From 12b4117668fd3c3c24f33279b8243cf44bba5825 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 26 Oct 2023 09:19:23 -0700
Subject: [PATCH 01/91] add scripts for reiding

---
 nmdc_automation/re_iding/re_id.py | 347 ++++++++++++++++++++++++++++++
 nmdc_automation/re_iding/utils.py |  31 +++
 2 files changed, 378 insertions(+)
 create mode 100755 nmdc_automation/re_iding/re_id.py
 create mode 100644 nmdc_automation/re_iding/utils.py

diff --git a/nmdc_automation/re_iding/re_id.py b/nmdc_automation/re_iding/re_id.py
new file mode 100755
index 00000000..8538c1e4
--- /dev/null
+++ b/nmdc_automation/re_iding/re_id.py
@@ -0,0 +1,347 @@
+#!/usr/bin/env python
+import os
+import sys
+import re
+from pymongo import MongoClient
+import hashlib
+import json
+from subprocess import check_output
+from nmdc_automation.api import NmdcRuntimeApi
+from nmdc_automation.config import Config
+
+base = "https://data.microbiomedata.org/data"
+base_dir = "/global/cfs/cdirs/m3408/results"
+
+
+sets = [
+        "read_qc_analysis_activity_set",
+        "metagenome_assembly_set",
+        "read_based_taxonomy_analysis_activity_set"
+        ]
+
+
+mapping_log = open("mapping.log", "a")
+
+
+def log_mapping(idtype, old, new):
+    """
+    Logs the mapping information.
+    
+    Parameters:
+    - idtype: The type of the ID (e.g., 'data', 'activity')
+    - old: The old ID value
+    - new: The new ID value
+    """
+    mapping_log.write(f"{idtype}\t{old}\t{new}\n")
+
+
+def read_map():
+    """
+    Reads a mapping list from a file and returns it as a dictionary.
+    
+    Returns:
+    - omap: A dictionary with old ID as key and new ID as value.
+    """
+    omap = {}
+    with open("map.lst") as f:
+        for line in f:
+            (k, v) = line.rstrip().split("\t")
+            omap[k] = v
+    return omap
+
+
+def find_dir(db, old_id):
+    """
+    Finds and returns the directory name associated with the given ID.
+    
+    Parameters:
+    - db: Database connection object
+    - old_id: The old ID for which the directory name is required
+    """
+    query_by_omics_id = {"was_informed_by": old_id}
+    activity_record = db.read_qc_analysis_activity_set.find_one(query_by_omics_id)
+    query_by_id = {"id": activity_record['has_output'][0]}
+    data_object_record = db.data_object_set.find_one(query_by_id)
+    return data_object_record['url'].split('/')[4]
+
+
+def process(db, old_id, new_id):
+    """
+    Process the given old ID and returns the associated data.
+    
+    Parameters:
+    - db: Database connection object
+    - old_id: The old ID to be processed
+    - new_id: The new ID to be used
+    
+    Returns:
+    - out: A dictionary containing processed data.
+    """
+    directory_name = find_dir(db, old_id)
+    assocaited_data_object = {"data_object_set": []}
+    for col in sets:
+        query_by_old_id = {"was_informed_by": old_id}
+        res = db[col].find(query_by_old_id)
+        count = 0
+        for doc in res:
+            count += 1
+        if count != 1:
+            raise ValueError("Too many matches.  Failing")
+        doc.pop("_id")
+        atype = doc['type']
+        func_name = atype.lower().replace("nmdc:", "")
+        func = globals()[func_name]
+        activity_records, data_object_records = func(db, doc, new_id)
+        assocaited_data_object[col] =[activity_records]
+        assocaited_data_object["data_object_set"].extend(data_object_records)
+    json.dump(assocaited_data_object, open(f"{new_id}.json", "w"), indent=2)
+    return assocaited_data_object
+
+
+def minter(config,shoulder):
+    """
+    Creates a new ID based on the provided shoulder.
+    
+    Parameters:
+    - shoulder: The base string for creating the new ID
+    
+    Returns:
+    - A new ID string
+    """
+    
+    runtime_api = NmdcRuntimeApi(config)
+    
+    return runtime_api.minter(shoulder)
+
+def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
+    """
+    Use the url to compute the new file name path and url
+    """
+    file_name = old_url.split("/")[-1]
+    file_extenstion = file_name.lstrip("nmdc_").split("_", maxsplit=1)[-1]
+    new_file_name = f"{act_id}_{file_extenstion}"
+    destination = os.path.join(new_base_dir, new_file_name)
+    new_url = f"{base}/{omic_id}/{act_id}/{new_file_name}"
+    return new_url, destination, new_file_name
+
+
+def md5_sum(fn):
+    """
+    Calculate the MD5 hash of a file.
+    
+    Args:
+    - fn (str): Path to the file for which the MD5 hash is to be computed.
+    
+    Returns:
+    - str: The MD5 hash of the file.
+    """
+    with open(fn, "rb") as f:
+        file_hash = hashlib.md5()
+        while chunk := f.read(8192):
+            file_hash.update(chunk)
+    return file_hash.hexdigest()
+
+
+def find_type(obj):
+    """
+    Determine the data type of an object based on its URL extension.
+    
+    Args:
+    - obj (dict): Dictionary containing the 'url' key which will be inspected to determine the data type.
+    
+    Returns:
+    - str: The determined data type or None if the type could not be determined.
+    """
+    if "data_object_type" in obj:
+        return obj["data_object_type"]
+    url = obj["url"]
+    if url.endswith("_covstats.txt"):
+        return "Assembly Coverage Stats"
+    elif url.endswith("_gottcha2_report.tsv"):
+        return "GOTTCHA2 Classification Report"
+    elif url.endswith("_gottcha2_report_full.tsv"):
+        return "GOTTCHA2 Report Full"
+    else:
+        sys.stderr.write(f"Missing type: {url}")
+        return None
+
+
+def copy_outputs(db, outputs, omic_id, act_id):
+    """
+    Copy output data objects and generate new metadata for them.
+    
+    Args:
+    - db (MongoClient): MongoDB client instance to fetch data.
+    - outputs (list): List of output object IDs.
+    - omic_id (str): ID of the omics process.
+    - act_id (str): ID of the activity.
+    
+    Returns:
+    - tuple: List of new object IDs and the new objects themselves.
+    """
+    new_data_objects = []
+    new_ids = []
+    new_base_dir = os.path.join(base_dir, omic_id, act_id)
+    os.makedirs(new_base_dir, exist_ok=True)
+    for data_obj_id in outputs:
+        data_obj = db.data_object_set.find_one({"id": data_obj_id})
+        old_url = data_obj["url"]
+        new_url, dst, new_fn = compute_new_paths(old_url, new_base_dir, omic_id, act_id)
+        new_id = minter("dobj")
+        log_mapping("data", data_obj["id"], new_id)
+
+        # Create new obj
+        data_obj.pop("_id")
+        desc = data_obj["description"]
+        data_obj["description"] = re.sub('[^ ]+$', f"{omic_id}", desc)
+        data_obj["url"] = new_url
+        data_obj["id"] = new_id
+        data_obj["name"] = new_fn
+        data_type = find_type(data_obj)
+        data_obj["data_object_type"] = data_type
+
+        # Link the file
+        src = old_url.replace(base, base_dir)
+        func_name = "bogus"
+        if data_type:
+            func_name = data_type.replace(" ", "_").lower()
+        if func_name in globals():
+            sys.stderr.write(f"Using func {func_name}\n")
+            func = globals()[func_name]
+            md5, size = func(src, dst, omic_id, act_id)
+            data_obj["file_size_bytes"] = size
+            data_obj["md5_checksum"] = md5
+        else:
+            os.link(src, dst)
+
+        # Add to the lists
+        new_ids.append(new_id)
+        new_data_objects.append(data_obj)
+    return new_ids, new_data_objects
+
+
+def rewrite_id(src, dst, old_id, new_id, prefix=None):
+    """
+    Rewrite lines in a file, replacing occurrences of an old ID with a new ID.
+    An optional prefix can be specified to limit which lines are modified.
+    
+    Args:
+    - src (str): Source file path.
+    - dst (str): Destination file path.
+    - old_id (str): ID to be replaced.
+    - new_id (str): Replacement ID.
+    - prefix (str, optional): Prefix character to determine which lines to modify. Defaults to None.
+    
+    Returns:
+    - tuple: MD5 checksum and size (in bytes) of the modified file.
+    """
+    fsrc = open(src)
+    fdst = open(dst, "w")
+    for line in fsrc:
+        if not prefix or (prefix and line[0] == prefix):
+            line = line.replace(old_id, new_id)
+        fdst.write(line)
+    fsrc.close()
+    fdst.close()
+    md5 = md5_sum(dst)
+    size = os.stat(dst).st_size
+    return md5, size
+
+
+def find_assembly_id(src):
+    fsrc = open(src)
+    line = fsrc.readline()
+    return "_".join(line[1:].split("_")[0:-1])
+
+
+def assembly_contigs(src, dst, omic_id, act_id):
+    scaf = src.replace("_contigs", "_scaffolds")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id, prefix=">")
+
+
+def assembly_scaffolds(src, dst, omic_id, act_id):
+    old_id = find_assembly_id(src)
+    return rewrite_id(src, dst, old_id, act_id, prefix=">")
+
+
+def assembly_coverage_stats(src, dst, omic_id, act_id):
+    scaf = src.replace("_covstats.txt", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id)
+
+
+def assembly_agp(src, dst, omic_id, act_id):
+    scaf = src.replace("_assembly.agp", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id)
+
+
+def convert_script(script, src, dst, old_id, act_id):
+    cmd = ["./rewrite_bam.sh", src, dst, old_id, act_id]
+    results = check_output(cmd)
+    md5 = md5_sum(dst)
+    size = os.stat(dst).st_size
+    return md5, size
+
+
+def assembly_coverage_bam(src, dst, omic_id, act_id):
+    scaf = src.replace("_pairedMapped_sorted.bam", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return convert_script("./rewrite_bam.sh", src, dst, old_id, act_id)
+
+
+def xassembly_info_file(src, dst, omic_id, act_id):
+    return []
+
+def readqcanalysisactivity(db, doc, new_omic_id):
+    new_act_id = minter("wfrqc") + ".1"
+    log_mapping("activity", doc["id"], new_act_id)
+    doc["id"] = new_act_id
+    doc["git_url"] = "https://github.com/microbiomedata/ReadsQC"
+    doc["version"] = "v1.0.8"
+    doc["was_informed_by"] = new_omic_id
+    doc["name"] = f"Read QC Activity for {new_act_id}"
+    new_ids, new_data_objects = copy_outputs(db, doc['has_output'], new_omic_id, new_act_id)
+    doc["has_output"] = new_ids
+    return doc, new_data_objects
+
+
+def metagenomeassembly(db, doc, new_omic_id):
+    new_act_id = minter("wfmgas") + ".1"
+    log_mapping("activity", doc["id"], new_act_id)
+    doc["id"] = new_act_id
+    doc["git_url"] = "https://github.com/microbiomedata/metaAssembly"
+    doc["version"] = "v1.0.3"
+    doc["was_informed_by"] = new_omic_id
+    doc["name"] = f"Metagenome Assembly Activity for {new_act_id}"
+    new_ids, new_data_objects = copy_outputs(db, doc['has_output'], new_omic_id, new_act_id)
+    doc["has_output"] = new_ids
+    return doc, new_data_objects
+
+def readbasedanalysis(db, doc, new_omic_id):
+    new_act_id = minter("wfrbt") + ".1"
+    log_mapping("activity", doc["id"], new_act_id)
+    doc["id"] = new_act_id
+    doc["git_url"] = "https://github.com/microbiomedata/ReadbasedAnalysis"
+    doc["version"] = "v1.0.5"
+    doc["was_informed_by"] = new_omic_id
+    doc["name"] = f"Metagenome Assembly Activity for {new_act_id}"
+    new_ids, new_data_objects = copy_outputs(db, doc['has_output'], new_omic_id, new_act_id)
+    doc["has_output"] = new_ids
+    return doc, new_data_objects
+
+if __name__ == "__main__":
+    mongo_url = os.environ["MONGO_URL"]
+    client = MongoClient(mongo_url, directConnection=True)
+    db = client.nmdc
+    # Read mapping list
+    # This should have:
+    # was_informed_by_old\twas_informed_by_new
+    # e.g.
+    # nmdc:mga0xxxxx    nmdc:omprc-11-xxxxx
+    omic_map = read_map()
+    for omic in omic_map:
+        process(db, omic, omic_map[omic])
+    # for each omics process
+    #     for act in [
diff --git a/nmdc_automation/re_iding/utils.py b/nmdc_automation/re_iding/utils.py
new file mode 100644
index 00000000..d77efc71
--- /dev/null
+++ b/nmdc_automation/re_iding/utils.py
@@ -0,0 +1,31 @@
+import subprocess
+import gzip 
+
+def rewrite_bam(type, old_bam, new_bam, old_id, new_id):
+    
+    if type == "inside":
+        print(f"Rewriting {new_bam}")
+
+        cmd1 = ["samtools", "view", "-h", old_bam]
+        cmd2 = ["sed", f"s/{old_id}/{new_id}/g"]
+        cmd3 = ["samtools", "view", "-hb", "-o", ]
+
+        # Create a pipeline: cmd1 | cmd2 | cmd3
+        p1 = subprocess.Popen(cmd1, stdout=subprocess.PIPE)
+        p2 = subprocess.Popen(cmd2, stdin=p1.stdout, stdout=subprocess.PIPE)
+        p1.stdout.close() 
+        p3 = subprocess.Popen(cmd3, stdin=p2.stdout)
+        p2.stdout.close()
+        p3.communicate() 
+
+    else:
+        with open(new_bam, 'w') as f:
+            pass  # touch file
+
+
+def rewrite_sam(input_sam, output_sam, old_id, new_id):
+    
+    with gzip.open(input_sam, 'rt') as f_in, gzip.open(output_sam, 'wt') as f_out:
+        for line in f_in:
+            f_out.write(line.replace(old_id, new_id))
+

From 913262d9f804f46be115bcf7dda4977395606d2c Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 26 Oct 2023 10:23:06 -0700
Subject: [PATCH 02/91] update .gitignore to exclude pycharm project files

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 01196e5a..0f010ee0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@ test_data/afile.sha256
 htmlcov/
 .coverage
 attic
+.idea/

From 04cc8eda04d219016ec297d995d840b5769eefbb Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 26 Oct 2023 11:45:03 -0700
Subject: [PATCH 03/91] initial script framework, Napa config file, and
 run_query method on API client

---
 configs/napa_config.toml                      | 29 ++++++++
 nmdc_automation/api/nmdcapi.py                |  6 ++
 .../rebuild_metagenome_workflow_records.py    | 69 +++++++++++++++++++
 3 files changed, 104 insertions(+)
 create mode 100644 configs/napa_config.toml
 create mode 100644 nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py

diff --git a/configs/napa_config.toml b/configs/napa_config.toml
new file mode 100644
index 00000000..de986b9e
--- /dev/null
+++ b/configs/napa_config.toml
@@ -0,0 +1,29 @@
+[cromwell]
+cromwell_url = "http://localhost:8088/api/workflows/v1"
+cromwell_api = "http://localhost:9999"
+
+[directories]
+stage_dir = "/path/to/stage/dir"
+template_dir = "/path/to/template/dir"
+data_dir = "/tmp"
+raw_dir = "/path/to/raw/data/files"
+
+[site]
+resource = "Resource Name"
+site = "Processing Site"
+
+[nmdc]
+url_root = "https://data.microbiomedata.org/data/"
+api_url = "https://api-napa.microbiomedata.org/"
+
+[state]
+watch_state = "State File"
+agent_state = "/tmp/agent.state"
+activity_id_state = "/Path/to/activity_id_state"
+
+[workflows]
+workflows_config = "./configs/workflows.yaml"
+
+[credentials]
+client_id = "xxxxxx"
+client_secret = "xxxxxxxx"
diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 1412dd02..a90a5370 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -304,6 +304,12 @@ def update_op(self, opid, done=None, results=None, meta=None):
         resp = requests.patch(url, headers=self.header, data=json.dumps(d))
         return resp.json()
 
+    @refresh_token
+    def run_query(self, query):
+        url = "%squeries:run" % self._base_url
+        resp = requests.post(url, headers=self.header, data=json.dumps(query))
+        return resp.json()
+
 
 def jprint(obj):
     print(json.dumps(obj, indent=2))
diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
new file mode 100644
index 00000000..09ecfee4
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+# coding: utf-8
+# nmdc_schema/napa_compliance/scripts/rebuild_metagenome_workflow_records.py
+"""
+rebuild_metagenome_workflow_records.py: Rebuild metagenome workflow records
+after re-ID-ing of OmicsProcessing records.
+"""
+import logging
+import os
+from pathlib import Path
+# import requests
+import time
+
+import click
+
+from nmdc_automation.config import Config
+from nmdc_automation.api import NmdcRuntimeApi
+
+GOLD_STUDY_ID = "gold:Gs0114663"
+STUDY_ID = "nmdc:sty-11-aygzgv51"
+NAPA_CONFIG = Path("../../../configs/napa_config.toml")
+
+@click.command()
+@click.option("--study_id", default=STUDY_ID, help="Updated study ID")
+@click.option("--site_config", type=click.Path(exists=True),
+              default=NAPA_CONFIG, help="Site configuration file")
+def rebuild_workflow_records(study_id: str, site_config: bool):
+    """
+    Rebuild metagenome workflow records after re-ID-ing of Study, Biosample, and
+    OmicsProcessing records by:
+    1. Retrieving all OmicsProcessing records for updated study ID
+    2. For each OmicsProcessing record, retrieve the corresponding
+    WorkflowExecutionActivity records:
+        a. ReadQcAnalysisActivity
+        b. ReadBasedTaxonomyAnalysisActivity
+        c. MetagenomeAssembly
+        d. MetagenomeAnnotationActivity
+        e. MagsAnalysisActivity
+    3. For each WorkflowExecutionActivity record:
+    TODO - summarize Michal's flowchart here
+
+    """
+    start_time = time.time()
+    logging.info("starting missing_neon_soils_ecosystem_data.py...")
+    logging.info(f"study_id: {study_id}")
+
+    runtime_api_client = NmdcRuntimeApi(site_config)
+
+
+
+    # 1. Retrieve all OmicsProcessing records for the given GOLD study ID
+    # https://api-napa.microbiomedata.org/omics_processing_sets?find=omics_processing_set&filter=part_of%3Agold:Gs0114663&per_page=99&page=1
+
+    params = {
+        "find": "omics_processing_set",
+        "filter": {
+            "part_of": {
+                "$elemMatch": {"$eq": study_id}
+            }
+        }
+    }
+    response = runtime_api_client.run_query(params)
+    print(response)
+
+    # 2. For each OmicsProcessing record, retrieve the corresponding
+
+
+if __name__ == "__main__":
+    rebuild_workflow_records()
\ No newline at end of file

From 1b118ba7bcee53a8e3f31cff9eadf1a2f5838cba Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 26 Oct 2023 12:05:30 -0700
Subject: [PATCH 04/91] added api_url reference

---
 configs/site_configuration.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/configs/site_configuration.toml b/configs/site_configuration.toml
index ff716dd0..866db4c9 100644
--- a/configs/site_configuration.toml
+++ b/configs/site_configuration.toml
@@ -14,6 +14,7 @@ site = "Processing Site"
 
 [nmdc]
 url_root = "https://data.microbiomedata.org/data/"
+api_url = "https://api.microbiomedata.org"
 
 [state]
 watch_state = "State File"
@@ -21,7 +22,7 @@ agent_state = "/tmp/agent.state"
 activity_id_state = "/Path/to/activity_id_state"
 
 [workflows]
-workflows_config = "./configs/workflows.yaml"
+workflows_config = "/configs/workflows.yaml"
 
 [credentials]
 client_id = "xxxxxx"

From 4ea1cf3cf85227ef7256dac1f8236ecba9fc13d6 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 26 Oct 2023 13:49:01 -0700
Subject: [PATCH 05/91] minimal config for reiding workflows

---
 configs/re_iding_worklfows.yaml | 184 ++++++++++++++++++++++++++++++++
 1 file changed, 184 insertions(+)
 create mode 100644 configs/re_iding_worklfows.yaml

diff --git a/configs/re_iding_worklfows.yaml b/configs/re_iding_worklfows.yaml
new file mode 100644
index 00000000..7fbce6ef
--- /dev/null
+++ b/configs/re_iding_worklfows.yaml
@@ -0,0 +1,184 @@
+Workflows:
+  - Name: Reads QC
+    Type: nmdc:ReadQcAnalysisActivity
+    Enabled: True
+    Git_repo: https://github.com/microbiomedata/ReadsQC
+    Version: v1.0.8
+    WDL: rqcfilter.wdl
+    Collection: read_qc_analysis_activity_set
+    Filter Input Objects:
+    - Metagenome Raw Reads
+    Predecessors:
+    - Sequencing
+    - Sequencing Interleaved
+    Input_prefix: nmdc_rqcfilter
+    Inputs:
+      input_files: do:Metagenome Raw Reads
+      proj: "{activity_id}"
+    Activity:
+      name: "Read QC Activity for {id}"
+      input_read_bases: "{outputs.stats.input_read_bases}"
+      input_read_count: "{outputs.stats.input_read_count}"
+      output_read_bases: "{outputs.stats.output_read_bases}"
+      output_read_count: "{outputs.stats.output_read_count}"
+      type: nmdc:ReadQcAnalysisActivity
+    Outputs:
+      - output: filtered_final
+        name: Reads QC result fastq (clean data)
+        suffix: "_filtered.fastq.gz"
+        data_object_type: Filtered Sequencing Reads
+        description: "Reads QC for {id}"
+      - output: filtered_stats_final
+        name: Reads QC summary statistics
+        suffix: "_filterStats.txt"
+        data_object_type: QC Statistics
+        description: "Reads QC summary for {id}"
+      - output: rqc_info
+        name: File containing read filtering information
+        suffix: "_readsQC.info"
+        data_object_type: Read Filtering Info File
+        description: "Read filtering info for {id}"
+
+  - Name: Metagenome Assembly
+    Type: nmdc:MetagenomeAssembly
+    Enabled: True
+    Git_repo: https://github.com/microbiomedata/metaAssembly
+    Version: v1.0.3
+    WDL: jgi_assembly.wdl
+    Collection: metagenome_assembly_set
+    Predecessors:
+    - Reads QC
+    - Reads QC Interleave
+    Input_prefix: jgi_metaASM
+    Inputs:
+      input_file: do:Filtered Sequencing Reads
+      rename_contig_prefix: "{activity_id}"
+      proj: "{activity_id}"
+    Activity:
+      name: "Metagenome Assembly Activity for {id}"
+      type: nmdc:MetagenomeAssembly
+      asm_score: "{outputs.stats.asm_score}"
+      contig_bp: "{outputs.stats.contig_bp}"
+      contigs: "{outputs.stats.contigs}"
+      ctg_l50: "{outputs.stats.ctg_l50}"
+      ctg_l90: "{outputs.stats.ctg_l90}"
+      ctg_logsum: "{outputs.stats.ctg_logsum}"
+      ctg_max: "{outputs.stats.ctg_max}"
+      ctg_n50: "{outputs.stats.ctg_n50}"
+      ctg_n90: "{outputs.stats.ctg_n90}"
+      ctg_powsum: "{outputs.stats.ctg_powsum}"
+      gap_pct: "{outputs.stats.gap_pct}"
+      gc_avg: "{outputs.stats.gc_avg}"
+      gc_std: "{outputs.stats.gc_std}"
+      scaf_bp: "{outputs.stats.scaf_bp}"
+      scaf_l50: "{outputs.stats.scaf_l50}"
+      scaf_l90: "{outputs.stats.scaf_l90}"
+      scaf_l_gt50k: "{outputs.stats.scaf_l_gt50k}"
+      scaf_logsum: "{outputs.stats.scaf_logsum}"
+      scaf_max: "{outputs.stats.scaf_max}"
+      scaf_n50: "{outputs.stats.scaf_n50}"
+      scaf_n90: "{outputs.stats.scaf_n90}"
+      scaf_n_gt50k: "{outputs.stats.scaf_n_gt50k}"
+      scaf_pct_gt50k: "{outputs.stats.scaf_pct_gt50k}"
+      scaf_powsum: "{outputs.stats.scaf_powsum}"
+      scaffolds: "{outputs.stats.scaffolds}"
+    Outputs:
+      - output: contig
+        name: Final assembly contigs fasta
+        suffix: "_contigs.fna"
+        data_object_type: Assembly Contigs
+        description: "Assembly contigs for {id}"
+      - output: scaffold
+        name: Final assembly scaffolds fasta
+        suffix: "_scaffolds.fna"
+        data_object_type: Assembly Scaffolds
+        description: "Assembly scaffolds for {id}"
+      - output: covstats
+        name: Assembled contigs coverage information
+        suffix: "_covstats.txt"
+        data_object_type: Assembly Coverage Stats
+        description: "Coverage Stats for {id}"
+      - output: agp
+        name: An AGP format file that describes the assembly
+        suffix: "_assembly.agp"
+        data_object_type: Assembly AGP
+        description: "AGP for {id}"
+      - output: bam
+        name: Sorted bam file of reads mapping back to the final assembly
+        suffix: "_pairedMapped_sorted.bam"
+        data_object_type: Assembly Coverage BAM
+        description: "Sorted Bam for {id}"
+      - output: asminfo
+        name: File containing assembly info
+        suffix: "_metaAsm.info"
+        data_object_type: Assembly Info File
+        description: "Assembly info for {id}"
+
+  - Name: Readbased Analysis
+    Type: nmdc:ReadBasedTaxonomyAnalysisActivity
+    Enabled: True
+    Git_repo: https://github.com/microbiomedata/ReadbasedAnalysis
+    Version: v1.0.5
+    WDL: ReadbasedAnalysis.wdl
+    Collection: read_based_taxonomy_analysis_activity_set
+    Predecessors:
+    - Reads QC
+    - Reads QC Interleave
+    Input_prefix: ReadbasedAnalysis
+    Inputs:
+      input_file: do:Filtered Sequencing Reads
+      proj: "{activity_id}"
+    Activity:
+      name: "Readbased Taxonomy Analysis Activity for {id}"
+      type: nmdc:ReadBasedTaxonomyAnalysisActivity
+    Outputs:
+    - output: final_gottcha2_report_tsv
+      data_object_type: GOTTCHA2 Classification Report
+      description: GOTTCHA2 Classification for {id}
+      name: GOTTCHA2 classification report file
+      suffix: _gottcha2_report.tsv
+    - output: final_gottcha2_full_tsv
+      data_object_type: GOTTCHA2 Report Full
+      description: GOTTCHA2 Full Report for {id}
+      name: GOTTCHA2 report file
+      suffix: _gottcha2_full_tsv
+    - output: final_gottcha2_krona_html
+      data_object_type: GOTTCHA2 Krona Plot
+      description: GOTTCHA2 Krona for {id}
+      name: GOTTCHA2 krona plot HTML file
+      suffix: _gottcha2_krona.html
+    - output: final_centrifuge_classification_tsv
+      data_object_type: Centrifuge Taxonomic Classification
+      description: Centrifuge Classification for {id}
+      name: Centrifuge output read classification file
+      suffix: _centrifuge_classification.tsv
+    - output: final_centrifuge_report_tsv
+      data_object_type: Centrifuge output report file
+      description: Centrifuge Report for {id}
+      name: Centrifuge Classification Report
+      suffix: _centrifuge_report.tsv
+    - output: final_centrifuge_krona_html
+      data_object_type: Centrifuge Krona Plot
+      description: Centrifuge Krona for {id}
+      name: Centrifug krona plot HTML file
+      suffix: _centrifuge_krona.html
+    - output: final_kraken2_classification_tsv
+      data_object_type: Kraken2 Taxonomic Classification
+      description: Kraken2 Classification for {id}
+      name: Kraken2 output read classification file
+      suffix: _kraken2_classification.tsv
+    - output: final_kraken2_report_tsv
+      data_object_type: Kraken2 Classification Report
+      description: Kraken2 Report for {id}
+      name: Kraken2 output report file
+      suffix: _kraken2_report.tsv
+    - output: final_kraken2_krona_html
+      data_object_type: Kraken2 Krona Plot
+      description: Kraken2 Krona for {id}
+      name: Kraken2 Krona plot HTML file
+      suffix: _kraken2_krona.html
+    - output: info_file
+      data_object_type: Read Based Analysis Info File
+      description: Read based analysis info for {id}
+      name: File containing reads based analysis information
+      suffix: profiler.info
\ No newline at end of file

From 210889068d21348b986fdc9f7c2fbe190135d18c Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 26 Oct 2023 13:53:01 -0700
Subject: [PATCH 06/91] added activity record and data object creation

---
 nmdc_automation/re_iding/re_id.py | 92 +++++++++++++++++++------------
 1 file changed, 56 insertions(+), 36 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id.py b/nmdc_automation/re_iding/re_id.py
index 8538c1e4..0acf2a3b 100755
--- a/nmdc_automation/re_iding/re_id.py
+++ b/nmdc_automation/re_iding/re_id.py
@@ -2,12 +2,20 @@
 import os
 import sys
 import re
+import yaml
+import datetime
+import pytz
 from pymongo import MongoClient
 import hashlib
 import json
 from subprocess import check_output
 from nmdc_automation.api import NmdcRuntimeApi
 from nmdc_automation.config import Config
+import nmdc_schema.nmdc as nmdc
+from linkml_runtime.dumpers import json_dumper
+
+###GLOBAL######
+nmdc_db = nmdc.Database()
 
 base = "https://data.microbiomedata.org/data"
 base_dir = "/global/cfs/cdirs/m3408/results"
@@ -22,6 +30,11 @@
 
 mapping_log = open("mapping.log", "a")
 
+def read_workflows_config(config_file):
+    with open(config_file, "r") as file:
+        workflow_data = yaml.safe_load(file)
+        
+    return workflow_data
 
 def log_mapping(idtype, old, new):
     """
@@ -113,6 +126,7 @@ def minter(config,shoulder):
     
     return runtime_api.minter(shoulder)
 
+
 def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
     """
     Use the url to compute the new file name path and url
@@ -294,42 +308,48 @@ def assembly_coverage_bam(src, dst, omic_id, act_id):
 def xassembly_info_file(src, dst, omic_id, act_id):
     return []
 
-def readqcanalysisactivity(db, doc, new_omic_id):
-    new_act_id = minter("wfrqc") + ".1"
-    log_mapping("activity", doc["id"], new_act_id)
-    doc["id"] = new_act_id
-    doc["git_url"] = "https://github.com/microbiomedata/ReadsQC"
-    doc["version"] = "v1.0.8"
-    doc["was_informed_by"] = new_omic_id
-    doc["name"] = f"Read QC Activity for {new_act_id}"
-    new_ids, new_data_objects = copy_outputs(db, doc['has_output'], new_omic_id, new_act_id)
-    doc["has_output"] = new_ids
-    return doc, new_data_objects
-
-
-def metagenomeassembly(db, doc, new_omic_id):
-    new_act_id = minter("wfmgas") + ".1"
-    log_mapping("activity", doc["id"], new_act_id)
-    doc["id"] = new_act_id
-    doc["git_url"] = "https://github.com/microbiomedata/metaAssembly"
-    doc["version"] = "v1.0.3"
-    doc["was_informed_by"] = new_omic_id
-    doc["name"] = f"Metagenome Assembly Activity for {new_act_id}"
-    new_ids, new_data_objects = copy_outputs(db, doc['has_output'], new_omic_id, new_act_id)
-    doc["has_output"] = new_ids
-    return doc, new_data_objects
-
-def readbasedanalysis(db, doc, new_omic_id):
-    new_act_id = minter("wfrbt") + ".1"
-    log_mapping("activity", doc["id"], new_act_id)
-    doc["id"] = new_act_id
-    doc["git_url"] = "https://github.com/microbiomedata/ReadbasedAnalysis"
-    doc["version"] = "v1.0.5"
-    doc["was_informed_by"] = new_omic_id
-    doc["name"] = f"Metagenome Assembly Activity for {new_act_id}"
-    new_ids, new_data_objects = copy_outputs(db, doc['has_output'], new_omic_id, new_act_id)
-    doc["has_output"] = new_ids
-    return doc, new_data_objects
+def make_activity_set(nmdc_db, omics_id, has_input, has_output,workflow_record):
+    database_activity_set = getattr(nmdc_db, workflow_record["Collection"])
+    # Lookup the nmdc schema range class
+    database_activity_range = getattr(nmdc_db, workflow_record["ActivityRange"])
+    # Mint an ID
+    new_id = minter(workflow_record["Type"])
+    
+    activity_id = new_id
+    database_activity_set.append(
+        database_activity_range(
+            id=activity_id,
+            name=workflow_record["Activity"]["name"].replace("{id}", activity_id),
+            git_url=workflow_record["Git_repo"],
+            version=workflow_record["Version"],
+            part_of=[omics_id],
+            execution_resource="Perlmutter - Nersc",
+            started_at_time=datetime.datetime.now(pytz.utc).isoformat(),
+            has_input=has_input,
+            has_output=has_output,
+            type=workflow_record["Type"],
+            ended_at_time=datetime.datetime.now(pytz.utc).isoformat(),
+            was_informed_by=omics_id,
+        )
+    )
+
+def make_data_object(data_object_record, omics_id):
+
+    nmdc_db.data_object_set.append(
+        nmdc.DataObject(
+            file_size_bytes=data_object_record["file_size"],
+            name=data_object_record["data_object_name"],
+            url=data_object_record["data_object_url"],
+            data_object_type=["data_object_type"],
+            type="nmdc:DataObject",
+            id=minter("nmdc:DataObject"),
+            md5_checksum=data_object_record["md5_checksum"],
+            description=data_object_record["description"].replace(
+                "{id}",omics_id
+            ),
+        )
+    )
+
 
 if __name__ == "__main__":
     mongo_url = os.environ["MONGO_URL"]

From 444ee0d76dd097c91e8bf407ca9f71cf87c4ec1b Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 26 Oct 2023 15:07:34 -0700
Subject: [PATCH 07/91] Add basic RuntimeUserApi client, and Napa specific
 configurations

---
 configs/napa_config.toml         |  8 ++++-
 nmdc_automation/api/__init__.py  |  2 +-
 nmdc_automation/api/nmdcapi.py   | 62 +++++++++++++++++++++++++++++++-
 nmdc_automation/config/config.py | 11 ++++++
 4 files changed, 80 insertions(+), 3 deletions(-)

diff --git a/configs/napa_config.toml b/configs/napa_config.toml
index de986b9e..c969d3a3 100644
--- a/configs/napa_config.toml
+++ b/configs/napa_config.toml
@@ -14,7 +14,13 @@ site = "Processing Site"
 
 [nmdc]
 url_root = "https://data.microbiomedata.org/data/"
-api_url = "https://api-napa.microbiomedata.org/"
+api_url = "https://api.microbiomedata.org/"
+
+[napa]
+base_url = "https://api-napa.microbiomedata.org/"
+username = "mbthornton"
+password = "H8jkYxc6rwrzA_k7g_fM"
+
 
 [state]
 watch_state = "State File"
diff --git a/nmdc_automation/api/__init__.py b/nmdc_automation/api/__init__.py
index f4c70039..eff0d2e4 100644
--- a/nmdc_automation/api/__init__.py
+++ b/nmdc_automation/api/__init__.py
@@ -1 +1 @@
-from .nmdcapi import NmdcRuntimeApi
+from .nmdcapi import NmdcRuntimeApi, NmdcRuntimeUserApi
diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index a90a5370..416fe993 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -4,11 +4,12 @@
 import sys
 import os
 from os.path import join, dirname
+from pydantic import BaseModel
 import requests
 import hashlib
 import mimetypes
 from time import time
-from datetime import datetime
+from datetime import datetime, timedelta, timezone
 from nmdc_automation.config import Config
 import logging
 
@@ -31,6 +32,10 @@ def _get_sha256(fn):
             f.write("\n")
     return sha
 
+def expiry_dt_from_now(days=0, hours=0, minutes=0, seconds=0):
+    return datetime.now(timezone.utc) + timedelta(days=days, hours=hours,
+                                          minutes=minutes,
+                              seconds=seconds)
 
 class NmdcRuntimeApi:
     token = None
@@ -311,6 +316,61 @@ def run_query(self, query):
         return resp.json()
 
 
+class NmdcRuntimeUserApi:
+    """
+    Basic Runtime API Client with user/password authentication.
+    """
+    def __init__(self, username: str, password: str, base_url: str):
+        self.username = username
+        self.password = password
+        self.base_url = base_url
+        self.headers = {}
+        self.token_response = None
+        self.refresh_token_after = None
+
+    def ensure_token(self):
+        if (self.refresh_token_after is None or datetime.now(timezone.utc) >
+                self.refresh_token_after):
+            self.get_token()
+    def get_token(self):
+        token_request_body = {
+            "grant_type": "password",
+            "username": self.username,
+            "password": self.password,
+            "scope": '',
+            "client_id": "",
+            "client_secret": "",
+        }
+        headers = {
+            'accept': 'application/json',
+            'Content-Type': 'application/x-www-form-urlencoded',
+        }
+        rv = requests.post(
+            self.base_url + "token", data=token_request_body
+            )
+        self.token_response = rv.json()
+        if "access_token" not in self.token_response:
+            raise Exception(f"Getting token failed: {self.token_response}")
+
+        self.headers[
+            "Authorization"] = f'Bearer {self.token_response["access_token"]}'
+        self.refresh_token_after = expiry_dt_from_now(
+            **self.token_response["expires"]
+        ) - timedelta(seconds=5)
+
+    def request(self, method, url_path, params_or_json_data=None):
+        self.ensure_token()
+        kwargs = {"url": self.base_url + url_path, "headers": self.headers}
+        if isinstance(params_or_json_data, BaseModel):
+            params_or_json_data = params_or_json_data.dict(exclude_unset=True)
+        if method.upper() == "GET":
+            kwargs["params"] = params_or_json_data
+        else:
+            kwargs["json"] = params_or_json_data
+        rv = requests.request(method, **kwargs)
+        rv.raise_for_status()
+        return rv
+
 def jprint(obj):
     print(json.dumps(obj, indent=2))
 
diff --git a/nmdc_automation/config/config.py b/nmdc_automation/config/config.py
index fd812a2a..8f515bc0 100644
--- a/nmdc_automation/config/config.py
+++ b/nmdc_automation/config/config.py
@@ -47,6 +47,17 @@ def url_root(self):
     def api_url(self):
         return self.config_data["nmdc"]["api_url"]
 
+    @property
+    def napa_base_url(self):
+        return self.config_data["napa"]["base_url"]
+    @property
+    def napa_username(self):
+        return self.config_data["napa"]["username"]
+
+    @property
+    def napa_password(self):
+        return self.config_data["napa"]["password"]
+
     @property
     def watch_state(self):
         return self.config_data["state"]["watch_state"]

From f06d7314e5e335dd89f212c0f7e97aaa7450265e Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 26 Oct 2023 15:08:19 -0700
Subject: [PATCH 08/91] Update rebuild_metagenome script - successfully calls
 queries:run endpoint

---
 .../rebuild_metagenome_workflow_records.py    | 46 ++++++++++---------
 1 file changed, 24 insertions(+), 22 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index 09ecfee4..a9300aee 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -6,24 +6,25 @@
 after re-ID-ing of OmicsProcessing records.
 """
 import logging
-import os
-from pathlib import Path
-# import requests
 import time
+from pathlib import Path
 
 import click
 
+from nmdc_automation.api import NmdcRuntimeUserApi
 from nmdc_automation.config import Config
-from nmdc_automation.api import NmdcRuntimeApi
 
 GOLD_STUDY_ID = "gold:Gs0114663"
 STUDY_ID = "nmdc:sty-11-aygzgv51"
 NAPA_CONFIG = Path("../../../configs/napa_config.toml")
 
+
 @click.command()
 @click.option("--study_id", default=STUDY_ID, help="Updated study ID")
-@click.option("--site_config", type=click.Path(exists=True),
-              default=NAPA_CONFIG, help="Site configuration file")
+@click.option(
+    "--site_config", type=click.Path(exists=True), default=NAPA_CONFIG,
+    help="Site configuration file"
+)
 def rebuild_workflow_records(study_id: str, site_config: bool):
     """
     Rebuild metagenome workflow records after re-ID-ing of Study, Biosample, and
@@ -44,26 +45,27 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
     logging.info("starting missing_neon_soils_ecosystem_data.py...")
     logging.info(f"study_id: {study_id}")
 
-    runtime_api_client = NmdcRuntimeApi(site_config)
-
-
+    config = Config(site_config)
+    query_api_client = NmdcRuntimeUserApi(
+        username=config.napa_username, password=config.napa_password,
+        base_url=config.napa_base_url, )
 
     # 1. Retrieve all OmicsProcessing records for the given GOLD study ID
-    # https://api-napa.microbiomedata.org/omics_processing_sets?find=omics_processing_set&filter=part_of%3Agold:Gs0114663&per_page=99&page=1
-
-    params = {
-        "find": "omics_processing_set",
-        "filter": {
-            "part_of": {
-                "$elemMatch": {"$eq": study_id}
-            }
-        }
-    }
-    response = runtime_api_client.run_query(params)
-    print(response)
+    url = "queries:run"
+    params = {"find": "omics_processing_set",
+              "filter": {"part_of": {"$elemMatch": {"$eq": study_id}}}}
+    response = query_api_client.request("POST", url, params_or_json_data=params)
+    if response.status_code != 200:
+        raise Exception(
+            f"Error retrieving OmicsProcessing records for study {study_id}"
+            )
+    omics_processing_records = response.json()["cursor"]["firstBatch"]
+    logging.info(
+        f"Retrieved {len(omics_processing_records)} OmicsProcessing records for study {study_id}"
+        )
 
     # 2. For each OmicsProcessing record, retrieve the corresponding
 
 
 if __name__ == "__main__":
-    rebuild_workflow_records()
\ No newline at end of file
+    rebuild_workflow_records()

From 4c88894170895e97547c4bdb6bf12b6bb27a8741 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 26 Oct 2023 15:08:58 -0700
Subject: [PATCH 09/91] ignore lock files

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 0f010ee0..8e4cb121 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ htmlcov/
 .coverage
 attic
 .idea/
+*.lock

From 0188da5984565ca4afa50558f56c71b385af45b0 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 26 Oct 2023 15:21:03 -0700
Subject: [PATCH 10/91] refactor get_omics_processing_records to the API client

---
 nmdc_automation/api/nmdcapi.py                    | 15 +++++++++++++++
 .../rebuild_metagenome_workflow_records.py        | 15 +++------------
 2 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 416fe993..43864a33 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -371,6 +371,21 @@ def request(self, method, url_path, params_or_json_data=None):
         rv.raise_for_status()
         return rv
 
+    def get_omics_processing_records_for_nmdc_study(self, nmdc_study_id: str):
+        """
+        Retrieve all OmicsProcessing records for the given NMDC study ID.
+        """
+        url = "queries:run"
+        params = {"find": "omics_processing_set",
+                  "filter": {"part_of": {"$elemMatch": {"$eq": nmdc_study_id}}}}
+        response = self.request("POST", url, params_or_json_data=params)
+        if response.status_code != 200:
+            raise Exception(
+                f"Error retrieving OmicsProcessing records for study {nmdc_study_id}"
+                )
+        omics_processing_records = response.json()["cursor"]["firstBatch"]
+        return omics_processing_records
+
 def jprint(obj):
     print(json.dumps(obj, indent=2))
 
diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index a9300aee..27ab84df 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -50,21 +50,12 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         username=config.napa_username, password=config.napa_password,
         base_url=config.napa_base_url, )
 
-    # 1. Retrieve all OmicsProcessing records for the given GOLD study ID
-    url = "queries:run"
-    params = {"find": "omics_processing_set",
-              "filter": {"part_of": {"$elemMatch": {"$eq": study_id}}}}
-    response = query_api_client.request("POST", url, params_or_json_data=params)
-    if response.status_code != 200:
-        raise Exception(
-            f"Error retrieving OmicsProcessing records for study {study_id}"
-            )
-    omics_processing_records = response.json()["cursor"]["firstBatch"]
+    # 1. Retrieve all OmicsProcessing records for the updated NMDC study ID
+    omics_processing_records = query_api_client.get_omics_processing_records_for_nmdc_study(study_id)
     logging.info(
         f"Retrieved {len(omics_processing_records)} OmicsProcessing records for study {study_id}"
         )
-
-    # 2. For each OmicsProcessing record, retrieve the corresponding
+    # 2. For each OmicsProcessing record, retrieve the informed_by records
 
 
 if __name__ == "__main__":

From 3d2144b314b5927e2f491672dc3d27f9689f7762 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 26 Oct 2023 15:42:52 -0700
Subject: [PATCH 11/91] update script to find legacy IDs

The old IDs can be either gold_sequencing_project_identifiers or alternative_identifiers
---
 .../rebuild_metagenome_workflow_records.py    | 37 +++++++++++++++++--
 1 file changed, 34 insertions(+), 3 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index 27ab84df..8b1d23be 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -19,6 +19,31 @@
 NAPA_CONFIG = Path("../../../configs/napa_config.toml")
 
 
+def _get_legacy_id(omics_processing_record: dict) -> str:
+    """
+    Get the legacy ID for the given OmicsProcessing record.
+    """
+    legacy_id = None
+    legacy_ids = []
+    gold_ids = omics_processing_record.get("gold_sequencing_project_identifiers", [])
+    legacy_ids.extend(gold_ids)
+    alternative_ids = omics_processing_record.get("alternative_identifiers", [])
+    legacy_ids.extend(alternative_ids)
+    if len(legacy_ids) == 0:
+        logging.warning(
+            f"No legacy IDs found for omics_processing_record: {omics_processing_record['id']}"
+        )
+        return None
+    elif len(legacy_ids) > 1:
+        logging.warning(
+            f"Multiple legacy IDs found for omics_processing_record: {omics_processing_record['id']}"
+        )
+        return None
+    else:
+        legacy_id = legacy_ids[0]
+    logging.info(f"legacy_id: {legacy_id}")
+    return legacy_id
+
 @click.command()
 @click.option("--study_id", default=STUDY_ID, help="Updated study ID")
 @click.option(
@@ -51,11 +76,17 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         base_url=config.napa_base_url, )
 
     # 1. Retrieve all OmicsProcessing records for the updated NMDC study ID
-    omics_processing_records = query_api_client.get_omics_processing_records_for_nmdc_study(study_id)
+    omics_processing_records = query_api_client.get_omics_processing_records_for_nmdc_study(
+        study_id
+        )
     logging.info(
         f"Retrieved {len(omics_processing_records)} OmicsProcessing records for study {study_id}"
-        )
-    # 2. For each OmicsProcessing record, retrieve the informed_by records
+    )
+    # 2. For each OmicsProcessing record, find the legacy identifier:
+    for omics_processing_record in omics_processing_records:
+        legacy_id = _get_legacy_id(omics_processing_record)
+        logging.info(f"legacy_id: {legacy_id}")
+
 
 
 if __name__ == "__main__":

From 5551b46e2e6e148eb596929b9b66cce6199e618e Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 26 Oct 2023 17:24:16 -0700
Subject: [PATCH 12/91] basic script framework - finds reads QC and downstream
 workflow activities

---
 nmdc_automation/api/nmdcapi.py                | 17 +++++++++++
 .../rebuild_metagenome_workflow_records.py    | 29 ++++++++++++++++++-
 2 files changed, 45 insertions(+), 1 deletion(-)

diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 43864a33..e8cad9f9 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -386,6 +386,23 @@ def get_omics_processing_records_for_nmdc_study(self, nmdc_study_id: str):
         omics_processing_records = response.json()["cursor"]["firstBatch"]
         return omics_processing_records
 
+    def get_workflow_activity_informed_by(self, workflow_activity_set: str,
+                                          informed_by_id: str):
+        """
+        Retrieve a workflow activity record for the given workflow activity set
+        and informed by a given OmicsProcessing ID.
+        """
+        url = "queries:run"
+        params = {"find": workflow_activity_set,
+                  "filter": {"was_informed_by": informed_by_id}}
+        response = self.request("POST", url, params_or_json_data=params)
+        if response.status_code != 200:
+            raise Exception(
+                f"Error retrieving {workflow_activity_set} record informed by {informed_by_id}"
+                )
+        workflow_activity_record = response.json()["cursor"]["firstBatch"]
+        return workflow_activity_record
+
 def jprint(obj):
     print(json.dumps(obj, indent=2))
 
diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index 8b1d23be..7ff618be 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -41,7 +41,6 @@ def _get_legacy_id(omics_processing_record: dict) -> str:
         return None
     else:
         legacy_id = legacy_ids[0]
-    logging.info(f"legacy_id: {legacy_id}")
     return legacy_id
 
 @click.command()
@@ -84,9 +83,37 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
     )
     # 2. For each OmicsProcessing record, find the legacy identifier:
     for omics_processing_record in omics_processing_records:
+        logging.info(f"omics_processing_record: "
+                     f"{omics_processing_record['id']}")
         legacy_id = _get_legacy_id(omics_processing_record)
         logging.info(f"legacy_id: {legacy_id}")
 
+        # reads QC records
+        # Downstream WorkflowExecutionActivity records depend on the `has_output`
+        # data object of the ReadQcAnalysisActivity record.
+        set_name = "read_qc_analysis_activity_set"
+        read_qc_records = query_api_client.get_workflow_activity_informed_by(
+            set_name, legacy_id
+        )
+        logging.info(f"Found {len(read_qc_records)} read_qc_records")
+
+        # downstream workflow activity sets
+        taxonomy_records, read_based_analysis_records, metagenome_assembly_records, \
+            metagenome_annotation_records, mags_records = [], [], [], [], []
+
+        downstream_workflow_activity_sets = {
+            "read_based_taxonomy_analysis_activity_set": taxonomy_records,
+            "read_based_analysis_activity_set": read_based_analysis_records,
+            "metagenome_assembly_set": metagenome_assembly_records,
+            "metagenome_annotation_activity_set": metagenome_annotation_records,
+            "mags_activity_set": mags_records,
+        }
+
+        for set_name, records in downstream_workflow_activity_sets.items():
+            records = query_api_client.get_workflow_activity_informed_by(
+                set_name, legacy_id
+            )
+            logging.info(f"Found {len(records)} {set_name} records")
 
 
 if __name__ == "__main__":

From f6a7908b237486f387454092ff604070f379bb8a Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Sat, 28 Oct 2023 07:01:28 -0700
Subject: [PATCH 13/91] added write out to json for study

---
 .../scripts/rebuild_metagenome_workflow_records.py     | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index 7ff618be..ab054665 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -8,7 +8,7 @@
 import logging
 import time
 from pathlib import Path
-
+import json
 import click
 
 from nmdc_automation.api import NmdcRuntimeUserApi
@@ -73,7 +73,7 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
     query_api_client = NmdcRuntimeUserApi(
         username=config.napa_username, password=config.napa_password,
         base_url=config.napa_base_url, )
-
+    
     # 1. Retrieve all OmicsProcessing records for the updated NMDC study ID
     omics_processing_records = query_api_client.get_omics_processing_records_for_nmdc_study(
         study_id
@@ -81,6 +81,8 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
     logging.info(
         f"Retrieved {len(omics_processing_records)} OmicsProcessing records for study {study_id}"
     )
+    
+    workflow_records_per_study = []
     # 2. For each OmicsProcessing record, find the legacy identifier:
     for omics_processing_record in omics_processing_records:
         logging.info(f"omics_processing_record: "
@@ -113,7 +115,11 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
             records = query_api_client.get_workflow_activity_informed_by(
                 set_name, legacy_id
             )
+            workflow_records_per_study.append(records)
             logging.info(f"Found {len(records)} {set_name} records")
+        
+    with open(f"{study_id}_assocated_record_dump.json", 'w') as json_file:
+        json.dump(workflow_records_per_study, json_file, indent=4)
 
 
 if __name__ == "__main__":

From e9e7267e06ac859409df1a0a870c835bec973ec9 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Sat, 28 Oct 2023 07:42:22 -0700
Subject: [PATCH 14/91] rename file, add database object post

---
 .../{utils.py => re_id_file_operations.py}    |   0
 .../re_iding/{re_id.py => re_id_process.py}   | 114 +++---------------
 2 files changed, 19 insertions(+), 95 deletions(-)
 rename nmdc_automation/re_iding/{utils.py => re_id_file_operations.py} (100%)
 rename nmdc_automation/re_iding/{re_id.py => re_id_process.py} (75%)

diff --git a/nmdc_automation/re_iding/utils.py b/nmdc_automation/re_iding/re_id_file_operations.py
similarity index 100%
rename from nmdc_automation/re_iding/utils.py
rename to nmdc_automation/re_iding/re_id_file_operations.py
diff --git a/nmdc_automation/re_iding/re_id.py b/nmdc_automation/re_iding/re_id_process.py
similarity index 75%
rename from nmdc_automation/re_iding/re_id.py
rename to nmdc_automation/re_iding/re_id_process.py
index 0acf2a3b..ec975584 100755
--- a/nmdc_automation/re_iding/re_id.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -6,17 +6,15 @@
 import datetime
 import pytz
 from pymongo import MongoClient
-import hashlib
 import json
-from subprocess import check_output
 from nmdc_automation.api import NmdcRuntimeApi
-from nmdc_automation.config import Config
+from re_id_file_operations import *
 import nmdc_schema.nmdc as nmdc
 from linkml_runtime.dumpers import json_dumper
 
 ###GLOBAL######
 nmdc_db = nmdc.Database()
-
+runtime_api = NmdcRuntimeApi("../../configs/site_configuration.toml")
 base = "https://data.microbiomedata.org/data"
 base_dir = "/global/cfs/cdirs/m3408/results"
 
@@ -139,23 +137,6 @@ def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
     return new_url, destination, new_file_name
 
 
-def md5_sum(fn):
-    """
-    Calculate the MD5 hash of a file.
-    
-    Args:
-    - fn (str): Path to the file for which the MD5 hash is to be computed.
-    
-    Returns:
-    - str: The MD5 hash of the file.
-    """
-    with open(fn, "rb") as f:
-        file_hash = hashlib.md5()
-        while chunk := f.read(8192):
-            file_hash.update(chunk)
-    return file_hash.hexdigest()
-
-
 def find_type(obj):
     """
     Determine the data type of an object based on its URL extension.
@@ -234,80 +215,6 @@ def copy_outputs(db, outputs, omic_id, act_id):
     return new_ids, new_data_objects
 
 
-def rewrite_id(src, dst, old_id, new_id, prefix=None):
-    """
-    Rewrite lines in a file, replacing occurrences of an old ID with a new ID.
-    An optional prefix can be specified to limit which lines are modified.
-    
-    Args:
-    - src (str): Source file path.
-    - dst (str): Destination file path.
-    - old_id (str): ID to be replaced.
-    - new_id (str): Replacement ID.
-    - prefix (str, optional): Prefix character to determine which lines to modify. Defaults to None.
-    
-    Returns:
-    - tuple: MD5 checksum and size (in bytes) of the modified file.
-    """
-    fsrc = open(src)
-    fdst = open(dst, "w")
-    for line in fsrc:
-        if not prefix or (prefix and line[0] == prefix):
-            line = line.replace(old_id, new_id)
-        fdst.write(line)
-    fsrc.close()
-    fdst.close()
-    md5 = md5_sum(dst)
-    size = os.stat(dst).st_size
-    return md5, size
-
-
-def find_assembly_id(src):
-    fsrc = open(src)
-    line = fsrc.readline()
-    return "_".join(line[1:].split("_")[0:-1])
-
-
-def assembly_contigs(src, dst, omic_id, act_id):
-    scaf = src.replace("_contigs", "_scaffolds")
-    old_id = find_assembly_id(scaf)
-    return rewrite_id(src, dst, old_id, act_id, prefix=">")
-
-
-def assembly_scaffolds(src, dst, omic_id, act_id):
-    old_id = find_assembly_id(src)
-    return rewrite_id(src, dst, old_id, act_id, prefix=">")
-
-
-def assembly_coverage_stats(src, dst, omic_id, act_id):
-    scaf = src.replace("_covstats.txt", "_scaffolds.fna")
-    old_id = find_assembly_id(scaf)
-    return rewrite_id(src, dst, old_id, act_id)
-
-
-def assembly_agp(src, dst, omic_id, act_id):
-    scaf = src.replace("_assembly.agp", "_scaffolds.fna")
-    old_id = find_assembly_id(scaf)
-    return rewrite_id(src, dst, old_id, act_id)
-
-
-def convert_script(script, src, dst, old_id, act_id):
-    cmd = ["./rewrite_bam.sh", src, dst, old_id, act_id]
-    results = check_output(cmd)
-    md5 = md5_sum(dst)
-    size = os.stat(dst).st_size
-    return md5, size
-
-
-def assembly_coverage_bam(src, dst, omic_id, act_id):
-    scaf = src.replace("_pairedMapped_sorted.bam", "_scaffolds.fna")
-    old_id = find_assembly_id(scaf)
-    return convert_script("./rewrite_bam.sh", src, dst, old_id, act_id)
-
-
-def xassembly_info_file(src, dst, omic_id, act_id):
-    return []
-
 def make_activity_set(nmdc_db, omics_id, has_input, has_output,workflow_record):
     database_activity_set = getattr(nmdc_db, workflow_record["Collection"])
     # Lookup the nmdc schema range class
@@ -350,6 +257,23 @@ def make_data_object(data_object_record, omics_id):
         )
     )
 
+def post_database_object_to_runtime(datase_object):
+    
+    nmdc_database_object = json.loads(
+            json_dumper.dumps(datase_object, inject_type=False)
+        )
+    res = runtime_api.post_objects(nmdc_database_object)
+    return res
+
+def main():
+    #TODO
+    #1. Read in json dump of analysis records 
+    #2. Process records for reads qc - generate new metadata, make new records and data objects (this will include file copies and renaming)
+    #3. save data of updated reads qc records
+    #4. Fetch old records for readbased analysis and assembly, generate new metadata, make new records and data objects (this will include file copies and renaming files and ids in files)
+    #5. Validate new records, submit them via runtime api
+    #6. Write seperate process to delete old records once we have
+    pass
 
 if __name__ == "__main__":
     mongo_url = os.environ["MONGO_URL"]

From 219b007130c8ddb8fb15d0f32e7413f23b25a3e8 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Sat, 28 Oct 2023 07:42:49 -0700
Subject: [PATCH 15/91] rename file, move all file operation here

---
 .../re_iding/re_id_file_operations.py         | 93 +++++++++++++++++++
 1 file changed, 93 insertions(+)

diff --git a/nmdc_automation/re_iding/re_id_file_operations.py b/nmdc_automation/re_iding/re_id_file_operations.py
index d77efc71..cf1d982d 100644
--- a/nmdc_automation/re_iding/re_id_file_operations.py
+++ b/nmdc_automation/re_iding/re_id_file_operations.py
@@ -1,5 +1,98 @@
 import subprocess
 import gzip 
+import os
+import hashlib
+from subprocess import check_output
+
+def md5_sum(fn):
+    """
+    Calculate the MD5 hash of a file.
+    
+    Args:
+    - fn (str): Path to the file for which the MD5 hash is to be computed.
+    
+    Returns:
+    - str: The MD5 hash of the file.
+    """
+    with open(fn, "rb") as f:
+        file_hash = hashlib.md5()
+        while chunk := f.read(8192):
+            file_hash.update(chunk)
+    return file_hash.hexdigest()
+
+def rewrite_id(src, dst, old_id, new_id, prefix=None):
+    """
+    Rewrite lines in a file, replacing occurrences of an old ID with a new ID.
+    An optional prefix can be specified to limit which lines are modified.
+    
+    Args:
+    - src (str): Source file path.
+    - dst (str): Destination file path.
+    - old_id (str): ID to be replaced.
+    - new_id (str): Replacement ID.
+    - prefix (str, optional): Prefix character to determine which lines to modify. Defaults to None.
+    
+    Returns:
+    - tuple: MD5 checksum and size (in bytes) of the modified file.
+    """
+    fsrc = open(src)
+    fdst = open(dst, "w")
+    for line in fsrc:
+        if not prefix or (prefix and line[0] == prefix):
+            line = line.replace(old_id, new_id)
+        fdst.write(line)
+    fsrc.close()
+    fdst.close()
+    md5 = md5_sum(dst)
+    size = os.stat(dst).st_size
+    return md5, size
+
+
+def find_assembly_id(src):
+    fsrc = open(src)
+    line = fsrc.readline()
+    return "_".join(line[1:].split("_")[0:-1])
+
+
+def assembly_contigs(src, dst, omic_id, act_id):
+    scaf = src.replace("_contigs", "_scaffolds")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id, prefix=">")
+
+
+def assembly_scaffolds(src, dst, omic_id, act_id):
+    old_id = find_assembly_id(src)
+    return rewrite_id(src, dst, old_id, act_id, prefix=">")
+
+
+def assembly_coverage_stats(src, dst, omic_id, act_id):
+    scaf = src.replace("_covstats.txt", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id)
+
+
+def assembly_agp(src, dst, omic_id, act_id):
+    scaf = src.replace("_assembly.agp", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id)
+
+
+def convert_script(script, src, dst, old_id, act_id):
+    cmd = ["./rewrite_bam.sh", src, dst, old_id, act_id]
+    results = check_output(cmd)
+    md5 = md5_sum(dst)
+    size = os.stat(dst).st_size
+    return md5, size
+
+
+def assembly_coverage_bam(src, dst, omic_id, act_id):
+    scaf = src.replace("_pairedMapped_sorted.bam", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return convert_script("./rewrite_bam.sh", src, dst, old_id, act_id)
+
+
+def xassembly_info_file(src, dst, omic_id, act_id):
+    return []
 
 def rewrite_bam(type, old_bam, new_bam, old_id, new_id):
     

From 0481caaa1b15e6ddeb99c82c96d296e9cc299722 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 31 Oct 2023 12:49:46 -0700
Subject: [PATCH 16/91] fixes for #23 Add read_qc_analysis_activity_set

---
 nmdc_automation/api/nmdcapi.py                |    13 +
 ...sty-11-aygzgv51_assocated_record_dump.json | 34722 ++++++++++++++++
 .../rebuild_metagenome_workflow_records.py    |    33 +-
 3 files changed, 34767 insertions(+), 1 deletion(-)
 create mode 100644 nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json

diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index e8cad9f9..2c86bcd7 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -403,6 +403,19 @@ def get_workflow_activity_informed_by(self, workflow_activity_set: str,
         workflow_activity_record = response.json()["cursor"]["firstBatch"]
         return workflow_activity_record
 
+    def get_data_object_by_id(self, data_object_id: str):
+        """
+        Retrieve a data object record for the given data object ID.
+        """
+        url = f"data_objects/{data_object_id}"
+        response = self.request("GET", url)
+        if response.status_code != 200:
+            raise Exception(
+                f"Error retrieving data object record for {data_object_id}"
+                )
+        data_object_record = response.json()
+        return data_object_record
+
 def jprint(obj):
     print(json.dumps(obj, indent=2))
 
diff --git a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
new file mode 100644
index 00000000..a7146766
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
@@ -0,0 +1,34722 @@
+[
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349b33"
+        },
+        "id": "nmdc:omprc-11-bn8jcq58",
+        "name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+        "description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
+        "has_input": [
+            "nmdc:bsm-11-qq8s6x03"
+        ],
+        "has_output": [
+            "jgi:55d740280d8785342fcf7e39"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "add_date": "2015-05-28",
+        "mod_date": "2021-06-15",
+        "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+        "omics_type": {
+            "has_raw_value": "Metagenome"
+        },
+        "principal_investigator": {
+            "has_raw_value": "James Stegen"
+        },
+        "processing_institution": "JGI",
+        "type": "nmdc:OmicsProcessing",
+        "gold_sequencing_project_identifiers": [
+            "gold:Gp0115663"
+        ],
+        "downstream_workflow_activity_records": [
+            {
+                "_id": {
+                    "$oid": "649b009d6bdd4fd20273c88b"
+                },
+                "has_input": [
+                    "nmdc:30a06664f29cffbbbc49abad86eae6fc"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef",
+                    "nmdc:b99ce8adc125c95f0bfdadf36a3f6848"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "input_read_count": 32238374,
+                "output_read_bases": 4608772924,
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "input_read_bases": 4867994474,
+                "name": "Read QC Activity for nmdc:mga0h9dt75",
+                "output_read_count": 30774080,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadQCAnalysisActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "output_data_objects": [
+                    {
+                        "name": "Gp0115663_Filtered Reads",
+                        "description": "Filtered Reads for Gp0115663",
+                        "data_object_type": "Filtered Sequencing Reads",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filtered.fastq.gz",
+                        "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                        "id": "nmdc:7bf778baef033d36f118f8591256d6ef",
+                        "file_size_bytes": 2571324879
+                    },
+                    {
+                        "name": "Gp0115663_Filtered Stats",
+                        "description": "Filtered Stats for Gp0115663",
+                        "data_object_type": "QC Statistics",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filterStats.txt",
+                        "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
+                        "id": "nmdc:b99ce8adc125c95f0bfdadf36a3f6848",
+                        "file_size_bytes": 290
+                    }
+                ]
+            },
+            {
+                "_id": {
+                    "$oid": "649b009bff710ae353f8cf4f"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                    "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                    "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                    "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                    "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                    "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                    "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                    "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                    "nmdc:94ee1bc2dc74830a21d5c3471d6cf223"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "name": "ReadBased Analysis Activity for nmdc:mga0h9dt75",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadbasedAnalysis",
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "output_data_objects": [
+                    {
+                        "name": "Gp0115663_Gottcha2 TSV report",
+                        "description": "Gottcha2 TSV report for Gp0115663",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
+                        "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
+                        "id": "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                        "file_size_bytes": 13174
+                    },
+                    {
+                        "name": "Gp0115663_Gottcha2 full TSV report",
+                        "description": "Gottcha2 full TSV report for Gp0115663",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
+                        "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
+                        "id": "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                        "file_size_bytes": 1035818
+                    },
+                    {
+                        "name": "Gp0115663_Gottcha2 Krona HTML report",
+                        "description": "Gottcha2 Krona HTML report for Gp0115663",
+                        "data_object_type": "GOTTCHA2 Krona Plot",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
+                        "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
+                        "id": "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                        "file_size_bytes": 262669
+                    },
+                    {
+                        "name": "Gp0115663_Centrifuge classification TSV report",
+                        "description": "Centrifuge classification TSV report for Gp0115663",
+                        "data_object_type": "Centrifuge Taxonomic Classification",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
+                        "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
+                        "id": "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                        "file_size_bytes": 2189843623
+                    },
+                    {
+                        "name": "Gp0115663_Centrifuge TSV report",
+                        "description": "Centrifuge TSV report for Gp0115663",
+                        "data_object_type": "Centrifuge Classification Report",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
+                        "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+                        "id": "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                        "file_size_bytes": 260134
+                    },
+                    {
+                        "name": "Gp0115663_Centrifuge Krona HTML report",
+                        "description": "Centrifuge Krona HTML report for Gp0115663",
+                        "data_object_type": "Centrifuge Krona Plot",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
+                        "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
+                        "id": "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                        "file_size_bytes": 2343980
+                    },
+                    {
+                        "name": "Gp0115663_Kraken classification TSV report",
+                        "description": "Kraken classification TSV report for Gp0115663",
+                        "data_object_type": "Kraken2 Taxonomic Classification",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
+                        "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
+                        "id": "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                        "file_size_bytes": 1785563917
+                    },
+                    {
+                        "name": "Gp0115663_Kraken2 TSV report",
+                        "description": "Kraken2 TSV report for Gp0115663",
+                        "data_object_type": "Kraken2 Classification Report",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
+                        "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+                        "id": "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                        "file_size_bytes": 699896
+                    },
+                    {
+                        "name": "Gp0115663_Kraken2 Krona HTML report",
+                        "description": "Kraken2 Krona HTML report for Gp0115663",
+                        "data_object_type": "Kraken2 Krona Plot",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
+                        "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+                        "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
+                        "file_size_bytes": 4221977
+                    }
+                ]
+            },
+            {
+                "_id": {
+                    "$oid": "61e71a31833bcf838a701ec1"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                    "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                    "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                    "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                    "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                    "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                    "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                    "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                    "nmdc:94ee1bc2dc74830a21d5c3471d6cf223"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "name": "ReadBased Analysis Activity for nmdc:mga0h9dt75",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadbasedAnalysis",
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "output_data_objects": [
+                    {
+                        "name": "Gp0115663_Gottcha2 TSV report",
+                        "description": "Gottcha2 TSV report for Gp0115663",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
+                        "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
+                        "id": "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                        "file_size_bytes": 13174
+                    },
+                    {
+                        "name": "Gp0115663_Gottcha2 full TSV report",
+                        "description": "Gottcha2 full TSV report for Gp0115663",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
+                        "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
+                        "id": "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                        "file_size_bytes": 1035818
+                    },
+                    {
+                        "name": "Gp0115663_Gottcha2 Krona HTML report",
+                        "description": "Gottcha2 Krona HTML report for Gp0115663",
+                        "data_object_type": "GOTTCHA2 Krona Plot",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
+                        "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
+                        "id": "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                        "file_size_bytes": 262669
+                    },
+                    {
+                        "name": "Gp0115663_Centrifuge classification TSV report",
+                        "description": "Centrifuge classification TSV report for Gp0115663",
+                        "data_object_type": "Centrifuge Taxonomic Classification",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
+                        "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
+                        "id": "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                        "file_size_bytes": 2189843623
+                    },
+                    {
+                        "name": "Gp0115663_Centrifuge TSV report",
+                        "description": "Centrifuge TSV report for Gp0115663",
+                        "data_object_type": "Centrifuge Classification Report",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
+                        "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+                        "id": "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                        "file_size_bytes": 260134
+                    },
+                    {
+                        "name": "Gp0115663_Centrifuge Krona HTML report",
+                        "description": "Centrifuge Krona HTML report for Gp0115663",
+                        "data_object_type": "Centrifuge Krona Plot",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
+                        "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
+                        "id": "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                        "file_size_bytes": 2343980
+                    },
+                    {
+                        "name": "Gp0115663_Kraken classification TSV report",
+                        "description": "Kraken classification TSV report for Gp0115663",
+                        "data_object_type": "Kraken2 Taxonomic Classification",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
+                        "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
+                        "id": "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                        "file_size_bytes": 1785563917
+                    },
+                    {
+                        "name": "Gp0115663_Kraken2 TSV report",
+                        "description": "Kraken2 TSV report for Gp0115663",
+                        "data_object_type": "Kraken2 Classification Report",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
+                        "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+                        "id": "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                        "file_size_bytes": 699896
+                    },
+                    {
+                        "name": "Gp0115663_Kraken2 Krona HTML report",
+                        "description": "Kraken2 Krona HTML report for Gp0115663",
+                        "data_object_type": "Kraken2 Krona Plot",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
+                        "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+                        "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
+                        "file_size_bytes": 4221977
+                    }
+                ]
+            },
+            {
+                "_id": {
+                    "$oid": "649b005f2ca5ee4adb139fb9"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "ctg_logsum": 214373,
+                "scaf_logsum": 215363,
+                "gap_pct": 0.00188,
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:deddd162bf0128fba13b3bc1ca38d1aa",
+                    "nmdc:b3573e3cda5a06611de71ca04c5c14cc",
+                    "nmdc:c6d0d4cea985ca6fb50a060e15b4a856",
+                    "nmdc:f450e3800e17691d5874c89fc46c186a",
+                    "nmdc:31dc958d116d02122509e90b0883954f"
+                ],
+                "asm_score": 6.577,
+                "was_informed_by": "gold:Gp0115663",
+                "ctg_powsum": 24284,
+                "scaf_max": 68135,
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "scaf_powsum": 24422,
+                "execution_resource": "NERSC-Cori",
+                "contigs": 169784,
+                "name": "Assembly Activity for nmdc:mga0h9dt75",
+                "ctg_max": 68135,
+                "gc_std": 0.11726,
+                "contig_bp": 83494920,
+                "gc_avg": 0.46001,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "scaf_bp": 83496490,
+                "type": "nmdc:MetagenomeAssembly",
+                "scaffolds": 169645,
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "ctg_l50": 470,
+                "ctg_l90": 290,
+                "ctg_n50": 45584,
+                "ctg_n90": 141996,
+                "scaf_l50": 470,
+                "scaf_l90": 290,
+                "scaf_n50": 45550,
+                "scaf_n90": 141870,
+                "scaf_l_gt50k": 68135,
+                "scaf_n_gt50k": 1,
+                "scaf_pct_gt50k": 0.08160224,
+                "output_data_objects": [
+                    {
+                        "name": "Gp0115663_Assembled contigs fasta",
+                        "description": "Assembled contigs fasta for Gp0115663",
+                        "data_object_type": "Assembly Contigs",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna",
+                        "md5_checksum": "deddd162bf0128fba13b3bc1ca38d1aa",
+                        "id": "nmdc:deddd162bf0128fba13b3bc1ca38d1aa",
+                        "file_size_bytes": 90115831
+                    },
+                    {
+                        "name": "Gp0115663_Assembled scaffold fasta",
+                        "description": "Assembled scaffold fasta for Gp0115663",
+                        "data_object_type": "Assembly Scaffolds",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna",
+                        "md5_checksum": "b3573e3cda5a06611de71ca04c5c14cc",
+                        "id": "nmdc:b3573e3cda5a06611de71ca04c5c14cc",
+                        "file_size_bytes": 89604715
+                    },
+                    {
+                        "name": "Gp0115663_Metagenome Contig Coverage Stats",
+                        "description": "Metagenome Contig Coverage Stats for Gp0115663",
+                        "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_covstats.txt",
+                        "md5_checksum": "c6d0d4cea985ca6fb50a060e15b4a856",
+                        "id": "nmdc:c6d0d4cea985ca6fb50a060e15b4a856",
+                        "file_size_bytes": 13412363
+                    },
+                    {
+                        "name": "Gp0115663_Assembled AGP file",
+                        "description": "Assembled AGP file for Gp0115663",
+                        "data_object_type": "Assembly AGP",
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+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456500"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349bf8"
+        },
+        "id": "nmdc:omprc-11-c1ngnw86",
+        "name": "SBR_FC_S1_00-10_H2Oext_15Oct15_Leopard_1_01_4531",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-m0hn5p98"
+        ],
+        "has_output": [
+            "emsl:output_456505"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456505"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349bf9"
+        },
+        "id": "nmdc:omprc-11-excmek32",
+        "name": "SBR_FC_S1_10-20_H2Oext_15Oct15_Leopard_1_01_4532",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-br7th280"
+        ],
+        "has_output": [
+            "emsl:output_456510"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456510"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349bfa"
+        },
+        "id": "nmdc:omprc-11-mefm4e20",
+        "name": "SBR_FC_S1_00-10_H2Oext_13Oct15_Leopard_1_01_4420",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-m0hn5p98"
+        ],
+        "has_output": [
+            "emsl:output_456504"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456504"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349bfb"
+        },
+        "id": "nmdc:omprc-11-fzgdcp80",
+        "name": "SBR_FC_S1_20-30_H2Oext_13Oct15_Leopard_1_01_4422",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-qyz13338"
+        ],
+        "has_output": [
+            "emsl:output_456514"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456514"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349bfc"
+        },
+        "id": "nmdc:omprc-11-3akts752",
+        "name": "SBR_FC_N3_50-60_H2Oext_13Oct15_Leopard_1_01_4419",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-8saj5c05"
+        ],
+        "has_output": [
+            "emsl:output_456499"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456499"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349bfd"
+        },
+        "id": "nmdc:omprc-11-6sq6j166",
+        "name": "SBR_FC_S1_10-20_H2Oext_13Oct15_Leopard_1_01_4421",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-br7th280"
+        ],
+        "has_output": [
+            "emsl:output_456509"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456509"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349bfe"
+        },
+        "id": "nmdc:omprc-11-3awbyv03",
+        "name": "SBR_FC_S1_30-40_H2Oext_13Oct15_Leopard_1_01_4423",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-pzv0cf30"
+        ],
+        "has_output": [
+            "emsl:output_456519"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456519"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349bff"
+        },
+        "id": "nmdc:omprc-11-4kgm5w41",
+        "name": "SBR_FC_S1_20-30_H2Oext_15Oct15_Leopard_1_01_4533",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-qyz13338"
+        ],
+        "has_output": [
+            "emsl:output_456515"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456515"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c00"
+        },
+        "id": "nmdc:omprc-11-6xm1va42",
+        "name": "SBR_FC_S1_50-60_H2Oext_13Oct15_Leopard_1_01_4425",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-pnzwey18"
+        ],
+        "has_output": [
+            "emsl:output_456529"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456529"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c01"
+        },
+        "id": "nmdc:omprc-11-t2yd9m69",
+        "name": "SBR_FC_S2_00-10_H2Oext_15Oct15_Leopard_1_01_4537",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-60ayn103"
+        ],
+        "has_output": [
+            "emsl:output_456535"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456535"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c02"
+        },
+        "id": "nmdc:omprc-11-9d9fxj83",
+        "name": "SBR_FC_S2_10-20_H2Oext_15Oct15_Leopard_1_01_4538",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-e3hp0a71"
+        ],
+        "has_output": [
+            "emsl:output_456540"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456540"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c03"
+        },
+        "id": "nmdc:omprc-11-1rkm8b52",
+        "name": "SBR_FC_S2_10-20_H2Oext_13Oct15_Leopard_1_01_4427",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-e3hp0a71"
+        ],
+        "has_output": [
+            "emsl:output_456539"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456539"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c04"
+        },
+        "id": "nmdc:omprc-11-bzhsj954",
+        "name": "SBR_FC_S2_30-40_H2Oext_15Oct15_Leopard_1_01_4540",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-73qw2q23"
+        ],
+        "has_output": [
+            "emsl:output_456550"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456550"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c05"
+        },
+        "id": "nmdc:omprc-11-ae716322",
+        "name": "SBR_FC_S2_20-30_H2Oext_13Oct15_Leopard_1_01_4428",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-pknfsy79"
+        ],
+        "has_output": [
+            "emsl:output_456544"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456544"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c06"
+        },
+        "id": "nmdc:omprc-11-ryy9gp08",
+        "name": "SBR_FC_S3_00-10_H2Oext_15Oct15_Leopard_1_01_4543",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-rs67sh23"
+        ],
+        "has_output": [
+            "emsl:output_456565"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456565"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c07"
+        },
+        "id": "nmdc:omprc-11-qx18h332",
+        "name": "SBR_FC_S3_10-20_H2Oext_13Oct15_Leopard_1_01_4433",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-83ghpk10"
+        ],
+        "has_output": [
+            "emsl:output_456569"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456569"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c08"
+        },
+        "id": "nmdc:omprc-11-k3e66918",
+        "name": "SBR_FC_S3_00-10_H2Oext_13Oct15_Leopard_1_01_4432",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-rs67sh23"
+        ],
+        "has_output": [
+            "emsl:output_456564"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456564"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c09"
+        },
+        "id": "nmdc:omprc-11-nq83nd29",
+        "name": "SBR_FC_S3_20-30_H2Oext_13Oct15_Leopard_1_01_4434",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-5p6f9e18"
+        ],
+        "has_output": [
+            "emsl:output_456574"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456574"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c0a"
+        },
+        "id": "nmdc:omprc-11-xsnaaj68",
+        "name": "SBR_FC_S2_20-30_H2Oext_15Oct15_Leopard_1_01_4539",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-pknfsy79"
+        ],
+        "has_output": [
+            "emsl:output_456545"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456545"
+        ],
+        "downstream_workflow_activity_records": []
+    },
+    {
+        "_id": {
+            "$oid": "649b009773e8249959349c0b"
+        },
+        "id": "nmdc:omprc-11-409hwb80",
+        "name": "SBR_FC_S3_30-40_H2Oext_13Oct15_Leopard_1_01_4435",
+        "description": "High resolution MS spectra only",
+        "has_input": [
+            "nmdc:bsm-11-ea7re871"
+        ],
+        "has_output": [
+            "emsl:output_456579"
+        ],
+        "part_of": [
+            "nmdc:sty-11-aygzgv51"
+        ],
+        "instrument_name": "12T_FTICR_B",
+        "omics_type": {
+            "has_raw_value": "Organic Matter Characterization"
+        },
+        "processing_institution": "EMSL",
+        "type": "nmdc:OmicsProcessing",
+        "alternative_identifiers": [
+            "emsl:456579"
+        ],
+        "downstream_workflow_activity_records": []
+    }
+]
\ No newline at end of file
diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index ab054665..d7a4442b 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -83,6 +83,7 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
     )
     
     workflow_records_per_study = []
+
     # 2. For each OmicsProcessing record, find the legacy identifier:
     for omics_processing_record in omics_processing_records:
         logging.info(f"omics_processing_record: "
@@ -90,6 +91,14 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         legacy_id = _get_legacy_id(omics_processing_record)
         logging.info(f"legacy_id: {legacy_id}")
 
+        omics_processing_record["downstream_workflow_activity_records"] = []
+
+        if (omics_processing_record["omics_type"]["has_raw_value"] !=
+                "Metagenome"):
+            logging.info(f"omics_processing_record {omics_processing_record['id']} "
+                         f"is not a Metagenome")
+            continue
+
         # reads QC records
         # Downstream WorkflowExecutionActivity records depend on the `has_output`
         # data object of the ReadQcAnalysisActivity record.
@@ -97,7 +106,19 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         read_qc_records = query_api_client.get_workflow_activity_informed_by(
             set_name, legacy_id
         )
+        # Add the data objects referenced by the `has_output` property
+        for record in read_qc_records:
+            record["output_data_objects"] = []
+            for data_object_id in record["has_output"]:
+                data_object_record = query_api_client.get_data_object_by_id(
+                    data_object_id
+                )
+                record["output_data_objects"].append(data_object_record)
+
+
         logging.info(f"Found {len(read_qc_records)} read_qc_records")
+        omics_processing_record[
+            "downstream_workflow_activity_records"].extend(read_qc_records)
 
         # downstream workflow activity sets
         taxonomy_records, read_based_analysis_records, metagenome_assembly_records, \
@@ -115,11 +136,21 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
             records = query_api_client.get_workflow_activity_informed_by(
                 set_name, legacy_id
             )
+            # Add the data objects referenced by the `has_output` property
+            for record in records:
+                record["output_data_objects"] = []
+                for data_object_id in record["has_output"]:
+                    data_object_record = query_api_client.get_data_object_by_id(
+                        data_object_id
+                    )
+                    record["output_data_objects"].append(data_object_record)
+            omics_processing_record[
+                "downstream_workflow_activity_records"].extend(records)
             workflow_records_per_study.append(records)
             logging.info(f"Found {len(records)} {set_name} records")
         
     with open(f"{study_id}_assocated_record_dump.json", 'w') as json_file:
-        json.dump(workflow_records_per_study, json_file, indent=4)
+        json.dump(omics_processing_records, json_file, indent=4)
 
 
 if __name__ == "__main__":

From 53b8c52345ceb28494a95405bfb57fa916f61955 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Tue, 31 Oct 2023 14:18:42 -0700
Subject: [PATCH 17/91] added json reader

---
 nmdc_automation/re_iding/re_id_file_operations.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/nmdc_automation/re_iding/re_id_file_operations.py b/nmdc_automation/re_iding/re_id_file_operations.py
index cf1d982d..8ca469c1 100644
--- a/nmdc_automation/re_iding/re_id_file_operations.py
+++ b/nmdc_automation/re_iding/re_id_file_operations.py
@@ -1,6 +1,7 @@
 import subprocess
 import gzip 
 import os
+import json
 import hashlib
 from subprocess import check_output
 
@@ -20,6 +21,20 @@ def md5_sum(fn):
             file_hash.update(chunk)
     return file_hash.hexdigest()
 
+def read_json_file(filename):
+    """
+    Read a JSON file and return its content as a dictionary.
+
+    Parameters:
+    - filename (str): The path to the JSON file.
+
+    Returns:
+    - dict: The content of the JSON file.
+    """
+    with open(filename, 'r') as json_file:
+        data = json.load(json_file)
+    return data
+
 def rewrite_id(src, dst, old_id, new_id, prefix=None):
     """
     Rewrite lines in a file, replacing occurrences of an old ID with a new ID.

