hitpicking complete, pre-addition of WW-Arctic parsers and models.
This commit is contained in:
Landon Wark
@@ -41,15 +41,11 @@ logger = logging.getLogger(f"submissions.{__name__}")
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def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]:
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result = None
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# from .custom_widgets.misc import ImportReagent
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# from .custom_widgets.pop_ups import AlertPop
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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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# set file dialog
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# home_dir = str(Path(obj.ctx["directory_path"]))
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# fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir)[0])
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fname = select_open_file(obj, 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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@@ -69,7 +65,6 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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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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# (?x)
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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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@@ -161,13 +156,11 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
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if hasattr(obj, 'ext_kit'):
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obj.kit_integrity_completion()
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logger.debug(f"Imported reagents: {obj.reagents}")
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return obj, result
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def kit_reload_function(obj:QMainWindow) -> QMainWindow:
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result = None
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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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if isinstance(item, QLabel):
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if item.text().startswith("Lot"):
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item.setParent(None)
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@@ -180,20 +173,22 @@ def kit_reload_function(obj:QMainWindow) -> QMainWindow:
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def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
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result = None
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# from .custom_widgets.misc import ImportReagent
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# from .custom_widgets.pop_ups import AlertPop
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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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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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obj.ext_kit = kit_widget.currentText()
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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.replace("lot_", "") for item in obj.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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# msg = AlertPop(message=kit_integrity['message'], status="critical")
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# msg.exec()
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result = dict(message=kit_integrity['message'], status="Warning")
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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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@@ -207,9 +202,9 @@ def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
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def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
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result = None
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# from .custom_widgets.misc import ImportReagent
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# from .custom_widgets.pop_ups import AlertPop, QuestionAsker
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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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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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@@ -268,12 +263,9 @@ 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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# print(dir(obj))
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if hasattr(obj, 'csv'):
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dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
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if dlg.exec():
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# home_dir = Path(obj.ctx["directory_path"]).joinpath(f"{base_submission.rsl_plate_num}.csv").resolve().__str__()
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# fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter=".csv")[0])
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fname = select_save_file(obj, f"{base_submission.rsl_plate_num}.csv", extension="csv")
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try:
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obj.csv.to_csv(fname.__str__(), index=False)
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@@ -282,8 +274,8 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
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return obj, result
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def generate_report_function(obj:QMainWindow) -> QMainWindow:
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# from .custom_widgets import ReportDatePicker
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result = None
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# ask for date ranges
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dlg = ReportDatePicker()
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if dlg.exec():
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info = extract_form_info(dlg)
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@@ -324,8 +316,6 @@ def generate_report_function(obj:QMainWindow) -> QMainWindow:
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def add_kit_function(obj:QMainWindow) -> QMainWindow:
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result = None
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# setup file dialog to find yaml flie
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# home_dir = str(Path(obj.ctx["directory_path"]))
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# fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "yml(*.yml)")[0])
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fname = select_open_file(obj, extension="yml")
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assert fname.exists()
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# read yaml file
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@@ -340,19 +330,11 @@ def add_kit_function(obj:QMainWindow) -> QMainWindow:
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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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# match result['code']:
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# case 0:
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# msg = AlertPop(message=result['message'], status='info')
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# case 1:
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# msg = AlertPop(message=result['message'], status='critical')
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# msg.exec()
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return obj, result
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def add_org_function(obj:QMainWindow) -> QMainWindow:
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result = None
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# setup file dialog to find yaml flie
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# home_dir = str(Path(obj.ctx["directory_path"]))
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# fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "yml(*.yml)")[0])
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fname = select_open_file(obj, extension="yml")
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assert fname.exists()
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# read yaml file
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@@ -367,12 +349,6 @@ def add_org_function(obj:QMainWindow) -> QMainWindow:
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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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# match result['code']:
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# case 0:
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# msg = AlertPop(message=result['message'], status='information')
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# case 1:
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# msg = AlertPop(message=result['message'], status='critical')
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# msg.exec()
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return obj, result
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def controls_getter_function(obj:QMainWindow) -> QMainWindow:
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@@ -391,7 +367,7 @@ def controls_getter_function(obj:QMainWindow) -> QMainWindow:
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obj.table_widget.datepicker.start_date.setDate(threemonthsago)
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obj._controls_getter()
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return obj, result
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# convert to python useable date object
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# convert to python useable date object
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obj.start_date = obj.table_widget.datepicker.start_date.date().toPyDate()
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obj.end_date = obj.table_widget.datepicker.end_date.date().toPyDate()
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obj.con_type = obj.table_widget.control_typer.currentText()
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@@ -412,8 +388,18 @@ def controls_getter_function(obj:QMainWindow) -> QMainWindow:
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return obj, result
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def chart_maker_function(obj:QMainWindow) -> QMainWindow:
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"""
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create html chart for controls reporting
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Args:
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obj (QMainWindow): original MainWindow
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Returns:
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QMainWindow: MainWindow with control display updates
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"""
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result = None
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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}")
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# set the subtype for kraken
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if obj.table_widget.sub_typer.currentText() == "":
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obj.subtype = None
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else:
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@@ -425,7 +411,7 @@ def chart_maker_function(obj:QMainWindow) -> QMainWindow:
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if controls == None:
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fig = None
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else:
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# change each control to list of dicts
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# change each control to list of dictionaries
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data = [control.convert_by_mode(mode=obj.mode) for control in controls]
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# flatten data to one dimensional list
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data = [item for sublist in data for item in sublist]
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@@ -646,7 +632,8 @@ def import_pcr_results_function(obj:QMainWindow) -> QMainWindow:
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logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
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logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
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obj.ctx["database_session"].commit()
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logger.debug(f"Got {len(parser.samples)} to update!")
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logger.debug(f"Got {len(parser.samples)} samples to update!")
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logger.debug(f"Parser samples: {parser.samples}")
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for sample in parser.samples:
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logger.debug(f"Running update on: {sample['sample']}")
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sample['plate_rsl'] = sub.rsl_plate_num
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@@ -655,11 +642,3 @@ def import_pcr_results_function(obj:QMainWindow) -> QMainWindow:
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return obj, result
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# dlg.exec()
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