Created omni-manager, omni-addit

src/scripts/import_irida.py

@@ -0,0 +1,58 @@
+import logging, sqlite3, json
+from pprint import pformat, pprint
+from datetime import datetime
+from tools import Settings
+
+from sqlalchemy.orm import Session
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+def import_irida(ctx: Settings):
+    """
+    Grabs Irida controls from secondary database.
+
+    Args:
+        ctx (Settings): Settings inherited from app.
+    """
+    from backend import BasicSample
+    from backend.db import IridaControl, ControlType
+    # NOTE: Because the main session will be busy in another thread, this requires a new session.
+    new_session = Session(ctx.database_session.get_bind())
+    ct = new_session.query(ControlType).filter(ControlType.name == "Irida Control").first()
+    existing_controls = [item.name for item in new_session.query(IridaControl)]
+    prm_list = ", ".join([f"'{thing}'" for thing in existing_controls])
+    ctrl_db_path = ctx.directory_path.joinpath("submissions_parser_output", "submissions.db")
+    try:
+        conn = sqlite3.connect(ctrl_db_path)
+    except AttributeError as e:
+        logger.error(f"Error, could not import from irida due to {e}")
+        return
+    sql = "SELECT name, submitted_date, submission_id, contains, matches, kraken, subtype, refseq_version, " \
+          "kraken2_version, kraken2_db_version, sample_id FROM _iridacontrol INNER JOIN _control on _control.id " \
+          f"= _iridacontrol.id WHERE _control.name NOT IN ({prm_list})"
+    cursor = conn.execute(sql)
+    records = [
+        dict(name=row[0], submitted_date=row[1], submission_id=row[2], contains=row[3], matches=row[4], kraken=row[5],
+             subtype=row[6], refseq_version=row[7], kraken2_version=row[8], kraken2_db_version=row[9],
+             sample_id=row[10]) for row in cursor]
+    for record in records:
+        instance = new_session.query(IridaControl).filter(IridaControl.name == record['name']).first()
+        if instance:
+            logger.warning(f"Irida Control {instance.name} already exists, skipping.")
+            continue
+        for thing in ['contains', 'matches', 'kraken']:
+            if record[thing]:
+                record[thing] = json.loads(record[thing])
+                assert isinstance(record[thing], dict)
+            else:
+                record[thing] = {}
+        record['submitted_date'] = datetime.strptime(record['submitted_date'], "%Y-%m-%d %H:%M:%S.%f")
+        assert isinstance(record['submitted_date'], datetime)
+        instance = IridaControl(controltype=ct, **record)
+        sample = new_session.query(BasicSample).filter(BasicSample.submitter_id == instance.name).first()
+        if sample:
+            instance.sample = sample
+            instance.submission = sample.submissions[0]
+        new_session.add(instance)
+    new_session.commit()
+    new_session.close()