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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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2
src/submissions/backend/db/models/__init__.py
View File

@@ -269,7 +269,7 @@ from .controls import *
from .organizations import *
from .kits import *
from .submissions import *
from .audit import AuditLog
from .audit import *
# NOTE: Add a creator to the submission for reagent association. Assigned here due to circular import constraints.
# https://docs.sqlalchemy.org/en/20/orm/extensions/associationproxy.html#sqlalchemy.ext.associationproxy.association_proxy.params.creator

1
src/submissions/backend/db/models/kits.py
View File

@@ -332,7 +332,6 @@ class KitType(BaseClass):
return new_kit
class ReagentRole(BaseClass):
"""
Base of reagent type abstract

2
src/submissions/backend/db/models/submissions.py
View File

@@ -1265,7 +1265,9 @@ class BasicSubmission(BaseClass, LogMixin):
logger.error(f"Couldn't save association with {equip} due to {e}")
if equip.tips:
for tips in equip.tips:
logger.debug(f"Attempting to add tips assoc: {tips} (pydantic)")
tassoc = tips.to_sql(submission=self)
logger.debug(f"Attempting to add tips assoc: {tips.__dict__} (sql)")
if tassoc not in self.submission_tips_associations:
tassoc.save()
else:

2
src/submissions/backend/excel/__init__.py
View File

@@ -2,6 +2,6 @@
Contains pandas and openpyxl convenience functions for interacting with excel workbooks
'''
from .reports import *
from .parser import *
from .reports import *
from .writer import *

50
src/submissions/backend/scripts/import_irida.py
View File

@@ -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()

19
src/submissions/backend/validators/pydant.py
View File

@@ -295,7 +295,8 @@ class PydTips(BaseModel):
Returns:
SubmissionTipsAssociation: Association between queried tips and submission
"""
tips = Tips.query(name=self.name, lot=self.lot, limit=1)
tips = Tips.query(name=self.name, limit=1)
logger.debug(f"Tips query has yielded: {tips}")
assoc = SubmissionTipsAssociation.query(tip_id=tips.id, submission_id=submission.id, role=self.role, limit=1)
if assoc is None:
assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
@@ -900,17 +901,20 @@ class PydSubmission(BaseModel, extra='allow'):
return render
# @report_result
def check_kit_integrity(self, extraction_kit: str | dict | None = None) -> Tuple[List[PydReagent], Report]:
def check_kit_integrity(self, extraction_kit: str | dict | None = None, exempt:List[PydReagent]=[]) -> Tuple[
List[PydReagent], Report]:
"""
Ensures all reagents expected in kit are listed in Submission
Args:
reagenttypes (list | None, optional): List to check against complete list. Defaults to None.
extraction_kit (str | dict | None, optional): kit to be checked. Defaults to None.
exempt (List[PydReagent], optional): List of reagents that don't need to be checked. Defaults to []
Returns:
Report: Result object containing a message and any missing components.
Tuple[List[PydReagent], Report]: List of reagents and Result object containing a message and any missing components.
"""
report = Report()
# logger.debug(f"The following reagents are exempt from the kit integrity check:\n{exempt}")
if isinstance(extraction_kit, str):
extraction_kit = dict(value=extraction_kit)
if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
@@ -922,7 +926,8 @@ class PydSubmission(BaseModel, extra='allow'):
expected_check = [item.role for item in ext_kit_rtypes]
output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
missing_check = [item.role for item in output_reagents]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check and rt.role not in exempt]
# logger.debug(f"Missing reagents: {missing_reagents}")
missing_reagents += [rt for rt in output_reagents if rt.missing]
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
# NOTE: if lists are equal return no problem
@@ -930,8 +935,8 @@ class PydSubmission(BaseModel, extra='allow'):
result = None
else:
result = Result(
msg=f"The excel sheet you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.role.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!",
status="Warning")
msg=f"The excel sheet you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.role.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!",
status="Warning")
report.add_result(result)
return output_reagents, report