From e06b4964cbd6d6167a329ddf3b8a62766e3a6177 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Tue, 31 Oct 2023 14:19:13 -0700
Subject: [PATCH 18/91] started to break down workflows updating process

---
 nmdc_automation/re_iding/re_id_process.py | 71 ++++++++++++++++++-----
 1 file changed, 56 insertions(+), 15 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index ec975584..633129bb 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -14,7 +14,7 @@
 
 ###GLOBAL######
 nmdc_db = nmdc.Database()
-runtime_api = NmdcRuntimeApi("../../configs/site_configuration.toml")
+runtime_api = NmdcRuntimeApi("../../configs/napa_config.toml")
 base = "https://data.microbiomedata.org/data"
 base_dir = "/global/cfs/cdirs/m3408/results"
 
@@ -32,7 +32,7 @@ def read_workflows_config(config_file):
     with open(config_file, "r") as file:
         workflow_data = yaml.safe_load(file)
         
-    return workflow_data
+    return workflow_data["Workflows"]
 
 def log_mapping(idtype, old, new):
     """
@@ -265,6 +265,56 @@ def post_database_object_to_runtime(datase_object):
     res = runtime_api.post_objects(nmdc_database_object)
     return res
 
+def get_omics_id(omics_record):
+    return omics_record["id"]
+
+def get_record_by_type(omics_children_records, record_type):
+    """
+    Reads a JSON file and returns the record that matches the given type.
+
+    Parameters:
+    - filename (str): The path to the JSON file.
+    - record_type (str): The desired type value to match.
+
+    Returns:
+    - dict: The first record that matches the given type, or None if not found.
+    """
+    
+    for analysis_record in omics_children_records["downstream_workflow_activity_records"]:
+        if analysis_record.get("type") == record_type:
+            return analysis_record
+                
+    return None
+
+def reads_qc_update(omics_record, template_file):
+    
+    workflow_type = "nmdc:ReadQCAnalysisActivity"
+    
+    reads_qc_record = get_record_by_type(omics_record, workflow_type)
+    for template in read_workflows_config(template_file):
+        if template['Type'] == "nmdc:ReadQcAnalysisActivity":
+            reads_qc_template = template
+            
+    #TODO:
+    #Use nmdc_schema db and update workflow recors and data objects for reads qc (update files)
+            
+    print(reads_qc_record, reads_qc_template)
+    
+    
+def process_analysis_sets(study_records, template_file,dry_run=False):
+    
+    count = 0
+    for omic_record in study_records:
+        omics_id = get_omics_id(omic_record)
+        print(omics_id)
+        reads_qc_update(omic_record, template_file)
+        if dry_run == True:
+            count += 1
+        if count == 1:
+            break
+    
+    
+
 def main():
     #TODO
     #1. Read in json dump of analysis records 
@@ -276,16 +326,7 @@ def main():
     pass
 
 if __name__ == "__main__":
-    mongo_url = os.environ["MONGO_URL"]
-    client = MongoClient(mongo_url, directConnection=True)
-    db = client.nmdc
-    # Read mapping list
-    # This should have:
-    # was_informed_by_old\twas_informed_by_new
-    # e.g.
-    # nmdc:mga0xxxxx    nmdc:omprc-11-xxxxx
-    omic_map = read_map()
-    for omic in omic_map:
-        process(db, omic, omic_map[omic])
-    # for each omics process
-    #     for act in [
+    test_file = "scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json"
+    template_file = "/global/cfs/cdirs/m3408/aim2/dev/reiding_scripts/nmdc_automation/configs/re_iding_worklfows.yaml"
+    stegen_data = read_json_file(test_file)
+    process_analysis_sets(stegen_data, template_file, dry_run=True)
\ No newline at end of file

From 2196856d33e87cc1ca6708b29b41208630668cae Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 31 Oct 2023 16:16:30 -0700
Subject: [PATCH 19/91] Change script output to a list of serialized Database
 instances

---
 ...sty-11-aygzgv51_assocated_record_dump.json | 60111 ++++++++--------
 .../rebuild_metagenome_workflow_records.py    |    48 +-
 2 files changed, 30055 insertions(+), 30104 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
index a7146766..37a912d9 100644
--- a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
@@ -1,301 +1,559 @@
 [
     {
-        "_id": {
-            "$oid": "649b009773e8249959349b33"
-        },
-        "id": "nmdc:omprc-11-bn8jcq58",
-        "name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
-        "description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
-        "has_input": [
-            "nmdc:bsm-11-qq8s6x03"
-        ],
-        "has_output": [
-            "jgi:55d740280d8785342fcf7e39"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "add_date": "2015-05-28",
-        "mod_date": "2021-06-15",
-        "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
-        "omics_type": {
-            "has_raw_value": "Metagenome"
-        },
-        "principal_investigator": {
-            "has_raw_value": "James Stegen"
-        },
-        "processing_institution": "JGI",
-        "type": "nmdc:OmicsProcessing",
-        "gold_sequencing_project_identifiers": [
-            "gold:Gp0115663"
-        ],
-        "downstream_workflow_activity_records": [
+        "functional_annotation_agg": [],
+        "library_preparation_set": [],
+        "processed_sample_set": [],
+        "extraction_set": [],
+        "activity_set": [],
+        "biosample_set": [],
+        "data_object_set": [
+            {
+                "name": "Gp0115663_Filtered Reads",
+                "description": "Filtered Reads for Gp0115663",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filtered.fastq.gz",
+                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                "id": "nmdc:7bf778baef033d36f118f8591256d6ef",
+                "file_size_bytes": 2571324879
+            },
+            {
+                "name": "Gp0115663_Filtered Stats",
+                "description": "Filtered Stats for Gp0115663",
+                "data_object_type": "QC Statistics",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filterStats.txt",
+                "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
+                "id": "nmdc:b99ce8adc125c95f0bfdadf36a3f6848",
+                "file_size_bytes": 290
+            },
+            {
+                "name": "Gp0115663_Gottcha2 TSV report",
+                "description": "Gottcha2 TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
+                "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
+                "id": "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                "file_size_bytes": 13174
+            },
+            {
+                "name": "Gp0115663_Gottcha2 full TSV report",
+                "description": "Gottcha2 full TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
+                "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
+                "id": "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                "file_size_bytes": 1035818
+            },
+            {
+                "name": "Gp0115663_Gottcha2 Krona HTML report",
+                "description": "Gottcha2 Krona HTML report for Gp0115663",
+                "data_object_type": "GOTTCHA2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
+                "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
+                "id": "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                "file_size_bytes": 262669
+            },
+            {
+                "name": "Gp0115663_Centrifuge classification TSV report",
+                "description": "Centrifuge classification TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
+                "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
+                "id": "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                "file_size_bytes": 2189843623
+            },
+            {
+                "name": "Gp0115663_Centrifuge TSV report",
+                "description": "Centrifuge TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
+                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+                "id": "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                "file_size_bytes": 260134
+            },
+            {
+                "name": "Gp0115663_Centrifuge Krona HTML report",
+                "description": "Centrifuge Krona HTML report for Gp0115663",
+                "data_object_type": "Centrifuge Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
+                "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
+                "id": "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                "file_size_bytes": 2343980
+            },
+            {
+                "name": "Gp0115663_Kraken classification TSV report",
+                "description": "Kraken classification TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
+                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
+                "id": "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                "file_size_bytes": 1785563917
+            },
+            {
+                "name": "Gp0115663_Kraken2 TSV report",
+                "description": "Kraken2 TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
+                "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+                "id": "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                "file_size_bytes": 699896
+            },
+            {
+                "name": "Gp0115663_Kraken2 Krona HTML report",
+                "description": "Kraken2 Krona HTML report for Gp0115663",
+                "data_object_type": "Kraken2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
+                "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+                "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
+                "file_size_bytes": 4221977
+            },
+            {
+                "name": "Gp0115663_Gottcha2 TSV report",
+                "description": "Gottcha2 TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
+                "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
+                "id": "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                "file_size_bytes": 13174
+            },
+            {
+                "name": "Gp0115663_Gottcha2 full TSV report",
+                "description": "Gottcha2 full TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
+                "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
+                "id": "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                "file_size_bytes": 1035818
+            },
+            {
+                "name": "Gp0115663_Gottcha2 Krona HTML report",
+                "description": "Gottcha2 Krona HTML report for Gp0115663",
+                "data_object_type": "GOTTCHA2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
+                "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
+                "id": "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                "file_size_bytes": 262669
+            },
+            {
+                "name": "Gp0115663_Centrifuge classification TSV report",
+                "description": "Centrifuge classification TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
+                "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
+                "id": "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                "file_size_bytes": 2189843623
+            },
+            {
+                "name": "Gp0115663_Centrifuge TSV report",
+                "description": "Centrifuge TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
+                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+                "id": "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                "file_size_bytes": 260134
+            },
+            {
+                "name": "Gp0115663_Centrifuge Krona HTML report",
+                "description": "Centrifuge Krona HTML report for Gp0115663",
+                "data_object_type": "Centrifuge Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
+                "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
+                "id": "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                "file_size_bytes": 2343980
+            },
+            {
+                "name": "Gp0115663_Kraken classification TSV report",
+                "description": "Kraken classification TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
+                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
+                "id": "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                "file_size_bytes": 1785563917
+            },
+            {
+                "name": "Gp0115663_Kraken2 TSV report",
+                "description": "Kraken2 TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
+                "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+                "id": "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                "file_size_bytes": 699896
+            },
+            {
+                "name": "Gp0115663_Kraken2 Krona HTML report",
+                "description": "Kraken2 Krona HTML report for Gp0115663",
+                "data_object_type": "Kraken2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
+                "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+                "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
+                "file_size_bytes": 4221977
+            },
+            {
+                "name": "Gp0115663_Assembled contigs fasta",
+                "description": "Assembled contigs fasta for Gp0115663",
+                "data_object_type": "Assembly Contigs",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna",
+                "md5_checksum": "deddd162bf0128fba13b3bc1ca38d1aa",
+                "id": "nmdc:deddd162bf0128fba13b3bc1ca38d1aa",
+                "file_size_bytes": 90115831
+            },
+            {
+                "name": "Gp0115663_Assembled scaffold fasta",
+                "description": "Assembled scaffold fasta for Gp0115663",
+                "data_object_type": "Assembly Scaffolds",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna",
+                "md5_checksum": "b3573e3cda5a06611de71ca04c5c14cc",
+                "id": "nmdc:b3573e3cda5a06611de71ca04c5c14cc",
+                "file_size_bytes": 89604715
+            },
+            {
+                "name": "Gp0115663_Metagenome Contig Coverage Stats",
+                "description": "Metagenome Contig Coverage Stats for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_covstats.txt",
+                "md5_checksum": "c6d0d4cea985ca6fb50a060e15b4a856",
+                "id": "nmdc:c6d0d4cea985ca6fb50a060e15b4a856",
+                "file_size_bytes": 13412363
+            },
+            {
+                "name": "Gp0115663_Assembled AGP file",
+                "description": "Assembled AGP file for Gp0115663",
+                "data_object_type": "Assembly AGP",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_assembly.agp",
+                "md5_checksum": "f450e3800e17691d5874c89fc46c186a",
+                "id": "nmdc:f450e3800e17691d5874c89fc46c186a",
+                "file_size_bytes": 12542171
+            },
+            {
+                "name": "Gp0115663_Metagenome Alignment BAM file",
+                "description": "Metagenome Alignment BAM file for Gp0115663",
+                "data_object_type": "Assembly Coverage BAM",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_pairedMapped_sorted.bam",
+                "md5_checksum": "31dc958d116d02122509e90b0883954f",
+                "id": "nmdc:31dc958d116d02122509e90b0883954f",
+                "file_size_bytes": 2773429299
+            },
+            {
+                "name": "Gp0115663_Protein FAA",
+                "description": "Protein FAA for Gp0115663",
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-            "emsl:output_456519"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456519"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349bff"
-        },
-        "id": "nmdc:omprc-11-4kgm5w41",
-        "name": "SBR_FC_S1_20-30_H2Oext_15Oct15_Leopard_1_01_4533",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-qyz13338"
-        ],
-        "has_output": [
-            "emsl:output_456515"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456515"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c00"
-        },
-        "id": "nmdc:omprc-11-6xm1va42",
-        "name": "SBR_FC_S1_50-60_H2Oext_13Oct15_Leopard_1_01_4425",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-pnzwey18"
-        ],
-        "has_output": [
-            "emsl:output_456529"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456529"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c01"
-        },
-        "id": "nmdc:omprc-11-t2yd9m69",
-        "name": "SBR_FC_S2_00-10_H2Oext_15Oct15_Leopard_1_01_4537",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-60ayn103"
-        ],
-        "has_output": [
-            "emsl:output_456535"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456535"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c02"
-        },
-        "id": "nmdc:omprc-11-9d9fxj83",
-        "name": "SBR_FC_S2_10-20_H2Oext_15Oct15_Leopard_1_01_4538",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-e3hp0a71"
-        ],
-        "has_output": [
-            "emsl:output_456540"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456540"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c03"
-        },
-        "id": "nmdc:omprc-11-1rkm8b52",
-        "name": "SBR_FC_S2_10-20_H2Oext_13Oct15_Leopard_1_01_4427",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-e3hp0a71"
-        ],
-        "has_output": [
-            "emsl:output_456539"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456539"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c04"
-        },
-        "id": "nmdc:omprc-11-bzhsj954",
-        "name": "SBR_FC_S2_30-40_H2Oext_15Oct15_Leopard_1_01_4540",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-73qw2q23"
-        ],
-        "has_output": [
-            "emsl:output_456550"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456550"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c05"
-        },
-        "id": "nmdc:omprc-11-ae716322",
-        "name": "SBR_FC_S2_20-30_H2Oext_13Oct15_Leopard_1_01_4428",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-pknfsy79"
-        ],
-        "has_output": [
-            "emsl:output_456544"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456544"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c06"
-        },
-        "id": "nmdc:omprc-11-ryy9gp08",
-        "name": "SBR_FC_S3_00-10_H2Oext_15Oct15_Leopard_1_01_4543",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-rs67sh23"
-        ],
-        "has_output": [
-            "emsl:output_456565"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456565"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c07"
-        },
-        "id": "nmdc:omprc-11-qx18h332",
-        "name": "SBR_FC_S3_10-20_H2Oext_13Oct15_Leopard_1_01_4433",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-83ghpk10"
-        ],
-        "has_output": [
-            "emsl:output_456569"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456569"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c08"
-        },
-        "id": "nmdc:omprc-11-k3e66918",
-        "name": "SBR_FC_S3_00-10_H2Oext_13Oct15_Leopard_1_01_4432",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-rs67sh23"
-        ],
-        "has_output": [
-            "emsl:output_456564"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456564"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c09"
-        },
-        "id": "nmdc:omprc-11-nq83nd29",
-        "name": "SBR_FC_S3_20-30_H2Oext_13Oct15_Leopard_1_01_4434",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-5p6f9e18"
-        ],
-        "has_output": [
-            "emsl:output_456574"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456574"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c0a"
-        },
-        "id": "nmdc:omprc-11-xsnaaj68",
-        "name": "SBR_FC_S2_20-30_H2Oext_15Oct15_Leopard_1_01_4539",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-pknfsy79"
-        ],
-        "has_output": [
-            "emsl:output_456545"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456545"
-        ],
-        "downstream_workflow_activity_records": []
-    },
-    {
-        "_id": {
-            "$oid": "649b009773e8249959349c0b"
-        },
-        "id": "nmdc:omprc-11-409hwb80",
-        "name": "SBR_FC_S3_30-40_H2Oext_13Oct15_Leopard_1_01_4435",
-        "description": "High resolution MS spectra only",
-        "has_input": [
-            "nmdc:bsm-11-ea7re871"
-        ],
-        "has_output": [
-            "emsl:output_456579"
-        ],
-        "part_of": [
-            "nmdc:sty-11-aygzgv51"
-        ],
-        "instrument_name": "12T_FTICR_B",
-        "omics_type": {
-            "has_raw_value": "Organic Matter Characterization"
-        },
-        "processing_institution": "EMSL",
-        "type": "nmdc:OmicsProcessing",
-        "alternative_identifiers": [
-            "emsl:456579"
-        ],
-        "downstream_workflow_activity_records": []
     }
 ]
\ No newline at end of file
diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index d7a4442b..04e78896 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -13,6 +13,7 @@
 
 from nmdc_automation.api import NmdcRuntimeUserApi
 from nmdc_automation.config import Config
+import nmdc_schema.nmdc as nmdc
 
 GOLD_STUDY_ID = "gold:Gs0114663"
 STUDY_ID = "nmdc:sty-11-aygzgv51"
@@ -82,75 +83,52 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         f"Retrieved {len(omics_processing_records)} OmicsProcessing records for study {study_id}"
     )
     
-    workflow_records_per_study = []
-
+    retrieved_databases = []
     # 2. For each OmicsProcessing record, find the legacy identifier:
     for omics_processing_record in omics_processing_records:
+        db = nmdc.Database()
         logging.info(f"omics_processing_record: "
                      f"{omics_processing_record['id']}")
         legacy_id = _get_legacy_id(omics_processing_record)
         logging.info(f"legacy_id: {legacy_id}")
 
-        omics_processing_record["downstream_workflow_activity_records"] = []
-
         if (omics_processing_record["omics_type"]["has_raw_value"] !=
                 "Metagenome"):
             logging.info(f"omics_processing_record {omics_processing_record['id']} "
                          f"is not a Metagenome")
             continue
-
-        # reads QC records
-        # Downstream WorkflowExecutionActivity records depend on the `has_output`
-        # data object of the ReadQcAnalysisActivity record.
-        set_name = "read_qc_analysis_activity_set"
-        read_qc_records = query_api_client.get_workflow_activity_informed_by(
-            set_name, legacy_id
-        )
-        # Add the data objects referenced by the `has_output` property
-        for record in read_qc_records:
-            record["output_data_objects"] = []
-            for data_object_id in record["has_output"]:
-                data_object_record = query_api_client.get_data_object_by_id(
-                    data_object_id
-                )
-                record["output_data_objects"].append(data_object_record)
-
-
-        logging.info(f"Found {len(read_qc_records)} read_qc_records")
-        omics_processing_record[
-            "downstream_workflow_activity_records"].extend(read_qc_records)
+        db.omics_processing_set.append(omics_processing_record)
 
         # downstream workflow activity sets
-        taxonomy_records, read_based_analysis_records, metagenome_assembly_records, \
-            metagenome_annotation_records, mags_records = [], [], [], [], []
+        (read_qc_records, taxonomy_records, read_based_analysis_records,
+         metagenome_assembly_records,
+            metagenome_annotation_records, mags_records) = [], [], [], [], [], []
 
         downstream_workflow_activity_sets = {
+            "read_qc_analysis_activity_set": read_qc_records,
             "read_based_taxonomy_analysis_activity_set": taxonomy_records,
             "read_based_analysis_activity_set": read_based_analysis_records,
             "metagenome_assembly_set": metagenome_assembly_records,
             "metagenome_annotation_activity_set": metagenome_annotation_records,
             "mags_activity_set": mags_records,
         }
-
         for set_name, records in downstream_workflow_activity_sets.items():
             records = query_api_client.get_workflow_activity_informed_by(
                 set_name, legacy_id
             )
+            db.__setattr__(set_name, records)
             # Add the data objects referenced by the `has_output` property
             for record in records:
-                record["output_data_objects"] = []
                 for data_object_id in record["has_output"]:
                     data_object_record = query_api_client.get_data_object_by_id(
                         data_object_id
                     )
-                    record["output_data_objects"].append(data_object_record)
-            omics_processing_record[
-                "downstream_workflow_activity_records"].extend(records)
-            workflow_records_per_study.append(records)
-            logging.info(f"Found {len(records)} {set_name} records")
+                    db.data_object_set.append(data_object_record)
+
+        retrieved_databases.append(db)
         
     with open(f"{study_id}_assocated_record_dump.json", 'w') as json_file:
-        json.dump(omics_processing_records, json_file, indent=4)
+        json.dump([o.__dict__ for o in retrieved_databases], json_file, indent=4)
 
 
 if __name__ == "__main__":

From 0538575103dd2b55349a1ee5274e0f86974ef201 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Wed, 1 Nov 2023 14:07:39 -0700
Subject: [PATCH 20/91] added dry run for reads qc transformation

---
 nmdc_automation/re_iding/re_id_process.py | 132 +++++++++++++++-------
 1 file changed, 93 insertions(+), 39 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index 633129bb..a47de8e5 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -11,6 +11,7 @@
 from re_id_file_operations import *
 import nmdc_schema.nmdc as nmdc
 from linkml_runtime.dumpers import json_dumper
+import shutil 
 
 ###GLOBAL######
 nmdc_db = nmdc.Database()
@@ -109,7 +110,7 @@ def process(db, old_id, new_id):
     return assocaited_data_object
 
 
-def minter(config,shoulder):
+def minter(shoulder):
     """
     Creates a new ID based on the provided shoulder.
     
@@ -120,8 +121,6 @@ def minter(config,shoulder):
     - A new ID string
     """
     
-    runtime_api = NmdcRuntimeApi(config)
-    
     return runtime_api.minter(shoulder)
 
 
@@ -130,9 +129,20 @@ def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
     Use the url to compute the new file name path and url
     """
     file_name = old_url.split("/")[-1]
+    suffix = old_url.split("https://data.microbiomedata.org/data/")[1]
+    old_file_path = base_dir + "/" + suffix
     file_extenstion = file_name.lstrip("nmdc_").split("_", maxsplit=1)[-1]
     new_file_name = f"{act_id}_{file_extenstion}"
     destination = os.path.join(new_base_dir, new_file_name)
+    
+    try:
+        os.link(old_file_path, destination)
+        print(f"Successfully created link between {old_file_path} and {destination}")
+    except OSError as e:
+        print(f"An error occurred while linking the file: {e}")
+    except Exception as e:
+        print(f"Unexpected error: {e}")
+    
     new_url = f"{base}/{omic_id}/{act_id}/{new_file_name}"
     return new_url, destination, new_file_name
 
@@ -215,47 +225,43 @@ def copy_outputs(db, outputs, omic_id, act_id):
     return new_ids, new_data_objects
 
 
-def make_activity_set(nmdc_db, omics_id, has_input, has_output,workflow_record):
-    database_activity_set = getattr(nmdc_db, workflow_record["Collection"])
+def make_activity_set(omics_id, activity_id, has_input, has_output, started_time, ended_time, workflow_record_template):
+    #look at activity range
+    database_activity_set = getattr(nmdc_db, workflow_record_template["Collection"])
     # Lookup the nmdc schema range class
-    database_activity_range = getattr(nmdc_db, workflow_record["ActivityRange"])
-    # Mint an ID
-    new_id = minter(workflow_record["Type"])
+    database_activity_range = getattr(nmdc, workflow_record_template["ActivityRange"])
     
-    activity_id = new_id
     database_activity_set.append(
         database_activity_range(
             id=activity_id,
-            name=workflow_record["Activity"]["name"].replace("{id}", activity_id),
-            git_url=workflow_record["Git_repo"],
-            version=workflow_record["Version"],
+            name=workflow_record_template["Activity"]["name"].replace("{id}", activity_id),
+            git_url=workflow_record_template["Git_repo"],
+            version=workflow_record_template["Version"],
             part_of=[omics_id],
             execution_resource="Perlmutter - Nersc",
-            started_at_time=datetime.datetime.now(pytz.utc).isoformat(),
+            started_at_time=started_time,
             has_input=has_input,
             has_output=has_output,
-            type=workflow_record["Type"],
-            ended_at_time=datetime.datetime.now(pytz.utc).isoformat(),
+            type=workflow_record_template["Type"],
+            ended_at_time=ended_time,
             was_informed_by=omics_id,
         )
     )
 
-def make_data_object(data_object_record, omics_id):
+def make_data_object(data_object_record, new_do_id, new_url, updated_name, updated_description):
 
     nmdc_db.data_object_set.append(
         nmdc.DataObject(
-            file_size_bytes=data_object_record["file_size"],
-            name=data_object_record["data_object_name"],
-            url=data_object_record["data_object_url"],
-            data_object_type=["data_object_type"],
+            file_size_bytes=data_object_record["file_size_bytes"],
+            name=updated_name,
+            url=new_url,
+            data_object_type=data_object_record["data_object_type"],
             type="nmdc:DataObject",
-            id=minter("nmdc:DataObject"),
+            id=new_do_id,
             md5_checksum=data_object_record["md5_checksum"],
-            description=data_object_record["description"].replace(
-                "{id}",omics_id
+            description=updated_description
             ),
         )
-    )
 
 def post_database_object_to_runtime(datase_object):
     
@@ -266,39 +272,80 @@ def post_database_object_to_runtime(datase_object):
     return res
 
 def get_omics_id(omics_record):
-    return omics_record["id"]
+    for rec in omics_record["omics_processing_set"]:
+        return rec["id"]
 
-def get_record_by_type(omics_children_records, record_type):
+def get_record_by_type(related_omic_records, record_type):
     """
-    Reads a JSON file and returns the record that matches the given type.
+    Returns the record that matches the given type.
 
     Parameters:
-    - filename (str): The path to the JSON file.
+    - related_omic_records (dict): records for an omics processing record.
     - record_type (str): The desired type value to match.
 
     Returns:
     - dict: The first record that matches the given type, or None if not found.
     """
     
-    for analysis_record in omics_children_records["downstream_workflow_activity_records"]:
-        if analysis_record.get("type") == record_type:
-            return analysis_record
-                
-    return None
+    return related_omic_records[record_type]
 
-def reads_qc_update(omics_record, template_file):
+def get_data_object_by_type(related_omic_records, old_activity_record):
+    
+    data_object_list = []
+    
+    for act_record in old_activity_record:
+        has_output_list = act_record["has_output"]
+    for do_record in related_omic_records["data_object_set"]:
+        if do_record["id"] in has_output_list:
+            data_object_list.append(do_record)
+            
+    return data_object_list
+        
+def get_associate_data_object_template(data_object_type,data_object_templates):
+    for data_object in data_object_templates:
+        if data_object_type == data_object["data_object_type"]:
+            return data_object
+    return None
     
-    workflow_type = "nmdc:ReadQCAnalysisActivity"
+def reads_qc_update(omics_record, template_file, omic_id):
+    
+    workflow_type = "read_qc_analysis_activity_set"
     
     reads_qc_record = get_record_by_type(omics_record, workflow_type)
+    reads_qc_data_objects = get_data_object_by_type(omics_record, reads_qc_record)
     for template in read_workflows_config(template_file):
         if template['Type'] == "nmdc:ReadQcAnalysisActivity":
             reads_qc_template = template
             
-    #TODO:
-    #Use nmdc_schema db and update workflow recors and data objects for reads qc (update files)
             
-    print(reads_qc_record, reads_qc_template)
+    new_act_id = minter(reads_qc_template["Type"])
+    new_qc_base_dir = os.path.join(base_dir, omic_id, new_act_id)
+    os.makedirs(new_qc_base_dir,exist_ok=True)
+    updated_has_output_list = []
+    
+    for data_object in reads_qc_data_objects:
+        dobj_tmpl = get_associate_data_object_template(data_object["data_object_type"],reads_qc_template["Outputs"])
+        new_do_id = minter("nmdc:DataObject")
+        new_description = re.sub('[^ ]+$', f"{omic_id}", data_object["description"])
+        new_url, destination, _ = compute_new_paths(data_object["url"], new_qc_base_dir, omic_id, new_act_id)
+        make_data_object(data_object, new_do_id, new_url, dobj_tmpl["name"], new_description)
+        updated_has_output_list.append(new_do_id)
+    
+    for rec in reads_qc_record:
+        has_input = rec["has_input"]
+        started_time = rec["started_at_time"]
+        ended_time = rec["ended_at_time"]
+    #need to change has input to be updated as well, 
+    make_activity_set(omic_id, new_act_id, has_input, updated_has_output_list, started_time, ended_time, reads_qc_template)
+        
+    
+    nmdc_database_object = json.loads(
+            json_dumper.dumps(nmdc_db, inject_type=False)
+        )
+        
+    print(nmdc_database_object)
+    
+    return destination
     
     
 def process_analysis_sets(study_records, template_file,dry_run=False):
@@ -307,9 +354,16 @@ def process_analysis_sets(study_records, template_file,dry_run=False):
     for omic_record in study_records:
         omics_id = get_omics_id(omic_record)
         print(omics_id)
-        reads_qc_update(omic_record, template_file)
+        destination = reads_qc_update(omic_record, template_file, omics_id)
         if dry_run == True:
             count += 1
+        dir_path = os.path.dirname(destination)
+        parent_dir_path = os.path.dirname(dir_path)
+        try:
+            shutil.rmtree(parent_dir_path)
+            print(f"Directory {parent_dir_path} and all its contents removed successfully!")
+        except OSError as e:
+            print(f"Error: {e}")
         if count == 1:
             break
     

From f59486a57887ba965e3f9550b775a87912ed68cf Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Wed, 1 Nov 2023 14:07:59 -0700
Subject: [PATCH 21/91] added ActivityRange for workflows

---
 configs/re_iding_worklfows.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/configs/re_iding_worklfows.yaml b/configs/re_iding_worklfows.yaml
index 7fbce6ef..b77da9a4 100644
--- a/configs/re_iding_worklfows.yaml
+++ b/configs/re_iding_worklfows.yaml
@@ -6,6 +6,7 @@ Workflows:
     Version: v1.0.8
     WDL: rqcfilter.wdl
     Collection: read_qc_analysis_activity_set
+    ActivityRange: ReadQcAnalysisActivity
     Filter Input Objects:
     - Metagenome Raw Reads
     Predecessors:
@@ -46,6 +47,7 @@ Workflows:
     Version: v1.0.3
     WDL: jgi_assembly.wdl
     Collection: metagenome_assembly_set
+    ActivityRange: MetagenomeAssembly
     Predecessors:
     - Reads QC
     - Reads QC Interleave
@@ -121,6 +123,7 @@ Workflows:
     Version: v1.0.5
     WDL: ReadbasedAnalysis.wdl
     Collection: read_based_taxonomy_analysis_activity_set
+    ActivityRange: ReadBasedTaxonomyAnalysisActivity
     Predecessors:
     - Reads QC
     - Reads QC Interleave

From 966d367d9f9c6a7fb3e0c224cf098d41cbb3a5be Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 1 Nov 2023 14:08:42 -0700
Subject: [PATCH 22/91] remove reads_based_analysis_acrtivity_set

---
 .../re_iding/scripts/rebuild_metagenome_workflow_records.py  | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index 04e78896..a32ceb99 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -100,14 +100,13 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         db.omics_processing_set.append(omics_processing_record)
 
         # downstream workflow activity sets
-        (read_qc_records, taxonomy_records, read_based_analysis_records,
+        (read_qc_records, taxonomy_records,
          metagenome_assembly_records,
-            metagenome_annotation_records, mags_records) = [], [], [], [], [], []
+            metagenome_annotation_records, mags_records) = [], [], [], [], []
 
         downstream_workflow_activity_sets = {
             "read_qc_analysis_activity_set": read_qc_records,
             "read_based_taxonomy_analysis_activity_set": taxonomy_records,
-            "read_based_analysis_activity_set": read_based_analysis_records,
             "metagenome_assembly_set": metagenome_assembly_records,
             "metagenome_annotation_activity_set": metagenome_annotation_records,
             "mags_activity_set": mags_records,

From ec7b528d72a03518cc46a63d44f02e16985f1d6d Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 2 Nov 2023 10:04:25 -0700
Subject: [PATCH 23/91] remove unused functions

---
 nmdc_automation/re_iding/re_id_process.py | 182 +++++++++-------------
 1 file changed, 75 insertions(+), 107 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index a47de8e5..7733cbca 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -62,54 +62,6 @@ def read_map():
     return omap
 
 
-def find_dir(db, old_id):
-    """
-    Finds and returns the directory name associated with the given ID.
-    
-    Parameters:
-    - db: Database connection object
-    - old_id: The old ID for which the directory name is required
-    """
-    query_by_omics_id = {"was_informed_by": old_id}
-    activity_record = db.read_qc_analysis_activity_set.find_one(query_by_omics_id)
-    query_by_id = {"id": activity_record['has_output'][0]}
-    data_object_record = db.data_object_set.find_one(query_by_id)
-    return data_object_record['url'].split('/')[4]
-
-
-def process(db, old_id, new_id):
-    """
-    Process the given old ID and returns the associated data.
-    
-    Parameters:
-    - db: Database connection object
-    - old_id: The old ID to be processed
-    - new_id: The new ID to be used
-    
-    Returns:
-    - out: A dictionary containing processed data.
-    """
-    directory_name = find_dir(db, old_id)
-    assocaited_data_object = {"data_object_set": []}
-    for col in sets:
-        query_by_old_id = {"was_informed_by": old_id}
-        res = db[col].find(query_by_old_id)
-        count = 0
-        for doc in res:
-            count += 1
-        if count != 1:
-            raise ValueError("Too many matches.  Failing")
-        doc.pop("_id")
-        atype = doc['type']
-        func_name = atype.lower().replace("nmdc:", "")
-        func = globals()[func_name]
-        activity_records, data_object_records = func(db, doc, new_id)
-        assocaited_data_object[col] =[activity_records]
-        assocaited_data_object["data_object_set"].extend(data_object_records)
-    json.dump(assocaited_data_object, open(f"{new_id}.json", "w"), indent=2)
-    return assocaited_data_object
-
-
 def minter(shoulder):
     """
     Creates a new ID based on the provided shoulder.
@@ -133,7 +85,8 @@ def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
     old_file_path = base_dir + "/" + suffix
     file_extenstion = file_name.lstrip("nmdc_").split("_", maxsplit=1)[-1]
     new_file_name = f"{act_id}_{file_extenstion}"
-    destination = os.path.join(new_base_dir, new_file_name)
+    modified_new_file_name = new_file_name.replace(":", "_")
+    destination = os.path.join(new_base_dir, modified_new_file_name)
     
     try:
         os.link(old_file_path, destination)
@@ -171,60 +124,6 @@ def find_type(obj):
         return None
 
 
-def copy_outputs(db, outputs, omic_id, act_id):
-    """
-    Copy output data objects and generate new metadata for them.
-    
-    Args:
-    - db (MongoClient): MongoDB client instance to fetch data.
-    - outputs (list): List of output object IDs.
-    - omic_id (str): ID of the omics process.
-    - act_id (str): ID of the activity.
-    
-    Returns:
-    - tuple: List of new object IDs and the new objects themselves.
-    """
-    new_data_objects = []
-    new_ids = []
-    new_base_dir = os.path.join(base_dir, omic_id, act_id)
-    os.makedirs(new_base_dir, exist_ok=True)
-    for data_obj_id in outputs:
-        data_obj = db.data_object_set.find_one({"id": data_obj_id})
-        old_url = data_obj["url"]
-        new_url, dst, new_fn = compute_new_paths(old_url, new_base_dir, omic_id, act_id)
-        new_id = minter("dobj")
-        log_mapping("data", data_obj["id"], new_id)
-
-        # Create new obj
-        data_obj.pop("_id")
-        desc = data_obj["description"]
-        data_obj["description"] = re.sub('[^ ]+$', f"{omic_id}", desc)
-        data_obj["url"] = new_url
-        data_obj["id"] = new_id
-        data_obj["name"] = new_fn
-        data_type = find_type(data_obj)
-        data_obj["data_object_type"] = data_type
-
-        # Link the file
-        src = old_url.replace(base, base_dir)
-        func_name = "bogus"
-        if data_type:
-            func_name = data_type.replace(" ", "_").lower()
-        if func_name in globals():
-            sys.stderr.write(f"Using func {func_name}\n")
-            func = globals()[func_name]
-            md5, size = func(src, dst, omic_id, act_id)
-            data_obj["file_size_bytes"] = size
-            data_obj["md5_checksum"] = md5
-        else:
-            os.link(src, dst)
-
-        # Add to the lists
-        new_ids.append(new_id)
-        new_data_objects.append(data_obj)
-    return new_ids, new_data_objects
-
-
 def make_activity_set(omics_id, activity_id, has_input, has_output, started_time, ended_time, workflow_record_template):
     #look at activity range
     database_activity_set = getattr(nmdc_db, workflow_record_template["Collection"])
@@ -238,7 +137,7 @@ def make_activity_set(omics_id, activity_id, has_input, has_output, started_time
             git_url=workflow_record_template["Git_repo"],
             version=workflow_record_template["Version"],
             part_of=[omics_id],
-            execution_resource="Perlmutter - Nersc",
+            execution_resource="NERSC - Perlmutter",
             started_at_time=started_time,
             has_input=has_input,
             has_output=has_output,
@@ -308,29 +207,47 @@ def get_associate_data_object_template(data_object_type,data_object_templates):
     return None
     
 def reads_qc_update(omics_record, template_file, omic_id):
+    """Extracts relevant information from omics record and template file, update data objects for reads qc
+        and the analysis activity set record. Performs necessary file operation as well
+
+    Args:
+        omics_record (dict): omics record corresponding to downstream workflows
+        template_file (file): template yaml file for relavant worklfows metadata
+        omic_id (str): string identifier of omics id
+
+    Returns:
+        nmdc_database_object: dump of nmdc object
+    """
     
     workflow_type = "read_qc_analysis_activity_set"
-    
+    #extract needed metaadata
     reads_qc_record = get_record_by_type(omics_record, workflow_type)
     reads_qc_data_objects = get_data_object_by_type(omics_record, reads_qc_record)
     for template in read_workflows_config(template_file):
         if template['Type'] == "nmdc:ReadQcAnalysisActivity":
             reads_qc_template = template
             
-            
+    #set up needed variables       
     new_act_id = minter(reads_qc_template["Type"])
     new_qc_base_dir = os.path.join(base_dir, omic_id, new_act_id)
     os.makedirs(new_qc_base_dir,exist_ok=True)
     updated_has_output_list = []
     
+    #hold input to downstream workflows
+    input_to_downstream_workflows = []
+    #make new data objects
     for data_object in reads_qc_data_objects:
         dobj_tmpl = get_associate_data_object_template(data_object["data_object_type"],reads_qc_template["Outputs"])
         new_do_id = minter("nmdc:DataObject")
+        #save filtered reads
+        if data_object["data_object_type"] == "Filtered Sequencing Reads":
+            input_to_downstream_workflows.append(new_do_id)
         new_description = re.sub('[^ ]+$', f"{omic_id}", data_object["description"])
         new_url, destination, _ = compute_new_paths(data_object["url"], new_qc_base_dir, omic_id, new_act_id)
         make_data_object(data_object, new_do_id, new_url, dobj_tmpl["name"], new_description)
         updated_has_output_list.append(new_do_id)
     
+    #make updated activity record
     for rec in reads_qc_record:
         has_input = rec["has_input"]
         started_time = rec["started_at_time"]
@@ -339,6 +256,57 @@ def reads_qc_update(omics_record, template_file, omic_id):
     make_activity_set(omic_id, new_act_id, has_input, updated_has_output_list, started_time, ended_time, reads_qc_template)
         
     
+    nmdc_database_object = json.loads(
+            json_dumper.dumps(nmdc_db, inject_type=False)
+        )
+        
+    print(nmdc_database_object)
+    
+    return input_to_downstream_workflows, destination
+
+def assembly_update(omics_record, template_file, omic_id, workflow_inputs):
+    """Extracts relevant information from omics record and template file, update data objects for assembly
+        and the analysis activity set record. Performs necessary file operation as well
+
+    Args:
+        omics_record (dict): omics record corresponding to downstream workflows
+        template_file (file): template yaml file for relavant worklfows metadata
+        omic_id (str): string identifier of omics id
+
+    Returns:
+        nmdc_database_object: dump of nmdc object
+    """
+    
+    workflow_type = "metagenome_assembly_set"
+    #extract needed metaadata
+    reads_qc_record = get_record_by_type(omics_record, workflow_type)
+    reads_qc_data_objects = get_data_object_by_type(omics_record, reads_qc_record)
+    for template in read_workflows_config(template_file):
+        if template['Type'] == "nmdc:MetagenomeAssembly":
+            reads_qc_template = template
+            
+    #set up needed variables       
+    new_act_id = minter(reads_qc_template["Type"])
+    new_qc_base_dir = os.path.join(base_dir, omic_id, new_act_id)
+    os.makedirs(new_qc_base_dir,exist_ok=True)
+    updated_has_output_list = []
+    
+    #make new data objects
+    for data_object in reads_qc_data_objects:
+        dobj_tmpl = get_associate_data_object_template(data_object["data_object_type"],reads_qc_template["Outputs"])
+        new_do_id = minter("nmdc:DataObject")
+        new_description = re.sub('[^ ]+$', f"{omic_id}", data_object["description"])
+        new_url, destination, _ = compute_new_paths(data_object["url"], new_qc_base_dir, omic_id, new_act_id)
+        make_data_object(data_object, new_do_id, new_url, dobj_tmpl["name"], new_description)
+        updated_has_output_list.append(new_do_id)
+    
+    for rec in reads_qc_record:
+        started_time = rec["started_at_time"]
+        ended_time = rec["ended_at_time"]
+    #need to change has input to be updated as well, 
+    make_activity_set(omic_id, new_act_id, workflow_inputs, updated_has_output_list, started_time, ended_time, reads_qc_template)
+        
+    
     nmdc_database_object = json.loads(
             json_dumper.dumps(nmdc_db, inject_type=False)
         )
@@ -354,7 +322,7 @@ def process_analysis_sets(study_records, template_file,dry_run=False):
     for omic_record in study_records:
         omics_id = get_omics_id(omic_record)
         print(omics_id)
-        destination = reads_qc_update(omic_record, template_file, omics_id)
+        downstream_input, destination = reads_qc_update(omic_record, template_file, omics_id)
         if dry_run == True:
             count += 1
         dir_path = os.path.dirname(destination)

From d3b1a30c8b21be2f960e435fd1a838272fb9d13f Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 2 Nov 2023 13:34:55 -0700
Subject: [PATCH 24/91] helper bash script to rename bam

---
 .../re_iding/scripts/rewrite_bam.sh           | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100755 nmdc_automation/re_iding/scripts/rewrite_bam.sh

diff --git a/nmdc_automation/re_iding/scripts/rewrite_bam.sh b/nmdc_automation/re_iding/scripts/rewrite_bam.sh
new file mode 100755
index 00000000..558e8c92
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/rewrite_bam.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+#
+
+# IMG=microbiomedata/workflowmeta:1.0.5.1
+IMG=biocontainers/samtools:1.3.1
+
+if [ "$1" = "inside" ] ; then
+	in=$2
+	out=$3
+	old=$4
+	new=$5
+	echo "Rewriting $out"
+	samtools view -h $in | sed "s/${old}/${new}/g" | \
+          samtools view -hb -o $out
+else 
+	touch $2
+	#shifter --image=$IMG $0 inside $@
+fi
+

From 789463d8b89585d2cca4c2662d04a0d2475c0eb4 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 2 Nov 2023 13:38:11 -0700
Subject: [PATCH 25/91] added operations for assembly

---
 .../re_iding/re_id_file_operations.py         | 80 +++++++++++--------
 1 file changed, 46 insertions(+), 34 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_file_operations.py b/nmdc_automation/re_iding/re_id_file_operations.py
index 8ca469c1..132b962c 100644
--- a/nmdc_automation/re_iding/re_id_file_operations.py
+++ b/nmdc_automation/re_iding/re_id_file_operations.py
@@ -1,17 +1,22 @@
 import subprocess
-import gzip 
+import gzip
 import os
 import json
 import hashlib
 from subprocess import check_output
 
+
+base_dir = "/global/cfs/cdirs/m3408/results"
+bam_script = "/global/u2/n/nmdcda/tasks/re_id/rewrite_bam.sh"
+
+
 def md5_sum(fn):
     """
     Calculate the MD5 hash of a file.
-    
+
     Args:
     - fn (str): Path to the file for which the MD5 hash is to be computed.
-    
+
     Returns:
     - str: The MD5 hash of the file.
     """
@@ -21,6 +26,7 @@ def md5_sum(fn):
             file_hash.update(chunk)
     return file_hash.hexdigest()
 
+
 def read_json_file(filename):
     """
     Read a JSON file and return its content as a dictionary.
@@ -31,22 +37,23 @@ def read_json_file(filename):
     Returns:
     - dict: The content of the JSON file.
     """
-    with open(filename, 'r') as json_file:
+    with open(filename, "r") as json_file:
         data = json.load(json_file)
     return data
 
+
 def rewrite_id(src, dst, old_id, new_id, prefix=None):
     """
     Rewrite lines in a file, replacing occurrences of an old ID with a new ID.
     An optional prefix can be specified to limit which lines are modified.
-    
+
     Args:
     - src (str): Source file path.
     - dst (str): Destination file path.
     - old_id (str): ID to be replaced.
     - new_id (str): Replacement ID.
     - prefix (str, optional): Prefix character to determine which lines to modify. Defaults to None.
-    
+
     Returns:
     - tuple: MD5 checksum and size (in bytes) of the modified file.
     """
@@ -69,71 +76,76 @@ def find_assembly_id(src):
     return "_".join(line[1:].split("_")[0:-1])
 
 
-def assembly_contigs(src, dst, omic_id, act_id):
+def assembly_contigs(src, dst, act_id):
     scaf = src.replace("_contigs", "_scaffolds")
     old_id = find_assembly_id(scaf)
     return rewrite_id(src, dst, old_id, act_id, prefix=">")
 
 
-def assembly_scaffolds(src, dst, omic_id, act_id):
+def assembly_scaffolds(src, dst, act_id):
     old_id = find_assembly_id(src)
     return rewrite_id(src, dst, old_id, act_id, prefix=">")
 
 
-def assembly_coverage_stats(src, dst, omic_id, act_id):
+def assembly_coverage_stats(src, dst, act_id):
     scaf = src.replace("_covstats.txt", "_scaffolds.fna")
     old_id = find_assembly_id(scaf)
     return rewrite_id(src, dst, old_id, act_id)
 
 
-def assembly_agp(src, dst, omic_id, act_id):
+def assembly_agp(src, dst, act_id):
     scaf = src.replace("_assembly.agp", "_scaffolds.fna")
     old_id = find_assembly_id(scaf)
     return rewrite_id(src, dst, old_id, act_id)
 
 
 def convert_script(script, src, dst, old_id, act_id):
-    cmd = ["./rewrite_bam.sh", src, dst, old_id, act_id]
+    cmd = [script, src, dst, old_id, act_id]
     results = check_output(cmd)
     md5 = md5_sum(dst)
     size = os.stat(dst).st_size
     return md5, size
 
 
-def assembly_coverage_bam(src, dst, omic_id, act_id):
+def assembly_coverage_bam(script, src, dst, act_id):
     scaf = src.replace("_pairedMapped_sorted.bam", "_scaffolds.fna")
     old_id = find_assembly_id(scaf)
-    return convert_script("./rewrite_bam.sh", src, dst, old_id, act_id)
+    return convert_script(script, src, dst, old_id, act_id)
 
 
 def xassembly_info_file(src, dst, omic_id, act_id):
     return []
 
-def rewrite_bam(type, old_bam, new_bam, old_id, new_id):
-    
-    if type == "inside":
-        print(f"Rewriting {new_bam}")
 
-        cmd1 = ["samtools", "view", "-h", old_bam]
-        cmd2 = ["sed", f"s/{old_id}/{new_id}/g"]
-        cmd3 = ["samtools", "view", "-hb", "-o", ]
+def rewrite_sam(input_sam, output_sam, old_id, new_id):
+    with gzip.open(input_sam, "rt") as f_in, gzip.open(output_sam, "wt") as f_out:
+        for line in f_in:
+            f_out.write(line.replace(old_id, new_id))
 
-        # Create a pipeline: cmd1 | cmd2 | cmd3
-        p1 = subprocess.Popen(cmd1, stdout=subprocess.PIPE)
-        p2 = subprocess.Popen(cmd2, stdin=p1.stdout, stdout=subprocess.PIPE)
-        p1.stdout.close() 
-        p3 = subprocess.Popen(cmd3, stdin=p2.stdout)
-        p2.stdout.close()
-        p3.communicate() 
 
-    else:
-        with open(new_bam, 'w') as f:
-            pass  # touch file
+def get_old_file_path(data_object_record):
+    old_url = data_object_record["url"]
+    suffix = old_url.split("https://data.microbiomedata.org/data/")[1]
+    old_file_path = base_dir + "/" + suffix
 
+    return old_file_path
 
-def rewrite_sam(input_sam, output_sam, old_id, new_id):
+
+def assembly_file_operations(data_object_record, destination, act_id):
+    # get old file path upfront
+    old_file_path = get_old_file_path(data_object_record)
     
-    with gzip.open(input_sam, 'rt') as f_in, gzip.open(output_sam, 'wt') as f_out:
-        for line in f_in:
-            f_out.write(line.replace(old_id, new_id))
+    if data_object_record["data_object_type"] == "Assembly Coverage Stats":
+        md5, size = assembly_coverage_stats(old_file_path, destination, act_id)
+    elif data_object_record["data_object_type"] == "Assembly Contigs":
+        md5, size = assembly_contigs(old_file_path, destination, act_id)
+    elif data_object_record["data_object_type"] == "Assembly Scaffolds":
+        md5, size = assembly_scaffolds(old_file_path, destination, act_id)
+    elif data_object_record["data_object_type"] == "Assembly AGP":
+        md5, size = assembly_agp(old_file_path, destination, act_id)
+    elif data_object_record["data_object_type"] == "Assembly Coverage BAM":
+        md5, size = assembly_coverage_bam(
+            bam_script, old_file_path, destination, act_id
+        )
 
+    return md5, size

From fc3b0d015f018d4aaf71a8a5be9387c8c40612df Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 2 Nov 2023 13:38:30 -0700
Subject: [PATCH 26/91] added support for assembly and readbased

---
 nmdc_automation/re_iding/re_id_process.py | 361 +++++++++++++++-------
 1 file changed, 253 insertions(+), 108 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index 7733cbca..bc16b7a5 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -11,7 +11,7 @@
 from re_id_file_operations import *
 import nmdc_schema.nmdc as nmdc
 from linkml_runtime.dumpers import json_dumper
-import shutil 
+import shutil
 
 ###GLOBAL######
 nmdc_db = nmdc.Database()
@@ -21,24 +21,26 @@
 
 
 sets = [
-        "read_qc_analysis_activity_set",
-        "metagenome_assembly_set",
-        "read_based_taxonomy_analysis_activity_set"
-        ]
+    "read_qc_analysis_activity_set",
+    "metagenome_assembly_set",
+    "read_based_taxonomy_analysis_activity_set",
+]
 
 
 mapping_log = open("mapping.log", "a")
 
+
 def read_workflows_config(config_file):
     with open(config_file, "r") as file:
         workflow_data = yaml.safe_load(file)
-        
+
     return workflow_data["Workflows"]
 
+
 def log_mapping(idtype, old, new):
     """
     Logs the mapping information.
-    
+
     Parameters:
     - idtype: The type of the ID (e.g., 'data', 'activity')
     - old: The old ID value
@@ -50,7 +52,7 @@ def log_mapping(idtype, old, new):
 def read_map():
     """
     Reads a mapping list from a file and returns it as a dictionary.
-    
+
     Returns:
     - omap: A dictionary with old ID as key and new ID as value.
     """
@@ -65,16 +67,29 @@ def read_map():
 def minter(shoulder):
     """
     Creates a new ID based on the provided shoulder.
-    
+
     Parameters:
     - shoulder: The base string for creating the new ID
-    
+
     Returns:
     - A new ID string
     """
-    
+
     return runtime_api.minter(shoulder)
 
+def get_new_paths(old_url, new_base_dir, omic_id, act_id):
+    """
+    Use the url to return the string value of name path and url
+    """
+    file_name = old_url.split("/")[-1]
+    file_extenstion = file_name.lstrip("nmdc_").split("_", maxsplit=1)[-1]
+    new_file_name = f"{act_id}_{file_extenstion}"
+    modified_new_file_name = new_file_name.replace(":", "_")
+    destination = os.path.join(new_base_dir, modified_new_file_name)
+
+    new_url = f"{base}/{omic_id}/{act_id}/{new_file_name}"
+    return new_url, destination, new_file_name
+
 
 def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
     """
@@ -87,7 +102,7 @@ def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
     new_file_name = f"{act_id}_{file_extenstion}"
     modified_new_file_name = new_file_name.replace(":", "_")
     destination = os.path.join(new_base_dir, modified_new_file_name)
-    
+
     try:
         os.link(old_file_path, destination)
         print(f"Successfully created link between {old_file_path} and {destination}")
@@ -95,7 +110,7 @@ def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
         print(f"An error occurred while linking the file: {e}")
     except Exception as e:
         print(f"Unexpected error: {e}")
-    
+
     new_url = f"{base}/{omic_id}/{act_id}/{new_file_name}"
     return new_url, destination, new_file_name
 
@@ -103,10 +118,10 @@ def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
 def find_type(obj):
     """
     Determine the data type of an object based on its URL extension.
-    
+
     Args:
     - obj (dict): Dictionary containing the 'url' key which will be inspected to determine the data type.
-    
+
     Returns:
     - str: The determined data type or None if the type could not be determined.
     """
@@ -124,16 +139,26 @@ def find_type(obj):
         return None
 
 
-def make_activity_set(omics_id, activity_id, has_input, has_output, started_time, ended_time, workflow_record_template):
-    #look at activity range
+def make_activity_set(
+    omics_id,
+    activity_id,
+    has_input,
+    has_output,
+    started_time,
+    ended_time,
+    workflow_record_template,
+):
+    # look at activity range
     database_activity_set = getattr(nmdc_db, workflow_record_template["Collection"])
     # Lookup the nmdc schema range class
     database_activity_range = getattr(nmdc, workflow_record_template["ActivityRange"])
-    
+
     database_activity_set.append(
         database_activity_range(
             id=activity_id,
-            name=workflow_record_template["Activity"]["name"].replace("{id}", activity_id),
+            name=workflow_record_template["Activity"]["name"].replace(
+                "{id}", activity_id
+            ),
             git_url=workflow_record_template["Git_repo"],
             version=workflow_record_template["Version"],
             part_of=[omics_id],
@@ -147,33 +172,38 @@ def make_activity_set(omics_id, activity_id, has_input, has_output, started_time
         )
     )
 
-def make_data_object(data_object_record, new_do_id, new_url, updated_name, updated_description):
 
+def make_data_object(
+    file_size, updated_name, new_url, do_type, new_do_id, updated_description, md5_value
+):
+    
     nmdc_db.data_object_set.append(
         nmdc.DataObject(
-            file_size_bytes=data_object_record["file_size_bytes"],
+            file_size_bytes=file_size,
             name=updated_name,
             url=new_url,
-            data_object_type=data_object_record["data_object_type"],
+            data_object_type=do_type,
             type="nmdc:DataObject",
             id=new_do_id,
-            md5_checksum=data_object_record["md5_checksum"],
-            description=updated_description
-            ),
-        )
+            md5_checksum=md5_value,
+            description=updated_description,
+        ),
+    )
+
 
 def post_database_object_to_runtime(datase_object):
-    
     nmdc_database_object = json.loads(
-            json_dumper.dumps(datase_object, inject_type=False)
-        )
+        json_dumper.dumps(datase_object, inject_type=False)
+    )
     res = runtime_api.post_objects(nmdc_database_object)
     return res
 
+
 def get_omics_id(omics_record):
     for rec in omics_record["omics_processing_set"]:
         return rec["id"]
 
+
 def get_record_by_type(related_omic_records, record_type):
     """
     Returns the record that matches the given type.
@@ -185,27 +215,48 @@ def get_record_by_type(related_omic_records, record_type):
     Returns:
     - dict: The first record that matches the given type, or None if not found.
     """
-    
+
     return related_omic_records[record_type]
 
+
 def get_data_object_by_type(related_omic_records, old_activity_record):
-    
+    """Find and return data objects for a activity record
+
+    Args:
+    - related_omic_records (dict): records for an omics processing record.
+    - old_activity_record (dict): old activty record of given ativity type
+
+    Returns:
+    - List[dict]: data objects for the given activity
+    """
+
     data_object_list = []
-    
+
     for act_record in old_activity_record:
         has_output_list = act_record["has_output"]
     for do_record in related_omic_records["data_object_set"]:
         if do_record["id"] in has_output_list:
             data_object_list.append(do_record)
-            
+
     return data_object_list
-        
-def get_associate_data_object_template(data_object_type,data_object_templates):
+
+
+def get_associate_data_object_template(data_object_type, data_object_templates):
+    """Get the associated data object template from yaml
+
+    Args:
+    - data_object_type (str): data object type
+    - data_object_templates (dict): workflows template
+
+    Returns:
+        data object record
+    """
     for data_object in data_object_templates:
         if data_object_type == data_object["data_object_type"]:
             return data_object
     return None
-    
+
+
 def reads_qc_update(omics_record, template_file, omic_id):
     """Extracts relevant information from omics record and template file, update data objects for reads qc
         and the analysis activity set record. Performs necessary file operation as well
@@ -218,52 +269,65 @@ def reads_qc_update(omics_record, template_file, omic_id):
     Returns:
         nmdc_database_object: dump of nmdc object
     """
-    
+
     workflow_type = "read_qc_analysis_activity_set"
-    #extract needed metaadata
+    # extract needed metaadata
     reads_qc_record = get_record_by_type(omics_record, workflow_type)
     reads_qc_data_objects = get_data_object_by_type(omics_record, reads_qc_record)
     for template in read_workflows_config(template_file):
-        if template['Type'] == "nmdc:ReadQcAnalysisActivity":
+        if template["Type"] == "nmdc:ReadQcAnalysisActivity":
             reads_qc_template = template
-            
-    #set up needed variables       
+
+    # set up needed variables
     new_act_id = minter(reads_qc_template["Type"])
     new_qc_base_dir = os.path.join(base_dir, omic_id, new_act_id)
-    os.makedirs(new_qc_base_dir,exist_ok=True)
+    os.makedirs(new_qc_base_dir, exist_ok=True)
     updated_has_output_list = []
-    
-    #hold input to downstream workflows
+
+    # hold input to downstream workflows
     input_to_downstream_workflows = []
-    #make new data objects
+    # make new data objects
     for data_object in reads_qc_data_objects:
-        dobj_tmpl = get_associate_data_object_template(data_object["data_object_type"],reads_qc_template["Outputs"])
+        dobj_tmpl = get_associate_data_object_template(
+            data_object["data_object_type"], reads_qc_template["Outputs"]
+        )
         new_do_id = minter("nmdc:DataObject")
-        #save filtered reads
+        # save filtered reads
         if data_object["data_object_type"] == "Filtered Sequencing Reads":
             input_to_downstream_workflows.append(new_do_id)
-        new_description = re.sub('[^ ]+$', f"{omic_id}", data_object["description"])
-        new_url, destination, _ = compute_new_paths(data_object["url"], new_qc_base_dir, omic_id, new_act_id)
-        make_data_object(data_object, new_do_id, new_url, dobj_tmpl["name"], new_description)
+        #get reusable slots
+        file_size = data_object["file_size_bytes"]
+        data_object_type = data_object["data_object_type"]
+        md5_sum = data_object["md5_checksum"]
+        #get new values for slots
+        new_description = re.sub("[^ ]+$", f"{omic_id}", data_object["description"])
+        new_url, destination, _ = compute_new_paths(
+            data_object["url"], new_qc_base_dir, omic_id, new_act_id
+        )
+        make_data_object(
+            file_size, dobj_tmpl["name"], new_url, data_object_type, new_do_id, new_description, md5_sum
+        )
         updated_has_output_list.append(new_do_id)
-    
-    #make updated activity record
+
+    # make updated activity record
     for rec in reads_qc_record:
         has_input = rec["has_input"]
         started_time = rec["started_at_time"]
         ended_time = rec["ended_at_time"]
-    #need to change has input to be updated as well, 
-    make_activity_set(omic_id, new_act_id, has_input, updated_has_output_list, started_time, ended_time, reads_qc_template)
-        
-    
-    nmdc_database_object = json.loads(
-            json_dumper.dumps(nmdc_db, inject_type=False)
-        )
-        
-    print(nmdc_database_object)
-    
+    # need to change has input to be updated as well,
+    make_activity_set(
+        omic_id,
+        new_act_id,
+        has_input,
+        updated_has_output_list,
+        started_time,
+        ended_time,
+        reads_qc_template,
+    )
+
     return input_to_downstream_workflows, destination
 
+
 def assembly_update(omics_record, template_file, omic_id, workflow_inputs):
     """Extracts relevant information from omics record and template file, update data objects for assembly
         and the analysis activity set record. Performs necessary file operation as well
@@ -276,79 +340,160 @@ def assembly_update(omics_record, template_file, omic_id, workflow_inputs):
     Returns:
         nmdc_database_object: dump of nmdc object
     """
-    
+
     workflow_type = "metagenome_assembly_set"
-    #extract needed metaadata
-    reads_qc_record = get_record_by_type(omics_record, workflow_type)
-    reads_qc_data_objects = get_data_object_by_type(omics_record, reads_qc_record)
+    # extract needed metaadata
+    assembly_record = get_record_by_type(omics_record, workflow_type)
+    assembly_data_objects = get_data_object_by_type(omics_record, assembly_record)
     for template in read_workflows_config(template_file):
-        if template['Type'] == "nmdc:MetagenomeAssembly":
-            reads_qc_template = template
-            
-    #set up needed variables       
-    new_act_id = minter(reads_qc_template["Type"])
-    new_qc_base_dir = os.path.join(base_dir, omic_id, new_act_id)
-    os.makedirs(new_qc_base_dir,exist_ok=True)
+        if template["Type"] == "nmdc:MetagenomeAssembly":
+            assembly_template = template
+
+    # set up needed variables
+    new_act_id = minter(assembly_template["Type"])
+    new_asm_base_dir = os.path.join(base_dir, omic_id, new_act_id)
+    os.makedirs(new_asm_base_dir, exist_ok=True)
     updated_has_output_list = []
-    
-    #make new data objects
-    for data_object in reads_qc_data_objects:
-        dobj_tmpl = get_associate_data_object_template(data_object["data_object_type"],reads_qc_template["Outputs"])
+
+    # make new data objects
+    for data_object in assembly_data_objects:
+        
+        data_object["data_object_type"] = find_type(data_object)
+        dobj_tmpl = get_associate_data_object_template(
+            data_object["data_object_type"], assembly_template["Outputs"]
+        )
+        #generate new dataobject type
         new_do_id = minter("nmdc:DataObject")
-        new_description = re.sub('[^ ]+$', f"{omic_id}", data_object["description"])
-        new_url, destination, _ = compute_new_paths(data_object["url"], new_qc_base_dir, omic_id, new_act_id)
-        make_data_object(data_object, new_do_id, new_url, dobj_tmpl["name"], new_description)
+        new_description = re.sub("[^ ]+$", f"{omic_id}", data_object["description"])
+        new_url, destination, _ = get_new_paths(data_object["url"], new_asm_base_dir, omic_id, new_act_id)
+        updated_md5, updated_file_size = assembly_file_operations(data_object, destination, new_act_id)
+        #get do_type
+        do_type = data_object["data_object_type"] 
+        make_data_object(
+            updated_file_size, dobj_tmpl["name"], new_url, do_type, new_do_id, new_description, updated_md5
+        )
         updated_has_output_list.append(new_do_id)
-    
-    for rec in reads_qc_record:
+
+    for rec in assembly_record:
         started_time = rec["started_at_time"]
         ended_time = rec["ended_at_time"]
-    #need to change has input to be updated as well, 
-    make_activity_set(omic_id, new_act_id, workflow_inputs, updated_has_output_list, started_time, ended_time, reads_qc_template)
+    # need to change has input to be updated as well,
+    make_activity_set(
+        omic_id,
+        new_act_id,
+        workflow_inputs,
+        updated_has_output_list,
+        started_time,
+        ended_time,
+        assembly_template,
+    )
+
+
+def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
+    """Extracts relevant information from omics record and template file, update data objects for assembly
+        and the analysis activity set record. Performs necessary file operation as well
+
+    Args:
+        omics_record (dict): omics record corresponding to downstream workflows
+        template_file (file): template yaml file for relavant worklfows metadata
+        omic_id (str): string identifier of omics id
+
+    Returns:
+        nmdc_database_object: dump of nmdc object
+    """
+
+    workflow_type = "read_based_taxonomy_analysis_activity_set"
+    # extract needed metaadata
+    readbased_record = get_record_by_type(omics_record, workflow_type)
+    readbased_data_objects = get_data_object_by_type(omics_record, readbased_record)
+    for template in read_workflows_config(template_file):
+        if template["Type"] == "nmdc:ReadBasedTaxonomyAnalysisActivity":
+            assembly_template = template
+
+    # set up needed variables
+    new_act_id = minter(assembly_template["Type"])
+    new_readbased_base_dir = os.path.join(base_dir, omic_id, new_act_id)
+    os.makedirs(new_readbased_base_dir, exist_ok=True)
+    updated_has_output_list = []
+
+    # make new data objects
+    for data_object in readbased_data_objects:
         
-    
-    nmdc_database_object = json.loads(
-            json_dumper.dumps(nmdc_db, inject_type=False)
+        data_object["data_object_type"] = find_type(data_object)
+           
+        dobj_tmpl = get_associate_data_object_template(
+            data_object["data_object_type"], assembly_template["Outputs"]
         )
-        
-    print(nmdc_database_object)
-    
-    return destination
-    
-    
-def process_analysis_sets(study_records, template_file,dry_run=False):
+        #generate new dataobject type
+        new_do_id = minter("nmdc:DataObject")
+        file_size = data_object["file_size_bytes"]
+        data_object_type = data_object["data_object_type"]
+        md5_sum = data_object["md5_checksum"]
+        #get new values for slots
+        new_description = re.sub("[^ ]+$", f"{omic_id}", data_object["description"])
+        new_url, destination, _ = compute_new_paths(
+            data_object["url"], new_readbased_base_dir, omic_id, new_act_id
+        )
+        make_data_object(
+            file_size, dobj_tmpl["name"], new_url, data_object_type, new_do_id, new_description, md5_sum
+        )
+        updated_has_output_list.append(new_do_id)
+
+    for rec in readbased_record:
+        started_time = rec["started_at_time"]
+        ended_time = rec["ended_at_time"]
     
+    make_activity_set(
+        omic_id,
+        new_act_id,
+        workflow_inputs,
+        updated_has_output_list,
+        started_time,
+        ended_time,
+        assembly_template,
+    )
+
+
+
+def process_analysis_sets(study_records, template_file, dry_run=False):
     count = 0
     for omic_record in study_records:
         omics_id = get_omics_id(omic_record)
         print(omics_id)
-        downstream_input, destination = reads_qc_update(omic_record, template_file, omics_id)
+        downstream_input, destination = reads_qc_update(
+            omic_record, template_file, omics_id
+        )
+        assembly_update(omic_record, template_file, omics_id, downstream_input)
+        readbased_update(omic_record, template_file, omics_id, downstream_input)
+        nmdc_database_object = json.loads(json_dumper.dumps(nmdc_db, inject_type=False))
+        print(nmdc_database_object)
         if dry_run == True:
             count += 1
         dir_path = os.path.dirname(destination)
         parent_dir_path = os.path.dirname(dir_path)
         try:
-            shutil.rmtree(parent_dir_path)
-            print(f"Directory {parent_dir_path} and all its contents removed successfully!")
+            # shutil.rmtree(parent_dir_path)
+            print(
+                f"Directory {parent_dir_path} and all its contents removed successfully!"
+            )
         except OSError as e:
             print(f"Error: {e}")
         if count == 1:
             break
-    
-    
 
 def main():
-    #TODO
-    #1. Read in json dump of analysis records 
-    #2. Process records for reads qc - generate new metadata, make new records and data objects (this will include file copies and renaming)
-    #3. save data of updated reads qc records
-    #4. Fetch old records for readbased analysis and assembly, generate new metadata, make new records and data objects (this will include file copies and renaming files and ids in files)
-    #5. Validate new records, submit them via runtime api
-    #6. Write seperate process to delete old records once we have
+    # TODO
+    # 1. Read in json dump of analysis records
+    # 2. Process records for reads qc - generate new metadata, make new records and data objects (this will include file copies and renaming)
+    # 3. save data of updated reads qc records
+    # 4. Fetch old records for readbased analysis and assembly, generate new metadata, make new records and data objects (this will include file copies and renaming files and ids in files)
+    # 5. Validate new records, submit them via runtime api
+    # 6. Write seperate process to delete old records once we have
     pass
 
+
 if __name__ == "__main__":
     test_file = "scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json"
-    template_file = "/global/cfs/cdirs/m3408/aim2/dev/reiding_scripts/nmdc_automation/configs/re_iding_worklfows.yaml"
+    template_file = "../../nmdc_automation/configs/re_iding_worklfows.yaml"
     stegen_data = read_json_file(test_file)
-    process_analysis_sets(stegen_data, template_file, dry_run=True)
\ No newline at end of file
+    process_analysis_sets(stegen_data, template_file, dry_run=True)

From b807215bf062d4a20972b8b6a7b90ed2f7159ef1 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 2 Nov 2023 13:48:04 -0700
Subject: [PATCH 27/91] find bam_script locally

---
 nmdc_automation/re_iding/re_id_file_operations.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_file_operations.py b/nmdc_automation/re_iding/re_id_file_operations.py
index 132b962c..a82181e5 100644
--- a/nmdc_automation/re_iding/re_id_file_operations.py
+++ b/nmdc_automation/re_iding/re_id_file_operations.py
@@ -7,7 +7,7 @@
 
 
 base_dir = "/global/cfs/cdirs/m3408/results"
-bam_script = "/global/u2/n/nmdcda/tasks/re_id/rewrite_bam.sh"
+bam_script = os.path.abspath("scripts/rewrite_bam.sh")
 
 
 def md5_sum(fn):
@@ -134,7 +134,7 @@ def get_old_file_path(data_object_record):
 def assembly_file_operations(data_object_record, destination, act_id):
     # get old file path upfront
     old_file_path = get_old_file_path(data_object_record)
-    
+
     if data_object_record["data_object_type"] == "Assembly Coverage Stats":
         md5, size = assembly_coverage_stats(old_file_path, destination, act_id)
     elif data_object_record["data_object_type"] == "Assembly Contigs":

From 8e53ff8e76733cb9e11fdda9799ecb92db117727 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 2 Nov 2023 13:48:16 -0700
Subject: [PATCH 28/91] reformat

---
 nmdc_automation/re_iding/re_id_process.py | 56 +++++++++++++++--------
 1 file changed, 38 insertions(+), 18 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index bc16b7a5..5cf8f7d6 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -77,6 +77,7 @@ def minter(shoulder):
 
     return runtime_api.minter(shoulder)
 
+
 def get_new_paths(old_url, new_base_dir, omic_id, act_id):
     """
     Use the url to return the string value of name path and url
@@ -176,7 +177,6 @@ def make_activity_set(
 def make_data_object(
     file_size, updated_name, new_url, do_type, new_do_id, updated_description, md5_value
 ):
-    
     nmdc_db.data_object_set.append(
         nmdc.DataObject(
             file_size_bytes=file_size,
@@ -295,17 +295,23 @@ def reads_qc_update(omics_record, template_file, omic_id):
         # save filtered reads
         if data_object["data_object_type"] == "Filtered Sequencing Reads":
             input_to_downstream_workflows.append(new_do_id)
-        #get reusable slots
+        # get reusable slots
         file_size = data_object["file_size_bytes"]
         data_object_type = data_object["data_object_type"]
         md5_sum = data_object["md5_checksum"]
-        #get new values for slots
+        # get new values for slots
         new_description = re.sub("[^ ]+$", f"{omic_id}", data_object["description"])
         new_url, destination, _ = compute_new_paths(
             data_object["url"], new_qc_base_dir, omic_id, new_act_id
         )
         make_data_object(
-            file_size, dobj_tmpl["name"], new_url, data_object_type, new_do_id, new_description, md5_sum
+            file_size,
+            dobj_tmpl["name"],
+            new_url,
+            data_object_type,
+            new_do_id,
+            new_description,
+            md5_sum,
         )
         updated_has_output_list.append(new_do_id)
 
@@ -357,20 +363,29 @@ def assembly_update(omics_record, template_file, omic_id, workflow_inputs):
 
     # make new data objects
     for data_object in assembly_data_objects:
-        
         data_object["data_object_type"] = find_type(data_object)
         dobj_tmpl = get_associate_data_object_template(
             data_object["data_object_type"], assembly_template["Outputs"]
         )
-        #generate new dataobject type
+        # generate new dataobject type
         new_do_id = minter("nmdc:DataObject")
         new_description = re.sub("[^ ]+$", f"{omic_id}", data_object["description"])
-        new_url, destination, _ = get_new_paths(data_object["url"], new_asm_base_dir, omic_id, new_act_id)
-        updated_md5, updated_file_size = assembly_file_operations(data_object, destination, new_act_id)
-        #get do_type
-        do_type = data_object["data_object_type"] 
+        new_url, destination, _ = get_new_paths(
+            data_object["url"], new_asm_base_dir, omic_id, new_act_id
+        )
+        updated_md5, updated_file_size = assembly_file_operations(
+            data_object, destination, new_act_id
+        )
+        # get do_type
+        do_type = data_object["data_object_type"]
         make_data_object(
-            updated_file_size, dobj_tmpl["name"], new_url, do_type, new_do_id, new_description, updated_md5
+            updated_file_size,
+            dobj_tmpl["name"],
+            new_url,
+            do_type,
+            new_do_id,
+            new_description,
+            updated_md5,
         )
         updated_has_output_list.append(new_do_id)
 
@@ -418,31 +433,36 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
 
     # make new data objects
     for data_object in readbased_data_objects:
-        
         data_object["data_object_type"] = find_type(data_object)
-           
+
         dobj_tmpl = get_associate_data_object_template(
             data_object["data_object_type"], assembly_template["Outputs"]
         )
-        #generate new dataobject type
+        # generate new dataobject type
         new_do_id = minter("nmdc:DataObject")
         file_size = data_object["file_size_bytes"]
         data_object_type = data_object["data_object_type"]
         md5_sum = data_object["md5_checksum"]
-        #get new values for slots
+        # get new values for slots
         new_description = re.sub("[^ ]+$", f"{omic_id}", data_object["description"])
         new_url, destination, _ = compute_new_paths(
             data_object["url"], new_readbased_base_dir, omic_id, new_act_id
         )
         make_data_object(
-            file_size, dobj_tmpl["name"], new_url, data_object_type, new_do_id, new_description, md5_sum
+            file_size,
+            dobj_tmpl["name"],
+            new_url,
+            data_object_type,
+            new_do_id,
+            new_description,
+            md5_sum,
         )
         updated_has_output_list.append(new_do_id)
 
     for rec in readbased_record:
         started_time = rec["started_at_time"]
         ended_time = rec["ended_at_time"]
-    
+
     make_activity_set(
         omic_id,
         new_act_id,
@@ -454,7 +474,6 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
     )
 
 
-
 def process_analysis_sets(study_records, template_file, dry_run=False):
     count = 0
     for omic_record in study_records:
@@ -481,6 +500,7 @@ def process_analysis_sets(study_records, template_file, dry_run=False):
         if count == 1:
             break
 
+
 def main():
     # TODO
     # 1. Read in json dump of analysis records

From 980a3a2234a35f1547e5a8ed6901869e2ce10fe4 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 2 Nov 2023 13:53:56 -0700
Subject: [PATCH 29/91] remove read_based_taxonomy_analysis

---
 .../re_iding/scripts/rebuild_metagenome_workflow_records.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index a32ceb99..b90621a8 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -100,13 +100,11 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         db.omics_processing_set.append(omics_processing_record)
 
