Update to autofill.
This commit is contained in:
Landon Wark
@@ -64,6 +64,7 @@ class App(QMainWindow):
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fileMenu = menuBar.addMenu("&File")
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# Creating menus using a title
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editMenu = menuBar.addMenu("&Edit")
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methodsMenu = menuBar.addMenu("&Methods")
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reportMenu = menuBar.addMenu("&Reports")
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maintenanceMenu = menuBar.addMenu("&Monthly")
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helpMenu = menuBar.addMenu("&Help")
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@@ -71,6 +72,7 @@ class App(QMainWindow):
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helpMenu.addAction(self.docsAction)
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fileMenu.addAction(self.importAction)
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fileMenu.addAction(self.importPCRAction)
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methodsMenu.addAction(self.constructFS)
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reportMenu.addAction(self.generateReportAction)
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maintenanceMenu.addAction(self.joinControlsAction)
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maintenanceMenu.addAction(self.joinExtractionAction)
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@@ -103,6 +105,7 @@ class App(QMainWindow):
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self.joinPCRAction = QAction("Link PCR Logs")
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self.helpAction = QAction("&About", self)
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self.docsAction = QAction("&Docs", self)
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self.constructFS = QAction("Make First Strand", self)
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def _connectActions(self):
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@@ -125,6 +128,7 @@ class App(QMainWindow):
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self.joinPCRAction.triggered.connect(self.linkPCR)
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self.helpAction.triggered.connect(self.showAbout)
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self.docsAction.triggered.connect(self.openDocs)
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self.constructFS.triggered.connect(self.construct_first_strand)
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def showAbout(self):
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"""
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@@ -290,6 +294,14 @@ class App(QMainWindow):
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self, result = import_pcr_results_function(self)
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self.result_reporter(result)
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def construct_first_strand(self):
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"""
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Converts first strand excel sheet to Biomek CSV
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"""
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from .main_window_functions import construct_first_strand_function
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self, result = construct_first_strand_function(self)
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self.result_reporter(result)
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class AddSubForm(QWidget):
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def __init__(self, parent):
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@@ -31,7 +31,7 @@ class AddReagentForm(QDialog):
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super().__init__()
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self.ctx = ctx
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if reagent_lot == None:
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reagent_lot = ""
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reagent_lot = reagent_type
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self.setWindowTitle("Add Reagent")
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@@ -257,7 +257,7 @@ class ControlsDatePicker(QWidget):
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class ImportReagent(QComboBox):
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def __init__(self, ctx:dict, reagent:PydReagent):
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def __init__(self, ctx:dict, reagent:PydReagent, extraction_kit:str):
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super().__init__()
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self.setEditable(True)
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# Ensure that all reagenttypes have a name that matches the items in the excel parser
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@@ -289,7 +289,7 @@ class ImportReagent(QComboBox):
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relevant_reagents.insert(0, str(reagent.lot))
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else:
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# TODO: look up the last used reagent of this type in the database
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looked_up_reg = lookup_last_used_reagenttype_lot(ctx=ctx, type_name=reagent.type)
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looked_up_reg = lookup_last_used_reagenttype_lot(ctx=ctx, type_name=reagent.type, extraction_kit=extraction_kit)
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logger.debug(f"Because there was no reagent listed for {reagent}, we will insert the last lot used: {looked_up_reg}")
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if looked_up_reg != None:
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relevant_reagents.remove(str(looked_up_reg.lot))
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@@ -26,12 +26,13 @@ from backend.db.functions import (
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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
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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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)
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from backend.excel.parser import SheetParser, PCRParser
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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
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from tools import check_not_nan, convert_well_to_row_column
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from .custom_widgets.pop_ups import AlertPop, QuestionAsker
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from .custom_widgets import ReportDatePicker
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from .custom_widgets.misc import ImportReagent, ParsedQLabel
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@@ -182,7 +183,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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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'])
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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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@@ -277,7 +278,7 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
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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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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))#item=item)
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add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)#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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@@ -310,7 +311,6 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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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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@@ -328,15 +328,11 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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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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# obj.ctx.database_session.rollback()
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return obj, dict(message="Failed integrity check", status="critical")
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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 +355,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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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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update_last_used(ctx=obj.ctx, reagent=reagent, kit=base_submission.extraction_kit)
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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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@@ -377,12 +374,8 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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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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logger.debug(f"We have the extraction kit: {extraction_kit.name}")
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# TODO replace below with function in KitType object. Update Kittype associations.
