Merge pull request #30 from WHOIGit/pandas-3.0

Removed /get from URLs

Author: joefutrelle

.github/workflows/publish-image-api.yml

@@ -3,7 +3,7 @@ on:
   push:
     branches:
       - "main"
-      - "order-by-date"
+      - "pandas-3.0"
 
 env:
   IMAGE_NAME: nes-lter-api-2

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.13-slim-bookworm
+FROM python:3.12-slim-bookworm
 
 # geospatial libraries
 RUN apt-get update && apt-get install -y binutils libproj-dev libgdal-dev libpoppler-dev git

api/core/templates/cruise_list.html

@@ -37,10 +37,10 @@ <h1><span class="emoji">{{ emoji }}</span>{{ label }}</h1>
                          style="width:24px;height:24px;vertical-align:-3px;margin-right:.35rem;border-radius:4px;">
                     Cruise Track
                 </a>
-                <a href="/api/ctd/cruises/get/{{ cruise.name|lower }}" target="_blank" class="link">
+                <a href="/api/ctd/cruises/{{ cruise.name|lower }}" target="_blank" class="link">
                     📊 Cruise Data
                 </a>
-                <a href="/api/ctd/casts/get/{{ cruise.name|lower }}" target="_blank" class="link">
+                <a href="/api/ctd/casts/{{ cruise.name|lower }}" target="_blank" class="link">
                     🪣 Casts
                 </a>
                 <a href="/api/ctd/bottles/{{ cruise.name|lower }}" target="_blank" class="link">
@@ -52,7 +52,7 @@ <h1><span class="emoji">{{ emoji }}</span>{{ label }}</h1>
                 <a href="/api/ctd/metadata/{{ cruise.name|lower }}" target="_blank" class="link">
                     🗒️ CTD Metadata
                 </a>
-                <a href="/api/events/get/{{ cruise.name|lower }}" target="_blank" class="link">
+                <a href="/api/events/{{ cruise.name|lower }}" target="_blank" class="link">
                     📅 Events
                 </a>
                 <a href="/api/events/instruments/{{ cruise.name|lower }}" target="_blank" class="link">
@@ -61,7 +61,7 @@ <h1><span class="emoji">{{ emoji }}</span>{{ label }}</h1>
                 <a href="/api/events/history/{{ cruise.name|lower }}" target="_blank" class="link">
                     🕰️ Event History
                 </a>
-                <a href="/api/underway/get/{{ cruise.name|lower }}" target="_blank" class="link">
+                <a href="/api/underway/{{ cruise.name|lower }}" target="_blank" class="link">
                     🚢 Underway Data
                 </a>
                 <a href="/api/underway/get_column_headers/{{ cruise.name|lower }}" target="_blank" class="link">

api/ctd/api.py

@@ -9,16 +9,10 @@
 
 router = Router()
 
-@router.get("/vessels/get/all", response=List[VesselOutput], tags=["Users"])
+@router.get("/vessels/all", response=List[VesselOutput], tags=["Users"])
 def get_vessels(request):
     return CtdService.get_vessels()
 
-
-@router.get("/vessels/get/{vessel_name}", response=VesselOutput, tags=["Users"])
-def get_vessel(request, vessel_name: str):
-    return CtdService.get_vessel(vessel_name)
-
-
 @router.post('/vessels/create', tags=["Admin"], auth=TokenAuthenticator())
 def create_vessel(request, input: AddVesselInput):
     try:
@@ -43,15 +37,19 @@ def delete_vessel(request, vessel_name: str):
     except ValueError as e:
         return {"status": "error", "message": str(e)}
 
-@router.get("/cruises/get/all", response=List[CruiseOutput], tags=["Users"])
-def get_cruises(request):
-    return CtdService.get_cruises()
+@router.get("/vessels/{vessel_name}", response=VesselOutput, tags=["Users"])
+def get_vessel(request, vessel_name: str):
+    return CtdService.get_vessel(vessel_name)
 
 
-@router.get("/cruises/get/{cruise_name}", response=CruiseOutput, tags=["Users"])
-def get_cruise(request, cruise_name: str):
-    return CtdService.get_cruise(cruise_name)
+@router.get("/cruises/all", response=List[CruiseOutput], tags=["Users"])
+def get_cruises(request):
+    return CtdService.get_cruises()
 
