diff --git a/nmdc_automation/nmdc_common/client.py b/nmdc_automation/nmdc_common/client.py index 9042cb20..e17124e8 100644 --- a/nmdc_automation/nmdc_common/client.py +++ b/nmdc_automation/nmdc_common/client.py @@ -77,7 +77,7 @@ def get_workflow_activities_informed_by(self, workflow_activity_set: str, } url = self.base_url + "nmdcschema/" + workflow_activity_set response = requests.get(url, params=params, headers=self.headers) - logger.info(response.url) + logger.debug(response.url) response.raise_for_status() workflow_activity_record = response.json()["resources"] return workflow_activity_record diff --git a/nmdc_automation/re_iding/db_utils.py b/nmdc_automation/re_iding/db_utils.py index 23f06e3e..481816de 100644 --- a/nmdc_automation/re_iding/db_utils.py +++ b/nmdc_automation/re_iding/db_utils.py @@ -12,8 +12,28 @@ OMICS_PROCESSING_SET = "omics_processing_set" DATA_OBJECT_SET = "data_object_set" READS_QC_SET = "read_qc_analysis_activity_set" +READS_BASED_TAXONOMY_ANALYSIS_ACTIVITY_SET = "read_based_taxonomy_analysis_activity_set" METAGENOME_ASSEMBLY_SET = "metagenome_assembly_set" +METAGENOME_ANNOTATION_ACTIVITY_SET = "metagenome_annotation_activity_set" +METAGENOME_SEQUENCING_ACTIVITY_SET = "metagenome_sequencing_activity_set" +MAGS_ACTIVITY_SET = "mags_activity_set" METATRANSCRIPTOME_ACTIVITY_SET = "metatranscriptome_activity_set" +METAPROTEOMICS_ANALYSIS_ACTIVITY_SET = "metaproteomics_analysis_activity_set" +METABOLOMICS_ANALYSIS_ACTIVITY_SET = "metabolomics_analysis_activity_set" +NOM_ANALYSIS_ACTIVITY_SET= "nom_analysis_activity_set" + +ANALYSIS_ACTIVITIES = [ + READS_QC_SET, + READS_BASED_TAXONOMY_ANALYSIS_ACTIVITY_SET, + METAGENOME_ANNOTATION_ACTIVITY_SET, + METAGENOME_SEQUENCING_ACTIVITY_SET, + METAGENOME_ASSEMBLY_SET, + MAGS_ACTIVITY_SET, + METATRANSCRIPTOME_ACTIVITY_SET, + METAPROTEOMICS_ANALYSIS_ACTIVITY_SET, + METABOLOMICS_ANALYSIS_ACTIVITY_SET, + NOM_ANALYSIS_ACTIVITY_SET +] diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py index 9d5b5c0f..b37a31cf 100755 --- a/nmdc_automation/re_iding/scripts/re_id_tool.py +++ b/nmdc_automation/re_iding/scripts/re_id_tool.py @@ -17,7 +17,7 @@ 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 +from nmdc_automation.re_iding.db_utils import get_omics_processing_id, ANALYSIS_ACTIVITIES # Defaults GOLD_STUDY_ID = "gold:Gs0114663" @@ -33,14 +33,11 @@ LOG_PATH = DATA_DIR.joinpath("re_id_tool.log") logging.basicConfig( - filename="re_id.log", - filemode="w", level=logging.INFO, format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", ) -logger = logging.getLogger(__name__) -logger.addHandler(logging.StreamHandler()) + @click.group() @@ -76,8 +73,8 @@ def extract_records(ctx, study_id, api_base_url): Write the results, as a list of nmdc-schema Database instances to a JSON file. """ start_time = time.time() - logger.info(f"Extracting workflow records for study_id: {study_id}") - logger.info(f"study_id: {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"] # api_client = NmdcRuntimeUserApi(config) @@ -88,7 +85,7 @@ def extract_records(ctx, study_id, api_base_url): api_client.get_omics_processing_records_part_of_study( study_id )) - logger.info( + logging.info( f"Retrieved {len(omics_processing_records)} OmicsProcessing records for study {study_id}" ) @@ -96,14 +93,14 @@ def extract_records(ctx, study_id, api_base_url): # 2. For each OmicsProcessing record, find the legacy identifier: for omics_processing_record in omics_processing_records: db = nmdc.Database() - logger.