Integrate tissues app

src/datasets_synchronization/admin.py

@@ -5,8 +5,9 @@
 
 class CGDSStudyAdmin(admin.ModelAdmin):
     list_display = ('name', 'description', 'version', 'date_last_synchronization', 'state')
-    list_filter = ('state',)
+    list_filter = ('state', 'tissues')
     search_fields = ('name', 'description')
+    filter_horizontal = ('tissues',)
 
     def delete_queryset(self, request, queryset):
         """

src/datasets_synchronization/migrations/0037_cgdsstudy_tissue.py

@@ -0,0 +1,28 @@
+# Generated by Django 4.2.19 on 2026-02-23 00:20
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("tissues", "0001_initial"),
+        (
+            "datasets_synchronization",
+            "0036_alter_cgdsstudy_clinical_patient_dataset_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="cgdsstudy",
+            name="tissue",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                to="tissues.tissue",
+            ),
+        ),
+    ]

src/datasets_synchronization/migrations/0038_remove_cgdsstudy_tissue_cgdsstudy_tissues.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.2.19 on 2026-03-05 22:27
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("tissues", "0002_tissue_code_and_initial_data"),
+        ("datasets_synchronization", "0037_cgdsstudy_tissue"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="cgdsstudy",
+            name="tissue",
+        ),
+        migrations.AddField(
+            model_name="cgdsstudy",
+            name="tissues",
+            field=models.ManyToManyField(blank=True, to="tissues.tissue"),
+        ),
+    ]

src/datasets_synchronization/models.py

@@ -10,6 +10,7 @@
 from common.methylation import MethylationPlatform
 from feature_selection.models import TrainedModel
 from statistical_properties.models import StatisticalValidation
+from tissues.models import Tissue
 from user_files.models import UserFile
 from user_files.models_choices import FileType
 from pandas import DataFrame
@@ -288,6 +289,7 @@ class CGDSStudy(models.Model):
         null=True,
         related_name='cgds_studies_as_clinical_sample_dataset'
     )
+    tissues = models.ManyToManyField(Tissue, blank=True)
     task_id: Optional[str] = models.CharField(max_length=100, blank=True, null=True)  # Celery Task ID
 
     def __str__(self) -> str:
@@ -327,4 +329,4 @@ def delete(self, *args, **kwargs) -> None:
                 dataset.delete()
 
             # Sends a websocket message to update the state in the frontend
-            send_update_cgds_studies_command()
+            send_update_cgds_studies_command()

src/datasets_synchronization/serializers.py

@@ -224,9 +224,10 @@ def create(self, validated_data) -> Optional[CGDSStudy]:
             methylation_dataset = self.__create_cgds_dataset(validated_data.pop('methylation_dataset'))
             clinical_patient_dataset = self.__create_cgds_dataset(validated_data.pop('clinical_patient_dataset'))
             clinical_sample_dataset = self.__create_cgds_dataset(validated_data.pop('clinical_sample_dataset'))
+            tissues = validated_data.pop('tissues', [])
 
             # Creates the CGDSStudy
-            return CGDSStudy.objects.create(
+            cgds_study = CGDSStudy.objects.create(
                 mrna_dataset=mrna_dataset,
                 mirna_dataset=mirna_dataset,
                 cna_dataset=cna_dataset,
@@ -235,6 +236,8 @@ def create(self, validated_data) -> Optional[CGDSStudy]:
                 clinical_sample_dataset=clinical_sample_dataset,
                 **validated_data
             )
+            cgds_study.tissues.set(tissues)
+            return cgds_study
 
     @staticmethod
     def __set_clinical_datasets_to_existing_experiments(cgds_study: CGDSStudy):
@@ -302,6 +305,10 @@ def update(self, instance: CGDSStudy, validated_data):
             instance.clinical_patient_dataset = clinical_patient_dataset
             instance.clinical_sample_dataset = clinical_sample_dataset
 
