Pre- pydsubmission toForm method.
This commit is contained in:
Landon Wark
@@ -38,7 +38,7 @@ from .custom_widgets import ReportDatePicker
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from .custom_widgets.misc import ImportReagent, ParsedQLabel
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from .visualizations.control_charts import create_charts, construct_html
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from pathlib import Path
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from frontend.custom_widgets.misc import FirstStrandSalvage, FirstStrandPlateList
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from frontend.custom_widgets.misc import FirstStrandSalvage, FirstStrandPlateList, ReagentFormWidget
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logger = logging.getLogger(f"submissions.{__name__}")
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@@ -78,8 +78,7 @@ def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[Q
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except Exception as e:
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return obj, dict(message= f"Problem creating pydantic model:\n\n{e}", status="critical")
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# destroy any widgets from previous imports
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for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
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item.setParent(None)
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obj.table_widget.formwidget.clear_form()
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obj.current_submission_type = pyd.submission_type['value']
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obj.current_file = pyd.filepath
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# Get list of fields from pydantic model.
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@@ -216,24 +215,26 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
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logger.debug(f"Kit selector: {kit_widget}")
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# get current kit being used
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obj.ext_kit = kit_widget.currentText()
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for item in obj.reagents:
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obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':True}, item.type, title=False, label_name=f"lot_{item.type}"))
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reagent = dict(type=item.type, lot=item.lot, exp=item.exp, name=item.name)
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add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
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for reagent in obj.reagents:
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# obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':True}, item.type, title=False, label_name=f"lot_{item.type}"))
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# reagent = dict(type=item.type, lot=item.lot, expiry=item.expiry, name=item.name)
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# add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
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# obj.table_widget.formlayout.addWidget(add_widget)
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add_widget = ReagentFormWidget(parent=obj.table_widget.formwidget, reagent=reagent, extraction_kit=obj.ext_kit)
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obj.table_widget.formlayout.addWidget(add_widget)
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logger.debug(f"Checking integrity of {obj.ext_kit}")
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# see if there are any missing reagents
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if len(obj.missing_reagents) > 0:
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result = dict(message=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in obj.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")
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for item in obj.missing_reagents:
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# Add label that has parsed as False to show "MISSING" label.
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obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False, label_name=f"missing_{item.type}"))
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# Set default parameters for the empty reagent.
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reagent = dict(type=item.type, lot=None, exp=date.today(), name=None)
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# create and add widget
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# add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)
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add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
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obj.table_widget.formlayout.addWidget(add_widget)
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# for item in obj.missing_reagents:
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# # Add label that has parsed as False to show "MISSING" label.
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# obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False, label_name=f"missing_{item.type}"))
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# # Set default parameters for the empty reagent.
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# reagent = dict(type=item.type, lot=None, expiry=date.today(), name=None)
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# # create and add widget
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# # add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)
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# add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
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# obj.table_widget.formlayout.addWidget(add_widget)
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# Add submit button to the form.
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submit_btn = QPushButton("Submit")
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submit_btn.setObjectName("submit_btn")
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@@ -264,34 +265,34 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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# info, reagents = obj.table_widget.formwidget.parse_form()
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submission: PydSubmission = obj.table_widget.formwidget.parse_form()
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logger.debug(f"Submission: {pprint.pformat(submission)}")
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parsed_reagents = []
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# parsed_reagents = []
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# compare reagents in form to reagent database
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for reagent in submission.reagents:
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# Lookup any existing reagent of this type with this lot number
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wanted_reagent = lookup_reagents(ctx=obj.ctx, lot_number=reagent.lot, reagent_type=reagent.name)
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logger.debug(f"Looked up reagent: {wanted_reagent}")
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# if reagent not found offer to add to database
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if wanted_reagent == None:
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# r_lot = reagent[reagent]
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dlg = QuestionAsker(title=f"Add {reagent.lot}?", message=f"Couldn't find reagent type {reagent.name.strip('Lot')}: {reagent.lot} in the database.\n\nWould you like to add it?")
