Release/4.5.1 alpha

docker-compose.yml

@@ -19,6 +19,8 @@ x-ifcb-common: &ifcb-common
 services:
   ifcbdb:
     <<: *ifcb-common
+    env_file:
+      - .env
     environment:
       - NGINX_HOST=${HOST:-localhost}
       - NGINX_HTTP_PORT=${HTTP_PORT:-80}

dotenv.template

@@ -20,3 +20,4 @@ DJANGO_SECRET_KEY=changeme
 POSTGRES_PASSWORD=changeme
 
 #LOCAL_SETTINGS=./local_settings.py
+

ifcbdb/common/auth.py

@@ -0,0 +1,53 @@
+from django.contrib.auth.models import User, Group
+from dashboard.models import TeamUser
+from .constants import TeamRoles
+
+# At the moment, this is simply a wrapper around the superadmin flag. In the future, this, and possibly other
+#   methods, will be used to determine access rules based on which teams a user is associated with and what
+#   their assigned role is for that team
+def is_admin(user):
+    if not user.is_authenticated:
+        return False
+
+    return user.is_superuser
+
+# This one is also just a wrapper around the staff flag. This is likely what will be used to determine if a user
+#   has access to things "quickly" without having to check through associated teams and roles on those records
+def is_staff(user):
+    if not user.is_authenticated:
+        return False
+
+    if not user.is_staff:
+        return False
+
+    return user.is_staff
+
+
+def can_manage_teams(user):
+    if not user.is_authenticated:
+        return False
+
+    if user.is_superuser or user.is_staff:
+        return True
+
+    # Team captains have limited access to the admin to manage their own teams
+    is_team_captain = TeamUser.objects \
+        .filter(user=user) \
+        .filter(role_id=TeamRoles.CAPTAIN.value) \
+        .exists()
+    if is_team_captain:
+        return True
+
+    return False
+
+def can_access_settings(user):
+    if not user.is_authenticated:
+        return False
+
+    if user.is_superuser or user.is_staff:
+        return True
+
+    if can_manage_teams(user):
+        return True
+
+    return False

ifcbdb/common/constants.py

@@ -0,0 +1,11 @@
+from enum import Enum
+
+class TeamRoles(Enum):
+    CAPTAIN = 1
+    MANAGER = 2
+    USER = 3
+
+# Values for this enum should map to their environment variable names
+class Features(Enum):
+    TEAMS = "Teams"
+

ifcbdb/dashboard/accession.py

@@ -61,17 +61,21 @@ def scan(self):
                 continue # skip and continue searching
             directory = ifcb.DataDirectory(dd.path)
             for b in directory:
-                yield b
+                yield (b, dd)
     def sync_one(self, pid):
         bin = None
+        dd_found = None
         for dd in self.dataset.directories.filter(kind=DataDirectory.RAW).order_by('priority'):
             if not os.path.exists(dd.path):
                 continue # skip and continue searching
             directory = ifcb.DataDirectory(dd.path)
             try:
                 bin = directory[pid]
+                dd_found = dd
             except KeyError:
                 continue
+            if bin is not None:
+                break
         if bin is None:
             return 'bin {} not found'.format(pid)
         # create instrument if necessary
@@ -86,11 +90,12 @@ def sync_one(self, pid):
             'timestamp': timestamp,
             'sample_time': timestamp,
             'instrument': instrument,
+            'path': os.path.splitext(bin.fileset.adc_path)[0], # path without extension
+            'data_directory': dd_found,
             'skip': True, # in case accession is interrupted
         })
-        if not created and not self.dataset in b.datasets:
-            self.dataset.bins.add(b)
-            return 
+        if not created:
+            return
         b2s, error = self.add_bin(bin, b)
         if error is not None:
             # there was an error. if we created a bin, delete it
@@ -115,13 +120,14 @@ def sync(self, progress_callback=do_nothing, log_callback=do_nothing):
         start_time = self.start_time()
         errors = {}
         while True:
-            bins = list(islice(scanner, self.batch_size))
-            if not bins:
+            bin_dds = list(islice(scanner, self.batch_size))
+            if not bin_dds:
                 break
-            total_bins += len(bins)
+            total_bins += len(bin_dds)
             # create instrument(s)
             instruments = {} # keyed by instrument number
-            for bin in bins:
+            for bin_dd in bin_dds:
+                bin, dd = bin_dd
                 i = bin.pid.instrument
                 if not i in instruments:
                     version = bin.pid.schema_version
@@ -132,7 +138,8 @@ def sync(self, progress_callback=do_nothing, log_callback=do_nothing):
             # create bins
             then = time.time()
             bins2save = []
-            for bin in bins:
+            for bin_dd in bin_dds:
+                bin, dd = bin_dd
                 pid = bin.lid
                 most_recent_bin_id = pid
                 log_callback('{} found'.format(pid))
@@ -144,10 +151,11 @@ def sync(self, progress_callback=do_nothing, log_callback=do_nothing):
                     'timestamp': timestamp,
                     'sample_time': timestamp,
                     'instrument': instrument,
+                    'path': os.path.splitext(bin.fileset.adc_path)[0], # path without extension
+                    'data_directory': dd,
                     'skip': True, # in case accession is interrupted
                 })
                 if not created:
-                    self.dataset.bins.add(b)
                     continue
                 b2s, error = self.add_bin(bin, b)
                 if error is not None:
@@ -200,6 +208,9 @@ def add_bin(self, bin, b): # IFCB bin, Bin instance
         except Exception as e:
             b.qc_bad = True
             return b, 'ml_analyzed: {}'.format(str(e))
+        # paths
+        if b.path is None:
+            b.path, _ = os.path.splitext(bin.fileset.adc_path)
         # metadata
         try:
             headers = bin.hdr_attributes

