Addition of autofilling excel forms. Improved pydantic validation.
This commit is contained in:
Landon Wark
@@ -29,24 +29,27 @@ from backend.db.functions import (
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)
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from backend.excel.parser import SheetParser, PCRParser
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from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
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from backend.pydant import PydReagent
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from tools import check_not_nan, check_kit_integrity
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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
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from .visualizations.control_charts import create_charts, construct_html
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from typing import List
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from openpyxl import load_workbook
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logger = logging.getLogger(f"submissions.{__name__}")
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def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]:
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"""
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_summary_
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Import a new submission to the app window
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Args:
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obj (QMainWindow): _description_
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obj (QMainWindow): original app window
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Returns:
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Tuple[QMainWindow, dict|None]: _description_
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Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict
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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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@@ -54,8 +57,10 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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# initialize samples
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obj.samples = []
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obj.reagents = {}
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obj.missing_reagents = []
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# set file dialog
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fname = select_open_file(obj, extension="xlsx")
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fname = select_open_file(obj, file_extension="xlsx")
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logger.debug(f"Attempting to parse file: {fname}")
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if not fname.exists():
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result = dict(message=f"File {fname.__str__()} not found.", status="critical")
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@@ -65,116 +70,37 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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prsr = SheetParser(ctx=obj.ctx, filepath=fname)
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except PermissionError:
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logger.error(f"Couldn't get permission to access file: {fname}")
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return
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return obj, result
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# obj.column_count = prsr.column_count
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try:
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logger.debug(f"Submission dictionary: {prsr.sub}")
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pyd = prsr.to_pydantic()
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logger.debug(f"Pydantic result: \n\n{pyd}\n\n")
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# with open("pickled.pkl", "wb") as f:
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# pickle.dump(pyd, f)
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logger.debug(f"Pydantic result: \n\n{pprint.pformat(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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# moved to pydantic model
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# if prsr.sub['rsl_plate_num'] == None:
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# prsr.sub['rsl_plate_num'] = RSLNamer(fname.__str__()).parsed_name
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# logger.debug(f"prsr.sub = {prsr.sub}")
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for sample in pyd.samples:
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if hasattr(sample, "elution_well"):
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logger.debug(f"Sample from import: {sample.elution_well}")
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# obj.current_submission_type = prsr.sub['submission_type']
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try:
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obj.xl = prsr.filepath
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except Exception as e:
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logger.error(f"Unable to make obj xl.")
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# for sample in pyd.samples:
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# if hasattr(sample, "elution_well"):
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# logger.debug(f"Sample from import: {sample.elution_well}")
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# I don't remember why this is here.
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missing_info = [k for k,v in pyd if v == None]
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obj.current_submission_type = pyd.submission_type
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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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# # regex to parser out different variable types for decision making
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# variable_parser = re.compile(r"""
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# (?P<extraction_kit>^extraction_kit$) |
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# (?P<submitted_date>^submitted_date$) |
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# (?P<submitting_lab>)^submitting_lab$ |
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# (?P<samples>)^samples$ |
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# (?P<reagent>^lot_.*$) |
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# (?P<csv>^csv$)
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# """, re.VERBOSE)
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# for item in prsr.sub:
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# logger.debug(f"Item: {item}")
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# # attempt to match variable name to regex group
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# try:
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# mo = variable_parser.fullmatch(item).lastgroup
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# except AttributeError:
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# mo = "other"
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# logger.debug(f"Mo: {mo}")
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# match mo:
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# case 'submitting_lab':
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# # create label
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# obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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# logger.debug(f"{item}: {prsr.sub[item]}")
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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_all_orgs(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(prsr.sub[item], 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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# # create label
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# obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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# # if extraction kit not available, all other values fail
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# if not check_not_nan(prsr.sub[item]):
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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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# uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=prsr.sub['submission_type'])]
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# if check_not_nan(prsr.sub[item]):
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# logger.debug(f"The extraction kit in parser was: {prsr.sub[item]}")
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# uses.insert(0, uses.pop(uses.index(prsr.sub[item])))
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# obj.ext_kit = prsr.sub[item]
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# else:
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# logger.error(f"Couldn't find {prsr.sub['extraction_kit']}")
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# obj.ext_kit = uses[0]
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# add_widget.addItems(uses)
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# case 'submitted_date':
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# # create label
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# obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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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(prsr.sub[item])
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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 'reagent':
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# # create label
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# reg_label = QLabel(item.replace("_", " ").title())
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# reg_label.setObjectName(f"lot_{item}_label")
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# obj.table_widget.formlayout.addWidget(reg_label)
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# # create reagent choice widget
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# add_widget = ImportReagent(ctx=obj.ctx, item=item, prsr=prsr)
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# obj.reagents[item] = prsr.sub[item]
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# case 'samples':
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# # hold samples in 'obj' until form submitted
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# logger.debug(f"{item}: {prsr.sub[item]}")
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# obj.samples = prsr.sub[item]
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# add_widget = None
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# case 'csv':
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# obj.csv = prsr.sub[item]
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# case _:
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# # anything else gets added in as a line edit
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# obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
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# add_widget = QLineEdit()
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# logger.debug(f"Setting widget text to {str(prsr.sub[item]).replace('_', ' ')}")
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# add_widget.setText(str(prsr.sub[item]).replace("_", " "))
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# Get list of fields from pydantic model.
