Pre- pydsubmission toForm method.
This commit is contained in:
Landon Wark
@@ -20,9 +20,10 @@ from backend.db.models import SubmissionTypeKitTypeAssociation
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from sqlalchemy import FLOAT, INTEGER
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import logging
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import numpy as np
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from .pop_ups import AlertPop
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from backend.validators import PydReagent
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from .pop_ups import AlertPop, QuestionAsker
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from backend.validators import PydReagent, PydKit, PydReagentType, PydSubmission
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from typing import Tuple
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from pprint import pformat
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logger = logging.getLogger(f"submissions.{__name__}")
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@@ -92,7 +93,7 @@ class AddReagentForm(QDialog):
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def parse_form(self):
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return dict(name=self.name_input.currentText(),
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lot=self.lot_input.text(),
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exp=self.exp_input.date().toPyDate(),
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expiry=self.exp_input.date().toPyDate(),
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type=self.type_input.currentText())
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def update_names(self):
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@@ -242,21 +243,22 @@ class KitAdder(QWidget):
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logger.debug(f"kit info: {pformat(info)}")
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logger.debug(f"kit reagents: {pformat(reagents)}")
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info['reagent_types'] = reagents
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# for reagent in reagents:
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# new_dict = {}
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# for k,v in reagent.items():
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# if "_" in k:
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# key, sub_key = k.split("_")
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# if key not in new_dict.keys():
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# new_dict[key] = {}
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# logger.debug(f"Adding key {key}, {sub_key} and value {v} to {new_dict}")
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# new_dict[key][sub_key] = v
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# else:
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# new_dict[k] = v
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# info['reagent_types'].append(new_dict)
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logger.debug(pformat(info))
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# send to kit constructor
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result = construct_kit_from_yaml(ctx=self.ctx, kit_dict=info)
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kit = PydKit(name=info['kit_name'])
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for reagent in info['reagent_types']:
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uses = {
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info['used_for']:
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{'sheet':reagent['sheet'],
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'name':reagent['name'],
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'lot':reagent['lot'],
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'expiry':reagent['expiry']
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}}
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kit.reagent_types.append(PydReagentType(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses))
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logger.debug(f"Output pyd object: {kit.__dict__}")
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# result = construct_kit_from_yaml(ctx=self.ctx, kit_dict=info)
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sqlobj, result = kit.toSQL(self.ctx)
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sqlobj.save(ctx=self.ctx)
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msg = AlertPop(message=result['message'], status=result['status'])
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msg.exec()
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self.__init__(self.ctx)
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@@ -521,5 +523,149 @@ class FirstStrandPlateList(QDialog):
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output.append(plate.currentText())
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return output
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class ReagentFormWidget(QWidget):
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def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
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super().__init__()
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self.setParent(parent)
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logger.debug(f"Reagent form widget parent is: {self.parent()}")
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logger.debug(f"It's great grandparent is {self.parent().parent.parent} which has a method [add_reagent]: {hasattr(self.parent().parent.parent, 'add_reagent')}")
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self.reagent = reagent
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self.extraction_kit = extraction_kit
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self.ctx = reagent.ctx
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layout = QVBoxLayout()
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self.label = self.ReagentParsedLabel(reagent=reagent)
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layout.addWidget(self.label)
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self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
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layout.addWidget(self.lot)
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self.setLayout(layout)
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self.setObjectName(reagent.name)
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self.missing = not reagent.parsed
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def parse_form(self) -> Tuple[PydReagent, dict]:
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lot = self.lot.currentText()
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# type = self.label.text().replace("_label")
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wanted_reagent = lookup_reagents(ctx=self.ctx, lot_number=lot, reagent_type=self.reagent.type)
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if wanted_reagent == None:
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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?")
