Bug fixes

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

@@ -1880,34 +1880,34 @@ class Wastewater(BasicSubmission):
             new_control.save()
         return report
 
-    def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
-        """
-        Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
-
-        Args:
-            sample (BasicSample): Associated sample.
-            input_dict (dict): values to be updated
-
-        Returns:
-            SubmissionSampleAssociation: Updated association
-        """
-        # logger.debug(f"Input dict: {pformat(input_dict)}")
+    # def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
+    #     """
+    #     Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
     #
-        assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
-        # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
-        # assert 0 < len(targets) <= 2
-        # for k, v in targets.items():
-        #     # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
-        #     # update_key = f"ct_n{i}"
-        #     current_value = getattr(assoc, k)
-        #     logger.debug(f"Current value came back as: {current_value}")
-        #     if current_value is None:
-        #         setattr(assoc, k, v)
-        #     else:
-        #         logger.debug(f"Have a value already, {current_value}... skipping.")
-        if assoc.column == 3:
-            logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
-        return assoc
+    #     Args:
+    #         sample (BasicSample): Associated sample.
+    #         input_dict (dict): values to be updated
+    #
+    #     Returns:
+    #         SubmissionSampleAssociation: Updated association
+    #     """
+    #     # logger.debug(f"Input dict: {pformat(input_dict)}")
+    #     #
+    #     assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
+    #     # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
+    #     # assert 0 < len(targets) <= 2
+    #     # for k, v in targets.items():
+    #     #     # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
+    #     #     # update_key = f"ct_n{i}"
+    #     #     current_value = getattr(assoc, k)
+    #     #     logger.debug(f"Current value came back as: {current_value}")
+    #     #     if current_value is None:
+    #     #         setattr(assoc, k, v)
+    #     #     else:
+    #     #         logger.debug(f"Have a value already, {current_value}... skipping.")
+    #     if assoc.column == 3:
+    #         logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
+    #     return assoc
 
 
 class WastewaterArtic(BasicSubmission):

src/submissions/backend/excel/reports.py

@@ -2,6 +2,7 @@
 Contains functions for generating summary reports
 """
 import itertools
+import re
 import sys
 from pprint import pformat
 from pandas import DataFrame, ExcelWriter
@@ -211,8 +212,13 @@ class ConcentrationMaker(ReportArchetype):
 
     @classmethod
     def build_record(cls, control) -> dict:
-
-        positive = not control.submitter_id.lower().startswith("en")
+        regex = re.compile(r"^(ATCC)|(MCS)", flags=re.IGNORECASE)
+        if bool(regex.match(control.submitter_id)):
+            positive = "positive"
+        elif control.submitter_id.lower().startswith("en"):
+            positive = "negative"
+        else:
+            positive = "sample"
         try:
             concentration = float(control.concentration)
         except (TypeError, ValueError):

src/submissions/frontend/visualizations/concentrations_chart.py

@@ -34,7 +34,7 @@ class ConcentrationsChart(CustomFigure):
             # logger.debug(f"DF after changes:\n{self.df}")
             scatter = px.scatter(data_frame=self.df, x='submission', y="concentration",
                                  hover_data=["name", "submission", "submitted_date", "concentration"],
-                                 color="positive", color_discrete_map={True: "red", False: "green"}
+                                 color="positive", color_discrete_map={"positive": "red", "negative": "green", "sample":"orange"}
                                  )
         except (ValueError, AttributeError) as e:
             logger.error(f"Error constructing chart: {e}")