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fields = list(pyd.model_fields.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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if not check_not_nan(value):
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continue
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logger.debug(f"Checking: {field}: {value}")
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# No longer necessary with addition of pydantic validations
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# if not check_not_nan(value):
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# continue
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match field:
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case 'submitting_lab':
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# create label
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@@ -194,17 +120,19 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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# create label
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label = QLabel(field.replace("_", " ").title())
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# if extraction kit not available, all other values fail
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if not check_not_nan(value):
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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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if not value['parsed']:
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missing_info.append(field)
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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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uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type)]
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if check_not_nan(value):
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logger.debug(f"The extraction kit in parser was: {value}")
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uses.insert(0, uses.pop(uses.index(value)))
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obj.ext_kit = 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 {prsr.sub['extraction_kit']}")
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obj.ext_kit = uses[0]
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@@ -225,23 +153,33 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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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 'csv':
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obj.csv = value
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case "ctx":
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continue
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case 'reagents':
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for reagent in value:
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# create label
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reg_label = QLabel(reagent['type'].replace("_", " ").title())
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reg_label.setObjectName(f"lot_{reagent['type']}_label")
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# obj.table_widget.formlayout.addWidget(reg_label)
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# reg_label = QLabel(reagent['type'].replace("_", " ").title())
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try:
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reg_label = QLabel(reagent.type.replace("_", " ").title())
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except AttributeError:
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continue
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# reg_label.setObjectName(f"lot_{reagent['type']}_label")
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reg_label.setObjectName(f"lot_{reagent.type}_label")
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# create reagent choice widget
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add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent)
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add_widget.setObjectName(f"lot_{reagent['type']}")
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add_widget.setObjectName(f"lot_{reagent.type}")
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logger.debug(f"Widget name set to: {add_widget.objectName()}")
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obj.table_widget.formlayout.addWidget(reg_label)
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obj.table_widget.formlayout.addWidget(add_widget)
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obj.reagents[reagent['type']] = reagent['lot']
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obj.reagents[reagent.type] = reagent
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continue
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case "rsl_plate_num":
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if not value['parsed']:
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missing_info.append(field)
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label = QLabel(field.replace("_", " ").title())
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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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case _:
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# anything else gets added in as a line edit
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label = QLabel(field.replace("_", " ").title())
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@@ -258,13 +196,27 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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# compare obj.reagents with expected reagents in kit
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if hasattr(obj, 'ext_kit'):
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obj.kit_integrity_completion()
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obj.missing_reagents = obj.missing_reagents + missing_info
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logger.debug(f"Imported reagents: {obj.reagents}")
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if prsr.sample_result != None:
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msg = AlertPop(message=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"All attributes of obj:\n{pprint.pformat(obj.__dict__)}")
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return obj, result
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def kit_reload_function(obj:QMainWindow) -> QMainWindow:
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def kit_reload_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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"""
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Reload the fields in the form
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Args:
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obj (QMainWindow): original app window
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Returns:
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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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@@ -277,7 +229,16 @@ def kit_reload_function(obj:QMainWindow) -> QMainWindow:
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obj.kit_integrity_completion_function()
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return obj, result
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def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
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def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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"""
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Compare kit contents to parsed contents
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Args:
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obj (QMainWindow): The original app window
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Returns:
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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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logger.debug(inspect.currentframe().f_back.f_code.co_name)
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# find the widget that contains lit info
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@@ -296,9 +257,11 @@ def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
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# if kit integrity comes back with an error, make widgets with missing reagents using default info
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if kit_integrity != None:
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result = dict(message=kit_integrity['message'], status="Warning")
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obj.missing_reagents = kit_integrity['missing']
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for item in kit_integrity['missing']:
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obj.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
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add_widget = ImportReagent(ctx=obj.ctx, reagent=dict(type=item, lot=None, exp=None))#item=item)
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reagent = dict(type=item, lot=None, exp=None)
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add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent))#item=item)
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obj.table_widget.formlayout.addWidget(add_widget)
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submit_btn = QPushButton("Submit")
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submit_btn.setObjectName("lot_submit_btn")
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@@ -306,38 +269,50 @@ def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
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submit_btn.clicked.connect(obj.submit_new_sample)
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return obj, result
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def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
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def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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"""
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Parse forms and add sample to the database.
