Ctd case sensitive filenames

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

@@ -3,7 +3,7 @@ on:
   push:
     branches:
       - "main"
-      - "test-bucketstore"
+      - "ctd-case-sensitive-filenames"
 
 env:
   IMAGE_NAME: nes-lter-api-2

api/core/migrations/0013_alter_cruise_type.py

@@ -0,0 +1,18 @@
+# Generated by Django 6.0.5 on 2026-06-09 20:18
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('core', '0012_alter_cruise_type'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='cruise',
+            name='type',
+            field=models.CharField(choices=[('NESLTER', 'Neslter'), ('JP Student', 'Jp Student'), ('OOI NES', 'Ooi Nes'), ('OOI MAB', 'Ooi Mab'), ('Opportunistic', 'Opportunistic')], default='NESLTER', max_length=32),
+        ),
+    ]

api/core/migrations/0014_alter_cruise_type.py

@@ -0,0 +1,18 @@
+# Generated by Django 6.0.6 on 2026-06-17 19:57
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('core', '0013_alter_cruise_type'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='cruise',
+            name='type',
+            field=models.CharField(choices=[('NES-LTER', 'Neslter'), ('JP Student', 'Jp Student'), ('OOI-NES', 'Ooi Nes'), ('OOI-MAB', 'Ooi Mab'), ('Opportunistic', 'Opportunistic')], default='NES-LTER', max_length=32),
+        ),
+    ]

api/core/models.py

@@ -160,9 +160,10 @@ def __str__(self):
 
 class Cruise(models.Model):
     class CruiseType(models.TextChoices):
-        NESLTER = "NESLTER"
+        NESLTER = "NES-LTER"
         JP_STUDENT = "JP Student"
-        OOI_PIONEER = "OOI Pioneer"
+        OOI_NES = "OOI-NES"   # pioneer
+        OOI_MAB = "OOI-MAB"   # pioneer
         OPPORTUNISTIC = "Opportunistic"
 
     name = models.CharField(max_length=100, unique=True) # e.g. "EN627"

api/core/templates/upload.html

@@ -56,6 +56,7 @@ <h1>📂 Drag and Drop Your Files</h1>
                     <option value="nutrient">LTERnut.xlsx</option>
                     <option value="sample_log">LTER_sample_log.xlsx</option>
                     <option value="station_list">NES-LTER_station_list_compilation.xlsx</option>
+                    <option value="cruise_types">NES-LTER_cruise_types.csv</option>
                     <option value="hplc">Sosik*report.xlsx</option>
                     <option value="chlorophyll">NESLTERchl.xlsx</option>
                 </select>

api/core/views.py

@@ -31,6 +31,7 @@ def file_upload_view(request):
                 'nutrient': Path('/data/raw/all/nut'),
                 'sample_log': Path('/data/raw/all'),
                 'station_list' : Path('/data/raw/all/metadata'),
+                'cruise_types' : Path('/data/raw/all/metadata'),
                 'hplc' : Path('/data/raw/all/hplc'),
                 'chlorophyll': Path('/data/raw/all/chl'),
             }
@@ -42,6 +43,7 @@ def file_upload_view(request):
                 'nutrient': Path('/vast/raw/all/nut'),
                 'sample_log': Path('/vast/raw/all'),
                 'station_list' : Path('/vast/raw/all/metadata'),
+                'cruise_types' : Path('/vast/raw/all/metadata'),
                 'hplc' : Path('/vast/raw/all/hplc'),
                 'chlorophyll': Path('/vast/raw/all/chl'),
             }    
@@ -101,6 +103,7 @@ def file_upload_view(request):
             'nutrient' : ['importnut'],
             'sample_log' : ['importnut'],
             'station_list' : ['importstations'],
+            'cruise_types' : ['importcruise'],
             'hplc' : ['importhplc'],
             'chlorophyll' : ['importchl']
         }
@@ -267,7 +270,8 @@ def cruises_for_season(request, season: str):
 TYPE_PREFIXES = [
     (Cruise.CruiseType.NESLTER,  "NESLTER",  "🚢"),
     (Cruise.CruiseType.JP_STUDENT,  "JP Student",  "🛳️"),
-    (Cruise.CruiseType.OOI_PIONEER, "OOI Pioneer", "🛥️"),
+    (Cruise.CruiseType.OOI_NES, "OOI NES", "🛥️"),
+    (Cruise.CruiseType.OOI_MAB, "OOI MAB", "⛴️"),
     (Cruise.CruiseType.OPPORTUNISTIC, "Opportunistic", "⛵"),
 ]
 

