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Code cleanup, dependency update, various bug fixes

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This commit is contained in:
lwark
2024-05-24 13:02:46 -05:00
parent 2814be8980
commit e047d1a9ee
24 changed files with 403 additions and 561 deletions
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136
src/submissions/frontend/widgets/submission_widget.py
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@@ -30,7 +30,7 @@ class SubmissionFormContainer(QWidget):
import_drag = pyqtSignal(Path)
def __init__(self, parent: QWidget) -> None:
logger.debug(f"Setting form widget...")
# logger.debug(f"Setting form widget...")
super().__init__(parent)
self.app = self.parent().parent()
self.report = Report()
@@ -52,7 +52,7 @@ class SubmissionFormContainer(QWidget):
Sets filename when file dropped
"""
fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
logger.debug(f"App: {self.app}")
# logger.debug(f"App: {self.app}")
self.app.last_dir = fname.parent
self.import_drag.emit(fname)
@@ -63,7 +63,7 @@ class SubmissionFormContainer(QWidget):
self.app.raise_()
self.app.activateWindow()
self.import_submission_function(fname)
logger.debug(f"Result from result reporter: {self.report.results}")
# logger.debug(f"Result from result reporter: {self.report.results}")
self.app.report.add_result(self.report)
self.report = Report()
self.app.result_reporter()
@@ -78,7 +78,7 @@ class SubmissionFormContainer(QWidget):
Returns:
Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict
"""
logger.debug(f"\n\nStarting Import...\n\n")
logger.info(f"\n\nStarting Import...\n\n")
report = Report()
try:
self.form.setParent(None)
@@ -90,7 +90,7 @@ class SubmissionFormContainer(QWidget):
# set file dialog
if isinstance(fname, bool) or fname == None:
fname = select_open_file(self, file_extension="xlsx")
logger.debug(f"Attempting to parse file: {fname}")
# logger.debug(f"Attempting to parse file: {fname}")
if not fname.exists():
report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
self.report.add_result(report)
@@ -103,16 +103,16 @@ class SubmissionFormContainer(QWidget):
return
except AttributeError:
self.prsr = SheetParser(filepath=fname)
logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
# logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
self.pyd = self.prsr.to_pydantic()
logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
# logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
self.form = self.pyd.to_form(parent=self)
self.layout().addWidget(self.form)
# if self.prsr.sample_result != None:
# report.add_result(msg=self.prsr.sample_result, status="Warning")
self.report.add_result(report)
logger.debug(f"Outgoing report: {self.report.results}")
logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
# logger.debug(f"Outgoing report: {self.report.results}")
# logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
"""
@@ -135,7 +135,7 @@ class SubmissionFormContainer(QWidget):
if dlg.exec():
# extract form info
info = dlg.parse_form()
logger.debug(f"Reagent info: {info}")
# logger.debug(f"Reagent info: {info}")
# create reagent object
reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
# send reagent to db
@@ -216,10 +216,10 @@ class SubmissionFormWidget(QWidget):
caller = inspect.stack()[1].function.__repr__().replace("'", "")
# self.reagents = []
# logger.debug(f"Self.reagents: {self.reagents}")
logger.debug(f"\n\n{pformat(caller)}\n\n")
# logger.debug(f"\n\n{pformat(caller)}\n\n")
# logger.debug(f"SubmissionType: {self.submission_type}")
report = Report()
logger.debug(f"Extraction kit: {extraction_kit}")
# logger.debug(f"Extraction kit: {extraction_kit}")
# Remove previous reagent widgets
try:
old_reagents = self.find_widgets()
@@ -249,7 +249,7 @@ class SubmissionFormWidget(QWidget):
add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit)
self.layout.addWidget(add_widget)
report.add_result(integrity_report)
logger.debug(f"Outgoing report: {report.results}")
# logger.debug(f"Outgoing report: {report.results}")
if hasattr(self.pyd, "csv"):
export_csv_btn = QPushButton("Export CSV")
export_csv_btn.setObjectName("export_csv_btn")
@@ -263,46 +263,6 @@ 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 clear_form(self):
"""
Removes all form widgets
@@ -335,24 +295,23 @@ class SubmissionFormWidget(QWidget):
Returns:
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
"""
logger.debug(f"\n\nBeginning Submission\n\n")
logger.info(f"\n\nBeginning Submission\n\n")
report = Report()
# self.pyd: PydSubmission = self.parse_form()
result = self.parse_form()
report.add_result(result)
logger.debug(f"Submission: {pformat(self.pyd)}")
logger.debug("Checking kit integrity...")
# logger.debug(f"Submission: {pformat(self.pyd)}")
# logger.debug("Checking kit integrity...")
_, result = self.pyd.check_kit_integrity()
report.add_result(result)
if len(result.results) > 0:
self.app.report.add_result(report)
self.app.result_reporter()
return
logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
# logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
base_submission, result = self.pyd.to_sql()
logger.debug(f"SQL object: {pformat(base_submission.__dict__)}")
# logger.debug(f"SQL object: {pformat(base_submission.__dict__)}")
# logger.debug(f"Base submission: {base_submission.to_dict()}")
# check output message for issues
# NOTE: check output message for issues
match result.code:
# code 0: everything is fine.
case 0:
@@ -379,11 +338,10 @@ class SubmissionFormWidget(QWidget):
# logger.debug(f"Updating: {reagent} with {reagent.lot}")
reagent.update_last_used(kit=base_submission.extraction_kit)
# logger.debug(f"Final reagents: {pformat(base_submission.reagents)}")
# sys.exit("Programmed stop submission_widget.py, line 381")
base_submission.save()
# update summary sheet
# NOTE: update summary sheet
self.app.table_widget.sub_wid.setData()
# reset form
# NOTE: reset form
self.setParent(None)
# logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
self.app.report.add_result(report)
@@ -396,16 +354,14 @@ class SubmissionFormWidget(QWidget):
Args:
fname (Path | None, optional): Input filename. Defaults to None.
"""
# self.parse_form()
if isinstance(fname, bool) or fname == None:
fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
try:
# logger.debug(f'')
# self.pyd.csv.to_csv(fname.__str__(), index=False)
workbook_2_csv(worksheet=self.pyd.csv, filename=fname)
except PermissionError:
logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
logger.warning(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
except AttributeError:
logger.error(f"No csv file found in the submission at this point.")
@@ -417,7 +373,7 @@ class SubmissionFormWidget(QWidget):
Report: Report on status of parse.
"""
report = Report()
logger.debug(f"Hello from form parser!")
logger.info(f"Hello from form parser!")
info = {}
reagents = []
for widget in self.findChildren(QWidget):
@@ -431,21 +387,19 @@ class SubmissionFormWidget(QWidget):
field, value = widget.parse_form()
if field is not None:
info[field] = value
logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents going into pyd: {pformat(reagents)}")
# logger.debug(f"Info: {pformat(info)}")
# 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}")
# logger.debug(f"Attempting to recover: {item}")
if hasattr(self, item):
value = getattr(self, item)
logger.debug(f"Setting {item}")
# logger.debug(f"Setting {item}")
info[item] = value
# submission = PydSubmission(reagents=reagents, **info)
for k,v in info.items():
self.pyd.set_attribute(key=k, value=v)
# return submission
# NOTE: return submission
report.add_result(report)
return report
@@ -510,7 +464,7 @@ class SubmissionFormWidget(QWidget):
except (TypeError, KeyError):
pass
obj = parent.parent().parent()
logger.debug(f"Creating widget for: {key}")
# logger.debug(f"Creating widget for: {key}")
match key:
case 'submitting_lab':
add_widget = QComboBox()
@@ -531,12 +485,12 @@ class SubmissionFormWidget(QWidget):
# create combobox to hold looked up kits
add_widget = QComboBox()
# lookup existing kits by 'submission_type' decided on by sheetparser
logger.debug(f"Looking up kits used for {submission_type}")
# logger.debug(f"Looking up kits used for {submission_type}")
uses = [item.name for item in KitType.query(used_for=submission_type)]
obj.uses = uses
logger.debug(f"Kits received for {submission_type}: {uses}")
# logger.debug(f"Kits received for {submission_type}: {uses}")
if check_not_nan(value):
logger.debug(f"The extraction kit in parser was: {value}")
# logger.debug(f"The extraction kit in parser was: {value}")
uses.insert(0, uses.pop(uses.index(value)))
obj.ext_kit = value
else:
@@ -565,7 +519,7 @@ class SubmissionFormWidget(QWidget):
case _:
# anything else gets added in as a line edit
add_widget = QLineEdit()
logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
# logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
add_widget.setText(str(value).replace("_", " "))
if add_widget != None:
add_widget.setObjectName(key)
@@ -639,14 +593,6 @@ class SubmissionFormWidget(QWidget):
# If changed set self.missing to True and update self.label
self.lot.currentTextChanged.connect(self.updated)
# def check_uncheck(self):
# if self.check_box.isChecked():
# self.lot.setCurrentIndex(0)
# self.lot.setEnabled(True)
# else:
# self.lot.setCurrentText("Not Applicable")
# self.lot.setEnabled(False)
def parse_form(self) -> Tuple[PydReagent, dict]:
"""
Pulls form info into PydReagent
@@ -657,17 +603,17 @@ class SubmissionFormWidget(QWidget):
# if not self.check_box.isChecked():
# return None, None
lot = self.lot.currentText()
logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
# logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
# if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
# NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
if wanted_reagent == None:
dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
return wanted_reagent, None
else:
# In this case we will have an empty reagent and the submission will fail kit integrity check
logger.debug("Will not add reagent.")
# NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
# logger.debug("Will not add reagent.")
return None, Result(msg="Failed integrity check", status="Critical")
else:
# Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
@@ -712,8 +658,8 @@ class SubmissionFormWidget(QWidget):
def __init__(self, reagent, extraction_kit:str) -> None:
super().__init__()
self.setEditable(True)
logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
# logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
# NOTE: below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
lookup = Reagent.query(reagent_type=reagent.type)
relevant_reagents = [str(item.lot) for item in lookup]
output_reg = []
@@ -725,8 +671,8 @@ class SubmissionFormWidget(QWidget):
elif isinstance(rel_reagent, str):
output_reg.append(rel_reagent)
relevant_reagents = output_reg
# if reagent in sheet is not found insert it into the front of relevant reagents so it shows
logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
# NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows
# logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
if str(reagent.lot) not in relevant_reagents:
if check_not_nan(reagent.lot):
relevant_reagents.insert(0, str(reagent.lot))