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#331 Rename hgvs router to transcripts. #367

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Merged
EstelleDa merged 1 commit into from
Dec 11, 2024
Merged

#331 Rename hgvs router to transcripts. #367

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10 changes: 5 additions & 5 deletions src/mavedb/routers/hgvs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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"}},
)

Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down
36 changes: 18 additions & 18 deletions tests/routers/test_hgvs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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"'
Expand All @@ -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()

Expand All @@ -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

Expand All @@ -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
Expand All @@ -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()

Expand All @@ -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
Expand All @@ -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
Expand All @@ -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

Expand All @@ -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
Expand All @@ -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
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