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Args:
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obj (QMainWindow): original app window
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Returns:
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Tuple[QMainWindow, dict]: Collection of new main app window and result 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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# seperate out reagents
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reagents = {k:v for k,v in info.items() if k.startswith("lot_")}
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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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logger.debug(f"Info: {info}")
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logger.debug(f"Reagents: {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 reagents:
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# TODO: have this lookup by type and lot
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# Lookup any existing reagent of this type with this lot number
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wanted_reagent = lookup_reagent(ctx=obj.ctx, reagent_lot=reagents[reagent], type_name=reagent)
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logger.debug(f"Looked up reagent: {wanted_reagent}")
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# logger.debug(f"\n\nLooking for {reagent} in {obj.reagents}\n\n")
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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 = reagents[reagent]
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dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent.replace('_', ' ').title().strip('Lot')}: {r_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"checking reagent: {reagent} in obj.reagents. Result: {obj.reagents[reagent]}")
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expiry_date = obj.reagents[reagent]['exp']
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expiry_date = obj.reagents[reagent].exp
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wanted_reagent = obj.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
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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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if wanted_reagent != None:
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parsed_reagents.append(wanted_reagent)
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wanted_reagent.type.last_used = reagents[reagent]
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# move samples into preliminary submission dict
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info['samples'] = obj.samples
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info['uploaded_by'] = getuser()
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# info['columns'] = obj.column_count
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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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base_submission, result = construct_submission_info(ctx=obj.ctx, info_dict=info)
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@@ -359,6 +334,7 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
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# add reagents to submission object
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for reagent in parsed_reagents:
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base_submission.reagents.append(reagent)
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logger.debug(f"Parsed reagents: {pprint.pformat(parsed_reagents)}")
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logger.debug("Checking kit integrity...")
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kit_integrity = check_kit_integrity(base_submission)
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if kit_integrity != None:
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@@ -371,7 +347,15 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
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# reset form
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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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logger.debug(f"All attributes of obj: {pprint.pprint(obj.__dict__)}")
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logger.debug(f"All attributes of obj: {pprint.pformat(obj.__dict__)}")
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if len(obj.missing_reagents) > 0:
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logger.debug(f"We have blank reagents in the excel sheet.\n\tLet's try to fill them in.")
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extraction_kit = lookup_kittype_by_name(obj.ctx, name=obj.ext_kit)
|
||||
logger.debug(f"We have the extraction kit: {extraction_kit.name}")
|
||||
logger.debug(f"Extraction kit map:\n\n{extraction_kit.used_for[obj.current_submission_type]}")
|
||||
excel_map = extraction_kit.used_for[obj.current_submission_type]
|
||||
input_reagents = [item.to_reagent_dict() for item in parsed_reagents]
|
||||
autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info)
|
||||
if hasattr(obj, 'csv'):
|
||||
dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
|
||||
if dlg.exec():
|
||||
@@ -384,13 +368,18 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
|
||||
delattr(obj, "csv")
|
||||
except AttributeError:
|
||||
pass
|
||||
# if obj.current_submission_type == "Bacterial_Culture":
|
||||
# hitpick = hitpick_plate(base_submission)
|
||||
# image = make_plate_map(hitpick)
|
||||
# image.show()
|
||||
return obj, result
|
||||
|
||||
def generate_report_function(obj:QMainWindow) -> QMainWindow:
|
||||
def generate_report_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Generate a summary of activities for a time period
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
# ask for date ranges
|
||||
dlg = ReportDatePicker()
|
||||
@@ -430,7 +419,16 @@ def generate_report_function(obj:QMainWindow) -> QMainWindow:
|
||||
writer.close()
|
||||
return obj, result
|
||||
|
||||
def add_kit_function(obj:QMainWindow) -> QMainWindow:
|
||||
def add_kit_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Add a new kit to the database.
