feat: add IGV.js search endpoint

bento_reference_service/models.py

@@ -106,6 +106,12 @@ class GenomeFeature(BaseModel):
     parents: tuple[str, ...]
 
 
+class GenomeFeatureIGV(BaseModel):
+    chromosome: str
+    start: int
+    end: int
+
+
 TaskStatus = Literal["queued", "running", "success", "error"]
 
 

bento_reference_service/routers/genomes.py

@@ -204,6 +204,20 @@ async def genomes_detail_features_detail(db: DatabaseDependency, genome_id: str,
     return await db.get_genome_feature_by_id(genome_id, feature_id)
 
 
+@genome_router.get("/{genome_id}/igv-js-features", dependencies=[authz_middleware.dep_public_endpoint()])
+async def genomes_detail_igv_js_features(
+    db: DatabaseDependency, genome_id: str, q: str | None = None
+) -> list[m.GenomeFeatureIGV]:
+    results, _ = await db.query_genome_features(
+        genome_id, name=q, name_fzy=True, feature_types=["mRNA", "gene", "transcript", "exon"], limit=1
+    )
+    return [
+        m.GenomeFeatureIGV(chromosome=r.contig_name, start=r.entries[0].start_pos, end=r.entries[-1].end_pos)
+        for r in results
+        if len(r.entries) > 0
+    ]
+
+
 @genome_router.get("/{genome_id}/features.gff3.gz", dependencies=[authz_middleware.dep_public_endpoint()])
 async def genomes_detail_features_gff3(
     config: ConfigDependency, db: DatabaseDependency, logger: LoggerDependency, request: Request, genome_id: str

tests/test_genome_routes.py

@@ -313,6 +313,7 @@ async def test_genome_feature_endpoints(test_client: TestClient, aioresponse: ai
     assert srd["pagination"]["total"] == 1
     assert isinstance(srd.get("time"), float)
     assert srd["time"] < 0.2  # this is a very basic operation on a small dataset and should be fast.
+    q_feature = srd["results"][0]
 
     #  - fuzzy search
     sr = test_client.get(f"/genomes/{genome.id}/features", params={"q": "ENSSASP00005000003", "q_fzy": "true"})
@@ -339,3 +340,12 @@ async def test_genome_feature_endpoints(test_client: TestClient, aioresponse: ai
     sr = test_client.get(f"/genomes/{genome.id}/features/CDS:ENSSASP00005000003")
     assert sr.status_code == 200
     assert sr.json()["feature_id"] == "CDS:ENSSASP00005000003"
+
+    # Test we can do an IGV.js search
+    sr = test_client.get(f"/genomes/{genome.id}/igv-js-features", params={"q": "ENSSASP00005000003"})
+    assert sr.status_code == 200
+    srd = sr.json()
+    assert len(srd) == 1
+    assert srd[0]["chromosome"] == q_feature["contig_name"]
+    assert srd[0]["start"] == q_feature["entries"][0]["start_pos"]
+    assert srd[0]["end"] == q_feature["entries"][0]["end_pos"]