Code cleanup and documentation
This commit is contained in:
Landon Wark
@@ -5,7 +5,7 @@ from PyQt6.QtWidgets import (
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from PyQt6.QtCore import pyqtSignal
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from pathlib import Path
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from . import select_open_file, select_save_file
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import logging, difflib, inspect, json, sys
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import logging, difflib, inspect, json
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from pathlib import Path
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from tools import Report, Result, check_not_nan
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from backend.excel.parser import SheetParser, PCRParser
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@@ -16,7 +16,6 @@ from backend.db import (
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)
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from pprint import pformat
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from .pop_ups import QuestionAsker, AlertPop
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# from .misc import ReagentFormWidget
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from typing import List, Tuple
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from datetime import date
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@@ -24,6 +23,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
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class SubmissionFormContainer(QWidget):
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# A signal carrying a path
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import_drag = pyqtSignal(Path)
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def __init__(self, parent: QWidget) -> None:
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@@ -31,19 +31,24 @@ class SubmissionFormContainer(QWidget):
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super().__init__(parent)
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self.app = self.parent().parent()
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self.report = Report()
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# self.parent = parent
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self.setAcceptDrops(True)
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# if import_drag is emitted, importSubmission will fire
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self.import_drag.connect(self.importSubmission)
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def dragEnterEvent(self, event):
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"""
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Allow drag if file.
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"""
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if event.mimeData().hasUrls():
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event.accept()
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else:
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event.ignore()
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def dropEvent(self, event):
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"""
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Sets filename when file dropped
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"""
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fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
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logger.debug(f"App: {self.app}")
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self.app.last_dir = fname.parent
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self.import_drag.emit(fname)
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@@ -52,7 +57,6 @@ class SubmissionFormContainer(QWidget):
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"""
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import submission from excel sheet into form
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"""
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# from .main_window_functions import import_submission_function
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self.app.raise_()
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self.app.activateWindow()
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self.import_submission_function(fname)
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@@ -62,6 +66,9 @@ class SubmissionFormContainer(QWidget):
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self.app.result_reporter()
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def scrape_reagents(self, *args, **kwargs):
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"""
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Called when a reagent is changed.
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"""
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caller = inspect.stack()[1].function.__repr__().replace("'", "")
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logger.debug(f"Args: {args}, kwargs: {kwargs}")
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self.scrape_reagents_function(args[0], caller=caller)
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@@ -80,7 +87,6 @@ class SubmissionFormContainer(QWidget):
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NOTE: this will not change self.reagents which should be fine
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since it's only used when looking up
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"""
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# from .main_window_functions import kit_integrity_completion_function
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self.kit_integrity_completion_function()
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self.app.report.add_result(self.report)
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self.report = Report()
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@@ -94,14 +100,12 @@ class SubmissionFormContainer(QWidget):
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"""
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Attempt to add sample to database when 'submit' button clicked
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"""
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# from .main_window_functions import submit_new_sample_function
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self.submit_new_sample_function()
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self.app.report.add_result(self.report)
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self.report = Report()
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self.app.result_reporter()
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def export_csv(self, fname:Path|None=None):
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# from .main_window_functions import export_csv_function
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self.export_csv_function(fname)
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def import_submission_function(self, fname:Path|None=None):
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@@ -116,12 +120,11 @@ class SubmissionFormContainer(QWidget):
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"""
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logger.debug(f"\n\nStarting Import...\n\n")
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report = Report()
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# logger.debug(obj.ctx)
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# initialize samples
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try:
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self.form.setParent(None)
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except AttributeError:
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pass
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# initialize samples
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self.samples = []
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self.missing_info = []
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# set file dialog
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@@ -129,7 +132,6 @@ class SubmissionFormContainer(QWidget):
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fname = select_open_file(self, 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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report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
