Pre-cleanup
This commit is contained in:
Landon Wark
@@ -7,6 +7,7 @@ from getpass import getuser
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import inspect
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import pprint
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import re
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import sys
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import yaml
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import json
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from typing import Tuple, List
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@@ -35,7 +36,6 @@ from backend.validators import PydSubmission, PydSample, PydReagent
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from tools import check_not_nan, convert_well_to_row_column
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from .custom_widgets.pop_ups import AlertPop, QuestionAsker
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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, ReagentFormWidget
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@@ -54,8 +54,12 @@ def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[Q
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"""
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logger.debug(f"\n\nStarting Import...\n\n")
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result = None
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logger.debug(obj.ctx)
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# logger.debug(obj.ctx)
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# initialize samples
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try:
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obj.form.setParent(None)
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except AttributeError:
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pass
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obj.samples = []
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obj.missing_info = []
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# set file dialog
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@@ -73,106 +77,114 @@ def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[Q
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return obj, result
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try:
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logger.debug(f"Submission dictionary:\n{pprint.pformat(obj.prsr.sub)}")
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pyd = obj.prsr.to_pydantic()
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logger.debug(f"Pydantic result: \n\n{pprint.pformat(pyd)}\n\n")
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obj.pyd = obj.prsr.to_pydantic()
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logger.debug(f"Pydantic result: \n\n{pprint.pformat(obj.pyd)}\n\n")
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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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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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# obj.table_widget.formwidget.set_parent(None)
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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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fields = list(pyd.model_fields.keys()) + list(pyd.model_extra.keys())
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fields.remove('filepath')
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logger.debug(f"pydantic fields: {fields}")
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for field in fields:
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value = getattr(pyd, field)
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logger.debug(f"Checking: {field}: {value}")
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# Get from pydantic model whether field was completed in the form
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if isinstance(value, dict) and field != 'ctx':
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logger.debug(f"The field {field} is a dictionary: {value}")
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if not value['parsed']:
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obj.missing_info.append(field)
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label = ParsedQLabel(value, field)
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match field:
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case 'submitting_lab':
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logger.debug(f"{field}: {value['value']}")
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# create combobox to hold looked up submitting labs
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add_widget = QComboBox()
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labs = [item.__str__() for item in lookup_organizations(ctx=obj.ctx)]
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# try to set closest match to top of list
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try:
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labs = difflib.get_close_matches(value['value'], labs, len(labs), 0)
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except (TypeError, ValueError):
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pass
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# set combobox values to lookedup values
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add_widget.addItems(labs)
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case 'extraction_kit':
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# if extraction kit not available, all other values fail
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if not check_not_nan(value['value']):
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msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
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msg.exec()
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# create combobox to hold looked up kits
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add_widget = QComboBox()
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# lookup existing kits by 'submission_type' decided on by sheetparser
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logger.debug(f"Looking up kits used for {pyd.submission_type['value']}")
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uses = [item.__str__() for item in lookup_kit_types(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
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logger.debug(f"Kits received for {pyd.submission_type['value']}: {uses}")
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if check_not_nan(value['value']):
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logger.debug(f"The extraction kit in parser was: {value['value']}")
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uses.insert(0, uses.pop(uses.index(value['value'])))
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obj.ext_kit = value['value']
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else:
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logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
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obj.ext_kit = uses[0]
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# Run reagent scraper whenever extraction kit is changed.