+@router.get("/cruises/readme", response=str, tags=["Users"])
+def get_cruise_readme_all(request):
+    return CtdService.get_cruise_readme_all()
+        
 @router.post('/cruises/create', tags=["Admin"], auth=TokenAuthenticator())
 def create_cruise(request, input: AddCruiseInput):
     try:
@@ -60,7 +58,6 @@ def create_cruise(request, input: AddCruiseInput):
     except ValueError as e:
         return {"status": "error", "message": str(e)}
 
-
 @router.post('/cruises/update/{cruise_name}', tags=["Admin"], auth=TokenAuthenticator())
 def update_cruise(request, cruise_name: str, input: UpdateCruiseInput):
     try:
@@ -78,22 +75,14 @@ def delete_cruise(request, cruise_name: str):
     except ValueError as e:
         return {"status": "error", "message": str(e)}
 
+@router.get("/cruises/{cruise_name}", response=CruiseOutput, tags=["Users"])
+def get_cruise(request, cruise_name: str):
+    return CtdService.get_cruise(cruise_name)
+
 @router.get("/cruises/readme/{cruise_name}", response=str, tags=["Users"])
 def get_cruise_readme(request, cruise_name: str):
     return CtdService.get_cruise_readme(cruise_name)
 
-@router.get("/cruises/readme", response=str, tags=["Users"])
-def get_cruise_readme_all(request):
-    return CtdService.get_cruise_readme_all()
-        
-@router.get("/casts/get/{cruise_name}", response=List[CastOutput], tags=["Users"])
-def get_casts(request, cruise_name: str):
-    return CtdService.get_casts(cruise_name)
-
-
-@router.get("/cast/get/{cruise_name}/{cast_number}", tags=["Users"])
-def get_cast(request, cruise_name: str, cast_number: str):
-    return CtdService.get_cast(cruise_name, cast_number)
 
 @router.post('/casts/create', tags=["Admin"], auth=TokenAuthenticator())
 def create_cast(request, input: CastInput):
@@ -111,15 +100,22 @@ def update_cast(request, cruise_name: str, cast_number: str, input: UpdateCastIn
     except ValueError as e:
         return {"status": "error", "message": str(e)}
 
-
 @router.delete('/casts/delete/{cruise_name}/{cast_number}', tags=["Admin"], auth=TokenAuthenticator())
 def delete_cast(request, cruise_name: str, cast_number: str):
     try:
         result = CtdService.delete_cast(cruise_name, cast_number)
         return result
     except ValueError as e:
         return {"status": "error", "message": str(e)}
+
+@router.get("/casts/{cruise_name}", response=List[CastOutput], tags=["Users"])
+def get_casts(request, cruise_name: str):
+    return CtdService.get_casts(cruise_name)
 
+@router.get("/cast/{cruise_name}/{cast_number}", tags=["Users"])
+def get_cast(request, cruise_name: str, cast_number: str):
+    return CtdService.get_cast(cruise_name, cast_number)
+
 
 @router.post('/niskins/create', tags=["Admin"], auth=TokenAuthenticator())
 def create_niskin(request, input: NiskinInput):
@@ -129,18 +125,14 @@ def create_niskin(request, input: NiskinInput):
     except ValueError as e:
         return {"status": "error", "message": str(e)}
 
-
-
-@router.get("/niskins/get/all/{cruise_name}/{cast_number}", response=List[NiskinOutput], tags=["Users"])
+@router.get("/niskins/all/{cruise_name}/{cast_number}", response=List[NiskinOutput], tags=["Users"])
 def get_niskins(request, cruise_name: str, cast_number: str):
     return CtdService.get_niskins(cruise_name, cast_number)
 
-
-@router.get("/niskins/get/{cruise_name}/{cast_number}/{niskin_number}", response=NiskinOutput, tags=["Users"])
+@router.get("/niskins/{cruise_name}/{cast_number}/{niskin_number}", response=NiskinOutput, tags=["Users"])
 def get_niskin(request, cruise_name: str, cast_number: str, niskin_number: int):
     return CtdService.get_niskin(cruise_name, cast_number, niskin_number)
 
