Bugfix for commenting submissions.

source/submissions.frontend.custom_widgets.rst

@@ -1,37 +0,0 @@
-submissions.frontend.custom\_widgets package
-============================================
-
-Submodules
-----------
-
-submissions.frontend.custom\_widgets.misc module
-------------------------------------------------
-
-.. automodule:: submissions.frontend.custom_widgets.misc
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-submissions.frontend.custom\_widgets.pop\_ups module
-----------------------------------------------------
-
-.. automodule:: submissions.frontend.custom_widgets.pop_ups
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-submissions.frontend.custom\_widgets.sub\_details module
---------------------------------------------------------
-
-.. automodule:: submissions.frontend.custom_widgets.sub_details
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: submissions.frontend.custom_widgets
-   :members:
-   :undoc-members:
-   :show-inheritance:

source/submissions.frontend.rst

@@ -7,27 +7,8 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
-   submissions.frontend.custom_widgets
    submissions.frontend.visualizations
-
+   submissions.frontend.widgets
-Submodules
-----------
-
-submissions.frontend.all\_window\_functions module
---------------------------------------------------
-
-.. automodule:: submissions.frontend.all_window_functions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-submissions.frontend.main\_window\_functions module
----------------------------------------------------
-
-.. automodule:: submissions.frontend.main_window_functions
-   :members:
-   :undoc-members:
-   :show-inheritance:
 
 Module contents
 ---------------

source/submissions.frontend.widgets.rst

@@ -0,0 +1,77 @@
+submissions.frontend.widgets package
+====================================
+
+Submodules
+----------
+
+submissions.frontend.widgets.app module
+---------------------------------------
+
+.. automodule:: submissions.frontend.widgets.app
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+submissions.frontend.widgets.controls\_chart module
+---------------------------------------------------
+
+.. automodule:: submissions.frontend.widgets.controls_chart
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+submissions.frontend.widgets.functions module
+---------------------------------------------
+
+.. automodule:: submissions.frontend.widgets.functions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+submissions.frontend.widgets.kit\_creator module
+------------------------------------------------
+
+.. automodule:: submissions.frontend.widgets.kit_creator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+submissions.frontend.widgets.misc module
+----------------------------------------
+
+.. automodule:: submissions.frontend.widgets.misc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+submissions.frontend.widgets.pop\_ups module
+--------------------------------------------
+
+.. automodule:: submissions.frontend.widgets.pop_ups
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+submissions.frontend.widgets.submission\_table module
+-----------------------------------------------------
+
+.. automodule:: submissions.frontend.widgets.submission_table
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+submissions.frontend.widgets.submission\_widget module
+------------------------------------------------------
+
+.. automodule:: submissions.frontend.widgets.submission_widget
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: submissions.frontend.widgets
+   :members:
+   :undoc-members:
+   :show-inheritance:

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

@@ -20,6 +20,7 @@ class ControlType(Base):
     """    
     __tablename__ = '_control_types'
     
+    
     id = Column(INTEGER, primary_key=True) #: primary key   
     name = Column(String(255), unique=True) #: controltype name (e.g. MCS)
     targets = Column(JSON) #: organisms checked for

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

@@ -360,12 +360,16 @@ class BasicSubmission(Base):
         logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
         return []
 
-    def save(self):
+    def save(self, original:bool=True):
-        self.uploaded_by = getuser()
+        if original:
+            self.uploaded_by = getuser()
         self.metadata.session.add(self)
         self.metadata.session.commit()
         return None
     
+    def update(self):
+        pass
+    
     def delete(self):
         backup = self.to_dict()
         try:
@@ -408,7 +412,7 @@ class BasicSubmission(Base):
         Returns:
             models.BasicSubmission | List[models.BasicSubmission]: Submission(s) of interest
         """    
-        logger.debug(kwargs)
+        logger.debug(f"kwargs coming into query: {kwargs}")
         # NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters
         if submission_type == None:
             model = cls.find_subclasses(attrs=kwargs)
@@ -651,7 +655,7 @@ class BacterialCulture(BasicSubmission):
         outstr = super().enforce_name(instr=instr, data=data)
         def construct(data:dict|None=None) -> str:
             """
-            DEPRECIATED due to slowness. Search for the largest rsl number and increment by 1
+            Create default plate name.
 
