Large scale refactor to improve db efficiency
This commit is contained in:
Landon Wark
@@ -22,16 +22,12 @@ from PyQt6.QtWidgets import (
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from .all_window_functions import extract_form_info, select_open_file, select_save_file
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from PyQt6.QtCore import QSignalBlocker
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from backend.db.functions import (
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lookup_all_orgs, lookup_kittype_by_use, lookup_kittype_by_name,
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construct_submission_info, lookup_reagent, store_submission, lookup_submissions_by_date_range,
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create_kit_from_yaml, create_org_from_yaml, get_control_subtypes, get_all_controls_by_type,
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lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_subsampassoc_with_pcr,
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check_kit_integrity, lookup_sub_samp_association_by_plate_sample, lookup_ww_sample_by_processing_number,
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lookup_sample_by_submitter_id, update_last_used
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construct_submission_info, lookup_reagents, construct_kit_from_yaml, construct_org_from_yaml, get_control_subtypes,
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update_subsampassoc_with_pcr, check_kit_integrity, update_last_used, lookup_organizations, lookup_kit_types,
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lookup_submissions, lookup_controls, lookup_samples, lookup_submission_sample_association, store_object
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)
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from backend.excel.parser import SheetParser, PCRParser, SampleParser
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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, 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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@@ -55,8 +51,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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logger.debug(obj.ctx)
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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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obj.missing_info = []
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# set file dialog
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@@ -67,31 +62,20 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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return obj, result
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# create sheetparser using excel sheet and context from gui
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try:
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prsr = SheetParser(ctx=obj.ctx, filepath=fname)
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obj.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 obj, result
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# prsr.sub = import_validation_check(ctx=obj.ctx, parser_sub=prsr.sub)
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# obj.column_count = prsr.column_count
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try:
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logger.debug(f"Submission dictionary:\n{pprint.pformat(prsr.sub)}")
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pyd = prsr.to_pydantic()
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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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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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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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obj.current_submission_type = pyd.submission_type['value']
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# destroy any widgets from previous imports
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for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
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item.setParent(None)
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obj.current_submission_type = pyd.submission_type['value']
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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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@@ -107,13 +91,11 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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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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# create label
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# label = QLabel(field.replace("_", " ").title())
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# label = ParsedQLabel(value, field)
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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_all_orgs(ctx=obj.ctx)]
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# labs = [item.__str__() for item in lookup_all_orgs(ctx=obj.ctx)]
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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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@@ -122,9 +104,6 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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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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# 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['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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@@ -132,21 +111,21 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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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['value'].lower())]
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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_kittype_by_use(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
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# uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, 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 {prsr.sub['extraction_kit']}")
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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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add_widget.addItems(uses)
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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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# add_widget.addItems(uses)
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case 'submitted_date':
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# create label
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# label = QLabel(field.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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@@ -163,40 +142,10 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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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 = ParsedQLabel(reagent, reagent['value'].type, title=False)
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if reagent['parsed']:
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# try:
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# reg_label = QLabel(f"Parsed Lot: {reagent['value'].type}")
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obj.reagents.append(reagent['value'])
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# except AttributeError:
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# continue
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else:
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# try:
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# reg_label = QLabel(f"MISSING Lot: {reagent['value'].type}")
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obj.missing_reagents.append(reagent['value'])
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continue
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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['value'].type}_label")
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# create reagent choice widget
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add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent['value'], extraction_kit=pyd.extraction_kit['value'])
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add_widget.setObjectName(f"lot_{reagent['value'].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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# NOTE: This is now set to run when the extraction kit is updated.
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continue
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# case "rsl_plate_num":
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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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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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@@ -207,13 +156,11 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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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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# 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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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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@@ -255,31 +202,30 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
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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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# 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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logger.debug(f"Kit selector: {kit_widget}")
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# get current kit info
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# get current kit being used
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obj.ext_kit = kit_widget.currentText()
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for item in obj.reagents:
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obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':True}, item.type, title=False, label_name=f"lot_{item.type}_label"))
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reagent = dict(type=item.type, lot=item.lot, exp=item.exp, name=item.name)
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add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
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obj.table_widget.formlayout.addWidget(add_widget)
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logger.debug(f"Checking integrity of {obj.ext_kit}")
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# get the kit from database using current kit info
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# kit = lookup_kittype_by_name(ctx=obj.ctx, name=obj.ext_kit)
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# get all reagents stored in the QWindow object
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# reagents_to_lookup = [item.name for item in obj.missing_reagents]
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# logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
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# make sure kit contains all necessary info
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# kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
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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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# see if there are any missing reagents
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if len(obj.missing_reagents) > 0:
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result = dict(message=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in obj.missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning")
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for item in obj.missing_reagents:
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obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False))
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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}_label"))
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# Set default parameters for the empty reagent.