         # downstream workflow activity sets
-        (read_qc_records, taxonomy_records,
-         metagenome_assembly_records,
-            metagenome_annotation_records, mags_records) = [], [], [], [], []
+        (read_qc_records, metagenome_assembly_records,
+            metagenome_annotation_records, mags_records) = [], [], [], []
 
         downstream_workflow_activity_sets = {
             "read_qc_analysis_activity_set": read_qc_records,
-            "read_based_taxonomy_analysis_activity_set": taxonomy_records,
             "metagenome_assembly_set": metagenome_assembly_records,
             "metagenome_annotation_activity_set": metagenome_annotation_records,
             "mags_activity_set": mags_records,

From 8386780742048c302e0920cbc09ecf4597960e06 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Fri, 3 Nov 2023 14:03:01 -0700
Subject: [PATCH 30/91] fix file path

---
 nmdc_automation/re_iding/re_id_process.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index 5cf8f7d6..75e9c312 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -438,6 +438,7 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
         dobj_tmpl = get_associate_data_object_template(
             data_object["data_object_type"], assembly_template["Outputs"]
         )
+        print(dobj_tmpl)
         # generate new dataobject type
         new_do_id = minter("nmdc:DataObject")
         file_size = data_object["file_size_bytes"]
@@ -514,6 +515,6 @@ def main():
 
 if __name__ == "__main__":
     test_file = "scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json"
-    template_file = "../../nmdc_automation/configs/re_iding_worklfows.yaml"
+    template_file = "../../configs/re_iding_worklfows.yaml"
     stegen_data = read_json_file(test_file)
     process_analysis_sets(stegen_data, template_file, dry_run=True)

From 62c5ddebb5829fda6e13c284cd6f7d85c57597c4 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Fri, 3 Nov 2023 14:04:01 -0700
Subject: [PATCH 31/91] remove superflous debugging

---
 nmdc_automation/re_iding/re_id_process.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index 75e9c312..d8cbe001 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -438,7 +438,7 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
         dobj_tmpl = get_associate_data_object_template(
             data_object["data_object_type"], assembly_template["Outputs"]
         )
-        print(dobj_tmpl)
+        
         # generate new dataobject type
         new_do_id = minter("nmdc:DataObject")
         file_size = data_object["file_size_bytes"]
@@ -446,7 +446,7 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
         md5_sum = data_object["md5_checksum"]
         # get new values for slots
         new_description = re.sub("[^ ]+$", f"{omic_id}", data_object["description"])
-        new_url, destination, _ = compute_new_paths(
+        new_url, _, _ = compute_new_paths(
             data_object["url"], new_readbased_base_dir, omic_id, new_act_id
         )
         make_data_object(

From 19f1d5f6311586a97fff2a61750147c9284952c9 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Fri, 3 Nov 2023 14:04:28 -0700
Subject: [PATCH 32/91] add back read_based_taxonomy_analysis_activity_set

---
 .../re_iding/scripts/rebuild_metagenome_workflow_records.py  | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
index b90621a8..fb5eca0a 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
@@ -100,11 +100,12 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         db.omics_processing_set.append(omics_processing_record)
 
         # downstream workflow activity sets
-        (read_qc_records, metagenome_assembly_records,
-            metagenome_annotation_records, mags_records) = [], [], [], []
+        (read_qc_records, readbased_records, metagenome_assembly_records,
+            metagenome_annotation_records, mags_records) = [], [], [], [], []
 
         downstream_workflow_activity_sets = {
             "read_qc_analysis_activity_set": read_qc_records,
+            "read_based_taxonomy_analysis_activity_set": readbased_records,
             "metagenome_assembly_set": metagenome_assembly_records,
             "metagenome_annotation_activity_set": metagenome_annotation_records,
             "mags_activity_set": mags_records,

From 2960932661b5b48b7466dfc5a7150145b9355073 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Fri, 3 Nov 2023 14:33:02 -0700
Subject: [PATCH 33/91] change centrifuge report do type

---
 configs/re_iding_worklfows.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/configs/re_iding_worklfows.yaml b/configs/re_iding_worklfows.yaml
index b77da9a4..5f71a7da 100644
--- a/configs/re_iding_worklfows.yaml
+++ b/configs/re_iding_worklfows.yaml
@@ -156,9 +156,9 @@ Workflows:
       name: Centrifuge output read classification file
       suffix: _centrifuge_classification.tsv
     - output: final_centrifuge_report_tsv
-      data_object_type: Centrifuge output report file
+      data_object_type: Centrifuge Classification Report
       description: Centrifuge Report for {id}
-      name: Centrifuge Classification Report
+      name: Centrifuge output report file
       suffix: _centrifuge_report.tsv
     - output: final_centrifuge_krona_html
       data_object_type: Centrifuge Krona Plot

From b88aa57ea9233d58d2552ea1cef9482b623b0b4c Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 6 Nov 2023 12:48:46 -0800
Subject: [PATCH 34/91] add example record

---
 ...zgv51_updated_records_example_dry_run.json | 243 ++++++++++++++++++
 1 file changed, 243 insertions(+)
 create mode 100644 nmdc_automation/re_iding/nmdc:sty-11-aygzgv51_updated_records_example_dry_run.json

diff --git a/nmdc_automation/re_iding/nmdc:sty-11-aygzgv51_updated_records_example_dry_run.json b/nmdc_automation/re_iding/nmdc:sty-11-aygzgv51_updated_records_example_dry_run.json
new file mode 100644
index 00000000..4d4beae5
--- /dev/null
+++ b/nmdc_automation/re_iding/nmdc:sty-11-aygzgv51_updated_records_example_dry_run.json
@@ -0,0 +1,243 @@
+{
+    "data_object_set": [
+        {
+            "id": "nmdc:dobj-12-3zw9ed72",
+            "name": "Reads QC result fastq (clean data)",
+            "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 2571324879,
+            "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+            "data_object_type": "Filtered Sequencing Reads",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-12-7bfbg150/nmdc_wfrqc-12-7bfbg150_filtered.fastq.gz",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-f992g204",
+            "name": "Reads QC summary statistics",
+            "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 290,
+            "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
+            "data_object_type": "QC Statistics",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-12-7bfbg150/nmdc_wfrqc-12-7bfbg150_filterStats.txt",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-g19r1r98",
+            "name": "Final assembly contigs fasta",
+            "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 90794959,
+            "md5_checksum": "148dffaee63c7eccc62db4022d916fe1",
+            "data_object_type": "Assembly Contigs",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-12-nv5zhv63/nmdc:wfmgas-12-nv5zhv63_contigs.fna",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-6qs0sb92",
+            "name": "Final assembly scaffolds fasta",
+            "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 90283295,
+            "md5_checksum": "5f66de5a1fa911f3f5e2e4027af8bb8c",
+            "data_object_type": "Assembly Scaffolds",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-12-nv5zhv63/nmdc:wfmgas-12-nv5zhv63_scaffolds.fna",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-0aqx6k97",
+            "name": "Assembled contigs coverage information",
+            "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 14091491,
+            "md5_checksum": "b2c4779abd596ab9604b06687f804360",
+            "data_object_type": "Assembly Coverage Stats",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-12-nv5zhv63/nmdc:wfmgas-12-nv5zhv63_covstats.txt",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-mxghxv82",
+            "name": "An AGP format file that describes the assembly",
+            "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 13901555,
+            "md5_checksum": "88e65190df33ce4082a224075e8e0ff4",
+            "data_object_type": "Assembly AGP",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-12-nv5zhv63/nmdc:wfmgas-12-nv5zhv63_assembly.agp",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-evyw0b45",
+            "name": "Sorted bam file of reads mapping back to the final assembly",
+            "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 0,
+            "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
+            "data_object_type": "Assembly Coverage BAM",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-12-nv5zhv63/nmdc:wfmgas-12-nv5zhv63_pairedMapped_sorted.bam",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-a1c08w33",
+            "name": "GOTTCHA2 classification report file",
+            "description": "Gottcha2 TSV report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 13174,
+            "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
+            "data_object_type": "GOTTCHA2 Classification Report",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_gottcha2_report.tsv",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-y7y6d813",
+            "name": "GOTTCHA2 report file",
+            "description": "Gottcha2 full TSV report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 1035818,
+            "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
+            "data_object_type": "GOTTCHA2 Report Full",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_gottcha2_report_full.tsv",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-5aweg275",
+            "name": "GOTTCHA2 krona plot HTML file",
+            "description": "Gottcha2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 262669,
+            "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
+            "data_object_type": "GOTTCHA2 Krona Plot",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_gottcha2_krona.html",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-1xzbt082",
+            "name": "Centrifuge output read classification file",
+            "description": "Centrifuge classification TSV report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 2189843623,
+            "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
+            "data_object_type": "Centrifuge Taxonomic Classification",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_centrifuge_classification.tsv",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-zaj6ec82",
+            "name": "Centrifuge output report file",
+            "description": "Centrifuge TSV report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 260134,
+            "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+            "data_object_type": "Centrifuge Classification Report",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_centrifuge_report.tsv",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-gnrpbj27",
+            "name": "Centrifug krona plot HTML file",
+            "description": "Centrifuge Krona HTML report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 2343980,
+            "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
+            "data_object_type": "Centrifuge Krona Plot",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_centrifuge_krona.html",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-avm4zb05",
+            "name": "Kraken2 output read classification file",
+            "description": "Kraken classification TSV report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 1785563917,
+            "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
+            "data_object_type": "Kraken2 Taxonomic Classification",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_kraken2_classification.tsv",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-mf77cq08",
+            "name": "Kraken2 output report file",
+            "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 699896,
+            "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+            "data_object_type": "Kraken2 Classification Report",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_kraken2_report.tsv",
+            "type": "nmdc:DataObject"
+        },
+        {
+            "id": "nmdc:dobj-12-gz9j7220",
+            "name": "Kraken2 Krona plot HTML file",
+            "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
+            "file_size_bytes": 4221977,
+            "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+            "data_object_type": "Kraken2 Krona Plot",
+            "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-12-bw74zf55/nmdc_wfrbt-12-bw74zf55_kraken2_krona.html",
+            "type": "nmdc:DataObject"
+        }
+    ],
+    "metagenome_assembly_set": [
+        {
+            "id": "nmdc:wfmgas-12-nv5zhv63",
+            "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
+            "started_at_time": "2021-10-11T02:28:26Z",
+            "ended_at_time": "2021-10-11T04:56:04+00:00",
+            "was_informed_by": "nmdc:omprc-11-bn8jcq58",
+            "execution_resource": "NERSC - Perlmutter",
+            "git_url": "https://github.com/microbiomedata/metaAssembly",
+            "has_input": [
+                "nmdc:dobj-12-3zw9ed72"
+            ],
+            "has_output": [
+                "nmdc:dobj-12-g19r1r98",
+                "nmdc:dobj-12-6qs0sb92",
+                "nmdc:dobj-12-0aqx6k97",
+                "nmdc:dobj-12-mxghxv82",
+                "nmdc:dobj-12-evyw0b45"
+            ],
+            "type": "nmdc:MetagenomeAssembly",
+            "part_of": [
+                "nmdc:omprc-11-bn8jcq58"
+            ],
+            "version": "v1.0.3"
+        }
+    ],
+    "read_qc_analysis_activity_set": [
+        {
+            "id": "nmdc:wfrqc-12-7bfbg150",
+            "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
+            "started_at_time": "2021-10-11T02:28:26Z",
+            "ended_at_time": "2021-10-11T04:56:04+00:00",
+            "was_informed_by": "nmdc:omprc-11-bn8jcq58",
+            "execution_resource": "NERSC - Perlmutter",
+            "git_url": "https://github.com/microbiomedata/ReadsQC",
+            "has_input": [
+                "nmdc:30a06664f29cffbbbc49abad86eae6fc"
+            ],
+            "has_output": [
+                "nmdc:dobj-12-3zw9ed72",
+                "nmdc:dobj-12-f992g204"
+            ],
+            "type": "nmdc:ReadQcAnalysisActivity",
+            "part_of": [
+                "nmdc:omprc-11-bn8jcq58"
+            ],
+            "version": "v1.0.8"
+        }
+    ],
+    "read_based_taxonomy_analysis_activity_set": [
+        {
+            "id": "nmdc:wfrbt-12-bw74zf55",
+            "name": "Readbased Taxonomy Analysis Activity for nmdc:omprc-11-bn8jcq58",
+            "started_at_time": "2021-10-11T02:28:26Z",
+            "ended_at_time": "2021-10-11T04:56:04+00:00",
+            "was_informed_by": "nmdc:omprc-11-bn8jcq58",
+            "execution_resource": "NERSC - Perlmutter",
+            "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
+            "has_input": [
+                "nmdc:dobj-12-3zw9ed72"
+            ],
+            "has_output": [
+                "nmdc:dobj-12-a1c08w33",
+                "nmdc:dobj-12-y7y6d813",
+                "nmdc:dobj-12-5aweg275",
+                "nmdc:dobj-12-1xzbt082",
+                "nmdc:dobj-12-zaj6ec82",
+                "nmdc:dobj-12-gnrpbj27",
+                "nmdc:dobj-12-avm4zb05",
+                "nmdc:dobj-12-mf77cq08",
+                "nmdc:dobj-12-gz9j7220"
+            ],
+            "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
+            "part_of": [
+                "nmdc:omprc-11-bn8jcq58"
+            ],
+            "version": "v1.0.5"
+        }
+    ]
+}
\ No newline at end of file

From d5f113d377b77276083b0cb9a7249e1af4334068 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 6 Nov 2023 12:48:57 -0800
Subject: [PATCH 35/91] added better logging

---
 nmdc_automation/re_iding/re_id_process.py | 106 +++++++++++++++-------
 1 file changed, 72 insertions(+), 34 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index d8cbe001..62b8e6c9 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -12,6 +12,7 @@
 import nmdc_schema.nmdc as nmdc
 from linkml_runtime.dumpers import json_dumper
 import shutil
+import logging
 
 ###GLOBAL######
 nmdc_db = nmdc.Database()
@@ -20,6 +21,16 @@
 base_dir = "/global/cfs/cdirs/m3408/results"
 
 
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+    handlers=[
+        logging.StreamHandler()
+    ]
+)
+
+logger = logging.getLogger(__name__)
+
 sets = [
     "read_qc_analysis_activity_set",
     "metagenome_assembly_set",
@@ -106,14 +117,14 @@ def compute_new_paths(old_url, new_base_dir, omic_id, act_id):
 
     try:
         os.link(old_file_path, destination)
-        print(f"Successfully created link between {old_file_path} and {destination}")
+        logging.info(f"Successfully created link between {old_file_path} and {destination}")
     except OSError as e:
-        print(f"An error occurred while linking the file: {e}")
+        logging.error(f"An error occurred while linking the file: {e}")
     except Exception as e:
-        print(f"Unexpected error: {e}")
+        logging.error(f"Unexpected error: {e}")
 
-    new_url = f"{base}/{omic_id}/{act_id}/{new_file_name}"
-    return new_url, destination, new_file_name
+    new_url = f"{base}/{omic_id}/{act_id}/{modified_new_file_name}"
+    return new_url, destination, modified_new_file_name
 
 
 def find_type(obj):
@@ -158,7 +169,7 @@ def make_activity_set(
         database_activity_range(
             id=activity_id,
             name=workflow_record_template["Activity"]["name"].replace(
-                "{id}", activity_id
+                "{id}", omics_id
             ),
             git_url=workflow_record_template["Git_repo"],
             version=workflow_record_template["Version"],
@@ -270,6 +281,8 @@ def reads_qc_update(omics_record, template_file, omic_id):
         nmdc_database_object: dump of nmdc object
     """
 
+    logging.info(f"Updating Reads QC for {omic_id}")
+
     workflow_type = "read_qc_analysis_activity_set"
     # extract needed metaadata
     reads_qc_record = get_record_by_type(omics_record, workflow_type)
@@ -283,6 +296,15 @@ def reads_qc_update(omics_record, template_file, omic_id):
     new_qc_base_dir = os.path.join(base_dir, omic_id, new_act_id)
     os.makedirs(new_qc_base_dir, exist_ok=True)
     updated_has_output_list = []
+    
+    # scrape useful old metadata
+    for rec in reads_qc_record:
+        has_input = rec["has_input"]
+        started_time = rec["started_at_time"]
+        ended_time = rec["ended_at_time"]
+        old_act_id = rec["id"]
+    
+    log_mapping("act_id", old_act_id, new_act_id)
 
     # hold input to downstream workflows
     input_to_downstream_workflows = []
@@ -292,6 +314,8 @@ def reads_qc_update(omics_record, template_file, omic_id):
             data_object["data_object_type"], reads_qc_template["Outputs"]
         )
         new_do_id = minter("nmdc:DataObject")
+        #log the new id
+        log_mapping("dobj", data_object["id"], new_do_id)
         # save filtered reads
         if data_object["data_object_type"] == "Filtered Sequencing Reads":
             input_to_downstream_workflows.append(new_do_id)
@@ -316,10 +340,6 @@ def reads_qc_update(omics_record, template_file, omic_id):
         updated_has_output_list.append(new_do_id)
 
     # make updated activity record
-    for rec in reads_qc_record:
-        has_input = rec["has_input"]
-        started_time = rec["started_at_time"]
-        ended_time = rec["ended_at_time"]
     # need to change has input to be updated as well,
     make_activity_set(
         omic_id,
@@ -347,6 +367,8 @@ def assembly_update(omics_record, template_file, omic_id, workflow_inputs):
         nmdc_database_object: dump of nmdc object
     """
 
+    logging.info(f"Updating Assembly for {omic_id}")
+
     workflow_type = "metagenome_assembly_set"
     # extract needed metaadata
     assembly_record = get_record_by_type(omics_record, workflow_type)
@@ -360,6 +382,14 @@ def assembly_update(omics_record, template_file, omic_id, workflow_inputs):
     new_asm_base_dir = os.path.join(base_dir, omic_id, new_act_id)
     os.makedirs(new_asm_base_dir, exist_ok=True)
     updated_has_output_list = []
+    
+    #get useful old metadata
+    for rec in assembly_record:
+        started_time = rec["started_at_time"]
+        ended_time = rec["ended_at_time"]
+        old_act_id = rec["id"]
+    
+    log_mapping("act_id", old_act_id, new_act_id)
 
     # make new data objects
     for data_object in assembly_data_objects:
@@ -369,6 +399,9 @@ def assembly_update(omics_record, template_file, omic_id, workflow_inputs):
         )
         # generate new dataobject type
         new_do_id = minter("nmdc:DataObject")
+        #log the new id
+        log_mapping("dobj", data_object["id"], new_do_id)
+        #continue updating metdata for data objects
         new_description = re.sub("[^ ]+$", f"{omic_id}", data_object["description"])
         new_url, destination, _ = get_new_paths(
             data_object["url"], new_asm_base_dir, omic_id, new_act_id
@@ -389,9 +422,6 @@ def assembly_update(omics_record, template_file, omic_id, workflow_inputs):
         )
         updated_has_output_list.append(new_do_id)
 
-    for rec in assembly_record:
-        started_time = rec["started_at_time"]
-        ended_time = rec["ended_at_time"]
     # need to change has input to be updated as well,
     make_activity_set(
         omic_id,
@@ -417,6 +447,8 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
         nmdc_database_object: dump of nmdc object
     """
 
+    logging.info(f"Updating Readbased for {omic_id}")
+
     workflow_type = "read_based_taxonomy_analysis_activity_set"
     # extract needed metaadata
     readbased_record = get_record_by_type(omics_record, workflow_type)
@@ -430,6 +462,15 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
     new_readbased_base_dir = os.path.join(base_dir, omic_id, new_act_id)
     os.makedirs(new_readbased_base_dir, exist_ok=True)
     updated_has_output_list = []
+    
+    #get useful old metadata
+    for rec in readbased_record:
+        started_time = rec["started_at_time"]
+        ended_time = rec["ended_at_time"]
+        old_act_id = rec["id"]
+
+    #log new activity id
+    log_mapping("act_id", old_act_id, new_act_id)
 
     # make new data objects
     for data_object in readbased_data_objects:
@@ -441,6 +482,9 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
         
         # generate new dataobject type
         new_do_id = minter("nmdc:DataObject")
+        #log the new id
+        log_mapping("dobj", data_object["id"], new_do_id)
+        #continue updating metdata for data objects
         file_size = data_object["file_size_bytes"]
         data_object_type = data_object["data_object_type"]
         md5_sum = data_object["md5_checksum"]
@@ -460,10 +504,7 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
         )
         updated_has_output_list.append(new_do_id)
 
-    for rec in readbased_record:
-        started_time = rec["started_at_time"]
-        ended_time = rec["ended_at_time"]
-
+    #make updated activity record
     make_activity_set(
         omic_id,
         new_act_id,
@@ -475,46 +516,43 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
     )
 
 
-def process_analysis_sets(study_records, template_file, dry_run=False):
+def process_analysis_sets(study_id,study_records, template_file, dry_run=False):
     count = 0
     for omic_record in study_records:
         omics_id = get_omics_id(omic_record)
-        print(omics_id)
+        logging.info(f"Starting re-iding process for {omics_id}")
+        log_mapping("omics_id", "gold", omics_id)
         downstream_input, destination = reads_qc_update(
             omic_record, template_file, omics_id
         )
         assembly_update(omic_record, template_file, omics_id, downstream_input)
         readbased_update(omic_record, template_file, omics_id, downstream_input)
         nmdc_database_object = json.loads(json_dumper.dumps(nmdc_db, inject_type=False))
-        print(nmdc_database_object)
+        logging.info(f"Writing nmdc database object dump to json file for {study_id}")
+        with open(f'{study_id}_updated_records.json', 'w') as json_file:
+            json.dump(nmdc_database_object, json_file, indent=4)
         if dry_run == True:
             count += 1
         dir_path = os.path.dirname(destination)
         parent_dir_path = os.path.dirname(dir_path)
         try:
-            # shutil.rmtree(parent_dir_path)
-            print(
-                f"Directory {parent_dir_path} and all its contents removed successfully!"
+            shutil.rmtree(parent_dir_path)
+            logging.info(
+                f"Running in dry_run mode, directory {parent_dir_path} and all its contents removed successfully!"
             )
         except OSError as e:
-            print(f"Error: {e}")
+            logging.info(f"Error: {e}")
         if count == 1:
             break
 
 
-def main():
-    # TODO
-    # 1. Read in json dump of analysis records
-    # 2. Process records for reads qc - generate new metadata, make new records and data objects (this will include file copies and renaming)
-    # 3. save data of updated reads qc records
-    # 4. Fetch old records for readbased analysis and assembly, generate new metadata, make new records and data objects (this will include file copies and renaming files and ids in files)
-    # 5. Validate new records, submit them via runtime api
-    # 6. Write seperate process to delete old records once we have
-    pass
+def main(study_id,study_data, template_file, dry_run=False):
+    process_analysis_sets(study_id,study_data, template_file, dry_run)
 
 
 if __name__ == "__main__":
     test_file = "scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json"
+    study_id = "nmdc:sty-11-aygzgv51"
     template_file = "../../configs/re_iding_worklfows.yaml"
     stegen_data = read_json_file(test_file)
-    process_analysis_sets(stegen_data, template_file, dry_run=True)
+    main(study_id,stegen_data, template_file, dry_run=True)

From 5cb1b7b97fe33639360be78d317fc5928cca4452 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 7 Nov 2023 09:15:41 -0800
Subject: [PATCH 36/91] Rename script

---
 ... => extract_metagenome_workflow_records.py} | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)
 rename nmdc_automation/re_iding/scripts/{rebuild_metagenome_workflow_records.py => extract_metagenome_workflow_records.py} (89%)

diff --git a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
similarity index 89%
rename from nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
rename to nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
index fb5eca0a..b655e534 100644
--- a/nmdc_automation/re_iding/scripts/rebuild_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
 # coding: utf-8
-# nmdc_schema/napa_compliance/scripts/rebuild_metagenome_workflow_records.py
+# nmdc_schema/napa_compliance/scripts/extract_metagenome_workflow_records.py
 """
-rebuild_metagenome_workflow_records.py: Rebuild metagenome workflow records
-after re-ID-ing of OmicsProcessing records.
+extract_metagenome_workflow_records.py: Extract metagenome workflow records
+for re-ID-ing of OmicsProcessing records.
 """
 import logging
 import time
@@ -50,9 +50,9 @@ def _get_legacy_id(omics_processing_record: dict) -> str:
     "--site_config", type=click.Path(exists=True), default=NAPA_CONFIG,
     help="Site configuration file"
 )
-def rebuild_workflow_records(study_id: str, site_config: bool):
+def extract_workflow_records(study_id: str, site_config: bool):
     """
-    Rebuild metagenome workflow records after re-ID-ing of Study, Biosample, and
+    Extract metagenome workflow records for re-ID-ing of Study, Biosample, and
     OmicsProcessing records by:
     1. Retrieving all OmicsProcessing records for updated study ID
     2. For each OmicsProcessing record, retrieve the corresponding
@@ -63,8 +63,10 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
         d. MetagenomeAnnotationActivity
         e. MagsAnalysisActivity
     3. For each WorkflowExecutionActivity record:
-    TODO - summarize Michal's flowchart here
-
+       a. Retrieve the corresponding DataObject records
+    4. Create a database object for each OmicsProcessing record and its
+    associated WorkflowExecutionActivity and DataObject records
+    5. Write the database object to a JSON file
     """
     start_time = time.time()
     logging.info("starting missing_neon_soils_ecosystem_data.py...")
@@ -130,4 +132,4 @@ def rebuild_workflow_records(study_id: str, site_config: bool):
 
 
 if __name__ == "__main__":
-    rebuild_workflow_records()
+    extract_workflow_records()

From f38ee0effdf9314bb9bed905b8ae895d07d051f4 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 7 Nov 2023 11:11:43 -0800
Subject: [PATCH 37/91] update to extract data object for omics processing
 has_output

---
 .../extract_metagenome_workflow_records.py    |    5 +
 ...sty-11-aygzgv51_assocated_record_dump.json | 6790 ++---------------
 2 files changed, 801 insertions(+), 5994 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
index b655e534..ebf25a64 100644
--- a/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
@@ -100,6 +100,11 @@ def extract_workflow_records(study_id: str, site_config: bool):
                          f"is not a Metagenome")
             continue
         db.omics_processing_set.append(omics_processing_record)
+        for data_object_id in omics_processing_record["has_output"]:
+            data_object_record = query_api_client.get_data_object_by_id(
+                data_object_id
+            )
+            db.data_object_set.append(data_object_record)
 
         # downstream workflow activity sets
         (read_qc_records, readbased_records, metagenome_assembly_records,
diff --git a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
index 37a912d9..cc5b8c9b 100644
--- a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
@@ -7,6 +7,13 @@
         "activity_set": [],
         "biosample_set": [],
         "data_object_set": [
+            {
+                "description": "Raw sequencer read data",
+                "file_size_bytes": 2861414297,
+                "type": "nmdc:DataObject",
+                "id": "jgi:55d740280d8785342fcf7e39",
+                "name": "9422.8.132674.GTTTCG.fastq.gz"
+            },
             {
                 "name": "Gp0115663_Filtered Reads",
                 "description": "Filtered Reads for Gp0115663",
@@ -104,85 +111,6 @@
                 "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
                 "file_size_bytes": 4221977
             },
-            {
-                "name": "Gp0115663_Gottcha2 TSV report",
-                "description": "Gottcha2 TSV report for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
-                "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
-                "id": "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
-                "file_size_bytes": 13174
-            },
-            {
-                "name": "Gp0115663_Gottcha2 full TSV report",
-                "description": "Gottcha2 full TSV report for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
-                "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
-                "id": "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
-                "file_size_bytes": 1035818
-            },
-            {
-                "name": "Gp0115663_Gottcha2 Krona HTML report",
-                "description": "Gottcha2 Krona HTML report for Gp0115663",
-                "data_object_type": "GOTTCHA2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
-                "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
-                "id": "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
-                "file_size_bytes": 262669
-            },
-            {
-                "name": "Gp0115663_Centrifuge classification TSV report",
-                "description": "Centrifuge classification TSV report for Gp0115663",
-                "data_object_type": "Centrifuge Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
-                "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
-                "id": "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
-                "file_size_bytes": 2189843623
-            },
-            {
-                "name": "Gp0115663_Centrifuge TSV report",
-                "description": "Centrifuge TSV report for Gp0115663",
-                "data_object_type": "Centrifuge Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
-                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
-                "id": "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
-                "file_size_bytes": 260134
-            },
-            {
-                "name": "Gp0115663_Centrifuge Krona HTML report",
-                "description": "Centrifuge Krona HTML report for Gp0115663",
-                "data_object_type": "Centrifuge Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
-                "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
-                "id": "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
-                "file_size_bytes": 2343980
-            },
-            {
-                "name": "Gp0115663_Kraken classification TSV report",
-                "description": "Kraken classification TSV report for Gp0115663",
-                "data_object_type": "Kraken2 Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
-                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
-                "id": "nmdc:7ca01ea379f0baed96f87d1435925f95",
-                "file_size_bytes": 1785563917
-            },
-            {
-                "name": "Gp0115663_Kraken2 TSV report",
-                "description": "Kraken2 TSV report for Gp0115663",
-                "data_object_type": "Kraken2 Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
-                "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
-                "id": "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
-                "file_size_bytes": 699896
-            },
-            {
-                "name": "Gp0115663_Kraken2 Krona HTML report",
-                "description": "Kraken2 Krona HTML report for Gp0115663",
-                "data_object_type": "Kraken2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
-                "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
-                "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
-                "file_size_bytes": 4221977
-            },
             {
                 "name": "Gp0115663_Assembled contigs fasta",
                 "description": "Assembled contigs fasta for Gp0115663",
@@ -707,39 +635,7 @@
         "collecting_biosamples_from_site_set": [],
         "date_created": null,
         "etl_software_version": null,
-        "pooling_set": [],
-        "read_based_analysis_activity_set": [
-            {
-                "_id": {
-                    "$oid": "61e71a31833bcf838a701ec1"
-                },
-                "has_input": [
-                    "nmdc:7bf778baef033d36f118f8591256d6ef"
-                ],
-                "part_of": [
-                    "nmdc:mga0h9dt75"
-                ],
-                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
-                "has_output": [
-                    "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
-                    "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
-                    "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
-                    "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
-                    "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
-                    "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
-                    "nmdc:7ca01ea379f0baed96f87d1435925f95",
-                    "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
-                    "nmdc:94ee1bc2dc74830a21d5c3471d6cf223"
-                ],
-                "was_informed_by": "gold:Gp0115663",
-                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
-                "execution_resource": "NERSC-Cori",
-                "name": "ReadBased Analysis Activity for nmdc:mga0h9dt75",
-                "started_at_time": "2021-10-11T02:28:26Z",
-                "type": "nmdc:ReadbasedAnalysis",
-                "ended_at_time": "2021-10-11T04:56:04+00:00"
-            }
-        ]
+        "pooling_set": []
     },
     {
         "functional_annotation_agg": [],
@@ -749,6 +645,13 @@
         "activity_set": [],
         "biosample_set": [],
         "data_object_set": [
+            {
+                "description": "Raw sequencer read data",
+                "file_size_bytes": 2080914094,
+                "type": "nmdc:DataObject",
+                "id": "jgi:55d817fc0d8785342fcf8274",
+                "name": "9387.2.132031.CCGTCC.fastq.gz"
+            },
             {
                 "name": "Gp0115666_Filtered Reads",
                 "description": "Filtered Reads for Gp0115666",
@@ -846,85 +749,6 @@
                 "id": "nmdc:b5091cfeed4fbea8316e50fbceea89bc",
                 "file_size_bytes": 3983935
             },
-            {
-                "name": "Gp0115666_Gottcha2 TSV report",
-                "description": "Gottcha2 TSV report for Gp0115666",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_gottcha2_report.tsv",
-                "md5_checksum": "17454627f873cc37e80700c4751c81d6",
-                "id": "nmdc:17454627f873cc37e80700c4751c81d6",
-                "file_size_bytes": 10721
-            },
-            {
-                "name": "Gp0115666_Gottcha2 full TSV report",
-                "description": "Gottcha2 full TSV report for Gp0115666",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_gottcha2_report_full.tsv",
-                "md5_checksum": "e0479eb7fd3345aaf134640e0b9e11b0",
-                "id": "nmdc:e0479eb7fd3345aaf134640e0b9e11b0",
-                "file_size_bytes": 920924
-            },
-            {
-                "name": "Gp0115666_Gottcha2 Krona HTML report",
-                "description": "Gottcha2 Krona HTML report for Gp0115666",
-                "data_object_type": "GOTTCHA2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_gottcha2_krona.html",
-                "md5_checksum": "a8433a0b17d7380fc836e4c9f85a7a54",
-                "id": "nmdc:a8433a0b17d7380fc836e4c9f85a7a54",
-                "file_size_bytes": 257441
-            },
-            {
-                "name": "Gp0115666_Centrifuge classification TSV report",
-                "description": "Centrifuge classification TSV report for Gp0115666",
-                "data_object_type": "Centrifuge Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_centrifuge_classification.tsv",
-                "md5_checksum": "9e061ad19d4a6a3f209d1992d02df9f9",
-                "id": "nmdc:9e061ad19d4a6a3f209d1992d02df9f9",
-                "file_size_bytes": 1468295025
-            },
-            {
-                "name": "Gp0115666_Centrifuge TSV report",
-                "description": "Centrifuge TSV report for Gp0115666",
-                "data_object_type": "Centrifuge Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_centrifuge_report.tsv",
-                "md5_checksum": "1d46eebd0f194f57dd9e92c9bc992891",
-                "id": "nmdc:1d46eebd0f194f57dd9e92c9bc992891",
-                "file_size_bytes": 257081
-            },
-            {
-                "name": "Gp0115666_Centrifuge Krona HTML report",
-                "description": "Centrifuge Krona HTML report for Gp0115666",
-                "data_object_type": "Centrifuge Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_centrifuge_krona.html",
-                "md5_checksum": "e5227b1cfdbc266c44d23028c92150a9",
-                "id": "nmdc:e5227b1cfdbc266c44d23028c92150a9",
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-            },
-            {
-                "name": "Gp0115666_Kraken classification TSV report",
-                "description": "Kraken classification TSV report for Gp0115666",
-                "data_object_type": "Kraken2 Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_kraken2_classification.tsv",
-                "md5_checksum": "05f7680c6646904cfb16fc146c0fed4a",
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-                "file_size_bytes": 1204548180
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-            {
-                "name": "Gp0115666_Kraken2 TSV report",
-                "description": "Kraken2 TSV report for Gp0115666",
-                "data_object_type": "Kraken2 Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_kraken2_report.tsv",
-                "md5_checksum": "368cf81424348cdf46d17c13908280e7",
-                "id": "nmdc:368cf81424348cdf46d17c13908280e7",
-                "file_size_bytes": 653697
-            },
-            {
-                "name": "Gp0115666_Kraken2 Krona HTML report",
-                "description": "Kraken2 Krona HTML report for Gp0115666",
-                "data_object_type": "Kraken2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0eehe16/ReadbasedAnalysis/nmdc_mga0eehe16_kraken2_krona.html",
-                "md5_checksum": "b5091cfeed4fbea8316e50fbceea89bc",
-                "id": "nmdc:b5091cfeed4fbea8316e50fbceea89bc",
-                "file_size_bytes": 3983935
-            },
             {
                 "name": "Gp0115666_Assembled contigs fasta",
                 "description": "Assembled contigs fasta for Gp0115666",
@@ -1389,39 +1213,7 @@
         "collecting_biosamples_from_site_set": [],
         "date_created": null,
         "etl_software_version": null,
-        "pooling_set": [],
-        "read_based_analysis_activity_set": [
-            {
-                "_id": {
-                    "$oid": "61e71a15833bcf838a701c88"
-                },
-                "has_input": [
-                    "nmdc:0b301d2dd917c2be31422dd0e986dd5e"
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-                "part_of": [
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-                ],
-                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
-                "has_output": [
-                    "nmdc:17454627f873cc37e80700c4751c81d6",
-                    "nmdc:e0479eb7fd3345aaf134640e0b9e11b0",
-                    "nmdc:a8433a0b17d7380fc836e4c9f85a7a54",
-                    "nmdc:9e061ad19d4a6a3f209d1992d02df9f9",
-                    "nmdc:1d46eebd0f194f57dd9e92c9bc992891",
-                    "nmdc:e5227b1cfdbc266c44d23028c92150a9",
-                    "nmdc:05f7680c6646904cfb16fc146c0fed4a",
-                    "nmdc:368cf81424348cdf46d17c13908280e7",
-                    "nmdc:b5091cfeed4fbea8316e50fbceea89bc"
-                ],
-                "was_informed_by": "gold:Gp0115666",
-                "id": "nmdc:db181675b157d27d9b0b2f35b5cbf03e",
-                "execution_resource": "NERSC-Cori",
-                "name": "ReadBased Analysis Activity for nmdc:mga0eehe16",
-                "started_at_time": "2021-10-11T02:28:09Z",
-                "type": "nmdc:ReadbasedAnalysis",
-                "ended_at_time": "2021-10-11T04:06:19+00:00"
-            }
-        ]
+        "pooling_set": []
     },
     {
         "functional_annotation_agg": [],
@@ -1431,6 +1223,13 @@
         "activity_set": [],
         "biosample_set": [],
         "data_object_set": [
+            {
+                "description": "Raw sequencer read data",
+                "file_size_bytes": 3050291373,
+                "type": "nmdc:DataObject",
+                "id": "jgi:55d740240d8785342fcf7e37",
+                "name": "9422.8.132674.GTGGCC.fastq.gz"
+            },
             {
                 "name": "Gp0115668_Filtered Reads",
                 "description": "Filtered Reads for Gp0115668",
@@ -1529,101 +1328,22 @@
                 "file_size_bytes": 4276256
             },
             {
-                "name": "Gp0115668_Gottcha2 TSV report",
-                "description": "Gottcha2 TSV report for Gp0115668",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0n66h21/ReadbasedAnalysis/nmdc_mga0n66h21_gottcha2_report.tsv",
-                "md5_checksum": "8bdf8bbee24242aaaee763c1d851c05e",
-                "id": "nmdc:8bdf8bbee24242aaaee763c1d851c05e",
-                "file_size_bytes": 13875
+                "name": "Gp0115668_Assembled contigs fasta",
+                "description": "Assembled contigs fasta for Gp0115668",
+                "data_object_type": "Assembly Contigs",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0n66h21/assembly/nmdc_mga0n66h21_contigs.fna",
+                "md5_checksum": "b2b862aede4f333acec79aac3afc7254",
+                "id": "nmdc:b2b862aede4f333acec79aac3afc7254",
+                "file_size_bytes": 182488593
             },
             {
-                "name": "Gp0115668_Gottcha2 full TSV report",
-                "description": "Gottcha2 full TSV report for Gp0115668",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0n66h21/ReadbasedAnalysis/nmdc_mga0n66h21_gottcha2_report_full.tsv",
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-                "name": "Gp0115668_Gottcha2 Krona HTML report",
-                "description": "Gottcha2 Krona HTML report for Gp0115668",
-                "data_object_type": "GOTTCHA2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0n66h21/ReadbasedAnalysis/nmdc_mga0n66h21_gottcha2_krona.html",
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-                "description": "Centrifuge classification TSV report for Gp0115668",
-                "data_object_type": "Centrifuge Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0n66h21/ReadbasedAnalysis/nmdc_mga0n66h21_centrifuge_classification.tsv",
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-                "url": "https://data.microbiomedata.org/data/nmdc:mga0n66h21/ReadbasedAnalysis/nmdc_mga0n66h21_centrifuge_report.tsv",
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-                "data_object_type": "Kraken2 Taxonomic Classification",
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@@ -33429,6 +28439,13 @@
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@@ -34092,6 +28998,13 @@
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-                "type": "nmdc:ReadbasedAnalysis",
-                "ended_at_time": "2021-11-13T18:52:13+00:00"
-            }
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+        "pooling_set": []
     }
 ]
\ No newline at end of file

From f33b6cea7cf99d5c85ee0c6b89e8338906395484 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Tue, 7 Nov 2023 12:44:27 -0800
Subject: [PATCH 38/91] updated with reabased_taxonomy

---
 ...sty-11-aygzgv51_assocated_record_dump.json | 6552 ++---------------
 1 file changed, 501 insertions(+), 6051 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
index 37a912d9..a23b6caa 100644
--- a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
@@ -104,85 +104,6 @@
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@@ -34658,38 +29140,6 @@
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-                    "nmdc:3219058371bf2f8081b2dd2b434ec145",
-                    "nmdc:be29ebcd7358653afec7381f9ca43431",
-                    "nmdc:a9e6ab6db23ddce02317e3e21ea3f618",
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-                "started_at_time": "2021-10-11T02:23:35Z",
-                "type": "nmdc:ReadbasedAnalysis",
-                "ended_at_time": "2021-11-13T18:52:13+00:00"
-            }
-        ]
+        "pooling_set": []
     }
 ]
\ No newline at end of file

From 50aad19632c6b28b8871f84fb59ddaf178c85c75 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 7 Nov 2023 13:02:42 -0800
Subject: [PATCH 39/91] add single-record extract output for testing purposes

---
 .../scripts/test_metagenome_record.json       | 640 ++++++++++++++++++
 1 file changed, 640 insertions(+)
 create mode 100644 nmdc_automation/re_iding/scripts/test_metagenome_record.json

diff --git a/nmdc_automation/re_iding/scripts/test_metagenome_record.json b/nmdc_automation/re_iding/scripts/test_metagenome_record.json
new file mode 100644
index 00000000..638c9f4d
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/test_metagenome_record.json
@@ -0,0 +1,640 @@
+[
+  {
+        "functional_annotation_agg": [],
+        "library_preparation_set": [],
+        "processed_sample_set": [],
+        "extraction_set": [],
+        "activity_set": [],
+        "biosample_set": [],
+        "data_object_set": [
+            {
+                "description": "Raw sequencer read data",
+                "file_size_bytes": 2861414297,
+                "type": "nmdc:DataObject",
+                "id": "jgi:55d740280d8785342fcf7e39",
+                "name": "9422.8.132674.GTTTCG.fastq.gz"
+            },
+            {
+                "name": "Gp0115663_Filtered Reads",
+                "description": "Filtered Reads for Gp0115663",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filtered.fastq.gz",
+                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                "id": "nmdc:7bf778baef033d36f118f8591256d6ef",
+                "file_size_bytes": 2571324879
+            },
+            {
+                "name": "Gp0115663_Filtered Stats",
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+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 4
+                    }
+                ],
+                "unbinned_contig_num": 9288,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:MAGsAnalysisActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "material_sample_set": [],
+        "material_sampling_activity_set": [],
+        "metabolomics_analysis_activity_set": [],
+        "metagenome_annotation_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b005bbf2caae0415ef9d6"
+                },
+                "has_input": [
+                    "nmdc:deddd162bf0128fba13b3bc1ca38d1aa"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:879988d212ecec46928b8598e2f8391f",
+                    "nmdc:884b95102f5965cc0ee2d9b7f198e5a4",
+                    "nmdc:002e4ebc728f8b91cb5f298d340ab013",
+                    "nmdc:6851078f29716d89e3f41f0969ae7bf0",
+                    "nmdc:4f88c89459f36655eb7c1eceec19602a",
+                    "nmdc:a068b9ce6ebb7deb15ff932b513817a9",
+                    "nmdc:618b18fa8635c80cc0091371f451a6f0",
+                    "nmdc:17e55a1a1a133ffbf8cbe4024d997a6f",
+                    "nmdc:8f80142c0f5723af5a3b44b7ff4e4339",
+                    "nmdc:fdd2e8741ffef40db383674a10bb4d11",
+                    "nmdc:8eb49ac20a6c2721d6db227f4fb3356a",
+                    "nmdc:75f481e0d98793cfb4f9508cb3e31622"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "name": "Annotation Activity for nmdc:mga0h9dt75",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:MetagenomeAnnotationActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "metagenome_assembly_set": [
+            {
+                "_id": {
+                    "$oid": "649b005f2ca5ee4adb139fb9"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "ctg_logsum": 214373,
+                "scaf_logsum": 215363,
+                "gap_pct": 0.00188,
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:deddd162bf0128fba13b3bc1ca38d1aa",
+                    "nmdc:b3573e3cda5a06611de71ca04c5c14cc",
+                    "nmdc:c6d0d4cea985ca6fb50a060e15b4a856",
+                    "nmdc:f450e3800e17691d5874c89fc46c186a",
+                    "nmdc:31dc958d116d02122509e90b0883954f"
+                ],
+                "asm_score": 6.577,
+                "was_informed_by": "gold:Gp0115663",
+                "ctg_powsum": 24284,
+                "scaf_max": 68135,
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "scaf_powsum": 24422,
+                "execution_resource": "NERSC-Cori",
+                "contigs": 169784,
+                "name": "Assembly Activity for nmdc:mga0h9dt75",
+                "ctg_max": 68135,
+                "gc_std": 0.11726,
+                "contig_bp": 83494920,
+                "gc_avg": 0.46001,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "scaf_bp": 83496490,
+                "type": "nmdc:MetagenomeAssembly",
+                "scaffolds": 169645,
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "ctg_l50": 470,
+                "ctg_l90": 290,
+                "ctg_n50": 45584,
+                "ctg_n90": 141996,
+                "scaf_l50": 470,
+                "scaf_l90": 290,
+                "scaf_n50": 45550,
+                "scaf_n90": 141870,
+                "scaf_l_gt50k": 68135,
+                "scaf_n_gt50k": 1,
+                "scaf_pct_gt50k": 0.08160224
+            }
+        ],
+        "metagenome_sequencing_activity_set": [],
+        "metaproteomics_analysis_activity_set": [],
+        "metatranscriptome_activity_set": [],
+        "nom_analysis_activity_set": [],
+        "omics_processing_set": [
+            {
+                "_id": {
+                    "$oid": "649b009773e8249959349b33"
+                },
+                "id": "nmdc:omprc-11-bn8jcq58",
+                "name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
+                "has_input": [
+                    "nmdc:bsm-11-qq8s6x03"
+                ],
+                "has_output": [
+                    "jgi:55d740280d8785342fcf7e39"
+                ],
+                "part_of": [
+                    "nmdc:sty-11-aygzgv51"
+                ],
+                "add_date": "2015-05-28",
+                "mod_date": "2021-06-15",
+                "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "omics_type": {
+                    "has_raw_value": "Metagenome"
+                },
+                "principal_investigator": {
+                    "has_raw_value": "James Stegen"
+                },
+                "processing_institution": "JGI",
+                "type": "nmdc:OmicsProcessing",
+                "gold_sequencing_project_identifiers": [
+                    "gold:Gp0115663"
+                ]
+            }
+        ],
+        "reaction_activity_set": [],
+        "read_qc_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009d6bdd4fd20273c88b"
+                },
+                "has_input": [
+                    "nmdc:30a06664f29cffbbbc49abad86eae6fc"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef",
+                    "nmdc:b99ce8adc125c95f0bfdadf36a3f6848"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "input_read_count": 32238374,
+                "output_read_bases": 4608772924,
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "input_read_bases": 4867994474,
+                "name": "Read QC Activity for nmdc:mga0h9dt75",
+                "output_read_count": 30774080,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadQCAnalysisActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "read_based_taxonomy_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009bff710ae353f8cf4f"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                    "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                    "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                    "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                    "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                    "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                    "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                    "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                    "nmdc:94ee1bc2dc74830a21d5c3471d6cf223"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "name": "ReadBased Analysis Activity for nmdc:mga0h9dt75",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadbasedAnalysis",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "study_set": [],
+        "field_research_site_set": [],
+        "collecting_biosamples_from_site_set": [],
+        "date_created": null,
+        "etl_software_version": null,
+        "pooling_set": []
+    }
+]
\ No newline at end of file

From bfac07ba6af342594787cc45ef31dd21c569b68a Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Tue, 7 Nov 2023 13:40:31 -0800
Subject: [PATCH 40/91] added click argument for process_analysis_set

---
 nmdc_automation/re_iding/re_id_process.py | 36 +++++++++++++++--------
 1 file changed, 23 insertions(+), 13 deletions(-)

diff --git a/nmdc_automation/re_iding/re_id_process.py b/nmdc_automation/re_iding/re_id_process.py
index 62b8e6c9..baef81d4 100755
--- a/nmdc_automation/re_iding/re_id_process.py
+++ b/nmdc_automation/re_iding/re_id_process.py
@@ -3,8 +3,7 @@
 import sys
 import re
 import yaml
-import datetime
-import pytz
+import click
 from pymongo import MongoClient
 import json
 from nmdc_automation.api import NmdcRuntimeApi
@@ -516,8 +515,25 @@ def readbased_update(omics_record, template_file, omic_id, workflow_inputs):
     )
 
 
-def process_analysis_sets(study_id,study_records, template_file, dry_run=False):
+@click.command()
+@click.argument('study_id')
+@click.argument('study_records_file', type=click.Path(exists=True))
+@click.argument('template_file', type=click.Path(exists=True))
+@click.option('--dry-run', is_flag=True, help='Run the script in dry-run mode without making any changes.')
+def process_analysis_sets(study_id,study_records_file, template_file, dry_run):
+    """
+    Process analysis activity sets for a given STUDY_ID using STUDY_RECORDS and TEMPLATE_FILE.
+
+    \b
+    STUDY_ID: The identifier for the study.
+    STUDY_RECORDS: The path to the JSON file containing study records.
+    TEMPLATE_FILE: The path to the template file containing .
+    """
     count = 0
+    
+    #read in json to memory:
+    study_records = read_json_file(study_records_file)
+    
     for omic_record in study_records:
         omics_id = get_omics_id(omic_record)
         logging.info(f"Starting re-iding process for {omics_id}")
@@ -545,14 +561,8 @@ def process_analysis_sets(study_id,study_records, template_file, dry_run=False):
         if count == 1:
             break
 
-
-def main(study_id,study_data, template_file, dry_run=False):
-    process_analysis_sets(study_id,study_data, template_file, dry_run)
-
-
 if __name__ == "__main__":
-    test_file = "scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json"
-    study_id = "nmdc:sty-11-aygzgv51"
-    template_file = "../../configs/re_iding_worklfows.yaml"
-    stegen_data = read_json_file(test_file)
-    main(study_id,stegen_data, template_file, dry_run=True)
+    # test_file = "scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json"
+    # study_id = "nmdc:sty-11-aygzgv51"
+    # template_file = "../../configs/re_iding_worklfows.yaml"
+    process_analysis_sets()

From 5da652225266b2d92014c2f6828fc9953d55be00 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 7 Nov 2023 13:56:02 -0800
Subject: [PATCH 41/91] update to search for orphaned data records and include
 in output

---
 nmdc_automation/api/nmdcapi.py                |    15 +
 nmdc_automation/re_iding/mapping.log          |     1 +
 .../extract_metagenome_workflow_records.py    |    14 +
 ...sty-11-aygzgv51_assocated_record_dump.json | 12546 +++++++++++++++-
 4 files changed, 11891 insertions(+), 685 deletions(-)
 create mode 100644 nmdc_automation/re_iding/mapping.log

diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 2c86bcd7..7a5988cf 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -403,6 +403,21 @@ def get_workflow_activity_informed_by(self, workflow_activity_set: str,
         workflow_activity_record = response.json()["cursor"]["firstBatch"]
         return workflow_activity_record
 
+    def get_data_objects_by_description(self, description: str):
+        """
+        Retrieve data objects the given description in its description.
+        """
+        response = self.request(
+            "POST",
+            "queries:run",
+            params_or_json_data={
+                "find": "data_object_set",
+                "filter": {"description": {"$regex": description, "$options": "i"}},
+            },
+        )
+        response.raise_for_status()
+        return response.json()["cursor"]["firstBatch"]
+
     def get_data_object_by_id(self, data_object_id: str):
         """
         Retrieve a data object record for the given data object ID.
diff --git a/nmdc_automation/re_iding/mapping.log b/nmdc_automation/re_iding/mapping.log
new file mode 100644
index 00000000..974bbbe8
--- /dev/null
+++ b/nmdc_automation/re_iding/mapping.log
@@ -0,0 +1 @@
+omics_id	gold	nmdc:omprc-11-bn8jcq58
diff --git a/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
index ebf25a64..079214e1 100644
--- a/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
@@ -124,12 +124,26 @@ def extract_workflow_records(study_id: str, site_config: bool):
             db.__setattr__(set_name, records)
             # Add the data objects referenced by the `has_output` property
             for record in records:
+                logging.info(f"record: {record['id']}, {record['name']}")
                 for data_object_id in record["has_output"]:
                     data_object_record = query_api_client.get_data_object_by_id(
                         data_object_id
                     )
+                    logging.info(f"data_object_record: "
+                                 f"{data_object_record['id']}, {data_object_record['description']}")
                     db.data_object_set.append(data_object_record)
 
+        # Search for orphaned data objects with the legacy ID in the description
+        orphaned_data_objects = query_api_client.get_data_objects_by_description(
+                legacy_id
+        )
+        # check that we don't already have the data object in the set
+        for data_object in orphaned_data_objects:
+            if data_object["id"] not in [d["id"] for d in db.data_object_set]:
+                db.data_object_set.append(data_object)
+                logging.info(f"Added orphaned data object: "
+                             f"{data_object['id']}, {data_object['description']}")
+
         retrieved_databases.append(db)
         
     with open(f"{study_id}_assocated_record_dump.json", 'w') as json_file:
diff --git a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
index cc5b8c9b..d3156d14 100644
--- a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
@@ -306,6 +306,224 @@
                 "md5_checksum": "27c07072f175571200b5931550adb8aa",
                 "id": "nmdc:27c07072f175571200b5931550adb8aa",
                 "file_size_bytes": 1114314
+            },
+            {
+                "_id": {
+                    "$oid": "649b003c1ae706d7b5b14d5a"
+                },
+                "description": "Assembled scaffold fasta for gold:Gp0115663",
+                "url": "https://data.microbiomedata.org/data/1781_86101/assembly/assembly_scaffolds.fna",
+                "file_size_bytes": 88756490,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:321a497bc1c3cf25affc8e659b746ba5",
+                "name": "assembly_scaffolds.fna",
+                "data_object_type": "Assembly Scaffolds"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003c1ae706d7b5b14d5d"
+                },
+                "description": "Metagenome Contig Coverage Stats for gold:Gp0115663",
+                "url": "https://data.microbiomedata.org/data/1781_86101/assembly/mapping_stats.txt",
+                "file_size_bytes": 12563453,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:ad47215b9b079c1d94a8fc56385dee36",
+                "name": "mapping_stats.txt",
+                "data_object_type": "Assembly Coverage Stats"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003c1ae706d7b5b14d5f"
+                },
+                "description": "Assembled contigs fasta for gold:Gp0115663",
+                "url": "https://data.microbiomedata.org/data/1781_86101/assembly/assembly_contigs.fna",
+                "file_size_bytes": 89266921,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:0a3d00715d01ad7b8f3aee59b674dfe9",
+                "name": "assembly_contigs.fna",
+                "data_object_type": "Assembly Contigs"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003c1ae706d7b5b14d61"
+                },
+                "description": "Assembled AGP file for gold:Gp0115663",
+                "url": "https://data.microbiomedata.org/data/1781_86101/assembly/assembly.agp",
+                "file_size_bytes": 10842941,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:bc01f0f507c9dac65d8a8e40e41a8c48",
+                "name": "assembly.agp",
+                "data_object_type": "Assembly AGP"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003c1ae706d7b5b14d63"
+                },
+                "description": "Metagenome Alignment BAM file for gold:Gp0115663",
+                "url": "https://data.microbiomedata.org/data/1781_86101/assembly/pairedMapped_sorted.bam",
+                "file_size_bytes": 2729039400,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:668d207be5ea844f988fbfb2813564cc",
+                "name": "pairedMapped_sorted.bam",
+                "data_object_type": "Assembly Coverage BAM"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b15979"
+                },
+                "id": "nmdc:9509adb5a013006dfda9754429cfc968",
+                "name": "1781_86101.krona.html",
+                "description": "Gold:Gp0115663 KRONA plot HTML file",
+                "url": "https://data.microbiomedata.org/1781_86101/ReadbasedAnalysis/centrifuge/1781_86101.krona.html",
+                "file_size_bytes": 3385,
+                "data_object_type": "Centrifuge Krona Plot",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b15980"
+                },
+                "id": "nmdc:6dea4c58f402b5c3935e8f1a545bec47",
+                "name": "1781_86101.json",
+                "description": "Gold:Gp0115663 ReadbasedAnalysis result JSON file",
+                "url": "https://data.microbiomedata.org/1781_86101/ReadbasedAnalysis/1781_86101.json",
+                "file_size_bytes": 3385,
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003f1ae706d7b5b16253"
+                },
+                "id": "nmdc:0c4c875e5b10c6b742c14c22e2926751",
+                "name": "bins.tooShort.fa",
+                "description": "tooShort (< 3kb) filtered contigs fasta file by metaBat2 for gold:Gp0115663",
+                "file_size_bytes": 68423774,
+                "url": "https://data.microbiomedata.org/data/1781_86101/img_MAGs/bins.tooShort.fa",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003f1ae706d7b5b16254"
+                },
+                "id": "nmdc:c55d6b00aa5d4af8cd46d349e17d4127",
+                "name": "bins.unbinned.fa",
+                "description": "unbinned fasta file from metabat2 for gold:Gp0115663",
+                "file_size_bytes": 16857267,
+                "url": "https://data.microbiomedata.org/data/1781_86101/img_MAGs/bins.unbinned.fa",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003f1ae706d7b5b16256"
+                },
+                "id": "nmdc:1346fe25b6ff22180eb3a51204e0b1fc",
+                "name": "gold:Gp0115663.bins.1.fa",
+                "description": "metabat2 binned contig file for gold:Gp0115663",
+                "file_size_bytes": 224772,
+                "url": "https://data.microbiomedata.org/data/1781_86101/img_MAGs/metabat-bins/bins.1.fa",
+                "type": "nmdc:DataObject",
+                "data_object_type": "Metagenome Bins"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003f1ae706d7b5b16258"
+                },
+                "id": "nmdc:818f5a47d1371295f9313909ea12eb50",
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+            {
+                "_id": {
+                    "$oid": "649b00401ae706d7b5b16d57"
+                },
+                "description": "EC TSV File for gold:Gp0127655",
+                "url": "https://data.microbiomedata.org/1781_100357/img_annotation/Ga0482216_ec.tsv",
+                "md5_checksum": "32c6c6dbce4a1c6ab92810a86f90c574",
+                "file_size_bytes": 3385,
+                "id": "nmdc:32c6c6dbce4a1c6ab92810a86f90c574",
+                "name": "gold:Gp0127655_EC TSV File",
+                "data_object_type": "Annotation Enzyme Commission",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b00401ae706d7b5b16d58"
+                },
+                "description": "Protein FAA for gold:Gp0127655",
+                "url": "https://data.microbiomedata.org/1781_100357/img_annotation/Ga0482216_proteins.faa",
+                "md5_checksum": "a31096eb3e473fd0c68d09096bc3fd85",
+                "file_size_bytes": 3385,
+                "id": "nmdc:a31096eb3e473fd0c68d09096bc3fd85",
+                "name": "gold:Gp0127655_Protein FAA",
+                "data_object_type": "Annotation Amino Acid FASTA",
+                "type": "nmdc:DataObject"
             }
         ],
         "dissolving_activity_set": [],
@@ -29264,6 +40270,176 @@
                 "md5_checksum": "1029b97dba32dab780f4267f8224619f",
                 "id": "nmdc:1029b97dba32dab780f4267f8224619f",
                 "file_size_bytes": 182
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b14ed2"
+                },
+                "description": "Metagenome Contig Coverage Stats for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/data/1781_100355/assembly/mapping_stats.txt",
+                "file_size_bytes": 3628417,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:59f6f5bd2480f717a09946125a0cac46",
+                "name": "mapping_stats.txt",
+                "data_object_type": "Assembly Coverage Stats"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b14ed3"
+                },
+                "description": "Assembled contigs fasta for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/data/1781_100355/assembly/assembly_contigs.fna",
+                "file_size_bytes": 18526584,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:c9708409d9e8f45dcc89e688b3482e5e",
+                "name": "assembly_contigs.fna",
+                "data_object_type": "Assembly Contigs"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b14ed4"
+                },
+                "description": "Assembled scaffold fasta for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/data/1781_100355/assembly/assembly_scaffolds.fna",
+                "file_size_bytes": 18379922,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:c76c1fdcd6be23a0d7add5ea3a23f754",
+                "name": "assembly_scaffolds.fna",
+                "data_object_type": "Assembly Scaffolds"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b14ed9"
+                },
+                "description": "Assembled AGP file for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/data/1781_100355/assembly/assembly.agp",
+                "file_size_bytes": 3159611,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:ac8be882728344819f210f42d5ea8577",
+                "name": "assembly.agp",
+                "data_object_type": "Assembly AGP"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b14edd"
+                },
+                "description": "Metagenome Alignment BAM file for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/data/1781_100355/assembly/pairedMapped_sorted.bam",
+                "file_size_bytes": 1732533897,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:fadc083a0534b4961c902c8af8a8ebba",
+                "name": "pairedMapped_sorted.bam",
+                "data_object_type": "Assembly Coverage BAM"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b15be6"
+                },
+                "id": "nmdc:2d6f886bc9561f305d3b15be14bc192f",
+                "name": "1781_100355.krona.html",
+                "description": "Gold:Gp0127653 KRONA plot HTML file",
+                "url": "https://data.microbiomedata.org/1781_100355/ReadbasedAnalysis/centrifuge/1781_100355.krona.html",
+                "file_size_bytes": 3385,
+                "data_object_type": "Centrifuge Krona Plot",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b15c08"
+                },
+                "id": "nmdc:bcf6968cd97d5db72fbe6d048a638fd7",
+                "name": "1781_100355.json",
+                "description": "Gold:Gp0127653 ReadbasedAnalysis result JSON file",
+                "url": "https://data.microbiomedata.org/1781_100355/ReadbasedAnalysis/1781_100355.json",
+                "file_size_bytes": 3385,
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003f1ae706d7b5b16642"
+                },
+                "id": "nmdc:9429c50986c3904bdd48e585bfc74dfd",
+                "name": "bins.tooShort.fa",
+                "description": "tooShort (< 3kb) filtered contigs fasta file by metaBat2 for gold:Gp0127653",
+                "file_size_bytes": 17290021,
+                "url": "https://data.microbiomedata.org/data/1781_100355/img_MAGs/bins.tooShort.fa",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003f1ae706d7b5b16647"
+                },
+                "id": "nmdc:eb6bfb2af22e43df303aa691a87889bc",
+                "name": "bins.unbinned.fa",
+                "description": "unbinned fasta file from metabat2 for gold:Gp0127653",
+                "file_size_bytes": 807307,
+                "url": "https://data.microbiomedata.org/data/1781_100355/img_MAGs/bins.unbinned.fa",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b00401ae706d7b5b16d4d"
+                },
+                "description": "EC TSV File for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/1781_100355/img_annotation/Ga0482218_ec.tsv",
+                "md5_checksum": "05cc9ce5321d6bc909ab63b8cbc59d02",
+                "file_size_bytes": 3385,
+                "id": "nmdc:05cc9ce5321d6bc909ab63b8cbc59d02",
+                "name": "gold:Gp0127653_EC TSV File",
+                "data_object_type": "Annotation Enzyme Commission",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b00401ae706d7b5b16d4f"
+                },
+                "description": "Protein FAA for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/1781_100355/img_annotation/Ga0482218_proteins.faa",
+                "md5_checksum": "658231efecf9d087ec2a6e9467f4e968",
+                "file_size_bytes": 3385,
+                "id": "nmdc:658231efecf9d087ec2a6e9467f4e968",
+                "name": "gold:Gp0127653_Protein FAA",
+                "data_object_type": "Annotation Amino Acid FASTA",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b00401ae706d7b5b16d51"
+                },
+                "description": "Functional annotation GFF file for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/1781_100355/img_annotation/Ga0482218_functional_annotation.gff",
+                "md5_checksum": "8d83e502a533b5db8cd3bc943ae8b18b",
+                "file_size_bytes": 3385,
+                "id": "nmdc:8d83e502a533b5db8cd3bc943ae8b18b",
+                "name": "gold:Gp0127653_Functional annotation GFF file",
+                "data_object_type": "Functional Annotation GFF",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b00401ae706d7b5b16d54"
+                },
+                "description": "KO TSV File for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/1781_100355/img_annotation/Ga0482218_ko.tsv",
+                "md5_checksum": "44f8e708349a1effdff745880f4fdd12",
+                "file_size_bytes": 3385,
+                "id": "nmdc:44f8e708349a1effdff745880f4fdd12",
+                "name": "gold:Gp0127653_KO TSV File",
+                "data_object_type": "Annotation KEGG Orthology",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "_id": {
+                    "$oid": "649b00401ae706d7b5b16d5b"
+                },
+                "description": "Structural annotation GFF file for gold:Gp0127653",
+                "url": "https://data.microbiomedata.org/1781_100355/img_annotation/Ga0482218_structural_annotation.gff",
+                "md5_checksum": "511ae319ddff2bdcbc3296d951e42d7e",
+                "file_size_bytes": 3385,
+                "id": "nmdc:511ae319ddff2bdcbc3296d951e42d7e",
+                "name": "gold:Gp0127653_Structural annotation GFF file",
+                "data_object_type": "Structural Annotation GFF",
+                "type": "nmdc:DataObject"
             }
         ],
         "dissolving_activity_set": [],

From d3ee0630e4d0513f3015403e8ae15a30f1b51d14 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 9 Nov 2023 17:00:16 -0800
Subject: [PATCH 42/91] Begin refactoring

Add packages in re_iding
add a basic unit test
combine both commands in single script
---
 nmdc_automation/re_iding/__init__.py          |   0
 nmdc_automation/re_iding/base.py              |  40 ++
 nmdc_automation/re_iding/db_utils.py          |  46 ++
 nmdc_automation/re_iding/mapping.log          |   1 +
 .../dryrun_associated_record_dump.json}       |   0
 ...sty-11-aygzgv51_assocated_record_dump.json |   0
 .../extract_metagenome_workflow_records.py    |   5 +-
 .../re_iding/scripts/re_id_tool.py            | 144 ++++
 nmdc_automation/re_iding/tests/__init__.py    |   0
 nmdc_automation/re_iding/tests/conftest.py    |  11 +
 .../re_iding/tests/test_data/db_record.json   | 638 ++++++++++++++++++
 .../re_iding/tests/test_re_iding_base.py      |  15 +
 12 files changed, 898 insertions(+), 2 deletions(-)
 create mode 100644 nmdc_automation/re_iding/__init__.py
 create mode 100644 nmdc_automation/re_iding/base.py
 create mode 100644 nmdc_automation/re_iding/db_utils.py
 rename nmdc_automation/re_iding/scripts/{test_metagenome_record.json => data/dryrun_associated_record_dump.json} (100%)
 rename nmdc_automation/re_iding/scripts/{ => data}/nmdc:sty-11-aygzgv51_assocated_record_dump.json (100%)
 create mode 100755 nmdc_automation/re_iding/scripts/re_id_tool.py
 create mode 100644 nmdc_automation/re_iding/tests/__init__.py
 create mode 100644 nmdc_automation/re_iding/tests/conftest.py
 create mode 100644 nmdc_automation/re_iding/tests/test_data/db_record.json
 create mode 100644 nmdc_automation/re_iding/tests/test_re_iding_base.py

diff --git a/nmdc_automation/re_iding/__init__.py b/nmdc_automation/re_iding/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
new file mode 100644
index 00000000..f3753246
--- /dev/null
+++ b/nmdc_automation/re_iding/base.py
@@ -0,0 +1,40 @@
+# nmdc_automation/nmddc_automation/re_iding/base.py
+"""
+base.py - Provides classes and functions for re-ID-ing NMDC metagenome workflow
+records and data objects.
+"""
+import logging
+from typing import List
+from pathlib import Path
+import json
+from typing import Dict, List
+
+from nmdc_schema.nmdc import Database, DataObject
+from nmdc_automation.re_iding.db_utils import (
+    OMICS_PROCESSING_SET,
+    DATA_OBJECT_SET,
+    check_for_single_omics_processing_record,
+)
+
+
+NAPA_TEMPLATE = "../../configs/re_iding_worklfows.yaml"
+
+
+def get_new_db_and_downstream_inputs(
+        db_record: Dict, config_file: str = None) -> (Database,
+                                                     List[DataObject]):
+    """
+    Return a new Database instance with the given new_omics_processing_record
+    and the data objects that are has_output of the given old_omics_processing_record
+    """
+    if config_file is None:
+        config_file = NAPA_TEMPLATE
+    config_file = Path(config_file)
+
+    new_db = Database()
+    downstream_inputs = []
+
+    check_for_single_omics_processing_record(db_record)
+    old_omics_processing_record = db_record[OMICS_PROCESSING_SET][0]
+
+    return new_db, downstream_inputs
\ No newline at end of file
diff --git a/nmdc_automation/re_iding/db_utils.py b/nmdc_automation/re_iding/db_utils.py
new file mode 100644
index 00000000..bdf5674b
--- /dev/null
+++ b/nmdc_automation/re_iding/db_utils.py
@@ -0,0 +1,46 @@
+# nmdc_automation/nmdc_automation/re_iding/db_utils.py
+"""
+nmdc_db_utils.py: Provides utility functions for working with NMDC Database
+records and data objects as dicts.
+"""
+from dataclasses import dataclass
+from typing import Dict, List
+from nmdc_schema.nmdc import Database, DataObject
+
+# Some constants for set names we care about
+OMICS_PROCESSING_SET = "omics_processing_set"
+DATA_OBJECT_SET = "data_object_set"
+
+
+
+
+def get_omics_processing_id(db_record: Dict) -> str:
+    """
+    Get the ID of the OmicsProcessing record in the given Database instance.
+    The OmicsProcessing record acts as the root of the workflow graph and
+    the data objects.
+    """
+    check_for_single_omics_processing_record(db_record)
+    omics_processing_set = db_record[OMICS_PROCESSING_SET]
+    return omics_processing_set[0]["id"]
+
+
+def check_for_single_omics_processing_record(old_db_record: Dict) -> bool:
+    """
+    Check that there is only one OmicsProcessing record in the Database.
+    """
+    omics_processing_set = old_db_record.get("omics_processing_set", [])
+    if len(omics_processing_set) == 0:
+        raise ValueError("No omics_processing_set found in db_record")
+    elif len(omics_processing_set) > 1:
+        raise ValueError("Multiple omics_processing_set found in db_record")
+    return True
+
+
+
+
+
+
+
+
+
diff --git a/nmdc_automation/re_iding/mapping.log b/nmdc_automation/re_iding/mapping.log
index 974bbbe8..c4b7fca5 100644
--- a/nmdc_automation/re_iding/mapping.log
+++ b/nmdc_automation/re_iding/mapping.log
@@ -1 +1,2 @@
 omics_id	gold	nmdc:omprc-11-bn8jcq58
+omics_id	gold	nmdc:omprc-11-bn8jcq58
diff --git a/nmdc_automation/re_iding/scripts/test_metagenome_record.json b/nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json
similarity index 100%
rename from nmdc_automation/re_iding/scripts/test_metagenome_record.json
rename to nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json
diff --git a/nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_assocated_record_dump.json
similarity index 100%
rename from nmdc_automation/re_iding/scripts/nmdc:sty-11-aygzgv51_assocated_record_dump.json
rename to nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_assocated_record_dump.json
diff --git a/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
index 079214e1..49c71c1f 100644
--- a/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
+++ b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
@@ -2,8 +2,9 @@
 # coding: utf-8
 # nmdc_schema/napa_compliance/scripts/extract_metagenome_workflow_records.py
 """
-extract_metagenome_workflow_records.py: Extract metagenome workflow records
-for re-ID-ing of OmicsProcessing records.
+extract_metagenome_workflow_records.py: Starting with OmicsProcessing, extract
+metagenome workflow activity records and their associated data objects. Write
+the results, as a list of nmdc-schema Database instances to a JSON file.
 """
 import logging
 import time
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
new file mode 100755
index 00000000..8fc4713c
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -0,0 +1,144 @@
+#!/usr/bin/env python3
+# nmdc_automation/nmdc_automation/re_iding/scripts/re_id_tool.py
+"""
+re_id_tool.py: Provides command-line tools to extract and re-ID NMDC metagenome
+workflow records.
+"""
+import logging
+import time
+from pathlib import Path
+import json
+import click
+
+from nmdc_automation.api import NmdcRuntimeUserApi
+from nmdc_automation.config import Config
+import nmdc_schema.nmdc as nmdc
+from nmdc_automation.re_iding.base import get_new_db_and_downstream_inputs
+from nmdc_automation.re_iding.db_utils import get_omics_processing_id
+
+# Defaults
+GOLD_STUDY_ID = "gold:Gs0114663"
+STUDY_ID = "nmdc:sty-11-aygzgv51"
+NAPA_CONFIG = Path("../../../configs/napa_config.toml")
+
+
+BASE_DATAFILE_DIR = "/global/cfs/cdirs/m3408/results"
+DRYRUN_DATAFILE_DIR = "./data/dryrun_data/results"
+
+DATA_DIR = Path(__file__).parent.absolute().joinpath("data")
+
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+    handlers=[
+        logging.StreamHandler()
+    ]
+)
+
+logger = logging.getLogger(__name__)
+
+
+
+@click.group()
+@click.option("--site-config", type=click.Path(exists=True),
+              default=NAPA_CONFIG,)
+@click.pass_context
+def cli(ctx, site_config):
+    """
+    NMDC re-ID tool
+    """
+    ctx.ensure_object(dict)
+    ctx.obj['site_config'] = site_config
+
+
+@cli.command()
+@click.option('--study_id', default=STUDY_ID,
+              help=f'Optional updated study ID. Default: {STUDY_ID}')
+@click.pass_context
+def extract_records(ctx, study_id):
+    """
+    Extract metagenome workflow activities and their data object records
+    that are informed_by the legacy ID (GOLD Study ID) for a re-ID-ed Study/
+    Biosample/OmicsProcessing.
+
+    Write the results, as a list of nmdc-schema Database instances to a JSON file.
+    """
+    start_time = time.time()
+    logging.info(f"Extracting workflow records for study_id: {study_id}")
+
+
+@cli.command()
+
+@click.option('--dryrun / --no-dryrun', is_flag=True, default=True,
+              help='Dryrun mode: use local data dir and do not save results')
+@click.option('--study_id', is_required=False, default=STUDY_ID,
+              help=f'Optional updated study ID. Default: {STUDY_ID}')
+@click.option('--data_dir', is_required=False, default=BASE_DATAFILE_DIR,
+              help=f'Optional base datafile directory. Default: {BASE_DATAFILE_DIR}')
+@click.pass_context
+def process_records(ctx, dryrun, study_id, data_dir):
+    """
+    Read the JSON file of extracted workflow records and their data objects and
+    re-ID the records with newly-minted NMDC IDs, update data file headers.
+
+    Write the results to a new JSON file of nmdc Database instances.
+    """
+    start_time = time.time()
+    logging.info(f"Processing workflow records for study_id: {study_id}")
+
+
+
+    # Get Database dump file paths and the data directory
+    db_infile, db_outfile = _get_database_paths(study_id, dryrun)
+    data_dir = _get_data_dir(data_dir, dryrun)
+
+
+    # Read extracted DB records
+    logging.info(f"Using db_infile: {db_infile}")
+    with open(db_infile, "r") as f:
+        db_records = json.load(f)
+    logging.info(f"Read {len(db_records)} records from db_infile")
+
+    re_ided_db_records = []
+    for db_record in db_records:
+        omics_processing_id = get_omics_processing_id(db_record)
+        logging.info(f"omics_processing_id: {omics_processing_id}")
+
+        # Get new Database instance and downstream data objects
+        new_db, downstream_inputs = get_new_db_and_downstream_inputs(db_record)
+        # Re-ID db_record
+        # Update data file headers
+        # Write re-IDed db_record to db_outfile
+        # Write updated data file to datafile_dir
+        # Log results
+
+
+def _get_data_dir(data_dir, dryrun):
+    """
+    Return the path to the data object files
+    """
+    if dryrun:
+        logging.info("Running in dryrun mode")
+        return DRYRUN_DATAFILE_DIR
+    elif not data_dir:
+        data_dir = BASE_DATAFILE_DIR
+    logging.info(f"Using datafile_dir: {data_dir}")
+    return data_dir
+
+def _get_database_paths(study_id, dryrun):
+    """
+    Return the paths to the input and output data files
+    """
+    db_infile_suffix = "_associated_record_dump.json"
+    db_outfile_suffix = "_re_ided_record_dump.json"
+    if dryrun:
+        db_infile = DATA_DIR.joinpath(f"dryrun{db_infile_suffix}")
+        db_outfile = DATA_DIR.joinpath(f"dryrun{db_outfile_suffix}")
+    else:
+        db_infile = DATA_DIR.joinpath(f"{study_id}{db_infile_suffix}")
+        db_outfile = DATA_DIR.joinpath(f"{study_id}{db_outfile_suffix}")
+    return db_infile, db_outfile
+
+
+if __name__ == '__main__':
+    cli(obj={})
diff --git a/nmdc_automation/re_iding/tests/__init__.py b/nmdc_automation/re_iding/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/nmdc_automation/re_iding/tests/conftest.py b/nmdc_automation/re_iding/tests/conftest.py
new file mode 100644
index 00000000..341ac2bc
--- /dev/null
+++ b/nmdc_automation/re_iding/tests/conftest.py
@@ -0,0 +1,11 @@
+import pytest
+from pathlib import Path
+import json
+
+TEST_DATA_DIR = Path(__file__).parent / "test_data"
+
+@pytest.fixture
+def db_record():
+    """Return a dict of a test Database instance"""
+    with open(TEST_DATA_DIR / "db_record.json", "r") as f:
+        return json.load(f)
diff --git a/nmdc_automation/re_iding/tests/test_data/db_record.json b/nmdc_automation/re_iding/tests/test_data/db_record.json
new file mode 100644
index 00000000..657e1469
--- /dev/null
+++ b/nmdc_automation/re_iding/tests/test_data/db_record.json
@@ -0,0 +1,638 @@
+{
+        "functional_annotation_agg": [],
+        "library_preparation_set": [],
+        "processed_sample_set": [],
+        "extraction_set": [],
+        "activity_set": [],
+        "biosample_set": [],
+        "data_object_set": [
+            {
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+                "name": "9422.8.132674.GTTTCG.fastq.gz"
+            },
+            {
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+                "description": "Filtered Reads for Gp0115663",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filtered.fastq.gz",
+                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                "id": "nmdc:7bf778baef033d36f118f8591256d6ef",
+                "file_size_bytes": 2571324879
+            },
+            {
+                "name": "Gp0115663_Filtered Stats",
+                "description": "Filtered Stats for Gp0115663",
+                "data_object_type": "QC Statistics",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filterStats.txt",
+                "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
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+            },
+            {
+                "name": "Gp0115663_Gottcha2 TSV report",
+                "description": "Gottcha2 TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
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+            },
+            {
+                "name": "Gp0115663_Gottcha2 full TSV report",
+                "description": "Gottcha2 full TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
+                "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
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+            },
+            {
+                "name": "Gp0115663_Gottcha2 Krona HTML report",
+                "description": "Gottcha2 Krona HTML report for Gp0115663",
+                "data_object_type": "GOTTCHA2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
+                "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
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+            },
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+                "description": "Centrifuge classification TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
+                "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
+                "id": "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
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+            },
+            {
+                "name": "Gp0115663_Centrifuge TSV report",
+                "description": "Centrifuge TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
+                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
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+            {
+                "name": "Gp0115663_Centrifuge Krona HTML report",
+                "description": "Centrifuge Krona HTML report for Gp0115663",
+                "data_object_type": "Centrifuge Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
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+                "description": "Kraken classification TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
+                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
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+                "name": "Gp0115663_Kraken2 TSV report",
+                "description": "Kraken2 TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
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+                "description": "Kraken2 Krona HTML report for Gp0115663",
+                "data_object_type": "Kraken2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
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+                "description": "Assembled contigs fasta for Gp0115663",
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+                "name": "Gp0115663_Assembled scaffold fasta",
+                "description": "Assembled scaffold fasta for Gp0115663",
+                "data_object_type": "Assembly Scaffolds",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna",
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+            {
+                "name": "Gp0115663_Metagenome Contig Coverage Stats",
+                "description": "Metagenome Contig Coverage Stats for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_covstats.txt",
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+                "description": "Assembled AGP file for Gp0115663",
+                "data_object_type": "Assembly AGP",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_assembly.agp",
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+                "description": "Protein FAA for Gp0115663",
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+                        "number_of_contig": 485,
+                        "completeness": 66.03,
+                        "bin_name": "bins.2",
+                        "gene_count": 2871,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 10.87,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 1,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 32
+                    },
+                    {
+                        "number_of_contig": 56,
+                        "completeness": 34.23,
+                        "bin_name": "bins.3",
+                        "gene_count": 337,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 9
+                    },
+                    {
+                        "number_of_contig": 63,
+                        "completeness": 6.9,
+                        "bin_name": "bins.4",
+                        "gene_count": 276,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 6
+                    },
+                    {
+                        "number_of_contig": 19,
+                        "completeness": 4.45,
+                        "bin_name": "bins.5",
+                        "gene_count": 463,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 4
+                    }
+                ],
+                "unbinned_contig_num": 9288,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:MAGsAnalysisActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "material_sample_set": [],
+        "material_sampling_activity_set": [],
+        "metabolomics_analysis_activity_set": [],
+        "metagenome_annotation_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b005bbf2caae0415ef9d6"
+                },
+                "has_input": [
+                    "nmdc:deddd162bf0128fba13b3bc1ca38d1aa"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:879988d212ecec46928b8598e2f8391f",
+                    "nmdc:884b95102f5965cc0ee2d9b7f198e5a4",
+                    "nmdc:002e4ebc728f8b91cb5f298d340ab013",
+                    "nmdc:6851078f29716d89e3f41f0969ae7bf0",
+                    "nmdc:4f88c89459f36655eb7c1eceec19602a",
+                    "nmdc:a068b9ce6ebb7deb15ff932b513817a9",
+                    "nmdc:618b18fa8635c80cc0091371f451a6f0",
+                    "nmdc:17e55a1a1a133ffbf8cbe4024d997a6f",
+                    "nmdc:8f80142c0f5723af5a3b44b7ff4e4339",
+                    "nmdc:fdd2e8741ffef40db383674a10bb4d11",
+                    "nmdc:8eb49ac20a6c2721d6db227f4fb3356a",
+                    "nmdc:75f481e0d98793cfb4f9508cb3e31622"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "name": "Annotation Activity for nmdc:mga0h9dt75",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:MetagenomeAnnotationActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "metagenome_assembly_set": [
+            {
+                "_id": {
+                    "$oid": "649b005f2ca5ee4adb139fb9"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "ctg_logsum": 214373,
+                "scaf_logsum": 215363,
+                "gap_pct": 0.00188,
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:deddd162bf0128fba13b3bc1ca38d1aa",
+                    "nmdc:b3573e3cda5a06611de71ca04c5c14cc",
+                    "nmdc:c6d0d4cea985ca6fb50a060e15b4a856",
+                    "nmdc:f450e3800e17691d5874c89fc46c186a",
+                    "nmdc:31dc958d116d02122509e90b0883954f"
+                ],
+                "asm_score": 6.577,
+                "was_informed_by": "gold:Gp0115663",
+                "ctg_powsum": 24284,
+                "scaf_max": 68135,
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "scaf_powsum": 24422,
+                "execution_resource": "NERSC-Cori",
+                "contigs": 169784,
+                "name": "Assembly Activity for nmdc:mga0h9dt75",
+                "ctg_max": 68135,
+                "gc_std": 0.11726,
+                "contig_bp": 83494920,
+                "gc_avg": 0.46001,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "scaf_bp": 83496490,
+                "type": "nmdc:MetagenomeAssembly",
+                "scaffolds": 169645,
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "ctg_l50": 470,
+                "ctg_l90": 290,
+                "ctg_n50": 45584,
+                "ctg_n90": 141996,
+                "scaf_l50": 470,
+                "scaf_l90": 290,
+                "scaf_n50": 45550,
+                "scaf_n90": 141870,
+                "scaf_l_gt50k": 68135,
+                "scaf_n_gt50k": 1,
+                "scaf_pct_gt50k": 0.08160224
+            }
+        ],
+        "metagenome_sequencing_activity_set": [],
+        "metaproteomics_analysis_activity_set": [],
+        "metatranscriptome_activity_set": [],
+        "nom_analysis_activity_set": [],
+        "omics_processing_set": [
+            {
+                "_id": {
+                    "$oid": "649b009773e8249959349b33"
+                },
+                "id": "nmdc:omprc-11-bn8jcq58",
+                "name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
+                "has_input": [
+                    "nmdc:bsm-11-qq8s6x03"
+                ],
+                "has_output": [
+                    "jgi:55d740280d8785342fcf7e39"
+                ],
+                "part_of": [
+                    "nmdc:sty-11-aygzgv51"
+                ],
+                "add_date": "2015-05-28",
+                "mod_date": "2021-06-15",
+                "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "omics_type": {
+                    "has_raw_value": "Metagenome"
+                },
+                "principal_investigator": {
+                    "has_raw_value": "James Stegen"
+                },
+                "processing_institution": "JGI",
+                "type": "nmdc:OmicsProcessing",
+                "gold_sequencing_project_identifiers": [
+                    "gold:Gp0115663"
+                ]
+            }
+        ],
+        "reaction_activity_set": [],
+        "read_qc_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009d6bdd4fd20273c88b"
+                },
+                "has_input": [
+                    "nmdc:30a06664f29cffbbbc49abad86eae6fc"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef",
+                    "nmdc:b99ce8adc125c95f0bfdadf36a3f6848"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "input_read_count": 32238374,
+                "output_read_bases": 4608772924,
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "input_read_bases": 4867994474,
+                "name": "Read QC Activity for nmdc:mga0h9dt75",
+                "output_read_count": 30774080,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadQCAnalysisActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "read_based_taxonomy_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009bff710ae353f8cf4f"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                    "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                    "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                    "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                    "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                    "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                    "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                    "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                    "nmdc:94ee1bc2dc74830a21d5c3471d6cf223"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "name": "ReadBased Analysis Activity for nmdc:mga0h9dt75",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadbasedAnalysis",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "study_set": [],
+        "field_research_site_set": [],
+        "collecting_biosamples_from_site_set": [],
+        "date_created": null,
+        "etl_software_version": null,
+        "pooling_set": []
+    }
\ No newline at end of file
diff --git a/nmdc_automation/re_iding/tests/test_re_iding_base.py b/nmdc_automation/re_iding/tests/test_re_iding_base.py
new file mode 100644
index 00000000..e2976676
--- /dev/null
+++ b/nmdc_automation/re_iding/tests/test_re_iding_base.py
@@ -0,0 +1,15 @@
+# nmdc_automation/re_iding/tests/test_re_iding_base.py
+
+from nmdc_schema.nmdc import Database
+from nmdc_automation.re_iding.base import get_new_db_and_downstream_inputs
+
+
+
+def test_get_new_db_and_downstream_inputs(db_record):
+    """
+    Test that we can get a new Database instance and downstream inputs from an
+    existing Database instance.
+    """
+    new_db, downstream_inputs = get_new_db_and_downstream_inputs(db_record)
+    assert isinstance(new_db, Database)
+    assert isinstance(downstream_inputs, list)
\ No newline at end of file

From fa5df3d4135b92fe6dde23cf346062fe26406d1a Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Fri, 10 Nov 2023 13:33:32 -0800
Subject: [PATCH 43/91] add omics processing update method and basic unit test

---
 nmdc_automation/re_iding/base.py              | 96 ++++++++++++++-----
 nmdc_automation/re_iding/db_utils.py          | 16 +++-
 .../re_iding/scripts/re_id_tool.py            | 21 ++--
 .../re_iding/tests/test_re_iding_base.py      | 28 ++++--
 pyproject.toml                                |  1 +
 5 files changed, 118 insertions(+), 44 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index f3753246..77226a6e 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -4,37 +4,81 @@
 records and data objects.
 """
 import logging
-from typing import List
-from pathlib import Path
-import json
-from typing import Dict, List
-
-from nmdc_schema.nmdc import Database, DataObject
-from nmdc_automation.re_iding.db_utils import (
-    OMICS_PROCESSING_SET,
-    DATA_OBJECT_SET,
-    check_for_single_omics_processing_record,
+from typing import Dict
+import yaml
+
+from nmdc_schema.nmdc import DataObject as NmdcDataObject, \
+    Database as NmdcDatabase, OmicsProcessing
+
+from nmdc_automation.api import NmdcRuntimeApi
+from nmdc_automation.re_iding.db_utils import (OMICS_PROCESSING_SET,
+                                               READS_QC_SET,
+                                               check_for_single_omics_processing_record,
+                                               get_data_object_record_by_id, )
+
+NAPA_TEMPLATE = "../../../configs/re_iding_worklfows.yaml"
+
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+    handlers=[logging.StreamHandler()]
 )
 
+logger = logging.getLogger(__name__)
 
-NAPA_TEMPLATE = "../../configs/re_iding_worklfows.yaml"
+class ReIdTool:
+    def __init__(self, api_client: NmdcRuntimeApi, template_file: str = None):
+        self.api_client = api_client
+        if template_file is None:
+            template_file = NAPA_TEMPLATE
+        with open(template_file, "r") as f:
+            self.template = yaml.safe_load(f)
 
+    def update_omics_processing_has_output(
+            self, db_record: Dict,
+            new_db: NmdcDatabase) -> (NmdcDatabase):
+        """
+        Return a new Database instance with the omics processing record has_output
+        data object IDs updated to new IDs.
 
