Frontend code cleanup finished.
This commit is contained in:
lwark
@@ -1,15 +1,13 @@
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"""
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Contains all procedure related frontend functions
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"""
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import sys
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import sys, logging
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from PyQt6.QtWidgets import (
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QWidget, QPushButton, QVBoxLayout,
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QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QHBoxLayout, QGridLayout
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)
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from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
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from .functions import select_open_file, select_save_file
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import logging
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from pathlib import Path
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from tools import Report, Result, check_not_nan, main_form_style, report_result, get_application_from_parent
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from backend.validators import PydReagent, PydClientSubmission, PydSample
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@@ -121,37 +119,16 @@ class SubmissionFormContainer(QWidget):
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report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
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return report
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# NOTE: create sheetparser using excel sheet and context from gui
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# try:
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# self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
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# except PermissionError:
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# logger.error(f"Couldn't get permission to access file: {fname}")
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# return
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# except AttributeError:
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# self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
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# try:
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# # self.prsr = SheetParser(filepath=fname)
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# self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
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# except PermissionError:
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# logger.error(f"Couldn't get permission to access file: {fname}")
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# return
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# except AttributeError:
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# self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
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# self.pydclientsubmission = self.clientsubmissionparser.to_pydantic()
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# self.pydsamples = self.sampleparser.to_pydantic()
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# logger.debug(f"Samples: {pformat(self.pydclientsubmission.sample)}")
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self.clientsubmission_manager = DefaultClientSubmissionManager(parent=self, input_object=fname)
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self.pydclientsubmission = self.clientsubmission_manager.to_pydantic()
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checker = SampleChecker(self, "Sample Checker", self.pydclientsubmission.sample)
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if checker.exec():
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# logger.debug(pformat(self.pydclientsubmission.sample))
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try:
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assert isinstance(self.pydclientsubmission, PydClientSubmission)
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except AssertionError as e:
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logger.error(f"Got wrong type for {self.pydclientsubmission}: {type(self.pydclientsubmission)}")
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raise e
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self.form = self.pydclientsubmission.to_form(parent=self)
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# self.form.samples = self.pydsamples
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self.layout().addWidget(self.form)
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else:
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message = "Submission cancelled."
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@@ -195,14 +172,11 @@ class SubmissionFormWidget(QWidget):
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self.pyd = pyd
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self.missing_info = []
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self.submissiontype = SubmissionType.query(name=self.pyd.submissiontype['value'])
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# basic_submission_class = self.submission_type.submission_class
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# logger.debug(f"Basic procedure class: {basic_submission_class}")
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defaults = Run.get_default_info("form_recover", "form_ignore", submissiontype=self.pyd.submissiontype['value'])
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self.recover = defaults['form_recover']
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self.ignore = defaults['form_ignore']
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self.layout = QVBoxLayout()
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for k in list(self.pyd.model_fields.keys()):# + list(self.pyd.model_extra.keys()):
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logger.debug(f"Pydantic field: {k}")
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if k in self.ignore:
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logger.warning(f"{k} in form_ignore {self.ignore}, not creating widget")
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continue
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@@ -218,7 +192,6 @@ class SubmissionFormWidget(QWidget):
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value = self.pyd.model_extra[k]
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except KeyError:
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value = dict(value=None, missing=True)
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logger.debug(f"Pydantic value: {value}")
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add_widget = self.create_widget(key=k, value=value, submission_type=self.submissiontype,
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run_object=Run(), disable=check)
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if add_widget is not None:
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@@ -230,7 +203,6 @@ class SubmissionFormWidget(QWidget):
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self.layout.addWidget(self.disabler)
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self.disabler.checkbox.checkStateChanged.connect(self.disable_reagents)
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self.setStyleSheet(main_form_style)
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# self.scrape_reagents(self.kittype)
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self.setLayout(self.layout)
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def disable_reagents(self):
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@@ -298,7 +270,6 @@ class SubmissionFormWidget(QWidget):
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if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
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reagent.setParent(None)
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reagents, integrity_report, missing_reagents = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
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# logger.debug(f"Reagents: {reagents}")
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expiry_report = self.pyd.check_reagent_expiries(exempt=missing_reagents)
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for reagent in reagents:
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add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.extraction_kit)
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@@ -364,34 +335,6 @@ class SubmissionFormWidget(QWidget):
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return report
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base_submission = self.pyd.to_sql()
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# NOTE: check output message for issues
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# try:
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# trigger = result.results[-1]
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# code = trigger.code
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# except IndexError as e:
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# logger.error(result.results)
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# logger.error(f"Problem getting error code: {e}")
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# code = 0
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# match code:
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# # NOTE: code 0: everything is fine.