api/ctd/management/commands/importall.py

@@ -42,6 +42,10 @@ def handle(self, *args, **options):
                 logger.error("Importing underway data...")
                 call_command('importunderwaydata', cruise_name=cruise_name)
 
+                self.stdout.write("Importing cruises again to set missing cruise start and end times from underway")
+                logger.error("Importing cruises again to set missing cruise start and end times from underway...")
+                call_command('importcruise', cruise_name=cruise_name)
+
                 self.stdout.write("Importing casts...")
                 logger.error("Importing casts...")
                 call_command('importcast', cruise_name=cruise_name)

api/ctd/management/commands/importcast.py

@@ -54,14 +54,19 @@ def parse_asc_fixed_width(self, asc_path):
 
     def create_cast_file(self, file, cruise, cast, time):
         delimiter = ';'
-        base_dir = os.path.dirname(file.name)
-        base_name = os.path.splitext(os.path.basename(file.name))[0]
+        hdr_path = Path(file)
+        base_dir = hdr_path.parent
+        base_name = hdr_path.stem.lower()
 
-        # Look for matching .asc file (case-sensitive)
+        # Look for matching .asc file, regardless of filename case
         ascfile = None
-        for f in os.listdir(base_dir):
-            if f.lower() == f"{base_name.lower()}.asc":
-                ascfile = os.path.join(base_dir, f)
+        for f in base_dir.iterdir():
+            if (
+                f.is_file()
+                and f.stem.lower() == base_name
+                and f.suffix.lower() == ".asc"
+            ):
+                ascfile = f
                 break
 
         if not ascfile:
@@ -110,14 +115,13 @@ def create_cast_file(self, file, cruise, cast, time):
             self.logger.error((f"{ascfile} not parsable."))
 
     def handle(self, *args, **options):
-        #self.stdout = options.get('stdout', sys.stdout) # removes /n's
         cruise_name = options['cruise_name']
 
         if cruise_name is None:
             parent_dir = Path('/vast/raw')
             cruises = [f.name for f in parent_dir.iterdir() if f.is_dir() and f.name != "all"]
         else:
-            cruises = [cruise_name]
+            cruises = [cruise_name.lower()]
 
         self.stdout.write(self.style.SUCCESS(f'For each .hdr file, look for a matching .asc file.'))
         self.logger.error((f'For each .hdr file, look for a matching .asc file.'))
@@ -127,7 +131,7 @@ def handle(self, *args, **options):
                 cruise = Cruise.objects.get(name__iexact=cruise_name)
                 directory = f'/vast/raw/{cruise_name}/ctd/'
                 hdr_files = sorted(glob.glob(os.path.join(directory, '*.hdr')))
-                if cruise_name.lower() == "en627":
+                if cruise_name == "en627":
                     added_dir = os.path.join(directory, "cast_1_files_used_for_corrected_cast_2")
                     hdr_files += sorted(glob.glob(os.path.join(added_dir, '*.hdr')))
 
@@ -148,12 +152,12 @@ def handle(self, *args, **options):
                         cast = cast.lstrip('0')
 
                         # get lat, lon and time from .hdr file
-                        with open(file, 'r', encoding='utf-8', errors='ignore') as file:
-                            content = file.read()
+                        with open(file, "r", encoding="utf-8", errors="ignore") as fh:
+                            content = fh.read()
 
                         latitude, longitude = parse_lat_lon(content)
                         start_time = parse_time(content)
-                        
+
                         if latitude != None and longitude != None and start_time != None:
                             Cast.objects.update_or_create(
                                 cruise=cruise,