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if dlg.exec():
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# logger.debug(f"Looking through {pformat(self.parent.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 = self.parent().parent.parent.add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
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return wanted_reagent, None
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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 None, dict(message="Failed integrity check", status="critical")
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else:
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rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
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return PydReagent(ctx=self.ctx, name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, parsed=not self.missing), None
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class ReagentParsedLabel(QLabel):
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def __init__(self, reagent:PydReagent):
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super().__init__()
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try:
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check = reagent.parsed
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except:
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return
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self.setObjectName(f"{reagent.type}_label")
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if check:
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self.setText(f"Parsed {reagent.type}")
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else:
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self.setText(f"MISSING {reagent.type}")
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class ReagentLot(QComboBox):
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def __init__(self, reagent, extraction_kit:str) -> None:
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super().__init__()
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self.ctx = reagent.ctx
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self.setEditable(True)
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if reagent.parsed:
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pass
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logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
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# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
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lookup = lookup_reagents(ctx=self.ctx, reagent_type=reagent.type)
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relevant_reagents = [item.__str__() for item in lookup]
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output_reg = []
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for rel_reagent in relevant_reagents:
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# extract strings from any sets.
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if isinstance(rel_reagent, set):
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for thing in rel_reagent:
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output_reg.append(thing)
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elif isinstance(rel_reagent, str):
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output_reg.append(rel_reagent)
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relevant_reagents = output_reg
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# if reagent in sheet is not found insert it into the front of relevant reagents so it shows
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logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
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if str(reagent.lot) not in relevant_reagents:
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if check_not_nan(reagent.lot):
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relevant_reagents.insert(0, str(reagent.lot))
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else:
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# TODO: look up the last used reagent of this type in the database
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looked_up_rt = lookup_reagenttype_kittype_association(ctx=self.ctx, reagent_type=reagent.type, kit_type=extraction_kit)
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looked_up_reg = lookup_reagents(ctx=self.ctx, lot_number=looked_up_rt.last_used)
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logger.debug(f"Because there was no reagent listed for {reagent}, we will insert the last lot used: {looked_up_reg}")
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if looked_up_reg != None:
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relevant_reagents.remove(str(looked_up_reg.lot))
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relevant_reagents.insert(0, str(looked_up_reg.lot))
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else:
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if len(relevant_reagents) > 1:
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logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")
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idx = relevant_reagents.index(str(reagent.lot))
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logger.debug(f"The index we got for {reagent.lot} in {relevant_reagents} was {idx}")
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moved_reag = relevant_reagents.pop(idx)
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relevant_reagents.insert(0, moved_reag)
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else:
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logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
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logger.debug(f"New relevant reagents: {relevant_reagents}")
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self.setObjectName(f"lot_{reagent.type}")
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self.addItems(relevant_reagents)
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class SubmissionFormWidget(QWidget):
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def __init__(self, parent: QWidget) -> None:
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super().__init__(parent)
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self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
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"qt_scrollarea_vcontainer", "submit_btn"
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]
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def clear_form(self):
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for item in self.findChildren(QWidget):
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item.setParent(None)
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def parse_form(self) -> PydSubmission:
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logger.debug(f"Hello from form parser!")
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info = {}
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reagents = []
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samples = self.parent.parent.samples
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logger.debug(f"Using samples: {pformat(samples)}")
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widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore]
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# widgets = [widget for widget in self.findChildren(QWidget)]
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for widget in widgets:
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logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)}")
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match widget:
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case ReagentFormWidget():
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reagent, _ = widget.parse_form()
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reagents.append(reagent)
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case ImportReagent():
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reagent = dict(name=widget.objectName().replace("lot_", ""), lot=widget.currentText(), type=None, expiry=None)
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reagents.append(PydReagent(ctx=self.parent.parent.ctx, **reagent))
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case QLineEdit():
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info[widget.objectName()] = dict(value=widget.text())
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case QComboBox():
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info[widget.objectName()] = dict(value=widget.currentText())
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case QDateEdit():
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info[widget.objectName()] = dict(value=widget.date().toPyDate())
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logger.debug(f"Info: {pformat(info)}")
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logger.debug(f"Reagents: {pformat(reagents)}")
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# sys.exit("Hi Landon. Check the reagents! frontend.__init__ line 442")
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submission = PydSubmission(ctx=self.parent.parent.ctx, filepath=self.parent.parent.current_file, reagents=reagents, samples=samples, **info)
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return submission
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