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add_widget.currentTextChanged.connect(obj.scrape_reagents)
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case 'submitted_date':
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# uses base calendar
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add_widget = QDateEdit(calendarPopup=True)
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# sets submitted date based on date found in excel sheet
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try:
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add_widget.setDate(value['value'])
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# if not found, use today
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except:
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add_widget.setDate(date.today())
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case 'samples':
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# hold samples in 'obj' until form submitted
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logger.debug(f"{field}:\n\t{value}")
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obj.samples = value
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continue
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case 'submission_category':
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add_widget = QComboBox()
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cats = ['Diagnostic', "Surveillance", "Research"]
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cats += [item.name for item in lookup_submission_type(ctx=obj.ctx)]
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try:
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cats.insert(0, cats.pop(cats.index(value['value'])))
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except ValueError:
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cats.insert(0, cats.pop(cats.index(pyd.submission_type['value'])))
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add_widget.addItems(cats)
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case "ctx" | 'reagents' | 'csv' | 'filepath':
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continue
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case _:
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# anything else gets added in as a line edit
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add_widget = QLineEdit()
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logger.debug(f"Setting widget text to {str(value['value']).replace('_', ' ')}")
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add_widget.setText(str(value['value']).replace("_", " "))
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try:
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add_widget.setObjectName(field)
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logger.debug(f"Widget name set to: {add_widget.objectName()}")
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obj.table_widget.formlayout.addWidget(label)
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obj.table_widget.formlayout.addWidget(add_widget)
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except AttributeError as e:
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logger.error(e)
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kit_widget = obj.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
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kit_widget.addItems(uses)
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# fields = list(pyd.model_fields.keys()) + list(pyd.model_extra.keys())
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# fields.remove('filepath')
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# logger.debug(f"pydantic fields: {fields}")
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# for field in fields:
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# value = getattr(pyd, field)
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# logger.debug(f"Checking: {field}: {value}")
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# # Get from pydantic model whether field was completed in the form
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# if isinstance(value, dict) and field != 'ctx':
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# logger.debug(f"The field {field} is a dictionary: {value}")
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# if not value['parsed']:
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# obj.missing_info.append(field)
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# label = ParsedQLabel(value, field)
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# match field:
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# case 'submitting_lab':
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# logger.debug(f"{field}: {value['value']}")
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# # create combobox to hold looked up submitting labs
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# add_widget = QComboBox()
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# labs = [item.__str__() for item in lookup_organizations(ctx=obj.ctx)]
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# # try to set closest match to top of list
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# try:
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# labs = difflib.get_close_matches(value['value'], labs, len(labs), 0)
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# except (TypeError, ValueError):
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# pass
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# # set combobox values to lookedup values
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# add_widget.addItems(labs)
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# case 'extraction_kit':
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# # if extraction kit not available, all other values fail
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# if not check_not_nan(value['value']):
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# msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
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# msg.exec()
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# # create combobox to hold looked up kits
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# add_widget = QComboBox()
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# # lookup existing kits by 'submission_type' decided on by sheetparser
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# logger.debug(f"Looking up kits used for {pyd.submission_type['value']}")
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# uses = [item.__str__() for item in lookup_kit_types(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
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# logger.debug(f"Kits received for {pyd.submission_type['value']}: {uses}")
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# if check_not_nan(value['value']):
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# logger.debug(f"The extraction kit in parser was: {value['value']}")
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# uses.insert(0, uses.pop(uses.index(value['value'])))
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# obj.ext_kit = value['value']
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# else:
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# logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
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# obj.ext_kit = uses[0]
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# # Run reagent scraper whenever extraction kit is changed.