-def get_new_db_and_downstream_inputs(
-        db_record: Dict, config_file: str = None) -> (Database,
-                                                     List[DataObject]):
-    """
-    Return a new Database instance with the given new_omics_processing_record
-    and the data objects that are has_output of the given old_omics_processing_record
-    """
-    if config_file is None:
-        config_file = NAPA_TEMPLATE
-    config_file = Path(config_file)
+        Note: This function assumes that there is only one omics processing record,
+        and that id and name have already been updated.
+        """
+        check_for_single_omics_processing_record(db_record)
+        omics_record = db_record[OMICS_PROCESSING_SET][0]
+        # Strip out and keep has_output and strip out _id
+        has_output = omics_record.pop("has_output", [])
+        omics_record.pop("_id", None)
+        # make a new omics processing record
+        new_omics = OmicsProcessing(**omics_record)
+
+        # make new data objects with updated IDs
+        for old_do_id in has_output:
+            old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
+            old_do_id = old_do_rec.pop("id")
+            new_do_id = self.api_client.minter("nmdc:DataObject")
+            logger.info(f"nmdcDataObject\t{old_do_id}\t{new_do_id}")
 
-    new_db = Database()
-    downstream_inputs = []
+            # Add new do ID to new OmicsProcessing has_output
+            new_omics.has_output.append(new_do_id)
+            # Make a new data object record with the new ID
+            new_db.data_object_set.append(
+                NmdcDataObject(**old_do_rec, id=new_do_id)
+            )
+        new_db.omics_processing_set.append(new_omics)
+        return new_db
 
-    check_for_single_omics_processing_record(db_record)
-    old_omics_processing_record = db_record[OMICS_PROCESSING_SET][0]
 
-    return new_db, downstream_inputs
\ No newline at end of file
+
+
+
+
+def update_reads_qc_analysis_activity_set(db_record: Dict, new_db: NmdcDatabase,
+                                          api_client: NmdcRuntimeApi) -> (NmdcDatabase):
+    """
+    Return a new Database instance with the reads_qc_analysis_activity_set
+    and its data objects updated to new IDs.
+    """
+    for reads_qc_rec in db_record[READS_QC_SET]:
+        pass
+
diff --git a/nmdc_automation/re_iding/db_utils.py b/nmdc_automation/re_iding/db_utils.py
index bdf5674b..f1c77c65 100644
--- a/nmdc_automation/re_iding/db_utils.py
+++ b/nmdc_automation/re_iding/db_utils.py
@@ -10,6 +10,7 @@
 # Some constants for set names we care about
 OMICS_PROCESSING_SET = "omics_processing_set"
 DATA_OBJECT_SET = "data_object_set"
+READS_QC_SET = "read_qc_analysis_activity_set"
 
 
 
@@ -25,17 +26,28 @@ def get_omics_processing_id(db_record: Dict) -> str:
     return omics_processing_set[0]["id"]
 
 
-def check_for_single_omics_processing_record(old_db_record: Dict) -> bool:
+def check_for_single_omics_processing_record(db_record: Dict) -> bool:
     """
     Check that there is only one OmicsProcessing record in the Database.
     """
-    omics_processing_set = old_db_record.get("omics_processing_set", [])
+    omics_processing_set = db_record.get("omics_processing_set", [])
     if len(omics_processing_set) == 0:
         raise ValueError("No omics_processing_set found in db_record")
     elif len(omics_processing_set) > 1:
         raise ValueError("Multiple omics_processing_set found in db_record")
     return True
 
+def get_data_object_record_by_id(db_record: Dict, id: str)-> Dict:
+    """
+    Return the data object record with the given ID.
+    """
+    data_objects = [d for d in db_record[DATA_OBJECT_SET] if d["id"] == id]
+    if len(data_objects) == 0:
+        raise ValueError(f"No data object found with id: {id}")
+    elif len(data_objects) > 1:
+        raise ValueError(f"Multiple data objects found with id: {id}")
+    return data_objects[0]
+
 
 
 
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 8fc4713c..a31ffed9 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -10,10 +10,10 @@
 import json
 import click
 
-from nmdc_automation.api import NmdcRuntimeUserApi
+from nmdc_automation.api import NmdcRuntimeApi
 from nmdc_automation.config import Config
 import nmdc_schema.nmdc as nmdc
-from nmdc_automation.re_iding.base import get_new_db_and_downstream_inputs
+from nmdc_automation.re_iding.base import update_omics_processing_has_output
 from nmdc_automation.re_iding.db_utils import get_omics_processing_id
 
 # Defaults
@@ -68,12 +68,11 @@ def extract_records(ctx, study_id):
 
 
 @cli.command()
-
 @click.option('--dryrun / --no-dryrun', is_flag=True, default=True,
               help='Dryrun mode: use local data dir and do not save results')
-@click.option('--study_id', is_required=False, default=STUDY_ID,
+@click.option('--study_id', default=STUDY_ID,
               help=f'Optional updated study ID. Default: {STUDY_ID}')
-@click.option('--data_dir', is_required=False, default=BASE_DATAFILE_DIR,
+@click.option('--data_dir', default=BASE_DATAFILE_DIR,
               help=f'Optional base datafile directory. Default: {BASE_DATAFILE_DIR}')
 @click.pass_context
 def process_records(ctx, dryrun, study_id, data_dir):
@@ -86,7 +85,9 @@ def process_records(ctx, dryrun, study_id, data_dir):
     start_time = time.time()
     logging.info(f"Processing workflow records for study_id: {study_id}")
 
-
+    # Get API client
+    config = ctx.obj['site_config']
+    api_client = NmdcRuntimeApi(config)
 
     # Get Database dump file paths and the data directory
     db_infile, db_outfile = _get_database_paths(study_id, dryrun)
@@ -104,8 +105,12 @@ def process_records(ctx, dryrun, study_id, data_dir):
         omics_processing_id = get_omics_processing_id(db_record)
         logging.info(f"omics_processing_id: {omics_processing_id}")
 
-        # Get new Database instance and downstream data objects
-        new_db, downstream_inputs = get_new_db_and_downstream_inputs(db_record)
+        new_db = nmdc.Database()
+        # update OmicsProcessing has_output and related DataObject records
+        new_db = update_omics_processing_has_output(db_record, new_db, api_client)
+
+
+
         # Re-ID db_record
         # Update data file headers
         # Write re-IDed db_record to db_outfile
diff --git a/nmdc_automation/re_iding/tests/test_re_iding_base.py b/nmdc_automation/re_iding/tests/test_re_iding_base.py
index e2976676..2459fc37 100644
--- a/nmdc_automation/re_iding/tests/test_re_iding_base.py
+++ b/nmdc_automation/re_iding/tests/test_re_iding_base.py
@@ -1,15 +1,27 @@
 # nmdc_automation/re_iding/tests/test_re_iding_base.py
+import pytest_mock
 
-from nmdc_schema.nmdc import Database
-from nmdc_automation.re_iding.base import get_new_db_and_downstream_inputs
+from nmdc_automation.api import NmdcRuntimeApi
+from nmdc_schema.nmdc import Database as NmdcDatabase
+from nmdc_automation.re_iding.base import ReIdTool
 
 
 
-def test_get_new_db_and_downstream_inputs(db_record):
+
+def test_update_omics_processing_has_output(db_record, mocker):
     """
-    Test that we can get a new Database instance and downstream inputs from an
-    existing Database instance.
+    Test that we can get a new Database with updated omics processing has_output
+    and re-IDed data objects.
     """
-    new_db, downstream_inputs = get_new_db_and_downstream_inputs(db_record)
-    assert isinstance(new_db, Database)
-    assert isinstance(downstream_inputs, list)
\ No newline at end of file
+    exp_do_id = "nmdc:dobj-1234-abcd12345"
+    mock_api = mocker.Mock(spec=NmdcRuntimeApi)
+    mock_api.minter.return_value = exp_do_id
+    reid_tool = ReIdTool(mock_api)
+    new_db = NmdcDatabase()
+    new_db = reid_tool.update_omics_processing_has_output(db_record, new_db)
+    assert isinstance(new_db, NmdcDatabase)
+    assert new_db.omics_processing_set
+
+    assert new_db.omics_processing_set[0].has_output[0] == exp_do_id
+
+
diff --git a/pyproject.toml b/pyproject.toml
index 98165d60..2d3b1673 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,6 +18,7 @@ pytz = "^2023.3"
 python-dotenv = "^1.0.0"
 click = "^8.1.3"
 pytest = "^7.3.1"
+pytest-mock = "^3.12.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"

From 360c37ecf8e670cf566406f3696033e0c93d2f6b Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 08:08:44 -0800
Subject: [PATCH 44/91] update re-id tool

---
 nmdc_automation/re_iding/base.py              | 158 +++++++++++++++---
 .../re_iding/scripts/re_id_tool.py            |   9 +-
 2 files changed, 139 insertions(+), 28 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 77226a6e..8194c58b 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -3,18 +3,22 @@
 base.py - Provides classes and functions for re-ID-ing NMDC metagenome workflow
 records and data objects.
 """
+import copy
 import logging
-from typing import Dict
+from typing import Dict, List
+import re
 import yaml
 
 from nmdc_schema.nmdc import DataObject as NmdcDataObject, \
-    Database as NmdcDatabase, OmicsProcessing
+    Database as NmdcDatabase, OmicsProcessing, WorkflowExecutionActivity
+import nmdc_schema.nmdc as nmdc
 
 from nmdc_automation.api import NmdcRuntimeApi
 from nmdc_automation.re_iding.db_utils import (OMICS_PROCESSING_SET,
                                                READS_QC_SET,
                                                check_for_single_omics_processing_record,
-                                               get_data_object_record_by_id, )
+                                               get_data_object_record_by_id,
+                                               get_omics_processing_id)
 
 NAPA_TEMPLATE = "../../../configs/re_iding_worklfows.yaml"
 
@@ -26,16 +30,60 @@
 
 logger = logging.getLogger(__name__)
 
+
 class ReIdTool:
-    def __init__(self, api_client: NmdcRuntimeApi, template_file: str = None):
+    def __init__(self, api_client: NmdcRuntimeApi, data_dir: str,
+                 template_file: str = None):
         self.api_client = api_client
+        self.data_dir = data_dir
         if template_file is None:
             template_file = NAPA_TEMPLATE
         with open(template_file, "r") as f:
-            self.template = yaml.safe_load(f)
+            self.workflow_template = yaml.safe_load(f)["Workflows"]
 
-    def update_omics_processing_has_output(
-            self, db_record: Dict,
+    def _workflow_template_for_type(self, workflow_type: str) -> Dict:
+        """
+        Return the workflow template for the given workflow name.
+        """
+        templates = []
+        for t in self.workflow_template:
+            type = t["Type"]
+            if type == workflow_type:
+                templates.append(t)
+
+        # templates = [t for t in self.workflow_template if
+        #              t["Type"] == workflow_type]
+        if len(templates) == 0:
+            raise ValueError(f"No workflow template found for {workflow_type}")
+        elif len(templates) > 1:
+            raise ValueError(
+                f"Multiple workflow templates found for "
+                f"{workflow_type}"
+                )
+        return templates[0]
+
+    def data_object_template(self, workflow_type: str,
+                             data_object_type: str) -> Dict:
+        """
+        Return the data object template for the given workflow name and data
+        object type.
+        """
+        template = self._workflow_template_for_type(workflow_type)
+        data_object_templates = [t for t in template["Outputs"] if
+                                 t["data_object_type"] == data_object_type]
+        if len(data_object_templates) == 0:
+            raise ValueError(
+                f"No data object template found for "
+                f"{workflow_type} and {data_object_type}"
+                )
+        elif len(data_object_templates) > 1:
+            raise ValueError(
+                f"Multiple data object templates found for "
+                f"{workflow_type} and {data_object_type}"
+                )
+        return data_object_templates[0]
+
+    def update_omics_processing_has_output(self, db_record: Dict,
             new_db: NmdcDatabase) -> (NmdcDatabase):
         """
         Return a new Database instance with the omics processing record has_output
@@ -47,15 +95,18 @@ def update_omics_processing_has_output(
         check_for_single_omics_processing_record(db_record)
         omics_record = db_record[OMICS_PROCESSING_SET][0]
         # Strip out and keep has_output and strip out _id
-        has_output = omics_record.pop("has_output", [])
-        omics_record.pop("_id", None)
+        params = copy.deepcopy(omics_record)
+        params.pop("has_output", [])
+        params.pop("_id", None)
         # make a new omics processing record
-        new_omics = OmicsProcessing(**omics_record)
+        new_omics = OmicsProcessing(**params)
 
         # make new data objects with updated IDs
-        for old_do_id in has_output:
+        for old_do_id in omics_record["has_output"]:
             old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
-            old_do_id = old_do_rec.pop("id")
+            old_do_id = old_do_rec.get("id")
+            params = copy.deepcopy(old_do_rec)
+            params.pop("id", None)
             new_do_id = self.api_client.minter("nmdc:DataObject")
             logger.info(f"nmdcDataObject\t{old_do_id}\t{new_do_id}")
 
@@ -63,22 +114,77 @@ def update_omics_processing_has_output(
             new_omics.has_output.append(new_do_id)
             # Make a new data object record with the new ID
             new_db.data_object_set.append(
-                NmdcDataObject(**old_do_rec, id=new_do_id)
+                NmdcDataObject(**params, id=new_do_id)
             )
         new_db.omics_processing_set.append(new_omics)
         return new_db
 
+    def update_reads_qc_analysis_activity_set(self, db_record: Dict,
+            new_db: NmdcDatabase) -> (NmdcDatabase):
+        """
+        Return a new Database instance with the reads_qc_analysis_activity_set
+        and its data objects updated to new IDs.
+        """
+        logger.info(
+            f"Updating reads_qc_analysis_activity_set for "
+            f"{db_record[OMICS_PROCESSING_SET][0]['id']}"
+            )
+        new_omics_processing = new_db.omics_processing_set[0]
+        logger.info(new_omics_processing)
+        for reads_qc_rec in db_record[READS_QC_SET]:
+            # old records have non-conforming type
+            activity_type = "nmdc:ReadQcAnalysisActivity"
+            omics_processing_id = new_omics_processing.id
+            has_input = new_omics_processing.has_output
+            updated_has_output = []
+            # Get ReadQC data objects and update IDs
+            for old_do_id in reads_qc_rec["has_output"]:
+                logger.info(f"old_do_id: {old_do_id}")
+                old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
+                new_do = self._make_new_data_object(
+                    omics_processing_id, activity_type, old_do_rec
+                )
+                new_db.data_object_set.append(new_do)
+                updated_has_output.append(new_do.id)
+        return new_db
 
-
-
-
-
-def update_reads_qc_analysis_activity_set(db_record: Dict, new_db: NmdcDatabase,
-                                          api_client: NmdcRuntimeApi) -> (NmdcDatabase):
-    """
-    Return a new Database instance with the reads_qc_analysis_activity_set
-    and its data objects updated to new IDs.
-    """
-    for reads_qc_rec in db_record[READS_QC_SET]:
-        pass
-
+    def _make_new_activity_set_object(self, omics_processing_id: str,
+            activity_set_rec: Dict, has_input: List,
+            has_output: List) -> WorkflowExecutionActivity:
+        """
+        Return a new activity set object with updated IDs.
+        """
+        activity_type = activity_set_rec["type"]
+        template = self.workflow_template(activity_type)
+        activity_class = getattr(nmdc, template["ActivityRange"])
+        new_activity_id = self.api_client.minter(activity_type)
+        logger.info(
+            f"{activity_type}\t{activity_set_rec['id']}\t{new_activity_id}"
+            )
+        activity = activity_class(
+            id=new_activity_id, name=template["Activity"]["name"].replace(
+                "{id}", omics_processing_id
+                ), git_url=template["Git_repo"], version=template["Version"],
+            part_of=[omics_processing_id],
+            execution_resource="NERSC - Perlmutter",
+            started_at_time=activity_set_rec["started_at_time"],
+            has_input=has_input, has_output=has_output,
+            ended_at_time=activity_set_rec["ended_at_time"],
+            was_informed_by=omics_processing_id, )
+        return activity
+
+    def _make_new_data_object(self, omics_processing_id: str,
+            activity_type: str, data_object_rec: Dict) -> NmdcDataObject:
+        """
+        Return a new data object with updated IDs.
+        """
+        data_object_type = data_object_rec["data_object_type"]
+        template = self.data_object_template(
+            activity_type, data_object_type
+            )
+        new_data_object_id = self.api_client.minter("nmdc:DataObject")
+        logger.info(f"nmdcDataObject\t{data_object_rec['id']}\t{new_data_object_id}")
+        new_description = re.sub(
+            "[^ ]+$", f"{omics_processing_id}", data_object_rec["description"]
+        )
+        logger.info(f"new_description: {new_description}")
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index a31ffed9..890ba8be 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -13,7 +13,7 @@
 from nmdc_automation.api import NmdcRuntimeApi
 from nmdc_automation.config import Config
 import nmdc_schema.nmdc as nmdc
-from nmdc_automation.re_iding.base import update_omics_processing_has_output
+from nmdc_automation.re_iding.base import ReIdTool
 from nmdc_automation.re_iding.db_utils import get_omics_processing_id
 
 # Defaults
@@ -89,10 +89,14 @@ def process_records(ctx, dryrun, study_id, data_dir):
     config = ctx.obj['site_config']
     api_client = NmdcRuntimeApi(config)
 
+
     # Get Database dump file paths and the data directory
     db_infile, db_outfile = _get_database_paths(study_id, dryrun)
     data_dir = _get_data_dir(data_dir, dryrun)
 
+    # Initialize re-ID tool
+    reid_tool = ReIdTool(api_client, data_dir)
+
 
     # Read extracted DB records
     logging.info(f"Using db_infile: {db_infile}")
@@ -107,7 +111,8 @@ def process_records(ctx, dryrun, study_id, data_dir):
 
         new_db = nmdc.Database()
         # update OmicsProcessing has_output and related DataObject records
-        new_db = update_omics_processing_has_output(db_record, new_db, api_client)
+        new_db = reid_tool.update_omics_processing_has_output(db_record, new_db)
+        new_db = reid_tool.update_reads_qc_analysis_activity_set(db_record, new_db)
 
 
 

From 68cd47a8d2098e31b34701369278a2e56aaeac50 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 09:17:42 -0800
Subject: [PATCH 45/91] _make_new_data_object

---
 nmdc_automation/re_iding/base.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 8194c58b..3bd74424 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -21,6 +21,7 @@
                                                get_omics_processing_id)
 
 NAPA_TEMPLATE = "../../../configs/re_iding_worklfows.yaml"
+BASE_DIR = "/global/cfs/cdirs/m3408/results"
 
 logging.basicConfig(
     level=logging.INFO,
@@ -188,3 +189,33 @@ def _make_new_data_object(self, omics_processing_id: str,
             "[^ ]+$", f"{omics_processing_id}", data_object_rec["description"]
         )
         logger.info(f"new_description: {new_description}")
+        new_filename = self._make_new_filename(new_data_object_id, data_object_rec)
+        logger.info(f"new_filename: {new_filename}")
+        new_url = f"{BASE_DIR}/{omics_processing_id}/{new_data_object_id}/{new_filename}"
+
+        data_object = NmdcDataObject(
+            id=new_data_object_id,
+            name=template["name"].replace("{id}", omics_processing_id),
+            description=new_description,
+            type="nmdc:Data_Object",
+            file_size_bytes=data_object_rec["file_size_bytes"],
+            md5_checksum=data_object_rec["md5_checksum"],
+            url=new_url,
+            )
+        return data_object
+
+    def _make_new_filename(self, new_data_object_id: str,
+            data_object_record: Dict) -> str:
+        """
+        Return the updated filename.
+        """
+        filename = data_object_record["url"].split("/")[-1]
+        file_extenstion = filename.lstrip("nmdc_").split("_", maxsplit=1)[-1]
+        new_filename = f"{new_data_object_id}_{file_extenstion}".replace(":",
+                                                                         "_")
+        return new_filename
+
+
+
+
+

From dff972636bb8a9d3dc137d9c4f11199d113752c9 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 09:40:14 -0800
Subject: [PATCH 46/91] Consolidate record extraction script to re_id_tool.py

---
 .../extract_metagenome_workflow_records.py    | 155 ------------------
 .../re_iding/scripts/re_id_tool.py            | 122 +++++++++++++-
 2 files changed, 116 insertions(+), 161 deletions(-)
 delete mode 100644 nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py

diff --git a/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py b/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
deleted file mode 100644
index 49c71c1f..00000000
--- a/nmdc_automation/re_iding/scripts/extract_metagenome_workflow_records.py
+++ /dev/null
@@ -1,155 +0,0 @@
-#!/usr/bin/env python3
-# coding: utf-8
-# nmdc_schema/napa_compliance/scripts/extract_metagenome_workflow_records.py
-"""
-extract_metagenome_workflow_records.py: Starting with OmicsProcessing, extract
-metagenome workflow activity records and their associated data objects. Write
-the results, as a list of nmdc-schema Database instances to a JSON file.
-"""
-import logging
-import time
-from pathlib import Path
-import json
-import click
-
-from nmdc_automation.api import NmdcRuntimeUserApi
-from nmdc_automation.config import Config
-import nmdc_schema.nmdc as nmdc
-
-GOLD_STUDY_ID = "gold:Gs0114663"
-STUDY_ID = "nmdc:sty-11-aygzgv51"
-NAPA_CONFIG = Path("../../../configs/napa_config.toml")
-
-
-def _get_legacy_id(omics_processing_record: dict) -> str:
-    """
-    Get the legacy ID for the given OmicsProcessing record.
-    """
-    legacy_id = None
-    legacy_ids = []
-    gold_ids = omics_processing_record.get("gold_sequencing_project_identifiers", [])
-    legacy_ids.extend(gold_ids)
-    alternative_ids = omics_processing_record.get("alternative_identifiers", [])
-    legacy_ids.extend(alternative_ids)
-    if len(legacy_ids) == 0:
-        logging.warning(
-            f"No legacy IDs found for omics_processing_record: {omics_processing_record['id']}"
-        )
-        return None
-    elif len(legacy_ids) > 1:
-        logging.warning(
-            f"Multiple legacy IDs found for omics_processing_record: {omics_processing_record['id']}"
-        )
-        return None
-    else:
-        legacy_id = legacy_ids[0]
-    return legacy_id
-
-@click.command()
-@click.option("--study_id", default=STUDY_ID, help="Updated study ID")
-@click.option(
-    "--site_config", type=click.Path(exists=True), default=NAPA_CONFIG,
-    help="Site configuration file"
-)
-def extract_workflow_records(study_id: str, site_config: bool):
-    """
-    Extract metagenome workflow records for re-ID-ing of Study, Biosample, and
-    OmicsProcessing records by:
-    1. Retrieving all OmicsProcessing records for updated study ID
-    2. For each OmicsProcessing record, retrieve the corresponding
-    WorkflowExecutionActivity records:
-        a. ReadQcAnalysisActivity
-        b. ReadBasedTaxonomyAnalysisActivity
-        c. MetagenomeAssembly
-        d. MetagenomeAnnotationActivity
-        e. MagsAnalysisActivity
-    3. For each WorkflowExecutionActivity record:
-       a. Retrieve the corresponding DataObject records
-    4. Create a database object for each OmicsProcessing record and its
-    associated WorkflowExecutionActivity and DataObject records
-    5. Write the database object to a JSON file
-    """
-    start_time = time.time()
-    logging.info("starting missing_neon_soils_ecosystem_data.py...")
-    logging.info(f"study_id: {study_id}")
-
-    config = Config(site_config)
-    query_api_client = NmdcRuntimeUserApi(
-        username=config.napa_username, password=config.napa_password,
-        base_url=config.napa_base_url, )
-    
-    # 1. Retrieve all OmicsProcessing records for the updated NMDC study ID
-    omics_processing_records = query_api_client.get_omics_processing_records_for_nmdc_study(
-        study_id
-        )
-    logging.info(
-        f"Retrieved {len(omics_processing_records)} OmicsProcessing records for study {study_id}"
-    )
-    
-    retrieved_databases = []
-    # 2. For each OmicsProcessing record, find the legacy identifier:
-    for omics_processing_record in omics_processing_records:
-        db = nmdc.Database()
-        logging.info(f"omics_processing_record: "
-                     f"{omics_processing_record['id']}")
-        legacy_id = _get_legacy_id(omics_processing_record)
-        logging.info(f"legacy_id: {legacy_id}")
-
-        if (omics_processing_record["omics_type"]["has_raw_value"] !=
-                "Metagenome"):
-            logging.info(f"omics_processing_record {omics_processing_record['id']} "
-                         f"is not a Metagenome")
-            continue
-        db.omics_processing_set.append(omics_processing_record)
-        for data_object_id in omics_processing_record["has_output"]:
-            data_object_record = query_api_client.get_data_object_by_id(
-                data_object_id
-            )
-            db.data_object_set.append(data_object_record)
-
-        # downstream workflow activity sets
-        (read_qc_records, readbased_records, metagenome_assembly_records,
-            metagenome_annotation_records, mags_records) = [], [], [], [], []
-
-        downstream_workflow_activity_sets = {
-            "read_qc_analysis_activity_set": read_qc_records,
-            "read_based_taxonomy_analysis_activity_set": readbased_records,
-            "metagenome_assembly_set": metagenome_assembly_records,
-            "metagenome_annotation_activity_set": metagenome_annotation_records,
-            "mags_activity_set": mags_records,
-        }
-        for set_name, records in downstream_workflow_activity_sets.items():
-            records = query_api_client.get_workflow_activity_informed_by(
-                set_name, legacy_id
-            )
-            db.__setattr__(set_name, records)
-            # Add the data objects referenced by the `has_output` property
-            for record in records:
-                logging.info(f"record: {record['id']}, {record['name']}")
-                for data_object_id in record["has_output"]:
-                    data_object_record = query_api_client.get_data_object_by_id(
-                        data_object_id
-                    )
-                    logging.info(f"data_object_record: "
-                                 f"{data_object_record['id']}, {data_object_record['description']}")
-                    db.data_object_set.append(data_object_record)
-
-        # Search for orphaned data objects with the legacy ID in the description
-        orphaned_data_objects = query_api_client.get_data_objects_by_description(
-                legacy_id
-        )
-        # check that we don't already have the data object in the set
-        for data_object in orphaned_data_objects:
-            if data_object["id"] not in [d["id"] for d in db.data_object_set]:
-                db.data_object_set.append(data_object)
-                logging.info(f"Added orphaned data object: "
-                             f"{data_object['id']}, {data_object['description']}")
-
-        retrieved_databases.append(db)
-        
-    with open(f"{study_id}_assocated_record_dump.json", 'w') as json_file:
-        json.dump([o.__dict__ for o in retrieved_databases], json_file, indent=4)
-
-
-if __name__ == "__main__":
-    extract_workflow_records()
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 890ba8be..0890f4db 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -10,7 +10,7 @@
 import json
 import click
 
-from nmdc_automation.api import NmdcRuntimeApi
+from nmdc_automation.api import NmdcRuntimeApi, NmdcRuntimeUserApi
 from nmdc_automation.config import Config
 import nmdc_schema.nmdc as nmdc
 from nmdc_automation.re_iding.base import ReIdTool
@@ -65,6 +65,93 @@ def extract_records(ctx, study_id):
     """
     start_time = time.time()
     logging.info(f"Extracting workflow records for study_id: {study_id}")
+    logging.info(f"study_id: {study_id}")
+
+    config = Config(ctx.obj['site_config'])
+    api_client = NmdcRuntimeUserApi(username=config.napa_username, password=config.napa_password,
+        base_url=config.napa_base_url)
+
+    # 1. Retrieve all OmicsProcessing records for the updated NMDC study ID
+    omics_processing_records = api_client.get_omics_processing_records_for_nmdc_study(
+        study_id
+    )
+    logging.info(
+        f"Retrieved {len(omics_processing_records)} OmicsProcessing records for study {study_id}"
+    )
+
+    retrieved_databases = []
+    # 2. For each OmicsProcessing record, find the legacy identifier:
+    for omics_processing_record in omics_processing_records:
+        db = nmdc.Database()
+        logging.info(
+            f"omics_processing_record: "
+            f"{omics_processing_record['id']}"
+            )
+        legacy_id = _get_legacy_id(omics_processing_record)
+        logging.info(f"legacy_id: {legacy_id}")
+
+        if (omics_processing_record["omics_type"]["has_raw_value"] !=
+                "Metagenome"):
+            logging.info(
+                f"omics_processing_record {omics_processing_record['id']} "
+                f"is not a Metagenome"
+                )
+            continue
+        db.omics_processing_set.append(omics_processing_record)
+        for data_object_id in omics_processing_record["has_output"]:
+            data_object_record = api_client.get_data_object_by_id(
+                data_object_id
+            )
+            db.data_object_set.append(data_object_record)
+
+        # downstream workflow activity sets
+        (read_qc_records, readbased_records, metagenome_assembly_records,
+         metagenome_annotation_records, mags_records) = [], [], [], [], []
+
+        downstream_workflow_activity_sets = {
+            "read_qc_analysis_activity_set": read_qc_records,
+            "read_based_taxonomy_analysis_activity_set": readbased_records,
+            "metagenome_assembly_set": metagenome_assembly_records,
+            "metagenome_annotation_activity_set": metagenome_annotation_records,
+            "mags_activity_set": mags_records,
+        }
+        for set_name, records in downstream_workflow_activity_sets.items():
+            records = api_client.get_workflow_activity_informed_by(
+                set_name, legacy_id
+            )
+            db.__setattr__(set_name, records)
+            # Add the data objects referenced by the `has_output` property
+            for record in records:
+                logging.info(f"record: {record['id']}, {record['name']}")
+                for data_object_id in record["has_output"]:
+                    data_object_record = api_client.get_data_object_by_id(
+                        data_object_id
+                    )
+                    logging.info(
+                        f"data_object_record: "
+                        f"{data_object_record['id']}, {data_object_record['description']}"
+                        )
+                    db.data_object_set.append(data_object_record)
+
+        # Search for orphaned data objects with the legacy ID in the description
+        orphaned_data_objects = api_client.get_data_objects_by_description(
+            legacy_id
+        )
+        # check that we don't already have the data object in the set
+        for data_object in orphaned_data_objects:
+            if data_object["id"] not in [d["id"] for d in db.data_object_set]:
+                db.data_object_set.append(data_object)
+                logging.info(
+                    f"Added orphaned data object: "
+                    f"{data_object['id']}, {data_object['description']}"
+                    )
+
+        retrieved_databases.append(db)
+
+    with open(f"{study_id}_assocated_record_dump.json", 'w') as json_file:
+        json.dump(
+            [o.__dict__ for o in retrieved_databases], json_file, indent=4
+            )
 
 
 @cli.command()
@@ -114,13 +201,13 @@ def process_records(ctx, dryrun, study_id, data_dir):
         new_db = reid_tool.update_omics_processing_has_output(db_record, new_db)
         new_db = reid_tool.update_reads_qc_analysis_activity_set(db_record, new_db)
 
+        re_ided_db_records.append(new_db)
 
 
-        # Re-ID db_record
-        # Update data file headers
-        # Write re-IDed db_record to db_outfile
-        # Write updated data file to datafile_dir
-        # Log results
+    with open(f"{study_id}_updated_record_dump.json", 'w') as json_file:
+        json.dump(
+            [o.__dict__ for o in re_ided_db_records], json_file, indent=4
+            )
 
 
 def _get_data_dir(data_dir, dryrun):
@@ -149,6 +236,29 @@ def _get_database_paths(study_id, dryrun):
         db_outfile = DATA_DIR.joinpath(f"{study_id}{db_outfile_suffix}")
     return db_infile, db_outfile
 
+def _get_legacy_id(omics_processing_record: dict) -> str:
+    """
+    Get the legacy ID for the given OmicsProcessing record.
+    """
+    legacy_id = None
+    legacy_ids = []
+    gold_ids = omics_processing_record.get("gold_sequencing_project_identifiers", [])
+    legacy_ids.extend(gold_ids)
+    alternative_ids = omics_processing_record.get("alternative_identifiers", [])
+    legacy_ids.extend(alternative_ids)
+    if len(legacy_ids) == 0:
+        logging.warning(
+            f"No legacy IDs found for omics_processing_record: {omics_processing_record['id']}"
+        )
+        return None
+    elif len(legacy_ids) > 1:
+        logging.warning(
+            f"Multiple legacy IDs found for omics_processing_record: {omics_processing_record['id']}"
+        )
+        return None
+    else:
+        legacy_id = legacy_ids[0]
+    return legacy_id
 
 if __name__ == '__main__':
     cli(obj={})

From 92f18b68b9536bad2c648cb0ef58f058c6020fbe Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 10:25:02 -0800
Subject: [PATCH 47/91] normalize QC vs Qc and output json for re-ided records

---
 nmdc_automation/api/nmdcapi.py                |   2 +-
 nmdc_automation/re_iding/base.py              |  28 ++-
 .../data/dryrun_re_ided_record_dump.json      | 198 ++++++++++++++++++
 .../re_iding/scripts/re_id_tool.py            |   9 +-
 4 files changed, 223 insertions(+), 14 deletions(-)
 create mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json

diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 7a5988cf..0927c23a 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -96,7 +96,7 @@ def minter(self, id_type, informed_by=None):
         data = {"schema_class": {"id": id_type}, "how_many": 1}
         resp = requests.post(url, data=json.dumps(data), headers=self.header)
         if not resp.ok:
-            raise ValueError("Failed to mint ID")
+            raise ValueError(f"Failed to mint ID of type {id_type}")
         id = resp.json()[0]
         if informed_by:
             url = f"{self._base_url}pids/bind"
diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 3bd74424..c6d0c7fa 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -47,13 +47,12 @@ def _workflow_template_for_type(self, workflow_type: str) -> Dict:
         Return the workflow template for the given workflow name.
         """
         templates = []
+        workflow_type = workflow_type.replace("QC", "Qc")
         for t in self.workflow_template:
             type = t["Type"]
             if type == workflow_type:
                 templates.append(t)
 
-        # templates = [t for t in self.workflow_template if
-        #              t["Type"] == workflow_type]
         if len(templates) == 0:
             raise ValueError(f"No workflow template found for {workflow_type}")
         elif len(templates) > 1:
@@ -137,6 +136,7 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             activity_type = "nmdc:ReadQcAnalysisActivity"
             omics_processing_id = new_omics_processing.id
             has_input = new_omics_processing.has_output
+
             updated_has_output = []
             # Get ReadQC data objects and update IDs
             for old_do_id in reads_qc_rec["has_output"]:
@@ -145,8 +145,15 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
                 new_do = self._make_new_data_object(
                     omics_processing_id, activity_type, old_do_rec
                 )
+                # add new data object to new database and update has_output
                 new_db.data_object_set.append(new_do)
                 updated_has_output.append(new_do.id)
+
+            # Get new ReadQC activity set
+            new_reads_qc = self._make_new_activity_set_object(
+                omics_processing_id, reads_qc_rec, has_input, updated_has_output
+            )
+            new_db.read_qc_analysis_activity_set.append(new_reads_qc)
         return new_db
 
     def _make_new_activity_set_object(self, omics_processing_id: str,
@@ -155,23 +162,26 @@ def _make_new_activity_set_object(self, omics_processing_id: str,
         """
         Return a new activity set object with updated IDs.
         """
-        activity_type = activity_set_rec["type"]
-        template = self.workflow_template(activity_type)
+        activity_type = activity_set_rec["type"].replace("QC", "Qc")
+        template = self._workflow_template_for_type(activity_type)
         activity_class = getattr(nmdc, template["ActivityRange"])
         new_activity_id = self.api_client.minter(activity_type)
         logger.info(
             f"{activity_type}\t{activity_set_rec['id']}\t{new_activity_id}"
             )
         activity = activity_class(
-            id=new_activity_id, name=template["Activity"]["name"].replace(
-                "{id}", omics_processing_id
-                ), git_url=template["Git_repo"], version=template["Version"],
+            id=new_activity_id,
+            name=template["Activity"]["name"].replace("{id}", omics_processing_id),
+            git_url=template["Git_repo"], version=template["Version"],
             part_of=[omics_processing_id],
             execution_resource="NERSC - Perlmutter",
             started_at_time=activity_set_rec["started_at_time"],
-            has_input=has_input, has_output=has_output,
+            has_input=has_input,
+            has_output=has_output,
             ended_at_time=activity_set_rec["ended_at_time"],
-            was_informed_by=omics_processing_id, )
+            was_informed_by=omics_processing_id,
+            type=template["Type"],
+        )
         return activity
 
     def _make_new_data_object(self, omics_processing_id: str,
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
new file mode 100644
index 00000000..94aeaf23
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -0,0 +1,198 @@
+[
+    {
+        "functional_annotation_agg": [],
+        "library_preparation_set": [],
+        "processed_sample_set": [],
+        "extraction_set": [],
+        "activity_set": [],
+        "biosample_set": [],
+        "data_object_set": [
+            {
+                "id": "nmdc:dobj-11-9t9hwj09",
+                "name": "9422.8.132674.GTTTCG.fastq.gz",
+                "description": "Raw sequencer read data",
+                "alternative_identifiers": [],
+                "file_size_bytes": 2861414297,
+                "md5_checksum": null,
+                "data_object_type": null,
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": null,
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-03dw0x03",
+                "name": "Reads QC result fastq (clean data)",
+                "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
+                "alternative_identifiers": [],
+                "file_size_bytes": 2571324879,
+                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                "data_object_type": null,
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-03dw0x03/nmdc_dobj-11-03dw0x03_filtered.fastq.gz",
+                "type": "nmdc:Data_Object"
+            },
+            {
+                "id": "nmdc:dobj-11-ds6gd769",
+                "name": "Reads QC summary statistics",
+                "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
+                "alternative_identifiers": [],
+                "file_size_bytes": 290,
+                "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
+                "data_object_type": null,
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-ds6gd769/nmdc_dobj-11-ds6gd769_filterStats.txt",
+                "type": "nmdc:Data_Object"
+            }
+        ],
+        "dissolving_activity_set": [],
+        "functional_annotation_set": [],
+        "genome_feature_set": [],
+        "mags_activity_set": [],
+        "material_sample_set": [],
+        "material_sampling_activity_set": [],
+        "metabolomics_analysis_activity_set": [],
+        "metagenome_annotation_activity_set": [],
+        "metagenome_assembly_set": [],
+        "metagenome_sequencing_activity_set": [],
+        "metaproteomics_analysis_activity_set": [],
+        "metatranscriptome_activity_set": [],
+        "nom_analysis_activity_set": [],
+        "omics_processing_set": [
+            {
+                "id": "nmdc:omprc-11-bn8jcq58",
+                "name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
+                "alternative_identifiers": [],
+                "has_input": [
+                    "nmdc:bsm-11-qq8s6x03"
+                ],
+                "add_date": "2015-05-28",
+                "chimera_check": null,
+                "gold_sequencing_project_identifiers": [
+                    "gold:Gp0115663"
+                ],
+                "has_output": [
+                    "nmdc:dobj-11-9t9hwj09"
+                ],
+                "insdc_experiment_identifiers": [],
+                "instrument_name": null,
+                "mod_date": "2021-06-15",
+                "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "nucl_acid_amp": null,
+                "nucl_acid_ext": null,
+                "omics_type": {
+                    "has_raw_value": "Metagenome",
+                    "was_generated_by": null,
+                    "type": null,
+                    "term": null
+                },
+                "part_of": [
+                    "nmdc:sty-11-aygzgv51"
+                ],
+                "pcr_cond": null,
+                "pcr_primers": null,
+                "principal_investigator": {
+                    "has_raw_value": "James Stegen",
+                    "was_generated_by": null,
+                    "type": null,
+                    "orcid": null,
+                    "profile_image_url": null,
+                    "email": null,
+                    "name": null,
+                    "websites": []
+                },
+                "processing_institution": {
+                    "_code": {
+                        "text": "JGI",
+                        "description": null,
+                        "meaning": null,
+                        "unit": null,
+                        "is_a": null,
+                        "mixins": [],
+                        "extensions": {},
+                        "annotations": {},
+                        "alt_descriptions": {},
+                        "title": null,
+                        "deprecated": null,
+                        "todos": [],
+                        "notes": [],
+                        "comments": [],
+                        "examples": [],
+                        "in_subset": [],
+                        "from_schema": null,
+                        "imported_from": null,
+                        "source": null,
+                        "in_language": null,
+                        "see_also": [],
+                        "deprecated_element_has_exact_replacement": null,
+                        "deprecated_element_has_possible_replacement": null,
+                        "aliases": [],
+                        "structured_aliases": {},
+                        "mappings": [],
+                        "exact_mappings": [],
+                        "close_mappings": [],
+                        "related_mappings": [],
+                        "narrow_mappings": [],
+                        "broad_mappings": [],
+                        "created_by": null,
+                        "contributors": [],
+                        "created_on": null,
+                        "last_updated_on": null,
+                        "modified_by": null,
+                        "status": null,
+                        "rank": null,
+                        "categories": [],
+                        "keywords": []
+                    }
+                },
+                "samp_vol_we_dna_ext": null,
+                "seq_meth": null,
+                "seq_quality_check": null,
+                "target_gene": null,
+                "target_subfragment": null,
+                "type": "nmdc:OmicsProcessing"
+            }
+        ],
+        "reaction_activity_set": [],
+        "read_qc_analysis_activity_set": [
+            {
+                "id": "nmdc:wfrqc-11-wt45ty13",
+                "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "was_informed_by": "nmdc:omprc-11-bn8jcq58",
+                "used": null,
+                "execution_resource": "NERSC - Perlmutter",
+                "git_url": "https://github.com/microbiomedata/ReadsQC",
+                "has_input": [
+                    "nmdc:dobj-11-9t9hwj09"
+                ],
+                "has_output": [
+                    "nmdc:dobj-11-03dw0x03",
+                    "nmdc:dobj-11-ds6gd769"
+                ],
+                "type": "nmdc:ReadQcAnalysisActivity",
+                "part_of": [
+                    "nmdc:omprc-11-bn8jcq58"
+                ],
+                "version": "v1.0.8",
+                "input_read_count": null,
+                "input_base_count": null,
+                "output_read_count": null,
+                "output_base_count": null,
+                "input_read_bases": null,
+                "output_read_bases": null
+            }
+        ],
+        "read_based_taxonomy_analysis_activity_set": [],
+        "study_set": [],
+        "field_research_site_set": [],
+        "collecting_biosamples_from_site_set": [],
+        "date_created": null,
+        "etl_software_version": null,
+        "pooling_set": []
+    }
+]
\ No newline at end of file
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 0890f4db..354a03de 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -199,15 +199,16 @@ def process_records(ctx, dryrun, study_id, data_dir):
         new_db = nmdc.Database()
         # update OmicsProcessing has_output and related DataObject records
         new_db = reid_tool.update_omics_processing_has_output(db_record, new_db)
+        # update ReadsQC
         new_db = reid_tool.update_reads_qc_analysis_activity_set(db_record, new_db)
 
         re_ided_db_records.append(new_db)
 
 
-    with open(f"{study_id}_updated_record_dump.json", 'w') as json_file:
-        json.dump(
-            [o.__dict__ for o in re_ided_db_records], json_file, indent=4
-            )
+    json_data = json.dumps(re_ided_db_records, default=lambda o: o.__dict__, indent=4)
+    logging.info(f"Writing re_ided_db_records to {db_outfile}")
+    with open(db_outfile, "w") as f:
+        f.write(json_data)
 
 
 def _get_data_dir(data_dir, dryrun):

From e0634acaca6859b9d2c39f4001bca7564a2a629e Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 10:39:05 -0800
Subject: [PATCH 48/91] update readQC specific properties

---
 nmdc_automation/re_iding/base.py              |  9 ++++++
 .../data/dryrun_re_ided_record_dump.json      | 28 +++++++++----------
 2 files changed, 23 insertions(+), 14 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index c6d0c7fa..1b745769 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -153,6 +153,15 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             new_reads_qc = self._make_new_activity_set_object(
                 omics_processing_id, reads_qc_rec, has_input, updated_has_output
             )
+            # update activity-specific properties
+            new_reads_qc.input_read_count = reads_qc_rec.get("input_read_count")
+            new_reads_qc.input_base_count = reads_qc_rec.get("input_base_count")
+            new_reads_qc.output_read_count = reads_qc_rec.get("output_read_count")
+            new_reads_qc.output_base_count = reads_qc_rec.get("output_base_count")
+            new_reads_qc.input_read_bases = reads_qc_rec.get("input_read_bases")
+            new_reads_qc.output_read_bases = reads_qc_rec.get("output_read_bases")
+
+
             new_db.read_qc_analysis_activity_set.append(new_reads_qc)
         return new_db
 
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index 94aeaf23..c4d5b59a 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -8,7 +8,7 @@
         "biosample_set": [],
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-9t9hwj09",
+                "id": "nmdc:dobj-11-3w7nex07",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "alternative_identifiers": [],
@@ -21,7 +21,7 @@
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-03dw0x03",
+                "id": "nmdc:dobj-11-aazp9v53",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -30,11 +30,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-03dw0x03/nmdc_dobj-11-03dw0x03_filtered.fastq.gz",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-aazp9v53/nmdc_dobj-11-aazp9v53_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-ds6gd769",
+                "id": "nmdc:dobj-11-wtayma27",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -43,7 +43,7 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-ds6gd769/nmdc_dobj-11-ds6gd769_filterStats.txt",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-wtayma27/nmdc_dobj-11-wtayma27_filterStats.txt",
                 "type": "nmdc:Data_Object"
             }
         ],
@@ -75,7 +75,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-9t9hwj09"
+                    "nmdc:dobj-11-3w7nex07"
                 ],
                 "insdc_experiment_identifiers": [],
                 "instrument_name": null,
@@ -159,7 +159,7 @@
         "reaction_activity_set": [],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-wt45ty13",
+                "id": "nmdc:wfrqc-11-08etj008",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -168,23 +168,23 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-9t9hwj09"
+                    "nmdc:dobj-11-3w7nex07"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-03dw0x03",
-                    "nmdc:dobj-11-ds6gd769"
+                    "nmdc:dobj-11-aazp9v53",
+                    "nmdc:dobj-11-wtayma27"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
                     "nmdc:omprc-11-bn8jcq58"
                 ],
                 "version": "v1.0.8",
-                "input_read_count": null,
+                "input_read_count": 32238374,
                 "input_base_count": null,
-                "output_read_count": null,
+                "output_read_count": 30774080,
                 "output_base_count": null,
-                "input_read_bases": null,
-                "output_read_bases": null
+                "input_read_bases": 4867994474,
+                "output_read_bases": 4608772924
             }
         ],
         "read_based_taxonomy_analysis_activity_set": [],

From 1354a52b29370982e38dc922c8fe35099f041eb8 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 11:17:18 -0800
Subject: [PATCH 49/91] add update_metagenome_assembly_set

---
 nmdc_automation/re_iding/base.py              | 46 +++++++++++-
 nmdc_automation/re_iding/db_utils.py          |  1 +
 .../data/dryrun_re_ided_record_dump.json      | 72 ++++++++++++++++---
 .../re_iding/scripts/re_id_tool.py            |  2 +
 4 files changed, 109 insertions(+), 12 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 1b745769..3207b271 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -16,6 +16,7 @@
 from nmdc_automation.api import NmdcRuntimeApi
 from nmdc_automation.re_iding.db_utils import (OMICS_PROCESSING_SET,
                                                READS_QC_SET,
+                                               METAGENOME_ASSEMBLY_SET,
                                                check_for_single_omics_processing_record,
                                                get_data_object_record_by_id,
                                                get_omics_processing_id)
@@ -130,7 +131,6 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             f"{db_record[OMICS_PROCESSING_SET][0]['id']}"
             )
         new_omics_processing = new_db.omics_processing_set[0]
-        logger.info(new_omics_processing)
         for reads_qc_rec in db_record[READS_QC_SET]:
             # old records have non-conforming type
             activity_type = "nmdc:ReadQcAnalysisActivity"
@@ -165,6 +165,48 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             new_db.read_qc_analysis_activity_set.append(new_reads_qc)
         return new_db
 
+    def update_metagenome_assembly_set(self, db_record: Dict,
+            new_db: NmdcDatabase) -> (NmdcDatabase):
+        """
+        Return a new Database instance with the metagenome_assembly_set
+        and its data objects updated to new IDs.
+        """
+        logger.info(f"Updating metagenome_assembly_set for "
+                    f"{db_record[OMICS_PROCESSING_SET][0]['id']}")
+        new_omics_processing = new_db.omics_processing_set[0]
+
+        for assembly_rec in db_record[METAGENOME_ASSEMBLY_SET]:
+            activity_type = "nmdc:MetagenomeAssembly"
+            omics_processing_id = new_omics_processing.id
+            new_read_qc = new_db.read_qc_analysis_activity_set[0]
+            has_input = new_read_qc.has_output
+            updated_has_output = []
+            for old_do_id in assembly_rec["has_output"]:
+                logger.info(f"old_do_id: {old_do_id}")
+                old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
+                # TODO we need to handle missing data_object_type - until
+                #  then though..
+                if not old_do_rec.get("data_object_type"):
+                    logger.warning(f"Skipping {old_do_id} - no "
+                                   f"data_object_type")
+                    continue
+                new_do = self._make_new_data_object(
+                    omics_processing_id, activity_type, old_do_rec
+                )
+                # add new data object to new database and update has_output
+                new_db.data_object_set.append(new_do)
+                updated_has_output.append(new_do.id)
+
+            # Get new Metagenome Assembly activity set
+            new_reads_qc = self._make_new_activity_set_object(
+                omics_processing_id, assembly_rec, has_input,
+                updated_has_output
+            )
+            # update activity-specific properties
+        return new_db
+
+
+
     def _make_new_activity_set_object(self, omics_processing_id: str,
             activity_set_rec: Dict, has_input: List,
             has_output: List) -> WorkflowExecutionActivity:
@@ -198,7 +240,7 @@ def _make_new_data_object(self, omics_processing_id: str,
         """
         Return a new data object with updated IDs.
         """
-        data_object_type = data_object_rec["data_object_type"]
+        data_object_type = data_object_rec.get("data_object_type")
         template = self.data_object_template(
             activity_type, data_object_type
             )
diff --git a/nmdc_automation/re_iding/db_utils.py b/nmdc_automation/re_iding/db_utils.py
index f1c77c65..6f99fb4b 100644
--- a/nmdc_automation/re_iding/db_utils.py
+++ b/nmdc_automation/re_iding/db_utils.py
@@ -11,6 +11,7 @@
 OMICS_PROCESSING_SET = "omics_processing_set"
 DATA_OBJECT_SET = "data_object_set"
 READS_QC_SET = "read_qc_analysis_activity_set"
+METAGENOME_ASSEMBLY_SET = "metagenome_assembly_set"
 
 
 
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index c4d5b59a..80692407 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -8,7 +8,7 @@
         "biosample_set": [],
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-3w7nex07",
+                "id": "nmdc:dobj-11-6bpfeq94",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "alternative_identifiers": [],
@@ -21,7 +21,7 @@
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-aazp9v53",
+                "id": "nmdc:dobj-11-dqtqva56",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -30,11 +30,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-aazp9v53/nmdc_dobj-11-aazp9v53_filtered.fastq.gz",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-dqtqva56/nmdc_dobj-11-dqtqva56_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-wtayma27",
+                "id": "nmdc:dobj-11-450z1443",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -43,7 +43,59 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-wtayma27/nmdc_dobj-11-wtayma27_filterStats.txt",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-450z1443/nmdc_dobj-11-450z1443_filterStats.txt",
+                "type": "nmdc:Data_Object"
+            },
+            {
+                "id": "nmdc:dobj-11-g1z1r257",
+                "name": "Final assembly contigs fasta",
+                "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
+                "alternative_identifiers": [],
+                "file_size_bytes": 90115831,
+                "md5_checksum": "deddd162bf0128fba13b3bc1ca38d1aa",
+                "data_object_type": null,
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-g1z1r257/nmdc_dobj-11-g1z1r257_contigs.fna",
+                "type": "nmdc:Data_Object"
+            },
+            {
+                "id": "nmdc:dobj-11-m0s9ek67",
+                "name": "Final assembly scaffolds fasta",
+                "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
+                "alternative_identifiers": [],
+                "file_size_bytes": 89604715,
+                "md5_checksum": "b3573e3cda5a06611de71ca04c5c14cc",
+                "data_object_type": null,
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-m0s9ek67/nmdc_dobj-11-m0s9ek67_scaffolds.fna",
+                "type": "nmdc:Data_Object"
+            },
+            {
+                "id": "nmdc:dobj-11-3degsk51",
+                "name": "An AGP format file that describes the assembly",
+                "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
+                "alternative_identifiers": [],
+                "file_size_bytes": 12542171,
+                "md5_checksum": "f450e3800e17691d5874c89fc46c186a",
+                "data_object_type": null,
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-3degsk51/nmdc_dobj-11-3degsk51_assembly.agp",
+                "type": "nmdc:Data_Object"
+            },
+            {
+                "id": "nmdc:dobj-11-zfemcr89",
+                "name": "Sorted bam file of reads mapping back to the final assembly",
+                "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
+                "alternative_identifiers": [],
+                "file_size_bytes": 2773429299,
+                "md5_checksum": "31dc958d116d02122509e90b0883954f",
+                "data_object_type": null,
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-zfemcr89/nmdc_dobj-11-zfemcr89_pairedMapped_sorted.bam",
                 "type": "nmdc:Data_Object"
             }
         ],
@@ -75,7 +127,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-3w7nex07"
+                    "nmdc:dobj-11-6bpfeq94"
                 ],
                 "insdc_experiment_identifiers": [],
                 "instrument_name": null,
@@ -159,7 +211,7 @@
         "reaction_activity_set": [],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-08etj008",
+                "id": "nmdc:wfrqc-11-rssxx935",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -168,11 +220,11 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-3w7nex07"
+                    "nmdc:dobj-11-6bpfeq94"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-aazp9v53",
-                    "nmdc:dobj-11-wtayma27"
+                    "nmdc:dobj-11-dqtqva56",
+                    "nmdc:dobj-11-450z1443"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 354a03de..1da55380 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -201,6 +201,8 @@ def process_records(ctx, dryrun, study_id, data_dir):
         new_db = reid_tool.update_omics_processing_has_output(db_record, new_db)
         # update ReadsQC
         new_db = reid_tool.update_reads_qc_analysis_activity_set(db_record, new_db)
+        # update Metagenome Assembly
+        new_db = reid_tool.update_metagenome_assembly_set(db_record, new_db)
 
         re_ided_db_records.append(new_db)
 

From 88e7471e496a411536f7dd1a5bcea26395ab4f3d Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 11:26:17 -0800
Subject: [PATCH 50/91] sketch in update read based analysis method

---
 nmdc_automation/re_iding/base.py              | 13 +++++++
 .../data/dryrun_re_ided_record_dump.json      | 36 +++++++++----------
 .../re_iding/scripts/re_id_tool.py            |  2 ++
 3 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 3207b271..9f4756a1 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -205,7 +205,20 @@ def update_metagenome_assembly_set(self, db_record: Dict,
             # update activity-specific properties
         return new_db
 
+    def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
+            new_db: NmdcDatabase) -> (NmdcDatabase):
+        """
+        Return a new Database instance with the read_based_taxonomy_analysis_activity_set
+        and its data objects updated to new IDs.
+        """
+        logger.info(f"Updating read_based_taxonomy_analysis_activity_set for "
+                    f"{db_record[OMICS_PROCESSING_SET][0]['id']}")
+        new_omics_processing = new_db.omics_processing_set[0]
 
+        for readbased_rec in db_record["read_based_taxonomy_analysis_activity_set"]:
+            pass
+
+        return new_db
 
     def _make_new_activity_set_object(self, omics_processing_id: str,
             activity_set_rec: Dict, has_input: List,
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index 80692407..524ca2e2 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -8,7 +8,7 @@
         "biosample_set": [],
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-6bpfeq94",
+                "id": "nmdc:dobj-11-4vnpfh80",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "alternative_identifiers": [],
@@ -21,7 +21,7 @@
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-dqtqva56",
+                "id": "nmdc:dobj-11-jt200525",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -30,11 +30,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-dqtqva56/nmdc_dobj-11-dqtqva56_filtered.fastq.gz",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-jt200525/nmdc_dobj-11-jt200525_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-450z1443",
+                "id": "nmdc:dobj-11-qvxhra11",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -43,11 +43,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-450z1443/nmdc_dobj-11-450z1443_filterStats.txt",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-qvxhra11/nmdc_dobj-11-qvxhra11_filterStats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-g1z1r257",
+                "id": "nmdc:dobj-11-9b3c8a90",
                 "name": "Final assembly contigs fasta",
                 "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -56,11 +56,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-g1z1r257/nmdc_dobj-11-g1z1r257_contigs.fna",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-9b3c8a90/nmdc_dobj-11-9b3c8a90_contigs.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-m0s9ek67",
+                "id": "nmdc:dobj-11-302hqy22",
                 "name": "Final assembly scaffolds fasta",
                 "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -69,11 +69,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-m0s9ek67/nmdc_dobj-11-m0s9ek67_scaffolds.fna",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-302hqy22/nmdc_dobj-11-302hqy22_scaffolds.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-3degsk51",
+                "id": "nmdc:dobj-11-8c4dad48",
                 "name": "An AGP format file that describes the assembly",
                 "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -82,11 +82,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-3degsk51/nmdc_dobj-11-3degsk51_assembly.agp",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-8c4dad48/nmdc_dobj-11-8c4dad48_assembly.agp",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-zfemcr89",
+                "id": "nmdc:dobj-11-sqshnm40",
                 "name": "Sorted bam file of reads mapping back to the final assembly",
                 "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -95,7 +95,7 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-zfemcr89/nmdc_dobj-11-zfemcr89_pairedMapped_sorted.bam",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-sqshnm40/nmdc_dobj-11-sqshnm40_pairedMapped_sorted.bam",
                 "type": "nmdc:Data_Object"
             }
         ],
@@ -127,7 +127,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-6bpfeq94"
+                    "nmdc:dobj-11-4vnpfh80"
                 ],
                 "insdc_experiment_identifiers": [],
                 "instrument_name": null,
@@ -211,7 +211,7 @@
         "reaction_activity_set": [],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-rssxx935",
+                "id": "nmdc:wfrqc-11-5d5fmd43",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -220,11 +220,11 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-6bpfeq94"
+                    "nmdc:dobj-11-4vnpfh80"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-dqtqva56",
-                    "nmdc:dobj-11-450z1443"
+                    "nmdc:dobj-11-jt200525",
+                    "nmdc:dobj-11-qvxhra11"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 1da55380..2ec0ce77 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -203,6 +203,8 @@ def process_records(ctx, dryrun, study_id, data_dir):
         new_db = reid_tool.update_reads_qc_analysis_activity_set(db_record, new_db)
         # update Metagenome Assembly
         new_db = reid_tool.update_metagenome_assembly_set(db_record, new_db)
+        # update Read Based Taxonomy Analysis
+        new_db = reid_tool.update_read_based_taxonomy_analysis_activity_set(db_record, new_db)
 
         re_ided_db_records.append(new_db)
 

From fe3f3d92004feded9f57f0bd10c39e3ed61017d0 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 12:07:50 -0800
Subject: [PATCH 51/91] Handle missing data_object_type

---
 nmdc_automation/re_iding/base.py              | 19 +++----
 nmdc_automation/re_iding/db_utils.py          |  2 +-
 nmdc_automation/re_iding/file_utils.py        | 38 ++++++++++++++
 .../data/dryrun_re_ided_record_dump.json      | 49 ++++++++++++-------
 .../re_iding/scripts/re_id_tool.py            |  5 +-
 5 files changed, 84 insertions(+), 29 deletions(-)
 create mode 100644 nmdc_automation/re_iding/file_utils.py

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 9f4756a1..0c23272a 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -20,6 +20,7 @@
                                                check_for_single_omics_processing_record,
                                                get_data_object_record_by_id,
                                                get_omics_processing_id)
+from nmdc_automation.re_iding.file_utils import find_data_object_type
 
 NAPA_TEMPLATE = "../../../configs/re_iding_worklfows.yaml"
 BASE_DIR = "/global/cfs/cdirs/m3408/results"
@@ -142,8 +143,10 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             for old_do_id in reads_qc_rec["has_output"]:
                 logger.info(f"old_do_id: {old_do_id}")
                 old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
+                data_object_type = find_data_object_type(old_do_rec)
                 new_do = self._make_new_data_object(
-                    omics_processing_id, activity_type, old_do_rec
+                    omics_processing_id, activity_type, old_do_rec,
+                    data_object_type,
                 )
                 # add new data object to new database and update has_output
                 new_db.data_object_set.append(new_do)
@@ -184,14 +187,11 @@ def update_metagenome_assembly_set(self, db_record: Dict,
             for old_do_id in assembly_rec["has_output"]:
                 logger.info(f"old_do_id: {old_do_id}")
                 old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
-                # TODO we need to handle missing data_object_type - until
-                #  then though..
-                if not old_do_rec.get("data_object_type"):
-                    logger.warning(f"Skipping {old_do_id} - no "
-                                   f"data_object_type")
+                data_object_type = find_data_object_type(old_do_rec)
+                if not data_object_type:
                     continue
                 new_do = self._make_new_data_object(
-                    omics_processing_id, activity_type, old_do_rec
+                    omics_processing_id, activity_type, old_do_rec, data_object_type
                 )
                 # add new data object to new database and update has_output
                 new_db.data_object_set.append(new_do)
@@ -249,11 +249,12 @@ def _make_new_activity_set_object(self, omics_processing_id: str,
         return activity
 
     def _make_new_data_object(self, omics_processing_id: str,
-            activity_type: str, data_object_rec: Dict) -> NmdcDataObject:
+                              activity_type: str,
+                              data_object_rec: Dict,
+                              data_object_type: str) -> NmdcDataObject:
         """
         Return a new data object with updated IDs.
         """
-        data_object_type = data_object_rec.get("data_object_type")
         template = self.data_object_template(
             activity_type, data_object_type
             )
diff --git a/nmdc_automation/re_iding/db_utils.py b/nmdc_automation/re_iding/db_utils.py
index 6f99fb4b..dee607eb 100644
--- a/nmdc_automation/re_iding/db_utils.py
+++ b/nmdc_automation/re_iding/db_utils.py
@@ -1,6 +1,6 @@
 # nmdc_automation/nmdc_automation/re_iding/db_utils.py
 """
-nmdc_db_utils.py: Provides utility functions for working with NMDC Database
+db_utils.py: Provides utility functions for working with NMDC Database
 records and data objects as dicts.
 """
 from dataclasses import dataclass
diff --git a/nmdc_automation/re_iding/file_utils.py b/nmdc_automation/re_iding/file_utils.py
new file mode 100644
index 00000000..b1ad8342
--- /dev/null
+++ b/nmdc_automation/re_iding/file_utils.py
@@ -0,0 +1,38 @@
+# nmdc_automation/re_iding/file_utils.py
+"""
+file_utils.py: Provides utility functions for working with files.
+"""
+import logging
+from typing import Dict, Optional
+
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+    handlers=[logging.StreamHandler()]
+)
+
+logger = logging.getLogger(__name__)
+
+def find_data_object_type(data_object_rec: Dict)-> Optional[str]:
+    """
+    Determine the data_object_type for a DO record based on its URL extension.
+
+    Args:
+    - data_object_record (dict): Dictionary containing the 'url' key which
+    will be inspected to determine the data type.
+
+    Returns:
+    - str: The determined data type or None if the type could not be determined.
+    """
+    if "data_object_type" in data_object_rec:
+        return data_object_rec["data_object_type"]
+    url = data_object_rec["url"]
+    if url.endswith("_covstats.txt"):
+        return "Assembly Coverage Stats"
+    elif url.endswith("_gottcha2_report.tsv"):
+        return "GOTTCHA2 Classification Report"
+    elif url.endswith("_gottcha2_report_full.tsv"):
+        return "GOTTCHA2 Report Full"
+    else:
+        logger.error(f"Missing type: {url}")
+        return None
\ No newline at end of file
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index 524ca2e2..99614bfd 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -8,7 +8,7 @@
         "biosample_set": [],
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-4vnpfh80",
+                "id": "nmdc:dobj-11-7ytdgk21",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "alternative_identifiers": [],
@@ -21,7 +21,7 @@
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-jt200525",
+                "id": "nmdc:dobj-11-xt71bd89",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -30,11 +30,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-jt200525/nmdc_dobj-11-jt200525_filtered.fastq.gz",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-xt71bd89/nmdc_dobj-11-xt71bd89_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-qvxhra11",
+                "id": "nmdc:dobj-11-3q6mm589",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -43,11 +43,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-qvxhra11/nmdc_dobj-11-qvxhra11_filterStats.txt",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-3q6mm589/nmdc_dobj-11-3q6mm589_filterStats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-9b3c8a90",
+                "id": "nmdc:dobj-11-1g293v37",
                 "name": "Final assembly contigs fasta",
                 "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -56,11 +56,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-9b3c8a90/nmdc_dobj-11-9b3c8a90_contigs.fna",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-1g293v37/nmdc_dobj-11-1g293v37_contigs.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-302hqy22",
+                "id": "nmdc:dobj-11-9a01ta97",
                 "name": "Final assembly scaffolds fasta",
                 "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -69,11 +69,24 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-302hqy22/nmdc_dobj-11-302hqy22_scaffolds.fna",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-9a01ta97/nmdc_dobj-11-9a01ta97_scaffolds.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-8c4dad48",
+                "id": "nmdc:dobj-11-33scvx87",
+                "name": "Assembled contigs coverage information",
+                "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
+                "alternative_identifiers": [],
+                "file_size_bytes": 13412363,
+                "md5_checksum": "c6d0d4cea985ca6fb50a060e15b4a856",
+                "data_object_type": null,
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-33scvx87/nmdc_dobj-11-33scvx87_covstats.txt",
+                "type": "nmdc:Data_Object"
+            },
+            {
+                "id": "nmdc:dobj-11-dnhkse46",
                 "name": "An AGP format file that describes the assembly",
                 "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -82,11 +95,11 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-8c4dad48/nmdc_dobj-11-8c4dad48_assembly.agp",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-dnhkse46/nmdc_dobj-11-dnhkse46_assembly.agp",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-sqshnm40",
+                "id": "nmdc:dobj-11-v9rgvc54",
                 "name": "Sorted bam file of reads mapping back to the final assembly",
                 "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -95,7 +108,7 @@
                 "data_object_type": null,
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-sqshnm40/nmdc_dobj-11-sqshnm40_pairedMapped_sorted.bam",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-v9rgvc54/nmdc_dobj-11-v9rgvc54_pairedMapped_sorted.bam",
                 "type": "nmdc:Data_Object"
             }
         ],
@@ -127,7 +140,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-4vnpfh80"
+                    "nmdc:dobj-11-7ytdgk21"
                 ],
                 "insdc_experiment_identifiers": [],
                 "instrument_name": null,
@@ -211,7 +224,7 @@
         "reaction_activity_set": [],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-5d5fmd43",
+                "id": "nmdc:wfrqc-11-jm2edq55",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -220,11 +233,11 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-4vnpfh80"
+                    "nmdc:dobj-11-7ytdgk21"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-jt200525",
-                    "nmdc:dobj-11-qvxhra11"
+                    "nmdc:dobj-11-xt71bd89",
+                    "nmdc:dobj-11-3q6mm589"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 2ec0ce77..26df0e81 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -199,8 +199,11 @@ def process_records(ctx, dryrun, study_id, data_dir):
         new_db = nmdc.Database()
         # update OmicsProcessing has_output and related DataObject records
         new_db = reid_tool.update_omics_processing_has_output(db_record, new_db)
-        # update ReadsQC
+        # update ReadsQC:
+        # db records
         new_db = reid_tool.update_reads_qc_analysis_activity_set(db_record, new_db)
+        # files
+        # TODO - update reads qc files
         # update Metagenome Assembly
         new_db = reid_tool.update_metagenome_assembly_set(db_record, new_db)
         # update Read Based Taxonomy Analysis

From c78dcb28031180ba993b61b1f788efe6e7fe29f7 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Mon, 13 Nov 2023 12:49:59 -0800
Subject: [PATCH 52/91] add data_object_type to new data objects

---
 nmdc_automation/re_iding/base.py              |  77 +-
 .../data/dryrun_re_ided_record_dump.json      | 984 +++++++++++++++++-
 2 files changed, 1005 insertions(+), 56 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 0c23272a..f9ea0831 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -49,7 +49,12 @@ def _workflow_template_for_type(self, workflow_type: str) -> Dict:
         Return the workflow template for the given workflow name.
         """
         templates = []
+        # There are some inconsistencies in the workflow names between
+        # template and object records
         workflow_type = workflow_type.replace("QC", "Qc")
+        if workflow_type == "nmdc:ReadbasedAnalysis":
+            workflow_type = "nmdc:ReadBasedTaxonomyAnalysisActivity"
+
         for t in self.workflow_template:
             type = t["Type"]
             if type == workflow_type:
@@ -157,13 +162,13 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
                 omics_processing_id, reads_qc_rec, has_input, updated_has_output
             )
             # update activity-specific properties
-            new_reads_qc.input_read_count = reads_qc_rec.get("input_read_count")
-            new_reads_qc.input_base_count = reads_qc_rec.get("input_base_count")
-            new_reads_qc.output_read_count = reads_qc_rec.get("output_read_count")
-            new_reads_qc.output_base_count = reads_qc_rec.get("output_base_count")
-            new_reads_qc.input_read_bases = reads_qc_rec.get("input_read_bases")
-            new_reads_qc.output_read_bases = reads_qc_rec.get("output_read_bases")
-
+            unset_properties = [
+                p for p in new_reads_qc.__dict__ if not new_reads_qc.__dict__[p]
+            ]
+            # check for that value in old record
+            for p in unset_properties:
+                if p in reads_qc_rec:
+                    setattr(new_reads_qc, p, reads_qc_rec[p])
 
             new_db.read_qc_analysis_activity_set.append(new_reads_qc)
         return new_db
@@ -198,11 +203,21 @@ def update_metagenome_assembly_set(self, db_record: Dict,
                 updated_has_output.append(new_do.id)
 
             # Get new Metagenome Assembly activity set
-            new_reads_qc = self._make_new_activity_set_object(
+            new_assembly = self._make_new_activity_set_object(
                 omics_processing_id, assembly_rec, has_input,
                 updated_has_output
             )
             # update activity-specific properties
+            # get new_assembly properties with no set value
+            unset_properties = [
+                p for p in new_assembly.__dict__ if not new_assembly.__dict__[p]
+            ]
+            # check for that value in old record
+            for p in unset_properties:
+                if p in assembly_rec:
+                    setattr(new_assembly, p, assembly_rec[p])
+
+            new_db.metagenome_assembly_set.append(new_assembly)
         return new_db
 
     def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
@@ -215,8 +230,42 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
                     f"{db_record[OMICS_PROCESSING_SET][0]['id']}")
         new_omics_processing = new_db.omics_processing_set[0]
 
