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Bug fixes.

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This commit is contained in:
lwark
2024-12-18 13:35:04 -06:00
parent b1544da730
commit 5fd36308b2
10 changed files with 70 additions and 43 deletions
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50
src/submissions/backend/scripts/import_irida.py
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@@ -4,20 +4,24 @@ from datetime import datetime
from tools import Settings
from backend import BasicSample
from backend.db import IridaControl, ControlType
from sqlalchemy.orm import Session
logger = logging.getLogger(f"submissions.{__name__}")
def script(ctx:Settings):
def script(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()]
# 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 = ControlType.query(name="Irida Control")
ct = new_session.query(ControlType).filter(ControlType.name == "Irida Control").first()
# existing_controls = [item.name for item in IridaControl.query()]
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:
@@ -25,29 +29,39 @@ def script(ctx:Settings):
except AttributeError as e:
logger.error(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 " \
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]
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 = IridaControl.query(name=record['name'])
# instance = IridaControl.query(name=record['name'])
instance = new_session.query(IridaControl).filter(IridaControl.name == record['name']).first()
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)
for thing in ['contains', 'matches', 'kraken']:
if record[thing]:
record[thing] = json.loads(record[thing])
assert isinstance(record[thing], dict)
else:
record[thing] = {}
# 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)
# sample = BasicSample.query(submitter_id=instance.name)
sample = new_session.query(BasicSample).filter(BasicSample.submitter_id == instance.name).first()
if sample:
instance.sample = sample
instance.submission = sample.submissions[0]
instance.save()
# instance.save()
new_session.add(instance)
new_session.commit()
new_session.close()