Merge pull request #58 from omics-datascience/swagger

Swagger UI

ModulectorBackend/settings.py

@@ -13,7 +13,7 @@
 import os
 
 # Modulector version
-VERSION: str = '2.2.0'
+VERSION: str = '2.2.1'
 
 # Default primary key field type
 # https://docs.djangoproject.com/en/4.0/ref/settings/#default-auto-field
@@ -53,7 +53,9 @@
     'modulector.apps.ModulectorConfig',
     'rest_framework',
     'django_filters',
-    'django_generate_secret_key'
+    'django_generate_secret_key',
+    'drf_spectacular',
+    'drf_spectacular_sidecar'
 ]
 
 CRONJOBS = [
@@ -78,8 +80,34 @@
     # 'DEFAULT_PERMISSION_CLASSES': (
     #  'rest_framework.permissions.DjangoModelPermissions',
     # )
+    'DEFAULT_SCHEMA_CLASS': 'drf_spectacular.openapi.AutoSchema',
+    'DEFAULT_AUTHENTICATION_CLASSES': [],
+    'DEFAULT_PERMISSION_CLASSES': []
 }
 
+SPECTACULAR_SETTINGS = {
+    'TITLE': 'Modulector',
+    'DESCRIPTION': """
+### An open platform which provides information about methylation sites, miRNAs and genes from different popular databases.  
+The platform is part of the Multiomix project. For more information, visit our [website](https://omicsdatascience.org/).
+To contribute: [OmicsDatascience](https://github.com/omics-datascience/modulector)""",
+    'VERSION': VERSION,
+    'SERVE_INCLUDE_SCHEMA': False,
+    'SWAGGER_UI_DIST': 'SIDECAR', 
+    'SWAGGER_UI_FAVICON_HREF': 'SIDECAR',
+    'REDOC_DIST': 'SIDECAR',
+    'SCHEMA_PATH_PREFIX': '/api/',
+    'SWAGGER_UI_SETTINGS': {
+            'defaultModelsExpandDepth': -1, 
+            'displayRequestDuration': False,
+            'docExpansion': 'none',
+            'filter': False,
+            'showExtensions': True,
+            'showCommonExtensions': True,
+    }
+}
+
+
 ROOT_URLCONF = 'ModulectorBackend.urls'
 
 TEMPLATES = [

ModulectorBackend/settings_prod.py

@@ -18,6 +18,7 @@
 
 # Disables Django REST Framework browsable API (in production only)
 REST_FRAMEWORK = {
+    'DEFAULT_SCHEMA_CLASS': 'drf_spectacular.openapi.AutoSchema',
     'DEFAULT_RENDERER_CLASSES': (
         'rest_framework.renderers.JSONRenderer',
     )

ModulectorBackend/urls.py

@@ -1,8 +1,13 @@
 from django.contrib import admin
 from django.urls import path
 from modulector import views
+from drf_spectacular.views import SpectacularAPIView, SpectacularRedocView, SpectacularSwaggerView
+
 
 urlpatterns = [
+    path('api/schema/', SpectacularAPIView.as_view(), name='schema'),
+    path('api/schema/swagger-ui/', SpectacularSwaggerView.as_view(url_name='schema'), name='swagger-ui'),
+    path('api/schema/redoc/', SpectacularRedocView.as_view(url_name='schema'), name='redoc'),
     path('admin/', admin.site.urls),
     path('mirna/', views.MirnaList.as_view({'get': 'list'}), name='mirna'),
     path('mirna-target-interactions/', views.MirnaTargetInteractions.as_view(),

README.md

@@ -53,7 +53,7 @@ Modulector obtains information from different bioinformatics databases or resour
 
 Modulector can be used through the graphical interfaces provided in [Multiomix][multiomix-site], or it can be hosted on your server (read [DEPLOYING.md](DEPLOYING.md) for more information). We strongly recommend using this software through the Multiomix application.
 
-All services are available through a web API accessible from a browser or any other web client. All the responses are in JSON format. In addition to the information provided, sorting, filtering, searching, and paging functions are also available. How to use these functions is explained below:
+All services are available through a web API accessible from a browser or web client, or you can try Modulector from its [Swagger interface](https://modulector.multiomix.org/api/schema/swagger-ui/). All the responses are in JSON format. In addition to the information provided, sorting, filtering, searching, and paging functions are also available. How to use these functions is explained below:
 
 
 ### General

config/requirements.txt

@@ -5,6 +5,8 @@ django-filter==23.3
 django-generate-secret-key==1.0.2
 django-stubs==4.2.7
 djangorestframework==3.14.0
+drf-spectacular==0.28.0
+drf-spectacular-sidecar==2024.12.1
 mypy==1.9.0
 pandas==2.1.2
 psycopg2-binary==2.9.9

docker-compose_dist.yml

@@ -29,7 +29,7 @@ services:
 
     # Django Backend Server
     web_modulector:
-        image: omicsdatascience/modulector:2.2.0
+        image: omicsdatascience/modulector:2.2.1
         restart: always
         depends_on:
             - db_modulector

modulector/serializers.py

@@ -48,7 +48,7 @@ class Meta:
         model = MirnaXGene
         fields = ['id', 'mirna', 'gene', 'score',
                   'source_name', 'pubmeds', 'sources', 'score_class']
-
+    
     def get_pubmeds(self, mirna_gene_interaction: MirnaXGene) -> Set[str]:
         """
         Gets a list of related Pubmed URLs to a miRNA-Gene interaction.

modulector/templates/index.html

@@ -41,5 +41,7 @@ <h2>Modulector v{{ version }}</h2>
         <a href="{% url 'methylation_sites_to_genes' %}">Illumina Methylation Sites to Genes</a>
     </li>
 </ul>
+<h3>You can use modulector features from the <a href="/api/schema/swagger-ui/" target="_blank">documentation</a> in Swagger</h3>
+<h3><a href="/api/schema/redoc/" target="_blank">Documentation</a> in Redoc</h3>
 </body>
 </html>