src/submissions/frontend/widgets/app.py

@@ -80,8 +80,8 @@ class App(QMainWindow):
         helpMenu.addAction(self.docsAction)
         helpMenu.addAction(self.githubAction)
         fileMenu.addAction(self.importAction)
-        fileMenu.addAction(self.yamlExportAction)
-        fileMenu.addAction(self.yamlImportAction)
+        # fileMenu.addAction(self.yamlExportAction)
+        # fileMenu.addAction(self.yamlImportAction)
         methodsMenu.addAction(self.searchSample)
         maintenanceMenu.addAction(self.joinExtractionAction)
         maintenanceMenu.addAction(self.joinPCRAction)
@@ -112,8 +112,8 @@ class App(QMainWindow):
         self.docsAction = QAction("&Docs", self)
         self.searchSample = QAction("Search Sample", self)
         self.githubAction = QAction("Github", self)
-        self.yamlExportAction = QAction("Export Type Example", self)
-        self.yamlImportAction = QAction("Import Type Template", self)
+        # self.yamlExportAction = QAction("Export Type Example", self)
+        # self.yamlImportAction = QAction("Import Type Template", self)
         self.editReagentAction = QAction("Edit Reagent", self)
         self.manageOrgsAction = QAction("Manage Clients", self)
         self.manageKitsAction = QAction("Manage Kits", self)
@@ -130,8 +130,8 @@ class App(QMainWindow):
         self.docsAction.triggered.connect(self.openDocs)
         self.searchSample.triggered.connect(self.runSampleSearch)
         self.githubAction.triggered.connect(self.openGithub)
-        self.yamlExportAction.triggered.connect(self.export_ST_yaml)
-        self.yamlImportAction.triggered.connect(self.import_ST_yaml)
+        # self.yamlExportAction.triggered.connect(self.export_ST_yaml)
+        # self.yamlImportAction.triggered.connect(self.import_ST_yaml)
         self.table_widget.pager.current_page.textChanged.connect(self.update_data)
         self.editReagentAction.triggered.connect(self.edit_reagent)
         self.manageOrgsAction.triggered.connect(self.manage_orgs)
@@ -186,46 +186,46 @@ class App(QMainWindow):
         dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")])
         dlg.exec()
 
-    def export_ST_yaml(self):
-        """
-        Copies submission type yaml to file system for editing and remport
+    # def export_ST_yaml(self):
+    #     """
+    #     Copies submission type yaml to file system for editing and remport
+    #
+    #     Returns:
+    #         None
+    #     """
+    #     if check_if_app():
+    #         yaml_path = Path(sys._MEIPASS).joinpath("files", "resources", "viral_culture.yml")
+    #     else:
+    #         yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
+    #     fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
+    #     shutil.copyfile(yaml_path, fname)
 
-        Returns:
-            None
-        """
-        if check_if_app():
-            yaml_path = Path(sys._MEIPASS).joinpath("files", "resources", "viral_culture.yml")
-        else:
-            yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
-        fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
-        shutil.copyfile(yaml_path, fname)
-
-    @check_authorization
-    def import_ST_yaml(self, *args, **kwargs):
-        """
-        Imports a yml form into a submission type.
-
-        Args:
-            *args ():
-            **kwargs ():
-
-        Returns:
-
-        """
-        fname = select_open_file(obj=self, file_extension="yml")
-        if not fname:
-            logger.info(f"Import cancelled.")
-            return
-        ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
-        ap.exec()
-        st = SubmissionType.import_from_json(filepath=fname)
-        if st:
-            # NOTE: Do not delete the print statement below.
-            choice = input("Save the above submission type? [y/N]: ")
-            if choice.lower() == "y":
-                pass
-            else:
-                logger.warning("Save of submission type cancelled.")
+    # @check_authorization
+    # def import_ST_yaml(self, *args, **kwargs):
+    #     """
+    #     Imports a yml form into a submission type.
+    #
+    #     Args:
+    #         *args ():
+    #         **kwargs ():
+    #
+    #     Returns:
+    #
+    #     """
+    #     fname = select_open_file(obj=self, file_extension="yml")
+    #     if not fname:
+    #         logger.info(f"Import cancelled.")
+    #         return
+    #     ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
+    #     ap.exec()
+    #     st = SubmissionType.import_from_json(filepath=fname)
+    #     if st:
+    #         # NOTE: Do not delete the print statement below.
+    #         choice = input("Save the above submission type? [y/N]: ")
+    #         if choice.lower() == "y":
+    #             pass
+    #         else:
+    #             logger.warning("Save of submission type cancelled.")
 
     def update_data(self):
         self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)