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# add_widget.currentTextChanged.connect(obj.scrape_reagents)
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# case 'submitted_date':
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# # uses base calendar
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# add_widget = QDateEdit(calendarPopup=True)
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# # sets submitted date based on date found in excel sheet
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# try:
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# add_widget.setDate(value['value'])
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# # if not found, use today
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# except:
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# add_widget.setDate(date.today())
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# case 'samples':
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# # hold samples in 'obj' until form submitted
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# logger.debug(f"{field}:\n\t{value}")
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# obj.samples = value
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# continue
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# case 'submission_category':
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# add_widget = QComboBox()
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# cats = ['Diagnostic', "Surveillance", "Research"]
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# cats += [item.name for item in lookup_submission_type(ctx=obj.ctx)]
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# try:
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# cats.insert(0, cats.pop(cats.index(value['value'])))
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# except ValueError:
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# cats.insert(0, cats.pop(cats.index(pyd.submission_type['value'])))
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# add_widget.addItems(cats)
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# case "ctx" | 'reagents' | 'csv' | 'filepath':
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# continue
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# case _:
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# # anything else gets added in as a line edit
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# add_widget = QLineEdit()
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# logger.debug(f"Setting widget text to {str(value['value']).replace('_', ' ')}")
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# add_widget.setText(str(value['value']).replace("_", " "))
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# try:
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# add_widget.setObjectName(field)
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# logger.debug(f"Widget name set to: {add_widget.objectName()}")
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# obj.table_widget.formlayout.addWidget(label)
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# obj.table_widget.formlayout.addWidget(add_widget)
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# except AttributeError as e:
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# logger.error(e)
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obj.form = obj.pyd.toForm(parent=obj)
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obj.table_widget.formlayout.addWidget(obj.form)
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# kit_widget = obj.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
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kit_widget = obj.form.find_widgets(object_name="extraction_kit")[0].input
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logger.debug(f"Kitwidget {kit_widget}")
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# block
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# with QSignalBlocker(kit_widget) as blocker:
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# kit_widget.addItems(obj.uses)
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obj.scrape_reagents(kit_widget.currentText())
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kit_widget.currentTextChanged.connect(obj.scrape_reagents)
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# compare obj.reagents with expected reagents in kit
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if obj.prsr.sample_result != None:
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msg = AlertPop(message=obj.prsr.sample_result, status="WARNING")
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msg.exec()
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logger.debug(f"Pydantic extra fields: {pyd.model_extra}")
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if "csv" in pyd.model_extra:
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obj.csv = pyd.model_extra['csv']
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# logger.debug(f"Pydantic extra fields: {obj.pyd.model_extra}")
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# if "csv" in pyd.model_extra:
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# obj.csv = pyd.model_extra['csv']
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logger.debug(f"All attributes of obj:\n{pprint.pformat(obj.__dict__)}")
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return obj, result
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@@ -187,15 +199,19 @@ def kit_reload_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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Tuple[QMainWindow, dict]: Collection of new main app window and result dict
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"""
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result = None
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for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
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if isinstance(item, QLabel):
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if item.text().startswith("Lot"):
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item.setParent(None)
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else:
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logger.debug(f"Type of {item.objectName()} is {type(item)}")
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if item.objectName().startswith("lot_"):
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item.setParent(None)
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obj.kit_integrity_completion_function()
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# for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
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logger.debug(f"Attempting to clear {obj.form.find_widgets()}")
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for item in obj.form.find_widgets():
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if isinstance(item, ReagentFormWidget):
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item.setParent(None)
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# if item.text().startswith("Lot"):
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# item.setParent(None)
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# else:
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# logger.debug(f"Type of {item.objectName()} is {type(item)}")
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# if item.objectName().startswith("lot_"):
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# item.setParent(None)
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kit_integrity_completion_function(obj)
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return obj, result
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def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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@@ -209,23 +225,31 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
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Tuple[QMainWindow, dict]: Collection of new main app window and result dict
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"""
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result = None
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missing_reagents = []
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# kit_reload_function(obj=obj)
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logger.debug(inspect.currentframe().f_back.f_code.co_name)
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# find the widget that contains kit info
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kit_widget = obj.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
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kit_widget = obj.form.find_widgets(object_name="extraction_kit")[0].input
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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 reagent in obj.reagents:
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# for reagent in obj.pyd.reagents:
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for reagent in obj.form.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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add_widget.setParent(obj.form)
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# obj.table_widget.formlayout.addWidget(add_widget)
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obj.form.layout().addWidget(add_widget)
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if reagent.missing:
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missing_reagents.append(reagent)
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logger.debug(f"Checking integrity of {obj.ext_kit}")
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# TODO: put check_kit_integrity here instead of what's here?
