Moved import PCR results to context menu.

CHANGELOG.md

@@ -1,6 +1,7 @@
 ## 202404.02
 
 - Various bug fixes.
+- Move import PCR results to context menu.
 - Added ability to sign off on submission in submission details.
 
 ## 202403.03

src/submissions/backend/db/models/submissions.py

@@ -3,7 +3,7 @@ Models for the main submission types.
 '''
 from __future__ import annotations
 from getpass import getuser
-import json, logging, uuid, tempfile, re, yaml, base64
+import logging, uuid, tempfile, re, yaml, base64
 from zipfile import ZipFile
 from tempfile import TemporaryDirectory
 from reportlab.graphics.barcode import createBarcodeImageInMemory
@@ -14,7 +14,6 @@ from pprint import pformat
 from . import Reagent, SubmissionType, KitType, Organization
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
 from sqlalchemy.orm import relationship, validates, Query
-from json.decoder import JSONDecodeError
 from sqlalchemy.ext.associationproxy import association_proxy
 import pandas as pd
 from openpyxl import Workbook
@@ -252,7 +251,7 @@ class BasicSubmission(BaseClass):
         sample_list = self.hitpick_plate()
         # logger.debug("Setting background colours")
         for sample in sample_list:
-            if sample['Positive']:
+            if sample['positive']:
                 sample['background_color'] = "#f10f07"
             else:
                 if "colour" in sample.keys():
@@ -1268,6 +1267,54 @@ class Wastewater(BasicSubmission):
         row = idx.index.to_list()[0]
         return row + 1
 
+    def custom_context_events(self) -> dict:
+        events = super().custom_context_events()
+        events['Link PCR'] = self.link_pcr
+        return events
+
+    def link_pcr(self, obj):
+        from backend.excel import PCRParser
+        from frontend.widgets import select_open_file
+        fname = select_open_file(obj=obj, file_extension="xlsx")
+        parser = PCRParser(filepath=fname)
+        # Check if PCR info already exists
+        if hasattr(self, 'pcr_info') and self.pcr_info != None:
+            # existing = json.loads(sub.pcr_info)
+            existing = self.pcr_info
+        else:
+            existing = None
+        if existing != None:
+            # update pcr_info
+            try:
+                logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
+                # if json.dumps(parser.pcr) not in sub.pcr_info:
+                if parser.pcr not in self.pcr_info:
+                    existing.append(parser.pcr)
+                logger.debug(f"Setting: {existing}")
+                # sub.pcr_info = json.dumps(existing)
+                self.pcr_info = existing
+            except TypeError:
+                logger.error(f"Error updating!")
+                # sub.pcr_info = json.dumps([parser.pcr])
+                self.pcr_info = [parser.pcr]
+            logger.debug(f"Final pcr info for {self.rsl_plate_num}: {self.pcr_info}")
+        else:
+            # sub.pcr_info = json.dumps([parser.pcr])
+            self.pcr_info = [parser.pcr]
+        logger.debug(f"Existing {type(self.pcr_info)}: {self.pcr_info}")
+        logger.debug(f"Inserting {type(parser.pcr)}: {parser.pcr}")
+        self.save(original=False)
+        logger.debug(f"Got {len(parser.samples)} samples to update!")
+        logger.debug(f"Parser samples: {parser.samples}")
+        for sample in self.samples:
+            logger.debug(f"Running update on: {sample}")
+            try:
+                sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
+            except IndexError:
+                continue
+            self.update_subsampassoc(sample=sample, input_dict=sample_dict)
+        # self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
+
 class WastewaterArtic(BasicSubmission):
     """
     derivative submission type for artic wastewater
@@ -2094,7 +2141,7 @@ class SubmissionSampleAssociation(BaseClass):
             logger.error(f"Unable to find row {self.row} in row_map.")
             sample['Well'] = None
         sample['Plate Name'] = self.submission.rsl_plate_num
-        sample['Positive'] = False
+        sample['positive'] = False
         sample['submitted_date'] = self.submission.submitted_date
         return sample
     

src/submissions/frontend/widgets/app.py

@@ -8,19 +8,16 @@ from PyQt6.QtWidgets import (
 )
 from PyQt6.QtGui import QAction
 from pathlib import Path
-from backend.validators import PydReagent
 from tools import check_if_app, Settings, Report
 from .pop_ups import  AlertPop
-from .misc import AddReagentForm, LogParser
+from .misc import LogParser
 import logging, webbrowser, sys
-from datetime import date
 from .submission_table import SubmissionsSheet
 from .submission_widget import SubmissionFormContainer
 from .controls_chart import ControlsViewer
 from .kit_creator import KitAdder
 from .submission_type_creator import SubmissionTypeAdder
 
-
 logger = logging.getLogger(f'submissions.{__name__}')
 logger.info("Hello, I am a logger")
 