-        for readbased_rec in db_record["read_based_taxonomy_analysis_activity_set"]:
-            pass
+        for read_based_rec in db_record[
+            "read_based_taxonomy_analysis_activity_set"]:
+            activity_type = "nmdc:ReadBasedTaxonomyAnalysisActivity"
+            omics_processing_id = new_omics_processing.id
+            new_assembly = new_db.metagenome_assembly_set[0]
+            has_input = new_assembly.has_output
+            updated_has_output = []
+            for old_do_id in read_based_rec["has_output"]:
+                logger.info(f"old_do_id: {old_do_id}")
+                old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
+                data_object_type = find_data_object_type(old_do_rec)
+                if not data_object_type:
+                    continue
+                new_do = self._make_new_data_object(
+                    omics_processing_id, activity_type, old_do_rec, data_object_type
+                )
+                # add new data object to new database and update has_output
+                new_db.data_object_set.append(new_do)
+                updated_has_output.append(new_do.id)
+
+            # Get new ReadBasedTaxonomyAnalysisActivity activity set
+            new_read_based = self._make_new_activity_set_object(
+                omics_processing_id, read_based_rec, has_input,
+                updated_has_output
+            )
+            # update activity-specific properties
+            # get new_read_based properties with no set value
+            unset_properties = [
+                p for p in new_read_based.__dict__ if not new_read_based.__dict__[p]
+            ]
+            # check for that value in old record
+            for p in unset_properties:
+                if p in read_based_rec:
+                    setattr(new_read_based, p, read_based_rec[p])
+
+            new_db.read_based_taxonomy_analysis_activity_set.append(new_read_based)
 
         return new_db
 
@@ -224,9 +273,14 @@ def _make_new_activity_set_object(self, omics_processing_id: str,
             activity_set_rec: Dict, has_input: List,
             has_output: List) -> WorkflowExecutionActivity:
         """
-        Return a new activity set object with updated IDs.
+        Return a new activity set object with updated IDs and common properties:
+        - id, name, git_url, version, part_of, execution_resource,
+        started_at_time, ended_at_time, was_informed_by, type, has_input,
+        has_output
         """
         activity_type = activity_set_rec["type"].replace("QC", "Qc")
+        if activity_type == "nmdc:ReadbasedAnalysis":
+            activity_type = "nmdc:ReadBasedTaxonomyAnalysisActivity"
         template = self._workflow_template_for_type(activity_type)
         activity_class = getattr(nmdc, template["ActivityRange"])
         new_activity_id = self.api_client.minter(activity_type)
@@ -276,6 +330,7 @@ def _make_new_data_object(self, omics_processing_id: str,
             file_size_bytes=data_object_rec["file_size_bytes"],
             md5_checksum=data_object_rec["md5_checksum"],
             url=new_url,
+            data_object_type=data_object_type,
             )
         return data_object
 
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index 99614bfd..d1e04d60 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -8,7 +8,7 @@
         "biosample_set": [],
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-7ytdgk21",
+                "id": "nmdc:dobj-11-q4pmsv93",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "alternative_identifiers": [],
@@ -21,94 +21,899 @@
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-xt71bd89",
+                "id": "nmdc:dobj-11-hfr31e20",
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                 "file_size_bytes": 2571324879,
                 "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
-                "data_object_type": null,
+                "data_object_type": {
+                    "_code": {
+                        "text": "Filtered Sequencing Reads",
+                        "description": "Reads QC result fastq (clean data)",
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+                        "unit": null,
+                        "is_a": null,
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-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-xt71bd89/nmdc_dobj-11-xt71bd89_filtered.fastq.gz",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-hfr31e20/nmdc_dobj-11-hfr31e20_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
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-                "id": "nmdc:dobj-11-3q6mm589",
+                "id": "nmdc:dobj-11-xc5jhn80",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
                 "file_size_bytes": 290,
                 "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
-                "data_object_type": null,
+                "data_object_type": {
+                    "_code": {
+                        "text": "QC Statistics",
+                        "description": "Reads QC summary statistics",
+                        "meaning": null,
+                        "unit": null,
+                        "is_a": null,
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+                        "mappings": [],
+                        "exact_mappings": [],
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+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-xc5jhn80/nmdc_dobj-11-xc5jhn80_filterStats.txt",
                 "type": "nmdc:Data_Object"
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-                "id": "nmdc:dobj-11-1g293v37",
+                "id": "nmdc:dobj-11-wz0zg037",
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-                "data_object_type": null,
+                "data_object_type": {
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+                "type": "nmdc:Data_Object"
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+                "md5_checksum": "b3573e3cda5a06611de71ca04c5c14cc",
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+                "type": "nmdc:Data_Object"
+            },
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+                "id": "nmdc:dobj-11-zr4b4z40",
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+                "type": "nmdc:Data_Object"
+            },
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+                "name": "An AGP format file that describes the assembly",
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+                        "last_updated_on": null,
+                        "modified_by": null,
+                        "status": null,
+                        "rank": null,
+                        "categories": [],
+                        "keywords": []
+                    }
+                },
+                "compression_type": null,
+                "was_generated_by": null,
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-h7mbw370/nmdc_dobj-11-h7mbw370_centrifuge_classification.tsv",
+                "type": "nmdc:Data_Object"
+            },
+            {
+                "id": "nmdc:dobj-11-8a9rmt95",
+                "name": "Centrifuge output report file",
+                "description": "Centrifuge TSV report for nmdc:omprc-11-bn8jcq58",
+                "alternative_identifiers": [],
+                "file_size_bytes": 260134,
+                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+                "data_object_type": {
+                    "_code": {
+                        "text": "Centrifuge Classification Report",
+                        "description": "Centrifuge output report file",
+                        "meaning": null,
+                        "unit": null,
+                        "is_a": null,
+                        "mixins": [],
+                        "extensions": {},
+                        "annotations": {},
+                        "alt_descriptions": {},
+                        "title": null,
+                        "deprecated": null,
+                        "todos": [],
+                        "notes": [],
+                        "comments": [],
+                        "examples": [],
+                        "in_subset": [],
+                        "from_schema": null,
+                        "imported_from": null,
+                        "source": null,
+                        "in_language": null,
+                        "see_also": [],
+                        "deprecated_element_has_exact_replacement": null,
+                        "deprecated_element_has_possible_replacement": null,
+                        "aliases": [],
+                        "structured_aliases": {},
+                        "mappings": [],
+                        "exact_mappings": [],
+                        "close_mappings": [],
+                        "related_mappings": [],
+                        "narrow_mappings": [],
+                        "broad_mappings": [],
+                        "created_by": null,
+                        "contributors": [],
+                        "created_on": null,
+                        "last_updated_on": null,
+                        "modified_by": null,
+                        "status": null,
+                        "rank": null,
+                        "categories": [],
+                        "keywords": []
+                    }
+                },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-1g293v37/nmdc_dobj-11-1g293v37_contigs.fna",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-8a9rmt95/nmdc_dobj-11-8a9rmt95_centrifuge_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-9a01ta97",
-                "name": "Final assembly scaffolds fasta",
-                "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
+                "id": "nmdc:dobj-11-wbynk051",
+                "name": "Centrifug krona plot HTML file",
+                "description": "Centrifuge Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 89604715,
-                "md5_checksum": "b3573e3cda5a06611de71ca04c5c14cc",
-                "data_object_type": null,
+                "file_size_bytes": 2343980,
+                "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
+                "data_object_type": {
+                    "_code": {
+                        "text": "Centrifuge Krona Plot",
+                        "description": "Centrifuge krona plot HTML file",
+                        "meaning": null,
+                        "unit": null,
+                        "is_a": null,
+                        "mixins": [],
+                        "extensions": {},
+                        "annotations": {},
+                        "alt_descriptions": {},
+                        "title": null,
+                        "deprecated": null,
+                        "todos": [],
+                        "notes": [],
+                        "comments": [],
+                        "examples": [],
+                        "in_subset": [],
+                        "from_schema": null,
+                        "imported_from": null,
+                        "source": null,
+                        "in_language": null,
+                        "see_also": [],
+                        "deprecated_element_has_exact_replacement": null,
+                        "deprecated_element_has_possible_replacement": null,
+                        "aliases": [],
+                        "structured_aliases": {},
+                        "mappings": [],
+                        "exact_mappings": [],
+                        "close_mappings": [],
+                        "related_mappings": [],
+                        "narrow_mappings": [],
+                        "broad_mappings": [],
+                        "created_by": null,
+                        "contributors": [],
+                        "created_on": null,
+                        "last_updated_on": null,
+                        "modified_by": null,
+                        "status": null,
+                        "rank": null,
+                        "categories": [],
+                        "keywords": []
+                    }
+                },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-9a01ta97/nmdc_dobj-11-9a01ta97_scaffolds.fna",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-wbynk051/nmdc_dobj-11-wbynk051_centrifuge_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-33scvx87",
-                "name": "Assembled contigs coverage information",
-                "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
+                "id": "nmdc:dobj-11-wpw7gs92",
+                "name": "Kraken2 output read classification file",
+                "description": "Kraken classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 13412363,
-                "md5_checksum": "c6d0d4cea985ca6fb50a060e15b4a856",
-                "data_object_type": null,
+                "file_size_bytes": 1785563917,
+                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
+                "data_object_type": {
+                    "_code": {
+                        "text": "Kraken2 Taxonomic Classification",
+                        "description": "Kraken2 output read classification file",
+                        "meaning": null,
+                        "unit": null,
+                        "is_a": null,
+                        "mixins": [],
+                        "extensions": {},
+                        "annotations": {},
+                        "alt_descriptions": {},
+                        "title": null,
+                        "deprecated": null,
+                        "todos": [],
+                        "notes": [],
+                        "comments": [],
+                        "examples": [],
+                        "in_subset": [],
+                        "from_schema": null,
+                        "imported_from": null,
+                        "source": null,
+                        "in_language": null,
+                        "see_also": [],
+                        "deprecated_element_has_exact_replacement": null,
+                        "deprecated_element_has_possible_replacement": null,
+                        "aliases": [],
+                        "structured_aliases": {},
+                        "mappings": [],
+                        "exact_mappings": [],
+                        "close_mappings": [],
+                        "related_mappings": [],
+                        "narrow_mappings": [],
+                        "broad_mappings": [],
+                        "created_by": null,
+                        "contributors": [],
+                        "created_on": null,
+                        "last_updated_on": null,
+                        "modified_by": null,
+                        "status": null,
+                        "rank": null,
+                        "categories": [],
+                        "keywords": []
+                    }
+                },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-33scvx87/nmdc_dobj-11-33scvx87_covstats.txt",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-wpw7gs92/nmdc_dobj-11-wpw7gs92_kraken2_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-dnhkse46",
-                "name": "An AGP format file that describes the assembly",
-                "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
+                "id": "nmdc:dobj-11-s4wxq602",
+                "name": "Kraken2 output report file",
+                "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 12542171,
-                "md5_checksum": "f450e3800e17691d5874c89fc46c186a",
-                "data_object_type": null,
+                "file_size_bytes": 699896,
+                "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+                "data_object_type": {
+                    "_code": {
+                        "text": "Kraken2 Classification Report",
+                        "description": "Kraken2 output report file",
+                        "meaning": null,
+                        "unit": null,
+                        "is_a": null,
+                        "mixins": [],
+                        "extensions": {},
+                        "annotations": {},
+                        "alt_descriptions": {},
+                        "title": null,
+                        "deprecated": null,
+                        "todos": [],
+                        "notes": [],
+                        "comments": [],
+                        "examples": [],
+                        "in_subset": [],
+                        "from_schema": null,
+                        "imported_from": null,
+                        "source": null,
+                        "in_language": null,
+                        "see_also": [],
+                        "deprecated_element_has_exact_replacement": null,
+                        "deprecated_element_has_possible_replacement": null,
+                        "aliases": [],
+                        "structured_aliases": {},
+                        "mappings": [],
+                        "exact_mappings": [],
+                        "close_mappings": [],
+                        "related_mappings": [],
+                        "narrow_mappings": [],
+                        "broad_mappings": [],
+                        "created_by": null,
+                        "contributors": [],
+                        "created_on": null,
+                        "last_updated_on": null,
+                        "modified_by": null,
+                        "status": null,
+                        "rank": null,
+                        "categories": [],
+                        "keywords": []
+                    }
+                },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-dnhkse46/nmdc_dobj-11-dnhkse46_assembly.agp",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-s4wxq602/nmdc_dobj-11-s4wxq602_kraken2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-v9rgvc54",
-                "name": "Sorted bam file of reads mapping back to the final assembly",
-                "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
+                "id": "nmdc:dobj-11-vf207x18",
+                "name": "Kraken2 Krona plot HTML file",
+                "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 2773429299,
-                "md5_checksum": "31dc958d116d02122509e90b0883954f",
-                "data_object_type": null,
+                "file_size_bytes": 4221977,
+                "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+                "data_object_type": {
+                    "_code": {
+                        "text": "Kraken2 Krona Plot",
+                        "description": "Kraken2 krona plot HTML file",
+                        "meaning": null,
+                        "unit": null,
+                        "is_a": null,
+                        "mixins": [],
+                        "extensions": {},
+                        "annotations": {},
+                        "alt_descriptions": {},
+                        "title": null,
+                        "deprecated": null,
+                        "todos": [],
+                        "notes": [],
+                        "comments": [],
+                        "examples": [],
+                        "in_subset": [],
+                        "from_schema": null,
+                        "imported_from": null,
+                        "source": null,
+                        "in_language": null,
+                        "see_also": [],
+                        "deprecated_element_has_exact_replacement": null,
+                        "deprecated_element_has_possible_replacement": null,
+                        "aliases": [],
+                        "structured_aliases": {},
+                        "mappings": [],
+                        "exact_mappings": [],
+                        "close_mappings": [],
+                        "related_mappings": [],
+                        "narrow_mappings": [],
+                        "broad_mappings": [],
+                        "created_by": null,
+                        "contributors": [],
+                        "created_on": null,
+                        "last_updated_on": null,
+                        "modified_by": null,
+                        "status": null,
+                        "rank": null,
+                        "categories": [],
+                        "keywords": []
+                    }
+                },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-v9rgvc54/nmdc_dobj-11-v9rgvc54_pairedMapped_sorted.bam",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-vf207x18/nmdc_dobj-11-vf207x18_kraken2_krona.html",
                 "type": "nmdc:Data_Object"
             }
         ],
@@ -120,7 +925,62 @@
         "material_sampling_activity_set": [],
         "metabolomics_analysis_activity_set": [],
         "metagenome_annotation_activity_set": [],
-        "metagenome_assembly_set": [],
+        "metagenome_assembly_set": [
+            {
+                "id": "nmdc:wfmgas-11-wa0zvp69",
+                "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "was_informed_by": "nmdc:omprc-11-bn8jcq58",
+                "used": null,
+                "execution_resource": "NERSC - Perlmutter",
+                "git_url": "https://github.com/microbiomedata/metaAssembly",
+                "has_input": [
+                    "nmdc:dobj-11-hfr31e20",
+                    "nmdc:dobj-11-xc5jhn80"
+                ],
+                "has_output": [
+                    "nmdc:dobj-11-wz0zg037",
+                    "nmdc:dobj-11-dc20ch29",
+                    "nmdc:dobj-11-zr4b4z40",
+                    "nmdc:dobj-11-fe6kea76",
+                    "nmdc:dobj-11-f8bj1b18"
+                ],
+                "type": "nmdc:MetagenomeAssembly",
+                "part_of": [
+                    "nmdc:omprc-11-bn8jcq58"
+                ],
+                "version": "v1.0.3",
+                "asm_score": 6.577,
+                "scaffolds": 169645,
+                "scaf_logsum": 215363,
+                "scaf_powsum": 24422,
+                "scaf_max": 68135,
+                "scaf_bp": 83496490,
+                "scaf_n50": 45550,
+                "scaf_n90": 141870,
+                "scaf_l50": 470,
+                "scaf_l90": 290,
+                "scaf_n_gt50k": 1,
+                "scaf_l_gt50k": 68135,
+                "scaf_pct_gt50k": 0.08160224,
+                "contigs": 169784,
+                "contig_bp": 83494920,
+                "ctg_n50": 45584,
+                "ctg_l50": 470,
+                "ctg_n90": 141996,
+                "ctg_l90": 290,
+                "ctg_logsum": 214373,
+                "ctg_powsum": 24284,
+                "ctg_max": 68135,
+                "gap_pct": 0.00188,
+                "gc_std": 0.11726,
+                "gc_avg": 0.46001,
+                "num_input_reads": null,
+                "num_aligned_reads": null,
+                "insdc_assembly_identifiers": null
+            }
+        ],
         "metagenome_sequencing_activity_set": [],
         "metaproteomics_analysis_activity_set": [],
         "metatranscriptome_activity_set": [],
@@ -140,7 +1000,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-7ytdgk21"
+                    "nmdc:dobj-11-q4pmsv93"
                 ],
                 "insdc_experiment_identifiers": [],
                 "instrument_name": null,
@@ -224,7 +1084,7 @@
         "reaction_activity_set": [],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-jm2edq55",
+                "id": "nmdc:wfrqc-11-wq4r6842",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -233,11 +1093,11 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-7ytdgk21"
+                    "nmdc:dobj-11-q4pmsv93"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-xt71bd89",
-                    "nmdc:dobj-11-3q6mm589"
+                    "nmdc:dobj-11-hfr31e20",
+                    "nmdc:dobj-11-xc5jhn80"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
@@ -252,7 +1112,41 @@
                 "output_read_bases": 4608772924
             }
         ],
-        "read_based_taxonomy_analysis_activity_set": [],
+        "read_based_taxonomy_analysis_activity_set": [
+            {
+                "id": "nmdc:wfrbt-11-psqmn810",
+                "name": "Readbased Taxonomy Analysis Activity for nmdc:omprc-11-bn8jcq58",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "was_informed_by": "nmdc:omprc-11-bn8jcq58",
+                "used": null,
+                "execution_resource": "NERSC - Perlmutter",
+                "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
+                "has_input": [
+                    "nmdc:dobj-11-wz0zg037",
+                    "nmdc:dobj-11-dc20ch29",
+                    "nmdc:dobj-11-zr4b4z40",
+                    "nmdc:dobj-11-fe6kea76",
+                    "nmdc:dobj-11-f8bj1b18"
+                ],
+                "has_output": [
+                    "nmdc:dobj-11-rw9dtn21",
+                    "nmdc:dobj-11-0wqjwr10",
+                    "nmdc:dobj-11-405tgq07",
+                    "nmdc:dobj-11-h7mbw370",
+                    "nmdc:dobj-11-8a9rmt95",
+                    "nmdc:dobj-11-wbynk051",
+                    "nmdc:dobj-11-wpw7gs92",
+                    "nmdc:dobj-11-s4wxq602",
+                    "nmdc:dobj-11-vf207x18"
+                ],
+                "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
+                "part_of": [
+                    "nmdc:omprc-11-bn8jcq58"
+                ],
+                "version": "v1.0.5"
+            }
+        ],
         "study_set": [],
         "field_research_site_set": [],
         "collecting_biosamples_from_site_set": [],

From 38c2dd7c0dfb4dc8b8454f6725753b2f07a75a9d Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 13 Nov 2023 14:19:42 -0800
Subject: [PATCH 53/91] exteded file operations for computing new paths and
 assembly operations

---
 nmdc_automation/re_iding/file_utils.py | 184 ++++++++++++++++++++++++-
 1 file changed, 183 insertions(+), 1 deletion(-)

diff --git a/nmdc_automation/re_iding/file_utils.py b/nmdc_automation/re_iding/file_utils.py
index b1ad8342..69b14f36 100644
--- a/nmdc_automation/re_iding/file_utils.py
+++ b/nmdc_automation/re_iding/file_utils.py
@@ -3,8 +3,18 @@
 file_utils.py: Provides utility functions for working with files.
 """
 import logging
+import os
+import hashlib
+import json
+import gzip
+from subprocess import check_output
 from typing import Dict, Optional
 
+
+base_dir = "/global/cfs/cdirs/m3408/results"
+bam_script = os.path.abspath("scripts/rewrite_bam.sh")
+base = "https://data.microbiomedata.org/data"
+
 logging.basicConfig(
     level=logging.INFO,
     format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
@@ -35,4 +45,176 @@ def find_data_object_type(data_object_rec: Dict)-> Optional[str]:
         return "GOTTCHA2 Report Full"
     else:
         logger.error(f"Missing type: {url}")
-        return None
\ No newline at end of file
+        return None
+    
+def md5_sum(fn):
+    """
+    Calculate the MD5 hash of a file.
+
+    Args:
+    - fn (str): Path to the file for which the MD5 hash is to be computed.
+
+    Returns:
+    - str: The MD5 hash of the file.
+    """
+    with open(fn, "rb") as f:
+        file_hash = hashlib.md5()
+        while chunk := f.read(8192):
+            file_hash.update(chunk)
+    return file_hash.hexdigest()
+
+
+def read_json_file(filename):
+    """
+    Read a JSON file and return its content as a dictionary.
+
+    Parameters:
+    - filename (str): The path to the JSON file.
+
+    Returns:
+    - dict: The content of the JSON file.
+    """
+    with open(filename, "r") as json_file:
+        data = json.load(json_file)
+    return data
+
+
+def rewrite_id(src, dst, old_id, new_id, prefix=None):
+    """
+    Rewrite lines in a file, replacing occurrences of an old ID with a new ID.
+    An optional prefix can be specified to limit which lines are modified.
+
+    Args:
+    - src (str): Source file path.
+    - dst (str): Destination file path.
+    - old_id (str): ID to be replaced.
+    - new_id (str): Replacement ID.
+    - prefix (str, optional): Prefix character to determine which lines to modify. Defaults to None.
+
+    Returns:
+    - tuple: MD5 checksum and size (in bytes) of the modified file.
+    """
+    fsrc = open(src)
+    fdst = open(dst, "w")
+    for line in fsrc:
+        if not prefix or (prefix and line[0] == prefix):
+            line = line.replace(old_id, new_id)
+        fdst.write(line)
+    fsrc.close()
+    fdst.close()
+    md5 = md5_sum(dst)
+    size = os.stat(dst).st_size
+    return md5, size
+
+
+def find_assembly_id(src):
+    fsrc = open(src)
+    line = fsrc.readline()
+    return "_".join(line[1:].split("_")[0:-1])
+
+
+def assembly_contigs(src, dst, act_id):
+    scaf = src.replace("_contigs", "_scaffolds")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id, prefix=">")
+
+
+def assembly_scaffolds(src, dst, act_id):
+    old_id = find_assembly_id(src)
+    return rewrite_id(src, dst, old_id, act_id, prefix=">")
+
+
+def assembly_coverage_stats(src, dst, act_id):
+    scaf = src.replace("_covstats.txt", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id)
+
+
+def assembly_agp(src, dst, act_id):
+    scaf = src.replace("_assembly.agp", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return rewrite_id(src, dst, old_id, act_id)
+
+
+def convert_script(script, src, dst, old_id, act_id):
+    cmd = [script, src, dst, old_id, act_id]
+    results = check_output(cmd)
+    md5 = md5_sum(dst)
+    size = os.stat(dst).st_size
+    return md5, size
+
+
+def assembly_coverage_bam(script, src, dst, act_id):
+    scaf = src.replace("_pairedMapped_sorted.bam", "_scaffolds.fna")
+    old_id = find_assembly_id(scaf)
+    return convert_script(script, src, dst, old_id, act_id)
+
+
+def rewrite_sam(input_sam, output_sam, old_id, new_id):
+    with gzip.open(input_sam, "rt") as f_in, gzip.open(output_sam, "wt") as f_out:
+        for line in f_in:
+            f_out.write(line.replace(old_id, new_id))
+
+
+def get_old_file_path(data_object_record):
+    old_url = data_object_record["url"]
+    suffix = old_url.split("https://data.microbiomedata.org/data/")[1]
+    old_file_path = base_dir + "/" + suffix
+
+    return old_file_path
+
+
+def assembly_file_operations(data_object_record, destination, act_id):
+    # get old file path upfront
+    old_file_path = get_old_file_path(data_object_record)
+
+    if data_object_record["data_object_type"] == "Assembly Coverage Stats":
+        md5, size = assembly_coverage_stats(old_file_path, destination, act_id)
+    elif data_object_record["data_object_type"] == "Assembly Contigs":
+        md5, size = assembly_contigs(old_file_path, destination, act_id)
+    elif data_object_record["data_object_type"] == "Assembly Scaffolds":
+        md5, size = assembly_scaffolds(old_file_path, destination, act_id)
+    elif data_object_record["data_object_type"] == "Assembly AGP":
+        md5, size = assembly_agp(old_file_path, destination, act_id)
+    elif data_object_record["data_object_type"] == "Assembly Coverage BAM":
+        md5, size = assembly_coverage_bam(
+            bam_script, old_file_path, destination, act_id
+        )
+
+    return md5, size
+
+def get_new_paths(old_url, new_base_dir, act_id):
+    """
+    Use the url to return the string value of name path and url
+    """
+    file_name = old_url.split("/")[-1]
+    file_extenstion = file_name.lstrip("nmdc_").split("_", maxsplit=1)[-1]
+    new_file_name = f"{act_id}_{file_extenstion}"
+    modified_new_file_name = new_file_name.replace(":", "_")
+    destination = os.path.join(new_base_dir, modified_new_file_name)
+
+    return destination
+
+
+def compute_new_paths(old_url, new_base_dir, act_id):
+    """
+    Use the url to compute the new file name path and url
+    """
+    file_name = old_url.split("/")[-1]
+    suffix = old_url.split("https://data.microbiomedata.org/data/")[1]
+    old_file_path = base_dir + "/" + suffix
+    file_extenstion = file_name.lstrip("nmdc_").split("_", maxsplit=1)[-1]
+    new_file_name = f"{act_id}_{file_extenstion}"
+    modified_new_file_name = new_file_name.replace(":", "_")
+    destination = os.path.join(new_base_dir, modified_new_file_name)
+
+    try:
+        os.link(old_file_path, destination)
+        logging.info(f"Successfully created link between {old_file_path} and {destination}")
+    except OSError as e:
+        logging.error(f"An error occurred while linking the file: {e}")
+    except Exception as e:
+        logging.error(f"Unexpected error: {e}")
+
+    
+    return destination
\ No newline at end of file

From e46924dddde0052d11be0e3b6b44bc5c614a0fde Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 13 Nov 2023 14:20:22 -0800
Subject: [PATCH 54/91] added file operations and fixed url names

---
 nmdc_automation/re_iding/base.py | 74 ++++++++++++++++++++++++--------
 1 file changed, 55 insertions(+), 19 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index f9ea0831..47d8bbd5 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -6,6 +6,7 @@
 import copy
 import logging
 from typing import Dict, List
+import os
 import re
 import yaml
 
@@ -20,7 +21,10 @@
                                                check_for_single_omics_processing_record,
                                                get_data_object_record_by_id,
                                                get_omics_processing_id)
-from nmdc_automation.re_iding.file_utils import find_data_object_type
+from nmdc_automation.re_iding.file_utils import (find_data_object_type,
+                                                compute_new_paths,
+                                                get_new_paths,
+                                                assembly_file_operations)
 
 NAPA_TEMPLATE = "../../../configs/re_iding_worklfows.yaml"
 BASE_DIR = "/global/cfs/cdirs/m3408/results"
@@ -142,6 +146,12 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             activity_type = "nmdc:ReadQcAnalysisActivity"
             omics_processing_id = new_omics_processing.id
             has_input = new_omics_processing.has_output
+            
+            new_activity_id = self.api_client.minter(activity_type)
+            logging.info("New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
+            
+            new_readsqc_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
+            os.makedirs(new_readsqc_base_dir, exist_ok=True)
 
             updated_has_output = []
             # Get ReadQC data objects and update IDs
@@ -149,8 +159,12 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
                 logger.info(f"old_do_id: {old_do_id}")
                 old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
                 data_object_type = find_data_object_type(old_do_rec)
+                new_file_path = compute_new_paths(
+                old_do_rec["url"], new_readsqc_base_dir, omics_processing_id, new_activity_id
+                )
+                logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
                 new_do = self._make_new_data_object(
-                    omics_processing_id, activity_type, old_do_rec,
+                    omics_processing_id, activity_type, new_activity_id, old_do_rec,
                     data_object_type,
                 )
                 # add new data object to new database and update has_output
@@ -159,7 +173,7 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
 
             # Get new ReadQC activity set
             new_reads_qc = self._make_new_activity_set_object(
-                omics_processing_id, reads_qc_rec, has_input, updated_has_output
+                omics_processing_id, new_activity_id, reads_qc_rec, has_input, updated_has_output
             )
             # update activity-specific properties
             unset_properties = [
@@ -189,14 +203,28 @@ def update_metagenome_assembly_set(self, db_record: Dict,
             new_read_qc = new_db.read_qc_analysis_activity_set[0]
             has_input = new_read_qc.has_output
             updated_has_output = []
+            
+            new_activity_id = self.api_client.minter(activity_type)
+            logging.info("New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
+            
+            new_assembly_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
+            os.makedirs(new_assembly_base_dir, exist_ok=True)
+            
             for old_do_id in assembly_rec["has_output"]:
                 logger.info(f"old_do_id: {old_do_id}")
                 old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
                 data_object_type = find_data_object_type(old_do_rec)
                 if not data_object_type:
                     continue
+                new_file_path = get_new_paths(old_do_rec["url"],new_assembly_base_dir, new_activity_id)
+                updated_md5, updated_file_size = assembly_file_operations(
+                old_do_rec, new_file_path, new_activity_id)
+                logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
+                #update md5 and file byte size in place to use _make_new_data_object function without functions
+                old_do_rec["file_size_bytes"] = updated_file_size
+                old_do_rec["md5_checksum"] = updated_md5
                 new_do = self._make_new_data_object(
-                    omics_processing_id, activity_type, old_do_rec, data_object_type
+                    omics_processing_id, activity_type, new_activity_id, old_do_rec, data_object_type
                 )
                 # add new data object to new database and update has_output
                 new_db.data_object_set.append(new_do)
@@ -204,7 +232,7 @@ def update_metagenome_assembly_set(self, db_record: Dict,
 
             # Get new Metagenome Assembly activity set
             new_assembly = self._make_new_activity_set_object(
-                omics_processing_id, assembly_rec, has_input,
+                omics_processing_id, new_activity_id, assembly_rec, has_input,
                 updated_has_output
             )
             # update activity-specific properties
@@ -234,8 +262,15 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
             "read_based_taxonomy_analysis_activity_set"]:
             activity_type = "nmdc:ReadBasedTaxonomyAnalysisActivity"
             omics_processing_id = new_omics_processing.id
-            new_assembly = new_db.metagenome_assembly_set[0]
-            has_input = new_assembly.has_output
+            new_read_qc = new_db.read_qc_analysis_activity_set[0]
+            has_input = new_read_qc.has_output
+            
+            new_activity_id = self.api_client.minter(activity_type)
+            logging.info("New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
+            
+            new_readbased_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
+            os.makedirs(new_readbased_base_dir, exist_ok=True)
+            
             updated_has_output = []
             for old_do_id in read_based_rec["has_output"]:
                 logger.info(f"old_do_id: {old_do_id}")
@@ -243,8 +278,12 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
                 data_object_type = find_data_object_type(old_do_rec)
                 if not data_object_type:
                     continue
+                new_file_path = compute_new_paths(
+                old_do_rec["url"], new_readbased_base_dir, omics_processing_id, new_activity_id
+                )
+                logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
                 new_do = self._make_new_data_object(
-                    omics_processing_id, activity_type, old_do_rec, data_object_type
+                    omics_processing_id, activity_type, new_activity_id, old_do_rec, data_object_type
                 )
                 # add new data object to new database and update has_output
                 new_db.data_object_set.append(new_do)
@@ -252,7 +291,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
 
             # Get new ReadBasedTaxonomyAnalysisActivity activity set
             new_read_based = self._make_new_activity_set_object(
-                omics_processing_id, read_based_rec, has_input,
+                omics_processing_id, new_activity_id,read_based_rec, has_input,
                 updated_has_output
             )
             # update activity-specific properties
@@ -269,7 +308,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
 
         return new_db
 
-    def _make_new_activity_set_object(self, omics_processing_id: str,
+    def _make_new_activity_set_object(self, omics_processing_id: str, new_activity_id: str,
             activity_set_rec: Dict, has_input: List,
             has_output: List) -> WorkflowExecutionActivity:
         """
@@ -283,7 +322,7 @@ def _make_new_activity_set_object(self, omics_processing_id: str,
             activity_type = "nmdc:ReadBasedTaxonomyAnalysisActivity"
         template = self._workflow_template_for_type(activity_type)
         activity_class = getattr(nmdc, template["ActivityRange"])
-        new_activity_id = self.api_client.minter(activity_type)
+        
         logger.info(
             f"{activity_type}\t{activity_set_rec['id']}\t{new_activity_id}"
             )
@@ -304,6 +343,7 @@ def _make_new_activity_set_object(self, omics_processing_id: str,
 
     def _make_new_data_object(self, omics_processing_id: str,
                               activity_type: str,
+                              new_activity_id: str,
                               data_object_rec: Dict,
                               data_object_type: str) -> NmdcDataObject:
         """
@@ -318,9 +358,9 @@ def _make_new_data_object(self, omics_processing_id: str,
             "[^ ]+$", f"{omics_processing_id}", data_object_rec["description"]
         )
         logger.info(f"new_description: {new_description}")
-        new_filename = self._make_new_filename(new_data_object_id, data_object_rec)
+        new_filename = self._make_new_filename(new_activity_id, data_object_rec)
         logger.info(f"new_filename: {new_filename}")
-        new_url = f"{BASE_DIR}/{omics_processing_id}/{new_data_object_id}/{new_filename}"
+        new_url = f"{BASE_DIR}/{omics_processing_id}/{new_activity_id}/{new_filename}"
 
         data_object = NmdcDataObject(
             id=new_data_object_id,
@@ -334,18 +374,14 @@ def _make_new_data_object(self, omics_processing_id: str,
             )
         return data_object
 
-    def _make_new_filename(self, new_data_object_id: str,
+    def _make_new_filename(self, new_activity_id: str,
             data_object_record: Dict) -> str:
         """
         Return the updated filename.
         """
         filename = data_object_record["url"].split("/")[-1]
         file_extenstion = filename.lstrip("nmdc_").split("_", maxsplit=1)[-1]
-        new_filename = f"{new_data_object_id}_{file_extenstion}".replace(":",
+        new_filename = f"{new_activity_id}_{file_extenstion}".replace(":",
                                                                          "_")
         return new_filename
 
-
-
-
-

From 0412ed0586eb1f0e56bf24d29a55307d19b06059 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 13 Nov 2023 14:36:40 -0800
Subject: [PATCH 55/91] pass data_object_type into assembly_file_operations to
 avoid records missing field

---
 nmdc_automation/re_iding/file_utils.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/nmdc_automation/re_iding/file_utils.py b/nmdc_automation/re_iding/file_utils.py
index 69b14f36..59b877c7 100644
--- a/nmdc_automation/re_iding/file_utils.py
+++ b/nmdc_automation/re_iding/file_utils.py
@@ -12,7 +12,7 @@
 
 
 base_dir = "/global/cfs/cdirs/m3408/results"
-bam_script = os.path.abspath("scripts/rewrite_bam.sh")
+bam_script = os.path.abspath("rewrite_bam.sh")
 base = "https://data.microbiomedata.org/data"
 
 logging.basicConfig(
@@ -164,19 +164,19 @@ def get_old_file_path(data_object_record):
     return old_file_path
 
 
-def assembly_file_operations(data_object_record, destination, act_id):
+def assembly_file_operations(data_object_record, data_object_type, destination, act_id):
     # get old file path upfront
     old_file_path = get_old_file_path(data_object_record)
 
-    if data_object_record["data_object_type"] == "Assembly Coverage Stats":
+    if data_object_type == "Assembly Coverage Stats":
         md5, size = assembly_coverage_stats(old_file_path, destination, act_id)
-    elif data_object_record["data_object_type"] == "Assembly Contigs":
+    elif data_object_type == "Assembly Contigs":
         md5, size = assembly_contigs(old_file_path, destination, act_id)
-    elif data_object_record["data_object_type"] == "Assembly Scaffolds":
+    elif data_object_type == "Assembly Scaffolds":
         md5, size = assembly_scaffolds(old_file_path, destination, act_id)
-    elif data_object_record["data_object_type"] == "Assembly AGP":
+    elif data_object_type == "Assembly AGP":
         md5, size = assembly_agp(old_file_path, destination, act_id)
-    elif data_object_record["data_object_type"] == "Assembly Coverage BAM":
+    elif data_object_type == "Assembly Coverage BAM":
         md5, size = assembly_coverage_bam(
             bam_script, old_file_path, destination, act_id
         )

From 74973531f14a191327c002aeee931a7cb89e7d3b Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 13 Nov 2023 14:37:38 -0800
Subject: [PATCH 56/91] pass data_object_type directly to
 assembly_file_operations

---
 nmdc_automation/re_iding/base.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 47d8bbd5..66ebab03 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -148,7 +148,7 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             has_input = new_omics_processing.has_output
             
             new_activity_id = self.api_client.minter(activity_type)
-            logging.info("New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
+            logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
             new_readsqc_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
             os.makedirs(new_readsqc_base_dir, exist_ok=True)
@@ -160,7 +160,7 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
                 old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
                 data_object_type = find_data_object_type(old_do_rec)
                 new_file_path = compute_new_paths(
-                old_do_rec["url"], new_readsqc_base_dir, omics_processing_id, new_activity_id
+                old_do_rec["url"], new_readsqc_base_dir, new_activity_id
                 )
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
                 new_do = self._make_new_data_object(
@@ -205,7 +205,7 @@ def update_metagenome_assembly_set(self, db_record: Dict,
             updated_has_output = []
             
             new_activity_id = self.api_client.minter(activity_type)
-            logging.info("New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
+            logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
             new_assembly_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
             os.makedirs(new_assembly_base_dir, exist_ok=True)
@@ -218,7 +218,7 @@ def update_metagenome_assembly_set(self, db_record: Dict,
                     continue
                 new_file_path = get_new_paths(old_do_rec["url"],new_assembly_base_dir, new_activity_id)
                 updated_md5, updated_file_size = assembly_file_operations(
-                old_do_rec, new_file_path, new_activity_id)
+                old_do_rec, data_object_type, new_file_path, new_activity_id)
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
                 #update md5 and file byte size in place to use _make_new_data_object function without functions
                 old_do_rec["file_size_bytes"] = updated_file_size
@@ -266,7 +266,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
             has_input = new_read_qc.has_output
             
             new_activity_id = self.api_client.minter(activity_type)
-            logging.info("New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
+            logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
             new_readbased_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
             os.makedirs(new_readbased_base_dir, exist_ok=True)
@@ -279,7 +279,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
                 if not data_object_type:
                     continue
                 new_file_path = compute_new_paths(
-                old_do_rec["url"], new_readbased_base_dir, omics_processing_id, new_activity_id
+                old_do_rec["url"], new_readbased_base_dir, new_activity_id
                 )
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
                 new_do = self._make_new_data_object(

From 5c8a4f0d9cf268307910639034a6f03919752ad1 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 13 Nov 2023 14:39:12 -0800
Subject: [PATCH 57/91] Added with file operations

---
 .../data/dryrun_re_ided_record_dump.json      | 139 +++++++++---------
 1 file changed, 68 insertions(+), 71 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index d1e04d60..74e29a57 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -8,7 +8,7 @@
         "biosample_set": [],
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-q4pmsv93",
+                "id": "nmdc:dobj-11-bgp6z123",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "alternative_identifiers": [],
@@ -21,7 +21,7 @@
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-hfr31e20",
+                "id": "nmdc:dobj-11-b20kzg40",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -73,11 +73,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-hfr31e20/nmdc_dobj-11-hfr31e20_filtered.fastq.gz",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-5sfwhy50/nmdc_wfrqc-11-5sfwhy50_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-xc5jhn80",
+                "id": "nmdc:dobj-11-mhccey92",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -129,16 +129,16 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-xc5jhn80/nmdc_dobj-11-xc5jhn80_filterStats.txt",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-5sfwhy50/nmdc_wfrqc-11-5sfwhy50_filterStats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-wz0zg037",
+                "id": "nmdc:dobj-11-b27rkd90",
                 "name": "Final assembly contigs fasta",
                 "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 90115831,
-                "md5_checksum": "deddd162bf0128fba13b3bc1ca38d1aa",
+                "file_size_bytes": 90794959,
+                "md5_checksum": "1a2ade31cf1edad5430ef0939d94ac43",
                 "data_object_type": {
                     "_code": {
                         "text": "Assembly Contigs",
@@ -185,16 +185,16 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-wz0zg037/nmdc_dobj-11-wz0zg037_contigs.fna",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-xc17b248/nmdc_wfmgas-11-xc17b248_contigs.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-dc20ch29",
+                "id": "nmdc:dobj-11-tcg9he98",
                 "name": "Final assembly scaffolds fasta",
                 "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 89604715,
-                "md5_checksum": "b3573e3cda5a06611de71ca04c5c14cc",
+                "file_size_bytes": 90283295,
+                "md5_checksum": "642e3bae5809fa7a2f0be592e0693a10",
                 "data_object_type": {
                     "_code": {
                         "text": "Assembly Scaffolds",
@@ -241,16 +241,16 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-dc20ch29/nmdc_dobj-11-dc20ch29_scaffolds.fna",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-xc17b248/nmdc_wfmgas-11-xc17b248_scaffolds.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-zr4b4z40",
+                "id": "nmdc:dobj-11-z5f6jq78",
                 "name": "Assembled contigs coverage information",
                 "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 13412363,
-                "md5_checksum": "c6d0d4cea985ca6fb50a060e15b4a856",
+                "file_size_bytes": 14091491,
+                "md5_checksum": "298156a0eddb0aa59ea3e312406fb56f",
                 "data_object_type": {
                     "_code": {
                         "text": "Assembly Coverage Stats",
@@ -297,16 +297,16 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-zr4b4z40/nmdc_dobj-11-zr4b4z40_covstats.txt",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-xc17b248/nmdc_wfmgas-11-xc17b248_covstats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-fe6kea76",
+                "id": "nmdc:dobj-11-kv8gp304",
                 "name": "An AGP format file that describes the assembly",
                 "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 12542171,
-                "md5_checksum": "f450e3800e17691d5874c89fc46c186a",
+                "file_size_bytes": 13901555,
+                "md5_checksum": "c319c47a6c2f2469ecdcaf972abd8f2b",
                 "data_object_type": {
                     "_code": {
                         "text": "Assembly AGP",
@@ -353,16 +353,16 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-fe6kea76/nmdc_dobj-11-fe6kea76_assembly.agp",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-xc17b248/nmdc_wfmgas-11-xc17b248_assembly.agp",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-f8bj1b18",
+                "id": "nmdc:dobj-11-xkzgxw24",
                 "name": "Sorted bam file of reads mapping back to the final assembly",
                 "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
-                "file_size_bytes": 2773429299,
-                "md5_checksum": "31dc958d116d02122509e90b0883954f",
+                "file_size_bytes": 0,
+                "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": {
                     "_code": {
                         "text": "Assembly Coverage BAM",
@@ -409,11 +409,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-f8bj1b18/nmdc_dobj-11-f8bj1b18_pairedMapped_sorted.bam",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-xc17b248/nmdc_wfmgas-11-xc17b248_pairedMapped_sorted.bam",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-rw9dtn21",
+                "id": "nmdc:dobj-11-vw7fz645",
                 "name": "GOTTCHA2 classification report file",
                 "description": "Gottcha2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -465,11 +465,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-rw9dtn21/nmdc_dobj-11-rw9dtn21_gottcha2_report.tsv",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_gottcha2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-0wqjwr10",
+                "id": "nmdc:dobj-11-bhnxqw16",
                 "name": "GOTTCHA2 report file",
                 "description": "Gottcha2 full TSV report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -521,11 +521,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-0wqjwr10/nmdc_dobj-11-0wqjwr10_gottcha2_report_full.tsv",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_gottcha2_report_full.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-405tgq07",
+                "id": "nmdc:dobj-11-hycy9b80",
                 "name": "GOTTCHA2 krona plot HTML file",
                 "description": "Gottcha2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -577,11 +577,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-405tgq07/nmdc_dobj-11-405tgq07_gottcha2_krona.html",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_gottcha2_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-h7mbw370",
+                "id": "nmdc:dobj-11-8prvd856",
                 "name": "Centrifuge output read classification file",
                 "description": "Centrifuge classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -633,11 +633,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-h7mbw370/nmdc_dobj-11-h7mbw370_centrifuge_classification.tsv",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_centrifuge_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-8a9rmt95",
+                "id": "nmdc:dobj-11-acryw383",
                 "name": "Centrifuge output report file",
                 "description": "Centrifuge TSV report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -689,11 +689,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-8a9rmt95/nmdc_dobj-11-8a9rmt95_centrifuge_report.tsv",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_centrifuge_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-wbynk051",
+                "id": "nmdc:dobj-11-f6j3wm49",
                 "name": "Centrifug krona plot HTML file",
                 "description": "Centrifuge Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -745,11 +745,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-wbynk051/nmdc_dobj-11-wbynk051_centrifuge_krona.html",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_centrifuge_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-wpw7gs92",
+                "id": "nmdc:dobj-11-xbn3d347",
                 "name": "Kraken2 output read classification file",
                 "description": "Kraken classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -801,11 +801,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-wpw7gs92/nmdc_dobj-11-wpw7gs92_kraken2_classification.tsv",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_kraken2_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-s4wxq602",
+                "id": "nmdc:dobj-11-sf23g974",
                 "name": "Kraken2 output report file",
                 "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -857,11 +857,11 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-s4wxq602/nmdc_dobj-11-s4wxq602_kraken2_report.tsv",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_kraken2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-vf207x18",
+                "id": "nmdc:dobj-11-cn18ys57",
                 "name": "Kraken2 Krona plot HTML file",
                 "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "alternative_identifiers": [],
@@ -913,7 +913,7 @@
                 },
                 "compression_type": null,
                 "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:dobj-11-vf207x18/nmdc_dobj-11-vf207x18_kraken2_krona.html",
+                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_kraken2_krona.html",
                 "type": "nmdc:Data_Object"
             }
         ],
@@ -927,7 +927,7 @@
         "metagenome_annotation_activity_set": [],
         "metagenome_assembly_set": [
             {
-                "id": "nmdc:wfmgas-11-wa0zvp69",
+                "id": "nmdc:wfmgas-11-xc17b248",
                 "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -936,15 +936,15 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/metaAssembly",
                 "has_input": [
-                    "nmdc:dobj-11-hfr31e20",
-                    "nmdc:dobj-11-xc5jhn80"
+                    "nmdc:dobj-11-b20kzg40",
+                    "nmdc:dobj-11-mhccey92"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-wz0zg037",
-                    "nmdc:dobj-11-dc20ch29",
-                    "nmdc:dobj-11-zr4b4z40",
-                    "nmdc:dobj-11-fe6kea76",
-                    "nmdc:dobj-11-f8bj1b18"
+                    "nmdc:dobj-11-b27rkd90",
+                    "nmdc:dobj-11-tcg9he98",
+                    "nmdc:dobj-11-z5f6jq78",
+                    "nmdc:dobj-11-kv8gp304",
+                    "nmdc:dobj-11-xkzgxw24"
                 ],
                 "type": "nmdc:MetagenomeAssembly",
                 "part_of": [
@@ -1000,7 +1000,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-q4pmsv93"
+                    "nmdc:dobj-11-bgp6z123"
                 ],
                 "insdc_experiment_identifiers": [],
                 "instrument_name": null,
@@ -1084,7 +1084,7 @@
         "reaction_activity_set": [],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-wq4r6842",
+                "id": "nmdc:wfrqc-11-5sfwhy50",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -1093,11 +1093,11 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-q4pmsv93"
+                    "nmdc:dobj-11-bgp6z123"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-hfr31e20",
-                    "nmdc:dobj-11-xc5jhn80"
+                    "nmdc:dobj-11-b20kzg40",
+                    "nmdc:dobj-11-mhccey92"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
@@ -1114,7 +1114,7 @@
         ],
         "read_based_taxonomy_analysis_activity_set": [
             {
-                "id": "nmdc:wfrbt-11-psqmn810",
+                "id": "nmdc:wfrbt-11-wy6fa249",
                 "name": "Readbased Taxonomy Analysis Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -1123,22 +1123,19 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
                 "has_input": [
-                    "nmdc:dobj-11-wz0zg037",
-                    "nmdc:dobj-11-dc20ch29",
-                    "nmdc:dobj-11-zr4b4z40",
-                    "nmdc:dobj-11-fe6kea76",
-                    "nmdc:dobj-11-f8bj1b18"
+                    "nmdc:dobj-11-b20kzg40",
+                    "nmdc:dobj-11-mhccey92"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-rw9dtn21",
-                    "nmdc:dobj-11-0wqjwr10",
-                    "nmdc:dobj-11-405tgq07",
-                    "nmdc:dobj-11-h7mbw370",
-                    "nmdc:dobj-11-8a9rmt95",
-                    "nmdc:dobj-11-wbynk051",
-                    "nmdc:dobj-11-wpw7gs92",
-                    "nmdc:dobj-11-s4wxq602",
-                    "nmdc:dobj-11-vf207x18"
+                    "nmdc:dobj-11-vw7fz645",
+                    "nmdc:dobj-11-bhnxqw16",
+                    "nmdc:dobj-11-hycy9b80",
+                    "nmdc:dobj-11-8prvd856",
+                    "nmdc:dobj-11-acryw383",
+                    "nmdc:dobj-11-f6j3wm49",
+                    "nmdc:dobj-11-xbn3d347",
+                    "nmdc:dobj-11-sf23g974",
+                    "nmdc:dobj-11-cn18ys57"
                 ],
                 "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
                 "part_of": [

From 62987ae4d189a98849473c08d078adae734e76c7 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 15 Nov 2023 09:51:16 -0800
Subject: [PATCH 58/91] localize data file ops and fix output serialization

---
 nmdc_automation/re_iding/base.py       | 21 +++++++++++++--------
 nmdc_automation/re_iding/file_utils.py | 15 ++++++++-------
 2 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 66ebab03..eff1de17 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -27,7 +27,7 @@
                                                 assembly_file_operations)
 
 NAPA_TEMPLATE = "../../../configs/re_iding_worklfows.yaml"
-BASE_DIR = "/global/cfs/cdirs/m3408/results"
+# BASE_DIR = "/global/cfs/cdirs/m3408/results"
 
 logging.basicConfig(
     level=logging.INFO,
@@ -150,7 +150,8 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             new_activity_id = self.api_client.minter(activity_type)
             logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
-            new_readsqc_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
+            new_readsqc_base_dir = os.path.join(self.data_dir, omics_processing_id,
+                                                new_activity_id)
             os.makedirs(new_readsqc_base_dir, exist_ok=True)
 
             updated_has_output = []
@@ -160,7 +161,7 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
                 old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
                 data_object_type = find_data_object_type(old_do_rec)
                 new_file_path = compute_new_paths(
-                old_do_rec["url"], new_readsqc_base_dir, new_activity_id
+                old_do_rec["url"], new_readsqc_base_dir, new_activity_id, self.data_dir
                 )
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
                 new_do = self._make_new_data_object(
@@ -207,7 +208,8 @@ def update_metagenome_assembly_set(self, db_record: Dict,
             new_activity_id = self.api_client.minter(activity_type)
             logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
-            new_assembly_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
+            new_assembly_base_dir = os.path.join(self.data_dir, omics_processing_id,
+                                                 new_activity_id)
             os.makedirs(new_assembly_base_dir, exist_ok=True)
             
             for old_do_id in assembly_rec["has_output"]:
@@ -218,7 +220,8 @@ def update_metagenome_assembly_set(self, db_record: Dict,
                     continue
                 new_file_path = get_new_paths(old_do_rec["url"],new_assembly_base_dir, new_activity_id)
                 updated_md5, updated_file_size = assembly_file_operations(
-                old_do_rec, data_object_type, new_file_path, new_activity_id)
+                old_do_rec, data_object_type, new_file_path, new_activity_id,
+                    self.data_dir)
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
                 #update md5 and file byte size in place to use _make_new_data_object function without functions
                 old_do_rec["file_size_bytes"] = updated_file_size
@@ -268,7 +271,8 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
             new_activity_id = self.api_client.minter(activity_type)
             logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
-            new_readbased_base_dir = os.path.join(BASE_DIR, omics_processing_id, new_activity_id)
+            new_readbased_base_dir = os.path.join(self.data_dir, omics_processing_id,
+                                                  new_activity_id)
             os.makedirs(new_readbased_base_dir, exist_ok=True)
             
             updated_has_output = []
@@ -279,7 +283,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
                 if not data_object_type:
                     continue
                 new_file_path = compute_new_paths(
-                old_do_rec["url"], new_readbased_base_dir, new_activity_id
+                old_do_rec["url"], new_readbased_base_dir, new_activity_id, self.data_dir
                 )
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
                 new_do = self._make_new_data_object(
@@ -360,7 +364,8 @@ def _make_new_data_object(self, omics_processing_id: str,
         logger.info(f"new_description: {new_description}")
         new_filename = self._make_new_filename(new_activity_id, data_object_rec)
         logger.info(f"new_filename: {new_filename}")
-        new_url = f"{BASE_DIR}/{omics_processing_id}/{new_activity_id}/{new_filename}"
+        new_url = (f"{self.data_dir}/{omics_processing_id}/{new_activity_id}"
+                   f"/{new_filename}")
 
         data_object = NmdcDataObject(
             id=new_data_object_id,
diff --git a/nmdc_automation/re_iding/file_utils.py b/nmdc_automation/re_iding/file_utils.py
index 59b877c7..b5bbae2e 100644
--- a/nmdc_automation/re_iding/file_utils.py
+++ b/nmdc_automation/re_iding/file_utils.py
@@ -11,7 +11,7 @@
 from typing import Dict, Optional
 
 
-base_dir = "/global/cfs/cdirs/m3408/results"
+# BASE_DIR = "/global/cfs/cdirs/m3408/results"
 bam_script = os.path.abspath("rewrite_bam.sh")
 base = "https://data.microbiomedata.org/data"
 
@@ -156,17 +156,18 @@ def rewrite_sam(input_sam, output_sam, old_id, new_id):
             f_out.write(line.replace(old_id, new_id))
 
 
-def get_old_file_path(data_object_record):
+def get_old_file_path(data_object_record, old_base_dir):
     old_url = data_object_record["url"]
     suffix = old_url.split("https://data.microbiomedata.org/data/")[1]
-    old_file_path = base_dir + "/" + suffix
+    old_file_path = old_base_dir + "/" + suffix
 
     return old_file_path
 
 
-def assembly_file_operations(data_object_record, data_object_type, destination, act_id):
+def assembly_file_operations(data_object_record, data_object_type,
+                             destination, act_id, old_base_dir):
     # get old file path upfront
-    old_file_path = get_old_file_path(data_object_record)
+    old_file_path = get_old_file_path(data_object_record, old_base_dir)
 
     if data_object_type == "Assembly Coverage Stats":
         md5, size = assembly_coverage_stats(old_file_path, destination, act_id)
@@ -196,13 +197,13 @@ def get_new_paths(old_url, new_base_dir, act_id):
     return destination
 
 
-def compute_new_paths(old_url, new_base_dir, act_id):
+def compute_new_paths(old_url, new_base_dir, act_id, old_base_dir):
     """
     Use the url to compute the new file name path and url
     """
     file_name = old_url.split("/")[-1]
     suffix = old_url.split("https://data.microbiomedata.org/data/")[1]
-    old_file_path = base_dir + "/" + suffix
+    old_file_path = old_base_dir + "/" + suffix
     file_extenstion = file_name.lstrip("nmdc_").split("_", maxsplit=1)[-1]
     new_file_name = f"{act_id}_{file_extenstion}"
     modified_new_file_name = new_file_name.replace(":", "_")

From 40e5ce586c4b4cd2c9171e9fe045a87cd3a001d0 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 15 Nov 2023 09:53:16 -0800
Subject: [PATCH 59/91] updated output dump

---
 .../data/dryrun_associated_record_dump.json   |   640 -
 ...sty-11-aygzgv51_assocated_record_dump.json | 40673 ----------------
 2 files changed, 41313 deletions(-)
 delete mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json
 delete mode 100644 nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_assocated_record_dump.json

diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json
deleted file mode 100644
index 638c9f4d..00000000
--- a/nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json
+++ /dev/null
@@ -1,640 +0,0 @@
-[
-  {
-        "functional_annotation_agg": [],
-        "library_preparation_set": [],
-        "processed_sample_set": [],
-        "extraction_set": [],
-        "activity_set": [],
-        "biosample_set": [],
-        "data_object_set": [
-            {
-                "description": "Raw sequencer read data",
-                "file_size_bytes": 2861414297,
-                "type": "nmdc:DataObject",
-                "id": "jgi:55d740280d8785342fcf7e39",
-                "name": "9422.8.132674.GTTTCG.fastq.gz"
-            },
-            {
-                "name": "Gp0115663_Filtered Reads",
-                "description": "Filtered Reads for Gp0115663",
-                "data_object_type": "Filtered Sequencing Reads",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filtered.fastq.gz",
-                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
-                "id": "nmdc:7bf778baef033d36f118f8591256d6ef",
-                "file_size_bytes": 2571324879
-            },
-            {
-                "name": "Gp0115663_Filtered Stats",
-                "description": "Filtered Stats for Gp0115663",
-                "data_object_type": "QC Statistics",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filterStats.txt",
-                "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
-                "id": "nmdc:b99ce8adc125c95f0bfdadf36a3f6848",
-                "file_size_bytes": 290
-            },
-            {
-                "name": "Gp0115663_Gottcha2 TSV report",
-                "description": "Gottcha2 TSV report for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
-                "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
-                "id": "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
-                "file_size_bytes": 13174
-            },
-            {
-                "name": "Gp0115663_Gottcha2 full TSV report",
-                "description": "Gottcha2 full TSV report for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
-                "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
-                "id": "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
-                "file_size_bytes": 1035818
-            },
-            {
-                "name": "Gp0115663_Gottcha2 Krona HTML report",
-                "description": "Gottcha2 Krona HTML report for Gp0115663",
-                "data_object_type": "GOTTCHA2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
-                "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
-                "id": "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
-                "file_size_bytes": 262669
-            },
-            {
-                "name": "Gp0115663_Centrifuge classification TSV report",
-                "description": "Centrifuge classification TSV report for Gp0115663",
-                "data_object_type": "Centrifuge Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
-                "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
-                "id": "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
-                "file_size_bytes": 2189843623
-            },
-            {
-                "name": "Gp0115663_Centrifuge TSV report",
-                "description": "Centrifuge TSV report for Gp0115663",
-                "data_object_type": "Centrifuge Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
-                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
-                "id": "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
-                "file_size_bytes": 260134
-            },
-            {
-                "name": "Gp0115663_Centrifuge Krona HTML report",
-                "description": "Centrifuge Krona HTML report for Gp0115663",
-                "data_object_type": "Centrifuge Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
-                "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
-                "id": "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
-                "file_size_bytes": 2343980
-            },
-            {
-                "name": "Gp0115663_Kraken classification TSV report",
-                "description": "Kraken classification TSV report for Gp0115663",
-                "data_object_type": "Kraken2 Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
-                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
-                "id": "nmdc:7ca01ea379f0baed96f87d1435925f95",
-                "file_size_bytes": 1785563917
-            },
-            {
-                "name": "Gp0115663_Kraken2 TSV report",
-                "description": "Kraken2 TSV report for Gp0115663",
-                "data_object_type": "Kraken2 Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
-                "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
-                "id": "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
-                "file_size_bytes": 699896
-            },
-            {
-                "name": "Gp0115663_Kraken2 Krona HTML report",
-                "description": "Kraken2 Krona HTML report for Gp0115663",
-                "data_object_type": "Kraken2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
-                "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
-                "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
-                "file_size_bytes": 4221977
-            },
-            {
-                "name": "Gp0115663_Assembled contigs fasta",
-                "description": "Assembled contigs fasta for Gp0115663",
-                "data_object_type": "Assembly Contigs",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna",
-                "md5_checksum": "deddd162bf0128fba13b3bc1ca38d1aa",
-                "id": "nmdc:deddd162bf0128fba13b3bc1ca38d1aa",
-                "file_size_bytes": 90115831
-            },
-            {
-                "name": "Gp0115663_Assembled scaffold fasta",
-                "description": "Assembled scaffold fasta for Gp0115663",
-                "data_object_type": "Assembly Scaffolds",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna",
-                "md5_checksum": "b3573e3cda5a06611de71ca04c5c14cc",
-                "id": "nmdc:b3573e3cda5a06611de71ca04c5c14cc",
-                "file_size_bytes": 89604715
-            },
-            {
-                "name": "Gp0115663_Metagenome Contig Coverage Stats",
-                "description": "Metagenome Contig Coverage Stats for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_covstats.txt",
-                "md5_checksum": "c6d0d4cea985ca6fb50a060e15b4a856",
-                "id": "nmdc:c6d0d4cea985ca6fb50a060e15b4a856",
-                "file_size_bytes": 13412363
-            },
-            {
-                "name": "Gp0115663_Assembled AGP file",
-                "description": "Assembled AGP file for Gp0115663",
-                "data_object_type": "Assembly AGP",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_assembly.agp",
-                "md5_checksum": "f450e3800e17691d5874c89fc46c186a",
-                "id": "nmdc:f450e3800e17691d5874c89fc46c186a",
-                "file_size_bytes": 12542171
-            },
-            {
-                "name": "Gp0115663_Metagenome Alignment BAM file",
-                "description": "Metagenome Alignment BAM file for Gp0115663",
-                "data_object_type": "Assembly Coverage BAM",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_pairedMapped_sorted.bam",
-                "md5_checksum": "31dc958d116d02122509e90b0883954f",
-                "id": "nmdc:31dc958d116d02122509e90b0883954f",
-                "file_size_bytes": 2773429299
-            },
-            {
-                "name": "Gp0115663_Protein FAA",
-                "description": "Protein FAA for Gp0115663",
-                "data_object_type": "Annotation Amino Acid FASTA",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_proteins.faa",
-                "md5_checksum": "879988d212ecec46928b8598e2f8391f",
-                "id": "nmdc:879988d212ecec46928b8598e2f8391f",
-                "file_size_bytes": 50165060
-            },
-            {
-                "name": "Gp0115663_Structural annotation GFF file",
-                "description": "Structural annotation GFF file for Gp0115663",
-                "data_object_type": "Structural Annotation GFF",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_structural_annotation.gff",
-                "md5_checksum": "884b95102f5965cc0ee2d9b7f198e5a4",
-                "id": "nmdc:884b95102f5965cc0ee2d9b7f198e5a4",
-                "file_size_bytes": 2767
-            },
-            {
-                "name": "Gp0115663_Functional annotation GFF file",
-                "description": "Functional annotation GFF file for Gp0115663",
-                "data_object_type": "Functional Annotation GFF",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_functional_annotation.gff",
-                "md5_checksum": "002e4ebc728f8b91cb5f298d340ab013",
-                "id": "nmdc:002e4ebc728f8b91cb5f298d340ab013",
-                "file_size_bytes": 55139586
-            },
-            {
-                "name": "Gp0115663_KO TSV file",
-                "description": "KO TSV file for Gp0115663",
-                "data_object_type": "Annotation KEGG Orthology",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_ko.tsv",
-                "md5_checksum": "6851078f29716d89e3f41f0969ae7bf0",
-                "id": "nmdc:6851078f29716d89e3f41f0969ae7bf0",
-                "file_size_bytes": 6023696
-            },
-            {
-                "name": "Gp0115663_EC TSV file",
-                "description": "EC TSV file for Gp0115663",
-                "data_object_type": "Annotation Enzyme Commission",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_ec.tsv",
-                "md5_checksum": "4f88c89459f36655eb7c1eceec19602a",
-                "id": "nmdc:4f88c89459f36655eb7c1eceec19602a",
-                "file_size_bytes": 3982918
-            },
-            {
-                "name": "Gp0115663_COG GFF file",
-                "description": "COG GFF file for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_cog.gff",
-                "md5_checksum": "a068b9ce6ebb7deb15ff932b513817a9",
-                "id": "nmdc:a068b9ce6ebb7deb15ff932b513817a9",
-                "file_size_bytes": 27362917
-            },
-            {
-                "name": "Gp0115663_PFAM GFF file",
-                "description": "PFAM GFF file for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_pfam.gff",
-                "md5_checksum": "618b18fa8635c80cc0091371f451a6f0",
-                "id": "nmdc:618b18fa8635c80cc0091371f451a6f0",
-                "file_size_bytes": 21572048
-            },
-            {
-                "name": "Gp0115663_TigrFam GFF file",
-                "description": "TigrFam GFF file for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_tigrfam.gff",
-                "md5_checksum": "17e55a1a1a133ffbf8cbe4024d997a6f",
-                "id": "nmdc:17e55a1a1a133ffbf8cbe4024d997a6f",
-                "file_size_bytes": 2900068
-            },
-            {
-                "name": "Gp0115663_SMART GFF file",
-                "description": "SMART GFF file for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_smart.gff",
-                "md5_checksum": "8f80142c0f5723af5a3b44b7ff4e4339",
-                "id": "nmdc:8f80142c0f5723af5a3b44b7ff4e4339",
-                "file_size_bytes": 6905519
-            },
-            {
-                "name": "Gp0115663_SuperFam GFF file",
-                "description": "SuperFam GFF file for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_supfam.gff",
-                "md5_checksum": "fdd2e8741ffef40db383674a10bb4d11",
-                "id": "nmdc:fdd2e8741ffef40db383674a10bb4d11",
-                "file_size_bytes": 38787856
-            },
-            {
-                "name": "Gp0115663_Cath FunFam GFF file",
-                "description": "Cath FunFam GFF file for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_cath_funfam.gff",
-                "md5_checksum": "8eb49ac20a6c2721d6db227f4fb3356a",
-                "id": "nmdc:8eb49ac20a6c2721d6db227f4fb3356a",
-                "file_size_bytes": 30134783
-            },
-            {
-                "name": "Gp0115663_KO_EC GFF file",
-                "description": "KO_EC GFF file for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_ko_ec.gff",
-                "md5_checksum": "75f481e0d98793cfb4f9508cb3e31622",
-                "id": "nmdc:75f481e0d98793cfb4f9508cb3e31622",
-                "file_size_bytes": 19194308
-            },
-            {
-                "name": "gold:Gp0452679_metabat2 bin checkm quality assessment result",
-                "description": "metabat2 bin checkm quality assessment result for gold:Gp0452679",
-                "data_object_type": "CheckM Statistics",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0fsjy84/MAGs/nmdc_mga0fsjy84_checkm_qa.out",
-                "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
-                "id": "nmdc:d41d8cd98f00b204e9800998ecf8427e",
-                "file_size_bytes": 0
-            },
-            {
-                "name": "Gp0115663_tooShort (< 3kb) filtered contigs fasta file by metaBat2",
-                "description": "tooShort (< 3kb) filtered contigs fasta file by metaBat2 for Gp0115663",
-                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/MAGs/nmdc_mga0h9dt75_bins.tooShort.fa",
-                "md5_checksum": "c092b018cb4652c4ca0620b37a4b3fad",
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diff --git a/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_assocated_record_dump.json b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_assocated_record_dump.json
deleted file mode 100644
index d3156d14..00000000
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-        "metagenome_sequencing_activity_set": [],
-        "metaproteomics_analysis_activity_set": [],
-        "metatranscriptome_activity_set": [],
-        "nom_analysis_activity_set": [],
-        "omics_processing_set": [
-            {
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-                },
-                "id": "nmdc:omprc-11-p1735e67",
-                "name": "Riverbed sediment microbial communities from areas with vegetation nearby in Columbia River, Washington, USA - GW-RW S2_0_10",
-                "description": "Riverbed sediment samples were collected from an area with a lot of surrounding vegetation in a hyporheic zone (subsurface groundwater - surface water mixing zone)",
-                "has_input": [
-                    "nmdc:bsm-11-k4wa0808"
-                ],
-                "has_output": [
-                    "jgi:574fde937ded5e3df1ee1428"
-                ],
-                "part_of": [
-                    "nmdc:sty-11-aygzgv51"
-                ],
-                "add_date": "2016-01-11",
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-                "omics_type": {
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-                },
-                "principal_investigator": {
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-                },
-                "processing_institution": "JGI",
-                "type": "nmdc:OmicsProcessing",
-                "gold_sequencing_project_identifiers": [
-                    "gold:Gp0127653"
-                ]
-            }
-        ],
-        "reaction_activity_set": [],
-        "read_qc_analysis_activity_set": [
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-                },
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-                ],
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-                "output_read_count": 19516330,
-                "started_at_time": "2021-10-11T02:23:35Z",
-                "type": "nmdc:ReadQCAnalysisActivity",
-                "ended_at_time": "2021-11-13T18:52:13+00:00"
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-        ],
-        "read_based_taxonomy_analysis_activity_set": [
-            {
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-                "execution_resource": "NERSC-Cori",
-                "name": "ReadBased Analysis Activity for nmdc:mga079y988",
-                "started_at_time": "2021-10-11T02:23:35Z",
-                "type": "nmdc:ReadbasedAnalysis",
-                "ended_at_time": "2021-11-13T18:52:13+00:00"
-            }
-        ],
-        "study_set": [],
-        "field_research_site_set": [],
-        "collecting_biosamples_from_site_set": [],
-        "date_created": null,
-        "etl_software_version": null,
-        "pooling_set": []
-    }
-]
\ No newline at end of file

From 1a1a8ab680e2eac4d1d9ab1250285cf65d5ca26a Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 15 Nov 2023 09:55:24 -0800
Subject: [PATCH 60/91] updated script and output

---
 ...ty-11-aygzgv51_associated_record_dump.json | 39520 ++++++++++++++++
 .../re_iding/scripts/re_id_tool.py            |    19 +-
 2 files changed, 39532 insertions(+), 7 deletions(-)
 create mode 100644 nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_associated_record_dump.json

diff --git a/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_associated_record_dump.json b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_associated_record_dump.json
new file mode 100644
index 00000000..935367d9
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_associated_record_dump.json
@@ -0,0 +1,39520 @@
+[
+    {
+        "data_object_set": [
+            {
+                "description": "Raw sequencer read data",
+                "file_size_bytes": 2861414297,
+                "type": "nmdc:DataObject",
+                "id": "jgi:55d740280d8785342fcf7e39",
+                "name": "9422.8.132674.GTTTCG.fastq.gz"
+            },
+            {
+                "name": "Gp0115663_Filtered Reads",
+                "description": "Filtered Reads for Gp0115663",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filtered.fastq.gz",
+                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                "id": "nmdc:7bf778baef033d36f118f8591256d6ef",
+                "file_size_bytes": 2571324879
+            },
+            {
+                "name": "Gp0115663_Filtered Stats",
+                "description": "Filtered Stats for Gp0115663",
+                "data_object_type": "QC Statistics",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filterStats.txt",
+                "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
+                "id": "nmdc:b99ce8adc125c95f0bfdadf36a3f6848",
+                "file_size_bytes": 290
+            },
+            {
+                "name": "Gp0115663_Gottcha2 TSV report",
+                "description": "Gottcha2 TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
+                "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
+                "id": "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                "file_size_bytes": 13174
+            },
+            {
+                "name": "Gp0115663_Gottcha2 full TSV report",
+                "description": "Gottcha2 full TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
+                "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
+                "id": "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                "file_size_bytes": 1035818
+            },
+            {
+                "name": "Gp0115663_Gottcha2 Krona HTML report",
+                "description": "Gottcha2 Krona HTML report for Gp0115663",
+                "data_object_type": "GOTTCHA2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
+                "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
+                "id": "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                "file_size_bytes": 262669
+            },
+            {
+                "name": "Gp0115663_Centrifuge classification TSV report",
+                "description": "Centrifuge classification TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
+                "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
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+                "file_size_bytes": 2189843623
+            },
+            {
+                "name": "Gp0115663_Centrifuge TSV report",
+                "description": "Centrifuge TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
+                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+                "id": "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                "file_size_bytes": 260134
+            },
+            {
+                "name": "Gp0115663_Centrifuge Krona HTML report",
+                "description": "Centrifuge Krona HTML report for Gp0115663",
+                "data_object_type": "Centrifuge Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
+                "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
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+            },
+            {
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+                "description": "Kraken classification TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
+                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
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+            },
+            {
+                "name": "Gp0115663_Kraken2 TSV report",
+                "description": "Kraken2 TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
+                "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+                "id": "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
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+            },
+            {
+                "name": "Gp0115663_Kraken2 Krona HTML report",
+                "description": "Kraken2 Krona HTML report for Gp0115663",
+                "data_object_type": "Kraken2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
+                "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+                "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
+                "file_size_bytes": 4221977
+            },
+            {
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+                "description": "Assembled contigs fasta for Gp0115663",
+                "data_object_type": "Assembly Contigs",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna",
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+            },
+            {
+                "name": "Gp0115663_Assembled scaffold fasta",
+                "description": "Assembled scaffold fasta for Gp0115663",
+                "data_object_type": "Assembly Scaffolds",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna",
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+            },
+            {
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+                "file_size_bytes": 13412363
+            },
+            {
+                "name": "Gp0115663_Assembled AGP file",
+                "description": "Assembled AGP file for Gp0115663",
+                "data_object_type": "Assembly AGP",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_assembly.agp",
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+                "id": "nmdc:f450e3800e17691d5874c89fc46c186a",
+                "file_size_bytes": 12542171
+            },
+            {
+                "name": "Gp0115663_Metagenome Alignment BAM file",
+                "description": "Metagenome Alignment BAM file for Gp0115663",
+                "data_object_type": "Assembly Coverage BAM",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_pairedMapped_sorted.bam",
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+                "id": "nmdc:31dc958d116d02122509e90b0883954f",
+                "file_size_bytes": 2773429299
+            },
+            {
+                "name": "Gp0115663_Protein FAA",
+                "description": "Protein FAA for Gp0115663",
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+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_proteins.faa",
+                "md5_checksum": "879988d212ecec46928b8598e2f8391f",
+                "id": "nmdc:879988d212ecec46928b8598e2f8391f",
+                "file_size_bytes": 50165060
+            },
+            {
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+        ],
+        "metagenome_annotation_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b005bbf2caae0415ef9be"
+                },
+                "has_input": [
+                    "nmdc:0f2b82878f54787c127bf03338d5c605"
+                ],
+                "part_of": [
+                    "nmdc:mga079y988"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:81f16ca99f73a3314a66e6b24d23376f",
+                    "nmdc:66bb16ef28196379647d319da50426dd",
+                    "nmdc:1e7dac5f12cc086509ff905f7133b15a",
+                    "nmdc:2a7343eb6364d769a1c43aa5c94daee8",
+                    "nmdc:b2cee4d35f68d1f5731bff3af5904fa4",
+                    "nmdc:1d45960b1ba5e27af42c736ec583ecd4",
+                    "nmdc:3dec47a0a04865ecdcd9ed7cbc78eca4",
+                    "nmdc:043322f3cd31d50faf4d4e0ffd1c8427",
+                    "nmdc:6bed0fc7a7be284936c69fc1faac4be6",
+                    "nmdc:052d3fb0080390255df5772f79e5ef2c",
+                    "nmdc:e66a3b85c713e8766e5181da2e393984",
+                    "nmdc:949e3b137b3a0591ed9de493ee5c530b"
+                ],
+                "was_informed_by": "gold:Gp0127653",
+                "id": "nmdc:676183a611b251dc6b8f0b8ca600181b",
+                "execution_resource": "NERSC-Cori",
+                "name": "Annotation Activity for nmdc:mga079y988",
+                "started_at_time": "2021-10-11T02:23:35Z",
+                "type": "nmdc:MetagenomeAnnotationActivity",
+                "ended_at_time": "2021-11-13T18:52:13+00:00"
+            }
+        ],
+        "metagenome_assembly_set": [
+            {
+                "_id": {
+                    "$oid": "649b005f2ca5ee4adb139faa"
+                },
+                "has_input": [
+                    "nmdc:8eec0e9c14abb418b906504d1675ecc5"
+                ],
+                "part_of": [
+                    "nmdc:mga079y988"
+                ],
+                "ctg_logsum": 9125.582,
+                "scaf_logsum": 9156.336,
+                "gap_pct": 0.00094,
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:0f2b82878f54787c127bf03338d5c605",
+                    "nmdc:02f8e7222e9e6f45c388a189ca66e1f9",
+                    "nmdc:eea8a4b58ca07019d0050b030be3a3d1",
+                    "nmdc:44b1ad59bd14c3367ac0fa2ca37aa057",
+                    "nmdc:ccd5ba8558a92751c59989aa81054e1a"
+                ],
+                "asm_score": 13.921,
+                "was_informed_by": "gold:Gp0127653",
+                "ctg_powsum": 1096.518,
+                "scaf_max": 58655,
+                "id": "nmdc:676183a611b251dc6b8f0b8ca600181b",
+                "scaf_powsum": 1101.795,
+                "execution_resource": "NERSC-Cori",
+                "contigs": 48932,
+                "name": "Assembly Activity for nmdc:mga079y988",
+                "ctg_max": 58655,
+                "gc_std": 0.10928,
+                "gc_avg": 0.57867,
+                "contig_bp": 16963869,
+                "started_at_time": "2021-10-11T02:23:35Z",
+                "scaf_bp": 16964029,
+                "type": "nmdc:MetagenomeAssembly",
+                "scaffolds": 48925,
+                "ended_at_time": "2021-11-13T18:52:13+00:00",
+                "ctg_l50": 309,
+                "ctg_l90": 281,
+                "ctg_n50": 19544,
+                "ctg_n90": 43034,
+                "scaf_l50": 309,
+                "scaf_l90": 281,
+                "scaf_n50": 19539,
+                "scaf_n90": 43028,
+                "scaf_l_gt50k": 58655,
+                "scaf_n_gt50k": 1,
+                "scaf_pct_gt50k": 0.34576103
+            }
+        ],
+        "omics_processing_set": [
+            {
+                "_id": {
+                    "$oid": "649b009773e8249959349b64"
+                },
+                "id": "nmdc:omprc-11-p1735e67",
+                "name": "Riverbed sediment microbial communities from areas with vegetation nearby in Columbia River, Washington, USA - GW-RW S2_0_10",
+                "description": "Riverbed sediment samples were collected from an area with a lot of surrounding vegetation in a hyporheic zone (subsurface groundwater - surface water mixing zone)",
+                "has_input": [
+                    "nmdc:bsm-11-k4wa0808"
+                ],
+                "has_output": [
+                    "jgi:574fde937ded5e3df1ee1428"
+                ],
+                "part_of": [
+                    "nmdc:sty-11-aygzgv51"
+                ],
+                "add_date": "2016-01-11",
+                "mod_date": "2021-06-15",
+                "ncbi_project_name": "Riverbed sediment microbial communities from areas with vegetation nearby in Columbia River, Washington, USA - GW-RW S2_0_10",
+                "omics_type": {
+                    "has_raw_value": "Metagenome"
+                },
+                "principal_investigator": {
+                    "has_raw_value": "James Stegen"
+                },
+                "processing_institution": "JGI",
+                "type": "nmdc:OmicsProcessing",
+                "gold_sequencing_project_identifiers": [
+                    "gold:Gp0127653"
+                ]
+            }
+        ],
+        "read_qc_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009d6bdd4fd20273c878"
+                },
+                "has_input": [
+                    "nmdc:84ffabc3fbd7e759cd2352ec513b89a0"
+                ],
+                "part_of": [
+                    "nmdc:mga079y988"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:8eec0e9c14abb418b906504d1675ecc5",
+                    "nmdc:5d07358bbc48f25e157ffc91ea7ae3e0"
+                ],
+                "was_informed_by": "gold:Gp0127653",
+                "input_read_count": 20780788,
+                "output_read_bases": 2918466866,
+                "id": "nmdc:676183a611b251dc6b8f0b8ca600181b",
+                "execution_resource": "NERSC-Cori",
+                "input_read_bases": 3137898988,
+                "name": "Read QC Activity for nmdc:mga079y988",
+                "output_read_count": 19516330,
+                "started_at_time": "2021-10-11T02:23:35Z",
+                "type": "nmdc:ReadQCAnalysisActivity",
+                "ended_at_time": "2021-11-13T18:52:13+00:00"
+            }
+        ],
+        "read_based_taxonomy_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009bff710ae353f8cf3d"
+                },
+                "has_input": [
+                    "nmdc:8eec0e9c14abb418b906504d1675ecc5"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:fbbad3e21108a372e3d53c9ee8fc3cd5",
+                    "nmdc:dbf03e26f7e1529762830161fe1f1906",
+                    "nmdc:284ce1b28b8964cb525025d678277dba",
+                    "nmdc:a379527f61806391e42b3512146013a8",
+                    "nmdc:3659ac6c99dea0fb1385c58eac8b1335",
+                    "nmdc:3219058371bf2f8081b2dd2b434ec145",
+                    "nmdc:be29ebcd7358653afec7381f9ca43431",
+                    "nmdc:a9e6ab6db23ddce02317e3e21ea3f618",
+                    "nmdc:4c1aae1a46e51359f9146e48fff0e7f0"
+                ],
+                "was_informed_by": "gold:Gp0127653",
+                "id": "nmdc:676183a611b251dc6b8f0b8ca600181b",
+                "execution_resource": "NERSC-Cori",
+                "name": "ReadBased Analysis Activity for nmdc:mga079y988",
+                "started_at_time": "2021-10-11T02:23:35Z",
+                "type": "nmdc:ReadbasedAnalysis",
+                "ended_at_time": "2021-11-13T18:52:13+00:00"
+            }
+        ]
+    }
+]
\ No newline at end of file
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 26df0e81..e784244a 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -10,6 +10,8 @@
 import json
 import click
 
