Addition of Equipment and SubmissionType creation.
This commit is contained in:
Landon Wark
@@ -18,6 +18,8 @@ from .submission_table import SubmissionsSheet
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from .submission_widget import SubmissionFormContainer
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from .controls_chart import ControlsViewer
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from .kit_creator import KitAdder
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from .submission_type_creator import SubbmissionTypeAdder
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logger = logging.getLogger(f'submissions.{__name__}')
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logger.info("Hello, I am a logger")
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@@ -207,11 +209,13 @@ class AddSubForm(QWidget):
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self.tab1 = QWidget()
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self.tab2 = QWidget()
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self.tab3 = QWidget()
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self.tab4 = QWidget()
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self.tabs.resize(300,200)
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# Add tabs
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self.tabs.addTab(self.tab1,"Submissions")
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self.tabs.addTab(self.tab2,"Controls")
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self.tabs.addTab(self.tab3, "Add Kit")
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self.tabs.addTab(self.tab3, "Add SubmissionType")
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self.tabs.addTab(self.tab4, "Add Kit")
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# Create submission adder form
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self.formwidget = SubmissionFormContainer(self)
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self.formlayout = QVBoxLayout(self)
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@@ -238,10 +242,14 @@ class AddSubForm(QWidget):
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self.tab2.layout.addWidget(self.controls_viewer)
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self.tab2.setLayout(self.tab2.layout)
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# create custom widget to add new tabs
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adder = KitAdder(self)
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ST_adder = SubbmissionTypeAdder(self)
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self.tab3.layout = QVBoxLayout(self)
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self.tab3.layout.addWidget(adder)
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self.tab3.layout.addWidget(ST_adder)
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self.tab3.setLayout(self.tab3.layout)
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kit_adder = KitAdder(self)
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self.tab4.layout = QVBoxLayout(self)
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self.tab4.layout.addWidget(kit_adder)
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self.tab4.setLayout(self.tab4.layout)
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# add tabs to main widget
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self.layout.addWidget(self.tabs)
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self.setLayout(self.layout)
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89
src/submissions/frontend/widgets/equipment_usage.py
Normal file
89
src/submissions/frontend/widgets/equipment_usage.py
Normal file
@@ -0,0 +1,89 @@
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from PyQt6.QtCore import Qt
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from PyQt6.QtWidgets import (QDialog, QComboBox, QCheckBox,
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QLabel, QWidget, QHBoxLayout,
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QVBoxLayout, QDialogButtonBox)
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from backend.db.models import SubmissionType
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from backend.validators.pydant import PydEquipment, PydEquipmentPool
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class EquipmentUsage(QDialog):
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def __init__(self, parent, submission_type:SubmissionType|str) -> QDialog:
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super().__init__(parent)
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self.setWindowTitle("Equipment Checklist")
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if isinstance(submission_type, str):
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submission_type = SubmissionType.query(name=submission_type)
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# self.static_equipment = submission_type.get_equipment()
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self.opt_equipment = submission_type.get_equipment()
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self.layout = QVBoxLayout()
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self.setLayout(self.layout)
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self.populate_form()
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def populate_form(self):
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QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
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self.buttonBox = QDialogButtonBox(QBtn)
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self.buttonBox.accepted.connect(self.accept)
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self.buttonBox.rejected.connect(self.reject)
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for eq in self.opt_equipment:
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self.layout.addWidget(eq.toForm(parent=self))
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self.layout.addWidget(self.buttonBox)
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def parse_form(self):
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output = []
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for widget in self.findChildren(QWidget):
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match widget:
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case (EquipmentCheckBox()|PoolComboBox()) :
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output.append(widget.parse_form())
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case _:
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pass
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return [item for item in output if item != None]
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class EquipmentCheckBox(QWidget):
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def __init__(self, parent, equipment:PydEquipment) -> None:
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super().__init__(parent)
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self.layout = QHBoxLayout()
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self.label = QLabel()
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self.label.setMaximumWidth(125)
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self.label.setMinimumWidth(125)
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self.check = QCheckBox()
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if equipment.static:
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self.check.setChecked(True)
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# self.check.setEnabled(False)
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if equipment.nickname != None:
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text = f"{equipment.name} ({equipment.nickname})"
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else:
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text = equipment.name
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self.setObjectName(equipment.name)
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self.label.setText(text)
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self.layout.addWidget(self.label)
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self.layout.addWidget(self.check)
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self.setLayout(self.layout)
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def parse_form(self) -> str|None:
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if self.check.isChecked():
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return self.objectName()
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else:
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return None
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class PoolComboBox(QWidget):
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def __init__(self, parent, pool:PydEquipmentPool) -> None:
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super().__init__(parent)
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self.layout = QHBoxLayout()
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# label = QLabel()