-
 @router.post('/niskins/update/{cruise_name}/{cast_number}/{niskin_number}', tags=["Admin"], auth=TokenAuthenticator())
 def update_niskin(request, cruise_name: str, cast_number: str, niskin_number: str, input: UpdateNiskinInput):
     try:
@@ -157,6 +149,7 @@ def delete_niskin(request, cruise_name: str, cast_number: str, niskin_number: in
     except ValueError as e:
         return {"status": "error", "message": str(e)}
 
+
 @router.get("/bottles/{cruise_name}", tags=["Users"])
 def get_bottles(request, cruise_name: str):
     return CtdService.get_bottles(cruise_name)

api/events/api.py

@@ -7,7 +7,7 @@
 
 router = Router()
 
-@router.get("/get/{cruise_name}", tags=["Users"])
+@router.get("/{cruise_name}", tags=["Users"])
 def get_events(request, cruise_name: str):
     return EventService.get_events(cruise_name)
 

api/nut/api.py

@@ -11,6 +11,10 @@ def getall(request):
 def get_readme(request):
     return NutService.get_readme()
 
+@router.get("/ar52_samplelog", tags=["Users"])
+def get_ar52_samplelog(request):
+    return NutService.ar52_samplelog()
+
 @router.get("/{cruise_name}", tags=["Users"])
 def get(request, cruise_name: str):
     return NutService.get(cruise_name)

api/nut/management/commands/importnut.py

@@ -233,7 +233,7 @@ def apply_flags(self, df):
             for param in DL_dict.keys():
                 if not close_rows.empty:
                     mean_value = (close_rows[param].mean() + row[param]) / 2
-                    ratio = 100 * (row[param] - mean_value) / mean_value           
+                    ratio = 100 * (row[param] - mean_value) / mean_value
                     if len(close_rows) >= 2: 
                        # Compare sample value against mean of the other rows
                        if abs(close_rows[param].mean() - row[param]) > diff_dict[param]:
@@ -246,6 +246,9 @@ def apply_flags(self, df):
                                elif abs(ratio) > 20:
                                    df.at[idx, flag_dict[param]] = 3
                            else:
+                               #if param == "silicate":
+                                   #print(len(close_rows), mean_value, flush=True)
+                                   #print(ratio,row, flush=True)
                                if abs(ratio) > 40:
                                    df.at[idx, flag_dict[param]] = 4
                                elif abs(ratio) > 15:

api/nut/services.py

@@ -2,6 +2,7 @@
 import os
 import csv
 import glob
+import pandas as pd
 from django.http import FileResponse, HttpResponse, Http404
 from core.utils import get_store
 from core.models import Cruise
@@ -73,4 +74,16 @@ def get_readme(cls) -> str:
         path = glob.glob(os.path.join(f'/vast/raw/all/nut/', 'README*'))[0]
         with open(path, 'r') as fin:
             content = fin.read()
-        return HttpResponse(content, content_type="text/plain")
+        return HttpResponse(content, content_type="text/plain")
+
+    @classmethod
+    def ar52_samplelog(cls) -> FileResponse:
+        path = "/vast/raw/all/LTER_sample_log.xlsx"
+        df = pd.read_excel(path, dtype=str)
+        cruises = {"AR52A", "AR52B"}
+        filtered = df[df["Cruise"].isin(cruises)]
+
+        # Convert to CSV
+        csv_content = filtered.to_csv(index=False)
+
+        return HttpResponse(csv_content,content_type="text/csv")

api/underway/api.py

@@ -6,7 +6,7 @@
 
 router = Router()
 
-@router.get("/get/{cruise_name}", tags=["Users"])
+@router.get("/{cruise_name}", tags=["Users"])
 def get_underway_data(request, cruise_name: str):
     return UnderwayService.get_data(cruise_name)
 

requirements.txt

@@ -2,7 +2,7 @@ django-ninja==1.5.1
 djangorestframework
 psycopg2
 django-simple-history
-pandas
+pandas==3.0
 python-dotenv
 requests
 openpyxl