Merge pull request #135 from VariantEffect/nick/check-hgvs-assembly-name

Tests & Fixups for /api/v1/hgvs endpoints

Author: ashsny

src/mavedb/routers/hgvs.py

@@ -7,6 +7,7 @@
 from cdot.hgvs.dataproviders import RESTDataProvider
 from fastapi import APIRouter, Depends, HTTPException
 from hgvs import parser, validator
+from hgvs.exceptions import HGVSDataNotAvailableError
 
 from mavedb.deps import hgvs_data_provider
 
@@ -22,7 +23,10 @@ def hgvs_fetch(accession: str, hdp: RESTDataProvider = Depends(hgvs_data_provide
     """
     List stored sequences
     """
-    return hdp.seqfetcher.fetch_seq(accession)
+    try:
+        return hdp.seqfetcher.fetch_seq(accession)
+    except HGVSDataNotAvailableError as e:
+        raise HTTPException(404, str(e))
 
 
 @router.post("/validate", status_code=200, response_model=Any)
@@ -75,6 +79,9 @@ def list_accessions(assembly: str, hdp: RESTDataProvider = Depends(hgvs_data_pro
     """
     List stored accessions
     """
+    if assembly not in hdp.assembly_maps:
+        raise HTTPException(404, f"Assembly '{assembly}' Not Found")
+
     return list(hdp.get_assembly_map(assembly_name=assembly).keys())
 
 
@@ -88,7 +95,7 @@ def list_genes():
     return list(chain.from_iterable(hgvs.dataproviders.uta.connect()._fetchall("select hgnc from gene")))
 
 
-@router.get("/genes/{gene}", status_code=200, response_model=list)
+@router.get("/genes/{gene}", status_code=200)
 def gene_info(gene: str, hdp: RESTDataProvider = Depends(hgvs_data_provider)):
     """
     List stored gene information for a specified gene
@@ -104,15 +111,15 @@ def list_transcripts_for_gene(gene: str, hdp: RESTDataProvider = Depends(hgvs_da
     return set([tx_info["tx_ac"] for tx_info in hdp.get_tx_for_gene(gene)])
 
 
-@router.get("/transcripts/{transcript}", status_code=200, response_model=list)
+@router.get("/transcripts/{transcript}", status_code=200)
 def transcript_info(transcript: str, hdp: RESTDataProvider = Depends(hgvs_data_provider)):
     """
     List transcript information for a particular transcript
     """
     return hdp.get_tx_identity_info(transcript)
 
 
-@router.get("/transcripts/protein/{transcript}", status_code=200, response_model=str)
+@router.get("/transcripts/protein/{transcript}", status_code=200)
 def convert_to_protein(transcript: str, hdp: RESTDataProvider = Depends(hgvs_data_provider)):
     """
     Convert a provided transcript from it's nucleotide accession identifier to its protein accession identifier