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# label.setText(pool.name)
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self.box = QComboBox()
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self.box.setMaximumWidth(125)
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self.box.setMinimumWidth(125)
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self.box.addItems([item.name for item in pool.equipment])
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self.check = QCheckBox()
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# self.layout.addWidget(label)
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self.layout.addWidget(self.box)
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self.layout.addWidget(self.check)
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self.setLayout(self.layout)
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def parse_form(self) -> str:
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if self.check.isChecked():
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return self.box.currentText()
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else:
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return None
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@@ -82,7 +82,7 @@ class KitAdder(QWidget):
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print(self.app)
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# get bottommost row
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maxrow = self.grid.rowCount()
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reg_form = ReagentTypeForm()
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reg_form = ReagentTypeForm(parent=self)
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reg_form.setObjectName(f"ReagentForm_{maxrow}")
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# self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
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self.grid.addWidget(reg_form, maxrow,0,1,4)
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@@ -139,8 +139,8 @@ class ReagentTypeForm(QWidget):
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"""
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custom widget to add information about a new reagenttype
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"""
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def __init__(self) -> None:
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super().__init__()
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def __init__(self, parent) -> None:
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super().__init__(parent)
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grid = QGridLayout()
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self.setLayout(grid)
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grid.addWidget(QLabel("Reagent Type Name"),0,0)
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@@ -53,7 +53,7 @@ class KitSelector(QDialog):
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super().__init__()
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self.setWindowTitle(title)
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self.widget = QComboBox()
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kits = [item.__str__() for item in KitType.query()]
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kits = [item.name for item in KitType.query()]
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self.widget.addItems(kits)
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self.widget.setEditable(False)
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# set yes/no buttons
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@@ -15,11 +15,12 @@ from PyQt6.QtWidgets import (
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from PyQt6.QtWebEngineWidgets import QWebEngineView
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from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
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from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
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from backend.db.models import BasicSubmission
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from backend.db.models import BasicSubmission, Equipment, SubmissionEquipmentAssociation
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from backend.excel import make_report_html, make_report_xlsx
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from tools import check_if_app, Report, Result, jinja_template_loading, get_first_blank_df_row, row_map
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from xhtml2pdf import pisa
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from .pop_ups import QuestionAsker
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from .equipment_usage import EquipmentUsage
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from ..visualizations import make_plate_barcode, make_plate_map, make_plate_map_html
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from .functions import select_save_file, select_open_file
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from .misc import ReportDatePicker
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@@ -159,22 +160,44 @@ class SubmissionsSheet(QTableView):
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# barcodeAction = QAction("Print Barcode", self)
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commentAction = QAction("Add Comment", self)
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backupAction = QAction("Backup", self)
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equipAction = QAction("Add Equipment", self)
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# hitpickAction = QAction("Hitpicks", self)
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renameAction.triggered.connect(lambda: self.delete_item(event))
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detailsAction.triggered.connect(lambda: self.show_details())
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# barcodeAction.triggered.connect(lambda: self.create_barcode())
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commentAction.triggered.connect(lambda: self.add_comment())
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backupAction.triggered.connect(lambda: self.regenerate_submission_form())
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equipAction.triggered.connect(lambda: self.add_equipment())
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# hitpickAction.triggered.connect(lambda: self.hit_pick())
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self.menu.addAction(detailsAction)
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self.menu.addAction(renameAction)
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# self.menu.addAction(barcodeAction)
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self.menu.addAction(commentAction)
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self.menu.addAction(backupAction)
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self.menu.addAction(equipAction)
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# self.menu.addAction(hitpickAction)
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# add other required actions
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self.menu.popup(QCursor.pos())
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def add_equipment(self):
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index = (self.selectionModel().currentIndex())
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value = index.sibling(index.row(),0).data()
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self.add_equipment_function(rsl_plate_id=value)
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def add_equipment_function(self, rsl_plate_id):
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submission = BasicSubmission.query(id=rsl_plate_id)
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submission_type = submission.submission_type_name
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dlg = EquipmentUsage(parent=self, submission_type=submission_type)
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if dlg.exec():
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equipment = dlg.parse_form()
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for equip in equipment:
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e = Equipment.query(name=equip)
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assoc = SubmissionEquipmentAssociation(submission=submission, equipment=e)
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# submission.submission_equipment_associations.append(assoc)
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logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}")
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# submission.save()
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assoc.save()
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def delete_item(self, event):
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"""
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Confirms user deletion and sends id to backend for deletion.