+            # Updates M2M tissues if provided
+            if 'tissues' in validated_data:
+                instance.tissues.set(validated_data['tissues'])
+
             # Saves new changes and returns instance
             instance.save()
             return instance

src/datasets_synchronization/views.py

@@ -13,6 +13,7 @@
 from .enums import SyncCGDSStudyResponseCode, SyncStrategy
 from .models import CGDSStudy, CGDSDatasetSynchronizationState, CGDSStudySynchronizationState, CGDSDataset
 from rest_framework import generics, permissions, filters
+from django_filters.rest_framework import DjangoFilterBackend
 from user_files.models_choices import FileType
 from .serializers import CGDSStudySerializer
 from django.shortcuts import render, get_object_or_404
@@ -82,7 +83,8 @@ def get_queryset(self):
     serializer_class = CGDSStudySerializer
     permission_classes = [permissions.IsAuthenticated]
     pagination_class = StandardResultsSetPagination
-    filter_backends = [filters.OrderingFilter, filters.SearchFilter]
+    filter_backends = [filters.OrderingFilter, filters.SearchFilter, DjangoFilterBackend]
+    filterset_fields = ['tissues']
     search_fields = ['name', 'description']
     ordering_fields = '__all__'
 

src/frontend/templates/frontend/base.html

@@ -48,6 +48,7 @@
         const urlTagsCRUD = "{% url 'tags' %}" {# REST CRUD URL User Tags #}
         const urlUserFilesCRUD = "{% url 'user_files' %}" {# REST CRUD URL User Files #}
         const urlCGDSStudiesCRUD = "{% url 'cgds_studies' %}" {# URL CGDS Studies #}
+        const urlTissuesCRUD = "{% url 'tissues' %}" {# REST URL for Tissues list #}
         const urlCurrentUser = "{% url 'current_user' %}" {# URL to get the current logged user #}
         const urlSitePolicy = "{% url 'site_policy' %}" {# URL to Site policy page #}
         const urlCGDSPanel = "{% url 'cgds_panel' %}" {# URL to the CGDS Panel #}

src/multiomics_intermediate/settings.py

@@ -63,6 +63,7 @@
     'molecules_details',
     'chunked_upload',
     'users',
+    'tissues',
 ]
 
 MIDDLEWARE = [

src/multiomics_intermediate/urls.py

@@ -38,4 +38,5 @@
     path('admin/', admin.site.urls),
     path('email/', include(mail_urls)),
     path('users/', include('users.urls')),
+    path('tissues/', include('tissues.urls')),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)

src/tissues/admin.py

@@ -0,0 +1,17 @@
+from django.contrib import admin
+from .models import Tissue
+
+
+@admin.register(Tissue)
+class TissueAdmin(admin.ModelAdmin):
+    list_display = ('id', 'name')
+    search_fields = ('name',)
+
+    def has_add_permission(self, request):
+        return False
+
+    def has_change_permission(self, request, obj=None):
+        return False
+
+    def has_delete_permission(self, request, obj=None):
+        return False

src/tissues/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class TissuesConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "tissues"

src/tissues/migrations/0001_initial.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.2.19 on 2026-02-23 00:19
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = []
+
+    operations = [
+        migrations.CreateModel(
+            name="Tissue",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("name", models.CharField(max_length=100, unique=True)),
+            ],
+            options={
+                "ordering": ["name"],
+            },
+        ),
+    ]

src/tissues/migrations/0002_tissue_code_and_initial_data.py

@@ -0,0 +1,57 @@
+from django.db import migrations, models
+
+TISSUES = [
+    ('Adrenal Gland', 'ADRENAL_GLAND'),
+    ('Bladder', 'BLADDER'),
+    ('Blood', 'BLOOD'),
+    ('Brain', 'BRAIN'),
+    ('Breast', 'BREAST'),
+    ('Cervix Uteri', 'CERVIX_UTERI'),
+    ('Colon', 'COLON'),
+    ('Esophagus', 'ESOPHAGUS'),
+    ('Kidney', 'KIDNEY'),
+    ('Liver', 'LIVER'),
+    ('Lung', 'LUNG'),
+    ('Ovary', 'OVARY'),
+    ('Pancreas', 'PANCREAS'),
+    ('Prostate', 'PROSTATE'),
+    ('Skin', 'SKIN'),
+    ('Stomach', 'STOMACH'),
+    ('Testis', 'TESTIS'),
+    ('Thyroid', 'THYROID'),
+    ('Uterus', 'UTERUS'),
+]
+
+
+def load_tissues(apps, schema_editor):
+    Tissue = apps.get_model('tissues', 'Tissue')
+    Tissue.objects.bulk_create([Tissue(name=name, code=code) for name, code in TISSUES])
+
+
+def unload_tissues(apps, schema_editor):
+    Tissue = apps.get_model('tissues', 'Tissue')
+    Tissue.objects.filter(name__in=[name for name, _ in TISSUES]).delete()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('tissues', '0001_initial'),
+    ]
+
+    operations = [
+        # Add code field as nullable first (so existing rows don't violate constraints)
+        migrations.AddField(
+            model_name='tissue',
+            name='code',
+            field=models.CharField(max_length=100, null=True, blank=True),
+        ),
+        # Insert the 19 English tissues (table is empty at this point in migration history)
+        migrations.RunPython(load_tissues, reverse_code=unload_tissues),
+        # Make code non-nullable and unique
+        migrations.AlterField(
+            model_name='tissue',
+            name='code',
+            field=models.CharField(max_length=100, unique=True),
+        ),
+    ]

