Addition of Equipment and SubmissionType creation.
This commit is contained in:
Landon Wark
@@ -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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