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reagent = dict(type=item.type, lot=None, exp=date.today(), name=None)
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add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)#item=item)
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# create and add widget
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# add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)
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add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
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obj.table_widget.formlayout.addWidget(add_widget)
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# Add submit button to the form.
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submit_btn = QPushButton("Submit")
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submit_btn.setObjectName("lot_submit_btn")
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obj.table_widget.formlayout.addWidget(submit_btn)
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@@ -309,7 +255,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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# compare reagents in form to reagent database
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for reagent in reagents:
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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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wanted_reagent = lookup_reagents(ctx=obj.ctx, lot_number=reagents[reagent], reagent_type=reagent)
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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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@@ -362,8 +308,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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if kit_integrity != None:
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return obj, dict(message=kit_integrity['message'], status="critical")
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logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
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result = store_submission(ctx=obj.ctx, base_submission=base_submission)
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# check result of storing for issues
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result = store_object(ctx=obj.ctx, object=base_submission)
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# update summary sheet
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obj.table_widget.sub_wid.setData()
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# reset form
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@@ -372,7 +317,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, 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 + obj.missing_info) > 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)
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extraction_kit = lookup_kit_types(ctx=obj.ctx, name=obj.ext_kit)
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logger.debug(f"We have the extraction kit: {extraction_kit.name}")
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excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type)
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logger.debug(f"Extraction kit map:\n\n{pprint.pformat(excel_map)}")
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@@ -410,7 +355,8 @@ def generate_report_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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info = extract_form_info(dlg)
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logger.debug(f"Report info: {info}")
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# find submissions based on date range
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subs = lookup_submissions_by_date_range(ctx=obj.ctx, start_date=info['start_date'], end_date=info['end_date'])
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# subs = lookup_submissions_by_date_range(ctx=obj.ctx, start_date=info['start_date'], end_date=info['end_date'])
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subs = lookup_submissions(ctx=obj.ctx, start_date=info['start_date'], end_date=info['end_date'])
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# convert each object to dict
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records = [item.report_dict() for item in subs]
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# make dataframe from record dictionaries
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@@ -452,7 +398,7 @@ def add_kit_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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# setup file dialog to find yaml flie
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# setup file dialog to find yaml file
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fname = select_open_file(obj, file_extension="yml")
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assert fname.exists()
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# read yaml file
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@@ -466,7 +412,7 @@ def add_kit_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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except PermissionError:
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return
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# send to kit creator function
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result = create_kit_from_yaml(ctx=obj.ctx, exp=exp)
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result = construct_kit_from_yaml(ctx=obj.ctx, exp=exp)
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return obj, result
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def add_org_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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@@ -494,7 +440,7 @@ def add_org_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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except PermissionError:
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return obj, result
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# send to kit creator function
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result = create_org_from_yaml(ctx=obj.ctx, org=org)
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result = construct_org_from_yaml(ctx=obj.ctx, org=org)
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return obj, result
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def controls_getter_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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@@ -531,6 +477,7 @@ def controls_getter_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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obj.table_widget.sub_typer.clear()
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# lookup subtypes
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sub_types = get_control_subtypes(ctx=obj.ctx, type=obj.con_type, mode=obj.mode)
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# sub_types = lookup_controls(ctx=obj.ctx, control_type=obj.con_type)
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if sub_types != []:
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# block signal that will rerun controls getter and update sub_typer
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with QSignalBlocker(obj.table_widget.sub_typer) as blocker:
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@@ -562,7 +509,8 @@ def chart_maker_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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obj.subtype = obj.table_widget.sub_typer.currentText()
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logger.debug(f"Subtype: {obj.subtype}")
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# query all controls using the type/start and end dates from the gui
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controls = get_all_controls_by_type(ctx=obj.ctx, con_type=obj.con_type, start_date=obj.start_date, end_date=obj.end_date)
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# controls = get_all_controls_by_type(ctx=obj.ctx, con_type=obj.con_type, start_date=obj.start_date, end_date=obj.end_date)
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controls = lookup_controls(ctx=obj.ctx, control_type=obj.con_type, start_date=obj.start_date, end_date=obj.end_date)
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# if no data found from query set fig to none for reporting in webview
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if controls == None:
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fig = None
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@@ -602,9 +550,11 @@ def link_controls_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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all_bcs = lookup_all_submissions_by_type(obj.ctx, "Bacterial Culture")
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# all_bcs = lookup_all_submissions_by_type(obj.ctx, "Bacterial Culture")
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all_bcs = lookup_submissions(ctx=obj.ctx, submission_type="Bacterial Culture")
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logger.debug(all_bcs)
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all_controls = get_all_controls(obj.ctx)
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# all_controls = get_all_controls(obj.ctx)
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all_controls = lookup_controls(ctx=obj.ctx)
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ac_list = [control.name for control in all_controls]
|
||||
count = 0
|
||||
for bcs in all_bcs:
|
||||
@@ -617,7 +567,6 @@ def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
if " " in sample:
|
||||
logger.warning(f"There is not supposed to be a space in the sample name!!!")