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if dlg.exec():
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logger.debug(f"Looking through {pprint.pformat(obj.reagents)} for reagent {reagent.name}")
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try:
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picked_reagent = [item for item in obj.reagents if item.type == reagent.name][0]
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except IndexError:
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logger.error(f"Couldn't find {reagent.name} in obj.reagents. Checking missing reagents {pprint.pformat(obj.missing_reagents)}")
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picked_reagent = [item for item in obj.missing_reagents if item.type == reagent.name][0]
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logger.debug(f"checking reagent: {reagent.name} in obj.reagents. Result: {picked_reagent}")
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expiry_date = picked_reagent.exp
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wanted_reagent = obj.add_reagent(reagent_lot=reagent.lot, reagent_type=reagent.name.replace("lot_", ""), expiry=expiry_date, name=picked_reagent.name)
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else:
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# In this case we will have an empty reagent and the submission will fail kit integrity check
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logger.debug("Will not add reagent.")
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return obj, dict(message="Failed integrity check", status="critical")
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# Append the PydReagent object o be added to the submission
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parsed_reagents.append(reagent)
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# move samples into preliminary submission dict
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submission.reagents = parsed_reagents
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# for reagent in submission.reagents:
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# # Lookup any existing reagent of this type with this lot number
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# wanted_reagent = lookup_reagents(ctx=obj.ctx, lot_number=reagent.lot, reagent_type=reagent.name)
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# logger.debug(f"Looked up reagent: {wanted_reagent}")
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# # if reagent not found offer to add to database
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# if wanted_reagent == None:
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# # r_lot = reagent[reagent]
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# dlg = QuestionAsker(title=f"Add {reagent.lot}?", message=f"Couldn't find reagent type {reagent.name.strip('Lot')}: {reagent.lot} in the database.\n\nWould you like to add it?")
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# if dlg.exec():
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# logger.debug(f"Looking through {pprint.pformat(obj.reagents)} for reagent {reagent.name}")
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# try:
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# picked_reagent = [item for item in obj.reagents if item.type == reagent.name][0]
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# except IndexError:
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# logger.error(f"Couldn't find {reagent.name} in obj.reagents. Checking missing reagents {pprint.pformat(obj.missing_reagents)}")
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# picked_reagent = [item for item in obj.missing_reagents if item.type == reagent.name][0]
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# logger.debug(f"checking reagent: {reagent.name} in obj.reagents. Result: {picked_reagent}")
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# expiry_date = picked_reagent.expiry
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# wanted_reagent = obj.add_reagent(reagent_lot=reagent.lot, reagent_type=reagent.name.replace("lot_", ""), expiry=expiry_date, name=picked_reagent.name)
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# else:
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# # In this case we will have an empty reagent and the submission will fail kit integrity check
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# logger.debug("Will not add reagent.")
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# return obj, dict(message="Failed integrity check", status="critical")
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# # Append the PydReagent object o be added to the submission
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# parsed_reagents.append(reagent)
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# # move samples into preliminary submission dict
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# submission.reagents = parsed_reagents
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# submission.uploaded_by = getuser()
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# construct submission object
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# logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
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@@ -1020,16 +1021,17 @@ def scrape_reagents(obj:QMainWindow, extraction_kit:str) -> Tuple[QMainWindow, d
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obj.reagents = []
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obj.missing_reagents = []
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# Remove previous reagent widgets
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[item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget) if item.objectName().startswith("lot_") or item.objectName().startswith("missing_")]
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[item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QPushButton)]
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# [item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget) if item.objectName().startswith("lot_") or item.objectName().startswith("missing_")]
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# [item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QPushButton)]
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reagents = obj.prsr.parse_reagents(extraction_kit=extraction_kit)
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logger.debug(f"Got reagents: {reagents}")
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for reagent in obj.prsr.sub['reagents']:
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# create label
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if reagent['parsed']:
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obj.reagents.append(reagent['value'])
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else:
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obj.missing_reagents.append(reagent['value'])
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# for reagent in obj.prsr.sub['reagents']:
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# # create label
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# if reagent.parsed:
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# obj.reagents.append(reagent)
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# else:
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# obj.missing_reagents.append(reagent)
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obj.reagents = obj.prsr.sub['reagents']
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logger.debug(f"Imported reagents: {obj.reagents}")
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logger.debug(f"Missing reagents: {obj.missing_reagents}")
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return obj, None
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