+from linkml_runtime.dumpers import json_dumper
+
 from nmdc_automation.api import NmdcRuntimeApi, NmdcRuntimeUserApi
 from nmdc_automation.config import Config
 import nmdc_schema.nmdc as nmdc
@@ -148,10 +150,10 @@ def extract_records(ctx, study_id):
 
         retrieved_databases.append(db)
 
-    with open(f"{study_id}_assocated_record_dump.json", 'w') as json_file:
-        json.dump(
-            [o.__dict__ for o in retrieved_databases], json_file, indent=4
-            )
+    json_data = json.loads(json_dumper.dumps(retrieved_databases, inject_type=False))
+    db_outfile = DATA_DIR.joinpath(f"{study_id}_associated_record_dump.json")
+    with open(db_outfile, "w") as f:
+        f.write(json.dumps(json_data, indent=4))
 
 
 @cli.command()
@@ -171,6 +173,8 @@ def process_records(ctx, dryrun, study_id, data_dir):
     """
     start_time = time.time()
     logging.info(f"Processing workflow records for study_id: {study_id}")
+    if dryrun:
+        logging.info("Running in dryrun mode")
 
     # Get API client
     config = ctx.obj['site_config']
@@ -180,6 +184,7 @@ def process_records(ctx, dryrun, study_id, data_dir):
     # Get Database dump file paths and the data directory
     db_infile, db_outfile = _get_database_paths(study_id, dryrun)
     data_dir = _get_data_dir(data_dir, dryrun)
+    logging.info(f"Using data_dir: {data_dir}")
 
     # Initialize re-ID tool
     reid_tool = ReIdTool(api_client, data_dir)
@@ -212,10 +217,10 @@ def process_records(ctx, dryrun, study_id, data_dir):
         re_ided_db_records.append(new_db)
 
 
-    json_data = json.dumps(re_ided_db_records, default=lambda o: o.__dict__, indent=4)
-    logging.info(f"Writing re_ided_db_records to {db_outfile}")
+    json_data = json.loads(json_dumper.dumps(re_ided_db_records,
+                                             inject_type=False))
     with open(db_outfile, "w") as f:
-        f.write(json_data)
+        f.write(json.dumps(json_data, indent=4))
 
 
 def _get_data_dir(data_dir, dryrun):

From c38070af6e6b97c146cbe26263aa3e443f6e5146 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 15 Nov 2023 09:57:33 -0800
Subject: [PATCH 61/91] Create dryrun_associated_record_dump.json

---
 .../data/dryrun_associated_record_dump.json   | 835 ++++++++++++++++++
 1 file changed, 835 insertions(+)
 create mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json

diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json
new file mode 100644
index 00000000..64fa1542
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_associated_record_dump.json
@@ -0,0 +1,835 @@
+[
+    {
+        "data_object_set": [
+            {
+                "description": "Raw sequencer read data",
+                "file_size_bytes": 2861414297,
+                "type": "nmdc:DataObject",
+                "id": "jgi:55d740280d8785342fcf7e39",
+                "name": "9422.8.132674.GTTTCG.fastq.gz"
+            },
+            {
+                "name": "Gp0115663_Filtered Reads",
+                "description": "Filtered Reads for Gp0115663",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filtered.fastq.gz",
+                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                "id": "nmdc:7bf778baef033d36f118f8591256d6ef",
+                "file_size_bytes": 2571324879
+            },
+            {
+                "name": "Gp0115663_Filtered Stats",
+                "description": "Filtered Stats for Gp0115663",
+                "data_object_type": "QC Statistics",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filterStats.txt",
+                "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
+                "id": "nmdc:b99ce8adc125c95f0bfdadf36a3f6848",
+                "file_size_bytes": 290
+            },
+            {
+                "name": "Gp0115663_Gottcha2 TSV report",
+                "description": "Gottcha2 TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report.tsv",
+                "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
+                "id": "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                "file_size_bytes": 13174
+            },
+            {
+                "name": "Gp0115663_Gottcha2 full TSV report",
+                "description": "Gottcha2 full TSV report for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_report_full.tsv",
+                "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
+                "id": "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                "file_size_bytes": 1035818
+            },
+            {
+                "name": "Gp0115663_Gottcha2 Krona HTML report",
+                "description": "Gottcha2 Krona HTML report for Gp0115663",
+                "data_object_type": "GOTTCHA2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_gottcha2_krona.html",
+                "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
+                "id": "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                "file_size_bytes": 262669
+            },
+            {
+                "name": "Gp0115663_Centrifuge classification TSV report",
+                "description": "Centrifuge classification TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_classification.tsv",
+                "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
+                "id": "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                "file_size_bytes": 2189843623
+            },
+            {
+                "name": "Gp0115663_Centrifuge TSV report",
+                "description": "Centrifuge TSV report for Gp0115663",
+                "data_object_type": "Centrifuge Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_report.tsv",
+                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+                "id": "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                "file_size_bytes": 260134
+            },
+            {
+                "name": "Gp0115663_Centrifuge Krona HTML report",
+                "description": "Centrifuge Krona HTML report for Gp0115663",
+                "data_object_type": "Centrifuge Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_centrifuge_krona.html",
+                "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
+                "id": "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                "file_size_bytes": 2343980
+            },
+            {
+                "name": "Gp0115663_Kraken classification TSV report",
+                "description": "Kraken classification TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_classification.tsv",
+                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
+                "id": "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                "file_size_bytes": 1785563917
+            },
+            {
+                "name": "Gp0115663_Kraken2 TSV report",
+                "description": "Kraken2 TSV report for Gp0115663",
+                "data_object_type": "Kraken2 Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_report.tsv",
+                "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+                "id": "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                "file_size_bytes": 699896
+            },
+            {
+                "name": "Gp0115663_Kraken2 Krona HTML report",
+                "description": "Kraken2 Krona HTML report for Gp0115663",
+                "data_object_type": "Kraken2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/ReadbasedAnalysis/nmdc_mga0h9dt75_kraken2_krona.html",
+                "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+                "id": "nmdc:94ee1bc2dc74830a21d5c3471d6cf223",
+                "file_size_bytes": 4221977
+            },
+            {
+                "name": "Gp0115663_Assembled contigs fasta",
+                "description": "Assembled contigs fasta for Gp0115663",
+                "data_object_type": "Assembly Contigs",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna",
+                "md5_checksum": "deddd162bf0128fba13b3bc1ca38d1aa",
+                "id": "nmdc:deddd162bf0128fba13b3bc1ca38d1aa",
+                "file_size_bytes": 90115831
+            },
+            {
+                "name": "Gp0115663_Assembled scaffold fasta",
+                "description": "Assembled scaffold fasta for Gp0115663",
+                "data_object_type": "Assembly Scaffolds",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna",
+                "md5_checksum": "b3573e3cda5a06611de71ca04c5c14cc",
+                "id": "nmdc:b3573e3cda5a06611de71ca04c5c14cc",
+                "file_size_bytes": 89604715
+            },
+            {
+                "name": "Gp0115663_Metagenome Contig Coverage Stats",
+                "description": "Metagenome Contig Coverage Stats for Gp0115663",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_covstats.txt",
+                "md5_checksum": "c6d0d4cea985ca6fb50a060e15b4a856",
+                "id": "nmdc:c6d0d4cea985ca6fb50a060e15b4a856",
+                "file_size_bytes": 13412363
+            },
+            {
+                "name": "Gp0115663_Assembled AGP file",
+                "description": "Assembled AGP file for Gp0115663",
+                "data_object_type": "Assembly AGP",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_assembly.agp",
+                "md5_checksum": "f450e3800e17691d5874c89fc46c186a",
+                "id": "nmdc:f450e3800e17691d5874c89fc46c186a",
+                "file_size_bytes": 12542171
+            },
+            {
+                "name": "Gp0115663_Metagenome Alignment BAM file",
+                "description": "Metagenome Alignment BAM file for Gp0115663",
+                "data_object_type": "Assembly Coverage BAM",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_pairedMapped_sorted.bam",
+                "md5_checksum": "31dc958d116d02122509e90b0883954f",
+                "id": "nmdc:31dc958d116d02122509e90b0883954f",
+                "file_size_bytes": 2773429299
+            },
+            {
+                "name": "Gp0115663_Protein FAA",
+                "description": "Protein FAA for Gp0115663",
+                "data_object_type": "Annotation Amino Acid FASTA",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_proteins.faa",
+                "md5_checksum": "879988d212ecec46928b8598e2f8391f",
+                "id": "nmdc:879988d212ecec46928b8598e2f8391f",
+                "file_size_bytes": 50165060
+            },
+            {
+                "name": "Gp0115663_Structural annotation GFF file",
+                "description": "Structural annotation GFF file for Gp0115663",
+                "data_object_type": "Structural Annotation GFF",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/annotation/nmdc_mga0h9dt75_structural_annotation.gff",
+                "md5_checksum": "884b95102f5965cc0ee2d9b7f198e5a4",
+                "id": "nmdc:884b95102f5965cc0ee2d9b7f198e5a4",
+                "file_size_bytes": 2767
+            },
+            {
+                "name": "Gp0115663_Functional annotation GFF file",
+                "description": "Functional annotation GFF file for Gp0115663",
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+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 6
+                    },
+                    {
+                        "number_of_contig": 19,
+                        "completeness": 4.45,
+                        "bin_name": "bins.5",
+                        "gene_count": 463,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 4
+                    }
+                ],
+                "unbinned_contig_num": 9288,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:MAGsAnalysisActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "metagenome_annotation_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b005bbf2caae0415ef9d6"
+                },
+                "has_input": [
+                    "nmdc:deddd162bf0128fba13b3bc1ca38d1aa"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:879988d212ecec46928b8598e2f8391f",
+                    "nmdc:884b95102f5965cc0ee2d9b7f198e5a4",
+                    "nmdc:002e4ebc728f8b91cb5f298d340ab013",
+                    "nmdc:6851078f29716d89e3f41f0969ae7bf0",
+                    "nmdc:4f88c89459f36655eb7c1eceec19602a",
+                    "nmdc:a068b9ce6ebb7deb15ff932b513817a9",
+                    "nmdc:618b18fa8635c80cc0091371f451a6f0",
+                    "nmdc:17e55a1a1a133ffbf8cbe4024d997a6f",
+                    "nmdc:8f80142c0f5723af5a3b44b7ff4e4339",
+                    "nmdc:fdd2e8741ffef40db383674a10bb4d11",
+                    "nmdc:8eb49ac20a6c2721d6db227f4fb3356a",
+                    "nmdc:75f481e0d98793cfb4f9508cb3e31622"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "name": "Annotation Activity for nmdc:mga0h9dt75",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:MetagenomeAnnotationActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "metagenome_assembly_set": [
+            {
+                "_id": {
+                    "$oid": "649b005f2ca5ee4adb139fb9"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "ctg_logsum": 214373,
+                "scaf_logsum": 215363,
+                "gap_pct": 0.00188,
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:deddd162bf0128fba13b3bc1ca38d1aa",
+                    "nmdc:b3573e3cda5a06611de71ca04c5c14cc",
+                    "nmdc:c6d0d4cea985ca6fb50a060e15b4a856",
+                    "nmdc:f450e3800e17691d5874c89fc46c186a",
+                    "nmdc:31dc958d116d02122509e90b0883954f"
+                ],
+                "asm_score": 6.577,
+                "was_informed_by": "gold:Gp0115663",
+                "ctg_powsum": 24284,
+                "scaf_max": 68135,
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "scaf_powsum": 24422,
+                "execution_resource": "NERSC-Cori",
+                "contigs": 169784,
+                "name": "Assembly Activity for nmdc:mga0h9dt75",
+                "ctg_max": 68135,
+                "gc_std": 0.11726,
+                "contig_bp": 83494920,
+                "gc_avg": 0.46001,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "scaf_bp": 83496490,
+                "type": "nmdc:MetagenomeAssembly",
+                "scaffolds": 169645,
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "ctg_l50": 470,
+                "ctg_l90": 290,
+                "ctg_n50": 45584,
+                "ctg_n90": 141996,
+                "scaf_l50": 470,
+                "scaf_l90": 290,
+                "scaf_n50": 45550,
+                "scaf_n90": 141870,
+                "scaf_l_gt50k": 68135,
+                "scaf_n_gt50k": 1,
+                "scaf_pct_gt50k": 0.08160224
+            }
+        ],
+        "omics_processing_set": [
+            {
+                "_id": {
+                    "$oid": "649b009773e8249959349b33"
+                },
+                "id": "nmdc:omprc-11-bn8jcq58",
+                "name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
+                "has_input": [
+                    "nmdc:bsm-11-qq8s6x03"
+                ],
+                "has_output": [
+                    "jgi:55d740280d8785342fcf7e39"
+                ],
+                "part_of": [
+                    "nmdc:sty-11-aygzgv51"
+                ],
+                "add_date": "2015-05-28",
+                "mod_date": "2021-06-15",
+                "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "omics_type": {
+                    "has_raw_value": "Metagenome"
+                },
+                "principal_investigator": {
+                    "has_raw_value": "James Stegen"
+                },
+                "processing_institution": "JGI",
+                "type": "nmdc:OmicsProcessing",
+                "gold_sequencing_project_identifiers": [
+                    "gold:Gp0115663"
+                ]
+            }
+        ],
+        "read_qc_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009d6bdd4fd20273c88b"
+                },
+                "has_input": [
+                    "nmdc:30a06664f29cffbbbc49abad86eae6fc"
+                ],
+                "part_of": [
+                    "nmdc:mga0h9dt75"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef",
+                    "nmdc:b99ce8adc125c95f0bfdadf36a3f6848"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "input_read_count": 32238374,
+                "output_read_bases": 4608772924,
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "input_read_bases": 4867994474,
+                "name": "Read QC Activity for nmdc:mga0h9dt75",
+                "output_read_count": 30774080,
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadQCAnalysisActivity",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ],
+        "read_based_taxonomy_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009bff710ae353f8cf4f"
+                },
+                "has_input": [
+                    "nmdc:7bf778baef033d36f118f8591256d6ef"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:bc7c1bda004aab357c8f6cf5a42242f9",
+                    "nmdc:9481434cadd0d6c154e2ec4c11ef0e04",
+                    "nmdc:6b5bc6ce7f11c1336a5f85a98fc18541",
+                    "nmdc:933c71bbc2f4a2e84d50f0d3864cf940",
+                    "nmdc:1a208e2519770ef50740ac39f1b9ba9a",
+                    "nmdc:f112a3840464ae7a9cf4a3bf295edd5c",
+                    "nmdc:7ca01ea379f0baed96f87d1435925f95",
+                    "nmdc:c85f2f2b4a518c4adb23970448a5cb45",
+                    "nmdc:94ee1bc2dc74830a21d5c3471d6cf223"
+                ],
+                "was_informed_by": "gold:Gp0115663",
+                "id": "nmdc:b31abf9d7fe53e2f802bb53e2d13542b",
+                "execution_resource": "NERSC-Cori",
+                "name": "ReadBased Analysis Activity for nmdc:mga0h9dt75",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "type": "nmdc:ReadbasedAnalysis",
+                "ended_at_time": "2021-10-11T04:56:04+00:00"
+            }
+        ]
+    }
+]
\ No newline at end of file

From dcda603c7f427a62fc20ce5b2ae88b6d8a128cdc Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 15 Nov 2023 09:59:05 -0800
Subject: [PATCH 62/91] local input files for dryrun

---
 .../assembly/nmdc_mga0h9dt75_assembly.agp     |    0
 .../assembly/nmdc_mga0h9dt75_contigs.fna      |    2 +
 .../assembly/nmdc_mga0h9dt75_covstats.txt     |    0
 .../assembly/nmdc_mga0h9dt75_scaffolds.fna    |    2 +
 .../data/dryrun_re_ided_record_dump.json      | 1015 ++---------------
 5 files changed, 91 insertions(+), 928 deletions(-)
 create mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_assembly.agp
 create mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna
 create mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_covstats.txt
 create mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna

diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_assembly.agp b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_assembly.agp
new file mode 100644
index 00000000..e69de29b
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna
new file mode 100644
index 00000000..aae2f9ae
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_contigs.fna
@@ -0,0 +1,2 @@
+>Contig_0001
+
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_covstats.txt b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_covstats.txt
new file mode 100644
index 00000000..e69de29b
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna
new file mode 100644
index 00000000..0f2c7e5b
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:mga0h9dt75/assembly/nmdc_mga0h9dt75_scaffolds.fna
@@ -0,0 +1,2 @@
+>sequenceID-001 description
+ACGT
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index 74e29a57..ad00210f 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -1,950 +1,193 @@
 [
     {
-        "functional_annotation_agg": [],
-        "library_preparation_set": [],
-        "processed_sample_set": [],
-        "extraction_set": [],
-        "activity_set": [],
-        "biosample_set": [],
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-bgp6z123",
+                "id": "nmdc:dobj-11-qadypq22",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
-                "alternative_identifiers": [],
                 "file_size_bytes": 2861414297,
-                "md5_checksum": null,
-                "data_object_type": null,
-                "compression_type": null,
-                "was_generated_by": null,
-                "url": null,
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-b20kzg40",
+                "id": "nmdc:dobj-11-r766y759",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
-                "alternative_identifiers": [],
                 "file_size_bytes": 2571324879,
                 "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
-                "data_object_type": {
-                    "_code": {
-                        "text": "Filtered Sequencing Reads",
-                        "description": "Reads QC result fastq (clean data)",
-                        "meaning": null,
-                        "unit": null,
-                        "is_a": null,
-                        "mixins": [],
-                        "extensions": {},
-                        "annotations": {},
-                        "alt_descriptions": {},
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-                        "todos": [],
-                        "notes": [],
-                        "comments": [],
-                        "examples": [],
-                        "in_subset": [],
-                        "from_schema": null,
-                        "imported_from": null,
-                        "source": null,
-                        "in_language": null,
-                        "see_also": [],
-                        "deprecated_element_has_exact_replacement": null,
-                        "deprecated_element_has_possible_replacement": null,
-                        "aliases": [],
-                        "structured_aliases": {},
-                        "mappings": [],
-                        "exact_mappings": [],
-                        "close_mappings": [],
-                        "related_mappings": [],
-                        "narrow_mappings": [],
-                        "broad_mappings": [],
-                        "created_by": null,
-                        "contributors": [],
-                        "created_on": null,
-                        "last_updated_on": null,
-                        "modified_by": null,
-                        "status": null,
-                        "rank": null,
-                        "categories": [],
-                        "keywords": []
-                    }
-                },
-                "compression_type": null,
-                "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-5sfwhy50/nmdc_wfrqc-11-5sfwhy50_filtered.fastq.gz",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-vap10912/nmdc_wfrqc-11-vap10912_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-mhccey92",
+                "id": "nmdc:dobj-11-k0bzwg32",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
-                "alternative_identifiers": [],
                 "file_size_bytes": 290,
                 "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
-                "data_object_type": {
-                    "_code": {
-                        "text": "QC Statistics",
-                        "description": "Reads QC summary statistics",
-                        "meaning": null,
-                        "unit": null,
-                        "is_a": null,
-                        "mixins": [],
-                        "extensions": {},
-                        "annotations": {},
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-                        "notes": [],
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-                        "examples": [],
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-                        "see_also": [],
-                        "deprecated_element_has_exact_replacement": null,
-                        "deprecated_element_has_possible_replacement": null,
-                        "aliases": [],
-                        "structured_aliases": {},
-                        "mappings": [],
-                        "exact_mappings": [],
-                        "close_mappings": [],
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-                        "narrow_mappings": [],
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-                        "rank": null,
-                        "categories": [],
-                        "keywords": []
-                    }
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-                "compression_type": null,
-                "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-5sfwhy50/nmdc_wfrqc-11-5sfwhy50_filterStats.txt",
+                "data_object_type": "QC Statistics",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-vap10912/nmdc_wfrqc-11-vap10912_filterStats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-b27rkd90",
+                "id": "nmdc:dobj-11-1dqfzb38",
                 "name": "Final assembly contigs fasta",
                 "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
-                "alternative_identifiers": [],
-                "file_size_bytes": 90794959,
-                "md5_checksum": "1a2ade31cf1edad5430ef0939d94ac43",
-                "data_object_type": {
-                    "_code": {
-                        "text": "Assembly Contigs",
-                        "description": "Final assembly contigs fasta",
-                        "meaning": null,
-                        "unit": null,
-                        "is_a": null,
-                        "mixins": [],
-                        "extensions": {},
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-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-xc17b248/nmdc_wfmgas-11-xc17b248_contigs.fna",
+                "file_size_bytes": 336,
+                "md5_checksum": "400d8dfa58189f35a3e754526470bf66",
+                "data_object_type": "Assembly Contigs",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_contigs.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-tcg9he98",
+                "id": "nmdc:dobj-11-9e1jhw75",
                 "name": "Final assembly scaffolds fasta",
                 "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
-                "alternative_identifiers": [],
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-                "md5_checksum": "642e3bae5809fa7a2f0be592e0693a10",
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-                        "mixins": [],
-                        "extensions": {},
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-                        "annotations": {},
-                        "alt_descriptions": {},
-                        "title": null,
-                        "deprecated": null,
-                        "todos": [],
-                        "notes": [],
-                        "comments": [],
-                        "examples": [],
-                        "in_subset": [],
-                        "from_schema": null,
-                        "imported_from": null,
-                        "source": null,
-                        "in_language": null,
-                        "see_also": [],
-                        "deprecated_element_has_exact_replacement": null,
-                        "deprecated_element_has_possible_replacement": null,
-                        "aliases": [],
-                        "structured_aliases": {},
-                        "mappings": [],
-                        "exact_mappings": [],
-                        "close_mappings": [],
-                        "related_mappings": [],
-                        "narrow_mappings": [],
-                        "broad_mappings": [],
-                        "created_by": null,
-                        "contributors": [],
-                        "created_on": null,
-                        "last_updated_on": null,
-                        "modified_by": null,
-                        "status": null,
-                        "rank": null,
-                        "categories": [],
-                        "keywords": []
-                    }
-                },
-                "compression_type": null,
-                "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_kraken2_classification.tsv",
+                "data_object_type": "Kraken2 Taxonomic Classification",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-sf23g974",
+                "id": "nmdc:dobj-11-1y04j389",
                 "name": "Kraken2 output report file",
                 "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
-                "alternative_identifiers": [],
                 "file_size_bytes": 699896,
                 "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
-                "data_object_type": {
-                    "_code": {
-                        "text": "Kraken2 Classification Report",
-                        "description": "Kraken2 output report file",
-                        "meaning": null,
-                        "unit": null,
-                        "is_a": null,
-                        "mixins": [],
-                        "extensions": {},
-                        "annotations": {},
-                        "alt_descriptions": {},
-                        "title": null,
-                        "deprecated": null,
-                        "todos": [],
-                        "notes": [],
-                        "comments": [],
-                        "examples": [],
-                        "in_subset": [],
-                        "from_schema": null,
-                        "imported_from": null,
-                        "source": null,
-                        "in_language": null,
-                        "see_also": [],
-                        "deprecated_element_has_exact_replacement": null,
-                        "deprecated_element_has_possible_replacement": null,
-                        "aliases": [],
-                        "structured_aliases": {},
-                        "mappings": [],
-                        "exact_mappings": [],
-                        "close_mappings": [],
-                        "related_mappings": [],
-                        "narrow_mappings": [],
-                        "broad_mappings": [],
-                        "created_by": null,
-                        "contributors": [],
-                        "created_on": null,
-                        "last_updated_on": null,
-                        "modified_by": null,
-                        "status": null,
-                        "rank": null,
-                        "categories": [],
-                        "keywords": []
-                    }
-                },
-                "compression_type": null,
-                "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_kraken2_report.tsv",
+                "data_object_type": "Kraken2 Classification Report",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-cn18ys57",
+                "id": "nmdc:dobj-11-0en1hj05",
                 "name": "Kraken2 Krona plot HTML file",
                 "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
-                "alternative_identifiers": [],
                 "file_size_bytes": 4221977,
                 "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
-                "data_object_type": {
-                    "_code": {
-                        "text": "Kraken2 Krona Plot",
-                        "description": "Kraken2 krona plot HTML file",
-                        "meaning": null,
-                        "unit": null,
-                        "is_a": null,
-                        "mixins": [],
-                        "extensions": {},
-                        "annotations": {},
-                        "alt_descriptions": {},
-                        "title": null,
-                        "deprecated": null,
-                        "todos": [],
-                        "notes": [],
-                        "comments": [],
-                        "examples": [],
-                        "in_subset": [],
-                        "from_schema": null,
-                        "imported_from": null,
-                        "source": null,
-                        "in_language": null,
-                        "see_also": [],
-                        "deprecated_element_has_exact_replacement": null,
-                        "deprecated_element_has_possible_replacement": null,
-                        "aliases": [],
-                        "structured_aliases": {},
-                        "mappings": [],
-                        "exact_mappings": [],
-                        "close_mappings": [],
-                        "related_mappings": [],
-                        "narrow_mappings": [],
-                        "broad_mappings": [],
-                        "created_by": null,
-                        "contributors": [],
-                        "created_on": null,
-                        "last_updated_on": null,
-                        "modified_by": null,
-                        "status": null,
-                        "rank": null,
-                        "categories": [],
-                        "keywords": []
-                    }
-                },
-                "compression_type": null,
-                "was_generated_by": null,
-                "url": "/global/cfs/cdirs/m3408/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-wy6fa249/nmdc_wfrbt-11-wy6fa249_kraken2_krona.html",
+                "data_object_type": "Kraken2 Krona Plot",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_krona.html",
                 "type": "nmdc:Data_Object"
             }
         ],
-        "dissolving_activity_set": [],
-        "functional_annotation_set": [],
-        "genome_feature_set": [],
-        "mags_activity_set": [],
-        "material_sample_set": [],
-        "material_sampling_activity_set": [],
-        "metabolomics_analysis_activity_set": [],
-        "metagenome_annotation_activity_set": [],
         "metagenome_assembly_set": [
             {
-                "id": "nmdc:wfmgas-11-xc17b248",
+                "id": "nmdc:wfmgas-11-7btyf478",
                 "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
                 "was_informed_by": "nmdc:omprc-11-bn8jcq58",
-                "used": null,
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/metaAssembly",
                 "has_input": [
-                    "nmdc:dobj-11-b20kzg40",
-                    "nmdc:dobj-11-mhccey92"
+                    "nmdc:dobj-11-r766y759",
+                    "nmdc:dobj-11-k0bzwg32"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-b27rkd90",
-                    "nmdc:dobj-11-tcg9he98",
-                    "nmdc:dobj-11-z5f6jq78",
-                    "nmdc:dobj-11-kv8gp304",
-                    "nmdc:dobj-11-xkzgxw24"
+                    "nmdc:dobj-11-1dqfzb38",
+                    "nmdc:dobj-11-9e1jhw75",
+                    "nmdc:dobj-11-7xk5gf96",
+                    "nmdc:dobj-11-w351h143",
+                    "nmdc:dobj-11-2jxf0086"
                 ],
                 "type": "nmdc:MetagenomeAssembly",
                 "part_of": [
@@ -975,129 +218,54 @@
                 "ctg_max": 68135,
                 "gap_pct": 0.00188,
                 "gc_std": 0.11726,
-                "gc_avg": 0.46001,
-                "num_input_reads": null,
-                "num_aligned_reads": null,
-                "insdc_assembly_identifiers": null
+                "gc_avg": 0.46001
             }
         ],
-        "metagenome_sequencing_activity_set": [],
-        "metaproteomics_analysis_activity_set": [],
-        "metatranscriptome_activity_set": [],
-        "nom_analysis_activity_set": [],
         "omics_processing_set": [
             {
                 "id": "nmdc:omprc-11-bn8jcq58",
                 "name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
                 "description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
-                "alternative_identifiers": [],
                 "has_input": [
                     "nmdc:bsm-11-qq8s6x03"
                 ],
                 "add_date": "2015-05-28",
-                "chimera_check": null,
                 "gold_sequencing_project_identifiers": [
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-bgp6z123"
+                    "nmdc:dobj-11-qadypq22"
                 ],
-                "insdc_experiment_identifiers": [],
-                "instrument_name": null,
                 "mod_date": "2021-06-15",
                 "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
-                "nucl_acid_amp": null,
-                "nucl_acid_ext": null,
                 "omics_type": {
-                    "has_raw_value": "Metagenome",
-                    "was_generated_by": null,
-                    "type": null,
-                    "term": null
+                    "has_raw_value": "Metagenome"
                 },
                 "part_of": [
                     "nmdc:sty-11-aygzgv51"
                 ],
-                "pcr_cond": null,
-                "pcr_primers": null,
                 "principal_investigator": {
-                    "has_raw_value": "James Stegen",
-                    "was_generated_by": null,
-                    "type": null,
-                    "orcid": null,
-                    "profile_image_url": null,
-                    "email": null,
-                    "name": null,
-                    "websites": []
+                    "has_raw_value": "James Stegen"
                 },
-                "processing_institution": {
-                    "_code": {
-                        "text": "JGI",
-                        "description": null,
-                        "meaning": null,
-                        "unit": null,
-                        "is_a": null,
-                        "mixins": [],
-                        "extensions": {},
-                        "annotations": {},
-                        "alt_descriptions": {},
-                        "title": null,
-                        "deprecated": null,
-                        "todos": [],
-                        "notes": [],
-                        "comments": [],
-                        "examples": [],
-                        "in_subset": [],
-                        "from_schema": null,
-                        "imported_from": null,
-                        "source": null,
-                        "in_language": null,
-                        "see_also": [],
-                        "deprecated_element_has_exact_replacement": null,
-                        "deprecated_element_has_possible_replacement": null,
-                        "aliases": [],
-                        "structured_aliases": {},
-                        "mappings": [],
-                        "exact_mappings": [],
-                        "close_mappings": [],
-                        "related_mappings": [],
-                        "narrow_mappings": [],
-                        "broad_mappings": [],
-                        "created_by": null,
-                        "contributors": [],
-                        "created_on": null,
-                        "last_updated_on": null,
-                        "modified_by": null,
-                        "status": null,
-                        "rank": null,
-                        "categories": [],
-                        "keywords": []
-                    }
-                },
-                "samp_vol_we_dna_ext": null,
-                "seq_meth": null,
-                "seq_quality_check": null,
-                "target_gene": null,
-                "target_subfragment": null,
+                "processing_institution": "JGI",
                 "type": "nmdc:OmicsProcessing"
             }
         ],
-        "reaction_activity_set": [],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-5sfwhy50",
+                "id": "nmdc:wfrqc-11-vap10912",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
                 "was_informed_by": "nmdc:omprc-11-bn8jcq58",
-                "used": null,
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-bgp6z123"
+                    "nmdc:dobj-11-qadypq22"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-b20kzg40",
-                    "nmdc:dobj-11-mhccey92"
+                    "nmdc:dobj-11-r766y759",
+                    "nmdc:dobj-11-k0bzwg32"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
@@ -1105,37 +273,34 @@
                 ],
                 "version": "v1.0.8",
                 "input_read_count": 32238374,
-                "input_base_count": null,
                 "output_read_count": 30774080,
-                "output_base_count": null,
                 "input_read_bases": 4867994474,
                 "output_read_bases": 4608772924
             }
         ],
         "read_based_taxonomy_analysis_activity_set": [
             {
-                "id": "nmdc:wfrbt-11-wy6fa249",
+                "id": "nmdc:wfrbt-11-k6swv922",
                 "name": "Readbased Taxonomy Analysis Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
                 "was_informed_by": "nmdc:omprc-11-bn8jcq58",
-                "used": null,
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
                 "has_input": [
-                    "nmdc:dobj-11-b20kzg40",
-                    "nmdc:dobj-11-mhccey92"
+                    "nmdc:dobj-11-r766y759",
+                    "nmdc:dobj-11-k0bzwg32"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-vw7fz645",
-                    "nmdc:dobj-11-bhnxqw16",
-                    "nmdc:dobj-11-hycy9b80",
-                    "nmdc:dobj-11-8prvd856",
-                    "nmdc:dobj-11-acryw383",
-                    "nmdc:dobj-11-f6j3wm49",
-                    "nmdc:dobj-11-xbn3d347",
-                    "nmdc:dobj-11-sf23g974",
-                    "nmdc:dobj-11-cn18ys57"
+                    "nmdc:dobj-11-101fqh28",
+                    "nmdc:dobj-11-a1vwvh45",
+                    "nmdc:dobj-11-28b66z83",
+                    "nmdc:dobj-11-bexrzt65",
+                    "nmdc:dobj-11-2ep63x87",
+                    "nmdc:dobj-11-jza95a63",
+                    "nmdc:dobj-11-a0babn50",
+                    "nmdc:dobj-11-1y04j389",
+                    "nmdc:dobj-11-0en1hj05"
                 ],
                 "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
                 "part_of": [
@@ -1143,12 +308,6 @@
                 ],
                 "version": "v1.0.5"
             }
-        ],
-        "study_set": [],
-        "field_research_site_set": [],
-        "collecting_biosamples_from_site_set": [],
-        "date_created": null,
-        "etl_software_version": null,
-        "pooling_set": []
+        ]
     }
 ]
\ No newline at end of file

From 22d0fac48e6c8c3a30b09759592ad36f350fa226 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Wed, 15 Nov 2023 11:11:03 -0800
Subject: [PATCH 63/91] fixed has_input for assembly and readbased

---
 nmdc_automation/re_iding/base.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index eff1de17..a6f9ae21 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -201,8 +201,8 @@ def update_metagenome_assembly_set(self, db_record: Dict,
         for assembly_rec in db_record[METAGENOME_ASSEMBLY_SET]:
             activity_type = "nmdc:MetagenomeAssembly"
             omics_processing_id = new_omics_processing.id
-            new_read_qc = new_db.read_qc_analysis_activity_set[0]
-            has_input = new_read_qc.has_output
+            has_input = [self._get_input_do_id(new_db, "Filtered Sequencing Reads")]
+            
             updated_has_output = []
             
             new_activity_id = self.api_client.minter(activity_type)
@@ -265,8 +265,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
             "read_based_taxonomy_analysis_activity_set"]:
             activity_type = "nmdc:ReadBasedTaxonomyAnalysisActivity"
             omics_processing_id = new_omics_processing.id
-            new_read_qc = new_db.read_qc_analysis_activity_set[0]
-            has_input = new_read_qc.has_output
+            has_input = [self._get_input_do_id(new_db, "Filtered Sequencing Reads")]
             
             new_activity_id = self.api_client.minter(activity_type)
             logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
@@ -311,6 +310,14 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
             new_db.read_based_taxonomy_analysis_activity_set.append(new_read_based)
 
         return new_db
+    
+    def _get_input_do_id(self, new_db, data_object_type: str):
+        """Returns the string representation of a data object id given data object type"""
+        
+        for rec in new_db.data_object_set:
+            print(type(rec.data_object_type))
+            if str(rec.data_object_type) == data_object_type:
+                return str(rec.id)        
 
     def _make_new_activity_set_object(self, omics_processing_id: str, new_activity_id: str,
             activity_set_rec: Dict, has_input: List,

From 6d3d81f6390716fda7c357e5ce2f946812431a0e Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Wed, 15 Nov 2023 11:11:24 -0800
Subject: [PATCH 64/91] updated has_inputs

---
 .../data/dryrun_re_ided_record_dump.json      | 118 +++++++++---------
 1 file changed, 58 insertions(+), 60 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index ad00210f..38b30ce3 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -2,176 +2,176 @@
     {
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-qadypq22",
+                "id": "nmdc:dobj-11-k18mgh67",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "file_size_bytes": 2861414297,
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-r766y759",
+                "id": "nmdc:dobj-11-40ms2n98",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2571324879,
                 "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
                 "data_object_type": "Filtered Sequencing Reads",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-vap10912/nmdc_wfrqc-11-vap10912_filtered.fastq.gz",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-7agz5x85/nmdc_wfrqc-11-7agz5x85_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-k0bzwg32",
+                "id": "nmdc:dobj-11-pz49a380",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 290,
                 "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
                 "data_object_type": "QC Statistics",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-vap10912/nmdc_wfrqc-11-vap10912_filterStats.txt",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-7agz5x85/nmdc_wfrqc-11-7agz5x85_filterStats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-1dqfzb38",
+                "id": "nmdc:dobj-11-s7hbx548",
                 "name": "Final assembly contigs fasta",
                 "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 336,
-                "md5_checksum": "400d8dfa58189f35a3e754526470bf66",
+                "md5_checksum": "1501f29ec969470773a42937d7050ee4",
                 "data_object_type": "Assembly Contigs",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_contigs.fna",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-wff05s57/nmdc_wfmgas-11-wff05s57_contigs.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-9e1jhw75",
+                "id": "nmdc:dobj-11-k4xtja04",
                 "name": "Final assembly scaffolds fasta",
                 "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 700,
-                "md5_checksum": "37c3fbca7955c4095feeada8325a2dc5",
+                "md5_checksum": "d9241051e6c263cf4cba013276fbce79",
                 "data_object_type": "Assembly Scaffolds",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_scaffolds.fna",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-wff05s57/nmdc_wfmgas-11-wff05s57_scaffolds.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-7xk5gf96",
+                "id": "nmdc:dobj-11-mn83rq32",
                 "name": "Assembled contigs coverage information",
                 "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly Coverage Stats",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_covstats.txt",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-wff05s57/nmdc_wfmgas-11-wff05s57_covstats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-w351h143",
+                "id": "nmdc:dobj-11-141yjx07",
                 "name": "An AGP format file that describes the assembly",
                 "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly AGP",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_assembly.agp",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-wff05s57/nmdc_wfmgas-11-wff05s57_assembly.agp",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-2jxf0086",
+                "id": "nmdc:dobj-11-gw706z78",
                 "name": "Sorted bam file of reads mapping back to the final assembly",
                 "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly Coverage BAM",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_pairedMapped_sorted.bam",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-wff05s57/nmdc_wfmgas-11-wff05s57_pairedMapped_sorted.bam",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-101fqh28",
+                "id": "nmdc:dobj-11-eb9w0c69",
                 "name": "GOTTCHA2 classification report file",
                 "description": "Gottcha2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 13174,
                 "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
                 "data_object_type": "GOTTCHA2 Classification Report",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_gottcha2_report.tsv",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_gottcha2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-a1vwvh45",
+                "id": "nmdc:dobj-11-wb0qzz63",
                 "name": "GOTTCHA2 report file",
                 "description": "Gottcha2 full TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 1035818,
                 "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
                 "data_object_type": "GOTTCHA2 Report Full",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_gottcha2_report_full.tsv",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_gottcha2_report_full.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-28b66z83",
+                "id": "nmdc:dobj-11-pnb7g686",
                 "name": "GOTTCHA2 krona plot HTML file",
                 "description": "Gottcha2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 262669,
                 "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
                 "data_object_type": "GOTTCHA2 Krona Plot",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_gottcha2_krona.html",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_gottcha2_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-bexrzt65",
+                "id": "nmdc:dobj-11-hfcn4m30",
                 "name": "Centrifuge output read classification file",
                 "description": "Centrifuge classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2189843623,
                 "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
                 "data_object_type": "Centrifuge Taxonomic Classification",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_centrifuge_classification.tsv",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_centrifuge_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-2ep63x87",
+                "id": "nmdc:dobj-11-e1y3vw77",
                 "name": "Centrifuge output report file",
                 "description": "Centrifuge TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 260134,
                 "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
                 "data_object_type": "Centrifuge Classification Report",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_centrifuge_report.tsv",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_centrifuge_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-jza95a63",
+                "id": "nmdc:dobj-11-6gt09871",
                 "name": "Centrifug krona plot HTML file",
                 "description": "Centrifuge Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2343980,
                 "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
                 "data_object_type": "Centrifuge Krona Plot",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_centrifuge_krona.html",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_centrifuge_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-a0babn50",
+                "id": "nmdc:dobj-11-1ytpbw47",
                 "name": "Kraken2 output read classification file",
                 "description": "Kraken classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 1785563917,
                 "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
                 "data_object_type": "Kraken2 Taxonomic Classification",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_classification.tsv",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_kraken2_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-1y04j389",
+                "id": "nmdc:dobj-11-1j604f63",
                 "name": "Kraken2 output report file",
                 "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 699896,
                 "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
                 "data_object_type": "Kraken2 Classification Report",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_report.tsv",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_kraken2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-0en1hj05",
+                "id": "nmdc:dobj-11-yjwsmg07",
                 "name": "Kraken2 Krona plot HTML file",
                 "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 4221977,
                 "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
                 "data_object_type": "Kraken2 Krona Plot",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_krona.html",
+                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-rvzhj731/nmdc_wfrbt-11-rvzhj731_kraken2_krona.html",
                 "type": "nmdc:Data_Object"
             }
         ],
         "metagenome_assembly_set": [
             {
-                "id": "nmdc:wfmgas-11-7btyf478",
+                "id": "nmdc:wfmgas-11-wff05s57",
                 "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -179,15 +179,14 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/metaAssembly",
                 "has_input": [
-                    "nmdc:dobj-11-r766y759",
-                    "nmdc:dobj-11-k0bzwg32"
+                    "nmdc:dobj-11-40ms2n98"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-1dqfzb38",
-                    "nmdc:dobj-11-9e1jhw75",
-                    "nmdc:dobj-11-7xk5gf96",
-                    "nmdc:dobj-11-w351h143",
-                    "nmdc:dobj-11-2jxf0086"
+                    "nmdc:dobj-11-s7hbx548",
+                    "nmdc:dobj-11-k4xtja04",
+                    "nmdc:dobj-11-mn83rq32",
+                    "nmdc:dobj-11-141yjx07",
+                    "nmdc:dobj-11-gw706z78"
                 ],
                 "type": "nmdc:MetagenomeAssembly",
                 "part_of": [
@@ -234,7 +233,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-qadypq22"
+                    "nmdc:dobj-11-k18mgh67"
                 ],
                 "mod_date": "2021-06-15",
                 "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
@@ -253,7 +252,7 @@
         ],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-vap10912",
+                "id": "nmdc:wfrqc-11-7agz5x85",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -261,11 +260,11 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-qadypq22"
+                    "nmdc:dobj-11-k18mgh67"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-r766y759",
-                    "nmdc:dobj-11-k0bzwg32"
+                    "nmdc:dobj-11-40ms2n98",
+                    "nmdc:dobj-11-pz49a380"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
@@ -280,7 +279,7 @@
         ],
         "read_based_taxonomy_analysis_activity_set": [
             {
-                "id": "nmdc:wfrbt-11-k6swv922",
+                "id": "nmdc:wfrbt-11-rvzhj731",
                 "name": "Readbased Taxonomy Analysis Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -288,19 +287,18 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
                 "has_input": [
-                    "nmdc:dobj-11-r766y759",
-                    "nmdc:dobj-11-k0bzwg32"
+                    "nmdc:dobj-11-40ms2n98"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-101fqh28",
-                    "nmdc:dobj-11-a1vwvh45",
-                    "nmdc:dobj-11-28b66z83",
-                    "nmdc:dobj-11-bexrzt65",
-                    "nmdc:dobj-11-2ep63x87",
-                    "nmdc:dobj-11-jza95a63",
-                    "nmdc:dobj-11-a0babn50",
-                    "nmdc:dobj-11-1y04j389",
-                    "nmdc:dobj-11-0en1hj05"
+                    "nmdc:dobj-11-eb9w0c69",
+                    "nmdc:dobj-11-wb0qzz63",
+                    "nmdc:dobj-11-pnb7g686",
+                    "nmdc:dobj-11-hfcn4m30",
+                    "nmdc:dobj-11-e1y3vw77",
+                    "nmdc:dobj-11-6gt09871",
+                    "nmdc:dobj-11-1ytpbw47",
+                    "nmdc:dobj-11-1j604f63",
+                    "nmdc:dobj-11-yjwsmg07"
                 ],
                 "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
                 "part_of": [

From eee1b50fd4f61092dcf6c8c66f7dd900ac266f51 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 15 Nov 2023 11:24:40 -0800
Subject: [PATCH 65/91] Update new data object URLs

---
 nmdc_automation/re_iding/base.py              |  29 +++--
 .../nmdc_wfmgas-11-3epd0s35_scaffolds.fna     |   2 +
 .../data/dryrun_re_ided_record_dump.json      | 120 +++++++++---------
 nmdc_automation/re_iding/tests/conftest.py    |  13 ++
 .../re_iding/tests/test_re_iding_base.py      |  26 +++-
 5 files changed, 114 insertions(+), 76 deletions(-)
 create mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index eff1de17..579bab3b 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -27,6 +27,7 @@
                                                 assembly_file_operations)
 
 NAPA_TEMPLATE = "../../../configs/re_iding_worklfows.yaml"
+DATA_BASE_URL = "https://data.microbiomedata.org/data"
 # BASE_DIR = "/global/cfs/cdirs/m3408/results"
 
 logging.basicConfig(
@@ -164,7 +165,7 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
                 old_do_rec["url"], new_readsqc_base_dir, new_activity_id, self.data_dir
                 )
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
-                new_do = self._make_new_data_object(
+                new_do = self.make_new_data_object(
                     omics_processing_id, activity_type, new_activity_id, old_do_rec,
                     data_object_type,
                 )
@@ -226,7 +227,7 @@ def update_metagenome_assembly_set(self, db_record: Dict,
                 #update md5 and file byte size in place to use _make_new_data_object function without functions
                 old_do_rec["file_size_bytes"] = updated_file_size
                 old_do_rec["md5_checksum"] = updated_md5
-                new_do = self._make_new_data_object(
+                new_do = self.make_new_data_object(
                     omics_processing_id, activity_type, new_activity_id, old_do_rec, data_object_type
                 )
                 # add new data object to new database and update has_output
@@ -286,7 +287,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
                 old_do_rec["url"], new_readbased_base_dir, new_activity_id, self.data_dir
                 )
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
-                new_do = self._make_new_data_object(
+                new_do = self.make_new_data_object(
                     omics_processing_id, activity_type, new_activity_id, old_do_rec, data_object_type
                 )
                 # add new data object to new database and update has_output
@@ -345,11 +346,11 @@ def _make_new_activity_set_object(self, omics_processing_id: str, new_activity_i
         )
         return activity
 
-    def _make_new_data_object(self, omics_processing_id: str,
-                              activity_type: str,
-                              new_activity_id: str,
-                              data_object_rec: Dict,
-                              data_object_type: str) -> NmdcDataObject:
+    def make_new_data_object(self, omics_processing_id: str,
+                             activity_type: str,
+                             new_activity_id: str,
+                             data_object_record: Dict,
+                             data_object_type: str) -> NmdcDataObject:
         """
         Return a new data object with updated IDs.
         """
@@ -357,14 +358,14 @@ def _make_new_data_object(self, omics_processing_id: str,
             activity_type, data_object_type
             )
         new_data_object_id = self.api_client.minter("nmdc:DataObject")
-        logger.info(f"nmdcDataObject\t{data_object_rec['id']}\t{new_data_object_id}")
+        logger.info(f"nmdcDataObject\t{data_object_record['id']}\t{new_data_object_id}")
         new_description = re.sub(
-            "[^ ]+$", f"{omics_processing_id}", data_object_rec["description"]
+            "[^ ]+$", f"{omics_processing_id}", data_object_record["description"]
         )
         logger.info(f"new_description: {new_description}")
-        new_filename = self._make_new_filename(new_activity_id, data_object_rec)
+        new_filename = self._make_new_filename(new_activity_id, data_object_record)
         logger.info(f"new_filename: {new_filename}")
-        new_url = (f"{self.data_dir}/{omics_processing_id}/{new_activity_id}"
+        new_url = (f"{DATA_BASE_URL}/{omics_processing_id}/{new_activity_id}"
                    f"/{new_filename}")
 
         data_object = NmdcDataObject(
@@ -372,8 +373,8 @@ def _make_new_data_object(self, omics_processing_id: str,
             name=template["name"].replace("{id}", omics_processing_id),
             description=new_description,
             type="nmdc:Data_Object",
-            file_size_bytes=data_object_rec["file_size_bytes"],
-            md5_checksum=data_object_rec["md5_checksum"],
+            file_size_bytes=data_object_record["file_size_bytes"],
+            md5_checksum=data_object_record["md5_checksum"],
             url=new_url,
             data_object_type=data_object_type,
             )
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna
new file mode 100644
index 00000000..93ef5e29
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna
@@ -0,0 +1,2 @@
+nmdc:wfmgas-11-3epd0s35>nmdc:wfmgas-11-3epd0s35snmdc:wfmgas-11-3epd0s35enmdc:wfmgas-11-3epd0s35qnmdc:wfmgas-11-3epd0s35unmdc:wfmgas-11-3epd0s35enmdc:wfmgas-11-3epd0s35nnmdc:wfmgas-11-3epd0s35cnmdc:wfmgas-11-3epd0s35enmdc:wfmgas-11-3epd0s35Inmdc:wfmgas-11-3epd0s35Dnmdc:wfmgas-11-3epd0s35-nmdc:wfmgas-11-3epd0s350nmdc:wfmgas-11-3epd0s350nmdc:wfmgas-11-3epd0s351nmdc:wfmgas-11-3epd0s35 nmdc:wfmgas-11-3epd0s35dnmdc:wfmgas-11-3epd0s35enmdc:wfmgas-11-3epd0s35snmdc:wfmgas-11-3epd0s35cnmdc:wfmgas-11-3epd0s35rnmdc:wfmgas-11-3epd0s35inmdc:wfmgas-11-3epd0s35pnmdc:wfmgas-11-3epd0s35tnmdc:wfmgas-11-3epd0s35inmdc:wfmgas-11-3epd0s35onmdc:wfmgas-11-3epd0s35nnmdc:wfmgas-11-3epd0s35
+nmdc:wfmgas-11-3epd0s35ACGT
diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index ad00210f..95d8bf1c 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -2,176 +2,176 @@
     {
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-qadypq22",
+                "id": "nmdc:dobj-11-y15shx96",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "file_size_bytes": 2861414297,
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-r766y759",
+                "id": "nmdc:dobj-11-26y4jr47",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2571324879,
                 "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
                 "data_object_type": "Filtered Sequencing Reads",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-vap10912/nmdc_wfrqc-11-vap10912_filtered.fastq.gz",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-nbsnr811/nmdc_wfrqc-11-nbsnr811_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-k0bzwg32",
+                "id": "nmdc:dobj-11-gf5yhj50",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 290,
                 "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
                 "data_object_type": "QC Statistics",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-vap10912/nmdc_wfrqc-11-vap10912_filterStats.txt",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-nbsnr811/nmdc_wfrqc-11-nbsnr811_filterStats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-1dqfzb38",
+                "id": "nmdc:dobj-11-wc9qnv48",
                 "name": "Final assembly contigs fasta",
                 "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 336,
-                "md5_checksum": "400d8dfa58189f35a3e754526470bf66",
+                "md5_checksum": "569e24922046a04cb49eeae4ac973c9d",
                 "data_object_type": "Assembly Contigs",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_contigs.fna",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_contigs.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-9e1jhw75",
+                "id": "nmdc:dobj-11-97rsby06",
                 "name": "Final assembly scaffolds fasta",
                 "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 700,
-                "md5_checksum": "37c3fbca7955c4095feeada8325a2dc5",
+                "md5_checksum": "4d0838d90aa7dec33f463c0d9a9148fe",
                 "data_object_type": "Assembly Scaffolds",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_scaffolds.fna",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-7xk5gf96",
+                "id": "nmdc:dobj-11-2740a986",
                 "name": "Assembled contigs coverage information",
                 "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly Coverage Stats",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_covstats.txt",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_covstats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-w351h143",
+                "id": "nmdc:dobj-11-yad0hz45",
                 "name": "An AGP format file that describes the assembly",
                 "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly AGP",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_assembly.agp",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_assembly.agp",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-2jxf0086",
+                "id": "nmdc:dobj-11-0yrnp384",
                 "name": "Sorted bam file of reads mapping back to the final assembly",
                 "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly Coverage BAM",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-7btyf478/nmdc_wfmgas-11-7btyf478_pairedMapped_sorted.bam",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_pairedMapped_sorted.bam",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-101fqh28",
+                "id": "nmdc:dobj-11-jrh4wg24",
                 "name": "GOTTCHA2 classification report file",
                 "description": "Gottcha2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 13174,
                 "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
                 "data_object_type": "GOTTCHA2 Classification Report",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_gottcha2_report.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_gottcha2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-a1vwvh45",
+                "id": "nmdc:dobj-11-j9dwnq42",
                 "name": "GOTTCHA2 report file",
                 "description": "Gottcha2 full TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 1035818,
                 "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
                 "data_object_type": "GOTTCHA2 Report Full",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_gottcha2_report_full.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_gottcha2_report_full.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-28b66z83",
+                "id": "nmdc:dobj-11-x0gyg366",
                 "name": "GOTTCHA2 krona plot HTML file",
                 "description": "Gottcha2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 262669,
                 "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
                 "data_object_type": "GOTTCHA2 Krona Plot",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_gottcha2_krona.html",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_gottcha2_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-bexrzt65",
+                "id": "nmdc:dobj-11-snpybq20",
                 "name": "Centrifuge output read classification file",
                 "description": "Centrifuge classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2189843623,
                 "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
                 "data_object_type": "Centrifuge Taxonomic Classification",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_centrifuge_classification.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_centrifuge_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-2ep63x87",
+                "id": "nmdc:dobj-11-gf3mxy83",
                 "name": "Centrifuge output report file",
                 "description": "Centrifuge TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 260134,
                 "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
                 "data_object_type": "Centrifuge Classification Report",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_centrifuge_report.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_centrifuge_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-jza95a63",
+                "id": "nmdc:dobj-11-8tg86t47",
                 "name": "Centrifug krona plot HTML file",
                 "description": "Centrifuge Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2343980,
                 "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
                 "data_object_type": "Centrifuge Krona Plot",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_centrifuge_krona.html",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_centrifuge_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-a0babn50",
+                "id": "nmdc:dobj-11-2xpzrv62",
                 "name": "Kraken2 output read classification file",
                 "description": "Kraken classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 1785563917,
                 "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
                 "data_object_type": "Kraken2 Taxonomic Classification",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_classification.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_kraken2_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-1y04j389",
+                "id": "nmdc:dobj-11-qspth853",
                 "name": "Kraken2 output report file",
                 "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 699896,
                 "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
                 "data_object_type": "Kraken2 Classification Report",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_report.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_kraken2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-0en1hj05",
+                "id": "nmdc:dobj-11-9msdy424",
                 "name": "Kraken2 Krona plot HTML file",
                 "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 4221977,
                 "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
                 "data_object_type": "Kraken2 Krona Plot",
-                "url": "./data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-k6swv922/nmdc_wfrbt-11-k6swv922_kraken2_krona.html",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_kraken2_krona.html",
                 "type": "nmdc:Data_Object"
             }
         ],
         "metagenome_assembly_set": [
             {
-                "id": "nmdc:wfmgas-11-7btyf478",
+                "id": "nmdc:wfmgas-11-3epd0s35",
                 "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -179,15 +179,15 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/metaAssembly",
                 "has_input": [
-                    "nmdc:dobj-11-r766y759",
-                    "nmdc:dobj-11-k0bzwg32"
+                    "nmdc:dobj-11-26y4jr47",
+                    "nmdc:dobj-11-gf5yhj50"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-1dqfzb38",
-                    "nmdc:dobj-11-9e1jhw75",
-                    "nmdc:dobj-11-7xk5gf96",
-                    "nmdc:dobj-11-w351h143",
-                    "nmdc:dobj-11-2jxf0086"
+                    "nmdc:dobj-11-wc9qnv48",
+                    "nmdc:dobj-11-97rsby06",
+                    "nmdc:dobj-11-2740a986",
+                    "nmdc:dobj-11-yad0hz45",
+                    "nmdc:dobj-11-0yrnp384"
                 ],
                 "type": "nmdc:MetagenomeAssembly",
                 "part_of": [
@@ -234,7 +234,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-qadypq22"
+                    "nmdc:dobj-11-y15shx96"
                 ],
                 "mod_date": "2021-06-15",
                 "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
@@ -253,7 +253,7 @@
         ],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-vap10912",
+                "id": "nmdc:wfrqc-11-nbsnr811",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -261,11 +261,11 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-qadypq22"
+                    "nmdc:dobj-11-y15shx96"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-r766y759",
-                    "nmdc:dobj-11-k0bzwg32"
+                    "nmdc:dobj-11-26y4jr47",
+                    "nmdc:dobj-11-gf5yhj50"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
@@ -280,7 +280,7 @@
         ],
         "read_based_taxonomy_analysis_activity_set": [
             {
-                "id": "nmdc:wfrbt-11-k6swv922",
+                "id": "nmdc:wfrbt-11-e30a2d23",
                 "name": "Readbased Taxonomy Analysis Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -288,19 +288,19 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
                 "has_input": [
-                    "nmdc:dobj-11-r766y759",
-                    "nmdc:dobj-11-k0bzwg32"
+                    "nmdc:dobj-11-26y4jr47",
+                    "nmdc:dobj-11-gf5yhj50"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-101fqh28",
-                    "nmdc:dobj-11-a1vwvh45",
-                    "nmdc:dobj-11-28b66z83",
-                    "nmdc:dobj-11-bexrzt65",
-                    "nmdc:dobj-11-2ep63x87",
-                    "nmdc:dobj-11-jza95a63",
-                    "nmdc:dobj-11-a0babn50",
-                    "nmdc:dobj-11-1y04j389",
-                    "nmdc:dobj-11-0en1hj05"
+                    "nmdc:dobj-11-jrh4wg24",
+                    "nmdc:dobj-11-j9dwnq42",
+                    "nmdc:dobj-11-x0gyg366",
+                    "nmdc:dobj-11-snpybq20",
+                    "nmdc:dobj-11-gf3mxy83",
+                    "nmdc:dobj-11-8tg86t47",
+                    "nmdc:dobj-11-2xpzrv62",
+                    "nmdc:dobj-11-qspth853",
+                    "nmdc:dobj-11-9msdy424"
                 ],
                 "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
                 "part_of": [
diff --git a/nmdc_automation/re_iding/tests/conftest.py b/nmdc_automation/re_iding/tests/conftest.py
index 341ac2bc..8141f20f 100644
--- a/nmdc_automation/re_iding/tests/conftest.py
+++ b/nmdc_automation/re_iding/tests/conftest.py
@@ -9,3 +9,16 @@ def db_record():
     """Return a dict of a test Database instance"""
     with open(TEST_DATA_DIR / "db_record.json", "r") as f:
         return json.load(f)
+
+@pytest.fixture
+def data_object_record():
+    """Return a dict of a test DataObject instance"""
+    return     {
+                "name": "Gp0115663_Filtered Reads",
+                "description": "Filtered Reads for Gp0115663",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0h9dt75/qa/nmdc_mga0h9dt75_filtered.fastq.gz",
+                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                "id": "nmdc:7bf778baef033d36f118f8591256d6ef",
+                "file_size_bytes": 2571324879
+            }
diff --git a/nmdc_automation/re_iding/tests/test_re_iding_base.py b/nmdc_automation/re_iding/tests/test_re_iding_base.py
index 2459fc37..53cca23f 100644
--- a/nmdc_automation/re_iding/tests/test_re_iding_base.py
+++ b/nmdc_automation/re_iding/tests/test_re_iding_base.py
@@ -1,12 +1,14 @@
 # nmdc_automation/re_iding/tests/test_re_iding_base.py
+from pathlib import Path
 import pytest_mock
 
 from nmdc_automation.api import NmdcRuntimeApi
 from nmdc_schema.nmdc import Database as NmdcDatabase
+from nmdc_schema.nmdc import DataObject as NmdcDataObject
 from nmdc_automation.re_iding.base import ReIdTool
 
 
-
+TEST_DATAFILE_DIR = "./test_data/results"
 
 def test_update_omics_processing_has_output(db_record, mocker):
     """
@@ -16,7 +18,7 @@ def test_update_omics_processing_has_output(db_record, mocker):
     exp_do_id = "nmdc:dobj-1234-abcd12345"
     mock_api = mocker.Mock(spec=NmdcRuntimeApi)
     mock_api.minter.return_value = exp_do_id
-    reid_tool = ReIdTool(mock_api)
+    reid_tool = ReIdTool(mock_api, TEST_DATAFILE_DIR)
     new_db = NmdcDatabase()
     new_db = reid_tool.update_omics_processing_has_output(db_record, new_db)
     assert isinstance(new_db, NmdcDatabase)
@@ -25,3 +27,23 @@ def test_update_omics_processing_has_output(db_record, mocker):
     assert new_db.omics_processing_set[0].has_output[0] == exp_do_id
 
 
+def test_make_new_data_object(data_object_record, mocker):
+    """
+    Test that we can make a new DataObject with a new ID and correct
+    URL and Path attributes.
+    """
+    exp_do_id = "nmdc:dobj-1234-abcd12345"
+    exp_url = 'https://data.microbiomedata.org/data/nmdc:omics_processing-1234-abcd12345/nmdc:activity-1234-abcd12345/nmdc_activity-1234-abcd12345_filtered.fastq.gz'
+    mock_api = mocker.Mock(spec=NmdcRuntimeApi)
+    mock_api.minter.return_value = exp_do_id
+    reid_tool = ReIdTool(mock_api, TEST_DATAFILE_DIR)
+    new_do = reid_tool.make_new_data_object(
+        omics_processing_id="nmdc:omics_processing-1234-abcd12345",
+        activity_type="nmdc:ReadQcAnalysisActivity",
+        new_activity_id="nmdc:activity-1234-abcd12345",
+        data_object_record=data_object_record,
+        data_object_type="Filtered Sequencing Reads",
+    )
+    assert isinstance(new_do, NmdcDataObject)
+    assert new_do.id == exp_do_id
+    assert new_do.url == exp_url

From 0b32b071cdc1aa69434c4c7b7fe42cde22782579 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 15 Nov 2023 11:27:47 -0800
Subject: [PATCH 66/91] updated processed dry run output

---
 .../data/dryrun_re_ided_record_dump.json      | 118 +++++++++---------
 1 file changed, 58 insertions(+), 60 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index 95d8bf1c..4972881a 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -2,176 +2,176 @@
     {
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-y15shx96",
+                "id": "nmdc:dobj-11-y134xn31",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "file_size_bytes": 2861414297,
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-26y4jr47",
+                "id": "nmdc:dobj-11-dz3wvm61",
                 "name": "Reads QC result fastq (clean data)",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2571324879,
                 "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
                 "data_object_type": "Filtered Sequencing Reads",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-nbsnr811/nmdc_wfrqc-11-nbsnr811_filtered.fastq.gz",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-8nssbh35/nmdc_wfrqc-11-8nssbh35_filtered.fastq.gz",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-gf5yhj50",
+                "id": "nmdc:dobj-11-1pp19646",
                 "name": "Reads QC summary statistics",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 290,
                 "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
                 "data_object_type": "QC Statistics",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-nbsnr811/nmdc_wfrqc-11-nbsnr811_filterStats.txt",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-8nssbh35/nmdc_wfrqc-11-8nssbh35_filterStats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-wc9qnv48",
+                "id": "nmdc:dobj-11-vfk56697",
                 "name": "Final assembly contigs fasta",
                 "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 336,
-                "md5_checksum": "569e24922046a04cb49eeae4ac973c9d",
+                "md5_checksum": "d4c4941391714c4d337bdf3444b2f108",
                 "data_object_type": "Assembly Contigs",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_contigs.fna",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_contigs.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-97rsby06",
+                "id": "nmdc:dobj-11-pdqkv709",
                 "name": "Final assembly scaffolds fasta",
                 "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 700,
-                "md5_checksum": "4d0838d90aa7dec33f463c0d9a9148fe",
+                "md5_checksum": "a57129f6b1ac8b75a42f4ab610b4c20a",
                 "data_object_type": "Assembly Scaffolds",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_scaffolds.fna",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-2740a986",
+                "id": "nmdc:dobj-11-ry36ec34",
                 "name": "Assembled contigs coverage information",
                 "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly Coverage Stats",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_covstats.txt",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_covstats.txt",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-yad0hz45",
+                "id": "nmdc:dobj-11-v2dcgb32",
                 "name": "An AGP format file that describes the assembly",
                 "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly AGP",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_assembly.agp",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_assembly.agp",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-0yrnp384",
+                "id": "nmdc:dobj-11-7f8z6a09",
                 "name": "Sorted bam file of reads mapping back to the final assembly",
                 "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly Coverage BAM",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_pairedMapped_sorted.bam",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_pairedMapped_sorted.bam",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-jrh4wg24",
+                "id": "nmdc:dobj-11-7q03xt64",
                 "name": "GOTTCHA2 classification report file",
                 "description": "Gottcha2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 13174,
                 "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
                 "data_object_type": "GOTTCHA2 Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_gottcha2_report.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_gottcha2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-j9dwnq42",
+                "id": "nmdc:dobj-11-qd17za87",
                 "name": "GOTTCHA2 report file",
                 "description": "Gottcha2 full TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 1035818,
                 "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
                 "data_object_type": "GOTTCHA2 Report Full",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_gottcha2_report_full.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_gottcha2_report_full.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-x0gyg366",
+                "id": "nmdc:dobj-11-f0pzg444",
                 "name": "GOTTCHA2 krona plot HTML file",
                 "description": "Gottcha2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 262669,
                 "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
                 "data_object_type": "GOTTCHA2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_gottcha2_krona.html",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_gottcha2_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-snpybq20",
+                "id": "nmdc:dobj-11-kmysd345",
                 "name": "Centrifuge output read classification file",
                 "description": "Centrifuge classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2189843623,
                 "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
                 "data_object_type": "Centrifuge Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_centrifuge_classification.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_centrifuge_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-gf3mxy83",
+                "id": "nmdc:dobj-11-mgdfaj98",
                 "name": "Centrifuge output report file",
                 "description": "Centrifuge TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 260134,
                 "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
                 "data_object_type": "Centrifuge Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_centrifuge_report.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_centrifuge_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-8tg86t47",
+                "id": "nmdc:dobj-11-g38md352",
                 "name": "Centrifug krona plot HTML file",
                 "description": "Centrifuge Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2343980,
                 "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
                 "data_object_type": "Centrifuge Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_centrifuge_krona.html",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_centrifuge_krona.html",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-2xpzrv62",
+                "id": "nmdc:dobj-11-d67rkh18",
                 "name": "Kraken2 output read classification file",
                 "description": "Kraken classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 1785563917,
                 "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
                 "data_object_type": "Kraken2 Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_kraken2_classification.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_kraken2_classification.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-qspth853",
+                "id": "nmdc:dobj-11-ptchwj55",
                 "name": "Kraken2 output report file",
                 "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 699896,
                 "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
                 "data_object_type": "Kraken2 Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_kraken2_report.tsv",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_kraken2_report.tsv",
                 "type": "nmdc:Data_Object"
             },
             {
-                "id": "nmdc:dobj-11-9msdy424",
+                "id": "nmdc:dobj-11-d0qt9513",
                 "name": "Kraken2 Krona plot HTML file",
                 "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 4221977,
                 "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
                 "data_object_type": "Kraken2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e30a2d23/nmdc_wfrbt-11-e30a2d23_kraken2_krona.html",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_kraken2_krona.html",
                 "type": "nmdc:Data_Object"
             }
         ],
         "metagenome_assembly_set": [
             {
-                "id": "nmdc:wfmgas-11-3epd0s35",
+                "id": "nmdc:wfmgas-11-ryns7t13",
                 "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -179,15 +179,14 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/metaAssembly",
                 "has_input": [
-                    "nmdc:dobj-11-26y4jr47",
-                    "nmdc:dobj-11-gf5yhj50"
+                    "nmdc:dobj-11-dz3wvm61"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-wc9qnv48",
-                    "nmdc:dobj-11-97rsby06",
-                    "nmdc:dobj-11-2740a986",
-                    "nmdc:dobj-11-yad0hz45",
-                    "nmdc:dobj-11-0yrnp384"
+                    "nmdc:dobj-11-vfk56697",
+                    "nmdc:dobj-11-pdqkv709",
+                    "nmdc:dobj-11-ry36ec34",
+                    "nmdc:dobj-11-v2dcgb32",
+                    "nmdc:dobj-11-7f8z6a09"
                 ],
                 "type": "nmdc:MetagenomeAssembly",
                 "part_of": [
@@ -234,7 +233,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-y15shx96"
+                    "nmdc:dobj-11-y134xn31"
                 ],
                 "mod_date": "2021-06-15",
                 "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
@@ -253,7 +252,7 @@
         ],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-nbsnr811",
+                "id": "nmdc:wfrqc-11-8nssbh35",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -261,11 +260,11 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-y15shx96"
+                    "nmdc:dobj-11-y134xn31"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-26y4jr47",
-                    "nmdc:dobj-11-gf5yhj50"
+                    "nmdc:dobj-11-dz3wvm61",
+                    "nmdc:dobj-11-1pp19646"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
@@ -280,7 +279,7 @@
         ],
         "read_based_taxonomy_analysis_activity_set": [
             {
-                "id": "nmdc:wfrbt-11-e30a2d23",
+                "id": "nmdc:wfrbt-11-mxr19q91",
                 "name": "Readbased Taxonomy Analysis Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
@@ -288,19 +287,18 @@
                 "execution_resource": "NERSC - Perlmutter",
                 "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
                 "has_input": [
-                    "nmdc:dobj-11-26y4jr47",
-                    "nmdc:dobj-11-gf5yhj50"
+                    "nmdc:dobj-11-dz3wvm61"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-jrh4wg24",
-                    "nmdc:dobj-11-j9dwnq42",
-                    "nmdc:dobj-11-x0gyg366",
-                    "nmdc:dobj-11-snpybq20",
-                    "nmdc:dobj-11-gf3mxy83",
-                    "nmdc:dobj-11-8tg86t47",
-                    "nmdc:dobj-11-2xpzrv62",
-                    "nmdc:dobj-11-qspth853",
-                    "nmdc:dobj-11-9msdy424"
+                    "nmdc:dobj-11-7q03xt64",
+                    "nmdc:dobj-11-qd17za87",
+                    "nmdc:dobj-11-f0pzg444",
+                    "nmdc:dobj-11-kmysd345",
+                    "nmdc:dobj-11-mgdfaj98",
+                    "nmdc:dobj-11-g38md352",
+                    "nmdc:dobj-11-d67rkh18",
+                    "nmdc:dobj-11-ptchwj55",
+                    "nmdc:dobj-11-d0qt9513"
                 ],
                 "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
                 "part_of": [

From 609d71c1afa9b3487b93fc85a396ef93a51e2a9f Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 15 Nov 2023 12:51:37 -0800
Subject: [PATCH 67/91] extracted workflow records for Gs0114675
 sty-11-8ft6t785