|
||||
sample = sample.replace(" ", "")
|
||||
# if sample not in ac_list:
|
||||
if not any([ac.startswith(sample) for ac in ac_list]):
|
||||
continue
|
||||
else:
|
||||
@@ -632,24 +581,15 @@ def link_controls_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
else:
|
||||
logger.debug(f"Adding {control.name} to {bcs.rsl_plate_num} as control")
|
||||
bcs.controls.append(control)
|
||||
# bcs.control_id.append(control.id)
|
||||
control.submission = bcs
|
||||
control.submission_id = bcs.id
|
||||
# obj.ctx["database_session"].add(control)
|
||||
obj.ctx.database_session.add(control)
|
||||
count += 1
|
||||
# obj.ctx["database_session"].add(bcs)
|
||||
obj.ctx.database_session.add(bcs)
|
||||
logger.debug(f"Here is the new control: {[control.name for control in bcs.controls]}")
|
||||
result = dict(message=f"We added {count} controls to bacterial cultures.", status="information")
|
||||
logger.debug(result)
|
||||
# obj.ctx['database_session'].commit()
|
||||
obj.ctx.database_session.commit()
|
||||
# msg = QMessageBox()
|
||||
# msg.setText("Controls added")
|
||||
# msg.setInformativeText(result)
|
||||
# msg.setWindowTitle("Controls added")
|
||||
# msg.exec()
|
||||
return obj, result
|
||||
|
||||
def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
@@ -681,7 +621,8 @@ def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
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'])
|
||||
# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
|
||||
sub = lookup_submissions(ctx=obj.ctx, rsl_number=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}")
|
||||
@@ -712,8 +653,6 @@ def link_extractions_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
|
||||
else:
|
||||
sub.extraction_info = json.dumps([new_run])
|
||||
# obj.ctx['database_session'].add(sub)
|
||||
# obj.ctx["database_session"].commit()
|
||||
obj.ctx.database_session.add(sub)
|
||||
obj.ctx.database_session.commit()
|
||||
result = dict(message=f"We added {count} logs to the database.", status='information')
|
||||
@@ -745,7 +684,8 @@ def link_pcr_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
end_time=run[5].strip()
|
||||
)
|
||||
# lookup imported submission
|
||||
sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
|
||||
# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
|
||||
sub = lookup_submissions(ctx=obj.ctx, rsl_number=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}")
|
||||
@@ -777,8 +717,6 @@ def link_pcr_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
|
||||
else:
|
||||
sub.pcr_info = json.dumps([new_run])
|
||||
# obj.ctx['database_session'].add(sub)
|
||||
# obj.ctx["database_session"].commit()
|
||||
obj.ctx.database_session.add(sub)
|
||||
obj.ctx.database_session.commit()
|
||||
result = dict(message=f"We added {count} logs to the database.", status='information')
|
||||
@@ -798,14 +736,16 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
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)
|
||||
# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
|
||||
sub = lookup_submissions(ctx=obj.ctx, rsl_number=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)
|
||||
# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
|
||||
sub = lookup_submissions(ctx=obj.ctx, rsl_number=parser.plate_num)
|
||||
try:
|
||||
logger.debug(f"Found submission: {sub.rsl_plate_num}")
|
||||
except AttributeError:
|
||||
@@ -830,11 +770,9 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
|
||||
else:
|
||||
sub.pcr_info = json.dumps([parser.pcr])
|
||||
# obj.ctx['database_session'].add(sub)
|
||||
obj.ctx.database_session.add(sub)
|
||||
logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
|
||||
logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
|
||||
# obj.ctx["database_session"].commit()
|
||||
obj.ctx.database_session.commit()
|
||||
logger.debug(f"Got {len(parser.samples)} samples to update!")