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@@ -193,65 +216,6 @@ class SubmissionsSheet(QTableView):
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return
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self.setData()
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# def hit_pick(self):
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# """
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# Extract positive samples from submissions with PCR results and export to csv.
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# NOTE: For this to work for arbitrary samples, positive samples must have 'positive' in their name
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# """
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# # Get all selected rows
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# indices = self.selectionModel().selectedIndexes()
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# # convert to id numbers
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# indices = [index.sibling(index.row(), 0).data() for index in indices]
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# # biomek can handle 4 plates maximum
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# if len(indices) > 4:
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# logger.error(f"Error: Had to truncate number of plates to 4.")
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# indices = indices[:4]
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# # lookup ids in the database
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# # subs = [lookup_submissions(ctx=self.ctx, id=id) for id in indices]
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# subs = [BasicSubmission.query(id=id) for id in indices]
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# # full list of samples
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# dicto = []
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# # list to contain plate images
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# images = []
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# for iii, sub in enumerate(subs):
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# # second check to make sure there aren't too many plates
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# if iii > 3:
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# logger.error(f"Error: Had to truncate number of plates to 4.")
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# continue
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# plate_dicto = sub.hitpick_plate(plate_number=iii+1)
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# if plate_dicto == None:
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# continue
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# image = make_plate_map(plate_dicto)
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# images.append(image)
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# for item in plate_dicto:
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# if len(dicto) < 94:
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# dicto.append(item)
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# else:
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# logger.error(f"We had to truncate the number of samples to 94.")
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# logger.debug(f"We found {len(dicto)} to hitpick")
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# # convert all samples to dataframe
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# df = make_hitpicks(dicto)
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# df = df[df.positive != False]
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# logger.debug(f"Size of the dataframe: {df.shape[0]}")
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# msg = AlertPop(message=f"We found {df.shape[0]} samples to hitpick", status="INFORMATION")
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# msg.exec()
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# if df.size == 0:
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# return
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# date = datetime.strftime(datetime.today(), "%Y-%m-%d")
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# # ask for filename and save as csv.
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# home_dir = Path(self.ctx.directory_path).joinpath(f"Hitpicks_{date}.csv").resolve().__str__()
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# fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".csv")[0])
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# if fname.__str__() == ".":
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# logger.debug("Saving csv was cancelled.")
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# return
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# df.to_csv(fname.__str__(), index=False)
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# # show plate maps
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# for image in images:
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# try:
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# image.show()
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# except Exception as e:
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# logger.error(f"Could not show image: {e}.")