---
 ...ty-11-8fb6t785_associated_record_dump.json | 26756 ++++++++++++++++
 1 file changed, 26756 insertions(+)
 create mode 100644 nmdc_automation/re_iding/scripts/data/nmdc:sty-11-8fb6t785_associated_record_dump.json

diff --git a/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-8fb6t785_associated_record_dump.json b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-8fb6t785_associated_record_dump.json
new file mode 100644
index 00000000..bb91c6e2
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-8fb6t785_associated_record_dump.json
@@ -0,0 +1,26756 @@
+[
+    {
+        "data_object_set": [
+            {
+                "description": "Raw sequencer read data",
+                "file_size_bytes": 4551741658,
+                "type": "nmdc:DataObject",
+                "id": "jgi:560df5b90d878540fd6fe202",
+                "name": "9567.8.137569.TAGGCAT-AGAGTAG.fastq.gz"
+            },
+            {
+                "name": "Gp0119849_Filtered Reads",
+                "description": "Filtered Reads for Gp0119849",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/qa/nmdc_mga0jfwq54_filtered.fastq.gz",
+                "md5_checksum": "f57b6f3aeda36484319fb9c345cfe600",
+                "id": "nmdc:f57b6f3aeda36484319fb9c345cfe600",
+                "file_size_bytes": 2421790995
+            },
+            {
+                "name": "Gp0119849_Filtered Stats",
+                "description": "Filtered Stats for Gp0119849",
+                "data_object_type": "QC Statistics",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/qa/nmdc_mga0jfwq54_filterStats.txt",
+                "md5_checksum": "a87566efafce97a9e99a3bb94e42b56c",
+                "id": "nmdc:a87566efafce97a9e99a3bb94e42b56c",
+                "file_size_bytes": 287
+            },
+            {
+                "name": "Gp0119849_Gottcha2 TSV report",
+                "description": "Gottcha2 TSV report for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_gottcha2_report.tsv",
+                "md5_checksum": "d33b8adac7c87df1a1706daae4aac29b",
+                "id": "nmdc:d33b8adac7c87df1a1706daae4aac29b",
+                "file_size_bytes": 6758
+            },
+            {
+                "name": "Gp0119849_Gottcha2 full TSV report",
+                "description": "Gottcha2 full TSV report for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_gottcha2_report_full.tsv",
+                "md5_checksum": "690ccd842d80dbd79294fd8efd7df668",
+                "id": "nmdc:690ccd842d80dbd79294fd8efd7df668",
+                "file_size_bytes": 289728
+            },
+            {
+                "name": "Gp0119849_Gottcha2 Krona HTML report",
+                "description": "Gottcha2 Krona HTML report for Gp0119849",
+                "data_object_type": "GOTTCHA2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_gottcha2_krona.html",
+                "md5_checksum": "d585fce17e6c7badda857c559faf9723",
+                "id": "nmdc:d585fce17e6c7badda857c559faf9723",
+                "file_size_bytes": 247651
+            },
+            {
+                "name": "Gp0119849_Centrifuge classification TSV report",
+                "description": "Centrifuge classification TSV report for Gp0119849",
+                "data_object_type": "Centrifuge Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_centrifuge_classification.tsv",
+                "md5_checksum": "3dd3d00f873c18b2e59b839ead67c778",
+                "id": "nmdc:3dd3d00f873c18b2e59b839ead67c778",
+                "file_size_bytes": 4801736282
+            },
+            {
+                "name": "Gp0119849_Centrifuge TSV report",
+                "description": "Centrifuge TSV report for Gp0119849",
+                "data_object_type": "Centrifuge Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_centrifuge_report.tsv",
+                "md5_checksum": "383e7886c9b93ecbf98bdd815ebe9f79",
+                "id": "nmdc:383e7886c9b93ecbf98bdd815ebe9f79",
+                "file_size_bytes": 209076
+            },
+            {
+                "name": "Gp0119849_Centrifuge Krona HTML report",
+                "description": "Centrifuge Krona HTML report for Gp0119849",
+                "data_object_type": "Centrifuge Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_centrifuge_krona.html",
+                "md5_checksum": "c543c400f77bd8e08636116c3a4681d6",
+                "id": "nmdc:c543c400f77bd8e08636116c3a4681d6",
+                "file_size_bytes": 2126517
+            },
+            {
+                "name": "Gp0119849_Kraken classification TSV report",
+                "description": "Kraken classification TSV report for Gp0119849",
+                "data_object_type": "Kraken2 Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_kraken2_classification.tsv",
+                "md5_checksum": "240a6e819568135189afedbc52a9f9f3",
+                "id": "nmdc:240a6e819568135189afedbc52a9f9f3",
+                "file_size_bytes": 3182616049
+            },
+            {
+                "name": "Gp0119849_Kraken2 TSV report",
+                "description": "Kraken2 TSV report for Gp0119849",
+                "data_object_type": "Kraken2 Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_kraken2_report.tsv",
+                "md5_checksum": "29445394b66469bbfd6972fae3b7be2a",
+                "id": "nmdc:29445394b66469bbfd6972fae3b7be2a",
+                "file_size_bytes": 443336
+            },
+            {
+                "name": "Gp0119849_Kraken2 Krona HTML report",
+                "description": "Kraken2 Krona HTML report for Gp0119849",
+                "data_object_type": "Kraken2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/ReadbasedAnalysis/nmdc_mga0jfwq54_kraken2_krona.html",
+                "md5_checksum": "b2b6fa1385acdad8f0827b029540a6c9",
+                "id": "nmdc:b2b6fa1385acdad8f0827b029540a6c9",
+                "file_size_bytes": 2949989
+            },
+            {
+                "name": "Gp0119849_Assembled contigs fasta",
+                "description": "Assembled contigs fasta for Gp0119849",
+                "data_object_type": "Assembly Contigs",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/assembly/nmdc_mga0jfwq54_contigs.fna",
+                "md5_checksum": "44b3fa54ba0cb93a37ed626b21354508",
+                "id": "nmdc:44b3fa54ba0cb93a37ed626b21354508",
+                "file_size_bytes": 15053260
+            },
+            {
+                "name": "Gp0119849_Assembled scaffold fasta",
+                "description": "Assembled scaffold fasta for Gp0119849",
+                "data_object_type": "Assembly Scaffolds",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/assembly/nmdc_mga0jfwq54_scaffolds.fna",
+                "md5_checksum": "e2a3484c735353d5e6d5b13c333bbeac",
+                "id": "nmdc:e2a3484c735353d5e6d5b13c333bbeac",
+                "file_size_bytes": 15014354
+            },
+            {
+                "name": "Gp0119849_Metagenome Contig Coverage Stats",
+                "description": "Metagenome Contig Coverage Stats for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/assembly/nmdc_mga0jfwq54_covstats.txt",
+                "md5_checksum": "59faa6c9e3228b3d7c7d1b80dc2ec9e3",
+                "id": "nmdc:59faa6c9e3228b3d7c7d1b80dc2ec9e3",
+                "file_size_bytes": 996899
+            },
+            {
+                "name": "Gp0119849_Assembled AGP file",
+                "description": "Assembled AGP file for Gp0119849",
+                "data_object_type": "Assembly AGP",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/assembly/nmdc_mga0jfwq54_assembly.agp",
+                "md5_checksum": "dcad1c15a762628715a1316e84badbbc",
+                "id": "nmdc:dcad1c15a762628715a1316e84badbbc",
+                "file_size_bytes": 914847
+            },
+            {
+                "name": "Gp0119849_Metagenome Alignment BAM file",
+                "description": "Metagenome Alignment BAM file for Gp0119849",
+                "data_object_type": "Assembly Coverage BAM",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/assembly/nmdc_mga0jfwq54_pairedMapped_sorted.bam",
+                "md5_checksum": "d712cc8ba2e860e2c7d6ed01305d875c",
+                "id": "nmdc:d712cc8ba2e860e2c7d6ed01305d875c",
+                "file_size_bytes": 3127591529
+            },
+            {
+                "name": "Gp0119849_Protein FAA",
+                "description": "Protein FAA for Gp0119849",
+                "data_object_type": "Annotation Amino Acid FASTA",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_proteins.faa",
+                "md5_checksum": "1ea616c9664276341a688252337ae0bf",
+                "id": "nmdc:1ea616c9664276341a688252337ae0bf",
+                "file_size_bytes": 7347943
+            },
+            {
+                "name": "Gp0119849_Structural annotation GFF file",
+                "description": "Structural annotation GFF file for Gp0119849",
+                "data_object_type": "Structural Annotation GFF",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_structural_annotation.gff",
+                "md5_checksum": "7314a7d70ba0f72dfafa856ef51ff77d",
+                "id": "nmdc:7314a7d70ba0f72dfafa856ef51ff77d",
+                "file_size_bytes": 2500
+            },
+            {
+                "name": "Gp0119849_Functional annotation GFF file",
+                "description": "Functional annotation GFF file for Gp0119849",
+                "data_object_type": "Functional Annotation GFF",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_functional_annotation.gff",
+                "md5_checksum": "4084daf80dc14c7a5d14fe387631ee68",
+                "id": "nmdc:4084daf80dc14c7a5d14fe387631ee68",
+                "file_size_bytes": 7323096
+            },
+            {
+                "name": "Gp0119849_KO TSV file",
+                "description": "KO TSV file for Gp0119849",
+                "data_object_type": "Annotation KEGG Orthology",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_ko.tsv",
+                "md5_checksum": "1d975322e1053cf6dc28c68557834f75",
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+            },
+            {
+                "name": "Gp0119849_EC TSV file",
+                "description": "EC TSV file for Gp0119849",
+                "data_object_type": "Annotation Enzyme Commission",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_ec.tsv",
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+            },
+            {
+                "name": "Gp0119849_COG GFF file",
+                "description": "COG GFF file for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_cog.gff",
+                "md5_checksum": "07cb4835969e2165d1b929e0350616a0",
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+            },
+            {
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+                "description": "PFAM GFF file for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_pfam.gff",
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+            },
+            {
+                "name": "Gp0119849_TigrFam GFF file",
+                "description": "TigrFam GFF file for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_tigrfam.gff",
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+            },
+            {
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+                "description": "SMART GFF file for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_smart.gff",
+                "md5_checksum": "dcd69fb1d06c2e0e81aa6c3e8a47a4d6",
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+            },
+            {
+                "name": "Gp0119849_SuperFam GFF file",
+                "description": "SuperFam GFF file for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_supfam.gff",
+                "md5_checksum": "919275eab1b2eff697b1f126a403d7a8",
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+            },
+            {
+                "name": "Gp0119849_Cath FunFam GFF file",
+                "description": "Cath FunFam GFF file for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_cath_funfam.gff",
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+            },
+            {
+                "name": "Gp0119849_KO_EC GFF file",
+                "description": "KO_EC GFF file for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/annotation/nmdc_mga0jfwq54_ko_ec.gff",
+                "md5_checksum": "6421ef4cc738c134eadfd5011c14563f",
+                "id": "nmdc:6421ef4cc738c134eadfd5011c14563f",
+                "file_size_bytes": 3865731
+            },
+            {
+                "name": "gold:Gp0452679_metabat2 bin checkm quality assessment result",
+                "description": "metabat2 bin checkm quality assessment result for gold:Gp0452679",
+                "data_object_type": "CheckM Statistics",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0fsjy84/MAGs/nmdc_mga0fsjy84_checkm_qa.out",
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+                "id": "nmdc:d41d8cd98f00b204e9800998ecf8427e",
+                "file_size_bytes": 0
+            },
+            {
+                "name": "Gp0119849_tooShort (< 3kb) filtered contigs fasta file by metaBat2",
+                "description": "tooShort (< 3kb) filtered contigs fasta file by metaBat2 for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/MAGs/nmdc_mga0jfwq54_bins.tooShort.fa",
+                "md5_checksum": "38c2006dc930f7cb8db52f4e2eda3bf1",
+                "id": "nmdc:38c2006dc930f7cb8db52f4e2eda3bf1",
+                "file_size_bytes": 4445685
+            },
+            {
+                "name": "Gp0119849_unbinned fasta file from metabat2",
+                "description": "unbinned fasta file from metabat2 for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/MAGs/nmdc_mga0jfwq54_bins.unbinned.fa",
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+                "id": "nmdc:fde7c45ed03675e4dd7b7fba9aa8a5a2",
+                "file_size_bytes": 4973295
+            },
+            {
+                "name": "Gp0119849_metabat2 bin checkm quality assessment result",
+                "description": "metabat2 bin checkm quality assessment result for Gp0119849",
+                "data_object_type": "CheckM Statistics",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/MAGs/nmdc_mga0jfwq54_checkm_qa.out",
+                "md5_checksum": "52d0bc80f4af44b60382600f8d1df96a",
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+                "description": "high-quality and medium-quality bins for Gp0119849",
+                "data_object_type": "Metagenome Bins",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/MAGs/nmdc_mga0jfwq54_hqmq_bin.zip",
+                "md5_checksum": "55b285e508b8a79e96355079a24d3b2f",
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+                "file_size_bytes": 1045591
+            },
+            {
+                "name": "Gp0119849_metabat2 bins",
+                "description": "metabat2 bins for Gp0119849",
+                "url": "https://data.microbiomedata.org/data/nmdc:mga0jfwq54/MAGs/nmdc_mga0jfwq54_metabat_bin.zip",
+                "md5_checksum": "7b2437d0d787888db28c6891ca5ad04a",
+                "id": "nmdc:7b2437d0d787888db28c6891ca5ad04a",
+                "file_size_bytes": 672086
+            },
+            {
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+                },
+                "description": "Metagenome Contig Coverage Stats for gold:Gp0119849",
+                "url": "https://data.microbiomedata.org/data/1777_95818/assembly/mapping_stats.txt",
+                "file_size_bytes": 935504,
+                "type": "nmdc:DataObject",
+                "id": "nmdc:32f196423fcede7cca7fe7ad99d5ec36",
+                "name": "mapping_stats.txt",
+                "data_object_type": "Assembly Coverage Stats"
+            },
+            {
+                "_id": {
+                    "$oid": "649b003d1ae706d7b5b14de9"
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+                        "contamination": 1.72,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 12
+                    },
+                    {
+                        "number_of_contig": 146,
+                        "completeness": 21.99,
+                        "bin_name": "bins.22",
+                        "gene_count": 680,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.85,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 4
+                    },
+                    {
+                        "number_of_contig": 359,
+                        "completeness": 58.43,
+                        "bin_name": "bins.3",
+                        "gene_count": 1968,
+                        "bin_quality": "MQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "BM002",
+                        "num_16s": 0,
+                        "gtdbtk_family": "BM002",
+                        "gtdbtk_domain": "Bacteria",
+                        "contamination": 0.68,
+                        "gtdbtk_class": "Syntrophobacteria",
+                        "gtdbtk_phylum": "Desulfobacterota",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 23
+                    },
+                    {
+                        "number_of_contig": 59,
+                        "completeness": 13.27,
+                        "bin_name": "bins.4",
+                        "gene_count": 239,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 0
+                    },
+                    {
+                        "number_of_contig": 50,
+                        "completeness": 19.19,
+                        "bin_name": "bins.5",
+                        "gene_count": 283,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 5
+                    },
+                    {
+                        "number_of_contig": 90,
+                        "completeness": 23.33,
+                        "bin_name": "bins.6",
+                        "gene_count": 434,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.91,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 13
+                    },
+                    {
+                        "number_of_contig": 94,
+                        "completeness": 15.52,
+                        "bin_name": "bins.7",
+                        "gene_count": 465,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 7
+                    },
+                    {
+                        "number_of_contig": 48,
+                        "completeness": 0.0,
+                        "bin_name": "bins.8",
+                        "gene_count": 260,
+                        "bin_quality": "LQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "",
+                        "num_16s": 0,
+                        "gtdbtk_family": "",
+                        "gtdbtk_domain": "",
+                        "contamination": 0.0,
+                        "gtdbtk_class": "",
+                        "gtdbtk_phylum": "",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "",
+                        "num_t_rna": 4
+                    },
+                    {
+                        "number_of_contig": 291,
+                        "completeness": 50.33,
+                        "bin_name": "bins.9",
+                        "gene_count": 1509,
+                        "bin_quality": "MQ",
+                        "gtdbtk_species": "",
+                        "gtdbtk_order": "Bacteroidales",
+                        "num_16s": 0,
+                        "gtdbtk_family": "vadinHA17",
+                        "gtdbtk_domain": "Bacteria",
+                        "contamination": 3.59,
+                        "gtdbtk_class": "Bacteroidia",
+                        "gtdbtk_phylum": "Bacteroidota",
+                        "num_5s": 0,
+                        "num_23s": 0,
+                        "gtdbtk_genus": "SR-FBR-E99",
+                        "num_t_rna": 15
+                    }
+                ],
+                "unbinned_contig_num": 104985,
+                "started_at_time": "2021-10-11T02:23:28Z",
+                "type": "nmdc:MAGsAnalysisActivity",
+                "ended_at_time": "2021-10-11T09:39:23+00:00"
+            }
+        ],
+        "metagenome_annotation_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b005bbf2caae0415ef9a1"
+                },
+                "has_input": [
+                    "nmdc:9a56bc21f20b6e1bc5edce3a88c469c9"
+                ],
+                "part_of": [
+                    "nmdc:mga0tc4144"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:7b83b2503caf6ef8448c50fc0a6c7199",
+                    "nmdc:b6e6beea1a1e2bc5fd3defefb4329096",
+                    "nmdc:e30b169c1a0529b20903cf960b162d84",
+                    "nmdc:16ffd084e72cab2403866158e5e6a6cb",
+                    "nmdc:dbc18fc26ae72645371911c8519549fa",
+                    "nmdc:3d67230b15a3119104d0a96c47e3a51e",
+                    "nmdc:69e4ba430ae17ea5e82d2ec1a8595ffd",
+                    "nmdc:cb48f118d9c407c955482ec145d1d705",
+                    "nmdc:8c880ce9cade09ededdca6d52db621d1",
+                    "nmdc:74b62c9e6ab9bd7d843b64b436361743",
+                    "nmdc:0dd92986c02650f665649b79cd95c3ad",
+                    "nmdc:cc9ac778259f4a97efb179d199561126"
+                ],
+                "was_informed_by": "gold:Gp0119868",
+                "id": "nmdc:9238b3016b2ebfeb268f6e32a396fead",
+                "execution_resource": "NERSC-Cori",
+                "name": "Annotation Activity for nmdc:mga0tc4144",
+                "started_at_time": "2021-10-11T02:23:28Z",
+                "type": "nmdc:MetagenomeAnnotationActivity",
+                "ended_at_time": "2021-10-11T09:39:23+00:00"
+            }
+        ],
+        "metagenome_assembly_set": [
+            {
+                "_id": {
+                    "$oid": "649b005f2ca5ee4adb139f8f"
+                },
+                "has_input": [
+                    "nmdc:f593f3aee7fc5760af7c039bdf62ba57"
+                ],
+                "part_of": [
+                    "nmdc:mga0tc4144"
+                ],
+                "ctg_logsum": 2099698,
+                "scaf_logsum": 2106188,
+                "gap_pct": 0.00141,
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:9a56bc21f20b6e1bc5edce3a88c469c9",
+                    "nmdc:9b82712bfcf3013e35482c9e68b9095b",
+                    "nmdc:76f1b90c58a3672147718346c40e81c9",
+                    "nmdc:0fe116e4fc9c24bf39029cafe4d2256d",
+                    "nmdc:bda4bbf191832c401a301364ceaa99b9"
+                ],
+                "asm_score": 5.69,
+                "was_informed_by": "gold:Gp0119868",
+                "ctg_powsum": 232346,
+                "scaf_max": 125304,
+                "id": "nmdc:9238b3016b2ebfeb268f6e32a396fead",
+                "scaf_powsum": 233179,
+                "execution_resource": "NERSC-Cori",
+                "contigs": 1343639,
+                "name": "Assembly Activity for nmdc:mga0tc4144",
+                "ctg_max": 125304,
+                "gc_std": 0.10463,
+                "contig_bp": 719936137,
+                "gc_avg": 0.56302,
+                "started_at_time": "2021-10-11T02:23:28Z",
+                "scaf_bp": 719946267,
+                "type": "nmdc:MetagenomeAssembly",
+                "scaffolds": 1342635,
+                "ended_at_time": "2021-10-11T09:39:23+00:00",
+                "ctg_l50": 550,
+                "ctg_l90": 300,
+                "ctg_n50": 346594,
+                "ctg_n90": 1096925,
+                "scaf_l50": 550,
+                "scaf_l90": 300,
+                "scaf_n50": 346521,
+                "scaf_n90": 1096070,
+                "scaf_l_gt50k": 1277940,
+                "scaf_n_gt50k": 18,
+                "scaf_pct_gt50k": 0.17750493
+            }
+        ],
+        "omics_processing_set": [
+            {
+                "_id": {
+                    "$oid": "649b009773e8249959349ba3"
+                },
+                "id": "nmdc:omprc-11-fy71mq09",
+                "name": "Enriched soil microbial communities from Old Woman Creek wetland in Ohio, USA - Methanogen_OWC",
+                "description": "Microbial controls on biogeochemical cycling in deep subsurface shale carbon reservoirs",
+                "has_input": [
+                    "nmdc:bsm-11-754aq706"
+                ],
+                "has_output": [
+                    "jgi:560df3660d878540fd6fe1b9"
+                ],
+                "part_of": [
+                    "nmdc:sty-11-8fb6t785"
+                ],
+                "add_date": "2015-08-15",
+                "mod_date": "2021-06-15",
+                "ncbi_project_name": "Deep subsurface shale carbon reservoir microbial communities from Ohio, USA - Methanogen_OWC",
+                "omics_type": {
+                    "has_raw_value": "Metagenome"
+                },
+                "principal_investigator": {
+                    "has_raw_value": "Kelly Wrighton"
+                },
+                "processing_institution": "JGI",
+                "type": "nmdc:OmicsProcessing",
+                "gold_sequencing_project_identifiers": [
+                    "gold:Gp0119868"
+                ]
+            }
+        ],
+        "read_qc_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009d6bdd4fd20273c85e"
+                },
+                "has_input": [
+                    "nmdc:fbcc8eac251f36bedf3497f34a05cd4a"
+                ],
+                "part_of": [
+                    "nmdc:mga0tc4144"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:f593f3aee7fc5760af7c039bdf62ba57",
+                    "nmdc:8aec820c1193dad3bb21ba4084d43a20"
+                ],
+                "was_informed_by": "gold:Gp0119868",
+                "input_read_count": 138421166,
+                "output_read_bases": 20393388409,
+                "id": "nmdc:9238b3016b2ebfeb268f6e32a396fead",
+                "execution_resource": "NERSC-Cori",
+                "input_read_bases": 20901596066,
+                "name": "Read QC Activity for nmdc:mga0tc4144",
+                "output_read_count": 136125146,
+                "started_at_time": "2021-10-11T02:23:28Z",
+                "type": "nmdc:ReadQCAnalysisActivity",
+                "ended_at_time": "2021-10-11T09:39:23+00:00"
+            }
+        ],
+        "read_based_taxonomy_analysis_activity_set": [
+            {
+                "_id": {
+                    "$oid": "649b009bff710ae353f8cf20"
+                },
+                "has_input": [
+                    "nmdc:f593f3aee7fc5760af7c039bdf62ba57"
+                ],
+                "git_url": "https://github.com/microbiomedata/metaG/releases/tag/0.1",
+                "has_output": [
+                    "nmdc:fe347ec8d4621fca2e07d8fe6cfcea55",
+                    "nmdc:73e3da946aae23b311d50688663ef847",
+                    "nmdc:abf78291d78d1c78eafe96d6cfb062aa",
+                    "nmdc:089f1a254b33552d2c8465e7e8de1186",
+                    "nmdc:c01688a45c35e13a9ebeea38e04fb8ef",
+                    "nmdc:d42c6a1ade379bfacea8a2abc762b45a",
+                    "nmdc:606adc1b169bba287f1d231635fe756f",
+                    "nmdc:9efccbd1e5bbb4d10ce94c2e8d2b33aa",
+                    "nmdc:0c7920c75acfbd3d3b2d654e3b2cd9ec"
+                ],
+                "was_informed_by": "gold:Gp0119868",
+                "id": "nmdc:9238b3016b2ebfeb268f6e32a396fead",
+                "execution_resource": "NERSC-Cori",
+                "name": "ReadBased Analysis Activity for nmdc:mga0tc4144",
+                "started_at_time": "2021-10-11T02:23:28Z",
+                "type": "nmdc:ReadbasedAnalysis",
+                "ended_at_time": "2021-10-11T09:39:23+00:00"
+            }
+        ]
+    }
+]
\ No newline at end of file

From 7fc1ef7da389d95c0e58c48c4fedc3ef6b053701 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Thu, 16 Nov 2023 10:39:15 -0800
Subject: [PATCH 68/91] delete dry-run output data files

---
 .../nmdc_wfmgas-11-3epd0s35_scaffolds.fna                       | 2 --
 1 file changed, 2 deletions(-)
 delete mode 100644 nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna

diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna b/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna
deleted file mode 100644
index 93ef5e29..00000000
--- a/nmdc_automation/re_iding/scripts/data/dryrun_data/results/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3epd0s35/nmdc_wfmgas-11-3epd0s35_scaffolds.fna
+++ /dev/null
@@ -1,2 +0,0 @@
-nmdc:wfmgas-11-3epd0s35>nmdc:wfmgas-11-3epd0s35snmdc:wfmgas-11-3epd0s35enmdc:wfmgas-11-3epd0s35qnmdc:wfmgas-11-3epd0s35unmdc:wfmgas-11-3epd0s35enmdc:wfmgas-11-3epd0s35nnmdc:wfmgas-11-3epd0s35cnmdc:wfmgas-11-3epd0s35enmdc:wfmgas-11-3epd0s35Inmdc:wfmgas-11-3epd0s35Dnmdc:wfmgas-11-3epd0s35-nmdc:wfmgas-11-3epd0s350nmdc:wfmgas-11-3epd0s350nmdc:wfmgas-11-3epd0s351nmdc:wfmgas-11-3epd0s35 nmdc:wfmgas-11-3epd0s35dnmdc:wfmgas-11-3epd0s35enmdc:wfmgas-11-3epd0s35snmdc:wfmgas-11-3epd0s35cnmdc:wfmgas-11-3epd0s35rnmdc:wfmgas-11-3epd0s35inmdc:wfmgas-11-3epd0s35pnmdc:wfmgas-11-3epd0s35tnmdc:wfmgas-11-3epd0s35inmdc:wfmgas-11-3epd0s35onmdc:wfmgas-11-3epd0s35nnmdc:wfmgas-11-3epd0s35
-nmdc:wfmgas-11-3epd0s35ACGT

From 0426dd2b99e8800e13776bab9f7873891ad5b3a4 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 16 Nov 2023 14:19:11 -0800
Subject: [PATCH 69/91] added iteration to activity ids

---
 nmdc_automation/re_iding/base.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index 5bf4aa58..b4876ab5 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -41,9 +41,10 @@
 
 class ReIdTool:
     def __init__(self, api_client: NmdcRuntimeApi, data_dir: str,
-                 template_file: str = None):
+                 template_file: str = None, iteration: str = "1"):
         self.api_client = api_client
         self.data_dir = data_dir
+        self.workflow_iteration = iteration
         if template_file is None:
             template_file = NAPA_TEMPLATE
         with open(template_file, "r") as f:
@@ -148,7 +149,7 @@ def update_reads_qc_analysis_activity_set(self, db_record: Dict,
             omics_processing_id = new_omics_processing.id
             has_input = new_omics_processing.has_output
             
-            new_activity_id = self.api_client.minter(activity_type)
+            new_activity_id = self.api_client.minter(activity_type) + "." + self.workflow_iteration
             logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
             new_readsqc_base_dir = os.path.join(self.data_dir, omics_processing_id,
@@ -206,7 +207,7 @@ def update_metagenome_assembly_set(self, db_record: Dict,
             
             updated_has_output = []
             
-            new_activity_id = self.api_client.minter(activity_type)
+            new_activity_id = self.api_client.minter(activity_type) + "." + self.workflow_iteration
             logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
             new_assembly_base_dir = os.path.join(self.data_dir, omics_processing_id,
@@ -268,7 +269,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
             omics_processing_id = new_omics_processing.id
             has_input = [self._get_input_do_id(new_db, "Filtered Sequencing Reads")]
             
-            new_activity_id = self.api_client.minter(activity_type)
+            new_activity_id = self.api_client.minter(activity_type) + "." + self.workflow_iteration
             logging.info(f"New activity id created for {omics_processing_id} activity type {activity_type}: {new_activity_id}")
             
             new_readbased_base_dir = os.path.join(self.data_dir, omics_processing_id,
@@ -316,7 +317,6 @@ def _get_input_do_id(self, new_db, data_object_type: str):
         """Returns the string representation of a data object id given data object type"""
         
         for rec in new_db.data_object_set:
-            print(type(rec.data_object_type))
             if str(rec.data_object_type) == data_object_type:
                 return str(rec.id)        
 

From 6b06e681c0f45ccb6959bd2e66238e7ac3137c1e Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Fri, 17 Nov 2023 10:26:46 -0800
Subject: [PATCH 70/91] fix id iteration and name slot

---
 nmdc_automation/re_iding/base.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/nmdc_automation/re_iding/base.py b/nmdc_automation/re_iding/base.py
index b4876ab5..ea9493f0 100644
--- a/nmdc_automation/re_iding/base.py
+++ b/nmdc_automation/re_iding/base.py
@@ -117,6 +117,7 @@ def update_omics_processing_has_output(self, db_record: Dict,
         # make new data objects with updated IDs
         for old_do_id in omics_record["has_output"]:
             old_do_rec = get_data_object_record_by_id(db_record, old_do_id)
+            old_do_rec["data_object_type"] = "Metagenome Raw Reads"
             old_do_id = old_do_rec.get("id")
             params = copy.deepcopy(old_do_rec)
             params.pop("id", None)
@@ -287,6 +288,7 @@ def update_read_based_taxonomy_analysis_activity_set(self, db_record: Dict,
                 old_do_rec["url"], new_readbased_base_dir, new_activity_id, self.data_dir
                 )
                 logging.info(f"New file path computed for {data_object_type}: {new_file_path}")
+                
                 new_do = self.make_new_data_object(
                     omics_processing_id, activity_type, new_activity_id, old_do_rec, data_object_type
                 )
@@ -343,7 +345,7 @@ def _make_new_activity_set_object(self, omics_processing_id: str, new_activity_i
             name=template["Activity"]["name"].replace("{id}", omics_processing_id),
             git_url=template["Git_repo"], version=template["Version"],
             part_of=[omics_processing_id],
-            execution_resource="NERSC - Perlmutter",
+            execution_resource="NERSC-Cori",
             started_at_time=activity_set_rec["started_at_time"],
             has_input=has_input,
             has_output=has_output,
@@ -377,9 +379,9 @@ def make_new_data_object(self, omics_processing_id: str,
 
         data_object = NmdcDataObject(
             id=new_data_object_id,
-            name=template["name"].replace("{id}", omics_processing_id),
+            name=new_filename,
             description=new_description,
-            type="nmdc:Data_Object",
+            type="nmdc:DataObject",
             file_size_bytes=data_object_record["file_size_bytes"],
             md5_checksum=data_object_record["md5_checksum"],
             url=new_url,

From 03bff679e63913cc30ccb8fc23329ee505cafa56 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Fri, 17 Nov 2023 10:33:00 -0800
Subject: [PATCH 71/91] change Dry run outdir for test with real files

---
 nmdc_automation/re_iding/scripts/re_id_tool.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index e784244a..9950c94e 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -25,7 +25,7 @@
 
 
 BASE_DATAFILE_DIR = "/global/cfs/cdirs/m3408/results"
-DRYRUN_DATAFILE_DIR = "./data/dryrun_data/results"
+DRYRUN_DATAFILE_DIR = "/global/cfs/cdirs/m3408/results"
 
 DATA_DIR = Path(__file__).parent.absolute().joinpath("data")
 

From 6d9945e92bf61ab972acb6bc42e62f887a854501 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Fri, 17 Nov 2023 10:33:28 -0800
Subject: [PATCH 72/91] dry run reflecting files on nersc

---
 .../data/dryrun_re_ided_record_dump.json      | 199 +++++++++---------
 1 file changed, 100 insertions(+), 99 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
index 4972881a..ee84252d 100644
--- a/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/dryrun_re_ided_record_dump.json
@@ -2,191 +2,192 @@
     {
         "data_object_set": [
             {
-                "id": "nmdc:dobj-11-y134xn31",
+                "id": "nmdc:dobj-11-k7vny888",
                 "name": "9422.8.132674.GTTTCG.fastq.gz",
                 "description": "Raw sequencer read data",
                 "file_size_bytes": 2861414297,
+                "data_object_type": "Metagenome Raw Reads",
                 "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-dz3wvm61",
-                "name": "Reads QC result fastq (clean data)",
+                "id": "nmdc:dobj-11-019yes10",
+                "name": "nmdc_wfrqc-11-zma0ys31.1_filtered.fastq.gz",
                 "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2571324879,
                 "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
                 "data_object_type": "Filtered Sequencing Reads",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-8nssbh35/nmdc_wfrqc-11-8nssbh35_filtered.fastq.gz",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-zma0ys31.1/nmdc_wfrqc-11-zma0ys31.1_filtered.fastq.gz",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-1pp19646",
-                "name": "Reads QC summary statistics",
+                "id": "nmdc:dobj-11-hty12n62",
+                "name": "nmdc_wfrqc-11-zma0ys31.1_filterStats.txt",
                 "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 290,
                 "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
                 "data_object_type": "QC Statistics",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-8nssbh35/nmdc_wfrqc-11-8nssbh35_filterStats.txt",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-zma0ys31.1/nmdc_wfrqc-11-zma0ys31.1_filterStats.txt",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-vfk56697",
-                "name": "Final assembly contigs fasta",
+                "id": "nmdc:dobj-11-gast3j11",
+                "name": "nmdc_wfmgas-11-3jvymb63.1_contigs.fna",
                 "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
-                "file_size_bytes": 336,
-                "md5_checksum": "d4c4941391714c4d337bdf3444b2f108",
+                "file_size_bytes": 91134523,
+                "md5_checksum": "b96c8e7796616a8eefe473bff2c62e52",
                 "data_object_type": "Assembly Contigs",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_contigs.fna",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3jvymb63.1/nmdc_wfmgas-11-3jvymb63.1_contigs.fna",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-pdqkv709",
-                "name": "Final assembly scaffolds fasta",
+                "id": "nmdc:dobj-11-bkza5366",
+                "name": "nmdc_wfmgas-11-3jvymb63.1_scaffolds.fna",
                 "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
-                "file_size_bytes": 700,
-                "md5_checksum": "a57129f6b1ac8b75a42f4ab610b4c20a",
+                "file_size_bytes": 90622585,
+                "md5_checksum": "6ca496a8b9b298278ad2b4010a7c8cb2",
                 "data_object_type": "Assembly Scaffolds",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_scaffolds.fna",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3jvymb63.1/nmdc_wfmgas-11-3jvymb63.1_scaffolds.fna",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-ry36ec34",
-                "name": "Assembled contigs coverage information",
+                "id": "nmdc:dobj-11-v9xfxp70",
+                "name": "nmdc_wfmgas-11-3jvymb63.1_covstats.txt",
                 "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
-                "file_size_bytes": 0,
-                "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
+                "file_size_bytes": 14431055,
+                "md5_checksum": "19782102f68575b03b7c12dd3d48e840",
                 "data_object_type": "Assembly Coverage Stats",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_covstats.txt",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3jvymb63.1/nmdc_wfmgas-11-3jvymb63.1_covstats.txt",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-v2dcgb32",
-                "name": "An AGP format file that describes the assembly",
+                "id": "nmdc:dobj-11-dz2mw103",
+                "name": "nmdc_wfmgas-11-3jvymb63.1_assembly.agp",
                 "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
-                "file_size_bytes": 0,
-                "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
+                "file_size_bytes": 14581247,
+                "md5_checksum": "419b294106e3fca4a06d18fd3c8e9181",
                 "data_object_type": "Assembly AGP",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_assembly.agp",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3jvymb63.1/nmdc_wfmgas-11-3jvymb63.1_assembly.agp",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-7f8z6a09",
-                "name": "Sorted bam file of reads mapping back to the final assembly",
+                "id": "nmdc:dobj-11-75skzn36",
+                "name": "nmdc_wfmgas-11-3jvymb63.1_pairedMapped_sorted.bam",
                 "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 0,
                 "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
                 "data_object_type": "Assembly Coverage BAM",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-ryns7t13/nmdc_wfmgas-11-ryns7t13_pairedMapped_sorted.bam",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-3jvymb63.1/nmdc_wfmgas-11-3jvymb63.1_pairedMapped_sorted.bam",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-7q03xt64",
-                "name": "GOTTCHA2 classification report file",
+                "id": "nmdc:dobj-11-ppa5pg23",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_gottcha2_report.tsv",
                 "description": "Gottcha2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 13174,
                 "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
                 "data_object_type": "GOTTCHA2 Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_gottcha2_report.tsv",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_gottcha2_report.tsv",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-qd17za87",
-                "name": "GOTTCHA2 report file",
+                "id": "nmdc:dobj-11-0yn4b055",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_gottcha2_report_full.tsv",
                 "description": "Gottcha2 full TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 1035818,
                 "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
                 "data_object_type": "GOTTCHA2 Report Full",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_gottcha2_report_full.tsv",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_gottcha2_report_full.tsv",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-f0pzg444",
-                "name": "GOTTCHA2 krona plot HTML file",
+                "id": "nmdc:dobj-11-ty0z3p61",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_gottcha2_krona.html",
                 "description": "Gottcha2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 262669,
                 "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
                 "data_object_type": "GOTTCHA2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_gottcha2_krona.html",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_gottcha2_krona.html",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-kmysd345",
-                "name": "Centrifuge output read classification file",
+                "id": "nmdc:dobj-11-e6h68y35",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_centrifuge_classification.tsv",
                 "description": "Centrifuge classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2189843623,
                 "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
                 "data_object_type": "Centrifuge Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_centrifuge_classification.tsv",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_centrifuge_classification.tsv",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-mgdfaj98",
-                "name": "Centrifuge output report file",
+                "id": "nmdc:dobj-11-chgp8k25",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_centrifuge_report.tsv",
                 "description": "Centrifuge TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 260134,
                 "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
                 "data_object_type": "Centrifuge Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_centrifuge_report.tsv",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_centrifuge_report.tsv",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-g38md352",
-                "name": "Centrifug krona plot HTML file",
+                "id": "nmdc:dobj-11-0wbjqw24",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_centrifuge_krona.html",
                 "description": "Centrifuge Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 2343980,
                 "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
                 "data_object_type": "Centrifuge Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_centrifuge_krona.html",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_centrifuge_krona.html",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-d67rkh18",
-                "name": "Kraken2 output read classification file",
+                "id": "nmdc:dobj-11-xteq6n75",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_kraken2_classification.tsv",
                 "description": "Kraken classification TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 1785563917,
                 "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
                 "data_object_type": "Kraken2 Taxonomic Classification",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_kraken2_classification.tsv",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_kraken2_classification.tsv",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-ptchwj55",
-                "name": "Kraken2 output report file",
+                "id": "nmdc:dobj-11-1n5y1278",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_kraken2_report.tsv",
                 "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 699896,
                 "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
                 "data_object_type": "Kraken2 Classification Report",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_kraken2_report.tsv",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_kraken2_report.tsv",
+                "type": "nmdc:DataObject"
             },
             {
-                "id": "nmdc:dobj-11-d0qt9513",
-                "name": "Kraken2 Krona plot HTML file",
+                "id": "nmdc:dobj-11-rtjb8n73",
+                "name": "nmdc_wfrbt-11-e79d5x03.1_kraken2_krona.html",
                 "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
                 "file_size_bytes": 4221977,
                 "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
                 "data_object_type": "Kraken2 Krona Plot",
-                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-mxr19q91/nmdc_wfrbt-11-mxr19q91_kraken2_krona.html",
-                "type": "nmdc:Data_Object"
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-e79d5x03.1/nmdc_wfrbt-11-e79d5x03.1_kraken2_krona.html",
+                "type": "nmdc:DataObject"
             }
         ],
         "metagenome_assembly_set": [
             {
-                "id": "nmdc:wfmgas-11-ryns7t13",
+                "id": "nmdc:wfmgas-11-3jvymb63.1",
                 "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
                 "was_informed_by": "nmdc:omprc-11-bn8jcq58",
-                "execution_resource": "NERSC - Perlmutter",
+                "execution_resource": "NERSC-Cori",
                 "git_url": "https://github.com/microbiomedata/metaAssembly",
                 "has_input": [
-                    "nmdc:dobj-11-dz3wvm61"
+                    "nmdc:dobj-11-019yes10"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-vfk56697",
-                    "nmdc:dobj-11-pdqkv709",
-                    "nmdc:dobj-11-ry36ec34",
-                    "nmdc:dobj-11-v2dcgb32",
-                    "nmdc:dobj-11-7f8z6a09"
+                    "nmdc:dobj-11-gast3j11",
+                    "nmdc:dobj-11-bkza5366",
+                    "nmdc:dobj-11-v9xfxp70",
+                    "nmdc:dobj-11-dz2mw103",
+                    "nmdc:dobj-11-75skzn36"
                 ],
                 "type": "nmdc:MetagenomeAssembly",
                 "part_of": [
@@ -233,7 +234,7 @@
                     "gold:Gp0115663"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-y134xn31"
+                    "nmdc:dobj-11-k7vny888"
                 ],
                 "mod_date": "2021-06-15",
                 "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
@@ -252,19 +253,19 @@
         ],
         "read_qc_analysis_activity_set": [
             {
-                "id": "nmdc:wfrqc-11-8nssbh35",
+                "id": "nmdc:wfrqc-11-zma0ys31.1",
                 "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
                 "was_informed_by": "nmdc:omprc-11-bn8jcq58",
-                "execution_resource": "NERSC - Perlmutter",
+                "execution_resource": "NERSC-Cori",
                 "git_url": "https://github.com/microbiomedata/ReadsQC",
                 "has_input": [
-                    "nmdc:dobj-11-y134xn31"
+                    "nmdc:dobj-11-k7vny888"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-dz3wvm61",
-                    "nmdc:dobj-11-1pp19646"
+                    "nmdc:dobj-11-019yes10",
+                    "nmdc:dobj-11-hty12n62"
                 ],
                 "type": "nmdc:ReadQcAnalysisActivity",
                 "part_of": [
@@ -279,26 +280,26 @@
         ],
         "read_based_taxonomy_analysis_activity_set": [
             {
-                "id": "nmdc:wfrbt-11-mxr19q91",
+                "id": "nmdc:wfrbt-11-e79d5x03.1",
                 "name": "Readbased Taxonomy Analysis Activity for nmdc:omprc-11-bn8jcq58",
                 "started_at_time": "2021-10-11T02:28:26Z",
                 "ended_at_time": "2021-10-11T04:56:04+00:00",
                 "was_informed_by": "nmdc:omprc-11-bn8jcq58",
-                "execution_resource": "NERSC - Perlmutter",
+                "execution_resource": "NERSC-Cori",
                 "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
                 "has_input": [
-                    "nmdc:dobj-11-dz3wvm61"
+                    "nmdc:dobj-11-019yes10"
                 ],
                 "has_output": [
-                    "nmdc:dobj-11-7q03xt64",
-                    "nmdc:dobj-11-qd17za87",
-                    "nmdc:dobj-11-f0pzg444",
-                    "nmdc:dobj-11-kmysd345",
-                    "nmdc:dobj-11-mgdfaj98",
-                    "nmdc:dobj-11-g38md352",
-                    "nmdc:dobj-11-d67rkh18",
-                    "nmdc:dobj-11-ptchwj55",
-                    "nmdc:dobj-11-d0qt9513"
+                    "nmdc:dobj-11-ppa5pg23",
+                    "nmdc:dobj-11-0yn4b055",
+                    "nmdc:dobj-11-ty0z3p61",
+                    "nmdc:dobj-11-e6h68y35",
+                    "nmdc:dobj-11-chgp8k25",
+                    "nmdc:dobj-11-0wbjqw24",
+                    "nmdc:dobj-11-xteq6n75",
+                    "nmdc:dobj-11-1n5y1278",
+                    "nmdc:dobj-11-rtjb8n73"
                 ],
                 "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
                 "part_of": [

From 836a0ca322be61faaca69162ed76907edc6cafae Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Fri, 17 Nov 2023 12:25:56 -0800
Subject: [PATCH 73/91] added command to ingest records

---
 .../re_iding/scripts/re_id_tool.py            | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 9950c94e..49e946f8 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -221,7 +221,29 @@ def process_records(ctx, dryrun, study_id, data_dir):
                                              inject_type=False))
     with open(db_outfile, "w") as f:
         f.write(json.dumps(json_data, indent=4))
+        
 
+@cli.command()
+@click.argument('reid_records_file', type=click.Path(exists=True))
+@click.pass_context
+def ingest_records(ctx, reid_records_file):
+    """
+    Read in json dump of re_id'd records and submit them to the /v1/workflows/activities endpoint
+    """
+    start_time = time.time()
+    logging.info(f"Submitting re id'd records from : {reid_records_file}")
+
+    config = Config(ctx.obj['site_config'])
+    api_client = NmdcRuntimeUserApi(username=config.napa_username, password=config.napa_password,
+        base_url=config.napa_base_url)
+    
+    with open(reid_records_file, "r") as f:
+        db_records = json.load(f)
+        
+    for record in db_records:
+        resp = api_client.post_objects(record)
+    
+        logger.info(f"{record} posted, got response: {resp}")
 
 def _get_data_dir(data_dir, dryrun):
     """

From ae75309564119c9461f2e010f0180397248bbf31 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 20 Nov 2023 13:43:52 -0800
Subject: [PATCH 74/91] update to reflect proper versions

---
 configs/re_iding_worklfows.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/configs/re_iding_worklfows.yaml b/configs/re_iding_worklfows.yaml
index 5f71a7da..3745401b 100644
--- a/configs/re_iding_worklfows.yaml
+++ b/configs/re_iding_worklfows.yaml
@@ -3,7 +3,7 @@ Workflows:
     Type: nmdc:ReadQcAnalysisActivity
     Enabled: True
     Git_repo: https://github.com/microbiomedata/ReadsQC
-    Version: v1.0.8
+    Version: v1.0.2
     WDL: rqcfilter.wdl
     Collection: read_qc_analysis_activity_set
     ActivityRange: ReadQcAnalysisActivity
@@ -44,7 +44,7 @@ Workflows:
     Type: nmdc:MetagenomeAssembly
     Enabled: True
     Git_repo: https://github.com/microbiomedata/metaAssembly
-    Version: v1.0.3
+    Version: v1.0.2
     WDL: jgi_assembly.wdl
     Collection: metagenome_assembly_set
     ActivityRange: MetagenomeAssembly
@@ -120,7 +120,7 @@ Workflows:
     Type: nmdc:ReadBasedTaxonomyAnalysisActivity
     Enabled: True
     Git_repo: https://github.com/microbiomedata/ReadbasedAnalysis
-    Version: v1.0.5
+    Version: v1.0.2
     WDL: ReadbasedAnalysis.wdl
     Collection: read_based_taxonomy_analysis_activity_set
     ActivityRange: ReadBasedTaxonomyAnalysisActivity

From da59e122fd11fb60c5c6f3b3986a0e2e6218b9dc Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 20 Nov 2023 14:07:13 -0800
Subject: [PATCH 75/91] added full stegen re-ided records

---
 ...c:sty-11-aygzgv51_re_ided_record_dump.json | 15395 ++++++++++++++++
 1 file changed, 15395 insertions(+)
 create mode 100644 nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_re_ided_record_dump.json

diff --git a/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_re_ided_record_dump.json
new file mode 100644
index 00000000..06d35da9
--- /dev/null
+++ b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_re_ided_record_dump.json
@@ -0,0 +1,15395 @@
+[
+    {
+        "data_object_set": [
+            {
+                "id": "nmdc:dobj-11-xkx6jy64",
+                "name": "9422.8.132674.GTTTCG.fastq.gz",
+                "description": "Raw sequencer read data",
+                "file_size_bytes": 2861414297,
+                "data_object_type": "Metagenome Raw Reads",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-ct3ee035",
+                "name": "nmdc_wfrqc-11-0ve6kv13.1_filtered.fastq.gz",
+                "description": "Filtered Reads for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 2571324879,
+                "md5_checksum": "7bf778baef033d36f118f8591256d6ef",
+                "data_object_type": "Filtered Sequencing Reads",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-0ve6kv13.1/nmdc_wfrqc-11-0ve6kv13.1_filtered.fastq.gz",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-8be0nr71",
+                "name": "nmdc_wfrqc-11-0ve6kv13.1_filterStats.txt",
+                "description": "Filtered Stats for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 290,
+                "md5_checksum": "b99ce8adc125c95f0bfdadf36a3f6848",
+                "data_object_type": "QC Statistics",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrqc-11-0ve6kv13.1/nmdc_wfrqc-11-0ve6kv13.1_filterStats.txt",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-36rmmb88",
+                "name": "nmdc_wfmgas-11-mm1xhm21.1_contigs.fna",
+                "description": "Assembled contigs fasta for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 91134523,
+                "md5_checksum": "058a25368fb61d9ae2ae0f9572cc7820",
+                "data_object_type": "Assembly Contigs",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-mm1xhm21.1/nmdc_wfmgas-11-mm1xhm21.1_contigs.fna",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-j5tv3r84",
+                "name": "nmdc_wfmgas-11-mm1xhm21.1_scaffolds.fna",
+                "description": "Assembled scaffold fasta for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 90622585,
+                "md5_checksum": "c981cbc33496f7e0cac7102d06f4e273",
+                "data_object_type": "Assembly Scaffolds",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-mm1xhm21.1/nmdc_wfmgas-11-mm1xhm21.1_scaffolds.fna",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-htqksg07",
+                "name": "nmdc_wfmgas-11-mm1xhm21.1_covstats.txt",
+                "description": "Metagenome Contig Coverage Stats for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 14431055,
+                "md5_checksum": "cb9b732dc061c51bf791f70028d6a132",
+                "data_object_type": "Assembly Coverage Stats",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-mm1xhm21.1/nmdc_wfmgas-11-mm1xhm21.1_covstats.txt",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-kykej776",
+                "name": "nmdc_wfmgas-11-mm1xhm21.1_assembly.agp",
+                "description": "Assembled AGP file for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 14581247,
+                "md5_checksum": "1e531b7998e50f6b71fd913cb9dcb027",
+                "data_object_type": "Assembly AGP",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-mm1xhm21.1/nmdc_wfmgas-11-mm1xhm21.1_assembly.agp",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-9153zz50",
+                "name": "nmdc_wfmgas-11-mm1xhm21.1_pairedMapped_sorted.bam",
+                "description": "Metagenome Alignment BAM file for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 0,
+                "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
+                "data_object_type": "Assembly Coverage BAM",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfmgas-11-mm1xhm21.1/nmdc_wfmgas-11-mm1xhm21.1_pairedMapped_sorted.bam",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-8j315t40",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_gottcha2_report.tsv",
+                "description": "Gottcha2 TSV report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 13174,
+                "md5_checksum": "bc7c1bda004aab357c8f6cf5a42242f9",
+                "data_object_type": "GOTTCHA2 Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_gottcha2_report.tsv",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-qgrfgk34",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_gottcha2_report_full.tsv",
+                "description": "Gottcha2 full TSV report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 1035818,
+                "md5_checksum": "9481434cadd0d6c154e2ec4c11ef0e04",
+                "data_object_type": "GOTTCHA2 Report Full",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_gottcha2_report_full.tsv",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-q439wj06",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_gottcha2_krona.html",
+                "description": "Gottcha2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 262669,
+                "md5_checksum": "6b5bc6ce7f11c1336a5f85a98fc18541",
+                "data_object_type": "GOTTCHA2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_gottcha2_krona.html",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-9dfrtv83",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_centrifuge_classification.tsv",
+                "description": "Centrifuge classification TSV report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 2189843623,
+                "md5_checksum": "933c71bbc2f4a2e84d50f0d3864cf940",
+                "data_object_type": "Centrifuge Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_centrifuge_classification.tsv",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-ydwz4r55",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_centrifuge_report.tsv",
+                "description": "Centrifuge TSV report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 260134,
+                "md5_checksum": "1a208e2519770ef50740ac39f1b9ba9a",
+                "data_object_type": "Centrifuge Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_centrifuge_report.tsv",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-nzqmzy34",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_centrifuge_krona.html",
+                "description": "Centrifuge Krona HTML report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 2343980,
+                "md5_checksum": "f112a3840464ae7a9cf4a3bf295edd5c",
+                "data_object_type": "Centrifuge Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_centrifuge_krona.html",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-ke6wvj86",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_kraken2_classification.tsv",
+                "description": "Kraken classification TSV report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 1785563917,
+                "md5_checksum": "7ca01ea379f0baed96f87d1435925f95",
+                "data_object_type": "Kraken2 Taxonomic Classification",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_kraken2_classification.tsv",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-91jzv767",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_kraken2_report.tsv",
+                "description": "Kraken2 TSV report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 699896,
+                "md5_checksum": "c85f2f2b4a518c4adb23970448a5cb45",
+                "data_object_type": "Kraken2 Classification Report",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_kraken2_report.tsv",
+                "type": "nmdc:DataObject"
+            },
+            {
+                "id": "nmdc:dobj-11-snxdsz38",
+                "name": "nmdc_wfrbt-11-ddtz8b82.1_kraken2_krona.html",
+                "description": "Kraken2 Krona HTML report for nmdc:omprc-11-bn8jcq58",
+                "file_size_bytes": 4221977,
+                "md5_checksum": "94ee1bc2dc74830a21d5c3471d6cf223",
+                "data_object_type": "Kraken2 Krona Plot",
+                "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-bn8jcq58/nmdc:wfrbt-11-ddtz8b82.1/nmdc_wfrbt-11-ddtz8b82.1_kraken2_krona.html",
+                "type": "nmdc:DataObject"
+            }
+        ],
+        "metagenome_assembly_set": [
+            {
+                "id": "nmdc:wfmgas-11-mm1xhm21.1",
+                "name": "Metagenome Assembly Activity for nmdc:omprc-11-bn8jcq58",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "was_informed_by": "nmdc:omprc-11-bn8jcq58",
+                "execution_resource": "NERSC-Cori",
+                "git_url": "https://github.com/microbiomedata/metaAssembly",
+                "has_input": [
+                    "nmdc:dobj-11-ct3ee035"
+                ],
+                "has_output": [
+                    "nmdc:dobj-11-36rmmb88",
+                    "nmdc:dobj-11-j5tv3r84",
+                    "nmdc:dobj-11-htqksg07",
+                    "nmdc:dobj-11-kykej776",
+                    "nmdc:dobj-11-9153zz50"
+                ],
+                "type": "nmdc:MetagenomeAssembly",
+                "part_of": [
+                    "nmdc:omprc-11-bn8jcq58"
+                ],
+                "version": "v1.0.2",
+                "asm_score": 6.577,
+                "scaffolds": 169645,
+                "scaf_logsum": 215363,
+                "scaf_powsum": 24422,
+                "scaf_max": 68135,
+                "scaf_bp": 83496490,
+                "scaf_n50": 45550,
+                "scaf_n90": 141870,
+                "scaf_l50": 470,
+                "scaf_l90": 290,
+                "scaf_n_gt50k": 1,
+                "scaf_l_gt50k": 68135,
+                "scaf_pct_gt50k": 0.08160224,
+                "contigs": 169784,
+                "contig_bp": 83494920,
+                "ctg_n50": 45584,
+                "ctg_l50": 470,
+                "ctg_n90": 141996,
+                "ctg_l90": 290,
+                "ctg_logsum": 214373,
+                "ctg_powsum": 24284,
+                "ctg_max": 68135,
+                "gap_pct": 0.00188,
+                "gc_std": 0.11726,
+                "gc_avg": 0.46001
+            }
+        ],
+        "omics_processing_set": [
+            {
+                "id": "nmdc:omprc-11-bn8jcq58",
+                "name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "description": "Sterilized sand packs were incubated back in the ground and collected at time point T2.",
+                "has_input": [
+                    "nmdc:bsm-11-qq8s6x03"
+                ],
+                "add_date": "2015-05-28",
+                "gold_sequencing_project_identifiers": [
+                    "gold:Gp0115663"
+                ],
+                "has_output": [
+                    "nmdc:dobj-11-xkx6jy64"
+                ],
+                "mod_date": "2021-06-15",
+                "ncbi_project_name": "Sand microcosm microbial communities from a hyporheic zone in Columbia River, Washington, USA - GW-RW T2_23-Sept-14",
+                "omics_type": {
+                    "has_raw_value": "Metagenome"
+                },
+                "part_of": [
+                    "nmdc:sty-11-aygzgv51"
+                ],
+                "principal_investigator": {
+                    "has_raw_value": "James Stegen"
+                },
+                "processing_institution": "JGI",
+                "type": "nmdc:OmicsProcessing"
+            }
+        ],
+        "read_qc_analysis_activity_set": [
+            {
+                "id": "nmdc:wfrqc-11-0ve6kv13.1",
+                "name": "Read QC Activity for nmdc:omprc-11-bn8jcq58",
+                "started_at_time": "2021-10-11T02:28:26Z",
+                "ended_at_time": "2021-10-11T04:56:04+00:00",
+                "was_informed_by": "nmdc:omprc-11-bn8jcq58",
+                "execution_resource": "NERSC-Cori",
+                "git_url": "https://github.com/microbiomedata/ReadsQC",
+                "has_input": [
+                    "nmdc:dobj-11-xkx6jy64"
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+                "was_informed_by": "nmdc:omprc-11-p1735e67",
+                "execution_resource": "NERSC-Cori",
+                "git_url": "https://github.com/microbiomedata/ReadbasedAnalysis",
+                "has_input": [
+                    "nmdc:dobj-11-b63t0y87"
+                ],
+                "has_output": [
+                    "nmdc:dobj-11-9wvf0h80",
+                    "nmdc:dobj-11-t83ze308",
+                    "nmdc:dobj-11-7bf4mb91",
+                    "nmdc:dobj-11-zx14g348",
+                    "nmdc:dobj-11-z1qw6j28",
+                    "nmdc:dobj-11-n5h02k27",
+                    "nmdc:dobj-11-46b3v052",
+                    "nmdc:dobj-11-f8p94069",
+                    "nmdc:dobj-11-3xwemf74"
+                ],
+                "type": "nmdc:ReadBasedTaxonomyAnalysisActivity",
+                "part_of": [
+                    "nmdc:omprc-11-p1735e67"
+                ],
+                "version": "v1.0.2"
+            }
+        ]
+    }
+]
\ No newline at end of file

From c13e93f25e27850717fb7e8d5cd21c45340587a0 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 20 Nov 2023 14:07:57 -0800
Subject: [PATCH 76/91] add delete method

---
 nmdc_automation/re_iding/re_id_file_operations.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/nmdc_automation/re_iding/re_id_file_operations.py b/nmdc_automation/re_iding/re_id_file_operations.py
index a82181e5..3e54e72c 100644
--- a/nmdc_automation/re_iding/re_id_file_operations.py
+++ b/nmdc_automation/re_iding/re_id_file_operations.py
@@ -1,4 +1,4 @@
-import subprocess
+import shutil
 import gzip
 import os
 import json
@@ -41,7 +41,19 @@ def read_json_file(filename):
         data = json.load(json_file)
     return data
 
+def delete_directory(path):
+    """Deletes the directory at the specified path along with all its contents.
 
+    Args:
+    path (str): Full path of the directory to be deleted.
+    """
+    if os.path.exists(path) and os.path.isdir(path):
+        shutil.rmtree(path)
+        print(f"Directory '{path}' has been deleted.")
+    else:
+        print(f"Directory '{path}' does not exist or is not a directory.")
+        
+        
 def rewrite_id(src, dst, old_id, new_id, prefix=None):
     """
     Rewrite lines in a file, replacing occurrences of an old ID with a new ID.

From 722f6ce342e7dedac57baee303c69a9e495df64d Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 20 Nov 2023 14:43:02 -0800
Subject: [PATCH 77/91] changed versions

---
 ...c:sty-11-aygzgv51_re_ided_record_dump.json | 200 +++++++++---------
 1 file changed, 100 insertions(+), 100 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_re_ided_record_dump.json b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_re_ided_record_dump.json
index 06d35da9..d054d989 100644
--- a/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_re_ided_record_dump.json
+++ b/nmdc_automation/re_iding/scripts/data/nmdc:sty-11-aygzgv51_re_ided_record_dump.json
@@ -193,7 +193,7 @@
                 "part_of": [
                     "nmdc:omprc-11-bn8jcq58"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 6.577,
                 "scaffolds": 169645,
                 "scaf_logsum": 215363,
@@ -271,7 +271,7 @@
                 "part_of": [
                     "nmdc:omprc-11-bn8jcq58"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 32238374,
                 "output_read_count": 30774080,
                 "input_read_bases": 4867994474,
@@ -503,7 +503,7 @@
                 "part_of": [
                     "nmdc:omprc-11-zp2ar437"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 5.224,
                 "scaffolds": 116565,
                 "scaf_logsum": 182081,
@@ -578,7 +578,7 @@
                 "part_of": [
                     "nmdc:omprc-11-zp2ar437"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 22183982,
                 "output_read_count": 20195754,
                 "input_read_bases": 3349781282,
@@ -810,7 +810,7 @@
                 "part_of": [
                     "nmdc:omprc-11-wepaa271"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.087,
                 "scaffolds": 322890,
                 "scaf_logsum": 491574,
@@ -888,7 +888,7 @@
                 "part_of": [
                     "nmdc:omprc-11-wepaa271"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 35064492,
                 "output_read_count": 33873238,
                 "input_read_bases": 5294738292,
@@ -1120,7 +1120,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hymrq852"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 12.582,
                 "scaffolds": 525116,
                 "scaf_logsum": 725191,
@@ -1198,7 +1198,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hymrq852"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 67696542,
                 "output_read_count": 67147510,
                 "input_read_bases": 10222177842,
@@ -1430,7 +1430,7 @@
                 "part_of": [
                     "nmdc:omprc-11-yt8css91"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 17.061,
                 "scaffolds": 116033,
                 "scaf_logsum": 196103,
@@ -1508,7 +1508,7 @@
                 "part_of": [
                     "nmdc:omprc-11-yt8css91"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 19416222,
                 "output_read_count": 18855352,
                 "input_read_bases": 2931849522,
@@ -1740,7 +1740,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hgehsc37"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.21,
                 "scaffolds": 78311,
                 "scaf_logsum": 60806,
@@ -1815,7 +1815,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hgehsc37"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 19058974,
                 "output_read_count": 17338778,
                 "input_read_bases": 2877905074,
@@ -2047,7 +2047,7 @@
                 "part_of": [
                     "nmdc:omprc-11-7vsv7h78"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 7.785,
                 "scaffolds": 383447,
                 "scaf_logsum": 496628,
@@ -2125,7 +2125,7 @@
                 "part_of": [
                     "nmdc:omprc-11-7vsv7h78"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 51286688,
                 "output_read_count": 48276864,
                 "input_read_bases": 7744289888,
@@ -2357,7 +2357,7 @@
                 "part_of": [
                     "nmdc:omprc-11-5r54nt37"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.626,
                 "scaffolds": 118391,
                 "scaf_logsum": 70885,
@@ -2432,7 +2432,7 @@
                 "part_of": [
                     "nmdc:omprc-11-5r54nt37"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 23705118,
                 "output_read_count": 22801896,
                 "input_read_bases": 3579472818,
@@ -2664,7 +2664,7 @@
                 "part_of": [
                     "nmdc:omprc-11-76ebsj44"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.923,
                 "scaffolds": 299890,
                 "scaf_logsum": 453436,
@@ -2739,7 +2739,7 @@
                 "part_of": [
                     "nmdc:omprc-11-76ebsj44"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 26227312,
                 "output_read_count": 25182244,
                 "input_read_bases": 3960324112,
@@ -2971,7 +2971,7 @@
                 "part_of": [
                     "nmdc:omprc-11-s6wqag22"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 7.629,
                 "scaffolds": 105366,
                 "scaf_logsum": 63657,
@@ -3046,7 +3046,7 @@
                 "part_of": [
                     "nmdc:omprc-11-s6wqag22"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 24223170,
                 "output_read_count": 22768968,
                 "input_read_bases": 3657698670,
@@ -3278,7 +3278,7 @@
                 "part_of": [
                     "nmdc:omprc-11-x0es2p18"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 5.95,
                 "scaffolds": 190940,
                 "scaf_logsum": 174680,
@@ -3353,7 +3353,7 @@
                 "part_of": [
                     "nmdc:omprc-11-x0es2p18"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 25674112,
                 "output_read_count": 22503352,
                 "input_read_bases": 3876790912,
@@ -3585,7 +3585,7 @@
                 "part_of": [
                     "nmdc:omprc-11-1nvcer55"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.305,
                 "scaffolds": 208427,
                 "scaf_logsum": 212917,
@@ -3660,7 +3660,7 @@
                 "part_of": [
                     "nmdc:omprc-11-1nvcer55"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 23886420,
                 "output_read_count": 22738452,
                 "input_read_bases": 3606849420,
@@ -3892,7 +3892,7 @@
                 "part_of": [
                     "nmdc:omprc-11-b051xn44"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.319,
                 "scaffolds": 157774,
                 "scaf_logsum": 111226,
@@ -3967,7 +3967,7 @@
                 "part_of": [
                     "nmdc:omprc-11-b051xn44"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 31715882,
                 "output_read_count": 30212248,
                 "input_read_bases": 4789098182,
@@ -4199,7 +4199,7 @@
                 "part_of": [
                     "nmdc:omprc-11-k8kt2j31"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.117,
                 "scaffolds": 237183,
                 "scaf_logsum": 307525,
@@ -4274,7 +4274,7 @@
                 "part_of": [
                     "nmdc:omprc-11-k8kt2j31"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 26419652,
                 "output_read_count": 25434840,
                 "input_read_bases": 3989367452,
@@ -4506,7 +4506,7 @@
                 "part_of": [
                     "nmdc:omprc-11-9pbab972"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 6.312,
                 "scaffolds": 127272,
                 "scaf_logsum": 77428,
@@ -4581,7 +4581,7 @@
                 "part_of": [
                     "nmdc:omprc-11-9pbab972"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 28569382,
                 "output_read_count": 26868700,
                 "input_read_bases": 4313976682,
@@ -4813,7 +4813,7 @@
                 "part_of": [
                     "nmdc:omprc-11-0g415160"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.48,
                 "scaffolds": 272628,
                 "scaf_logsum": 380592,
@@ -4888,7 +4888,7 @@
                 "part_of": [
                     "nmdc:omprc-11-0g415160"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 23291434,
                 "output_read_count": 22556158,
                 "input_read_bases": 3517006534,
@@ -5120,7 +5120,7 @@
                 "part_of": [
                     "nmdc:omprc-11-z5qv0f24"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.807,
                 "scaffolds": 51180,
                 "scaf_logsum": 6368.36,
@@ -5195,7 +5195,7 @@
                 "part_of": [
                     "nmdc:omprc-11-z5qv0f24"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 20505370,
                 "output_read_count": 19995028,
                 "input_read_bases": 3096310870,
@@ -5427,7 +5427,7 @@
                 "part_of": [
                     "nmdc:omprc-11-8qms8262"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 5.986,
                 "scaffolds": 132455,
                 "scaf_logsum": 81839,
@@ -5502,7 +5502,7 @@
                 "part_of": [
                     "nmdc:omprc-11-8qms8262"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 27906294,
                 "output_read_count": 26116440,
                 "input_read_bases": 4213850394,
@@ -5734,7 +5734,7 @@
                 "part_of": [
                     "nmdc:omprc-11-k675bw84"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.618,
                 "scaffolds": 95584,
                 "scaf_logsum": 36615,
@@ -5809,7 +5809,7 @@
                 "part_of": [
                     "nmdc:omprc-11-k675bw84"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 31642056,
                 "output_read_count": 29115818,
                 "input_read_bases": 4777950456,
@@ -6041,7 +6041,7 @@
                 "part_of": [
                     "nmdc:omprc-11-mbv2jc69"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 5.751,
                 "scaffolds": 175734,
                 "scaf_logsum": 142614,
@@ -6116,7 +6116,7 @@
                 "part_of": [
                     "nmdc:omprc-11-mbv2jc69"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 29872658,
                 "output_read_count": 27896694,
                 "input_read_bases": 4510771358,
@@ -6348,7 +6348,7 @@
                 "part_of": [
                     "nmdc:omprc-11-kc23zq65"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.934,
                 "scaffolds": 206599,
                 "scaf_logsum": 270403,
@@ -6423,7 +6423,7 @@
                 "part_of": [
                     "nmdc:omprc-11-kc23zq65"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 25320866,
                 "output_read_count": 24600396,
                 "input_read_bases": 3823450766,
@@ -6655,7 +6655,7 @@
                 "part_of": [
                     "nmdc:omprc-11-c8dzx197"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 5.062,
                 "scaffolds": 214737,
                 "scaf_logsum": 272416,
@@ -6730,7 +6730,7 @@
                 "part_of": [
                     "nmdc:omprc-11-c8dzx197"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 24239336,
                 "output_read_count": 19917090,
                 "input_read_bases": 3660139736,
@@ -6962,7 +6962,7 @@
                 "part_of": [
                     "nmdc:omprc-11-tgxmb243"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 6.89,
                 "scaffolds": 169622,
                 "scaf_logsum": 141966,
@@ -7037,7 +7037,7 @@
                 "part_of": [
                     "nmdc:omprc-11-tgxmb243"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 21721428,
                 "output_read_count": 19723416,
                 "input_read_bases": 3279935628,
@@ -7269,7 +7269,7 @@
                 "part_of": [
                     "nmdc:omprc-11-t0xjjc50"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 12.57,
                 "scaffolds": 152330,
                 "scaf_logsum": 274450,
@@ -7347,7 +7347,7 @@
                 "part_of": [
                     "nmdc:omprc-11-t0xjjc50"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 36554212,
                 "output_read_count": 33663942,
                 "input_read_bases": 5519686012,
@@ -7579,7 +7579,7 @@
                 "part_of": [
                     "nmdc:omprc-11-1avd3d16"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 18.19,
                 "scaffolds": 139236,
                 "scaf_logsum": 272657,
@@ -7657,7 +7657,7 @@
                 "part_of": [
                     "nmdc:omprc-11-1avd3d16"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 26546332,
                 "output_read_count": 25776010,
                 "input_read_bases": 4008496132,
@@ -7889,7 +7889,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hk1bje46"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 6.419,
                 "scaffolds": 89660,
                 "scaf_logsum": 161291,
@@ -7964,7 +7964,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hk1bje46"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 17796788,
                 "output_read_count": 16817496,
                 "input_read_bases": 2687314988,
@@ -8196,7 +8196,7 @@
                 "part_of": [
                     "nmdc:omprc-11-qtje8r57"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.588,
                 "scaffolds": 120242,
                 "scaf_logsum": 112140,
@@ -8271,7 +8271,7 @@
                 "part_of": [
                     "nmdc:omprc-11-qtje8r57"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 22298982,
                 "output_read_count": 20445042,
                 "input_read_bases": 3367146282,
@@ -8503,7 +8503,7 @@
                 "part_of": [
                     "nmdc:omprc-11-7ey2jr63"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 10.939,
                 "scaffolds": 186895,
                 "scaf_logsum": 337025,
@@ -8581,7 +8581,7 @@
                 "part_of": [
                     "nmdc:omprc-11-7ey2jr63"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 39069214,
                 "output_read_count": 37037822,
                 "input_read_bases": 5899451314,
@@ -8813,7 +8813,7 @@
                 "part_of": [
                     "nmdc:omprc-11-qngh7497"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 13.853,
                 "scaffolds": 543003,
                 "scaf_logsum": 442802,
@@ -8891,7 +8891,7 @@
                 "part_of": [
                     "nmdc:omprc-11-qngh7497"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 65434428,
                 "output_read_count": 64887080,
                 "input_read_bases": 9880598628,
@@ -9123,7 +9123,7 @@
                 "part_of": [
                     "nmdc:omprc-11-jk7zjz92"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.718,
                 "scaffolds": 80703,
                 "scaf_logsum": 116377,
@@ -9198,7 +9198,7 @@
                 "part_of": [
                     "nmdc:omprc-11-jk7zjz92"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 18827380,
                 "output_read_count": 16749572,
                 "input_read_bases": 2842934380,
@@ -9430,7 +9430,7 @@
                 "part_of": [
                     "nmdc:omprc-11-2jt0jk84"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 5.768,
                 "scaffolds": 351728,
                 "scaf_logsum": 429769,
@@ -9505,7 +9505,7 @@
                 "part_of": [
                     "nmdc:omprc-11-2jt0jk84"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 50719572,
                 "output_read_count": 47896142,
                 "input_read_bases": 7658655372,
@@ -9737,7 +9737,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hqmmwn16"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.733,
                 "scaffolds": 114011,
                 "scaf_logsum": 152336,
@@ -9812,7 +9812,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hqmmwn16"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 20957834,
                 "output_read_count": 20454422,
                 "input_read_bases": 3164632934,
@@ -10044,7 +10044,7 @@
                 "part_of": [
                     "nmdc:omprc-11-qsxwf517"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 13.127,
                 "scaffolds": 220853,
                 "scaf_logsum": 448446,
@@ -10122,7 +10122,7 @@
                 "part_of": [
                     "nmdc:omprc-11-qsxwf517"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 34522052,
                 "output_read_count": 33454554,
                 "input_read_bases": 5212829852,
@@ -10354,7 +10354,7 @@
                 "part_of": [
                     "nmdc:omprc-11-932jcd76"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 5.471,
                 "scaffolds": 106645,
                 "scaf_logsum": 42987,
@@ -10429,7 +10429,7 @@
                 "part_of": [
                     "nmdc:omprc-11-932jcd76"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 28754670,
                 "output_read_count": 27981268,
                 "input_read_bases": 4341955170,
@@ -10661,7 +10661,7 @@
                 "part_of": [
                     "nmdc:omprc-11-p0jdew93"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.367,
                 "scaffolds": 191777,
                 "scaf_logsum": 225846,
@@ -10736,7 +10736,7 @@
                 "part_of": [
                     "nmdc:omprc-11-p0jdew93"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 24261468,
                 "output_read_count": 22362924,
                 "input_read_bases": 3663481668,
@@ -10968,7 +10968,7 @@
                 "part_of": [
                     "nmdc:omprc-11-dtsr6z90"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.329,
                 "scaffolds": 208793,
                 "scaf_logsum": 260132,
@@ -11043,7 +11043,7 @@
                 "part_of": [
                     "nmdc:omprc-11-dtsr6z90"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 25305566,
                 "output_read_count": 23508042,
                 "input_read_bases": 3821140466,
@@ -11276,7 +11276,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hwadfm25"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.712,
                 "scaffolds": 46121,
                 "scaf_logsum": 38062,
@@ -11351,7 +11351,7 @@
                 "part_of": [
                     "nmdc:omprc-11-hwadfm25"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 11431762,
                 "output_read_count": 8322164,
                 "input_read_bases": 1726196062,
@@ -11583,7 +11583,7 @@
                 "part_of": [
                     "nmdc:omprc-11-vnnn4722"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.397,
                 "scaffolds": 212379,
                 "scaf_logsum": 318786,
@@ -11658,7 +11658,7 @@
                 "part_of": [
                     "nmdc:omprc-11-vnnn4722"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 23535784,
                 "output_read_count": 20011156,
                 "input_read_bases": 3553903384,
@@ -11890,7 +11890,7 @@
                 "part_of": [
                     "nmdc:omprc-11-p21wp875"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 7.947,
                 "scaffolds": 103181,
                 "scaf_logsum": 50816,
@@ -11965,7 +11965,7 @@
                 "part_of": [
                     "nmdc:omprc-11-p21wp875"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 28024960,
                 "output_read_count": 27378404,
                 "input_read_bases": 4231768960,
@@ -12197,7 +12197,7 @@
                 "part_of": [
                     "nmdc:omprc-11-vs67yj43"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 17.863,
                 "scaffolds": 81627,
                 "scaf_logsum": 20954,
@@ -12275,7 +12275,7 @@
                 "part_of": [
                     "nmdc:omprc-11-vs67yj43"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 27835800,
                 "output_read_count": 25862834,
                 "input_read_bases": 4203205800,
@@ -12507,7 +12507,7 @@
                 "part_of": [
                     "nmdc:omprc-11-nhf5m035"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.996,
                 "scaffolds": 147272,
                 "scaf_logsum": 91521,
@@ -12582,7 +12582,7 @@
                 "part_of": [
                     "nmdc:omprc-11-nhf5m035"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 28064750,
                 "output_read_count": 26438892,
                 "input_read_bases": 4237777250,
@@ -12814,7 +12814,7 @@
                 "part_of": [
                     "nmdc:omprc-11-w3v30q48"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 14.664,
                 "scaffolds": 97316,
                 "scaf_logsum": 37899,
@@ -12892,7 +12892,7 @@
                 "part_of": [
                     "nmdc:omprc-11-w3v30q48"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 24906858,
                 "output_read_count": 24128544,
                 "input_read_bases": 3760935558,
@@ -13124,7 +13124,7 @@
                 "part_of": [
                     "nmdc:omprc-11-vykcbs96"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 2.823,
                 "scaffolds": 106821,
                 "scaf_logsum": 65979,
@@ -13199,7 +13199,7 @@
                 "part_of": [
                     "nmdc:omprc-11-vykcbs96"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 24139032,
                 "output_read_count": 23262948,
                 "input_read_bases": 3644993832,
@@ -13431,7 +13431,7 @@
                 "part_of": [
                     "nmdc:omprc-11-dw7shd52"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.279,
                 "scaffolds": 189880,
                 "scaf_logsum": 158661,
@@ -13506,7 +13506,7 @@
                 "part_of": [
                     "nmdc:omprc-11-dw7shd52"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 24889788,
                 "output_read_count": 23803802,
                 "input_read_bases": 3758357988,
@@ -13738,7 +13738,7 @@
                 "part_of": [
                     "nmdc:omprc-11-j43hz774"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.266,
                 "scaffolds": 216046,
                 "scaf_logsum": 294510,
@@ -13813,7 +13813,7 @@
                 "part_of": [
                     "nmdc:omprc-11-j43hz774"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 26604768,
                 "output_read_count": 24717950,
                 "input_read_bases": 4017319968,
@@ -14045,7 +14045,7 @@
                 "part_of": [
                     "nmdc:omprc-11-kgxpef29"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.409,
                 "scaffolds": 197600,
                 "scaf_logsum": 130537,
@@ -14123,7 +14123,7 @@
                 "part_of": [
                     "nmdc:omprc-11-kgxpef29"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 30951192,
                 "output_read_count": 30289044,
                 "input_read_bases": 4673629992,
@@ -14355,7 +14355,7 @@
                 "part_of": [
                     "nmdc:omprc-11-qrsway30"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 2.914,
                 "scaffolds": 169419,
                 "scaf_logsum": 99077,
@@ -14430,7 +14430,7 @@
                 "part_of": [
                     "nmdc:omprc-11-qrsway30"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 27317020,
                 "output_read_count": 26481746,
                 "input_read_bases": 4124870020,
@@ -14662,7 +14662,7 @@
                 "part_of": [
                     "nmdc:omprc-11-nry91b19"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 4.164,
                 "scaffolds": 180310,
                 "scaf_logsum": 193641,
@@ -14737,7 +14737,7 @@
                 "part_of": [
                     "nmdc:omprc-11-nry91b19"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 23728904,
                 "output_read_count": 22416634,
                 "input_read_bases": 3583064504,
@@ -14969,7 +14969,7 @@
                 "part_of": [
                     "nmdc:omprc-11-0n8y1d07"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 3.393,
                 "scaffolds": 182865,
                 "scaf_logsum": 171254,
@@ -15044,7 +15044,7 @@
                 "part_of": [
                     "nmdc:omprc-11-0n8y1d07"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 23985924,
                 "output_read_count": 22751496,
                 "input_read_bases": 3621874524,
@@ -15276,7 +15276,7 @@
                 "part_of": [
                     "nmdc:omprc-11-p1735e67"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "asm_score": 13.921,
                 "scaffolds": 48925,
                 "scaf_logsum": 9156.336,
@@ -15354,7 +15354,7 @@
                 "part_of": [
                     "nmdc:omprc-11-p1735e67"
                 ],
-                "version": "v1.0.2",
+                "version": "1.0.2",
                 "input_read_count": 20780788,
                 "output_read_count": 19516330,
                 "input_read_bases": 3137898988,

From a06695dd88b617c661cafc0edaa847548201792b Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Mon, 20 Nov 2023 14:43:18 -0800
Subject: [PATCH 78/91] changed versions

---
 configs/re_iding_worklfows.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/configs/re_iding_worklfows.yaml b/configs/re_iding_worklfows.yaml
index 3745401b..a763e3e0 100644
--- a/configs/re_iding_worklfows.yaml
+++ b/configs/re_iding_worklfows.yaml
@@ -3,7 +3,7 @@ Workflows:
     Type: nmdc:ReadQcAnalysisActivity
     Enabled: True
     Git_repo: https://github.com/microbiomedata/ReadsQC
-    Version: v1.0.2
+    Version: 1.0.2
     WDL: rqcfilter.wdl
     Collection: read_qc_analysis_activity_set
     ActivityRange: ReadQcAnalysisActivity
@@ -44,7 +44,7 @@ Workflows:
     Type: nmdc:MetagenomeAssembly
     Enabled: True
     Git_repo: https://github.com/microbiomedata/metaAssembly
-    Version: v1.0.2
+    Version: 1.0.2
     WDL: jgi_assembly.wdl
     Collection: metagenome_assembly_set
     ActivityRange: MetagenomeAssembly

From db5581ab00f55b6cda2e7175ec07618d69677b9e Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Tue, 21 Nov 2023 12:01:15 -0800
Subject: [PATCH 79/91] exclude omics_processing_set from ingest

---
 nmdc_automation/re_iding/scripts/re_id_tool.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 49e946f8..1f808039 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -180,7 +180,6 @@ def process_records(ctx, dryrun, study_id, data_dir):
     config = ctx.obj['site_config']
     api_client = NmdcRuntimeApi(config)
 
-
     # Get Database dump file paths and the data directory
     db_infile, db_outfile = _get_database_paths(study_id, dryrun)
     data_dir = _get_data_dir(data_dir, dryrun)
@@ -233,14 +232,17 @@ def ingest_records(ctx, reid_records_file):
     start_time = time.time()
     logging.info(f"Submitting re id'd records from : {reid_records_file}")
 
-    config = Config(ctx.obj['site_config'])
-    api_client = NmdcRuntimeUserApi(username=config.napa_username, password=config.napa_password,
-        base_url=config.napa_base_url)
+    # Get API client
+    config = ctx.obj['site_config']
+    api_client = NmdcRuntimeApi(config)
     
     with open(reid_records_file, "r") as f:
         db_records = json.load(f)
         
     for record in db_records:
+        time.sleep(3)
+        if 'omics_processing_set' in record:
+            del record['omics_processing_set']
         resp = api_client.post_objects(record)
     
         logger.info(f"{record} posted, got response: {resp}")

From 35cae661ab139c0ab2af31d2ea7ad8a4b08071fc Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 21 Nov 2023 14:59:38 -0800
Subject: [PATCH 80/91] add changesheet-only logic to re-id-ing ingest_records