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self.report.add_result(report)
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return
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@@ -141,14 +143,9 @@ class SubmissionFormContainer(QWidget):
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return
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except AttributeError:
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self.prsr = SheetParser(ctx=self.app.ctx, filepath=fname)
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# try:
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logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
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self.pyd = self.prsr.to_pydantic()
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logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
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# except Exception as e:
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# report.add_result(Result(msg=f"Problem creating pydantic model:\n\n{e}", status="Critical"))
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# self.report.add_result(report)
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# return
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self.form = self.pyd.toForm(parent=self)
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self.layout().addWidget(self.form)
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kit_widget = self.form.find_widgets(object_name="extraction_kit")[0].input
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@@ -176,11 +173,8 @@ class SubmissionFormContainer(QWidget):
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"""
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self.form.reagents = []
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logger.debug(f"\n\n{caller}\n\n")
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# assert caller == "import_submission_function"
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report = Report()
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logger.debug(f"Extraction kit: {extraction_kit}")
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# obj.reagents = []
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# obj.missing_reagents = []
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# Remove previous reagent widgets
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try:
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old_reagents = self.form.find_widgets()
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@@ -191,14 +185,6 @@ class SubmissionFormContainer(QWidget):
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for reagent in old_reagents:
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if isinstance(reagent, ReagentFormWidget) or isinstance(reagent, QPushButton):
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reagent.setParent(None)
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# reagents = obj.prsr.parse_reagents(extraction_kit=extraction_kit)
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# logger.debug(f"Got reagents: {reagents}")
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# for reagent in obj.prsr.sub['reagents']:
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# # create label
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# if reagent.parsed:
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# obj.reagents.append(reagent)
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# else:
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# obj.missing_reagents.append(reagent)
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match caller:
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case "import_submission_function":
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self.form.reagents = self.prsr.sub['reagents']
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@@ -231,11 +217,9 @@ class SubmissionFormContainer(QWidget):
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logger.debug(f"Kit selector: {kit_widget}")
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# get current kit being used
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self.ext_kit = kit_widget.currentText()
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# for reagent in obj.pyd.reagents:
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for reagent in self.form.reagents:
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logger.debug(f"Creating widget for {reagent}")
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add_widget = ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
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# add_widget.setParent(sub_form_container.form)
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self.form.layout().addWidget(add_widget)
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if reagent.missing:
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missing_reagents.append(reagent)
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@@ -275,7 +259,6 @@ class SubmissionFormContainer(QWidget):
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self.pyd: PydSubmission = self.form.parse_form()
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logger.debug(f"Submission: {pformat(self.pyd)}")
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logger.debug("Checking kit integrity...")
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# result = check_kit_integrity(sub=self.pyd)
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result = self.pyd.check_kit_integrity()
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report.add_result(result)
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if len(result.results) > 0:
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@@ -283,7 +266,6 @@ class SubmissionFormContainer(QWidget):
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return
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base_submission, result = self.pyd.toSQL()
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# logger.debug(f"Base submission: {base_submission.to_dict()}")
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# sys.exit()
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# check output message for issues
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match result.code:
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# code 0: everything is fine.
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@@ -309,9 +291,7 @@ class SubmissionFormContainer(QWidget):
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# add reagents to submission object
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for reagent in base_submission.reagents:
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# logger.debug(f"Updating: {reagent} with {reagent.lot}")
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# update_last_used(reagent=reagent, kit=base_submission.extraction_kit)
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reagent.update_last_used(kit=base_submission.extraction_kit)
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# sys.exit()
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# logger.debug(f"Here is the final submission: {pformat(base_submission.__dict__)}")
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# logger.debug(f"Parsed reagents: {pformat(base_submission.reagents)}")
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# logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
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@@ -324,24 +304,15 @@ class SubmissionFormContainer(QWidget):
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# reset form
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self.form.setParent(None)
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# logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
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# wkb = self.pyd.autofill_excel()
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# if wkb != None:
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# fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="xlsx")
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# try:
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# wkb.save(filename=fname.__str__())
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# except PermissionError:
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# logger.error("Hit a permission error when saving workbook. Cancelled?")