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def link_extractions(self):
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self.link_extractions_function()
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self.app.report.add_result(self.report)
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118
src/submissions/frontend/widgets/submission_type_creator.py
Normal file
118
src/submissions/frontend/widgets/submission_type_creator.py
Normal file
@@ -0,0 +1,118 @@
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from PyQt6.QtCore import Qt
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from PyQt6.QtWidgets import (
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QWidget, QVBoxLayout, QScrollArea,
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QGridLayout, QPushButton, QLabel,
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QLineEdit, QComboBox, QDoubleSpinBox,
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QSpinBox, QDateEdit
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)
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from sqlalchemy import FLOAT, INTEGER
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from sqlalchemy.orm.attributes import InstrumentedAttribute
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from backend.db import SubmissionType, Equipment, SubmissionTypeEquipmentAssociation, BasicSubmission
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from backend.validators import PydReagentType, PydKit
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import logging
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from pprint import pformat
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from tools import Report
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from typing import Tuple
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from .functions import select_open_file
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logger = logging.getLogger(f"submissions.{__name__}")
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class SubbmissionTypeAdder(QWidget):
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def __init__(self, parent) -> None:
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super().__init__(parent)
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self.report = Report()
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self.app = parent.parent()
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self.template_path = ""
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main_box = QVBoxLayout(self)
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scroll = QScrollArea(self)
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main_box.addWidget(scroll)
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scroll.setWidgetResizable(True)
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scrollContent = QWidget(scroll)
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self.grid = QGridLayout()
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scrollContent.setLayout(self.grid)
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# insert submit button at top
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self.submit_btn = QPushButton("Submit")
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self.grid.addWidget(self.submit_btn,0,0,1,1)
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self.grid.addWidget(QLabel("Submission Type Name:"),2,0)
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# widget to get kit name
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self.st_name = QLineEdit()
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self.st_name.setObjectName("submission_type_name")
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self.grid.addWidget(self.st_name,2,1,1,2)
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self.grid.addWidget(QLabel("Template File"),3,0)
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template_selector = QPushButton("Select")
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self.grid.addWidget(template_selector,3,1)
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self.template_label = QLabel("None")
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self.grid.addWidget(self.template_label,3,2)
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# self.grid.addWidget(QLabel("Used For Submission Type:"),3,0)
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# widget to get uses of kit
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exclude = ['id', 'submitting_lab_id', 'extraction_kit_id', 'reagents_id', 'extraction_info', 'pcr_info', 'run_cost']
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self.columns = {key:value for key, value in BasicSubmission.__dict__.items() if isinstance(value, InstrumentedAttribute)}
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self.columns = {key:value for key, value in self.columns.items() if hasattr(value, "type") and key not in exclude}
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for iii, key in enumerate(self.columns):
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idx = iii + 4
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# convert field name to human readable.
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# field_name = key
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# self.grid.addWidget(QLabel(field_name),idx,0)
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# print(self.columns[key].type)
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# match self.columns[key].type:
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# case FLOAT():
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# add_widget = QDoubleSpinBox()
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# add_widget.setMinimum(0)
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# add_widget.setMaximum(9999)
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# case INTEGER():
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# add_widget = QSpinBox()
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# add_widget.setMinimum(0)
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# add_widget.setMaximum(9999)
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# case _:
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# add_widget = QLineEdit()
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# add_widget.setObjectName(key)
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self.grid.addWidget(InfoWidget(parent=self, key=key), idx,0,1,3)
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scroll.setWidget(scrollContent)
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self.submit_btn.clicked.connect(self.submit)
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template_selector.clicked.connect(self.get_template_path)