src/tissues/models.py

@@ -0,0 +1,17 @@
+from django.core.exceptions import PermissionDenied
+from django.db import models
+
+
+class Tissue(models.Model):
+    """Reference model for tissue types. Tissues are read-only and cannot be deleted."""
+    name = models.CharField(max_length=100, unique=True)
+    code = models.CharField(max_length=100, unique=True)  # noqa: populated by migration 0003
+
+    class Meta:
+        ordering = ['name']
+
+    def __str__(self) -> str:
+        return self.name
+
+    def delete(self, *args, **kwargs):
+        raise PermissionDenied("Tissues cannot be deleted")

src/tissues/serializers.py

@@ -0,0 +1,8 @@
+from rest_framework import serializers
+from .models import Tissue
+
+
+class TissueSerializer(serializers.ModelSerializer):
+    class Meta:
+        model = Tissue
+        fields = ['id', 'name', 'code']

src/tissues/urls.py

@@ -0,0 +1,6 @@
+from django.urls import path
+from . import views
+
+urlpatterns = [
+    path('', views.TissueList.as_view(), name='tissues'),
+]

src/tissues/views.py

@@ -0,0 +1,12 @@
+from rest_framework import generics, permissions, filters
+from .models import Tissue
+from .serializers import TissueSerializer
+
+
+class TissueList(generics.ListAPIView):
+    """REST endpoint: read-only list for Tissue model."""
+    queryset = Tissue.objects.all()
+    serializer_class = TissueSerializer
+    permission_classes = [permissions.IsAuthenticated]
+    filter_backends = [filters.SearchFilter]
+    search_fields = ['name']

src/user_files/admin.py

@@ -4,9 +4,15 @@
 
 class UserFileAdmin(admin.ModelAdmin):
     list_display = ('name', 'description', 'file_type', 'upload_date', 'contains_nan_values', 'number_of_rows',
-                    'number_of_samples', 'decimal_separator', 'is_public', 'is_cpg_site_id', 'platform')
-    list_filter = ('file_type', 'upload_date', 'is_public', 'is_cpg_site_id')
+                    'number_of_samples', 'decimal_separator', 'is_public', 'is_cpg_site_id', 'platform',
+                    'tissue_list')
+    list_filter = ('file_type', 'upload_date', 'is_public', 'is_cpg_site_id', 'tissues')
     search_fields = ('name', 'description', 'user__username')
+    filter_horizontal = ('tissues',)
+
+    def tissue_list(self, obj):
+        return ', '.join(obj.tissues.values_list('name', flat=True))
+    tissue_list.short_description = 'Tissues'
 
 
 admin.site.register(UserFile, UserFileAdmin)

src/user_files/migrations/0016_userfile_tissue.py

@@ -0,0 +1,25 @@
+# Generated by Django 4.2.19 on 2026-02-23 00:20
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("tissues", "0001_initial"),
+        ("user_files", "0015_alter_userfile_options"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="userfile",
+            name="tissue",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                to="tissues.tissue",
+            ),
+        ),
+    ]

src/user_files/migrations/0017_remove_userfile_tissue_userfile_tissues.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.2.19 on 2026-03-05 22:27
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("tissues", "0002_tissue_code_and_initial_data"),
+        ("user_files", "0016_userfile_tissue"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="userfile",
+            name="tissue",
+        ),
+        migrations.AddField(
+            model_name="userfile",
+            name="tissues",
+            field=models.ManyToManyField(blank=True, to="tissues.tissue"),
+        ),
+    ]