tests/routers/test_hgvs.py

@@ -0,0 +1,145 @@
+VALID_MAJOR_ASSEMBLY = "GRCh38"
+VALID_MINOR_ASSEMBLY = "GRCh38.p3"
+INVALID_ASSEMBLY = "undefined"
+VALID_ACCESSION = "NC_000001.11"
+INVALID_ACCESSION = "NC_999999.99"
+SMALL_ACCESSION = "NM_002977.4"
+VALID_GENE = "BRCA1"
+INVALID_GENE = "fnord"
+VALID_TRANSCRIPT = 'NM_001408458.1'
+INVALID_TRANSCRIPT = 'NX_99999.1'
+VALID_VARIANT = VALID_ACCESSION + ":g.1_2insA"
+INVALID_VARIANT = VALID_ACCESSION + ":g.1delA"
+HAS_PROTEIN_ACCESSION = "NM_000014.4"
+PROTEIN_ACCESSION = "NP_000005.2"
+
+
+def test_hgvs_fetch_valid(client, setup_router_db):
+    # VALID_ACCESSION is rather large so use a smaller one
+    response = client.get(f"/api/v1/hgvs/fetch/{SMALL_ACCESSION}")
+    assert response.status_code == 200
+
+
+def test_hgvs_fetch_invalid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/fetch/{INVALID_ACCESSION}")
+    assert response.status_code == 404
+
+
+def test_hgvs_validate_valid(client, setup_router_db):
+    payload = {'variant': VALID_VARIANT}
+    response = client.post("/api/v1/hgvs/validate", json=payload)
+    assert response.status_code == 200
+
+
+def test_hgvs_validate_invalid(client, setup_router_db):
+    payload = {'variant': INVALID_VARIANT}
+    response = client.post("/api/v1/hgvs/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")
+    assert response.status_code == 200
+    assert VALID_MAJOR_ASSEMBLY in response.json()
+    assert VALID_MINOR_ASSEMBLY in response.json()
+
+
+def test_hgvs_grouped_assemblies(client, setup_router_db):
+    response = client.get("/api/v1/hgvs/grouped-assemblies")
+    assert response.status_code == 200
+
+    groups = {group['type'] : group['assemblies'] for group in response.json()}
+    assert 'Major Assembly Versions' in groups
+    assert 'Minor Assembly Versions' in groups
+    assert VALID_MAJOR_ASSEMBLY in groups['Major Assembly Versions']
+    assert VALID_MINOR_ASSEMBLY in groups['Minor Assembly Versions']
+
+
+def test_hgvs_accessions_major(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/{VALID_MAJOR_ASSEMBLY}/accessions")
+    assert response.status_code == 200
+    assert VALID_ACCESSION in response.json()
+
+
+def test_hgvs_accessions_minor(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/{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")
+    assert response.status_code == 404
+
+
+def test_hgvs_genes(client, setup_router_db):
+    response = client.get("/api/v1/hgvs/genes")
+    assert response.status_code == 200
+    assert VALID_GENE in response.json()
+
+
+def test_hgvs_gene_info_valid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/genes/{VALID_GENE}")
+    assert response.status_code == 200
+    assert response.json()['hgnc'] == VALID_GENE
+    assert response.json()['descr'] is not None
+
+
+def test_hgvs_gene_info_invalid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/genes/{INVALID_GENE}")
+    # XXX this probably SHOULD return a 404, but currently returns a 200 with None
+    # assert response.status_code == 404
+    assert response.status_code == 200
+    assert response.json() is None
+
+
+def test_hgvs_gene_transcript_valid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/transcripts/gene/{VALID_GENE}")
+    assert response.status_code == 200
+    assert VALID_TRANSCRIPT in response.json()
+
+
+def test_hgvs_gene_transcript_invalid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/transcripts/gene/{INVALID_GENE}")
+    # XXX this probably SHOULD return a 404, but currently returns a 200 with empty list
+    # assert response.status_code == 404
+    assert response.status_code == 200
+    assert response.json() == []
+
+
+def test_hgvs_transcript_valid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/transcripts/{VALID_TRANSCRIPT}")
+    assert response.status_code == 200
+    assert response.json()['hgnc'] == VALID_GENE
+
+
+def test_hgvs_transcript_invalid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/transcripts/{INVALID_TRANSCRIPT}")
+    # XXX this probably SHOULD return a 404, but currently returns a 200 with None
+    # assert response.status_code == 404
+    assert response.status_code == 200
+    assert response.json() is None
+
+
+def test_hgvs_transcript_protein_valid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/transcripts/protein/{HAS_PROTEIN_ACCESSION}")
+    assert response.status_code == 200
+    assert response.json() == PROTEIN_ACCESSION
+
+
+def test_hgvs_transcript_protein_no_protein(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/transcripts/protein/{SMALL_ACCESSION}")
+    # XXX this probably SHOULD return a 404, but currently returns a 200 with None
+    # assert response.status_code == 404
+    assert response.status_code == 200
+    assert response.json() is None
+
+
+def test_hgvs_transcript_protein_invalid(client, setup_router_db):
+    response = client.get(f"/api/v1/hgvs/transcripts/protein/{INVALID_ACCESSION}")
+    # XXX this probably SHOULD return a 400, but currently returns a 200 with None
+    # assert response.status_code == 404
+    assert response.status_code == 200
+    assert response.json() is None
+
+