Automated Tests

api/chl/services.py

@@ -17,7 +17,7 @@ def get(cls, cruise_name: str) -> FileResponse:
 
         try:
             Cruise.objects.get(name__iexact=cruise_name) 
-            object_key = f"{cruise_name}{cls.FILE_SUFFIX}"
+            object_key = f"{cruise_name.lower()}{cls.FILE_SUFFIX}"
             with MediaStore(cls.URL, token=cls.TOKEN) as store:
                 prefix = PrefixStore(store, cls.MEDIASTORE_PREFIX)
                 try:

api/core/views.py

@@ -153,25 +153,25 @@ def cruise_track_view(request, cruise_name):
         # Non-clickable track points (no labels or popups)
         try:
             track_points = [
-                {"lat": row[" Dec_LAT"], "lng": row[" Dec_LON"]}
+                {"lat": row["dec_lat"], "lng": row["dec_lon"]}   # ar
                 for _, row in underway_data.iterrows()
             ]
         except KeyError:
             try:
                 track_points = [
-                    {"lat": row["Latitude_Deg"], "lng": row["Longitude_Deg"]}   # hrs2303
+                    {"lat": row["latitude_deg"], "lng": row["longitude_deg"]}   # hrs2303
                     for _, row in underway_data.iterrows()
                 ]
             except KeyError:
                 try:
                     track_points = [
-                        {"lat": row["GPS-Furuno-Latitude"], "lng": row["GPS-Furuno-Longitude"]}   # en
+                        {"lat": row["gps_furuno_latitude"], "lng": row["gps_furuno_longitude"]}   # en
                         for _, row in underway_data.iterrows()
                     ]
                 except KeyError:
 
                     track_points = [
-                        {"lat": row["Latitude"], "lng": row["Longitude"]}   # ae2426
+                        {"lat": row["latitude"], "lng": row["longitude"]}   # ae2426
                         for _, row in underway_data.iterrows()
                     ]
 
@@ -286,4 +286,8 @@ def ctd_plot_view(request, cruise_name, cast_number):
     plt.close()
     buffer.seek(0)
 
-    return HttpResponse(buffer.getvalue(), content_type='image/png')
+    # The title will be verified in cruise_track.js automated test
+    resp = HttpResponse(buffer.getvalue(), content_type="image/png")
+    resp["X-Plot-Title"] = f"{cruise_name} Cast {cast_number} - CTD Profile"
+    return resp
+

api/ctd/api.py

@@ -35,6 +35,13 @@ def update_vessel(request, vessel_name: str, input: UpdateVesselInput):
     except ValueError as e:
         return {"status": "error", "message": str(e)}
 
+@router.delete('/vessels/delete/{vessel_name}', tags=["Admin"], auth=TokenAuthenticator())
+def delete_vessel(request, vessel_name: str):
+    try:
+        result = CtdService.delete_vessel(vessel_name)
+        return result
+    except ValueError as e:
+        return {"status": "error", "message": str(e)}
 
 @router.get("/cruises/get/all", response=List[CruiseOutput], tags=["Users"])
 def get_cruises(request):

api/ctd/services.py

@@ -1,4 +1,5 @@
 import io, os
+import csv
 from typing import Optional, List, Tuple
 from datetime import datetime
 
@@ -160,6 +161,16 @@ def create_vessel(cls, input: AddVesselInput) -> VesselOutput:
         except Vessel.DoesNotExist:
             pass
 
+    @classmethod
+    def delete_vessel(cls, vessel_name: str):
+        vessel = Vessel.objects.filter(name__iexact=vessel_name)
+        if not vessel.exists():
+            raise HttpError(404, f"Vessel with name '{vessel_name}' does not exist.")
+        try:
+            vessel.delete()
+            return {"message": f"Vessel '{vessel_name}' deleted"}
+        except Exception as e:
+            raise HttpError(500, f"Failed to delete vessel: {str(e)}")
 
     @classmethod
     def update_vessel(cls, vessel_name: str, input: UpdateVesselInput) -> VesselOutput:
@@ -194,9 +205,27 @@ def serialize_cruise(cruise: Cruise) -> CruiseOutput:
         )
 
     @classmethod
-    def get_cruises(cls) -> list[CruiseOutput]:
+    def get_cruises(cls) -> HttpResponse:
         cruises = Cruise.objects.all()
-        return [cls.serialize_cruise(cruise) for cruise in cruises]
+
+        buffer = io.StringIO()
+        writer = csv.writer(buffer)
+
+        # Write header row
+        writer.writerow(["name", "vessel", "start_time", "end_time"])
+
+        for cruise in cruises:
+            writer.writerow([
+                cruise.name,
+                cruise.vessel.name,
+                cruise.start_time,
+                cruise.end_time
+            ])
+
+        # Convert to HttpResponse
+        response = HttpResponse(buffer.getvalue(), content_type='text/csv')
+        response['Content-Disposition'] = 'attachment; filename="cruises.csv"'
+        return response
 
