Major refactor for improved documentation and readability
This commit is contained in:
Landon Wark
@@ -1,80 +1,53 @@
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# from ..models import *
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from backend.db.models import *
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import logging
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from PyQt6.QtWidgets import (
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QMainWindow, QLabel, QToolBar,
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QTabWidget, QWidget, QVBoxLayout,
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QPushButton, QFileDialog,
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QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
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QSpinBox, QScrollArea
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)
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logger = logging.getLogger(f"submissions.{__name__}")
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def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None) -> dict|None:
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def extract_form_info(object) -> dict:
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"""
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Ensures all reagents expected in kit are listed in Submission
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retrieves object names and values from form
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Args:
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sub (BasicSubmission | KitType): Object containing complete list of reagent types.
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reagenttypes (list | None, optional): List to check against complete list. Defaults to None.
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object (_type_): the form widget
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Returns:
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dict|None: Result object containing a message and any missing components.
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"""
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logger.debug(type(sub))
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# What type is sub?
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match sub:
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case BasicSubmission():
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ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
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# Overwrite function parameter reagenttypes
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reagenttypes = [reagent.type.name for reagent in sub.reagents]
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case KitType():
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ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types]
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logger.debug(f"Kit reagents: {ext_kit_rtypes}")
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logger.debug(f"Submission reagents: {reagenttypes}")
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# check if lists are equal
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check = set(ext_kit_rtypes) == set(reagenttypes)
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logger.debug(f"Checking if reagents match kit contents: {check}")
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# what reagent types are in both lists?
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# common = list(set(ext_kit_rtypes).intersection(reagenttypes))
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missing = list(set(ext_kit_rtypes).difference(reagenttypes))
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logger.debug(f"Missing reagents types: {missing}")
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# if lists are equal return no problem
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if len(missing)==0:
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result = None
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else:
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# missing = [x for x in ext_kit_rtypes if x not in common]
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result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.", 'missing': missing}
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return result
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# Below is depreciated:
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# def insert_reagent_import(ctx:dict, item:str, prsr:SheetParser|None=None) -> QComboBox:
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# add_widget = QComboBox()
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# add_widget.setEditable(True)
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# # Ensure that all reagenttypes have a name that matches the items in the excel parser
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# query_var = item.replace("lot_", "")
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# logger.debug(f"Query for: {query_var}")
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# if prsr != None:
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# if isinstance(prsr.sub[item], np.float64):
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# logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
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# try:
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# prsr.sub[item] = int(prsr.sub[item]['lot'])
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# except ValueError:
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# pass
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# # query for reagents using type name from sheet and kit from sheet
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# logger.debug(f"Attempting lookup of reagents by type: {query_var}")
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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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# relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
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# output_reg = []
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# for reagent in relevant_reagents:
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# if isinstance(reagent, set):
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# for thing in reagent:
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# output_reg.append(thing)
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# elif isinstance(reagent, str):
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# output_reg.append(reagent)
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# relevant_reagents = output_reg
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# # if reagent in sheet is not found insert it into items
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# if prsr != None:
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# logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
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# if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
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# if check_not_nan(prsr.sub[item]['lot']):
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# relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
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# logger.debug(f"New relevant reagents: {relevant_reagents}")
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# add_widget.addItems(relevant_reagents)
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# return add_widget
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dict: dictionary of objectName:text items
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"""
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from frontend.custom_widgets import ReagentTypeForm
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dicto = {}
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reagents = {}
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logger.debug(f"Object type: {type(object)}")
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# grab all widgets in form
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try:
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all_children = object.layout.parentWidget().findChildren(QWidget)
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except AttributeError:
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all_children = object.layout().parentWidget().findChildren(QWidget)
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for item in all_children:
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logger.debug(f"Looking at: {item.objectName()}")
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match item:
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case QLineEdit():
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dicto[item.objectName()] = item.text()
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case QComboBox():
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dicto[item.objectName()] = item.currentText()
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case QDateEdit():
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dicto[item.objectName()] = item.date().toPyDate()
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case QSpinBox():
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dicto[item.objectName()] = item.value()
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case ReagentTypeForm():
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reagent = extract_form_info(item)
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# reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
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logger.debug(reagent)
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# reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
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reagents[reagent["name"].strip()] = {'eol_ext':int(reagent['eol'])}
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# value for ad hoc check above
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if reagents != {}:
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return dicto, reagents
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return dicto
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