Merge pull request #367 from VariantEffect/estelle/renameHgvsToTranscripts

#331 Rename hgvs router to transcripts.

Author: EstelleDa

src/mavedb/routers/hgvs.py

@@ -10,8 +10,8 @@
 from mavedb.deps import hgvs_data_provider
 
 router = APIRouter(
-    prefix="/api/v1/hgvs",
-    tags=["hgvs"],
+    prefix="/api/v1/transcripts",
+    tags=["transcripts"],
     responses={404: {"description": "Not found"}},
 )
 
@@ -85,7 +85,7 @@ def gene_info(gene: str, hdp: RESTDataProvider = Depends(hgvs_data_provider)) ->
     return gene_info
 
 
-@router.get("/transcripts/gene/{gene}", status_code=200, response_model=list[str])
+@router.get("/gene/{gene}", status_code=200, response_model=list[str])
 def list_transcripts_for_gene(gene: str, hdp: RESTDataProvider = Depends(hgvs_data_provider)) -> list[str]:
     """
     List transcripts associated with a particular gene
@@ -98,7 +98,7 @@ def list_transcripts_for_gene(gene: str, hdp: RESTDataProvider = Depends(hgvs_da
     return list(transcripts)
 
 
-@router.get("/transcripts/{transcript}", status_code=200, response_model=dict[str, Any])
+@router.get("/{transcript}", status_code=200, response_model=dict[str, Any])
 def transcript_info(transcript: str, hdp: RESTDataProvider = Depends(hgvs_data_provider)) -> dict[str, Any]:
     """
     List transcript information for a particular transcript
@@ -111,7 +111,7 @@ def transcript_info(transcript: str, hdp: RESTDataProvider = Depends(hgvs_data_p
     return transcript_info
 
 
-@router.get("/transcripts/protein/{transcript}", status_code=200, response_model=str)
+@router.get("/protein/{transcript}", status_code=200, response_model=str)
 def convert_to_protein(transcript: str, hdp: RESTDataProvider = Depends(hgvs_data_provider)) -> str:
     """
     Convert a provided transcript from it's nucleotide accession identifier to its protein accession identifier

tests/routers/test_hgvs.py

@@ -21,7 +21,7 @@
 
 
 def test_hgvs_fetch_valid(client, setup_router_db):
-    response = client.get(f"/api/v1/hgvs/fetch/{VALID_ACCESSION}")
+    response = client.get(f"/api/v1/transcripts/fetch/{VALID_ACCESSION}")
 
     assert response.status_code == 200
     assert response.text == '"GATTACAGATTACAGATTACAGATTACAGATTACAGATTACAGATTACA"'
@@ -31,51 +31,51 @@ def test_hgvs_fetch_invalid(client, setup_router_db):
     with patch.object(
         cdot.hgvs.dataproviders.ChainedSeqFetcher, "fetch_seq", side_effect=HGVSDataNotAvailableError()
     ) as p:
-        response = client.get(f"/api/v1/hgvs/fetch/{SMALL_ACCESSION}")
+        response = client.get(f"/api/v1/transcripts/fetch/{SMALL_ACCESSION}")
         p.assert_called_once()
         assert response.status_code == 404
 
 
 def test_hgvs_validate_valid(client, setup_router_db):
     with patch.object(cdot.hgvs.dataproviders.RESTDataProvider, "_get_transcript", return_value=TEST_CDOT_TRANSCRIPT):
         payload = {"variant": VALID_VARIANT}
-        response = client.post("/api/v1/hgvs/validate", json=payload)
+        response = client.post("/api/v1/transcripts/validate", json=payload)
         assert response.status_code == 200
 
 
 def test_hgvs_validate_invalid(client, setup_router_db):
     with patch.object(cdot.hgvs.dataproviders.RESTDataProvider, "_get_transcript", return_value=TEST_CDOT_TRANSCRIPT):
         payload = {"variant": INVALID_VARIANT}
-        response = client.post("/api/v1/hgvs/validate", json=payload)
+        response = client.post("/api/v1/transcripts/validate", json=payload)
 
         assert response.status_code == 400
         assert "does not agree" in response.json()["detail"]
 
 
 def test_hgvs_list_assemblies(client, setup_router_db):
-    response = client.get("/api/v1/hgvs/assemblies")
+    response = client.get("/api/v1/transcripts/assemblies")
     assert response.status_code == 200
     assert VALID_MAJOR_ASSEMBLY in response.json()
 
 
 def test_hgvs_accessions_major(client, setup_router_db):
-    response = client.get(f"/api/v1/hgvs/{VALID_MAJOR_ASSEMBLY}/accessions")
+    response = client.get(f"/api/v1/transcripts/{VALID_MAJOR_ASSEMBLY}/accessions")
     assert response.status_code == 200
     assert "NC_000001.11" in response.json()
 
 
 def test_hgvs_accessions_minor(client, setup_router_db):
-    response = client.get(f"/api/v1/hgvs/{VALID_MINOR_ASSEMBLY}/accessions")
+    response = client.get(f"/api/v1/transcripts/{VALID_MINOR_ASSEMBLY}/accessions")
     assert response.status_code == 404
 
 
 def test_hgvs_accessions_invalid(client, setup_router_db):
-    response = client.get(f"/api/v1/hgvs/{INVALID_ASSEMBLY}/accessions")
+    response = client.get(f"/api/v1/transcripts/{INVALID_ASSEMBLY}/accessions")
     assert response.status_code == 404
 
 
 def test_hgvs_genes(client, setup_router_db):
-    response = client.get("/api/v1/hgvs/genes")
+    response = client.get("/api/v1/transcripts/genes")
     assert response.status_code == 200
     assert VALID_GENE in response.json()
 