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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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if len(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 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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@@ -238,7 +262,7 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
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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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obj.table_widget.formlayout.addWidget(submit_btn)
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obj.form.layout().addWidget(submit_btn)
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submit_btn.clicked.connect(obj.submit_new_sample)
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return obj, result
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@@ -254,61 +278,25 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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"""
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logger.debug(f"\n\nBeginning Submission\n\n")
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result = None
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# extract info from the form widgets
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# info = extract_form_info(obj.table_widget.tab1)
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# if isinstance(info, tuple):
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# logger.warning(f"Got tuple for info for some reason.")
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# info = info[0]
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# # seperate out reagents
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# reagents = {k.replace("lot_", ""):v for k,v in info.items() if k.startswith("lot_")}
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# info = {k:v for k,v in info.items() if not k.startswith("lot_")}
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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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# 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.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
|
||||
# submission.uploaded_by = getuser()
|
||||
# construct submission object
|
||||
# logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
|
||||
# base_submission, result = construct_submission_info(ctx=obj.ctx, info_dict=info)
|
||||
base_submission, result = submission.toSQL()
|
||||
# delattr(base_submission, "ctx")
|
||||
# raise ValueError(base_submission.__dict__)
|
||||
obj.pyd: PydSubmission = obj.form.parse_form()
|
||||
logger.debug(f"Submission: {pprint.pformat(obj.pyd)}")
|
||||
logger.debug("Checking kit integrity...")
|
||||
kit_integrity = check_kit_integrity(ctx=obj.ctx, sub=obj.pyd)
|
||||
if kit_integrity != None:
|
||||
return obj, dict(message=kit_integrity['message'], status="critical")
|
||||
base_submission, result = obj.pyd.toSQL()
|
||||
# check output message for issues
|
||||
match result['code']:
|
||||
# code 0: everything is fine.
|
||||
case 0:
|
||||
result = None
|
||||
# code 1: ask for overwrite
|
||||
case 1:
|
||||
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
|
||||
if dlg.exec():
|
||||
# Do not add duplicate reagents.
|
||||
# base_submission.reagents = []
|
||||
pass
|
||||
result = None
|
||||
else:
|
||||
obj.ctx.database_session.rollback()
|
||||
return obj, dict(message="Overwrite cancelled", status="Information")
|
||||
@@ -321,31 +309,19 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
for reagent in base_submission.reagents:
|
||||
update_last_used(ctx=obj.ctx, reagent=reagent, kit=base_submission.extraction_kit)
|
||||
logger.debug(f"Here is the final submission: {pprint.pformat(base_submission.__dict__)}")
|
||||
logger.debug(f"Parsed reagents: {pprint.pformat(base_submission.reagents)}")
|
||||
logger.debug("Checking kit integrity...")
|
||||
kit_integrity = check_kit_integrity(base_submission)
|
||||
if kit_integrity != None:
|
||||
return obj, dict(message=kit_integrity['message'], status="critical")
|
||||
logger.debug(f"Parsed reagents: {pprint.pformat(base_submission.reagents)}")
|
||||
logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
|
||||
# result = store_object(ctx=obj.ctx, object=base_submission)
|
||||
base_submission.save(ctx=obj.ctx)
|
||||
# update summary sheet
|
||||
obj.table_widget.sub_wid.setData()
|
||||
# reset form
|
||||
for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
|
||||
item.setParent(None)
|
||||
obj.form.setParent(None)
|
||||
logger.debug(f"All attributes of obj: {pprint.pformat(obj.__dict__)}")
|
||||
if len(obj.missing_reagents + obj.missing_info) > 0:
|
||||
logger.debug(f"We have blank reagents in the excel sheet.\n\tLet's try to fill them in.")