---
 nmdc_automation/api/nmdcapi.py                |  11 +-
 nmdc_automation/re_iding/changesheets.py      |  87 +++++++++++++++
 .../dryrun_changesheet-20231121-142444.tsv    |   3 +
 ...1-aygzgv51_changesheet-20231121-142542.tsv | 101 ++++++++++++++++++
 .../re_iding/scripts/re_id_tool.py            |  72 ++++++++++---
 5 files changed, 258 insertions(+), 16 deletions(-)
 create mode 100644 nmdc_automation/re_iding/changesheets.py
 create mode 100644 nmdc_automation/re_iding/changesheets_output/dryrun_changesheet-20231121-142444.tsv
 create mode 100644 nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet-20231121-142542.tsv

diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 0927c23a..2c1e5031 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -320,10 +320,13 @@ class NmdcRuntimeUserApi:
     """
     Basic Runtime API Client with user/password authentication.
     """
-    def __init__(self, username: str, password: str, base_url: str):
-        self.username = username
-        self.password = password
-        self.base_url = base_url
+    def __init__(self, site_configuration):
+        self.config = Config(site_configuration)
+
+        # TODO: remove hard-coded values here
+        self.username = self.config.napa_username
+        self.password = self.config.napa_password
+        self.base_url = self.config.napa_base_url
         self.headers = {}
         self.token_response = None
         self.refresh_token_after = None
diff --git a/nmdc_automation/re_iding/changesheets.py b/nmdc_automation/re_iding/changesheets.py
new file mode 100644
index 00000000..df962c40
--- /dev/null
+++ b/nmdc_automation/re_iding/changesheets.py
@@ -0,0 +1,87 @@
+# nmdc_automation/re_iding/changesheets.py
+"""
+changesheets.py: Provides data classes for creating changesheets for NMDC
+database objects.
+"""
+
+import logging
+import time
+from dataclasses import dataclass, field
+from pathlib import Path
+import requests
+from typing import Any, ClassVar, Dict, Optional
+
+
+logging.basicConfig(
+    level=logging.INFO, format="%(asctime)s %(levelname)s %(" "message)s"
+)
+
+CHANGESHEETS_DIR = Path(__file__).parent.absolute().joinpath("changesheets_output")
+
+
+@dataclass
+class ChangesheetLineItem:
+    """
+    A line item in a changesheet
+    """
+
+    id: str
+    action: str
+    attribute: str
+    value: str
+
+    @property
+    def line(self) -> str:
+        """
+        Return the line item as a tab-separated string
+        """
+        cleaned_value = self.value.replace("\n", " ").replace("\t", " ").strip()
+        return f"{self.id}\t{self.action}\t{self.attribute}\t{cleaned_value}"
+
+
+@dataclass
+class Changesheet:
+    """
+    A changesheet
+    """
+
+    name: str
+    line_items: list = field(default_factory=list)
+    header: ClassVar[str] = "id\taction\tattribute\tvalue"
+    output_dir: Optional[Path] = None
+
+    def __post_init__(self):
+        self.line_items = []
+        if self.output_dir is None:
+            self.output_dir = CHANGESHEETS_DIR
+        self.output_dir.mkdir(parents=True, exist_ok=True)
+        self.output_filename_root: str = f"{self.name}-{time.strftime('%Y%m%d-%H%M%S')}"
+        self.output_filename: str = f"{self.output_filename_root}.tsv"
+        self.output_filepath: Path = self.output_dir.joinpath(self.output_filename)
+
+    def validate_changesheet(self, base_url: str) -> bool:
+        """
+        Validate the changesheet
+        :return: None
+        """
+        logging.info(f"Validating changesheet {self.output_filepath}")
+        url = f"{base_url}metadata/changesheets:validate"
+        logging.info(f"Posting to {url}")
+        resp = requests.post(
+            url,
+            files={"uploaded_file": open(self.output_filepath, "rb")},
+        )
+        if not resp.ok:
+            logging.error(f"Changesheet validation failed: {resp.text}")
+        return resp.ok
+
+    def write_changesheet(self) -> None:
+        """
+        Write the changesheet to a file
+        :return: None
+        """
+        with open(self.output_filepath, "w") as f:
+            logging.info(f"Writing changesheet to {self.output_filepath}")
+            f.write(self.header + "\n")
+            for line_item in self.line_items:
+                f.write(line_item.line + "\n")
diff --git a/nmdc_automation/re_iding/changesheets_output/dryrun_changesheet-20231121-142444.tsv b/nmdc_automation/re_iding/changesheets_output/dryrun_changesheet-20231121-142444.tsv
new file mode 100644
index 00000000..69b360ec
--- /dev/null
+++ b/nmdc_automation/re_iding/changesheets_output/dryrun_changesheet-20231121-142444.tsv
@@ -0,0 +1,3 @@
+id	action	attribute	value
+nmdc:omprc-11-bn8jcq58	remove item	has_output	jgi:55d740280d8785342fcf7e39|
+nmdc:omprc-11-bn8jcq58	insert	has_output	nmdc:dobj-11-k7vny888|
diff --git a/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet-20231121-142542.tsv b/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet-20231121-142542.tsv
new file mode 100644
index 00000000..5c7dccb0
--- /dev/null
+++ b/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet-20231121-142542.tsv
@@ -0,0 +1,101 @@
+id	action	attribute	value
+nmdc:omprc-11-bn8jcq58	remove item	has_output	jgi:55d740280d8785342fcf7e39|
+nmdc:omprc-11-bn8jcq58	insert	has_output	nmdc:dobj-11-xkx6jy64|
+nmdc:omprc-11-zp2ar437	remove item	has_output	jgi:55d817fc0d8785342fcf8274|
+nmdc:omprc-11-zp2ar437	insert	has_output	nmdc:dobj-11-26xaf448|
+nmdc:omprc-11-wepaa271	remove item	has_output	jgi:55d740240d8785342fcf7e37|
+nmdc:omprc-11-wepaa271	insert	has_output	nmdc:dobj-11-ee1cn292|
+nmdc:omprc-11-hymrq852	remove item	has_output	jgi:55a9cb010d87852b21508920|
+nmdc:omprc-11-hymrq852	insert	has_output	nmdc:dobj-11-kt904y47|
+nmdc:omprc-11-yt8css91	remove item	has_output	jgi:55d818010d8785342fcf8278|
+nmdc:omprc-11-yt8css91	insert	has_output	nmdc:dobj-11-1qqy8057|
+nmdc:omprc-11-hgehsc37	remove item	has_output	jgi:55d817f20d8785342fcf826c|
+nmdc:omprc-11-hgehsc37	insert	has_output	nmdc:dobj-11-d8vd2744|
+nmdc:omprc-11-7vsv7h78	remove item	has_output	jgi:55f23d790d8785306f96497e|
+nmdc:omprc-11-7vsv7h78	insert	has_output	nmdc:dobj-11-xhvk5873|
+nmdc:omprc-11-5r54nt37	remove item	has_output	jgi:574fde547ded5e3df1ee13fa|
+nmdc:omprc-11-5r54nt37	insert	has_output	nmdc:dobj-11-ym2gpg27|
+nmdc:omprc-11-76ebsj44	remove item	has_output	jgi:574fde787ded5e3df1ee1416|
+nmdc:omprc-11-76ebsj44	insert	has_output	nmdc:dobj-11-mgpw8m22|
+nmdc:omprc-11-s6wqag22	remove item	has_output	jgi:574fde7b7ded5e3df1ee1418|
+nmdc:omprc-11-s6wqag22	insert	has_output	nmdc:dobj-11-vkxna711|
+nmdc:omprc-11-x0es2p18	remove item	has_output	jgi:574fde577ded5e3df1ee13fc|
+nmdc:omprc-11-x0es2p18	insert	has_output	nmdc:dobj-11-38txm578|
+nmdc:omprc-11-1nvcer55	remove item	has_output	jgi:574fde587ded5e3df1ee13fd|
+nmdc:omprc-11-1nvcer55	insert	has_output	nmdc:dobj-11-h7t4fx79|
+nmdc:omprc-11-b051xn44	remove item	has_output	jgi:574fe09a7ded5e3df1ee1485|
+nmdc:omprc-11-b051xn44	insert	has_output	nmdc:dobj-11-zc62cx90|
+nmdc:omprc-11-k8kt2j31	remove item	has_output	jgi:574fde5b7ded5e3df1ee13ff|
+nmdc:omprc-11-k8kt2j31	insert	has_output	nmdc:dobj-11-ba1s7a39|
+nmdc:omprc-11-9pbab972	remove item	has_output	jgi:574fde7c7ded5e3df1ee1419|
+nmdc:omprc-11-9pbab972	insert	has_output	nmdc:dobj-11-s1m79s13|
+nmdc:omprc-11-0g415160	remove item	has_output	jgi:574fde5e7ded5e3df1ee1401|
+nmdc:omprc-11-0g415160	insert	has_output	nmdc:dobj-11-br8p6y08|
+nmdc:omprc-11-z5qv0f24	remove item	has_output	jgi:574fe0967ded5e3df1ee1482|
+nmdc:omprc-11-z5qv0f24	insert	has_output	nmdc:dobj-11-pk311p17|
+nmdc:omprc-11-8qms8262	remove item	has_output	jgi:574fde807ded5e3df1ee141b|
+nmdc:omprc-11-8qms8262	insert	has_output	nmdc:dobj-11-rbvvgr79|
+nmdc:omprc-11-k675bw84	remove item	has_output	jgi:574fe09f7ded5e3df1ee1489|
+nmdc:omprc-11-k675bw84	insert	has_output	nmdc:dobj-11-ezyfxj50|
+nmdc:omprc-11-mbv2jc69	remove item	has_output	jgi:574fe09c7ded5e3df1ee1487|
+nmdc:omprc-11-mbv2jc69	insert	has_output	nmdc:dobj-11-y27yqy58|
+nmdc:omprc-11-kc23zq65	remove item	has_output	jgi:574fde607ded5e3df1ee1403|
+nmdc:omprc-11-kc23zq65	insert	has_output	nmdc:dobj-11-mmsvm346|
+nmdc:omprc-11-c8dzx197	remove item	has_output	jgi:574fde647ded5e3df1ee1406|
+nmdc:omprc-11-c8dzx197	insert	has_output	nmdc:dobj-11-0vpq2471|
+nmdc:omprc-11-tgxmb243	remove item	has_output	jgi:574fde837ded5e3df1ee141d|
+nmdc:omprc-11-tgxmb243	insert	has_output	nmdc:dobj-11-assd7y33|
+nmdc:omprc-11-t0xjjc50	remove item	has_output	jgi:55d7402a0d8785342fcf7e3b|
+nmdc:omprc-11-t0xjjc50	insert	has_output	nmdc:dobj-11-1v0g7c04|
+nmdc:omprc-11-1avd3d16	remove item	has_output	jgi:55d7402c0d8785342fcf7e3e|
+nmdc:omprc-11-1avd3d16	insert	has_output	nmdc:dobj-11-k5qf8f61|
+nmdc:omprc-11-hk1bje46	remove item	has_output	jgi:55d817f70d8785342fcf8270|
+nmdc:omprc-11-hk1bje46	insert	has_output	nmdc:dobj-11-wvje1j80|
+nmdc:omprc-11-qtje8r57	remove item	has_output	jgi:55d817fa0d8785342fcf8272|
+nmdc:omprc-11-qtje8r57	insert	has_output	nmdc:dobj-11-sp1dx351|
+nmdc:omprc-11-7ey2jr63	remove item	has_output	jgi:55d740220d8785342fcf7e35|
+nmdc:omprc-11-7ey2jr63	insert	has_output	nmdc:dobj-11-h4fha619|
+nmdc:omprc-11-qngh7497	remove item	has_output	jgi:55a9caff0d87852b2150891e|
+nmdc:omprc-11-qngh7497	insert	has_output	nmdc:dobj-11-p9rq4261|
+nmdc:omprc-11-jk7zjz92	remove item	has_output	jgi:55d817f30d8785342fcf826d|
+nmdc:omprc-11-jk7zjz92	insert	has_output	nmdc:dobj-11-phjw3w62|
+nmdc:omprc-11-2jt0jk84	remove item	has_output	jgi:55f23d820d8785306f964980|
+nmdc:omprc-11-2jt0jk84	insert	has_output	nmdc:dobj-11-7pwab132|
+nmdc:omprc-11-hqmmwn16	remove item	has_output	jgi:55d817fe0d8785342fcf8276|
+nmdc:omprc-11-hqmmwn16	insert	has_output	nmdc:dobj-11-7g54r371|
+nmdc:omprc-11-qsxwf517	remove item	has_output	jgi:55d7402b0d8785342fcf7e3c|
+nmdc:omprc-11-qsxwf517	insert	has_output	nmdc:dobj-11-zx1hkd49|
+nmdc:omprc-11-932jcd76	remove item	has_output	jgi:574fe0a17ded5e3df1ee148a|
+nmdc:omprc-11-932jcd76	insert	has_output	nmdc:dobj-11-zb61bz69|
+nmdc:omprc-11-p0jdew93	remove item	has_output	jgi:574fde697ded5e3df1ee140a|
+nmdc:omprc-11-p0jdew93	insert	has_output	nmdc:dobj-11-r2hspr31|
+nmdc:omprc-11-dtsr6z90	remove item	has_output	jgi:574fde6c7ded5e3df1ee140c|
+nmdc:omprc-11-dtsr6z90	insert	has_output	nmdc:dobj-11-dvy2av42|
+nmdc:omprc-11-hwadfm25	remove item	has_output	jgi:574fe0a87ded5e3df1ee148e|
+nmdc:omprc-11-hwadfm25	insert	has_output	nmdc:dobj-11-h1bew282|
+nmdc:omprc-11-vnnn4722	remove item	has_output	jgi:574fde667ded5e3df1ee1407|
+nmdc:omprc-11-vnnn4722	insert	has_output	nmdc:dobj-11-5mt10622|
+nmdc:omprc-11-p21wp875	remove item	has_output	jgi:574fe0a67ded5e3df1ee148d|
+nmdc:omprc-11-p21wp875	insert	has_output	nmdc:dobj-11-ggn5ha23|
+nmdc:omprc-11-vs67yj43	remove item	has_output	jgi:574fde867ded5e3df1ee1420|
+nmdc:omprc-11-vs67yj43	insert	has_output	nmdc:dobj-11-1jxf0m20|
+nmdc:omprc-11-nhf5m035	remove item	has_output	jgi:574fe0ac7ded5e3df1ee1491|
+nmdc:omprc-11-nhf5m035	insert	has_output	nmdc:dobj-11-aw4wks31|
+nmdc:omprc-11-w3v30q48	remove item	has_output	jgi:574fde8a7ded5e3df1ee1422|
+nmdc:omprc-11-w3v30q48	insert	has_output	nmdc:dobj-11-a52d6695|
+nmdc:omprc-11-vykcbs96	remove item	has_output	jgi:574fde6e7ded5e3df1ee140d|
+nmdc:omprc-11-vykcbs96	insert	has_output	nmdc:dobj-11-yjmvgb38|
+nmdc:omprc-11-dw7shd52	remove item	has_output	jgi:574fde8c7ded5e3df1ee1424|
+nmdc:omprc-11-dw7shd52	insert	has_output	nmdc:dobj-11-pr8zqm21|
+nmdc:omprc-11-j43hz774	remove item	has_output	jgi:574fe0af7ded5e3df1ee1493|
+nmdc:omprc-11-j43hz774	insert	has_output	nmdc:dobj-11-srrrsz66|
+nmdc:omprc-11-kgxpef29	remove item	has_output	jgi:574fe0b17ded5e3df1ee1494|
+nmdc:omprc-11-kgxpef29	insert	has_output	nmdc:dobj-11-qjrhfc82|
+nmdc:omprc-11-qrsway30	remove item	has_output	jgi:574fe0b47ded5e3df1ee1496|
+nmdc:omprc-11-qrsway30	insert	has_output	nmdc:dobj-11-zqgnfj09|
+nmdc:omprc-11-nry91b19	remove item	has_output	jgi:574fde907ded5e3df1ee1426|
+nmdc:omprc-11-nry91b19	insert	has_output	nmdc:dobj-11-hkern724|
+nmdc:omprc-11-0n8y1d07	remove item	has_output	jgi:574fde947ded5e3df1ee1429|
+nmdc:omprc-11-0n8y1d07	insert	has_output	nmdc:dobj-11-9wykaf95|
+nmdc:omprc-11-p1735e67	remove item	has_output	jgi:574fde937ded5e3df1ee1428|
+nmdc:omprc-11-p1735e67	insert	has_output	nmdc:dobj-11-r0ygq360|
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 1f808039..2eca95ba 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -16,6 +16,7 @@
 from nmdc_automation.config import Config
 import nmdc_schema.nmdc as nmdc
 from nmdc_automation.re_iding.base import ReIdTool
+from nmdc_automation.re_iding.changesheets import Changesheet, ChangesheetLineItem
 from nmdc_automation.re_iding.db_utils import get_omics_processing_id
 
 # Defaults
@@ -69,9 +70,8 @@ def extract_records(ctx, study_id):
     logging.info(f"Extracting workflow records for study_id: {study_id}")
     logging.info(f"study_id: {study_id}")
 
-    config = Config(ctx.obj['site_config'])
-    api_client = NmdcRuntimeUserApi(username=config.napa_username, password=config.napa_password,
-        base_url=config.napa_base_url)
+    config = ctx.obj['site_config']
+    api_client = NmdcRuntimeUserApi(config)
 
     # 1. Retrieve all OmicsProcessing records for the updated NMDC study ID
     omics_processing_records = api_client.get_omics_processing_records_for_nmdc_study(
@@ -224,28 +224,76 @@ def process_records(ctx, dryrun, study_id, data_dir):
 
 @cli.command()
 @click.argument('reid_records_file', type=click.Path(exists=True))
+@click.option('--changesheet_only', is_flag=True, default=False,)
 @click.pass_context
-def ingest_records(ctx, reid_records_file):
+def ingest_records(ctx, reid_records_file, changesheet_only):
     """
-    Read in json dump of re_id'd records and submit them to the /v1/workflows/activities endpoint
+    Read in json dump of re_id'd records and:
+    submit them to the
+    /v1/workflows/activities endpoint
     """
     start_time = time.time()
     logging.info(f"Submitting re id'd records from : {reid_records_file}")
+    reid_records_filename = Path(reid_records_file).name
+    reid_base_name = reid_records_filename.split("_")[0]
 
-    # Get API client
+    # Get API client(s)
     config = ctx.obj['site_config']
     api_client = NmdcRuntimeApi(config)
+    api_user_client = NmdcRuntimeUserApi(config)
     
     with open(reid_records_file, "r") as f:
         db_records = json.load(f)
-        
+
+    changesheet = Changesheet(name=f"{reid_base_name}_changesheet")
     for record in db_records:
         time.sleep(3)
-        if 'omics_processing_set' in record:
-            del record['omics_processing_set']
-        resp = api_client.post_objects(record)
-    
-        logger.info(f"{record} posted, got response: {resp}")
+        # remove the omics_processing_set and use it to generate
+        # changes to omics_processing has_output
+        omics_processing_set = record.pop("omics_processing_set")
+        for omics_processing_record in omics_processing_set:
+            omics_processing_id = omics_processing_record["id"]
+            logging.info(f"omics_processing_id: {omics_processing_id}")
+            # find legacy has_output and create change to remove it
+            # need to strip the nmdc: prefix for the objects endpoint
+            trimmed_omics_processing_id = omics_processing_id.split(":")[1]
+            resp = api_user_client.request(
+                "GET", f"objects/{trimmed_omics_processing_id}"
+            )
+            legacy_omics_processing_record = resp.json()
+            # delete legacy has_output
+            change = ChangesheetLineItem(
+                id=omics_processing_id, action="remove item",
+                attribute="has_output",
+                value="|".join(legacy_omics_processing_record["has_output"]) + "|", )
+            changesheet.line_items.append(change)
+            logging.info(f"changes: {change}")
+
+
+
+            # insert new has_output
+            change = ChangesheetLineItem(
+                id=omics_processing_id, action="insert",
+                attribute="has_output",
+                value="|".join(omics_processing_record["has_output"]) + "|", )
+            changesheet.line_items.append(change)
+            logging.info(f"changes: {change}")
+
+        # submit the record to the workflows endpoint
+        if not changesheet_only:
+            resp = api_client.post_objects(record)
+            logger.info(f"{record} posted, got response: {resp}")
+        else:
+            logger.info(f"changesheet_only is True, skipping ingest")
+
+    changesheet.write_changesheet()
+    logging.info(f"changesheet written to {changesheet.output_filepath}")
+    if changesheet.validate_changesheet(api_client.config.napa_base_url):
+        logging.info(f"changesheet validated")
+    else:
+        logging.info(f"changesheet validation failed")
+
+
 
 def _get_data_dir(data_dir, dryrun):
     """

From c76f63b867cd43117662d0cd56b4cb1c25e34a57 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Wed, 29 Nov 2023 09:15:19 -0800
Subject: [PATCH 81/91] split changesheet to test api

---
 ...1-aygzgv51_changesheet-20231121-142542.tsv | 52 +------------------
 .../nmdc:sty-11-aygzgv51_changesheet_pt2.tsv  | 52 +++++++++++++++++++
 2 files changed, 53 insertions(+), 51 deletions(-)
 create mode 100644 nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet_pt2.tsv

diff --git a/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet-20231121-142542.tsv b/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet-20231121-142542.tsv
index 5c7dccb0..5f7a9c5f 100644
--- a/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet-20231121-142542.tsv
+++ b/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet-20231121-142542.tsv
@@ -48,54 +48,4 @@ nmdc:omprc-11-tgxmb243	insert	has_output	nmdc:dobj-11-assd7y33|
 nmdc:omprc-11-t0xjjc50	remove item	has_output	jgi:55d7402a0d8785342fcf7e3b|
 nmdc:omprc-11-t0xjjc50	insert	has_output	nmdc:dobj-11-1v0g7c04|
 nmdc:omprc-11-1avd3d16	remove item	has_output	jgi:55d7402c0d8785342fcf7e3e|
-nmdc:omprc-11-1avd3d16	insert	has_output	nmdc:dobj-11-k5qf8f61|
-nmdc:omprc-11-hk1bje46	remove item	has_output	jgi:55d817f70d8785342fcf8270|
-nmdc:omprc-11-hk1bje46	insert	has_output	nmdc:dobj-11-wvje1j80|
-nmdc:omprc-11-qtje8r57	remove item	has_output	jgi:55d817fa0d8785342fcf8272|
-nmdc:omprc-11-qtje8r57	insert	has_output	nmdc:dobj-11-sp1dx351|
-nmdc:omprc-11-7ey2jr63	remove item	has_output	jgi:55d740220d8785342fcf7e35|
-nmdc:omprc-11-7ey2jr63	insert	has_output	nmdc:dobj-11-h4fha619|
-nmdc:omprc-11-qngh7497	remove item	has_output	jgi:55a9caff0d87852b2150891e|
-nmdc:omprc-11-qngh7497	insert	has_output	nmdc:dobj-11-p9rq4261|
-nmdc:omprc-11-jk7zjz92	remove item	has_output	jgi:55d817f30d8785342fcf826d|
-nmdc:omprc-11-jk7zjz92	insert	has_output	nmdc:dobj-11-phjw3w62|
-nmdc:omprc-11-2jt0jk84	remove item	has_output	jgi:55f23d820d8785306f964980|
-nmdc:omprc-11-2jt0jk84	insert	has_output	nmdc:dobj-11-7pwab132|
-nmdc:omprc-11-hqmmwn16	remove item	has_output	jgi:55d817fe0d8785342fcf8276|
-nmdc:omprc-11-hqmmwn16	insert	has_output	nmdc:dobj-11-7g54r371|
-nmdc:omprc-11-qsxwf517	remove item	has_output	jgi:55d7402b0d8785342fcf7e3c|
-nmdc:omprc-11-qsxwf517	insert	has_output	nmdc:dobj-11-zx1hkd49|
-nmdc:omprc-11-932jcd76	remove item	has_output	jgi:574fe0a17ded5e3df1ee148a|
-nmdc:omprc-11-932jcd76	insert	has_output	nmdc:dobj-11-zb61bz69|
-nmdc:omprc-11-p0jdew93	remove item	has_output	jgi:574fde697ded5e3df1ee140a|
-nmdc:omprc-11-p0jdew93	insert	has_output	nmdc:dobj-11-r2hspr31|
-nmdc:omprc-11-dtsr6z90	remove item	has_output	jgi:574fde6c7ded5e3df1ee140c|
-nmdc:omprc-11-dtsr6z90	insert	has_output	nmdc:dobj-11-dvy2av42|
-nmdc:omprc-11-hwadfm25	remove item	has_output	jgi:574fe0a87ded5e3df1ee148e|
-nmdc:omprc-11-hwadfm25	insert	has_output	nmdc:dobj-11-h1bew282|
-nmdc:omprc-11-vnnn4722	remove item	has_output	jgi:574fde667ded5e3df1ee1407|
-nmdc:omprc-11-vnnn4722	insert	has_output	nmdc:dobj-11-5mt10622|
-nmdc:omprc-11-p21wp875	remove item	has_output	jgi:574fe0a67ded5e3df1ee148d|
-nmdc:omprc-11-p21wp875	insert	has_output	nmdc:dobj-11-ggn5ha23|
-nmdc:omprc-11-vs67yj43	remove item	has_output	jgi:574fde867ded5e3df1ee1420|
-nmdc:omprc-11-vs67yj43	insert	has_output	nmdc:dobj-11-1jxf0m20|
-nmdc:omprc-11-nhf5m035	remove item	has_output	jgi:574fe0ac7ded5e3df1ee1491|
-nmdc:omprc-11-nhf5m035	insert	has_output	nmdc:dobj-11-aw4wks31|
-nmdc:omprc-11-w3v30q48	remove item	has_output	jgi:574fde8a7ded5e3df1ee1422|
-nmdc:omprc-11-w3v30q48	insert	has_output	nmdc:dobj-11-a52d6695|
-nmdc:omprc-11-vykcbs96	remove item	has_output	jgi:574fde6e7ded5e3df1ee140d|
-nmdc:omprc-11-vykcbs96	insert	has_output	nmdc:dobj-11-yjmvgb38|
-nmdc:omprc-11-dw7shd52	remove item	has_output	jgi:574fde8c7ded5e3df1ee1424|
-nmdc:omprc-11-dw7shd52	insert	has_output	nmdc:dobj-11-pr8zqm21|
-nmdc:omprc-11-j43hz774	remove item	has_output	jgi:574fe0af7ded5e3df1ee1493|
-nmdc:omprc-11-j43hz774	insert	has_output	nmdc:dobj-11-srrrsz66|
-nmdc:omprc-11-kgxpef29	remove item	has_output	jgi:574fe0b17ded5e3df1ee1494|
-nmdc:omprc-11-kgxpef29	insert	has_output	nmdc:dobj-11-qjrhfc82|
-nmdc:omprc-11-qrsway30	remove item	has_output	jgi:574fe0b47ded5e3df1ee1496|
-nmdc:omprc-11-qrsway30	insert	has_output	nmdc:dobj-11-zqgnfj09|
-nmdc:omprc-11-nry91b19	remove item	has_output	jgi:574fde907ded5e3df1ee1426|
-nmdc:omprc-11-nry91b19	insert	has_output	nmdc:dobj-11-hkern724|
-nmdc:omprc-11-0n8y1d07	remove item	has_output	jgi:574fde947ded5e3df1ee1429|
-nmdc:omprc-11-0n8y1d07	insert	has_output	nmdc:dobj-11-9wykaf95|
-nmdc:omprc-11-p1735e67	remove item	has_output	jgi:574fde937ded5e3df1ee1428|
-nmdc:omprc-11-p1735e67	insert	has_output	nmdc:dobj-11-r0ygq360|
+
diff --git a/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet_pt2.tsv b/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet_pt2.tsv
new file mode 100644
index 00000000..b0be76c3
--- /dev/null
+++ b/nmdc_automation/re_iding/changesheets_output/nmdc:sty-11-aygzgv51_changesheet_pt2.tsv
@@ -0,0 +1,52 @@
+id	action	attribute	value
+nmdc:omprc-11-1avd3d16	insert	has_output	nmdc:dobj-11-k5qf8f61|
+nmdc:omprc-11-hk1bje46	remove item	has_output	jgi:55d817f70d8785342fcf8270|
+nmdc:omprc-11-hk1bje46	insert	has_output	nmdc:dobj-11-wvje1j80|
+nmdc:omprc-11-qtje8r57	remove item	has_output	jgi:55d817fa0d8785342fcf8272|
+nmdc:omprc-11-qtje8r57	insert	has_output	nmdc:dobj-11-sp1dx351|
+nmdc:omprc-11-7ey2jr63	remove item	has_output	jgi:55d740220d8785342fcf7e35|
+nmdc:omprc-11-7ey2jr63	insert	has_output	nmdc:dobj-11-h4fha619|
+nmdc:omprc-11-qngh7497	remove item	has_output	jgi:55a9caff0d87852b2150891e|
+nmdc:omprc-11-qngh7497	insert	has_output	nmdc:dobj-11-p9rq4261|
+nmdc:omprc-11-jk7zjz92	remove item	has_output	jgi:55d817f30d8785342fcf826d|
+nmdc:omprc-11-jk7zjz92	insert	has_output	nmdc:dobj-11-phjw3w62|
+nmdc:omprc-11-2jt0jk84	remove item	has_output	jgi:55f23d820d8785306f964980|
+nmdc:omprc-11-2jt0jk84	insert	has_output	nmdc:dobj-11-7pwab132|
+nmdc:omprc-11-hqmmwn16	remove item	has_output	jgi:55d817fe0d8785342fcf8276|
+nmdc:omprc-11-hqmmwn16	insert	has_output	nmdc:dobj-11-7g54r371|
+nmdc:omprc-11-qsxwf517	remove item	has_output	jgi:55d7402b0d8785342fcf7e3c|
+nmdc:omprc-11-qsxwf517	insert	has_output	nmdc:dobj-11-zx1hkd49|
+nmdc:omprc-11-932jcd76	remove item	has_output	jgi:574fe0a17ded5e3df1ee148a|
+nmdc:omprc-11-932jcd76	insert	has_output	nmdc:dobj-11-zb61bz69|
+nmdc:omprc-11-p0jdew93	remove item	has_output	jgi:574fde697ded5e3df1ee140a|
+nmdc:omprc-11-p0jdew93	insert	has_output	nmdc:dobj-11-r2hspr31|
+nmdc:omprc-11-dtsr6z90	remove item	has_output	jgi:574fde6c7ded5e3df1ee140c|
+nmdc:omprc-11-dtsr6z90	insert	has_output	nmdc:dobj-11-dvy2av42|
+nmdc:omprc-11-hwadfm25	remove item	has_output	jgi:574fe0a87ded5e3df1ee148e|
+nmdc:omprc-11-hwadfm25	insert	has_output	nmdc:dobj-11-h1bew282|
+nmdc:omprc-11-vnnn4722	remove item	has_output	jgi:574fde667ded5e3df1ee1407|
+nmdc:omprc-11-vnnn4722	insert	has_output	nmdc:dobj-11-5mt10622|
+nmdc:omprc-11-p21wp875	remove item	has_output	jgi:574fe0a67ded5e3df1ee148d|
+nmdc:omprc-11-p21wp875	insert	has_output	nmdc:dobj-11-ggn5ha23|
+nmdc:omprc-11-vs67yj43	remove item	has_output	jgi:574fde867ded5e3df1ee1420|
+nmdc:omprc-11-vs67yj43	insert	has_output	nmdc:dobj-11-1jxf0m20|
+nmdc:omprc-11-nhf5m035	remove item	has_output	jgi:574fe0ac7ded5e3df1ee1491|
+nmdc:omprc-11-nhf5m035	insert	has_output	nmdc:dobj-11-aw4wks31|
+nmdc:omprc-11-w3v30q48	remove item	has_output	jgi:574fde8a7ded5e3df1ee1422|
+nmdc:omprc-11-w3v30q48	insert	has_output	nmdc:dobj-11-a52d6695|
+nmdc:omprc-11-vykcbs96	remove item	has_output	jgi:574fde6e7ded5e3df1ee140d|
+nmdc:omprc-11-vykcbs96	insert	has_output	nmdc:dobj-11-yjmvgb38|
+nmdc:omprc-11-dw7shd52	remove item	has_output	jgi:574fde8c7ded5e3df1ee1424|
+nmdc:omprc-11-dw7shd52	insert	has_output	nmdc:dobj-11-pr8zqm21|
+nmdc:omprc-11-j43hz774	remove item	has_output	jgi:574fe0af7ded5e3df1ee1493|
+nmdc:omprc-11-j43hz774	insert	has_output	nmdc:dobj-11-srrrsz66|
+nmdc:omprc-11-kgxpef29	remove item	has_output	jgi:574fe0b17ded5e3df1ee1494|
+nmdc:omprc-11-kgxpef29	insert	has_output	nmdc:dobj-11-qjrhfc82|
+nmdc:omprc-11-qrsway30	remove item	has_output	jgi:574fe0b47ded5e3df1ee1496|
+nmdc:omprc-11-qrsway30	insert	has_output	nmdc:dobj-11-zqgnfj09|
+nmdc:omprc-11-nry91b19	remove item	has_output	jgi:574fde907ded5e3df1ee1426|
+nmdc:omprc-11-nry91b19	insert	has_output	nmdc:dobj-11-hkern724|
+nmdc:omprc-11-0n8y1d07	remove item	has_output	jgi:574fde947ded5e3df1ee1429|
+nmdc:omprc-11-0n8y1d07	insert	has_output	nmdc:dobj-11-9wykaf95|
+nmdc:omprc-11-p1735e67	remove item	has_output	jgi:574fde937ded5e3df1ee1428|
+nmdc:omprc-11-p1735e67	insert	has_output	nmdc:dobj-11-r0ygq360|
\ No newline at end of file

From b4de0b5b8c4fbb67a8d88c2426ddf3506e0cd715 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 7 Dec 2023 11:29:21 -0800
Subject: [PATCH 82/91] added function to delete old records from db

---
 .../re_iding/scripts/re_id_tool.py            | 62 +++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 2eca95ba..3d501808 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -294,6 +294,68 @@ def ingest_records(ctx, reid_records_file, changesheet_only):
         logging.info(f"changesheet validation failed")
 
 
+@cli.command()
+@click.argument('old_records_file', type=click.Path(exists=True))
+@click.pass_context
+def delete_old_records(ctx, old_records_file):
+    """
+    Read in json dump of old records and:
+    delete them using
+    /queries/run endpoint
+    """
+    
+    logging.info(f"Deleting old objects found in : {old_records_file}")
+    old_records_filename = Path(old_records_file).name
+    old_base_name = old_records_filename.split("_")[0]
+
+    # Get API client(s)
+    config = ctx.obj['site_config']
+    api_user_client = NmdcRuntimeUserApi(config)
+    
+    #get old db records
+    with open(old_records_file, "r") as f:
+        old_db_records = json.load(f)
+    
+    #set list to capture annotation genes for agg set    
+    gene_id_list = []
+    
+    for record in old_db_records:
+        for set_name, object_record in record.items():
+            if set_name == "omics_processing_set":
+                continue
+            if isinstance(object_record, list):
+                for item in object_record:
+                    if "id" in item:
+                        if set_name == "metagenome_annotation_activity_set":
+                            gene_id_list.append(item["id"])
+                        delete_query = {
+                            "delete": set_name,
+                            "deletes": [{"q": {"id": item['id']}, "limit": 1}]
+                            }
+                        logging.info(f"Running query: {delete_query}, deleting {set_name} with id: {item['id']}")
+                        
+                        run_query_response = api_user_client.delete_query(delete_query)
+                        
+                        logging.info(f"Deleting query posted with response: {run_query_response}")
+                        
+    for annotation_id in gene_id_list:
+        logging.info(f"Deleting functional aggregate record with id: {annotation_id}")
+        delete_query_agg = {
+            "delete": "functional_annotation_agg",
+            "deletes": [{"q": {"id": annotation_id}}]
+            } 
+        
+        run_query_agg_response = api_user_client.delete_query(delete_query_agg)
+        
+        logging.info(f"Response for deleting function annotation agg record returned: {run_query_agg_response}")
+                        
+                        
+                        
+    
+    
+
+        
+        
 
 def _get_data_dir(data_dir, dryrun):
     """

From 9fb3f274aefec3c9fb24ecbc1e9ad414e211e408 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 7 Dec 2023 11:29:59 -0800
Subject: [PATCH 83/91] added  method for /qeuries/run

---
 nmdc_automation/api/nmdcapi.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 2c1e5031..29861d8c 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -433,6 +433,23 @@ def get_data_object_by_id(self, data_object_id: str):
                 )
         data_object_record = response.json()
         return data_object_record
+    
+    def run_query(self, query: dict):
+        """
+        Function to run a query using the Microbiome Data API.
+        
+        Parameters:
+        query (dict): The query to be run in JSON format.
+        
+        Returns:
+        dict: The response from the API.
+        """
+        
+        self.ensure_token()
+        url = "https://api.microbiomedata.org/queries/run"
+        
+        response = requests.post(url, json=query, headers=self.headers)
+        return response.json()
 
 def jprint(obj):
     print(json.dumps(obj, indent=2))

From d09597dff30ad0b4028c515633a2b81b820f7acc Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 7 Dec 2023 11:39:43 -0800
Subject: [PATCH 84/91] fixed query key for deleting functional agg record

---
 .../re_iding/scripts/re_id_tool.py            | 179 ++++++++++--------
 1 file changed, 97 insertions(+), 82 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 3d501808..cb7dda3e 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -32,31 +32,34 @@
 
 logging.basicConfig(
     level=logging.INFO,
-    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
-    handlers=[
-        logging.StreamHandler()
-    ]
+    format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
+    handlers=[logging.StreamHandler()],
 )
 
 logger = logging.getLogger(__name__)
 
 
-
 @click.group()
-@click.option("--site-config", type=click.Path(exists=True),
-              default=NAPA_CONFIG,)
+@click.option(
+    "--site-config",
+    type=click.Path(exists=True),
+    default=NAPA_CONFIG,
+)
 @click.pass_context
 def cli(ctx, site_config):
     """
     NMDC re-ID tool
     """
     ctx.ensure_object(dict)
-    ctx.obj['site_config'] = site_config
+    ctx.obj["site_config"] = site_config
 
 
 @cli.command()
-@click.option('--study_id', default=STUDY_ID,
-              help=f'Optional updated study ID. Default: {STUDY_ID}')
+@click.option(
+    "--study_id",
+    default=STUDY_ID,
+    help=f"Optional updated study ID. Default: {STUDY_ID}",
+)
 @click.pass_context
 def extract_records(ctx, study_id):
     """
@@ -70,7 +73,7 @@ def extract_records(ctx, study_id):
     logging.info(f"Extracting workflow records for study_id: {study_id}")
     logging.info(f"study_id: {study_id}")
 
-    config = ctx.obj['site_config']
+    config = ctx.obj["site_config"]
     api_client = NmdcRuntimeUserApi(config)
 
     # 1. Retrieve all OmicsProcessing records for the updated NMDC study ID
@@ -85,30 +88,29 @@ def extract_records(ctx, study_id):
     # 2. For each OmicsProcessing record, find the legacy identifier:
     for omics_processing_record in omics_processing_records:
         db = nmdc.Database()
-        logging.info(
-            f"omics_processing_record: "
-            f"{omics_processing_record['id']}"
-            )
+        logging.info(f"omics_processing_record: " f"{omics_processing_record['id']}")
         legacy_id = _get_legacy_id(omics_processing_record)
         logging.info(f"legacy_id: {legacy_id}")
 
-        if (omics_processing_record["omics_type"]["has_raw_value"] !=
-                "Metagenome"):
+        if omics_processing_record["omics_type"]["has_raw_value"] != "Metagenome":
             logging.info(
                 f"omics_processing_record {omics_processing_record['id']} "
                 f"is not a Metagenome"
-                )
+            )
             continue
         db.omics_processing_set.append(omics_processing_record)
         for data_object_id in omics_processing_record["has_output"]:
-            data_object_record = api_client.get_data_object_by_id(
-                data_object_id
-            )
+            data_object_record = api_client.get_data_object_by_id(data_object_id)
             db.data_object_set.append(data_object_record)
 
         # downstream workflow activity sets
-        (read_qc_records, readbased_records, metagenome_assembly_records,
-         metagenome_annotation_records, mags_records) = [], [], [], [], []
+        (
+            read_qc_records,
+            readbased_records,
+            metagenome_assembly_records,
+            metagenome_annotation_records,
+            mags_records,
+        ) = ([], [], [], [], [])
 
         downstream_workflow_activity_sets = {
             "read_qc_analysis_activity_set": read_qc_records,
@@ -118,9 +120,7 @@ def extract_records(ctx, study_id):
             "mags_activity_set": mags_records,
         }
         for set_name, records in downstream_workflow_activity_sets.items():
-            records = api_client.get_workflow_activity_informed_by(
-                set_name, legacy_id
-            )
+            records = api_client.get_workflow_activity_informed_by(set_name, legacy_id)
             db.__setattr__(set_name, records)
             # Add the data objects referenced by the `has_output` property
             for record in records:
@@ -132,13 +132,11 @@ def extract_records(ctx, study_id):
                     logging.info(
                         f"data_object_record: "
                         f"{data_object_record['id']}, {data_object_record['description']}"
-                        )
+                    )
                     db.data_object_set.append(data_object_record)
 
         # Search for orphaned data objects with the legacy ID in the description
-        orphaned_data_objects = api_client.get_data_objects_by_description(
-            legacy_id
-        )
+        orphaned_data_objects = api_client.get_data_objects_by_description(legacy_id)
         # check that we don't already have the data object in the set
         for data_object in orphaned_data_objects:
             if data_object["id"] not in [d["id"] for d in db.data_object_set]:
@@ -146,7 +144,7 @@ def extract_records(ctx, study_id):
                 logging.info(
                     f"Added orphaned data object: "
                     f"{data_object['id']}, {data_object['description']}"
-                    )
+                )
 
         retrieved_databases.append(db)
 
@@ -157,12 +155,22 @@ def extract_records(ctx, study_id):
 
 
 @cli.command()
-@click.option('--dryrun / --no-dryrun', is_flag=True, default=True,
-              help='Dryrun mode: use local data dir and do not save results')
-@click.option('--study_id', default=STUDY_ID,
-              help=f'Optional updated study ID. Default: {STUDY_ID}')
-@click.option('--data_dir', default=BASE_DATAFILE_DIR,
-              help=f'Optional base datafile directory. Default: {BASE_DATAFILE_DIR}')
+@click.option(
+    "--dryrun / --no-dryrun",
+    is_flag=True,
+    default=True,
+    help="Dryrun mode: use local data dir and do not save results",
+)
+@click.option(
+    "--study_id",
+    default=STUDY_ID,
+    help=f"Optional updated study ID. Default: {STUDY_ID}",
+)
+@click.option(
+    "--data_dir",
+    default=BASE_DATAFILE_DIR,
+    help=f"Optional base datafile directory. Default: {BASE_DATAFILE_DIR}",
+)
 @click.pass_context
 def process_records(ctx, dryrun, study_id, data_dir):
     """
@@ -177,7 +185,7 @@ def process_records(ctx, dryrun, study_id, data_dir):
         logging.info("Running in dryrun mode")
 
     # Get API client
-    config = ctx.obj['site_config']
+    config = ctx.obj["site_config"]
     api_client = NmdcRuntimeApi(config)
 
     # Get Database dump file paths and the data directory
@@ -188,7 +196,6 @@ def process_records(ctx, dryrun, study_id, data_dir):
     # Initialize re-ID tool
     reid_tool = ReIdTool(api_client, data_dir)
 
-
     # Read extracted DB records
     logging.info(f"Using db_infile: {db_infile}")
     with open(db_infile, "r") as f:
@@ -211,20 +218,24 @@ def process_records(ctx, dryrun, study_id, data_dir):
         # update Metagenome Assembly
         new_db = reid_tool.update_metagenome_assembly_set(db_record, new_db)
         # update Read Based Taxonomy Analysis
-        new_db = reid_tool.update_read_based_taxonomy_analysis_activity_set(db_record, new_db)
+        new_db = reid_tool.update_read_based_taxonomy_analysis_activity_set(
+            db_record, new_db
+        )
 
         re_ided_db_records.append(new_db)
 
-
-    json_data = json.loads(json_dumper.dumps(re_ided_db_records,
-                                             inject_type=False))
+    json_data = json.loads(json_dumper.dumps(re_ided_db_records, inject_type=False))
     with open(db_outfile, "w") as f:
         f.write(json.dumps(json_data, indent=4))
-        
+
 
 @cli.command()
-@click.argument('reid_records_file', type=click.Path(exists=True))
-@click.option('--changesheet_only', is_flag=True, default=False,)
+@click.argument("reid_records_file", type=click.Path(exists=True))
+@click.option(
+    "--changesheet_only",
+    is_flag=True,
+    default=False,
+)
 @click.pass_context
 def ingest_records(ctx, reid_records_file, changesheet_only):
     """
@@ -238,10 +249,10 @@ def ingest_records(ctx, reid_records_file, changesheet_only):
     reid_base_name = reid_records_filename.split("_")[0]
 
     # Get API client(s)
-    config = ctx.obj['site_config']
+    config = ctx.obj["site_config"]
     api_client = NmdcRuntimeApi(config)
     api_user_client = NmdcRuntimeUserApi(config)
-    
+
     with open(reid_records_file, "r") as f:
         db_records = json.load(f)
 
@@ -263,19 +274,21 @@ def ingest_records(ctx, reid_records_file, changesheet_only):
             legacy_omics_processing_record = resp.json()
             # delete legacy has_output
             change = ChangesheetLineItem(
-                id=omics_processing_id, action="remove item",
+                id=omics_processing_id,
+                action="remove item",
                 attribute="has_output",
-                value="|".join(legacy_omics_processing_record["has_output"]) + "|", )
+                value="|".join(legacy_omics_processing_record["has_output"]) + "|",
+            )
             changesheet.line_items.append(change)
             logging.info(f"changes: {change}")
 
-
-
             # insert new has_output
             change = ChangesheetLineItem(
-                id=omics_processing_id, action="insert",
+                id=omics_processing_id,
+                action="insert",
                 attribute="has_output",
-                value="|".join(omics_processing_record["has_output"]) + "|", )
+                value="|".join(omics_processing_record["has_output"]) + "|",
+            )
             changesheet.line_items.append(change)
             logging.info(f"changes: {change}")
 
@@ -295,7 +308,7 @@ def ingest_records(ctx, reid_records_file, changesheet_only):
 
 
 @cli.command()
-@click.argument('old_records_file', type=click.Path(exists=True))
+@click.argument("old_records_file", type=click.Path(exists=True))
 @click.pass_context
 def delete_old_records(ctx, old_records_file):
     """
@@ -303,22 +316,22 @@ def delete_old_records(ctx, old_records_file):
     delete them using
     /queries/run endpoint
     """
-    
+
     logging.info(f"Deleting old objects found in : {old_records_file}")
     old_records_filename = Path(old_records_file).name
     old_base_name = old_records_filename.split("_")[0]
 
     # Get API client(s)
-    config = ctx.obj['site_config']
+    config = ctx.obj["site_config"]
     api_user_client = NmdcRuntimeUserApi(config)
-    
-    #get old db records
+
+    # get old db records
     with open(old_records_file, "r") as f:
         old_db_records = json.load(f)
-    
-    #set list to capture annotation genes for agg set    
+
+    # set list to capture annotation genes for agg set
     gene_id_list = []
-    
+
     for record in old_db_records:
         for set_name, object_record in record.items():
             if set_name == "omics_processing_set":
@@ -330,32 +343,31 @@ def delete_old_records(ctx, old_records_file):
                             gene_id_list.append(item["id"])
                         delete_query = {
                             "delete": set_name,
-                            "deletes": [{"q": {"id": item['id']}, "limit": 1}]
-                            }
-                        logging.info(f"Running query: {delete_query}, deleting {set_name} with id: {item['id']}")
-                        
+                            "deletes": [{"q": {"id": item["id"]}, "limit": 1}],
+                        }
+                        logging.info(
+                            f"Running query: {delete_query}, deleting {set_name} with id: {item['id']}"
+                        )
+
                         run_query_response = api_user_client.delete_query(delete_query)
-                        
-                        logging.info(f"Deleting query posted with response: {run_query_response}")
-                        
+
+                        logging.info(
+                            f"Deleting query posted with response: {run_query_response}"
+                        )
+
     for annotation_id in gene_id_list:
         logging.info(f"Deleting functional aggregate record with id: {annotation_id}")
         delete_query_agg = {
             "delete": "functional_annotation_agg",
-            "deletes": [{"q": {"id": annotation_id}}]
-            } 
-        
+            "deletes": [{"q": {"metagenome_annotation_id": annotation_id}}],
+        }
+
         run_query_agg_response = api_user_client.delete_query(delete_query_agg)
-        
-        logging.info(f"Response for deleting function annotation agg record returned: {run_query_agg_response}")
-                        
-                        
-                        
-    
-    
 
-        
-        
+        logging.info(
+            f"Response for deleting function annotation agg record returned: {run_query_agg_response}"
+        )
+
 
 def _get_data_dir(data_dir, dryrun):
     """
@@ -369,6 +381,7 @@ def _get_data_dir(data_dir, dryrun):
     logging.info(f"Using datafile_dir: {data_dir}")
     return data_dir
 
+
 def _get_database_paths(study_id, dryrun):
     """
     Return the paths to the input and output data files
@@ -383,6 +396,7 @@ def _get_database_paths(study_id, dryrun):
         db_outfile = DATA_DIR.joinpath(f"{study_id}{db_outfile_suffix}")
     return db_infile, db_outfile
 
+
 def _get_legacy_id(omics_processing_record: dict) -> str:
     """
     Get the legacy ID for the given OmicsProcessing record.
@@ -407,5 +421,6 @@ def _get_legacy_id(omics_processing_record: dict) -> str:
         legacy_id = legacy_ids[0]
     return legacy_id
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     cli(obj={})

From e4fd0272f776753742f6299705e54544b766410f Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Thu, 7 Dec 2023 11:53:26 -0800
Subject: [PATCH 85/91] added try-except block to catch errors

---
 .../re_iding/scripts/re_id_tool.py            | 52 ++++++++++++-------
 1 file changed, 33 insertions(+), 19 deletions(-)

diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index cb7dda3e..8a9c1498 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -9,7 +9,7 @@
 from pathlib import Path
 import json
 import click
-
+import requests
 from linkml_runtime.dumpers import json_dumper
 
 from nmdc_automation.api import NmdcRuntimeApi, NmdcRuntimeUserApi
@@ -345,28 +345,42 @@ def delete_old_records(ctx, old_records_file):
                             "delete": set_name,
                             "deletes": [{"q": {"id": item["id"]}, "limit": 1}],
                         }
-                        logging.info(
-                            f"Running query: {delete_query}, deleting {set_name} with id: {item['id']}"
-                        )
-
-                        run_query_response = api_user_client.delete_query(delete_query)
-
-                        logging.info(
-                            f"Deleting query posted with response: {run_query_response}"
-                        )
+                        try:
+                            logging.info(
+                                f"Running query: {delete_query}, deleting {set_name} with id: {item['id']}"
+                            )
+
+                            run_query_response = api_user_client.delete_query(
+                                delete_query
+                            )
+
+                            logging.info(
+                                f"Deleting query posted with response: {run_query_response}"
+                            )
+                        except:
+                            logging.info(
+                                f"An error occured while running: {delete_query}, response retutrned: {e}"
+                            )
 
     for annotation_id in gene_id_list:
-        logging.info(f"Deleting functional aggregate record with id: {annotation_id}")
-        delete_query_agg = {
-            "delete": "functional_annotation_agg",
-            "deletes": [{"q": {"metagenome_annotation_id": annotation_id}}],
-        }
+        try:
+            logging.info(
+                f"Deleting functional aggregate record with id: {annotation_id}"
+            )
+            delete_query_agg = {
+                "delete": "functional_annotation_agg",
+                "deletes": [{"q": {"metagenome_annotation_id": annotation_id}}],
+            }
 
-        run_query_agg_response = api_user_client.delete_query(delete_query_agg)
+            run_query_agg_response = api_user_client.delete_query(delete_query_agg)
 
-        logging.info(
-            f"Response for deleting function annotation agg record returned: {run_query_agg_response}"
-        )
+            logging.info(
+                f"Response for deleting functional annotation agg record returned: {run_query_agg_response}"
+            )
+        except requests.exceptions.RequestException as e:
+            logging.error(
+                f"An error occurred while deleting annotation id {annotation_id}: {e}"
+            )
 
 
 def _get_data_dir(data_dir, dryrun):

From afb0a740b873464c7da53d52457d4e68078b9b25 Mon Sep 17 00:00:00 2001
From: Michal Babinski <mbabinski@lanl.gov>
Date: Tue, 19 Dec 2023 12:15:46 -0800
Subject: [PATCH 86/91] fixed functional annotation agg

---
 nmdc_automation/api/nmdcapi.py                 | 4 ++--
 nmdc_automation/re_iding/scripts/re_id_tool.py | 9 ++++-----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 29861d8c..aa386997 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -446,8 +446,8 @@ def run_query(self, query: dict):
         """
         
         self.ensure_token()
-        url = "https://api.microbiomedata.org/queries/run"
-        
+        url = "https://api.microbiomedata.org/queries:run"
+      
         response = requests.post(url, json=query, headers=self.headers)
         return response.json()
 
diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py
index 8a9c1498..f39d83d9 100755
--- a/nmdc_automation/re_iding/scripts/re_id_tool.py
+++ b/nmdc_automation/re_iding/scripts/re_id_tool.py
@@ -331,7 +331,6 @@ def delete_old_records(ctx, old_records_file):
 
     # set list to capture annotation genes for agg set
     gene_id_list = []
-
     for record in old_db_records:
         for set_name, object_record in record.items():
             if set_name == "omics_processing_set":
@@ -350,14 +349,14 @@ def delete_old_records(ctx, old_records_file):
                                 f"Running query: {delete_query}, deleting {set_name} with id: {item['id']}"
                             )
 
-                            run_query_response = api_user_client.delete_query(
+                            run_query_response = api_user_client.run_query(
                                 delete_query
                             )
 
                             logging.info(
                                 f"Deleting query posted with response: {run_query_response}"
                             )
-                        except:
+                        except requests.exceptions.RequestException as e:
                             logging.info(
                                 f"An error occured while running: {delete_query}, response retutrned: {e}"
                             )
@@ -369,10 +368,10 @@ def delete_old_records(ctx, old_records_file):
             )
             delete_query_agg = {
                 "delete": "functional_annotation_agg",
-                "deletes": [{"q": {"metagenome_annotation_id": annotation_id}}],
+                "deletes": [{"q": {"metagenome_annotation_id": annotation_id}, "limit": 1}],
             }
 
-            run_query_agg_response = api_user_client.delete_query(delete_query_agg)
+            run_query_agg_response = api_user_client.run_query(delete_query_agg)
 
             logging.info(
                 f"Response for deleting functional annotation agg record returned: {run_query_agg_response}"

From 65fa67ea55ba3db2ba8d78eb20e34d1edb3e5c41 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 9 Jan 2024 07:59:21 -0800
Subject: [PATCH 87/91] update make test to use poetry

remove max_page_size args from test
---
 Makefile              | 2 +-
 tests/test_nmdcapi.py | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index 51500800..a1dce99a 100644
--- a/Makefile
+++ b/Makefile
@@ -1,3 +1,3 @@
 
 test:
-	PYTHONPATH=$(shell pwd) pytest --cov-report term --cov=nmdc_automation ./tests
+	poetry run pytest --cov-report term --cov=nmdc_automation ./tests
diff --git a/tests/test_nmdcapi.py b/tests/test_nmdcapi.py
index a5525c34..2d93ceeb 100644
--- a/tests/test_nmdcapi.py
+++ b/tests/test_nmdcapi.py
@@ -58,15 +58,15 @@ def test_list_funcs(mock_api, requests_mock):
 
     # TODO: ccheck the full url
     requests_mock.get("http://localhost/jobs", json=mock_resp)
-    resp = n.list_jobs(filt="a=b", max_page_size=10)
+    resp = n.list_jobs(filt="a=b")
     assert resp is not None
 
     requests_mock.get("http://localhost/operations", json=[])
-    resp = n.list_ops(filt="a=b", max_page_size=10)
+    resp = n.list_ops(filt="a=b")
     assert resp is not None
 
     requests_mock.get("http://localhost/objects", json=[])
-    resp = n.list_objs(filt="a=b", max_page_size=10)
+    resp = n.list_objs(filt="a=b")
     assert resp is not None
 
 

From e1161d8fb5899cd334c8accdf6cd2cdc4dc77df5 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 9 Jan 2024 08:07:24 -0800
Subject: [PATCH 88/91] poetry add flake8

---
 poetry.lock    | 1039 +++++++++++++++++-------------------------------
 pyproject.toml |    2 +
 2 files changed, 375 insertions(+), 666 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 05fa8c4a..08a4c1ea 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -42,21 +42,22 @@ test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
-    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
 ]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
+dev = ["attrs[tests]", "pre-commit"]
 docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
 tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "cachetools"
@@ -228,73 +229,6 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
-[[package]]
-name = "coverage"
-version = "7.3.2"
-description = "Code coverage measurement for Python"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "coverage-7.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d872145f3a3231a5f20fd48500274d7df222e291d90baa2026cc5152b7ce86bf"},
-    {file = "coverage-7.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:310b3bb9c91ea66d59c53fa4989f57d2436e08f18fb2f421a1b0b6b8cc7fffda"},
-    {file = "coverage-7.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f47d39359e2c3779c5331fc740cf4bce6d9d680a7b4b4ead97056a0ae07cb49a"},
-    {file = "coverage-7.3.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:aa72dbaf2c2068404b9870d93436e6d23addd8bbe9295f49cbca83f6e278179c"},
-    {file = "coverage-7.3.2-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:beaa5c1b4777f03fc63dfd2a6bd820f73f036bfb10e925fce067b00a340d0f3f"},
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-
-[package.extras]
-toml = ["tomli"]
-
 [[package]]
 name = "curies"
 version = "0.7.4"
@@ -356,13 +290,13 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 
 [[package]]
 name = "distlib"
-version = "0.3.7"
+version = "0.3.8"
 description = "Distribution utilities"
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+version = "7.0.0"
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 [[package]]
 name = "fqdn"
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 [package.extras]
-docs = ["Sphinx"]
+docs = ["Sphinx", "furo"]
 test = ["objgraph", "psutil"]
 
 [[package]]
@@ -726,13 +661,13 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
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 files = [
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 [package.dependencies]
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 [[package]]
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 description = "Linked Open Data Modeling Language"
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 [package.dependencies]
@@ -795,13 +730,13 @@ linkml-runtime = ">=1.1.6"
 
 [[package]]
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 description = "Runtime environment for LinkML, the Linked open data modeling language"
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 python-versions = ">=3.7.6,<4.0.0"
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-
-[package.dependencies]
-packaging = "*"
-sentinels = "*"
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 [[package]]
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 version = "7.8.0"
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 linkml-runtime = ">=1.5.4,<2.0.0"
 
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 [package.dependencies]
@@ -1321,13 +1128,13 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pyflakes"
-version = "3.1.0"
+version = "3.2.0"
 description = "passive checker of Python programs"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -1447,20 +1254,6 @@ snappy = ["python-snappy"]
 test = ["pytest (>=7)"]
 zstd = ["zstandard"]
 
-[[package]]
-name = "pymongo-inmemory"
-version = "0.4.0"
-description = "A mongo mocking library with an ephemeral MongoDB running in memory."
-optional = false
-python-versions = ">=3.9,<4.0"
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-
-[package.dependencies]
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-
 [[package]]
 name = "pyparsing"
 version = "3.1.1"
@@ -1537,13 +1330,13 @@ shexjsg = ">=0.8.1"
 
 [[package]]
 name = "pytest"
-version = "7.4.3"
+version = "7.4.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1557,41 +1350,6 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
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-
-[package.extras]
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-
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-description = "Generate local badges (shields) reporting your test suite status."
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-
 [[package]]
 name = "pytest-logging"
 version = "2015.11.4"
@@ -1785,13 +1543,13 @@ rdflib-jsonld = "0.6.1"
 
 [[package]]
 name = "referencing"
-version = "0.31.1"
+version = "0.32.1"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -1819,25 +1577,6 @@ urllib3 = ">=1.21.1,<3"
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
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-
-[package.extras]
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-test = ["fixtures", "mock", "purl", "pytest", "requests-futures", "sphinx", "testtools"]
-
 [[package]]
 name = "rfc3339-validator"
 version = "0.1.4"
@@ -1865,110 +1604,110 @@ files = [
 
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
 greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""}
-typing-extensions = ">=4.2.0"
+typing-extensions = ">=4.6.0"
 
 [package.extras]
 aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
 aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
 mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
@@ -2232,7 +1950,7 @@ mssql-pyodbc = ["pyodbc"]
 mypy = ["mypy (>=0.910)"]
 mysql = ["mysqlclient (>=1.4.0)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx-oracle (>=8)"]
+oracle = ["cx_oracle (>=8)"]
 oracle-oracledb = ["oracledb (>=1.0.1)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
@@ -2242,7 +1960,7 @@ postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
 postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
 pymysql = ["pymysql"]
-sqlcipher = ["sqlcipher3-binary"]
+sqlcipher = ["sqlcipher3_binary"]
 
 [[package]]
 name = "tomli"
@@ -2284,35 +2002,24 @@ testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pol
 
 [[package]]
 name = "types-python-dateutil"
-version = "2.8.19.14"
+version = "2.8.19.20240106"
 description = "Typing stubs for python-dateutil"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "types-python-dateutil-2.8.19.14.tar.gz", hash = "sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b"},
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+    {file = "types-python-dateutil-2.8.19.20240106.tar.gz", hash = "sha256:1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f"},
+    {file = "types_python_dateutil-2.8.19.20240106-py3-none-any.whl", hash = "sha256:efbbdc54590d0f16152fa103c9879c7d4a00e82078f6e2cf01769042165acaa2"},
 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.8.0"
+version = "4.9.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
-    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
-]
-
-[[package]]
-name = "tzdata"
-version = "2023.3"
-description = "Provider of IANA time zone data"
-optional = false
-python-versions = ">=2"
-files = [
-    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
-    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+    {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
+    {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
 ]
 
 [[package]]
@@ -2501,4 +2208,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "211c7b05291828dc0859f1df7e90d97cb941e420bae65330b930a582627565c1"
+content-hash = "a2274b559edcfe85dfa748761736502fe4769dde2c29c05f406e0df8ed800aab"
diff --git a/pyproject.toml b/pyproject.toml
index 2d3b1673..8aed7640 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,6 +19,8 @@ python-dotenv = "^1.0.0"
 click = "^8.1.3"
 pytest = "^7.3.1"
 pytest-mock = "^3.12.0"
+flake8 = "^7.0.0"
+setuptools = "^69.0.3"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"

From 0a08bf0ab80ccbb768e8cb80358d017756311848 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 9 Jan 2024 08:54:30 -0800
Subject: [PATCH 89/91] update poetry env somehow dropped pandas

---
 poetry.lock    | 126 ++++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml |   1 +
 2 files changed, 126 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index 08a4c1ea..a621e8a1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -849,6 +849,51 @@ files = [
 linkml = ">=1.5.6,<2.0.0"
 linkml-runtime = ">=1.5.4,<2.0.0"
 
+[[package]]
+name = "numpy"
+version = "1.26.3"
+description = "Fundamental package for array computing in Python"
+optional = false
+python-versions = ">=3.9"
+files = [
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+    {file = "numpy-1.26.3-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:3c67423b3703f8fbd90f5adaa37f85b5794d3366948efe9a5190a5f3a83fc34e"},
+    {file = "numpy-1.26.3-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:46f47ee566d98849323f01b349d58f2557f02167ee301e5e28809a8c0e27a2d0"},
+    {file = "numpy-1.26.3-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:a8474703bffc65ca15853d5fd4d06b18138ae90c17c8d12169968e998e448bb5"},
+    {file = "numpy-1.26.3.tar.gz", hash = "sha256:697df43e2b6310ecc9d95f05d5ef20eacc09c7c4ecc9da3f235d39e71b7da1e4"},
+]
+
 [[package]]
 name = "openpyxl"
 version = "3.1.2"
@@ -888,6 +933,74 @@ files = [
     {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
 ]
 
+[[package]]
+name = "pandas"
+version = "2.1.4"
+description = "Powerful data structures for data analysis, time series, and statistics"
+optional = false
+python-versions = ">=3.9"
+files = [
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+
+[package.dependencies]
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+    {version = ">=1.23.2,<2", markers = "python_version == \"3.11\""},
+    {version = ">=1.26.0,<2", markers = "python_version >= \"3.12\""},
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+python-dateutil = ">=2.8.2"
+pytz = ">=2020.1"
+tzdata = ">=2022.1"
+
+[package.extras]
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+computation = ["scipy (>=1.8.1)", "xarray (>=2022.03.0)"]
+consortium-standard = ["dataframe-api-compat (>=0.1.7)"]
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+feather = ["pyarrow (>=7.0.0)"]
+fss = ["fsspec (>=2022.05.0)"]
+gcp = ["gcsfs (>=2022.05.0)", "pandas-gbq (>=0.17.5)"]
+hdf5 = ["tables (>=3.7.0)"]
+html = ["beautifulsoup4 (>=4.11.1)", "html5lib (>=1.1)", "lxml (>=4.8.0)"]
+mysql = ["SQLAlchemy (>=1.4.36)", "pymysql (>=1.0.2)"]
+output-formatting = ["jinja2 (>=3.1.2)", "tabulate (>=0.8.10)"]
+parquet = ["pyarrow (>=7.0.0)"]
+performance = ["bottleneck (>=1.3.4)", "numba (>=0.55.2)", "numexpr (>=2.8.0)"]
+plot = ["matplotlib (>=3.6.1)"]
+postgresql = ["SQLAlchemy (>=1.4.36)", "psycopg2 (>=2.9.3)"]
+spss = ["pyreadstat (>=1.1.5)"]
+sql-other = ["SQLAlchemy (>=1.4.36)"]
+test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-xdist (>=2.2.0)"]
+xml = ["lxml (>=4.8.0)"]
+
 [[package]]
 name = "parse"
 version = "1.20.0"
@@ -2022,6 +2135,17 @@ files = [
     {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
 ]
 
+[[package]]
+name = "tzdata"
+version = "2023.4"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+    {file = "tzdata-2023.4-py2.py3-none-any.whl", hash = "sha256:aa3ace4329eeacda5b7beb7ea08ece826c28d761cda36e747cfbf97996d39bf3"},
+    {file = "tzdata-2023.4.tar.gz", hash = "sha256:dd54c94f294765522c77399649b4fefd95522479a664a0cec87f41bebc6148c9"},
+]
+
 [[package]]
 name = "uri-template"
 version = "1.3.0"
@@ -2208,4 +2332,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "a2274b559edcfe85dfa748761736502fe4769dde2c29c05f406e0df8ed800aab"
+content-hash = "b24f0167717021cc1dff5c4194b9e68f252ffc89158b068b783d37673fae9fac"
diff --git a/pyproject.toml b/pyproject.toml
index 8aed7640..4a00c350 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,6 +21,7 @@ pytest = "^7.3.1"
 pytest-mock = "^3.12.0"
 flake8 = "^7.0.0"
 setuptools = "^69.0.3"
+pandas = "^2.1.4"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"

From 27c80b9291e88cec28f7a5720ba50dcc8f075e3c Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 9 Jan 2024 08:57:30 -0800
Subject: [PATCH 90/91] update reqs somehow dropped from poetry env

---
 poetry.lock    | 170 ++++++++++++++++++++++++++++++++++++++++++++++++-
 pyproject.toml |   4 ++
 2 files changed, 173 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index a621e8a1..0cb077e9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -229,6 +229,73 @@ files = [
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
 
+[[package]]
+name = "coverage"
+version = "7.4.0"
+description = "Code coverage measurement for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "coverage-7.4.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:36b0ea8ab20d6a7564e89cb6135920bc9188fb5f1f7152e94e8300b7b189441a"},
+    {file = "coverage-7.4.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0676cd0ba581e514b7f726495ea75aba3eb20899d824636c6f59b0ed2f88c471"},
+    {file = "coverage-7.4.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d0ca5c71a5a1765a0f8f88022c52b6b8be740e512980362f7fdbb03725a0d6b9"},
+    {file = "coverage-7.4.0-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a7c97726520f784239f6c62506bc70e48d01ae71e9da128259d61ca5e9788516"},
+    {file = "coverage-7.4.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:815ac2d0f3398a14286dc2cea223a6f338109f9ecf39a71160cd1628786bc6f5"},
+    {file = "coverage-7.4.0-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:80b5ee39b7f0131ebec7968baa9b2309eddb35b8403d1869e08f024efd883566"},
+    {file = "coverage-7.4.0-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:5b2ccb7548a0b65974860a78c9ffe1173cfb5877460e5a229238d985565574ae"},
+    {file = "coverage-7.4.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:995ea5c48c4ebfd898eacb098164b3cc826ba273b3049e4a889658548e321b43"},
+    {file = "coverage-7.4.0-cp310-cp310-win32.whl", hash = "sha256:79287fd95585ed36e83182794a57a46aeae0b64ca53929d1176db56aacc83451"},
+    {file = "coverage-7.4.0-cp310-cp310-win_amd64.whl", hash = "sha256:5b14b4f8760006bfdb6e08667af7bc2d8d9bfdb648351915315ea17645347137"},
+    {file = "coverage-7.4.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:04387a4a6ecb330c1878907ce0dc04078ea72a869263e53c72a1ba5bbdf380ca"},
+    {file = "coverage-7.4.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:ea81d8f9691bb53f4fb4db603203029643caffc82bf998ab5b59ca05560f4c06"},
+    {file = "coverage-7.4.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:74775198b702868ec2d058cb92720a3c5a9177296f75bd97317c787daf711505"},
+    {file = "coverage-7.4.0-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:76f03940f9973bfaee8cfba70ac991825611b9aac047e5c80d499a44079ec0bc"},
+    {file = "coverage-7.4.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:485e9f897cf4856a65a57c7f6ea3dc0d4e6c076c87311d4bc003f82cfe199d25"},
+    {file = "coverage-7.4.0-cp311-cp311-musllinux_1_1_aarch64.whl", hash = "sha256:6ae8c9d301207e6856865867d762a4b6fd379c714fcc0607a84b92ee63feff70"},
+    {file = "coverage-7.4.0-cp311-cp311-musllinux_1_1_i686.whl", hash = "sha256:bf477c355274a72435ceb140dc42de0dc1e1e0bf6e97195be30487d8eaaf1a09"},
+    {file = "coverage-7.4.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:83c2dda2666fe32332f8e87481eed056c8b4d163fe18ecc690b02802d36a4d26"},
+    {file = "coverage-7.4.0-cp311-cp311-win32.whl", hash = "sha256:697d1317e5290a313ef0d369650cfee1a114abb6021fa239ca12b4849ebbd614"},
+    {file = "coverage-7.4.0-cp311-cp311-win_amd64.whl", hash = "sha256:26776ff6c711d9d835557ee453082025d871e30b3fd6c27fcef14733f67f0590"},
+    {file = "coverage-7.4.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:13eaf476ec3e883fe3e5fe3707caeb88268a06284484a3daf8250259ef1ba143"},
+    {file = "coverage-7.4.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:846f52f46e212affb5bcf131c952fb4075b55aae6b61adc9856222df89cbe3e2"},
+    {file = "coverage-7.4.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:26f66da8695719ccf90e794ed567a1549bb2644a706b41e9f6eae6816b398c4a"},
+    {file = "coverage-7.4.0-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:164fdcc3246c69a6526a59b744b62e303039a81e42cfbbdc171c91a8cc2f9446"},
+    {file = "coverage-7.4.0-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:316543f71025a6565677d84bc4df2114e9b6a615aa39fb165d697dba06a54af9"},
+    {file = "coverage-7.4.0-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:bb1de682da0b824411e00a0d4da5a784ec6496b6850fdf8c865c1d68c0e318dd"},
+    {file = "coverage-7.4.0-cp312-cp312-musllinux_1_1_i686.whl", hash = "sha256:0e8d06778e8fbffccfe96331a3946237f87b1e1d359d7fbe8b06b96c95a5407a"},
+    {file = "coverage-7.4.0-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:a56de34db7b7ff77056a37aedded01b2b98b508227d2d0979d373a9b5d353daa"},
+    {file = "coverage-7.4.0-cp312-cp312-win32.whl", hash = "sha256:51456e6fa099a8d9d91497202d9563a320513fcf59f33991b0661a4a6f2ad450"},
+    {file = "coverage-7.4.0-cp312-cp312-win_amd64.whl", hash = "sha256:cd3c1e4cb2ff0083758f09be0f77402e1bdf704adb7f89108007300a6da587d0"},
+    {file = "coverage-7.4.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:e9d1bf53c4c8de58d22e0e956a79a5b37f754ed1ffdbf1a260d9dcfa2d8a325e"},
+    {file = "coverage-7.4.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:109f5985182b6b81fe33323ab4707011875198c41964f014579cf82cebf2bb85"},
+    {file = "coverage-7.4.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3cc9d4bc55de8003663ec94c2f215d12d42ceea128da8f0f4036235a119c88ac"},
+    {file = "coverage-7.4.0-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:cc6d65b21c219ec2072c1293c505cf36e4e913a3f936d80028993dd73c7906b1"},
+    {file = "coverage-7.4.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5a10a4920def78bbfff4eff8a05c51be03e42f1c3735be42d851f199144897ba"},
+    {file = "coverage-7.4.0-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:b8e99f06160602bc64da35158bb76c73522a4010f0649be44a4e167ff8555952"},
+    {file = "coverage-7.4.0-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:7d360587e64d006402b7116623cebf9d48893329ef035278969fa3bbf75b697e"},
+    {file = "coverage-7.4.0-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:29f3abe810930311c0b5d1a7140f6395369c3db1be68345638c33eec07535105"},
+    {file = "coverage-7.4.0-cp38-cp38-win32.whl", hash = "sha256:5040148f4ec43644702e7b16ca864c5314ccb8ee0751ef617d49aa0e2d6bf4f2"},
+    {file = "coverage-7.4.0-cp38-cp38-win_amd64.whl", hash = "sha256:9864463c1c2f9cb3b5db2cf1ff475eed2f0b4285c2aaf4d357b69959941aa555"},
+    {file = "coverage-7.4.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:936d38794044b26c99d3dd004d8af0035ac535b92090f7f2bb5aa9c8e2f5cd42"},
+    {file = "coverage-7.4.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:799c8f873794a08cdf216aa5d0531c6a3747793b70c53f70e98259720a6fe2d7"},
+    {file = "coverage-7.4.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e7defbb9737274023e2d7af02cac77043c86ce88a907c58f42b580a97d5bcca9"},
+    {file = "coverage-7.4.0-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a1526d265743fb49363974b7aa8d5899ff64ee07df47dd8d3e37dcc0818f09ed"},
+    {file = "coverage-7.4.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bf635a52fc1ea401baf88843ae8708591aa4adff875e5c23220de43b1ccf575c"},
+    {file = "coverage-7.4.0-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:756ded44f47f330666843b5781be126ab57bb57c22adbb07d83f6b519783b870"},
+    {file = "coverage-7.4.0-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:0eb3c2f32dabe3a4aaf6441dde94f35687224dfd7eb2a7f47f3fd9428e421058"},
+    {file = "coverage-7.4.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:bfd5db349d15c08311702611f3dccbef4b4e2ec148fcc636cf8739519b4a5c0f"},
+    {file = "coverage-7.4.0-cp39-cp39-win32.whl", hash = "sha256:53d7d9158ee03956e0eadac38dfa1ec8068431ef8058fe6447043db1fb40d932"},
+    {file = "coverage-7.4.0-cp39-cp39-win_amd64.whl", hash = "sha256:cfd2a8b6b0d8e66e944d47cdec2f47c48fef2ba2f2dff5a9a75757f64172857e"},
+    {file = "coverage-7.4.0-pp38.pp39.pp310-none-any.whl", hash = "sha256:c530833afc4707fe48524a44844493f36d8727f04dcce91fb978c414a8556cc6"},
+    {file = "coverage-7.4.0.tar.gz", hash = "sha256:707c0f58cb1712b8809ece32b68996ee1e609f71bd14615bd8f87a1293cb610e"},
+]
+
+[package.dependencies]
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
+
+[package.extras]
+toml = ["tomli"]
+
 [[package]]
 name = "curies"
 version = "0.7.4"
@@ -834,6 +901,21 @@ files = [
     {file = "mccabe-0.7.0.tar.gz", hash = "sha256:348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325"},
 ]
 
+[[package]]
+name = "mongomock"
+version = "4.1.2"
+description = "Fake pymongo stub for testing simple MongoDB-dependent code"
+optional = false
+python-versions = "*"
+files = [
+    {file = "mongomock-4.1.2-py2.py3-none-any.whl", hash = "sha256:08a24938a05c80c69b6b8b19a09888d38d8c6e7328547f94d46cadb7f47209f2"},
+    {file = "mongomock-4.1.2.tar.gz", hash = "sha256:f06cd62afb8ae3ef63ba31349abd220a657ef0dd4f0243a29587c5213f931b7d"},
+]
+
+[package.dependencies]
+packaging = "*"
+sentinels = "*"
+
 [[package]]
 name = "nmdc-schema"
 version = "7.8.0"
@@ -1463,6 +1545,52 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
+[[package]]
+name = "pytest-cov"
+version = "4.1.0"
+description = "Pytest plugin for measuring coverage."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"},
+    {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"},
+]
+
+[package.dependencies]
+coverage = {version = ">=5.2.1", extras = ["toml"]}
+pytest = ">=4.6"
+
+[package.extras]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
+
+[[package]]
+name = "pytest-cover"
+version = "3.0.0"
+description = "Pytest plugin for measuring coverage. Forked from `pytest-cov`."
+optional = false
+python-versions = "*"
+files = [
+    {file = "pytest-cover-3.0.0.tar.gz", hash = "sha256:5bdb6c1cc3dd75583bb7bc2c57f5e1034a1bfcb79d27c71aceb0b16af981dbf4"},
+    {file = "pytest_cover-3.0.0-py2.py3-none-any.whl", hash = "sha256:578249955eb3b5f3991209df6e532bb770b647743b7392d3d97698dc02f39ebb"},
+]
+
+[package.dependencies]
+pytest-cov = ">=2.0"
+
+[[package]]
+name = "pytest-coverage"
+version = "0.0"
+description = "Pytest plugin for measuring coverage. Forked from `pytest-cov`."
+optional = false
+python-versions = "*"
+files = [
+    {file = "pytest-coverage-0.0.tar.gz", hash = "sha256:db6af2cbd7e458c7c9fd2b4207cee75258243c8a81cad31a7ee8cfad5be93c05"},
+    {file = "pytest_coverage-0.0-py2.py3-none-any.whl", hash = "sha256:dedd084c5e74d8e669355325916dc011539b190355021b037242514dee546368"},
+]
+
+[package.dependencies]
+pytest-cover = "*"
+
 [[package]]
 name = "pytest-logging"
 version = "2015.11.4"
@@ -1690,6 +1818,25 @@ urllib3 = ">=1.21.1,<3"
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
+[[package]]
+name = "requests-mock"
+version = "1.11.0"
+description = "Mock out responses from the requests package"
+optional = false
+python-versions = "*"
+files = [
+    {file = "requests-mock-1.11.0.tar.gz", hash = "sha256:ef10b572b489a5f28e09b708697208c4a3b2b89ef80a9f01584340ea357ec3c4"},
+    {file = "requests_mock-1.11.0-py2.py3-none-any.whl", hash = "sha256:f7fae383f228633f6bececebdab236c478ace2284d6292c6e7e2867b9ab74d15"},
+]
+
+[package.dependencies]
+requests = ">=2.3,<3"
+six = "*"
+
+[package.extras]
+fixture = ["fixtures"]
+test = ["fixtures", "mock", "purl", "pytest", "requests-futures", "sphinx", "testtools"]
+
 [[package]]
 name = "rfc3339-validator"
 version = "0.1.4"
@@ -1900,6 +2047,27 @@ files = [
     {file = "ruamel.yaml.clib-0.2.8.tar.gz", hash = "sha256:beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512"},
 ]
 
+[[package]]
+name = "semver"
+version = "3.0.2"
+description = "Python helper for Semantic Versioning (https://semver.org)"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "semver-3.0.2-py3-none-any.whl", hash = "sha256:b1ea4686fe70b981f85359eda33199d60c53964284e0cfb4977d243e37cf4bf4"},
+    {file = "semver-3.0.2.tar.gz", hash = "sha256:6253adb39c70f6e51afed2fa7152bcd414c411286088fb4b9effb133885ab4cc"},
+]
+
+[[package]]
+name = "sentinels"
+version = "1.0.0"
+description = "Various objects to denote special meanings in python"
+optional = false
+python-versions = "*"
+files = [
+    {file = "sentinels-1.0.0.tar.gz", hash = "sha256:7be0704d7fe1925e397e92d18669ace2f619c92b5d4eb21a89f31e026f9ff4b1"},
+]
+
 [[package]]
 name = "setuptools"
 version = "69.0.3"
@@ -2332,4 +2500,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "b24f0167717021cc1dff5c4194b9e68f252ffc89158b068b783d37673fae9fac"
+content-hash = "ba9830cf7d267f38ced14561877761cb1e853e5a794177952be073450dbf2a3b"
diff --git a/pyproject.toml b/pyproject.toml
index 4a00c350..9b09c50f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,6 +22,10 @@ pytest-mock = "^3.12.0"
 flake8 = "^7.0.0"
 setuptools = "^69.0.3"
 pandas = "^2.1.4"
+pytest-coverage = "^0.0"
+semver = "^3.0.2"
+mongomock = "^4.1.2"
+requests-mock = "^1.11.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"

From e7596c7aa5a4929c03662a1f4fe6b69931168ca6 Mon Sep 17 00:00:00 2001
From: Michael Thornton <mbthornton@lbl.gov>
Date: Tue, 9 Jan 2024 09:20:33 -0800
Subject: [PATCH 91/91] add pytest-local-badge

---
 poetry.lock    | 19 ++++++++++++++++++-
 pyproject.toml |  1 +
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index 0cb077e9..bc045e4d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1591,6 +1591,23 @@ files = [
 [package.dependencies]
 pytest-cover = "*"
 
+[[package]]
+name = "pytest-local-badge"
+version = "1.0.3"
+description = "Generate local badges (shields) reporting your test suite status."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pytest-local-badge-1.0.3.tar.gz", hash = "sha256:e13274cc9cadf91a1e3fa290d0bbbd371a365f9d719411e475596f722c2725a5"},
+    {file = "pytest_local_badge-1.0.3-py3-none-any.whl", hash = "sha256:e14dc79922598e5b27ef4398a3537535ad115df2229ebba0259f6c6d92c6047b"},
+]
+
+[package.dependencies]
+pytest = ">=6.1.0"
+
+[package.extras]
+develop = ["black (>=22.12.0)", "build", "flake8-bugbear", "flake8-comprehensions", "flake8-import-order", "flake8-print", "pep8-naming", "pytest (>=7.1.0,<8)", "pytest-cov", "pytest-mock"]
+
 [[package]]
 name = "pytest-logging"
 version = "2015.11.4"
@@ -2500,4 +2517,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "ba9830cf7d267f38ced14561877761cb1e853e5a794177952be073450dbf2a3b"
+content-hash = "76e09a3ecb5e07197345b22578b7389f6a2c61c8f1a6077c6ded64dbc369c504"
diff --git a/pyproject.toml b/pyproject.toml
index 9b09c50f..4eb20f8a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,6 +26,7 @@ pytest-coverage = "^0.0"
 semver = "^3.0.2"
 mongomock = "^4.1.2"
 requests-mock = "^1.11.0"
+pytest-local-badge = "^1.0.3"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"