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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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19
src/submissions/backend/validators/pydant.py
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@@ -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