change get_ena_submission_list to a cronjob and add trigger_submissio…

…n_to_ena which gets approved sequences from a github repo

ena-submission/.gitignore

@@ -1,2 +1,3 @@
 .snakemake/
-results/
+results/
+__pycache__

ena-submission/Snakefile

@@ -63,13 +63,34 @@ rule get_ena_submission_list:
                 --log-level {params.log_level} \
         """
 
-rule get_ena_submission_list_and_sleep:
+rule trigger_submission_to_ena:
     input:
-        file="results/ena_submission_list.json"
+        script="scripts/trigger_submission_to_ena.py",
+        config="results/config.yaml",
+    output:
+        submitted=touch("results/triggered"),
+    params:
+        log_level=LOG_LEVEL,
+    shell:
+        """
+        python {input.script} \
+                --config-file {input.config} \
+                --log-level {params.log_level} \
+        """
+
+rule trigger_submission_to_ena_from_file:  # for testing
+    input:
+        script="scripts/trigger_submission_to_ena.py",
+        input_file="results/approved_ena_submission_list.json",
+        config="results/config.yaml",
     output:
-        file="results/sleep.txt"
+        submitted=touch("results/triggered_from_file"),
+    params:
+        log_level=LOG_LEVEL,
     shell:
         """
-        sleep 360
-        touch {output.file}
+        python {input.script} \
+                --config-file {input.config} \
+                --input-file {input.input_file} \
+                --log-level {params.log_level} \
         """

ena-submission/config/defaults.yaml

@@ -2,3 +2,6 @@ username: external_metadata_updater
 password: external_metadata_updater
 keycloak_client_id: backend-client
 ingest_pipeline_submitter: insdc_ingest_user
+github_username: fake_username
+github_pat: fake_pat
+github_url: https://api.github.com/repos/pathoplexus/ena-submission/contents/test/approved_ena_submission_list.json?ref=main

ena-submission/flyway/sql/V1__Initial_Schema.sql

@@ -2,26 +2,28 @@ CREATE TABLE submission_table (
     accession text not null,
     version bigint not null,
     organism text not null,
-    groupId bigint not null,
+    group_id bigint not null,
     errors jsonb,
     warnings jsonb,
     status_all text not null,
     started_at timestamp not null,
     finished_at timestamp,
+    metadata jsonb,
+    aligned_nucleotide_sequences jsonb,
     external_metadata jsonb,
     primary key (accession, version)
 );
 
 CREATE TABLE project_table (
-    groupId bigint not null,
+    group_id bigint not null,
     organism text not null,
     errors jsonb,
     warnings jsonb,
     status text not null,
     started_at timestamp not null,
     finished_at timestamp,
-    project_metadata jsonb,
-    primary key (groupId, organism)
+    result jsonb,
+    primary key (group_id, organism)
 );
 
 CREATE TABLE sample_table (
@@ -32,7 +34,7 @@ CREATE TABLE sample_table (
     status text not null,
     started_at timestamp not null,
     finished_at timestamp,
-    sample_metadata jsonb,
+    result jsonb,
     primary key (accession, version)
 );
 
@@ -44,6 +46,6 @@ CREATE TABLE assembly_table (
     status text not null,
     started_at timestamp not null,
     finished_at timestamp,
-    assembly_metadata jsonb,
+    result jsonb,
     primary key (accession, version)
 );

ena-submission/scripts/get_ena_submission_list.py

@@ -9,7 +9,7 @@
 import yaml
 from call_loculus import get_released_data
 from notifications import get_slack_config, notify, upload_file_with_comment
-from submission_db import get_db_config, in_submission_table
+from submission_db_helper import get_db_config, in_submission_table
 
 logger = logging.getLogger(__name__)
 logging.basicConfig(

ena-submission/scripts/submission_db_helper.py

@@ -0,0 +1,130 @@
+import os
+from dataclasses import dataclass
+from datetime import datetime
+from enum import Enum
+
+import psycopg2
+import pytz
+
+
+@dataclass
+class DBConfig:
+    username: str
+    password: str
+    host: str
+
+
+def get_db_config(db_password_default: str, db_username_default: str, db_host_default: str):
+    db_password = os.getenv("DB_PASSWORD")
+    if not db_password:
+        db_password = db_password_default
+
+    db_username = os.getenv("DB_USERNAME")
+    if not db_username:
+        db_username = db_username_default
+
+    db_host = os.getenv("DB_HOST")
+    if not db_host:
+        db_host = db_host_default
+
+    db_params = {
+        "username": db_username,
+        "password": db_password,
+        "host": db_host,
+    }
+
+    return DBConfig(**db_params)
+
+
+class StatusAll(Enum):
+    READY_TO_SUBMIT = 0
+    SUBMITTING_PROJECT = 1
+    SUBMITTING_SAMPLE = 2
+    SUBMITTING_ASSEMBLY = 3
+    SUBMITTED_ALL = 4
+    SENT_TO_LOCULUS = 5
+    HAS_ERRORS_PROJECT = 6
+    HAS_ERRORS_ASSEMBLY = 7
+    HAS_ERRORS_SAMPLE = 8
+
+    def __str__(self):
+        return self.name
+
+
+class Status(Enum):
+    READY = 0
+    SUBMITTING = 1
+    SUBMITTED = 2
+    HAS_ERRORS = 3
+
+    def __str__(self):
+        return self.name
+
+
+@dataclass
+class SubmissionTableEntry:
+    accession: str
+    version: str
+    organism: str
+    group_id: int
+    errors: str | None = None
+    warnings: str | None = None
+    status_all: StatusAll = StatusAll.READY_TO_SUBMIT
+    started_at: datetime | None = None
+    finished_at: datetime | None = None
+    metadata: str | None = None
+    aligned_nucleotide_sequences: str | None = None
+    external_metadata: str | None = None
+
+
+def connect_to_db(db_config: DBConfig):
+    """
+    Establish connection to ena_submitter DB, if DB doesn't exist create it.
+    """
+    try:
+        con = psycopg2.connect(
+            dbname="loculus",
+            user=db_config.username,
+            host=db_config.host,
+            password=db_config.password,
+            options="-c search_path=ena-submission",
+        )
+    except ConnectionError as e:
+        raise ConnectionError("Could not connect to loculus DB") from e
+    return con
+
+
+def in_submission_table(accession: str, version: int, db_config: DBConfig) -> bool:
+    con = connect_to_db(db_config)
+    cur = con.cursor()
+    cur.execute(
+        "select * from submission_table where accession=%s and version=%s",
+        (f"{accession}", f"{version}"),
+    )
+    return bool(cur.rowcount)
+
+
+def add_to_submission_table(db_config: DBConfig, submission_table_entry: SubmissionTableEntry):
+    con = connect_to_db(db_config)
+    cur = con.cursor()
+    submission_table_entry.started_at = datetime.now(tz=pytz.utc)
+
+    cur.execute(
+        "insert into submission_table values(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)",
+        (
+            submission_table_entry.accession,
+            submission_table_entry.version,
+            submission_table_entry.organism,
+            submission_table_entry.group_id,
+            submission_table_entry.errors,
+            submission_table_entry.warnings,
+            str(submission_table_entry.status_all),
+            submission_table_entry.started_at,
+            submission_table_entry.finished_at,
+            submission_table_entry.metadata,
+            submission_table_entry.aligned_nucleotide_sequences,
+            submission_table_entry.external_metadata,
+        ),
+    )
+    con.commit()
+    con.close()