     @classmethod
     def get_cruise(cls, cruise_name: str) -> CruiseOutput:
@@ -446,7 +475,7 @@ def delete_niskin(cruise_name: str, cast_number: str, niskin_number: int):
             cast = Cast.objects.get(cruise=cruise, number__iexact=cast_number)
             niskin = Niskin.objects.get(cast=cast, number=niskin_number)
             niskin.delete()
-            return {"status": "success", "message": f"Cast {cast_number} on cruise {cruise_name} deleted."}   
+            return {"status": "success", "message": f"Niskin {niskin_number} on cruise {cruise_name} for cast {cast_number} deleted."}   
         except Cruise.DoesNotExist:
             raise Http404(f"Cruise {cruise_name} not found.")
         except Cast.DoesNotExist:
@@ -462,7 +491,7 @@ def get_bottles(cls, cruise_name: str) -> FileResponse:
         FILE_SUFFIX = '_ctd_bottles.csv'
         try:
             Cruise.objects.get(name__iexact=cruise_name) 
-            object_key = f"{cruise_name}{FILE_SUFFIX}"
+            object_key = f"{cruise_name.lower()}{FILE_SUFFIX}"
             with MediaStore(URL, token=TOKEN) as store:
                 prefix = PrefixStore(store, MEDIASTORE_PREFIX)
                 try:
@@ -485,7 +514,7 @@ def get_bottle_summary(cls, cruise_name: str) -> FileResponse:
         FILE_SUFFIX = '_ctd_bottle_summary.csv'
         try:
             Cruise.objects.get(name__iexact=cruise_name) 
-            object_key = f"{cruise_name}{FILE_SUFFIX}"
+            object_key = f"{cruise_name.lower()}{FILE_SUFFIX}"
             with MediaStore(URL, token=TOKEN) as store:
                 prefix = PrefixStore(store, MEDIASTORE_PREFIX)
                 try:
@@ -508,7 +537,7 @@ def get_metadata(cls, cruise_name: str) -> FileResponse:
         FILE_SUFFIX = '_ctd_metadata.csv'
         try:
             Cruise.objects.get(name__iexact=cruise_name) 
-            object_key = f"{cruise_name}{FILE_SUFFIX}"
+            object_key = f"{cruise_name.lower()}{FILE_SUFFIX}"
             with MediaStore(URL, token=TOKEN) as store:
                 prefix = PrefixStore(store, MEDIASTORE_PREFIX)
                 try:

api/events/api.py

@@ -11,14 +11,17 @@
 def get_events(request, cruise_name: str):
     return EventService.get_events(cruise_name)
 
+@router.get("/instruments/{cruise_name}", response=List[str], tags=["Users"])
+def get_instruments(request, cruise_name: str):
+    return EventService.get_instruments(cruise_name)
 
-@router.post("/filter/{cruise_name}", response=List[EventOutput], tags=["Users"])
+@router.post("/filter/{cruise_name}", response=List[EventOutput], tags=["Users"], auth=TokenAuthenticator())
 def filter_events(request, cruise_name: str, input: FilterEventInput):
     return EventService.filter_events(cruise_name, input)
 
-@router.post("/edit/{cruise_name}/{message_id}", response=EventOutput, tags=["Admin"], auth=TokenAuthenticator())
-def edit_events(request, cruise_name: str, message_id: int, input: EditEventInput):
-    return EventService.edit_events(cruise_name, message_id, input)
+@router.post("/edit/{cruise_name}/{r2r_event}", response=EventOutput, tags=["Admin"], auth=TokenAuthenticator())
+def edit_events(request, cruise_name: str, r2r_event: str, input: EditEventInput):
+    return EventService.edit_events(cruise_name, r2r_event, input)
 