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# excel_map = extraction_kit.used_for[obj.current_submission_type.replace('_', ' ')]
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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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# excel_map.update(extraction_kit.used_for[obj.current_submission_type.replace('_', ' ').title()])
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input_reagents = [item.to_reagent_dict(extraction_kit=base_submission.extraction_kit) for item in parsed_reagents]
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logger.debug(f"Parsed reagents going into autofile: {pprint.pformat(input_reagents)}")
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autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info, missing_info=obj.missing_info)
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@@ -881,17 +874,8 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
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# pare down reagents to only what's missing
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logger.debug(f"Checking {[item['type'] for item in reagents]} against {[reagent.type for reagent in missing_reagents]}")
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relevant_reagents = [item for item in reagents if item['type'] in [reagent.type for reagent in missing_reagents]]
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# relevant_reagents = []
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# for item in reagents:
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# logger.debug(f"Checking {item['type']} in {[reagent.type for reagent in missing_reagents]}")
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# if item['type'] in [reagent.type for reagent in missing_reagents]:
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# logger.debug("Hit!")
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# relevant_reagents.append(item)
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# else:
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# logger.debug('Miss.')
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logger.debug(f"Here are the relevant reagents: {pprint.pformat(relevant_reagents)}")
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# hacky manipulation of submission type so it looks better.
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# info['submission_type'] = info['submission_type'].replace("_", " ").title()
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# pare down info to just what's missing
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relevant_info_map = {k:v for k,v in xl_map['info'].items() if k in missing_info and k != 'samples'}
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relevant_info = {k:v for k,v in info.items() if k in missing_info}
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@@ -910,9 +894,9 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
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# name is only present for Bacterial Culture
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try:
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new_reagent['name'] = relevant_reagent_map[new_reagent['type']]['name']
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new_reagent['name']['value'] = reagent['type']
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except:
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pass
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new_reagent['name']['value'] = reagent['name']
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except Exception as e:
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logger.error(f"Couldn't get name due to {e}")
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new_reagents.append(new_reagent)
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# construct new info objects to put into excel sheets
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new_info = []
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@@ -936,21 +920,98 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
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# Get relevant reagents for that sheet
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sheet_reagents = [item for item in new_reagents if sheet in item['sheet']]
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for reagent in sheet_reagents:
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logger.debug(f"Attempting: {reagent['type']}:")
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logger.debug(f"Attempting to write lot {reagent['lot']['value']} in: row {reagent['lot']['row']}, column {reagent['lot']['column']}")
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worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'], value=reagent['lot']['value'])
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logger.debug(f"Attempting to write expiry {reagent['expiry']['value']} in: row {reagent['expiry']['row']}, column {reagent['expiry']['column']}")
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worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value'])
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try:
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worksheet.cell(row=reagent['name']['row'], column=reagent['name']['column'], value=reagent['name']['value'].replace("_", " ").upper())
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except:
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pass
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logger.debug(f"Attempting to write name {reagent['name']['value']} in: row {reagent['name']['row']}, column {reagent['name']['column']}")
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worksheet.cell(row=reagent['name']['row'], column=reagent['name']['column'], value=reagent['name']['value'])
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except Exception as e:
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logger.error(f"Could not write name {reagent['name']['value']} due to {e}")
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# Get relevant info for that sheet
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sheet_info = [item for item in new_info if sheet in item['location']['sheets']]
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for item in sheet_info:
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logger.debug(f"Attempting: {item['type']}")
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worksheet.cell(row=item['location']['row'], column=item['location']['column'], value=item['value'])
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# Hacky way to
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# Hacky way to pop in 'signed by'
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if info['submission_type'] == "Bacterial Culture":
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workbook["Sample List"].cell(row=14, column=2, value=getuser()[0:2].upper())