@@ -93,7 +93,7 @@ def test_hgvs_gene_info_valid(client, setup_router_db):
                 "summary": "This gene, etc",
             },
         )
-        response = client.get(f"/api/v1/hgvs/genes/{VALID_GENE}")
+        response = client.get(f"/api/v1/transcripts/genes/{VALID_GENE}")
 
         assert m.called
 
@@ -108,7 +108,7 @@ def test_hgvs_gene_info_invalid(client, setup_router_db):
             "https://cdot.cc/gene/fnord",
             status_code=404,
         )
-        response = client.get(f"/api/v1/hgvs/genes/{INVALID_GENE}")
+        response = client.get(f"/api/v1/transcripts/genes/{INVALID_GENE}")
 
         assert m.called
         assert response.status_code == 404
@@ -122,7 +122,7 @@ def test_hgvs_gene_transcript_valid(client, setup_router_db):
             json={"results": [{"hgnc": f"{VALID_GENE}", "tx_ac": VALID_TRANSCRIPT}]},
         )
 
-        response = client.get(f"/api/v1/hgvs/transcripts/gene/{VALID_GENE}")
+        response = client.get(f"/api/v1/transcripts/gene/{VALID_GENE}")
         assert response.status_code == 200
         assert VALID_TRANSCRIPT in response.json()
 
@@ -131,15 +131,15 @@ def test_hgvs_gene_transcript_invalid(client, setup_router_db):
     with requests_mock.mock() as m:
         m.get(f"https://cdot.cc/transcripts/gene/{INVALID_GENE}", status_code=404)
 
-        response = client.get(f"/api/v1/hgvs/transcripts/gene/{INVALID_GENE}")
+        response = client.get(f"/api/v1/transcripts/gene/{INVALID_GENE}")
 
         assert m.called
         assert response.status_code == 404
 
 
 def test_hgvs_transcript_valid(client, setup_router_db):
     with patch.object(cdot.hgvs.dataproviders.RESTDataProvider, "_get_transcript", return_value=TEST_CDOT_TRANSCRIPT):
-        response = client.get(f"/api/v1/hgvs/transcripts/{VALID_TRANSCRIPT}")
+        response = client.get(f"/api/v1/transcripts/{VALID_TRANSCRIPT}")
 
     assert response.status_code == 200
     assert response.json()["hgnc"] == VALID_GENE
@@ -149,7 +149,7 @@ def test_hgvs_transcript_invalid(client, setup_router_db):
     with requests_mock.mock() as m:
         m.get(f"https://cdot.cc/transcript/{INVALID_TRANSCRIPT}", status_code=404)
 
-        response = client.get(f"/api/v1/hgvs/transcripts/{INVALID_TRANSCRIPT}")
+        response = client.get(f"/api/v1/transcripts/{INVALID_TRANSCRIPT}")
 
         assert m.called
         assert response.status_code == 404
@@ -163,7 +163,7 @@ def test_hgvs_transcript_protein_valid(client, setup_router_db):
             json={"biotype": ["protein_coding"], "gene_name": "A2M", "gene_vesion": "2", "protein": "NP_000005.2"},
         )
 
-        response = client.get(f"/api/v1/hgvs/transcripts/protein/{HAS_PROTEIN_ACCESSION}")
+        response = client.get(f"/api/v1/transcripts/protein/{HAS_PROTEIN_ACCESSION}")
 
         assert m.called
 
@@ -175,7 +175,7 @@ def test_hgvs_transcript_protein_no_protein(client, setup_router_db):
     with requests_mock.mock() as m:
         m.get(f"https://cdot.cc/transcript/{SMALL_ACCESSION}", status_code=404)
 
-        response = client.get(f"/api/v1/hgvs/transcripts/protein/{SMALL_ACCESSION}")
+        response = client.get(f"/api/v1/transcripts/protein/{SMALL_ACCESSION}")
 
         assert m.called
         assert response.status_code == 404
@@ -185,7 +185,7 @@ def test_hgvs_transcript_protein_invalid(client, setup_router_db):
     with requests_mock.mock() as m:
         m.get(f"https://cdot.cc/transcript/{INVALID_ACCESSION}", status_code=404)
 
-        response = client.get(f"/api/v1/hgvs/transcripts/protein/{INVALID_ACCESSION}")
+        response = client.get(f"/api/v1/transcripts/protein/{INVALID_ACCESSION}")
 
         assert m.called
         assert response.status_code == 404