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# if hasattr(self.pyd, '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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# fname = select_save_file(self, f"{self.pyd.construct_filename()}.csv", extension="csv")
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# try:
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# self.pyd.csv.to_csv(fname.__str__(), index=False)
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# except PermissionError:
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# logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
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self.report.add_result(report)
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def export_csv_function(self, fname:Path|None=None):
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"""
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Save the submission's csv file.
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Args:
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fname (Path | None, optional): Input filename. Defaults to None.
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"""
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if isinstance(fname, bool) or fname == None:
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fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
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try:
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@@ -351,6 +322,9 @@ class SubmissionFormContainer(QWidget):
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logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
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def import_pcr_results(self):
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"""
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Pull QuantStudio results into db
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"""
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self.import_pcr_results_function()
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self.app.report.add_result(self.report)
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self.report = Report()
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@@ -370,7 +344,6 @@ class SubmissionFormContainer(QWidget):
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fname = select_open_file(self, file_extension="xlsx")
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parser = PCRParser(filepath=fname)
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logger.debug(f"Attempting lookup for {parser.plate_num}")
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# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
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sub = BasicSubmission.query(rsl_number=parser.plate_num)
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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@@ -378,14 +351,11 @@ class SubmissionFormContainer(QWidget):
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# If no plate is found, may be because this is a repeat. Lop off the '-1' or '-2' and repeat
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logger.error(f"Submission of number {parser.plate_num} not found. Attempting rescue of plate repeat.")
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parser.plate_num = "-".join(parser.plate_num.split("-")[:-1])
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# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
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# sub = lookup_submissions(ctx=obj.ctx, rsl_number=parser.plate_num)
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sub = BasicSubmission.query(rsl_number=parser.plate_num)
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try:
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logger.debug(f"Found submission: {sub.rsl_plate_num}")
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except AttributeError:
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logger.error(f"Rescue of {parser.plate_num} failed.")
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# return obj, dict(message="Couldn't find a submission with that RSL number.", status="warning")
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self.report.add_result(Result(msg="Couldn't find a submission with that RSL number.", status="Warning"))
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return
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# Check if PCR info already exists
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@@ -407,7 +377,6 @@ class SubmissionFormContainer(QWidget):
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logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
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else:
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sub.pcr_info = json.dumps([parser.pcr])
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# obj.ctx.database_session.add(sub)
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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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sub.save(original=False)
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@@ -419,18 +388,13 @@ class SubmissionFormContainer(QWidget):
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sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
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except IndexError:
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continue
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# update_subsampassoc_with_pcr(submission=sub, sample=sample, input_dict=sample_dict)
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sub.update_subsampassoc(sample=sample, input_dict=sample_dict)
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self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
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# return obj, result
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class SubmissionFormWidget(QWidget):
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def __init__(self, parent: QWidget, **kwargs) -> None:
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super().__init__(parent)
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# self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
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# "qt_scrollarea_vcontainer", "submit_btn"
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# ]
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self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment', 'equipment']
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self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
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layout = QVBoxLayout()
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@@ -441,25 +405,53 @@ class SubmissionFormWidget(QWidget):
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layout.addWidget(add_widget)
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else:
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setattr(self, k, v)
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self.setLayout(layout)
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def create_widget(self, key:str, value:dict, submission_type:str|None=None):
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def create_widget(self, key:str, value:dict, submission_type:str|None=None) -> "self.InfoItem":
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"""
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Make an InfoItem widget to hold a field
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Args:
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key (str): Name of the field
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value (dict): Value of field
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submission_type (str | None, optional): Submissiontype as str. Defaults to None.
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Returns:
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self.InfoItem: Form widget to hold name:value
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"""
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if key not in self.ignore:
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return self.InfoItem(self, key=key, value=value, submission_type=submission_type)
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return None
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def clear_form(self):
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"""
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Removes all form widgets
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"""
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for item in self.findChildren(QWidget):
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item.setParent(None)
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def find_widgets(self, object_name:str|None=None) -> List[QWidget]:
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"""
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Gets all widgets filtered by object name
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Args:
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object_name (str | None, optional): name to filter by. Defaults to None.