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fname = select_save_file(obj=obj, default_name=info['rsl_plate_num'], extension="xlsx")
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workbook.save(filename=fname.__str__())
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def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
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def get_plates(input_sample_number:str, plates:list) -> Tuple[int, str]:
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logger.debug(f"Looking up {input_sample_number} in {plates}")
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samp = lookup_ww_sample_by_processing_number(ctx=obj.ctx, processing_number=input_sample_number)
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if samp == None:
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samp = lookup_sample_by_submitter_id(ctx=obj.ctx, submitter_id=input_sample_number)
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logger.debug(f"Got sample: {samp}")
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# if samp != None:
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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)]
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# for iii, plate in enumerate(plates):
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# lplate = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate)
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# if lplate == None:
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# continue
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# else:
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# logger.debug(f"Got a plate: {lplate}")
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# new_plates.append((iii, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lplate)))
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logger.debug(f"Associations: {pprint.pformat(new_plates)}")
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try:
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plate_num, plate = next(assoc for assoc in new_plates if assoc[1] is not None)
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except StopIteration:
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plate_num, plate = None, None
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logger.debug(f"Plate number {plate_num} is {plate}")
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return plate_num, plate
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fname = select_open_file(obj=obj, file_extension="xlsx")
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xl = pd.ExcelFile(fname)
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sprsr = SampleParser(ctx=obj.ctx, xl=xl, submission_type="First Strand")
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_, samples = sprsr.parse_samples(generate=False)
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plates = sprsr.grab_plates()
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output_samples = []
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logger.debug(f"Samples: {pprint.pformat(samples)}")
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old_plate_number = 1
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for item in samples:
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new_dict = {}
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new_dict['sample'] = item['submitter_id']
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if item['submitter_id'] == "NTC1":
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new_dict['destination_row'] = 8
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new_dict['destination_column'] = 2
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new_dict['plate_number'] = 'control'
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elif item['submitter_id'] == "NTC2":
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new_dict['destination_row'] = 8
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new_dict['destination_column'] = 5
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new_dict['plate_number'] = 'control'
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else:
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new_dict['destination_row'] = item['row']
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new_dict['destination_column'] = item['column']
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# 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)]
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plate_num, plate = get_plates(input_sample_number=new_dict['sample'], plates=plates)
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if plate_num == None:
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plate_num = str(old_plate_number) + "*"
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else:
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old_plate_number = plate_num
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logger.debug(f"Got plate number: {plate_num}, plate: {plate}")
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if plate == None:
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try:
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new_dict['source_row'], new_dict['source_column'] = convert_well_to_row_column(item['well'])
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new_dict['plate_number'] = plate_num
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except KeyError:
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pass
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else:
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new_dict['plate_number'] = plate_num
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new_dict['plate'] = plate.submission.rsl_plate_num
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new_dict['source_row'] = plate.row
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new_dict['source_column'] = plate.column
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output_samples.append(new_dict)
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df = pd.DataFrame.from_records(output_samples)
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df.sort_values(by=['destination_column', 'destination_row'], ascending=True, inplace=True)
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columnsTitles = ['sample', 'destination_column', 'destination_row', 'plate_number', 'plate', "source_column", 'source_row']
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df = df.reindex(columns=columnsTitles)
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ofname = select_save_file(obj=obj, default_name=f"First Strand {date.today()}", extension="csv")
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df.to_csv(ofname, index=False)
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return obj, None
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