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
# setup file dialog to find yaml flie
|
||||
fname = select_open_file(obj, extension="yml")
|
||||
@@ -449,7 +447,16 @@ def add_kit_function(obj:QMainWindow) -> QMainWindow:
|
||||
result = create_kit_from_yaml(ctx=obj.ctx, exp=exp)
|
||||
return obj, result
|
||||
|
||||
def add_org_function(obj:QMainWindow) -> QMainWindow:
|
||||
def add_org_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Add a new organization to the database.
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
# setup file dialog to find yaml flie
|
||||
fname = select_open_file(obj, extension="yml")
|
||||
@@ -468,7 +475,16 @@ def add_org_function(obj:QMainWindow) -> QMainWindow:
|
||||
result = create_org_from_yaml(ctx=obj.ctx, org=org)
|
||||
return obj, result
|
||||
|
||||
def controls_getter_function(obj:QMainWindow) -> QMainWindow:
|
||||
def controls_getter_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Get controls based on start/end dates
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
# subtype defaults to disabled
|
||||
try:
|
||||
@@ -480,11 +496,12 @@ def controls_getter_function(obj:QMainWindow) -> QMainWindow:
|
||||
logger.warning("Start date after end date is not allowed!")
|
||||
threemonthsago = obj.table_widget.datepicker.end_date.date().addDays(-60)
|
||||
# block signal that will rerun controls getter and set start date
|
||||
# Without triggering this function again
|
||||
with QSignalBlocker(obj.table_widget.datepicker.start_date) as blocker:
|
||||
obj.table_widget.datepicker.start_date.setDate(threemonthsago)
|
||||
obj._controls_getter()
|
||||
return obj, result
|
||||
# convert to python useable date object
|
||||
# convert to python useable date objects
|
||||
obj.start_date = obj.table_widget.datepicker.start_date.date().toPyDate()
|
||||
obj.end_date = obj.table_widget.datepicker.end_date.date().toPyDate()
|
||||
obj.con_type = obj.table_widget.control_typer.currentText()
|
||||
@@ -504,15 +521,15 @@ def controls_getter_function(obj:QMainWindow) -> QMainWindow:
|
||||
obj._chart_maker()
|
||||
return obj, result
|
||||
|
||||
def chart_maker_function(obj:QMainWindow) -> QMainWindow:
|
||||
def chart_maker_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
create html chart for controls reporting
|
||||
Create html chart for controls reporting
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original MainWindow
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
QMainWindow: MainWindow with control display updates
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
logger.debug(f"Control getter context: \n\tControl type: {obj.con_type}\n\tMode: {obj.mode}\n\tStart Date: {obj.start_date}\n\tEnd Date: {obj.end_date}")
|
||||
@@ -552,7 +569,16 @@ def chart_maker_function(obj:QMainWindow) -> QMainWindow:
|
||||
logger.debug("Figure updated... I hope.")
|
||||
return obj, result
|
||||
|
||||
def link_controls_function(obj:QMainWindow) -> QMainWindow:
|
||||
def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Link scraped controls to imported submissions.
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
all_bcs = lookup_all_submissions_by_type(obj.ctx, "Bacterial Culture")
|
||||
logger.debug(all_bcs)
|
||||
@@ -601,12 +627,20 @@ def link_controls_function(obj:QMainWindow) -> QMainWindow:
|
||||
# msg.exec()
|
||||
return obj, result
|
||||
|
||||
def link_extractions_function(obj:QMainWindow) -> QMainWindow:
|
||||
def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Link extractions from runlogs to imported submissions
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
# home_dir = str(Path(obj.ctx["directory_path"]))
|
||||
# fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "csv(*.csv)")[0])
|
||||
fname = select_open_file(obj, extension="csv")
|
||||
fname = select_open_file(obj, file_extension="csv")
|
||||
with open(fname.__str__(), 'r') as f:
|
||||
# split csv on commas
|
||||
runs = [col.strip().split(",") for col in f.readlines()]
|
||||
count = 0
|
||||
for run in runs:
|
||||
@@ -618,9 +652,12 @@ def link_extractions_function(obj:QMainWindow) -> QMainWindow:
|
||||
experiment_name=run[4].strip(),
|
||||
end_time=run[5].strip()
|
||||
)
|
||||
# elution columns are item 6 in the comma split list to the end
|
||||
for ii in range(6, len(run)):
|
||||
new_run[f"column{str(ii-5)}_vol"] = run[ii]
|
||||
# Lookup imported submissions
|
||||
sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
|
||||
# If no such submission exists, move onto the next run
|
||||
try:
|
||||
logger.debug(f"Found submission: {sub.rsl_plate_num}")
|
||||
count += 1
|
||||
@@ -630,12 +667,14 @@ def link_extractions_function(obj:QMainWindow) -> QMainWindow:
|
||||
existing = json.loads(sub.extraction_info)
|
||||
else:
|
||||
existing = None
|
||||
# Check if the new info already exists in the imported submission
|
||||
try:
|
||||
if json.dumps(new_run) in sub.extraction_info:
|
||||
logger.debug(f"Looks like we already have that info.")
