Fixed issue with missing sample id in btl file dfo-mar-odis#173

core/parsers/SampleParser.py

@@ -262,7 +262,17 @@ def parse_data_frame(mission: core_models.Mission, sample_config: settings_model
             value = row[value_field]
 
             if sample_id not in bottle_keys:
-                message = f"Could not find bottle matching id {sample_id} in file {file_name}"
+                message = f"Could not find bottle matching id {sample_id} in file {file_name} \n"
+                event = mission.events.filter(sample_id__lte=sample_id, end_sample_id__gte=sample_id)
+                if event:
+                    event = event.first()
+                    message += (_("Possible Event") + f" #{event.event_id} " + _("Bottle IDs") +
+                                f" {event.sample_id} - {event.end_sample_id}")
+                    message += _("\nEvent Comments : ")
+                    for action in event.actions.all():
+                        if action.comment:
+                            message += f"\n{action.get_type_display()} : {action.comment}"
+
                 error = core_models.FileError(mission=mission, file_name=file_name, line=sample_id, message=message,
                                               type=core_models.ErrorType.sample)
                 errors.append(error)

core/parsers/ctd.py

@@ -337,10 +337,15 @@ def process_data(event: core_models.Event, data_frame: pandas.DataFrame, column_
     update_discrete_samples: [core_models.DiscreteSampleValue] = []
     # validate and remove bottles that don't exist
     if data_frame_avg.shape[0] > (event.total_samples + 1):
-        message = _('Event contained more than the expected number of bottles. Additional bottles will be dropped. ')
-        message += _("Event") + f" #{event.event_id} "
-        message += _("Expected") + f"[{(event.total_samples+1)}] "
-        message += _("Found") + f"[{data_frame_avg.shape[0]}]"
+        message = _('Event contained more than the expected number of bottles. Additional bottles will be dropped. \n')
+        message += _("Event") + f" #{event.event_id} \n"
+        message += _("Expected") + f"[{(event.total_samples+1)}] \n"
+        message += _("Found") + f"[{data_frame_avg.shape[0]}]\n"
+        message += _("\nEvent Comments : ")
+        for action in event.actions.all():
+            if action.comment:
+                message += f"\n{action.get_type_display()} : {action.comment}"
+
         logger.warning(message)
 
         core_models.FileError(mission=mission, file_name=file_name, line=skipped_rows, message=message,
@@ -373,11 +378,29 @@ def process_data(event: core_models.Event, data_frame: pandas.DataFrame, column_
 
         # if the Bottle S/N column is present then use that values as the bottle ID
         if 'bottle_' in row[1]:
-            bottle_id = int(row[1]['bottle_'])
+            try:
+                bottle_id = int(row[1]['bottle_'])
+            except ValueError as ex:
+                logger.exception(ex)
+                message = _("There was an error parsing a bottle id - ")
+                message += _("\nEvent Comments : ")
+                for action in event.actions.all():
+                    if action.comment:
+                        message += f"\n{action.get_type_display()} : {action.comment}"
+
+                logger.error(message)
+
+                core_models.FileError(mission=mission, file_name=file_name, line=skipped_rows, message=message,
+                                      type=core_models.ErrorType.validation).save()
+                continue
 
         if not bottles.filter(bottle_id=bottle_id).exists():
-            message = _("Bottle does not exist for event")
+            message = _("Bottle does not exist for event \n")
             message += _("Event") + f" #{event.event_id} " + _("Bottle ID") + f" #{bottle_id}"
+            message += _("\nEvent Comments : ")
+            for action in event.actions.all():
+                if action.comment:
+                    message += f"\n{action.get_type_display()} : {action.comment}"
 
             logger.warning(message)
             continue

core/tests/TestAndesParser.py

@@ -152,6 +152,7 @@ def test_andeis_parser_events(self):
                 {
                     "event_number": 11.0,
                     "instrument": "Plankton net (202μm)",
+                    "instrument_type": "NET",
                     "wire_out": "1000 m",
                     "wire_angle": "45 degrees",
                     "flow_meter_start": 2068,

core/views_mission_sample.py

@@ -168,7 +168,10 @@ def get_file_error_card(request, database, mission_id):
             li_id = f'error_{error.pk}'
             li = soup.new_tag('li', attrs={'class': 'list-group-item', 'id': li_id})
             div = soup.new_tag('div', attrs={'class': 'col'})
-            div.string = error.message
+            msgs = error.message.split("\n")
+            for msg in msgs:
+                div.append(msg_div:=soup.new_tag('div'))
+                msg_div.string = msg
 
             url = reverse_lazy('core:mission_samples_delete_file_error', args=(database, error.pk))
             btn_attrs = {

start_dart.bat

@@ -4,7 +4,7 @@ if not exist ".\logs\" (
   mkdir logs
 )
 
-set dart_version=3.3.0.2
+set dart_version=3.3.1
 
 REM if this is not a git repo, and the application was installed from zip file we just want to run update
 REM if this is a cloned version of the git repo we want to pull from master, then run the update

update.bat

@@ -7,7 +7,7 @@ if not exist ".\logs\" (
 REM If this was run from a clone repo we can force an update of the python libraries, collectstatic or a
 REM migration on the database by changing the update version
 
-set update_version=3.3.0.2
+set update_version=3.3.1
 
 set first_run=0
 set server_path=.\dart_env\Scripts\activate.bat