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Pre-sample/control connect

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This commit is contained in:
Landon Wark
2023-12-05 10:20:46 -06:00
parent 283e77fee5
commit cddb947ec8
29 changed files with 1357 additions and 1042 deletions
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16
src/submissions/frontend/widgets/submission_widget.py
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@@ -65,9 +65,6 @@ class SubmissionFormContainer(QWidget):
self.app.result_reporter()
def scrape_reagents(self, *args, **kwargs):
# from .main_window_functions import scrape_reagents
# logger.debug(f"Args: {args}")
# logger.debug(F"kwargs: {kwargs}")
print(f"\n\n{inspect.stack()[1].function}\n\n")
self.scrape_reagents_function(args[0])
self.kit_integrity_completion()
@@ -140,7 +137,7 @@ class SubmissionFormContainer(QWidget):
return
# create sheetparser using excel sheet and context from gui
try:
self.prsr = SheetParser(ctx=self.ctx, filepath=fname)
self.prsr = SheetParser(ctx=self.app.ctx, filepath=fname)
except PermissionError:
logger.error(f"Couldn't get permission to access file: {fname}")
return
@@ -519,7 +516,7 @@ class SubmissionFormWidget(QWidget):
case 'submitting_lab':
add_widget = QComboBox()
# lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
labs = [item.__str__() for item in Organization.query()]
labs = [item.name for item in Organization.query()]
# try to set closest match to top of list
try:
labs = difflib.get_close_matches(value, labs, len(labs), 0)
@@ -536,7 +533,7 @@ class SubmissionFormWidget(QWidget):
add_widget = QComboBox()
# lookup existing kits by 'submission_type' decided on by sheetparser
logger.debug(f"Looking up kits used for {submission_type}")
uses = [item.__str__() for item in KitType.query(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}")
if check_not_nan(value):
@@ -616,6 +613,8 @@ class ReagentFormWidget(QWidget):
def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
super().__init__(parent)
# self.setParent(parent)
self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
self.reagent = reagent
self.extraction_kit = extraction_kit
# self.ctx = reagent.ctx
@@ -640,7 +639,8 @@ class ReagentFormWidget(QWidget):
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().parent().parent().parent().parent().parent().parent().parent.add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
print(self.app)
wanted_reagent = self.app.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
@@ -690,7 +690,7 @@ class ReagentFormWidget(QWidget):
# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
# lookup = lookup_reagents(ctx=self.ctx, reagent_type=reagent.type)
lookup = Reagent.query(reagent_type=reagent.type)
relevant_reagents = [item.__str__() for item in lookup]
relevant_reagents = [str(item.lot) for item in lookup]
output_reg = []
for rel_reagent in relevant_reagents:
# extract strings from any sets.