|
||||
continue
|
||||
except TypeError:
|
||||
pass
|
||||
# Update or create the extraction info
|
||||
if existing != None:
|
||||
try:
|
||||
logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
|
||||
@@ -653,12 +692,20 @@ def link_extractions_function(obj:QMainWindow) -> QMainWindow:
|
||||
result = dict(message=f"We added {count} logs to the database.", status='information')
|
||||
return obj, result
|
||||
|
||||
def link_pcr_function(obj:QMainWindow) -> QMainWindow:
|
||||
def link_pcr_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Link PCR data from run logs to an imported submission
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
# home_dir = str(Path(obj.ctx["directory_path"]))
|
||||
# fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "csv(*.csv)")[0])
|
||||
fname = select_open_file(obj, extension="csv")
|
||||
fname = select_open_file(obj, file_extension="csv")
|
||||
with open(fname.__str__(), 'r') as f:
|
||||
# split csv rows on comma
|
||||
runs = [col.strip().split(",") for col in f.readlines()]
|
||||
count = 0
|
||||
for run in runs:
|
||||
@@ -670,17 +717,19 @@ def link_pcr_function(obj:QMainWindow) -> QMainWindow:
|
||||
experiment_name=run[4].strip(),
|
||||
end_time=run[5].strip()
|
||||
)
|
||||
# for ii in range(6, len(run)):
|
||||
# obj[f"column{str(ii-5)}_vol"] = run[ii]
|
||||
# lookup imported submission
|
||||
sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
|
||||
# if imported submission doesn't exist move on to next run
|
||||
try:
|
||||
logger.debug(f"Found submission: {sub.rsl_plate_num}")
|
||||
except AttributeError:
|
||||
continue
|
||||
# check if pcr_info already exists
|
||||
if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
|
||||
existing = json.loads(sub.pcr_info)
|
||||
else:
|
||||
existing = None
|
||||
# check if this entry already exists in imported submission
|
||||
try:
|
||||
if json.dumps(new_run) in sub.pcr_info:
|
||||
logger.debug(f"Looks like we already have that info.")
|
||||
@@ -706,17 +755,25 @@ def link_pcr_function(obj:QMainWindow) -> QMainWindow:
|
||||
result = dict(message=f"We added {count} logs to the database.", status='information')
|
||||
return obj, result
|
||||
|
||||
def import_pcr_results_function(obj:QMainWindow) -> QMainWindow:
|
||||
def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Import Quant-studio PCR data to an imported submission
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): original app window
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
|
||||
"""
|
||||
result = None
|
||||
# home_dir = str(Path(obj.ctx["directory_path"]))
|
||||
# fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "xlsx(*.xlsx)")[0])
|
||||
fname = select_open_file(obj, extension="xlsx")
|
||||
fname = select_open_file(obj, file_extension="xlsx")
|
||||
parser = PCRParser(ctx=obj.ctx, filepath=fname)
|
||||
logger.debug(f"Attempting lookup for {parser.plate_num}")
|
||||
sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
|
||||
try:
|
||||
logger.debug(f"Found submission: {sub.rsl_plate_num}")
|
||||
except AttributeError:
|
||||
# If no plate is found, may be because this is a repeat. Lop off the '-1' or '-2' and repeat
|
||||
logger.error(f"Submission of number {parser.plate_num} not found. Attempting rescue of plate repeat.")
