Merge branch 'master' of https://github.com/RNAcentral/rnacentral-web…

…code into update-gunicorn

rnacentral/apiv1/views.py

@@ -48,6 +48,7 @@
 from django.http import Http404, HttpResponse
 from django.shortcuts import get_object_or_404
 from django_filters import rest_framework as filters
+from drf_spectacular.utils import extend_schema
 from portal.config.expert_databases import expert_dbs
 from portal.models import (
     Accession,
@@ -109,6 +110,7 @@ def get_database(region):
     return providing_databases
 
 
+@extend_schema(exclude=True)
 class GenomeAnnotations(APIView):
     """
     Ensembl-like genome coordinates endpoint.
@@ -182,6 +184,7 @@ def get(self, request, species, chromosome, start, end, format=None):
         return Response(features)
 
 
+@extend_schema(exclude=True)
 class APIRoot(APIView):
     """
     This is the root of the RNAcentral API Version 1.
@@ -457,6 +460,7 @@ def get_queryset(self):
         return Rna.objects.get(upi=upi).get_xrefs(taxid=taxid)
 
 
+@extend_schema(exclude=True)
 class SecondaryStructureSpeciesSpecificList(generics.ListAPIView):
     """
     List of secondary structures for a particular RNA sequence in a specific species.
@@ -630,7 +634,12 @@ class CitationsView(generics.ListAPIView):
 
     def get_queryset(self):
         pk = self.kwargs["pk"]
-        return Accession.objects.select_related().get(pk=pk).refs.all()
+        try:
+            citations = Accession.objects.select_related().get(pk=pk).refs.all()
+        except Accession.DoesNotExist:
+            citations = Accession.objects.none()
+
+        return citations
 
 
 class RnaPublicationsView(generics.ListAPIView):
@@ -691,6 +700,7 @@ def _normalize_expert_db_label(expert_db_label):
     #     return Database.objects.get(expert_db_name).references
 
 
+@extend_schema(exclude=True)
 class ExpertDatabasesStatsViewSet(RetrieveModelMixin, ListModelMixin, GenericViewSet):
     """
     API endpoint with statistics of databases, comprising RNAcentral.

rnacentral/portal/templates/portal/docs/sab.md

@@ -6,7 +6,6 @@
 [RNAcentral](/) and [Rfam](https://rfam.org) share a Scientific Advisory Board (SAB)
 which includes six RNA biologists covering a wide range of expertise from wet lab to computational research.
 
-- [Yann Ponty](http://www.lix.polytechnique.fr/~ponty/) CNRS École Politechnique, France
 - [Lovorka Stojic](https://www.bartscancer.london/staff/dr-lovorka-stojic/) Barts Centre CRUK, UK
 - [Alain Laederach](https://ribosnitch.bio.unc.edu/) UNC Chapel Hill, USA
 - [Madeline Sherlock](https://profiles.ucdenver.edu/display/20414874) New York Structural Biology Center, USA
@@ -26,4 +25,6 @@ The SAB oversees the progress of the project during annual meetings.
 - [Mihaela Zavolan](https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/) (University of Basel) *SAB member between 2016-2020*
 - [Eric Westhof](http://www-ibmc.u-strasbg.fr/upr9002/westhof/index.html) University of Strasbourg *SAB member between 2015-2021*
 - [Michelle Meyer](https://bioinformatics.bc.edu/meyerlab/) Boston College *SAB member between 2016-2021*
-- [Manja Marz](http://www.rna.uni-jena.de/members/manja-marz/) Friedrich Schiller University Jena, Germany
+- [Manja Marz](http://www.rna.uni-jena.de/members/manja-marz/) Friedrich Schiller University Jena, Germany *SAB member between 2017-2022*
+- [Yiliang Ding](https://www.jic.ac.uk/people/yilliang-ding/) John Innes Centre, UK *SAB member between 2021-2023*
+- [Yann Ponty](http://www.lix.polytechnique.fr/~ponty/) CNRS École Politechnique, France *SAB member between 2019-2024*

rnacentral/portal/templates/portal/header.html

@@ -91,6 +91,7 @@
           <ul class="dropdown-menu">
             <li><a href="{% url 'api-v1-root' %}">Browsable API</a></li>
             <li><a href="{% url 'api-docs' %}">API Documentation</a></li>
+            <li><a href="{% url 'swagger-ui' %}" target="_blank">OpenAPI Schema</a></li>
           </ul>
         </li>
 