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# case 0:
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# pass
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# # NOTE: code 1: ask for overwrite
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# case 1:
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# dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_number}?", message=trigger.msg)
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# if dlg.exec():
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# # NOTE: Do not add duplicate reagents.
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# pass
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# else:
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# self.app.ctx.database_session.rollback()
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# report.add_result(Result(msg="Overwrite cancelled", status="Information"))
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# return report
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# # NOTE: code 2: No RSL plate number given
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# case 2:
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# report.add_result(result)
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# return report
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# case _:
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# pass
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# NOTE: add reagents to procedure object
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if base_submission is None:
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return
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for reagent in base_submission.reagents:
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@@ -450,7 +393,6 @@ class SubmissionFormWidget(QWidget):
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if field is not None:
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info[field] = value
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self.pyd.reagents = reagents
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# logger.debug(f"Reagents from form: {reagents}")
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for item in self.recover:
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if hasattr(self, item):
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value = getattr(self, item)
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@@ -558,29 +500,29 @@ class SubmissionFormWidget(QWidget):
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# NOTE: set combobox values to lookedup values
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add_widget.addItems(labs)
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add_widget.setToolTip("Select submitting lab.")
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case 'kittype':
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# NOTE: if extraction kittype not available, all other values fail
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if not check_not_nan(value):
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msg = AlertPop(message="Make sure to check your extraction kittype in the excel sheet!",
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status="warning")
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msg.exec()
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# NOTE: create combobox to hold looked up kits
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add_widget = MyQComboBox(scrollWidget=parent)
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# NOTE: lookup existing kits by 'proceduretype' decided on by sheetparser
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uses = [item.name for item in submission_type.kit_types]
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obj.uses = uses
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if check_not_nan(value):
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try:
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uses.insert(0, uses.pop(uses.index(value)))
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except ValueError:
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logger.warning(f"Couldn't find kittype in list, skipping move to top of list.")
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obj.ext_kit = value
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else:
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logger.error(f"Couldn't find {obj.prsr.sub['kittype']}")
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obj.ext_kit = uses[0]
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add_widget.addItems(uses)
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add_widget.setToolTip("Select extraction kittype.")
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parent.extraction_kit = add_widget.currentText()
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# case 'kittype':
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# # NOTE: if extraction kittype not available, all other values fail
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# if not check_not_nan(value):
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# msg = AlertPop(message="Make sure to check your extraction kittype in the excel sheet!",
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# status="warning")
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# msg.exec()
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# # NOTE: create combobox to hold looked up kits
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# add_widget = MyQComboBox(scrollWidget=parent)
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# # NOTE: lookup existing kits by 'proceduretype' decided on by sheetparser
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# uses = [item.name for item in submission_type.kit_types]
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# obj.uses = uses
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# if check_not_nan(value):
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# try:
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# uses.insert(0, uses.pop(uses.index(value)))
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# except ValueError:
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# logger.warning(f"Couldn't find kittype in list, skipping move to top of list.")
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# obj.ext_kit = value
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# else:
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# logger.error(f"Couldn't find {obj.prsr.sub['kittype']}")
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# obj.ext_kit = uses[0]
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# add_widget.addItems(uses)
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# add_widget.setToolTip("Select extraction kittype.")
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# parent.extraction_kit = add_widget.currentText()
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case 'submission_category':
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add_widget = MyQComboBox(scrollWidget=parent)
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categories = ['Diagnostic', "Surveillance", "Research"]
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@@ -813,11 +755,8 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
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self.disabler.setHidden(True)
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except AttributeError:
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pass
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# save_btn = QPushButton("Save")
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self.sample = samples
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logger.debug(f"Samples: {self.sample}")
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start_run_btn = QPushButton("Save")
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# self.layout.addWidget(save_btn)
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self.layout.addWidget(start_run_btn)
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start_run_btn.clicked.connect(self.create_new_submission)
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@@ -846,7 +785,6 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
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field, value = widget.parse_form()
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if field is not None:
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info[field] = value
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# logger.debug(f"Reagents from form: {reagents}")
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for item in self.recover:
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if hasattr(self, item):
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value = getattr(self, item)
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@@ -865,7 +803,6 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
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@report_result
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def create_new_submission(self, *args) -> Report:
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pyd = self.to_pydantic()
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logger.debug(f"Pydantic: {pyd}")
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sql = pyd.to_sql()
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for sample in pyd.sample:
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if isinstance(sample, PydSample):
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@@ -874,9 +811,7 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
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if sample.sample_id.lower() in ["", "blank"]:
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continue
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sample.save()
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# if sample not in sql.sample:
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sql.add_sample(sample=sample)
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logger.debug(pformat(sql.__dict__))
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try:
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del sql._misc_info['sample']
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except KeyError:
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