|
||||
parser.plate_num = "-".join(parser.plate_num.split("-")[:-1])
|
||||
sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
|
||||
@@ -725,14 +782,13 @@ def import_pcr_results_function(obj:QMainWindow) -> QMainWindow:
|
||||
except AttributeError:
|
||||
logger.error(f"Rescue of {parser.plate_num} failed.")
|
||||
return obj, dict(message="Couldn't find a submission with that RSL number.", status="warning")
|
||||
# jout = json.dumps(parser.pcr)
|
||||
count = 0
|
||||
# Check if PCR info already exists
|
||||
if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
|
||||
existing = json.loads(sub.pcr_info)
|
||||
else:
|
||||
# jout = None
|
||||
existing = None
|
||||
if existing != None:
|
||||
# update pcr_info
|
||||
try:
|
||||
logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
|
||||
if json.dumps(parser.pcr) not in sub.pcr_info:
|
||||
@@ -757,5 +813,59 @@ def import_pcr_results_function(obj:QMainWindow) -> QMainWindow:
|
||||
update_ww_sample(ctx=obj.ctx, sample_obj=sample)
|
||||
result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
|
||||
return obj, result
|
||||
# dlg.exec()
|
||||
|
||||
def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_reagents:List[str], info:dict):
|
||||
"""
|
||||
Automatically fills in excel cells with reagent info.
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): Original main app window
|
||||
xl_map (dict): Map of where each reagent goes in the excel workbook.
|
||||
reagents (List[dict]): All reagents used in the kit.
|
||||
missing_reagents (List[str]): Reagents that are required for the kit that were not present.
|
||||
"""
|
||||
# logger.debug(reagents)
|
||||
|
||||
logger.debug(f"Here is the info dict coming in:\n{pprint.pformat(info)}")
|
||||
logger.debug(f"Here are the missing reagents:\n{missing_reagents}")
|
||||
relevant_map = {k:v for k,v in xl_map.items() if k in missing_reagents}
|
||||
# logger.debug(relevant_map)
|
||||
relevant_reagents = [item for item in reagents if item['type'] in missing_reagents]
|
||||
relevant_info = {k:v for k,v in info.items() if k in missing_reagents}
|
||||
logger.debug(f"Here is the relevant info: {pprint.pformat(relevant_info)}")
|
||||
# logger.debug(f"Relevant reagents:\n{relevant_reagents}")
|
||||
# construct new objects to put into excel sheets:
|
||||
new_reagents = []
|
||||
for reagent in relevant_reagents:
|
||||
new_reagent = {}
|
||||
new_reagent['type'] = reagent['type']
|
||||
new_reagent['lot'] = relevant_map[new_reagent['type']]['lot']
|
||||
new_reagent['lot']['value'] = reagent['lot']
|
||||
new_reagent['expiry'] = relevant_map[new_reagent['type']]['expiry']
|
||||
new_reagent['expiry']['value'] = reagent['expiry']
|
||||
new_reagent['sheet'] = relevant_map[new_reagent['type']]['sheet']
|
||||
new_reagents.append(new_reagent)
|
||||
new_info = []
|
||||
for item in relevant_info:
|
||||
new_item = {}
|
||||
new_item['type'] = item
|
||||
new_item['location'] = relevant_map[item]
|
||||
new_item['value'] = relevant_info[item]
|
||||
new_info.append(new_item)
|
||||
logger.debug(f"New reagents: {new_reagents}")
|
||||
workbook = load_workbook(obj.xl)
|
||||
sheets = workbook.sheetnames
|
||||
logger.debug(workbook.sheetnames)
|
||||
for sheet in sheets:
|
||||
worksheet=workbook[sheet]
|
||||
sheet_reagents = [item for item in new_reagents if item['sheet'] == sheet]
|
||||
for reagent in sheet_reagents:
|
||||
logger.debug(f"Attempting: {reagent['type']}:")
|
||||
worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'], value=reagent['lot']['value'])
|
||||
worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value'])
|
||||
sheet_info = [item for item in new_info if item['location']['sheet'] == sheet]
|
||||
for item in sheet_info:
|
||||
logger.debug(f"Attempting: {item['type']}")
|
||||
worksheet.cell(row=item['location']['row'], column=item['location']['column'], value=item['value'])
|
||||
fname = select_save_file(obj=obj, default_name=Path(obj.xl).stem, extension="xlsx")
|
||||
workbook.save(filename=fname.__str__())
|
||||
|
||||
Reference in New Issue
Block a user