             Returns:
                 str: new RSL number
@@ -912,9 +916,10 @@ class WastewaterArtic(BasicSubmission):
                 source_row = lookup_ssa.row
                 source_column = lookup_ssa.column
             except AttributeError:
-                plate = ""
+                plate = "Error"
                 source_row = 0
                 source_column = 0
+                # continue
             samples.append(dict(
                 sample=sample.submitter_id,
                 destination_column=destination_column, 
@@ -931,7 +936,7 @@ class WastewaterArtic(BasicSubmission):
         df = pd.DataFrame.from_records(samples).fillna(value="")
         df.source_row = df.source_row.astype(int)
         df.source_column = df.source_column.astype(int)
-        df.sort_values(by=['destination_column', 'destination_row'], inplace=True)
+        df.sort_values(by=['plate_number', 'source_column', 'source_row'], inplace=True)
         input_dict['csv'] = df
         return input_dict
         

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(rsl=value)
+        dlg = SubmissionComment(parent=self, rsl=value)
         if dlg.exec():
             dlg.add_comment()
 
@@ -455,8 +455,10 @@ class SubmissionDetails(QDialog):
 
         super().__init__(parent)
         # self.ctx = ctx
-        self.app = parent.parent().parent().parent().parent().parent().parent
+        try:
-        print(f"App: {self.app}")
+            self.app = parent.parent().parent().parent().parent().parent().parent
+        except AttributeError:
+            self.app = None
         self.setWindowTitle("Submission Details")
         # create scrollable interior
         interior = QScrollArea()
@@ -605,10 +607,12 @@ class SubmissionComment(QDialog):
     """
     a window for adding comment text to a submission
     """    
-    def __init__(self, rsl:str) -> None:
+    def __init__(self, parent, rsl:str) -> None:
 
-        super().__init__()
+        super().__init__(parent)
         # self.ctx = ctx
+        self.app = parent.parent().parent().parent().parent().parent().parent
+        print(f"App: {self.app}")
         self.rsl = rsl
         self.setWindowTitle(f"{self.rsl} Submission Comment")
         # create text field
@@ -632,16 +636,18 @@ class SubmissionComment(QDialog):
         commenter = getuser()
         comment = self.txt_editor.toPlainText()
         dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
-        full_comment = {"name":commenter, "time": dt, "text": comment}
+        
+        full_comment = [{"name":commenter, "time": dt, "text": comment}]
         logger.debug(f"Full comment: {full_comment}")
-        # sub = lookup_submission_by_rsl_num(ctx = self.ctx, rsl_num=self.rsl)
-        # sub = lookup_submissions(ctx = self.ctx, rsl_number=self.rsl)
         sub = BasicSubmission.query(rsl_number=self.rsl)
         try:
-            sub.comment.append(full_comment)
+            # For some reason .append results in new comment being ignores, so have to concatenate lists.
-        except AttributeError:
+            sub.comment = sub.comment + full_comment
-            sub.comment = [full_comment]
+        except AttributeError as e:
-        logger.debug(sub.__dict__)
+            logger.error(f"Hit error {e} creating comment")
-        sub.save()
+            sub.comment = full_comment
+        # logger.debug(sub.comment)
+        sub.save(original=False)
+        # logger.debug(f"Save result: {result}")
 
         

src/submissions/frontend/widgets/submission_widget.py

@@ -400,7 +400,7 @@ class SubmissionFormContainer(QWidget):
         # obj.ctx.database_session.add(sub)
         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()
+        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: