Bugs squashed.

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202311.2b"
+__version__ = "202311.3b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 

src/submissions/__main__.py

@@ -1,9 +1,11 @@
 import sys
 import os
 # environment variable must be set to enable qtwebengine in network path
-if getattr(sys, 'frozen', False):
+# if getattr(sys, 'frozen', False):
+#     os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
+from tools import get_config, setup_logger, check_if_app
+if check_if_app():
     os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
-from tools import get_config, setup_logger
 # setup custom logger
 logger = setup_logger(verbosity=3)
 # create settings object

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

@@ -471,6 +471,21 @@ class Reagent(Base):
                 pass
         return query_return(query=query, limit=limit)
 
+    def update_last_used(self, kit:KitType):
+        report = Report()
+        logger.debug(f"Attempting update of reagent type at intersection of ({self}), ({kit})")
+        rt = ReagentType.query(kit_type=kit, reagent=self, limit=1)
+        if rt != None:
+            logger.debug(f"got reagenttype {rt}")
+            assoc = KitTypeReagentTypeAssociation.query(kit_type=kit, reagent_type=rt)
+            if assoc != None:
+                if assoc.last_used != self.lot:
+                    logger.debug(f"Updating {assoc} last used to {self.lot}")
+                    assoc.last_used = self.lot
+                    result = assoc.save()
+                    return(report.add_result(result))
+        return report.add_result(Result(msg=f"Updating last used {rt} was not performed.", status="Information"))
+
 class Discount(Base):
     """
     Relationship table for client labs for certain kits.

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

@@ -25,7 +25,6 @@ from dateutil.parser._parser import ParserError
 import yaml
 from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError
 from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
-import sys
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -572,6 +571,17 @@ class BasicSubmission(Base):
         except AttributeError:
             logger.error(f"Could not set {self} attribute {key} to {value}")
 
+    def update_subsampassoc(self, sample:BasicSample, input_dict:dict):
+        assoc = SubmissionSampleAssociation.query(submission=self, sample=sample, limit=1)
+        for k,v in input_dict.items():
+            try:
+                setattr(assoc, k, v)
+            except AttributeError:
+                logger.error(f"Can't set {k} to {v}")
+        # result = store_object(ctx=ctx, object=assoc)
+        result = assoc.save()
+        return result
+
 # Below are the custom submission types
 
 class BacterialCulture(BasicSubmission):
@@ -925,6 +935,8 @@ class WastewaterArtic(BasicSubmission):
         input_dict['csv'] = df
         return input_dict
         
+# Sample Classes
+
 class BasicSample(Base):
     """
     Base of basic sample which polymorphs into BCSample and WWSample
@@ -1115,6 +1127,8 @@ class BasicSample(Base):
             instance.sample_type = sample_type
         return instance
 
+#Below are the custom sample types
+
 class WastewaterSample(BasicSample):
     """
     Derivative wastewater sample
@@ -1199,6 +1213,8 @@ class BacterialCultureSample(BasicSample):
         sample['name'] = f"{self.submitter_id} - ({self.organism})"
         return sample
 
+# Submission to Sample Associations
+
 class SubmissionSampleAssociation(Base):
     """
     table containing submission/sample associations

src/submissions/backend/validators/pydant.py

@@ -13,7 +13,7 @@ import re
 import logging
 from tools import check_not_nan, convert_nans_to_nones, jinja_template_loading, Report, Result
 from backend.db.models import *
-from sqlalchemy.exc import StatementError
+from sqlalchemy.exc import StatementError, IntegrityError
 from PyQt6.QtWidgets import QComboBox, QWidget
 from pprint import pformat
 from openpyxl import load_workbook
@@ -172,7 +172,10 @@ class PydSample(BaseModel, extra='allow'):
                                                                           submission=submission, 
                                                                           sample=instance, 
                                                                           row=row, column=column)
+                try:
                     instance.sample_submission_associations.append(association)
+                except IntegrityError:
+                    instance.metadata.session.rollback()
         return instance, result
 
 class PydSubmission(BaseModel, extra='allow'):
@@ -408,9 +411,9 @@ class PydSubmission(BaseModel, extra='allow'):
         extraction_kit = KitType.query(name=self.extraction_kit['value'])
         logger.debug(f"We have the extraction kit: {extraction_kit.name}")
         excel_map = extraction_kit.construct_xl_map_for_use(self.submission_type['value'])
-        logger.debug(f"Extraction kit map:\n\n{pformat(excel_map)}")
+        # logger.debug(f"Extraction kit map:\n\n{pformat(excel_map)}")
-        logger.debug(f"Missing reagents going into autofile: {pformat(reagents)}")
+        # logger.debug(f"Missing reagents going into autofile: {pformat(reagents)}")
-        logger.debug(f"Missing info going into autofile: {pformat(info)}")
+        # logger.debug(f"Missing info going into autofile: {pformat(info)}")
         new_reagents = []
         for reagent in reagents:
             new_reagent = {}

src/submissions/frontend/widgets/submission_table.py

@@ -145,7 +145,7 @@ class SubmissionsSheet(QTableView):
         index = (self.selectionModel().currentIndex())
         value = index.sibling(index.row(),1).data()
         logger.debug(f"Selected value: {value}")
-        dlg = SubmissionComment(ctx=self.ctx, rsl=value)
+        dlg = SubmissionComment(rsl=value)
         if dlg.exec():
             dlg.add_comment()
 