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def submit(self):
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info = self.parse_form()
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ST = SubmissionType(name=self.st_name.text(), info_map=info)
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with open(self.template_path, "rb") as f:
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ST.template_file = f.read()
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logger.debug(ST.__dict__)
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def parse_form(self):
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widgets = [widget for widget in self.findChildren(QWidget) if isinstance(widget, InfoWidget)]
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return [{widget.objectName():widget.parse_form()} for widget in widgets]
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def get_template_path(self):
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self.template_path = select_open_file(obj=self, file_extension="xlsx")
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self.template_label.setText(self.template_path.__str__())
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class InfoWidget(QWidget):
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def __init__(self, parent: QWidget, key) -> None:
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super().__init__(parent)
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grid = QGridLayout()
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self.setLayout(grid)
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grid.addWidget(QLabel(key.replace("_", " ").title()),0,0,1,4)
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self.setObjectName(key)
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grid.addWidget(QLabel("Sheet Names (comma seperated):"),1,0)
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self.sheet = QLineEdit()
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self.sheet.setObjectName("sheets")
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grid.addWidget(self.sheet, 1,1,1,3)
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grid.addWidget(QLabel("Row:"),2,0,alignment=Qt.AlignmentFlag.AlignRight)
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self.row = QSpinBox()
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self.row.setObjectName("row")
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grid.addWidget(self.row,2,1)
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grid.addWidget(QLabel("Column:"),2,2,alignment=Qt.AlignmentFlag.AlignRight)
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self.column = QSpinBox()
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self.column.setObjectName("column")
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grid.addWidget(self.column,2,3)
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def parse_form(self):
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return dict(
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sheets = self.sheet.text().split(","),
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row = self.row.value(),
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column = self.column.value()
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)
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@@ -62,12 +62,13 @@ class SubmissionFormContainer(QWidget):
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self.app.result_reporter()
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def scrape_reagents(self, *args, **kwargs):
|
||||
print(f"\n\n{inspect.stack()[1].function}\n\n")
|
||||
self.scrape_reagents_function(args[0])
|
||||
caller = inspect.stack()[1].function.__repr__().replace("'", "")
|
||||
logger.debug(f"Args: {args}, kwargs: {kwargs}")
|
||||
self.scrape_reagents_function(args[0], caller=caller)
|
||||
self.kit_integrity_completion()
|
||||
self.app.report.add_result(self.report)
|
||||
self.report = Report()
|
||||
match inspect.stack()[1].function:
|
||||
match inspect.stack()[1].function.__repr__():
|
||||
case "import_submission_function":
|
||||
pass
|
||||
case _:
|
||||
@@ -83,7 +84,7 @@ class SubmissionFormContainer(QWidget):
|
||||
self.kit_integrity_completion_function()
|
||||
self.app.report.add_result(self.report)
|
||||
self.report = Report()
|
||||
match inspect.stack()[1].function:
|
||||
match inspect.stack()[1].function.__repr__():
|
||||
case "import_submission_function":
|
||||
pass
|
||||
case _:
|
||||
@@ -161,7 +162,7 @@ class SubmissionFormContainer(QWidget):
|
||||
logger.debug(f"Outgoing report: {self.report.results}")
|
||||
logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
|
||||
|
||||
def scrape_reagents_function(self, extraction_kit:str):
|
||||
def scrape_reagents_function(self, extraction_kit:str, caller:str|None=None):
|
||||
"""
|
||||
Extracted scrape reagents function that will run when
|
||||
form 'extraction_kit' widget is updated.
|
||||
@@ -173,6 +174,9 @@ class SubmissionFormContainer(QWidget):
|
||||
Returns:
|
||||
Tuple[QMainWindow, dict]: Updated application and result
|
||||
"""
|
||||
self.form.reagents = []
|
||||
logger.debug(f"\n\n{caller}\n\n")
|
||||
# assert caller == "import_submission_function"
|
||||
report = Report()
|
||||
logger.debug(f"Extraction kit: {extraction_kit}")
|
||||
# obj.reagents = []
|
||||
@@ -195,7 +199,15 @@ class SubmissionFormContainer(QWidget):
|
||||
# obj.reagents.append(reagent)
|
||||
# else:
|
||||
# obj.missing_reagents.append(reagent)
|
||||
self.form.reagents = self.prsr.sub['reagents']
|
||||
match caller:
|
||||
case "import_submission_function":
|
||||
self.form.reagents = self.prsr.sub['reagents']
|
||||
case _:
|
||||
already_have = [reagent for reagent in self.prsr.sub['reagents'] if not reagent.missing]
|
||||
names = list(set([item.type for item in already_have]))
|
||||
logger.debug(f"reagents: {already_have}")
|
||||
reagents = [item.to_pydantic() for item in KitType.query(name=extraction_kit).get_reagents(submission_type=self.pyd.submission_type) if item.name not in names]
|
||||
self.form.reagents = already_have + reagents
|
||||
# logger.debug(f"Imported reagents: {obj.reagents}")
|
||||
# logger.debug(f"Missing reagents: {obj.missing_reagents}")
|
||||
self.report.add_result(report)
|
||||
@@ -221,6 +233,7 @@ class SubmissionFormContainer(QWidget):
|
||||
self.ext_kit = kit_widget.currentText()
|
||||
# for reagent in obj.pyd.reagents:
|
||||
for reagent in self.form.reagents:
|
||||
logger.debug(f"Creating widget for {reagent}")
|
||||
add_widget = ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
|
||||
# add_widget.setParent(sub_form_container.form)
|
||||
self.form.layout().addWidget(add_widget)
|
||||
|
||||
Reference in New Issue
Block a user