|
||||
extraction_kit = lookup_kit_types(ctx=obj.ctx, name=obj.ext_kit)
|
||||
logger.debug(f"We have the extraction kit: {extraction_kit.name}")
|
||||
excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type)
|
||||
logger.debug(f"Extraction kit map:\n\n{pprint.pformat(excel_map)}")
|
||||
input_reagents = [item.to_reagent_dict(extraction_kit=base_submission.extraction_kit) for item in base_submission.reagents]
|
||||
logger.debug(f"Parsed reagents going into autofile: {pprint.pformat(input_reagents)}")
|
||||
# autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info, missing_info=obj.missing_info)
|
||||
autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=base_submission.__dict__, missing_info=obj.missing_info)
|
||||
if hasattr(obj, 'csv'):
|
||||
wkb = obj.pyd.autofill_excel()
|
||||
if wkb != None:
|
||||
fname = select_save_file(obj=obj, default_name=obj.pyd.rsl_plate_num['value'], extension="xlsx")
|
||||
wkb.save(filename=fname.__str__())
|
||||
if hasattr(obj.pyd, 'csv'):
|
||||
dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
|
||||
if dlg.exec():
|
||||
fname = select_save_file(obj, f"{base_submission.rsl_plate_num}.csv", extension="csv")
|
||||
@@ -353,10 +329,6 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
obj.csv.to_csv(fname.__str__(), index=False)
|
||||
except PermissionError:
|
||||
logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
|
||||
try:
|
||||
delattr(obj, "csv")
|
||||
except AttributeError:
|
||||
pass
|
||||
return obj, result
|
||||
|
||||
def generate_report_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
@@ -905,6 +877,8 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
|
||||
fname = select_save_file(obj=obj, default_name=info['rsl_plate_num'], extension="xlsx")
|
||||
workbook.save(filename=fname.__str__())
|
||||
|
||||
|
||||
|
||||
def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Generates a csv file from client submitted xlsx file.
|
||||
@@ -1016,23 +990,29 @@ def scrape_reagents(obj:QMainWindow, extraction_kit:str) -> Tuple[QMainWindow, d
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Updated application and result
|
||||
"""
|
||||
logger.debug("\n\nHello from reagent scraper!!\n\n")
|
||||
logger.debug(f"Extraction kit: {extraction_kit}")
|
||||
obj.reagents = []
|
||||
obj.missing_reagents = []
|
||||
# obj.reagents = []
|
||||
# obj.missing_reagents = []
|
||||
# Remove previous reagent widgets
|
||||
# [item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget) if item.objectName().startswith("lot_") or item.objectName().startswith("missing_")]
|
||||
# [item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QPushButton)]
|
||||
reagents = obj.prsr.parse_reagents(extraction_kit=extraction_kit)
|
||||
logger.debug(f"Got reagents: {reagents}")
|
||||
try:
|
||||
old_reagents = obj.form.find_widgets()
|
||||
except AttributeError:
|
||||
logger.error(f"Couldn't find old reagents.")
|
||||
old_reagents = []
|
||||
# logger.debug(f"\n\nAttempting to clear: {old_reagents}\n\n")
|
||||
for reagent in old_reagents:
|
||||
if isinstance(reagent, ReagentFormWidget) or isinstance(reagent, QPushButton):
|
||||
reagent.setParent(None)
|
||||
# reagents = obj.prsr.parse_reagents(extraction_kit=extraction_kit)
|
||||
# logger.debug(f"Got reagents: {reagents}")
|
||||
# for reagent in obj.prsr.sub['reagents']:
|
||||
# # create label
|
||||
# if reagent.parsed:
|
||||
# obj.reagents.append(reagent)
|
||||
# else:
|
||||
# obj.missing_reagents.append(reagent)
|
||||
obj.reagents = obj.prsr.sub['reagents']
|
||||
logger.debug(f"Imported reagents: {obj.reagents}")
|
||||
logger.debug(f"Missing reagents: {obj.missing_reagents}")
|
||||
obj.form.reagents = obj.prsr.sub['reagents']
|
||||
# logger.debug(f"Imported reagents: {obj.reagents}")
|
||||
# logger.debug(f"Missing reagents: {obj.missing_reagents}")
|
||||
return obj, None
|
||||
|
||||
|
||||
Reference in New Issue
Block a user