ifcbdb/dashboard/management/commands/bintool.py

@@ -16,6 +16,7 @@ def add_arguments(self, parser):
         parser.add_argument('--sample-type', type=str, help='Sample type')
         parser.add_argument('--remove-dataset', type=str, help='Dataset name to remove filtered bins from')
         parser.add_argument('--add-dataset', type=str, help='Dataset name to add filtered bins to')
+        parser.add_argument('--cache-paths', action='store_true', help='Cache paths for filtered bins')
 
     def handle(self, *args, **options):
         dataset_name = options['dataset']
@@ -58,5 +59,9 @@ def handle(self, *args, **options):
             except Dataset.DoesNotExist:
                 self.stderr.write(f"Dataset '{add_dataset_name}' does not exist.")
 
+        if options['cache_paths']:
+            for b in bins:
+                b._get_bin() # this will cache the path if it isn't already
+
         for bin_id in bin_ids:
             self.stdout.write(bin_id)

ifcbdb/dashboard/migrations/0039_team_teamuser_teamdataset_team_datasets_team_users.py

@@ -0,0 +1,56 @@
+# Generated by Django 4.2.20 on 2025-06-04 02:42
+
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('dashboard', '0038_remove_datadirectory_unique_path_and_more'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Team',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('timestamp', models.DateTimeField(auto_now_add=True)),
+                ('name', models.CharField(max_length=50)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='TeamUser',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('team', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='dashboard.team')),
+                ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'unique_together': {('user', 'team')},
+            },
+        ),
+        migrations.CreateModel(
+            name='TeamDataset',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('dataset', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='dashboard.dataset')),
+                ('team', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='dashboard.team')),
+            ],
+            options={
+                'unique_together': {('dataset', 'team')},
+            },
+        ),
+        migrations.AddField(
+            model_name='team',
+            name='datasets',
+            field=models.ManyToManyField(related_name='teams', through='dashboard.TeamDataset', to='dashboard.dataset'),
+        ),
+        migrations.AddField(
+            model_name='team',
+            name='users',
+            field=models.ManyToManyField(related_name='teams', through='dashboard.TeamUser', to=settings.AUTH_USER_MODEL),
+        ),
+    ]

ifcbdb/dashboard/migrations/0040_teamuser_is_manager.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.21 on 2025-07-04 16:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dashboard', '0039_team_teamuser_teamdataset_team_datasets_team_users'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='teamuser',
+            name='is_manager',
+            field=models.BooleanField(default=False),
+        ),
+    ]

ifcbdb/dashboard/migrations/0041_auto_20250718_0247.py

@@ -0,0 +1,35 @@
+# Generated by Django 4.2.21 on 2025-07-18 02:47
+
+from django.db import migrations
+from common.constants import Features
+
+
+def apply_migration(apps, schema_editor):
+    Switch = apps.get_model('waffle', 'Switch')
+    Switch.objects.update_or_create(
+        name=Features.TEAMS.value,
+        defaults={
+            'active': False,
+            'note': 'Enables the teams feature'
+        }
+    )
+
+def revert_migration(apps, schema_editor):
+    try:
+        Switch = apps.get_model('waffle', 'Switch')
+        Switch.objects.filter(name=Features.TEAMS.value).delete()
+    except LookupError:
+        # Waffle isn't installed
+        pass
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dashboard', '0040_teamuser_is_manager'),
+        ('waffle', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.RunPython(apply_migration, revert_migration),
+    ]

ifcbdb/dashboard/migrations/0042_teamrole_remove_teamuser_is_manager.py

@@ -0,0 +1,24 @@
+# Generated by Django 4.2.21 on 2025-07-18 03:45
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dashboard', '0041_auto_20250718_0247'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='TeamRole',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=50)),
+            ],
+        ),
+        migrations.RemoveField(
+            model_name='teamuser',
+            name='is_manager',
+        ),
+    ]

ifcbdb/dashboard/migrations/0043_auto_20250718_0346.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.2.21 on 2025-07-18 03:46
+
+from django.db import migrations
+from common.constants import TeamRoles
+
+
+def apply_migration(apps, schema_editor):
+    TeamRole = apps.get_model('dashboard', 'TeamRole')
+    TeamRole.objects.bulk_create([
+        TeamRole(id=TeamRoles.CAPTAIN.value, name="Captain"),
+        TeamRole(id=TeamRoles.MANAGER.value, name="Manager"),
+        TeamRole(id=TeamRoles.USER.value, name="User"),
+    ])
+
+def revert_migration(apps, schema_editor):
+    TeamRole = apps.get_model('dashboard', 'TeamRole')
+    TeamRole.objects.filter(id__in=[
+        TeamRoles.CAPTAIN.value,
+        TeamRoles.MANAGER.value,
+        TeamRoles.USER.value
+    ]).delete()
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dashboard', '0042_teamrole_remove_teamuser_is_manager'),
+    ]
+
+    operations = [
+        migrations.RunPython(apply_migration, revert_migration),
+    ]

ifcbdb/dashboard/migrations/0044_teamuser_role.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.2.21 on 2025-07-18 03:54
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dashboard', '0043_auto_20250718_0346'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='teamuser',
+            name='role',
+            field=models.ForeignKey(default=3, on_delete=django.db.models.deletion.CASCADE, to='dashboard.teamrole'),
+        ),
+    ]