 
 @router.get("/history/{cruise_name}", response=str, tags=["Users"])

api/events/management/commands/importevent.py

@@ -83,7 +83,7 @@ def store_csv_file(self, cruise_name, csv_data):
 
     def handle(self, *args, **options):
         cruise_name = options['cruise_name']
-        
+
         if cruise_name is None:
             cruises = list(Cruise.objects.values_list('name', flat=True))
         else:

api/events/services.py

@@ -29,6 +29,7 @@
 MESSAGE_ID = 'Message ID'  
 
 class EventOutput(BaseModel):
+    r2r_event: str
     message_id: int
     instrument: str
     action: str
@@ -43,18 +44,19 @@ class EventOutput(BaseModel):
 class FilterEventInput(BaseModel):
     instrument: Optional[str] = None
     action: Optional[str] = None
-    station: Optional[str] = None
-    cast: Optional[str] = None
-    comment: Optional[str] = None
+    station: Optional[str] = ""
+    cast: Optional[str] = ""
+    comment: Optional[str] = ""
 
 class EditEventInput(BaseModel):
+    message_id: Optional[int] = None
     instrument: Optional[str] = None
     action: Optional[str] = None
-    station: Optional[str] = None
-    cast: Optional[str] = None
+    station: Optional[str] = ""
+    cast: Optional[str] = ""
     latitude: Optional[float] = None
     longitude: Optional[float] = None
-    comment: Optional[str] = None
+    comment: Optional[str] = ""
     datetime: Optional[datetime] = None
 
 
@@ -71,6 +73,7 @@ def serialize_event(event: Event) -> EventOutput:
             longitude = None
 
         return EventOutput(
+                r2r_event=event.r2r_event,
                 message_id=event.message_id,
                 instrument=event.instrument,
                 action=event.action,
@@ -90,6 +93,8 @@ def store_csv_file(self, cruise_name, csv_data):
         df = pd.DataFrame(csv_data)
         df[DATETIME] = pd.to_datetime(df[DATETIME])
         df = df.sort_values(by=DATETIME)
+        df["Station"] = df["Station"].replace("nan", "")
+        df["Cast"] = df["Cast"].replace("nan", "")
         csv_buffer = io.StringIO()
         df.to_csv(csv_buffer, index=False)
         csv_binary = csv_buffer.getvalue().encode("utf-8")
@@ -129,7 +134,7 @@ def get_events(cls, cruise_name: str) -> FileResponse:
         try:
             cruise = Cruise.objects.get(name__iexact=cruise_name) 
             if Event.objects.filter(cruise=cruise).exists():
-                object_key = f"{cruise_name}{FILE_SUFFIX}"
+                object_key = f"{cruise_name.lower()}{FILE_SUFFIX}"
                 with MediaStore(URL, token=TOKEN) as store:
                     prefix = PrefixStore(store, MEDIASTORE_PREFIX)
                     try:
@@ -144,7 +149,27 @@ def get_events(cls, cruise_name: str) -> FileResponse:
             else:
                 raise Http404(f"Event data not imported.")    
         except Cruise.DoesNotExist:
-           raise Http404(f"Cruise {cruise_name} not found.")    
+           raise Http404(f"Cruise {cruise_name} not found.")  
+
+    @classmethod
+    def get_instruments(cls, cruise_name: str) -> List[str]:
+        URL = os.getenv("URL")
+        TOKEN = os.getenv("TOKEN")
+        MEDIASTORE_PREFIX = os.getenv("MEDIASTORE_PREFIX")
+
+        try:
+            cruise = Cruise.objects.get(name__iexact=cruise_name) 
+            if Event.objects.filter(cruise=cruise).exists():
+                events = Event.objects.filter(cruise=cruise)
+
+                # Extract unique instruments, sorted alphabetically
+                instruments = events.values_list('instrument', flat=True).distinct().order_by('instrument')
+                return list(instruments)
+            else:
+                raise Http404("Event data not imported.")
+                return []
+        except Cruise.DoesNotExist:
+            raise Http404(f"Cruise {cruise_name} not found.")    
 
 
     @classmethod
@@ -162,23 +187,28 @@ def filter_events(cls, cruise_name: str, input: FilterEventInput) -> List[EventO
                 events = events.filter(cast__iexact=input.cast)
             if input.comment:
                 events = events.filter(comment__icontains=input.comment)
+            print(events.query, flush=True)
+            print([e.id for e in events], flush=True)
+
             return [EventService.serialize_event(event) for event in events]
         except Cruise.DoesNotExist:
            raise Http404(f"Cruise {cruise_name} not found.")  
 