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Returns:
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List[QWidget]: Widgets matching filter
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"""
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query = self.findChildren(QWidget)
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if object_name != None:
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query = [widget for widget in query if widget.objectName()==object_name]
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return query
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def parse_form(self) -> PydSubmission:
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"""
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Transforms form info into PydSubmission
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Returns:
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PydSubmission: Pydantic submission object
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"""
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logger.debug(f"Hello from form parser!")
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info = {}
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reagents = []
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@@ -483,8 +475,6 @@ class SubmissionFormWidget(QWidget):
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value = getattr(self, item)
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logger.debug(f"Setting {item}")
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info[item] = value
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# app = self.parent().parent().parent().parent().parent().parent().parent().parent
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# submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
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submission = PydSubmission(reagents=reagents, **info)
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return submission
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@@ -513,7 +503,13 @@ class SubmissionFormWidget(QWidget):
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case QLineEdit():
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self.input.textChanged.connect(self.update_missing)
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def parse_form(self):
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def parse_form(self) -> Tuple[str, dict]:
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"""
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Pulls info from widget into dict
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Returns:
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Tuple[str, dict]: name of field, {value, missing}
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"""
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match self.input:
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case QLineEdit():
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value = self.input.text()
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@@ -526,6 +522,18 @@ class SubmissionFormWidget(QWidget):
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return self.input.objectName(), dict(value=value, missing=self.missing)
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def set_widget(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> QWidget:
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"""
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Creates form widget
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Args:
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parent (QWidget): parent widget
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key (str): name of field
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value (dict): value, and is it missing from scrape
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submission_type (str | None, optional): SubmissionType as str. Defaults to None.
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Returns:
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QWidget: Form object
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"""
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try:
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value = value['value']
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except (TypeError, KeyError):
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@@ -565,7 +573,6 @@ class SubmissionFormWidget(QWidget):
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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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case 'submitted_date':
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# uses base calendar
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add_widget = QDateEdit(calendarPopup=True)
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@@ -578,7 +585,6 @@ class SubmissionFormWidget(QWidget):
|
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case 'submission_category':
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add_widget = QComboBox()
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cats = ['Diagnostic', "Surveillance", "Research"]
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# cats += [item.name for item in lookup_submission_type(ctx=obj.ctx)]
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cats += [item.name for item in SubmissionType.query()]
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try:
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cats.insert(0, cats.pop(cats.index(value)))
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@@ -593,10 +599,12 @@ class SubmissionFormWidget(QWidget):
|
||||
if add_widget != None:
|
||||
add_widget.setObjectName(key)
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||||
add_widget.setParent(parent)
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||||
|
||||
return add_widget
|
||||
|
||||
def update_missing(self):
|
||||
"""
|
||||
Set widget status to updated
|
||||
"""
|
||||
self.missing = True
|
||||
self.label.updated(self.objectName())
|
||||
|
||||
@@ -622,6 +630,13 @@ class SubmissionFormWidget(QWidget):
|
||||
self.setText(f"MISSING {output}")
|
||||
|
||||
def updated(self, key:str, title:bool=True):
|
||||
"""
|
||||
Mark widget as updated
|
||||
|
||||
Args:
|
||||
key (str): Name of the field
|
||||
title (bool, optional): Use title case. Defaults to True.
|
||||
"""
|
||||
if title:
|
||||
output = key.replace('_', ' ').title()
|
||||
else:
|
||||
@@ -632,12 +647,9 @@ class ReagentFormWidget(QWidget):
|
||||
|
||||
def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
|
||||
super().__init__(parent)
|
||||
# self.setParent(parent)
|
||||
self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
|
||||
|
||||
self.reagent = reagent
|
||||
self.extraction_kit = extraction_kit
|
||||
# self.ctx = reagent.ctx
|
||||
layout = QVBoxLayout()
|
||||
self.label = self.ReagentParsedLabel(reagent=reagent)
|
||||
layout.addWidget(self.label)
|
||||
@@ -652,14 +664,18 @@ class ReagentFormWidget(QWidget):
|
||||
self.lot.currentTextChanged.connect(self.updated)
|
||||
|
||||
def parse_form(self) -> Tuple[PydReagent, dict]:
|
||||
"""
|
||||
Pulls form info into PydReagent
|
||||
|
||||
Returns:
|
||||
Tuple[PydReagent, dict]: PydReagent and Report(?)