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) - logger.info(f"legacy_id: {legacy_id}") + logging.info(f"legacy_id: {legacy_id}") omics_type = omics_processing_record["omics_type"]["has_raw_value"] omics_id = omics_processing_record["id"] if omics_type not in ["Metagenome", "Metatranscriptome"]: - logger.info( + logging.info( f"omics_processing_record {omics_id}: {omics_type}] " f"is not a Metagenome or Metatranscriptome, skipping" ) @@ -112,11 +109,11 @@ def extract_records(ctx, study_id, api_base_url): for data_object_id in omics_processing_record["has_output"]: data_object_record = api_client.get_data_object(data_object_id) if not data_object_record: - logger.warning(f"no data object found for {data_object_id}") + logging.warning(f"no data object found for {data_object_id}") continue data_object_type = data_object_record.get("data_object_type") data_object_description = data_object_record.get("description") - logger.info( + logging.info( f"has_output: " f"{data_object_record['id']}, " f"Type: {data_object_type}, " @@ -143,13 +140,13 @@ def extract_records(ctx, study_id, api_base_url): "metatranscriptome_activity_set": metatranscriptome_activity_records, } for set_name, workflow_records in downstream_workflow_activity_sets.items(): - logger.info(f"set_name: {set_name} for {legacy_id}") + logging.info(f"set_name: {set_name} for {legacy_id}") workflow_records = api_client.get_workflow_activities_informed_by(set_name, legacy_id) - logger.info(f"found {len(workflow_records)} records") + logging.info(f"found {len(workflow_records)} records") db.__setattr__(set_name, workflow_records) for workflow_record in workflow_records: - logger.info(f"record: {workflow_record['id']}, {workflow_record['name']}") + logging.info(f"record: {workflow_record['id']}, {workflow_record['name']}") input_output_data_object_ids = [] if "has_input" in workflow_record: input_output_data_object_ids.extend(workflow_record["has_input"]) @@ -161,11 +158,11 @@ def extract_records(ctx, study_id, api_base_url): data_object_id ) if not data_object_record: - logger.warning(f"no data object found for {data_object_id}") + logging.warning(f"no data object found for {data_object_id}") continue data_object_type = data_object_record.get("data_object_type") data_object_description = data_object_record.get("description") - logger.info( + logging.info( f"has_output: " f"{data_object_record['id']}, " f"Type: {data_object_type}, " @@ -180,7 +177,7 @@ def extract_records(ctx, study_id, api_base_url): for data_object in orphaned_data_objects: if data_object not in db.data_object_set: db.data_object_set.append(data_object) - logger.info( + logging.info( f"Added orphaned data object: " f"{data_object['id']}, {data_object['description']}" ) @@ -189,8 +186,8 @@ def extract_records(ctx, study_id, api_base_url): json_data = json.loads(json_dumper.dumps(retrieved_databases, inject_type=False)) db_outfile = DATA_DIR.joinpath(f"{study_id}_associated_record_dump.json") - logger.info(f"Writing {len(retrieved_databases)} records to {db_outfile}") - logger.info(f"Elapsed time: {time.time() - start_time}") + logging.info(f"Writing {len(retrieved_databases)} records to {db_outfile}") + logging.info(f"Elapsed time: {time.time() - start_time}") with open(db_outfile, "w") as f: f.write(json.dumps(json_data, indent=4)) @@ -267,8 +264,8 @@ def process_records(ctx, dryrun, study_id, data_dir): re_ided_db_records.append(new_db) - logger.info(f"Writing {len(re_ided_db_records)} records to {db_outfile}") - logger.info(f"Elapsed time: {time.time() - start_time}") + logging.info(f"Writing {len(re_ided_db_records)} records to {db_outfile}") + logging.info(f"Elapsed time: {time.time() - start_time}") 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)) @@ -340,9 +337,9 @@ def ingest_records(ctx, reid_records_file, changesheet_only): # 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}") + logging.info(f"{record} posted, got response: {resp}") else: - logger.info(f"changesheet_only is True, skipping ingest") + logging.info(f"changesheet_only is True, skipping ingest") changesheet.write_changesheet() logging.info(f"changesheet written to {changesheet.output_filepath}") @@ -427,6 +424,91 @@ def delete_old_records(ctx, old_records_file): ) +@cli.command() +@click.option("--study-id", default=STUDY_ID, help="NMDC study ID") +@click.option("--api-base-url", default=NAPA_BASE_URL, + help=f"Optional base URL for the NMDC API. Default: {NAPA_BASE_URL}") +@click.pass_context +def