Added ability to not import reagents on first import.

src/submissions/backend/scripts/__init__.py

@@ -0,0 +1,7 @@
+from .irida import import_irida
+
+def hello(ctx):
+    print("\n\nHello!\n\n")
+
+def goodbye(ctx):
+    print("\n\nGoodbye\n\n")

src/submissions/backend/scripts/irida.py

@@ -0,0 +1,56 @@
+import logging, sqlite3, json
+from pprint import pformat, pprint
+from datetime import datetime
+from tools import Settings
+from backend import BasicSample
+from backend.db import IridaControl, ControlType
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+def import_irida(ctx:Settings):
+    """
+    Grabs Irida controls from secondary database.
+
+    Args:
+        ctx (Settings): Settings inherited from app.
+
+    """
+    ct = ControlType.query(name="Irida Control")
+    existing_controls = [item.name for item in IridaControl.query()]
+    prm_list = ", ".join([f"'{thing}'" for thing in existing_controls])
+    ctrl_db_path = ctx.directory_path.joinpath("submissions_parser_output", "submissions.db")
+    # print(f"Incoming settings: {pformat(ctx)}")
+    try:
+        conn = sqlite3.connect(ctrl_db_path)
+    except AttributeError as e:
+        print(f"Error, could not import from irida due to {e}")
+        return
+    sql = f"SELECT name, submitted_date, submission_id, contains, matches, kraken, subtype, refseq_version, " \
+          f"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]
+    # incoming_controls = set(item['name'] for item in records)
+    # relevant = list(incoming_controls - existing_controls)
+    for record in records:
+        instance = IridaControl.query(name=record['name'])
+        if instance:
+            logger.warning(f"Irida Control {instance.name} already exists, skipping.")
+            continue
+        record['contains'] = json.loads(record['contains'])
+        assert isinstance(record['contains'], dict)
+        record['matches'] = json.loads(record['matches'])
+        assert isinstance(record['matches'], dict)
+        record['kraken'] = json.loads(record['kraken'])
+        assert isinstance(record['kraken'], dict)
+        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 = BasicSample.query(submitter_id=instance.name)
+        if sample:
+            instance.sample = sample
+            instance.submission = sample.submissions[0]
+        # pprint(instance.__dict__)
+        instance.save()