@@ -70,7 +67,7 @@ class App(QMainWindow):
         helpMenu.addAction(self.helpAction)
         helpMenu.addAction(self.docsAction)
         fileMenu.addAction(self.importAction)
-        fileMenu.addAction(self.importPCRAction)
+        # fileMenu.addAction(self.importPCRAction)
         methodsMenu.addAction(self.searchLog)
         reportMenu.addAction(self.generateReportAction)
         maintenanceMenu.addAction(self.joinExtractionAction)
@@ -93,7 +90,7 @@ class App(QMainWindow):
         """        
         logger.debug(f"Creating actions...")
         self.importAction = QAction("&Import Submission", self)
-        self.importPCRAction = QAction("&Import PCR Results", self)
+        # self.importPCRAction = QAction("&Import PCR Results", self)
         self.addReagentAction = QAction("Add Reagent", self)
         self.generateReportAction = QAction("Make Report", self)
         self.addKitAction = QAction("Import Kit", self)
@@ -110,7 +107,7 @@ class App(QMainWindow):
         """
         logger.debug(f"Connecting actions...")
         self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
-        self.importPCRAction.triggered.connect(self.table_widget.formwidget.import_pcr_results)
+        # self.importPCRAction.triggered.connect(self.table_widget.formwidget.import_pcr_results)
         self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
         self.generateReportAction.triggered.connect(self.table_widget.sub_wid.generate_report)
         self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions)
@@ -157,8 +154,6 @@ class App(QMainWindow):
             self.report = Report()
         else:
             self.statusBar().showMessage("Action completed sucessfully.", 5000)
-        
-    
 
     def runSearch(self):
         dlg = LogParser(self)

src/submissions/frontend/widgets/submission_details.py

@@ -95,10 +95,12 @@ class SubmissionDetails(QDialog):
         self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
         self.webview.setHtml(self.html)
         self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
+        with open("details.html", "w") as f:
+            f.write(self.html)
 
     @pyqtSlot(str)
     def sign_off(self, submission:str|BasicSubmission):
-        logger.debug(f"Signing off on {submission}")
+        logger.debug(f"Signing off on {submission} - ({getuser()})")
         if isinstance(submission, str):
             submission = BasicSubmission.query(rsl_number=submission)
         submission.uploaded_by = getuser()

src/submissions/frontend/widgets/submission_widget.py

@@ -112,81 +112,6 @@ class SubmissionFormContainer(QWidget):
         logger.debug(f"Outgoing report: {self.report.results}")
         logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
 
-    def import_pcr_results(self):
-        """
-        Pull QuantStudio results into db
-        """        
-        self.import_pcr_results_function()
-        self.app.report.add_result(self.report)
-        self.report = Report()
-        self.app.result_reporter()
-
-    def import_pcr_results_function(self):
-        """
-        Import Quant-studio PCR data to an imported submission
-
-        Args:
-            obj (QMainWindow): original app window
-
-        Returns:
-            Tuple[QMainWindow, dict]: Collection of new main app window and result dict
-        """    
-        report = Report()
-        fname = select_open_file(self, file_extension="xlsx")
-        parser = PCRParser(filepath=fname)
-        logger.debug(f"Attempting lookup for {parser.plate_num}")
-        sub = BasicSubmission.query(rsl_number=parser.plate_num)
-        try:
-            logger.debug(f"Found submission: {sub.rsl_plate_num}")
-        except AttributeError:
-            # If no plate is found, may be because this is a repeat. Lop off the '-1' or '-2' and repeat
-            logger.error(f"Submission of number {parser.plate_num} not found. Attempting rescue of plate repeat.")
-            parser.plate_num = "-".join(parser.plate_num.split("-")[:-1])
-            sub = BasicSubmission.query(rsl_number=parser.plate_num)
-            try:
-                logger.debug(f"Found submission: {sub.rsl_plate_num}")
-            except AttributeError:
-                logger.error(f"Rescue of {parser.plate_num} failed.")
-                self.report.add_result(Result(msg="Couldn't find a submission with that RSL number.", status="Warning"))
-                return
-        # Check if PCR info already exists
-        if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
-            # existing = json.loads(sub.pcr_info)
-            existing = sub.pcr_info
-        else:
-            existing = None
-        if existing != None:
-            # update pcr_info
-            try:
-                logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
-                # if json.dumps(parser.pcr) not in sub.pcr_info:
-                if parser.pcr not in sub.pcr_info:
-                    existing.append(parser.pcr)
-                logger.debug(f"Setting: {existing}")
-                # sub.pcr_info = json.dumps(existing)
-                sub.pcr_info = existing
-            except TypeError:
-                logger.error(f"Error updating!")
-                # sub.pcr_info = json.dumps([parser.pcr])
-                sub.pcr_info = [parser.pcr]
-            logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
-        else:
-            # sub.pcr_info = json.dumps([parser.pcr])
-            sub.pcr_info = [parser.pcr]
-        logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
-        logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
-        sub.save(original=False)
-        logger.debug(f"Got {len(parser.samples)} samples to update!")
-        logger.debug(f"Parser samples: {parser.samples}")
-        for sample in sub.samples:
-            logger.debug(f"Running update on: {sample}")
-            try:
-                sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
-            except IndexError:
-                continue
-            sub.update_subsampassoc(sample=sample, input_dict=sample_dict)
-        self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
-
     def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
         """
         Action to create new reagent in DB.