     @classmethod
-    def edit_events(cls, cruise_name: str, message_id: int, input: EditEventInput) -> EventOutput:
+    def edit_events(cls, cruise_name: str, r2r_event: str, input: EditEventInput) -> EventOutput:
         try:
             cruise = Cruise.objects.get(name__iexact=cruise_name) 
-            event = Event.objects.get(cruise=cruise, message_id=message_id)
+            event = Event.objects.get(cruise=cruise, r2r_event=r2r_event)
+            if input.message_id:
+                event.message_id = input.message_id
             if input.instrument:
                 event.instrument = input.instrument
             if input.action:
                 event.action = input.action
             if input.station:
                 event.station = input.station
             if input.cast:
-                event.cast = input.cast
+                event.cast = input.cast            
             if input.latitude and input.longitude:
                 event.geolocation = Point(float(input.longitude), float(input.latitude), srid=4326)    
             if input.comment:
@@ -191,6 +221,7 @@ def edit_events(cls, cruise_name: str, message_id: int, input: EditEventInput) -
             events = Event.objects.filter(cruise=cruise)
             data = [
                 {
+                    "R2R_Event": e.r2r_event,
                     MESSAGE_ID: e.message_id,
                     DATETIME: e.datetime,
                     "Instrument": e.instrument,
@@ -210,7 +241,7 @@ def edit_events(cls, cruise_name: str, message_id: int, input: EditEventInput) -
         except Cruise.DoesNotExist:
            raise Http404(f"Cruise {cruise_name} not found.")  
         except Event.DoesNotExist:
-            raise Http404(f"Event {message_id} not found for {cruise_name} .")
+            raise Http404(f"Event {r2r_event} not found for {cruise_name} .")
 
     @classmethod
     def history_events(cls, cruise_name: str) -> str:
@@ -224,6 +255,7 @@ def history_events(cls, cruise_name: str) -> str:
                         diff = record.diff_against(record.prev_record)
                         if diff.changed_fields:
                             history_data.append({
+                                'r2r_event': event.r2r_event,
                                 'message_id': event.message_id,
                                 'history_date': record.history_date,
                                 'history_user': record.history_user,

api/hplc/services.py

@@ -19,7 +19,7 @@ def get(cls, cruise_name: str) -> FileResponse:
         try:
             if cruise_name.lower() != "mvco":
                 Cruise.objects.get(name__iexact=cruise_name) 
-            object_key = f"{cruise_name}{FILE_SUFFIX}"
+            object_key = f"{cruise_name.lower()}{FILE_SUFFIX}"
             with MediaStore(URL, token=TOKEN) as store:
                 prefix = PrefixStore(store, MEDIASTORE_PREFIX)
                 try:

api/nut/services.py

@@ -17,7 +17,7 @@ def get(cls, cruise_name: str) -> FileResponse:
 
         try:
             Cruise.objects.get(name__iexact=cruise_name) 
-            object_key = f"{cruise_name}{cls.FILE_SUFFIX}"
+            object_key = f"{cruise_name.lower()}{cls.FILE_SUFFIX}"
             with MediaStore(cls.URL, token=cls.TOKEN) as store:
                 prefix = PrefixStore(store, cls.MEDIASTORE_PREFIX)
                 try:

api/stations/api.py

@@ -41,7 +41,7 @@ def set_location(request, input: StationLocationInput):
     return 204
 
 
-@router.post('/add_nearest', response=AddNearestStationOutput, tags=["Users"])
+@router.post('/add_nearest', response=AddNearestStationOutput, tags=["Users"], auth=TokenAuthenticator())
 def add_nearest_station(request, input: AddNearestStationInput):
     return StationService.add_nearest_station(
         latitude=input.latitude,

api/underway/management/commands/importunderwaydata.py

@@ -6,6 +6,7 @@
 import pandas as pd
 from core.models import Cruise
 from core.models import Underway
+from core.utils import clean_column_names
 from storage.fs import FilesystemStore
 from storage.mediastore import MediaStore
 from storage.utils import PrefixStore
@@ -87,6 +88,9 @@ def handle(self, *args, **options):
                     else:
                         start_datetime = pd.to_datetime(combined_data[date_column].iloc[0])
                         end_datetime = pd.to_datetime(combined_data[date_column].iloc[-1])
+
+                    df_data = clean_column_names(combined_data)
+
                 else:
                     raise ValueError(f"Unsupported cruise type for cruise_name: {cruise_name}")
                 start_datetime = None if pd.isna(start_datetime) else self.make_aware_if_naive(start_datetime)
@@ -100,7 +104,7 @@ def handle(self, *args, **options):
                         )       
 
                 csv_buffer = StringIO()
-                combined_data.to_csv(csv_buffer, index=False)
+                df_data.to_csv(csv_buffer, index=False)
                 csv_binary = csv_buffer.getvalue().encode('utf-8')
                 # Use the put method to store the CSV in the vast media store
                 object_key = f"{cruise_name}{self.FILE_SUFFIX}"