Handle transcipt stable IDs

app/api/models/resolver.py

@@ -4,9 +4,9 @@
 
 
 class SearchPayload(BaseModel):
-    stable_id: str = Field(default=None, title="Stable ID of a gene")
-    type: Literal["gene"] | None = Field(
-        default=None, title="Type of stable id, e.g. gene"
+    stable_id: str = Field(default=None, title="Stable ID")
+    type: Literal["gene", "transcript", "protein"] | None = Field(
+        default=None, title="Optional stable-ID type filter"
     )
     per_page: int = 1
     app: Literal["genome-browser", "feature-explorer"] = Field(
@@ -15,8 +15,9 @@ class SearchPayload(BaseModel):
 
 
 class SearchMatch(BaseModel):
-    genome: str
+    genome_id: str
     unversioned_stable_id: str
+    type: Literal["gene", "transcript", "protein"] | None = None
 
 
 class SearchResult(BaseModel):
@@ -89,6 +90,7 @@ class UrlResolverResponse(BaseModel):
 
 
 class StableIdResolverContent(MetadataResult):
+    stable_id_type: Literal["gene", "transcript", "protein"] = "gene"
     feature_explorer_url: str | None = None
     genome_browser_url: str | None = None
     release_type: str | None = None

app/api/resources/resolver_view.py

@@ -26,7 +26,7 @@
 async def resolve(
     request: Request,
     stable_id: str,
-    type: Optional[str] = "gene",
+    type: Optional[Literal["gene", "transcript", "protein"]] = None,
     gca: Optional[str] = "",
     app: Optional[Literal["genome-browser", "feature-explorer"]] = DEFAULT_APP,
 ):

app/api/resources/templates/shared/id_content.html

@@ -3,7 +3,7 @@
 <div class="id-redirect-content">
     <div class="redirect-info">
         <div class="search-param">
-            <span class="search-param-label">Gene</span>
+            <span class="search-param-label">Stable ID</span>
             <span class="search-param-value">{{ response.stable_id }}</span>
         </div>
         {% if (response.code == 404 or response.code == 500) and response.message %}

app/api/utils/commons.py

@@ -13,10 +13,14 @@ def build_stable_id_resolver_content(metadata_results) -> list[StableIdResolverC
 
         content = StableIdResolverContent(
             feature_explorer_url=build_feature_explorer_url(
-                genome_id, metadata["unversioned_stable_id"]
+                genome_id,
+                metadata["unversioned_stable_id"],
+                metadata.get("stable_id_type", "gene"),
             ),
             genome_browser_url=build_genome_browser_url(
-                genome_id, metadata["unversioned_stable_id"]
+                genome_id,
+                metadata["unversioned_stable_id"],
+                metadata.get("stable_id_type", "gene"),
             ),
             release_type=metadata.get("release", {}).get("type", ""),
             release_name=metadata.get("release", {}).get("name", ""),
@@ -27,12 +31,19 @@ def build_stable_id_resolver_content(metadata_results) -> list[StableIdResolverC
     return results
 
 
-def build_feature_explorer_url(genome_id: str, stable_id: str) -> str:
-    return f"{ENSEMBL_URL}/feature-explorer/{genome_id}/gene:{stable_id}"
+def build_feature_explorer_url(
+    genome_id: str, stable_id: str, stable_id_type: str = "gene"
+) -> str:
+    return f"{ENSEMBL_URL}/feature-explorer/{genome_id}/{stable_id_type}:{stable_id}"
 
 
-def build_genome_browser_url(genome_id: str, stable_id: str) -> str:
-    return f"{ENSEMBL_URL}/genome-browser/{genome_id}?focus=gene:{stable_id}"
+def build_genome_browser_url(
+    genome_id: str, stable_id: str, stable_id_type: str = "gene"
+) -> str:
+    return (
+        f"{ENSEMBL_URL}/genome-browser/{genome_id}"
+        f"?focus={stable_id_type}:{stable_id}"
+    )
 
 
 def is_json_request(request) -> bool:

app/api/utils/metadata.py

@@ -25,6 +25,11 @@ def get_metadata(matches: List[SearchMatch] = []):
                 metadata_results[genome_id]["unversioned_stable_id"] = match.get(
                     "unversioned_stable_id"
                 )
+                # Fast-match supplies this field. Keep the historical gene
+                # default for search-hub responses that do not yet include it.
+                metadata_results[genome_id]["stable_id_type"] = (
+                    match.get("type") or match.get("doc_type") or "gene"
+                )
         except Exception as e:
             raise Exception(
                 f"Failed to fetch metadata for genome '{genome_id}': {e}"

app/api/utils/search.py

@@ -71,7 +71,7 @@ def get_fast_match_results(params: SearchPayload):
     # version suffixes (for example, ``ENSG00000127720.3``) are removed.
     unversioned_stable_id = re.sub(r"\.\d+$", "", params.stable_id)
     matches = []
-    seen_genome_ids = set()
+    seen_matches = set()
 
     for raw_match in raw_matches.split("+"):
         try:
@@ -89,14 +89,19 @@ def get_fast_match_results(params: SearchPayload):
         if params.type and doc_type != params.type:
             continue
 