|
||||
"""
|
||||
lot = self.lot.currentText()
|
||||
# wanted_reagent = lookup_reagents(ctx=self.ctx, lot_number=lot, reagent_type=self.reagent.type)
|
||||
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
|
||||
# if reagent doesn't exist in database, off to add it (uses App.add_reagent)
|
||||
if wanted_reagent == None:
|
||||
dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
|
||||
if dlg.exec():
|
||||
print(self.app)
|
||||
wanted_reagent = self.app.add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
|
||||
return wanted_reagent, None
|
||||
else:
|
||||
@@ -669,15 +685,15 @@ class ReagentFormWidget(QWidget):
|
||||
else:
|
||||
# Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
|
||||
# from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
|
||||
# rt = lookup_reagent_types(ctx=self.ctx, name=self.reagent.type)
|
||||
# rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
|
||||
rt = ReagentType.query(name=self.reagent.type)
|
||||
if rt == None:
|
||||
# rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
|
||||
rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
|
||||
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, parsed=not self.missing), None
|
||||
|
||||
def updated(self):
|
||||
"""
|
||||
Set widget status to updated
|
||||
"""
|
||||
self.missing = True
|
||||
self.label.updated(self.reagent.type)
|
||||
|
||||
@@ -696,19 +712,21 @@ class ReagentFormWidget(QWidget):
|
||||
self.setText(f"MISSING {reagent.type}")
|
||||
|
||||
def updated(self, reagent_type:str):
|
||||
"""
|
||||
Marks widget as updated
|
||||
|
||||
Args:
|
||||
reagent_type (str): _description_
|
||||
"""
|
||||
self.setText(f"UPDATED {reagent_type}")
|
||||
|
||||
class ReagentLot(QComboBox):
|
||||
|
||||
def __init__(self, reagent, extraction_kit:str) -> None:
|
||||
super().__init__()
|
||||
# self.ctx = reagent.ctx
|
||||
self.setEditable(True)
|
||||
# if reagent.parsed:
|
||||
# pass
|
||||
logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
|
||||
# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
|
||||
# lookup = lookup_reagents(ctx=self.ctx, reagent_type=reagent.type)
|
||||
lookup = Reagent.query(reagent_type=reagent.type)
|
||||
relevant_reagents = [str(item.lot) for item in lookup]
|
||||
output_reg = []
|
||||
@@ -726,11 +744,8 @@ class ReagentFormWidget(QWidget):
|
||||
if check_not_nan(reagent.lot):
|
||||
relevant_reagents.insert(0, str(reagent.lot))
|
||||
else:
|
||||
# TODO: look up the last used reagent of this type in the database
|
||||
# looked_up_rt = lookup_reagenttype_kittype_association(ctx=self.ctx, reagent_type=reagent.type, kit_type=extraction_kit)
|
||||
looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type, kit_type=extraction_kit)
|
||||
try:
|
||||
# looked_up_reg = lookup_reagents(ctx=self.ctx, lot_number=looked_up_rt.last_used)
|
||||
looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
|
||||
except AttributeError:
|
||||
looked_up_reg = None
|
||||
@@ -752,4 +767,3 @@ class ReagentFormWidget(QWidget):
|
||||
logger.debug(f"New relevant reagents: {relevant_reagents}")
|
||||
self.setObjectName(f"lot_{reagent.type}")
|
||||
self.addItems(relevant_reagents)
|
||||
|
||||
|
||||
Reference in New Issue
Block a user