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During code cleanup

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This commit is contained in:
lwark
2024-05-23 15:06:22 -05:00
parent d1bf12e8d1
commit 2814be8980
10 changed files with 297 additions and 356 deletions
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100
src/submissions/frontend/widgets/submission_widget.py
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@@ -263,45 +263,45 @@ class SubmissionFormWidget(QWidget):
self.app.report.add_result(report)
self.app.result_reporter()
def kit_integrity_completion_function(self, extraction_kit:str|None=None):
"""
Compare kit contents to parsed contents and creates widgets.
Args:
obj (QMainWindow): The original app window
Returns:
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
"""
report = Report()
missing_reagents = []
# logger.debug(inspect.currentframe().f_back.f_code.co_name)
# find the widget that contains kit info
if extraction_kit is None:
kit_widget = self.find_widgets(object_name="extraction_kit")[0].input
logger.debug(f"Kit selector: {kit_widget}")
# get current kit being used
self.ext_kit = kit_widget.currentText()
else:
self.ext_kit = extraction_kit
for reagent in self.reagents:
logger.debug(f"Creating widget for {reagent}")
add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
# self.form.layout().addWidget(add_widget)
self.layout.addWidget(add_widget)
if reagent.missing:
missing_reagents.append(reagent)
logger.debug(f"Checking integrity of {self.ext_kit}")
# TODO: put check_kit_integrity here instead of what's here?
# see if there are any missing reagents
if len(missing_reagents) > 0:
result = Result(msg=f"""The submission you are importing is missing some reagents expected by the kit.\n\n
It looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\n
Alternatively, 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!""".replace(" ", ""), status="Warning")
report.add_result(result)
self.report.add_result(report)
logger.debug(f"Outgoing report: {self.report.results}")
# def kit_integrity_completion_function(self, extraction_kit:str|None=None):
# """
# Compare kit contents to parsed contents and creates widgets.
#
# Args:
# obj (QMainWindow): The original app window
#
# Returns:
# Tuple[QMainWindow, dict]: Collection of new main app window and result dict
# """
# report = Report()
# missing_reagents = []
# # logger.debug(inspect.currentframe().f_back.f_code.co_name)
# # find the widget that contains kit info
# if extraction_kit is None:
# kit_widget = self.find_widgets(object_name="extraction_kit")[0].input
# logger.debug(f"Kit selector: {kit_widget}")
# # get current kit being used
# self.ext_kit = kit_widget.currentText()
# else:
# self.ext_kit = extraction_kit
# for reagent in self.reagents:
# logger.debug(f"Creating widget for {reagent}")
# add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
# # self.form.layout().addWidget(add_widget)
# self.layout.addWidget(add_widget)
# if reagent.missing:
# missing_reagents.append(reagent)
# logger.debug(f"Checking integrity of {self.ext_kit}")
# # TODO: put check_kit_integrity here instead of what's here?
# # see if there are any missing reagents
# if len(missing_reagents) > 0:
# result = Result(msg=f"""The submission you are importing is missing some reagents expected by the kit.\n\n
# It looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\n
# Alternatively, 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!""".replace(" ", ""), status="Warning")
# report.add_result(result)
# self.report.add_result(report)
# logger.debug(f"Outgoing report: {self.report.results}")
def clear_form(self):
"""
@@ -374,17 +374,12 @@ class SubmissionFormWidget(QWidget):
return
case _:
pass
# assert base_submission.reagents != []
# add reagents to submission object
# NOTE: add reagents to submission object
for reagent in base_submission.reagents:
# logger.debug(f"Updating: {reagent} with {reagent.lot}")
reagent.update_last_used(kit=base_submission.extraction_kit)
# logger.debug(f"Here is the final submission: {pformat(base_submission.__dict__)}")
# logger.debug(f"Parsed reagents: {pformat(base_submission.reagents)}")
# logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
# logger.debug(f"Samples from pyd: {pformat(self.pyd.samples)}")
# logger.debug(f"Samples SQL: {pformat([item.__dict__ for item in base_submission.samples])}")
# logger.debug(f"")
# logger.debug(f"Final reagents: {pformat(base_submission.reagents)}")
# sys.exit("Programmed stop submission_widget.py, line 381")
base_submission.save()
# update summary sheet
self.app.table_widget.sub_wid.setData()
@@ -414,12 +409,12 @@ class SubmissionFormWidget(QWidget):
except AttributeError:
logger.error(f"No csv file found in the submission at this point.")
def parse_form(self) -> PydSubmission:
def parse_form(self) -> Report:
"""
Transforms form info into PydSubmission
Returns:
PydSubmission: Pydantic submission object
Report: Report on status of parse.
"""
report = Report()
logger.debug(f"Hello from form parser!")
@@ -430,15 +425,16 @@ class SubmissionFormWidget(QWidget):
match widget:
case self.ReagentFormWidget():
reagent, _ = widget.parse_form()
if reagent != None:
if reagent is not None:
reagents.append(reagent)
case self.InfoItem():
field, value = widget.parse_form()
if field != None:
if field is not None:
info[field] = value
logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents: {pformat(reagents)}")
logger.debug(f"Reagents going into pyd: {pformat(reagents)}")
self.pyd.reagents = reagents
# logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
for item in self.recover:
logger.debug(f"Attempting to recover: {item}")