-        if genome_id not in seen_genome_ids:
+        # A stable ID normally identifies one feature type, but retain the type
+        # in both the result and deduplication key when no filter was supplied.
+        # The resolver needs it to construct a gene or transcript destination.
+        match_key = (genome_id, doc_type)
+        if match_key not in seen_matches:
             matches.append(
                 {
                     "genome_id": genome_id,
                     "unversioned_stable_id": unversioned_stable_id,
+                    "type": doc_type,
                 }
             )
-            seen_genome_ids.add(genome_id)
+            seen_matches.add(match_key)
 
     logger.info(
             f"Fast-match stable ID lookup result: {len(matches)} matches "

app/static/APISpecification.yaml

@@ -42,19 +42,19 @@ paths:
       parameters:
         - name: stable_id
           in: path
-          description: Gene stable id used to represent a gene in a genome.
+          description: Gene, transcript, or protein stable ID.
           required: true
           explode: true
           schema:
             type: string
             example: ENSG00000221914.11
         - name: type
           in: query
-          description: Defines a type - gene/transcript/variant etc
+          description: Optional stable-ID type filter. If omitted, all supported types are searched.
           required: false
           schema:
             type: string
-            enum: [ gene, transcript, variant ]
+            enum: [ gene, transcript, protein ]
             example:
               gene
         - name: app

tests/test_fast_match_search.py

@@ -51,10 +51,12 @@ def test_returns_matches_with_unversioned_stable_id(self, mock_fm_py):
                     {
                         "genome_id": "genome-1",
                         "unversioned_stable_id": "ENSG00000127720",
+                        "type": "gene",
                     },
                     {
                         "genome_id": "genome-2",
                         "unversioned_stable_id": "ENSG00000127720",
+                        "type": "gene",
                     },
                 ]
             },
@@ -80,11 +82,39 @@ def test_filters_other_document_types_and_duplicate_genomes(self, mock_fm_py):
                     {
                         "genome_id": "genome-2",
                         "unversioned_stable_id": "ENSG00000127720",
+                        "type": "gene",
                     }
                 ]
             },
         )
 
+    @patch("app.api.utils.search.fm_py")
+    @patch("app.api.utils.search.FAST_MATCH_ENABLED", True)
+    @patch("app.api.utils.search.FAST_MATCH_DB_PATH", "/data/stable-ids.redb")
+    def test_returns_supported_types_when_no_type_filter_is_supplied(self, mock_fm_py):
+        mock_fm_py.find_key.return_value = "genome-1|gene+genome-1|transcript"
+        params = SearchPayload(stable_id="ENSX000001", type=None, per_page=10)
+
+        result = get_search_results(params)
+
+        self.assertEqual(
+            result,
+            {
+                "matches": [
+                    {
+                        "genome_id": "genome-1",
+                        "unversioned_stable_id": "ENSX000001",
+                        "type": "gene",
+                    },
+                    {
+                        "genome_id": "genome-1",
+                        "unversioned_stable_id": "ENSX000001",
+                        "type": "transcript",
+                    },
+                ]
+            },
+        )
+
     @patch("app.api.utils.search.fm_py")
     @patch("app.api.utils.search.FAST_MATCH_ENABLED", True)
     @patch("app.api.utils.search.FAST_MATCH_DB_PATH", "/data/stable-ids.redb")

tests/test_resolver.py

@@ -106,6 +106,39 @@ def test_resolve_success_with_redirect(
             response.headers["location"], self.mock_resolved_url["genome1"]
         )
 
+    @patch("app.api.resources.resolver_view.get_search_results")
+    @patch("app.api.resources.resolver_view.get_metadata")
+    def test_resolves_transcript_using_the_matched_type(
+        self, mock_get_metadata, mock_get_search_results
+    ):
+        transcript_id = "ENST00000357654"
+        mock_get_search_results.return_value = {
+            "matches": [
+                {
+                    "genome_id": "genome1",
+                    "unversioned_stable_id": transcript_id,
+                    "type": "transcript",
+                }
+            ]
+        }
+        mock_get_metadata.return_value = {
+            "genome1": {
+                **self.mock_single_metadata_results_success["genome1"],
+                "unversioned_stable_id": transcript_id,
+                "stable_id_type": "transcript",
+            }
+        }
+
+        response = self.client.get(
+            f"/id/{transcript_id}", params={"app": "genome-browser"}, follow_redirects=False
+        )
+
+        self.assertEqual(response.status_code, 307)
+        self.assertEqual(
+            response.headers["location"],
+            f"{ENSEMBL_URL}/genome-browser/genome1?focus=transcript:{transcript_id}",
+        )
+
     @patch("app.api.resources.resolver_view.get_search_results")
     @patch("app.api.resources.resolver_view.get_metadata")
     def test_resolve_success_with_html_response(