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Removed logger.debugs for proven functions.

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This commit is contained in:
lwark
2024-12-12 12:17:21 -06:00
parent b174eb1221
commit 67520cb784
32 changed files with 80 additions and 758 deletions
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4
src/submissions/backend/scripts/__init__.py
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@@ -1,7 +1,7 @@
from .irida import import_irida
def hello(ctx):
print("\n\nHello!\n\n")
print("\n\nHello! Welcome to Robotics Submission Tracker.\n\n")
def goodbye(ctx):
print("\n\nGoodbye\n\n")
print("\n\nGoodbye. Thank you for using Robotics Submission Tracker.\n\n")

8
src/submissions/backend/scripts/irida.py
View File

@@ -19,11 +19,10 @@ def import_irida(ctx:Settings):
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}")
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 " \
@@ -32,8 +31,6 @@ def import_irida(ctx:Settings):
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:
@@ -52,5 +49,4 @@ def import_irida(ctx:Settings):
if sample:
instance.sample = sample
instance.submission = sample.submissions[0]
# pprint(instance.__dict__)
instance.save()
instance.save()