|
||||
logger.debug(f"Parser samples: {parser.samples}")
|
||||
@@ -844,8 +782,6 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
|
||||
except IndexError:
|
||||
continue
|
||||
# sample['plate_rsl'] = sub.rsl_plate_num
|
||||
# update_ww_sample(ctx=obj.ctx, sample_obj=sample)
|
||||
update_subsampassoc_with_pcr(ctx=obj.ctx, submission=sub, sample=sample, input_dict=sample_dict)
|
||||
|
||||
result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
|
||||
@@ -909,8 +845,8 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
|
||||
new_info.append(new_item)
|
||||
logger.debug(f"New reagents: {new_reagents}")
|
||||
logger.debug(f"New info: {new_info}")
|
||||
# open the workbook using openpyxl
|
||||
workbook = load_workbook(obj.xl)
|
||||
# open a new workbook using openpyxl
|
||||
workbook = load_workbook(obj.prsr.xl.io)
|
||||
# get list of sheet names
|
||||
sheets = workbook.sheetnames
|
||||
# logger.debug(workbook.sheetnames)
|
||||
@@ -941,22 +877,25 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
|
||||
workbook.save(filename=fname.__str__())
|
||||
|
||||
def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Generates a csv file from client submitted xlsx file.
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): Main application
|
||||
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Updated main application and result
|
||||
"""
|
||||
def get_plates(input_sample_number:str, plates:list) -> Tuple[int, str]:
|
||||
logger.debug(f"Looking up {input_sample_number} in {plates}")
|
||||
samp = lookup_ww_sample_by_processing_number(ctx=obj.ctx, processing_number=input_sample_number)
|
||||
# samp = lookup_ww_sample_by_processing_number(ctx=obj.ctx, processing_number=input_sample_number)
|
||||
samp = lookup_samples(ctx=obj.ctx, ww_processing_num=input_sample_number)
|
||||
if samp == None:
|
||||
samp = lookup_sample_by_submitter_id(ctx=obj.ctx, submitter_id=input_sample_number)
|
||||
# samp = lookup_sample_by_submitter_id(ctx=obj.ctx, submitter_id=input_sample_number)
|
||||
samp = lookup_samples(ctx=obj.ctx, submitter_id=input_sample_number)
|
||||
logger.debug(f"Got sample: {samp}")
|
||||
# if samp != None:
|
||||
new_plates = [(iii+1, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate))) for iii, plate in enumerate(plates)]
|
||||
# for iii, plate in enumerate(plates):
|
||||
# lplate = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate)
|
||||
# if lplate == None:
|
||||
# continue
|
||||
# else:
|
||||
# logger.debug(f"Got a plate: {lplate}")
|
||||
# new_plates.append((iii, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lplate)))
|
||||
# new_plates = [(iii+1, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate))) for iii, plate in enumerate(plates)]
|
||||
new_plates = [(iii+1, lookup_submission_sample_association(ctx=obj.ctx, sample=samp, submission=plate)) for iii, plate in enumerate(plates)]
|
||||
logger.debug(f"Associations: {pprint.pformat(new_plates)}")
|
||||
try:
|
||||
plate_num, plate = next(assoc for assoc in new_plates if assoc[1] is not None)
|
||||
@@ -964,8 +903,6 @@ def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]
|
||||
plate_num, plate = None, None
|
||||
logger.debug(f"Plate number {plate_num} is {plate}")
|
||||
return plate_num, plate
|
||||
|
||||
|
||||
fname = select_open_file(obj=obj, file_extension="xlsx")
|
||||
xl = pd.ExcelFile(fname)
|
||||
sprsr = SampleParser(ctx=obj.ctx, xl=xl, submission_type="First Strand")
|
||||
@@ -988,7 +925,6 @@ def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]
|
||||
else:
|
||||
new_dict['destination_row'] = item['row']
|
||||
new_dict['destination_column'] = item['column']
|
||||
# assocs = [(iii, lookup_ww_sample_by_processing_number_and_plate(ctx=obj.ctx, processing_number=new_dict['sample'], plate_number=plate)) for iii, plate in enumerate(plates)]
|
||||
plate_num, plate = get_plates(input_sample_number=new_dict['sample'], plates=plates)
|
||||
if plate_num == None:
|
||||
plate_num = str(old_plate_number) + "*"
|
||||
@@ -1015,3 +951,34 @@ def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]
|
||||
df.to_csv(ofname, index=False)
|
||||
return obj, None
|
||||
|
||||
def scrape_reagents(obj:QMainWindow, extraction_kit:str) -> Tuple[QMainWindow, dict]:
|
||||
"""
|
||||
Extracted scrape reagents function that will run when
|
||||
form 'extraction_kit' widget is updated.
|
||||
|
||||
Args:
|
||||
obj (QMainWindow): updated main application
|
||||
extraction_kit (str): name of extraction kit (in 'extraction_kit' widget)
|
||||
|
||||
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 = []
|
||||
[item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget) if item.objectName().startswith("lot_") or item.objectName().startswith("missing_")]
|
||||
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['value'])
|
||||
else:
|
||||
obj.missing_reagents.append(reagent['value'])
|
||||
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