orphan_data_objects(ctx, study_id, api_base_url): + """ + Scan project data directories, read in the data object records from 'data_objects.json' + and find data objects that: + - are associated with one or more workflow activities has_input or has_output + - are not present in the data_objects collection in the NMDC database + + Write the results to a JSON file of nmdc DataObject instances. + """ + start_time = time.time() + logging.info(f"Scanning for orphaned data objects for {study_id}") + + + api_client = NmdcApi(api_base_url) + with open("unique_data_objects.json", "r") as f: + data_objects = json.load(f) + # index the data objects by ID + data_objects_by_id = {data_object["id"]: data_object for data_object in data_objects} + + + # 1. Retrieve all OmicsProcessing records for the updated NMDC study ID + omics_processing_records = ( + api_client.get_omics_processing_records_part_of_study( + study_id + )) + orphan_data_object_ids = set() + # 2. For each OmicsProcessing record, find the legacy identifier: + for omics_processing_record in omics_processing_records: + informed_by_id = _get_legacy_id(omics_processing_record) + for activity_set_name in ANALYSIS_ACTIVITIES: + workflow_records = api_client.get_workflow_activities_informed_by(activity_set_name, informed_by_id) + for workflow_record in workflow_records: + data_object_ids = set() + data_object_ids.update(workflow_record["has_input"]) + data_object_ids.update(workflow_record["has_output"]) + + # Search the data object IDs + for data_object_id in data_object_ids: + data_object_record = api_client.get_data_object(data_object_id) + if not data_object_record: + logging.warning(f"{informed_by_id} : {workflow_record['id']} " + f"{workflow_record['name']} missing: {data_object_id}") + orphan_data_object_ids.add(data_object_id) + continue + logging.info(f"Elapsed time: {time.time() - start_time}") + logging.info(f"Found {len(orphan_data_object_ids)} orphaned data objects") + # get orphaned data objects from the data_objects_by_id if present + orphaned_data_objects = [] + for data_object_id in orphan_data_object_ids: + if data_object_id in data_objects_by_id: + orphaned_data_objects.append(data_objects_by_id[data_object_id]) + else: + logging.warning(f"orphaned data object {data_object_id} not found in data_objects.json") + logging.info(f"Writing {len(orphaned_data_objects)} orphaned data objects to orphaned_data_objects.json") + if orphaned_data_objects: + with open(f"{study_id}_orphaned_data_objects.json", "w") as f: + f.write(json.dumps(orphaned_data_objects, indent=4)) + + +@cli.command() +@click.argument("data-objects-file", type=click.Path(exists=True)) +def get_unique_data_objects(data_objects_file): + """ + Read in a raw json dump of data objects and return a list of unique data objects + as a json dump. + """ + with open(data_objects_file, "r") as f: + data_objects = json.load(f) + + unique_data_objects = [] + unique_data_object_ids = set() + for data_object in data_objects: + if data_object["id"] not in unique_data_object_ids: + unique_data_objects.append(data_object) + unique_data_object_ids.add(data_object["id"]) + with open("unique_data_objects.json", "w") as f: + f.write(json.dumps(unique_data_objects, indent=4)) + + + def _get_data_dir(data_dir, dryrun): """ Return the path to the data object files @@ -466,7 +548,7 @@ def _get_legacy_id(omics_processing_record: dict) -> str: alternative_ids = omics_processing_record.get("alternative_identifiers", []) legacy_ids.extend(alternative_ids) if len(legacy_ids) == 0: - logging.warning( + logging.debug( f"No legacy IDs found for: {omics_processing_record['id']} using ID instead" ) return omics_processing_record["id"] diff --git a/nmdc_automation/re_iding/scripts/unique_data_objects.json b/nmdc_automation/re_iding/scripts/unique_data_objects.json new file mode 100644 index 00000000..e18791b5 --- /dev/null +++ b/nmdc_automation/re_iding/scripts/unique_data_objects.json @@ -0,0 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