rnacentral/portal/templates/portal/r2dt.html

@@ -26,7 +26,7 @@ <h1><i class="fa fa-search"></i> R2DT</h1>
     </p>
     <r2dt-web
         examples='[
-          {"description": "3SKZ_B", "sequence": "GGCCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGGUC\n.((((((((A..((((((.....BB))))))(.....a)(((((((bb..)))))))..))))))))."},
+          {"description": "3SKZ_B", "descriptionNote": "Dot-bracket notation", "sequence": "GGCCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGGUC\n.((((((((A..((((((.....BB))))))(.....a)(((((((bb..)))))))..))))))))."},
           {"description": "MT-RNR1", "sequence": "AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC"},
           {"description": "SAM", "sequence": "CTCTTATCGAGAGTTGGGCGAGGGATTTGGCCTTTTGACCCCAAAAGCAACCGACCGTAATTCCATTGTGAAATGGGGCGCATTTTTTTCGCGCCGAGACGCTGGTCTCTTAAGGCACGGTGCTAATTCCATTCAGATCTGATCTGAGAGATAAGAG"},
           {"description": "RNVU1-1", "sequence": "AUACUUACCUGGCAGGGGAGAUACGAUGAUCACGAAGGUGGUUUUCCCAGGGAGAGGCUUAUCCAUUGCACUCCGGAUGUGCUGACCCCUGCCGUUUCCCCAAAUGUGGGAAACUCGACUGCAUAAUUUGUGGUAGUGGGGGACUGCGUUCGCGCUGUCCUCUG"},

rnacentral/requirements.txt

@@ -34,3 +34,6 @@ django-cache-machine==1.1.0
 
 # AWS SDK for Python
 boto3==1.17.54
+
+# drf-spectacular for OpenAPI schema generation
+drf_spectacular

rnacentral/rnacentral/settings.py

@@ -186,6 +186,7 @@
     "rest_framework",
     "compressor",
     "markdown_deux",
+    "drf_spectacular",
     # Uncomment the next line to enable admin documentation:
     # 'django.contrib.admindocs',
 )
@@ -246,6 +247,7 @@
     "DEFAULT_PERMISSION_CLASSES": [
         "rest_framework.permissions.DjangoModelPermissionsOrAnonReadOnly"
     ],
+    "DEFAULT_AUTHENTICATION_CLASSES": [],
     # API results pagination
     "DEFAULT_PAGINATION_CLASS": "rnacentral.utils.pagination.Pagination",
     "PAGE_SIZE": 10,
@@ -266,6 +268,19 @@
         "rest_framework_yaml.renderers.YAMLRenderer",
         "rest_framework.renderers.BrowsableAPIRenderer",
     ),
+    "DEFAULT_SCHEMA_CLASS": "drf_spectacular.openapi.AutoSchema",
+}
+
+SPECTACULAR_SETTINGS = {
+    "TITLE": "RNAcentral API",
+    "DESCRIPTION": "RNAcentral API provides programmatic access to RNAcentral data",
+    "VERSION": "1.0.0",
+    "SERVE_INCLUDE_SCHEMA": False,
+    "POSTPROCESSING_HOOKS": [
+        "rnacentral.utils.drf_spectacular.remove_path",
+        "rnacentral.utils.drf_spectacular.fix_path",
+    ],
+    "SCHEMA_PATH_PREFIX": r"/api/v[0-9]",
 }
 
 # django-debug-toolbar

rnacentral/rnacentral/urls.py

@@ -15,6 +15,7 @@
 
 from django.conf.urls import include, url
 from django.views.generic import TemplateView
+from drf_spectacular.views import SpectacularAPIView, SpectacularSwaggerView
 
 urlpatterns = [
     # RNAcentral portal
@@ -27,6 +28,13 @@
     # new sequence search
     url(r"^sequence-search/", include("sequence_search.urls")),
     # Django Debug Toolbar
+    # OpenAPI schema
+    url(r"^api/schema/$", SpectacularAPIView.as_view(), name="schema"),
+    url(
+        r"^api/schema/swagger-ui/$",
+        SpectacularSwaggerView.as_view(url_name="schema"),
+        name="swagger-ui",
+    ),
 ]
 
 # robots.txt extras

rnacentral/rnacentral/utils/drf_spectacular.py

@@ -0,0 +1,31 @@
+def remove_path(result, generator, request, public):
+    """
+    Post-processing hook to remove /api/current/ and /sequence-search/ from the schema
+    """
+    paths = result.get("paths", {})
+    excluded_prefixes = ("/api/current/", "/sequence-search/")
+    paths = {
+        key: value
+        for key, value in paths.items()
+        if not key.startswith(excluded_prefixes)
+    }
+    result["paths"] = paths
+    return result
+
+
+def fix_path(result, generator, request, public):
+    """
+    Post-processing hook to normalize paths in the OpenAPI schema:
+    - Fix RNA path patterns containing [_/] to only show /.
+    """
+    paths = result.get("paths", {})
+    updated_paths = {}
+
+    for path, details in paths.items():
+        if "[/_]" in path:
+            path = path.replace("[/_]", "/")
+
+        updated_paths[path] = details
+
+    result["paths"] = updated_paths
+    return result