@@ -455,6 +455,8 @@ class SubmissionDetails(QDialog):
 
         super().__init__(parent)
         # self.ctx = ctx
+        self.app = parent.parent().parent().parent().parent().parent().parent
+        print(f"App: {self.app}")
         self.setWindowTitle("Submission Details")
         # create scrollable interior
         interior = QScrollArea()
@@ -603,10 +605,10 @@ class SubmissionComment(QDialog):
     """
     a window for adding comment text to a submission
     """    
-    def __init__(self, ctx:Settings, rsl:str) -> None:
+    def __init__(self, rsl:str) -> None:
 
         super().__init__()
-        self.ctx = ctx
+        # self.ctx = ctx
         self.rsl = rsl
         self.setWindowTitle(f"{self.rsl} Submission Comment")
         # create text field
@@ -640,7 +642,6 @@ class SubmissionComment(QDialog):
         except AttributeError:
             sub.comment = [full_comment]
         logger.debug(sub.__dict__)
-        self.ctx.database_session.add(sub)
+        sub.save()
-        self.ctx.database_session.commit()
 
         

src/submissions/frontend/widgets/submission_widget.py

@@ -11,7 +11,7 @@ from tools import Report, Result, check_not_nan
 from backend.excel.parser import SheetParser, PCRParser
 from backend.validators import PydSubmission, PydReagent
 from backend.db import (
-    check_kit_integrity, update_last_used, KitType, Organization, SubmissionType, Reagent, 
+    check_kit_integrity, KitType, Organization, SubmissionType, Reagent, 
     ReagentType, KitTypeReagentTypeAssociation, BasicSubmission, update_subsampassoc_with_pcr
 )
 from pprint import pformat
@@ -22,7 +22,7 @@ import difflib
 from datetime import date
 import inspect
 import json
-
+import sys
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -80,27 +80,6 @@ class SubmissionFormContainer(QWidget):
             case _:
                 self.app.result_reporter()
 
-    # def kit_reload_function(self):
-    #     """
-    #     Reload the fields in the form
-
-    #     Args:
-    #         obj (QMainWindow): original app window
-
-    #     Returns:
-    #         Tuple[QMainWindow, dict]: Collection of new main app window and result dict
-    #     """    
-    #     report = Report()
-    #     # for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
-    #     logger.debug(f"Attempting to clear {obj.form.find_widgets()}")
-    #     for item in self.form.find_widgets():
-    #         if isinstance(item, ReagentFormWidget):
-    #             item.setParent(None)
-    #     self.kit_integrity_completion_function()
-    #     self.report.add_result(report)
-
-
-
     def kit_integrity_completion(self):
         """
         Performs check of imported reagents
@@ -296,6 +275,8 @@ class SubmissionFormContainer(QWidget):
             self.report.add_result(report)
             return
         base_submission, result = self.pyd.toSQL()
+        # logger.debug(f"Base submission: {base_submission.to_dict()}")
+        # sys.exit()
         # check output message for issues
         match result.code:
             # code 0: everything is fine.
@@ -303,7 +284,7 @@ class SubmissionFormContainer(QWidget):
                 self.report.add_result(None)
             # code 1: ask for overwrite
             case 1:
-                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
+                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
                 if dlg.exec():
                     # Do not add duplicate reagents.
                     # base_submission.reagents = []
@@ -320,7 +301,10 @@ class SubmissionFormContainer(QWidget):
                 pass
         # add reagents to submission object
         for reagent in base_submission.reagents:
-            update_last_used(reagent=reagent, kit=base_submission.extraction_kit)
+            # logger.debug(f"Updating: {reagent} with {reagent.lot}")
+            # update_last_used(reagent=reagent, kit=base_submission.extraction_kit)
+            reagent.update_last_used(kit=base_submission.extraction_kit)
+        # sys.exit()
         logger.debug(f"Here is the final submission: {pformat(base_submission.__dict__)}")
         logger.debug(f"Parsed reagents: {pformat(base_submission.reagents)}")    
         logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
@@ -329,7 +313,7 @@ class SubmissionFormContainer(QWidget):
         self.app.table_widget.sub_wid.setData()
         # reset form
         self.form.setParent(None)
-        logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
+        # logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
         wkb = self.pyd.autofill_excel()
         if wkb != None:
             fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="xlsx")
@@ -352,6 +336,7 @@ class SubmissionFormContainer(QWidget):
             fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
         try:
             self.pyd.csv.to_csv(fname.__str__(), index=False)
+            del self.pyd.csv
         except PermissionError:
             logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
 
@@ -424,7 +409,8 @@ class SubmissionFormContainer(QWidget):
                 sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
             except IndexError:
                 continue
-            update_subsampassoc_with_pcr(submission=sub, sample=sample, input_dict=sample_dict)
+            # update_subsampassoc_with_pcr(submission=sub, sample=sample, input_dict=sample_dict)
+            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'))
         # return obj, result
 
@@ -481,6 +467,7 @@ class SubmissionFormWidget(QWidget):
                         info[field] = value
         logger.debug(f"Info: {pformat(info)}")
         logger.debug(f"Reagents: {pformat(reagents)}")
+        # sys.exit()
         # app = self.parent().parent().parent().parent().parent().parent().parent().parent
         submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
         return submission

src/submissions/templates/submission_details.html

@@ -35,7 +35,7 @@
             </style>
         <title>Submission Details for {{ sub['Plate Number'] }}</title>
     </head>
-    {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments', 'barcode', 'platemap'] %}
+    {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments', 'barcode', 'platemap', 'export_map'] %}
     <body>
         <h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>&nbsp;&nbsp;&nbsp;{% if sub['barcode'] %}<img align='right' height="30px" width="120px" src="data:image/jpeg;base64,{{ sub['barcode'] | safe }}">{% endif %}
         <p>{% for key, value in sub.items() if key not in excluded %}