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jsstevensonjsstevenson
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update tests
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+185
-7
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3 files changed

+185
-7
lines changed

‎tests/conftest.py‎

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Original file line numberDiff line numberDiff line change
@@ -6,6 +6,8 @@
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from ga4gh.vrs import models
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from pydantic import BaseModel
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from anyvlm.anyvar.http_client import HttpAnyVarClient
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@pytest.fixture(scope="session", autouse=True)
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def load_env():
@@ -58,3 +60,12 @@ def vcr_config():
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"before_record_response": remove_response_headers,
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"decode_compressed_response": True,
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}
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@pytest.fixture
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def anyvar_client() -> HttpAnyVarClient:
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"""Provide AnyVar client fixture for tests.
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Uses HTTP because that's auto-mockable with pytest-record
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"""
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return HttpAnyVarClient()

‎tests/unit/functions/cassettes/test_ingest_vcf/test_ingest_vcf.yaml‎

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interactions:
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:chr1
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response:
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body:
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string: "{\n \"added\": \"2016-08-27T21:17:00Z\",\n \"aliases\": [\n \"GRCh38:1\",\n
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\ \"GRCh38:chr1\",\n \"GRCh38.p1:1\",\n \"GRCh38.p1:chr1\",\n \"GRCh38.p10:1\",\n
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\ \"GRCh38.p10:chr1\",\n \"GRCh38.p11:1\",\n \"GRCh38.p11:chr1\",\n
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\ \"GRCh38.p12:1\",\n \"GRCh38.p12:chr1\",\n \"GRCh38.p2:1\",\n \"GRCh38.p2:chr1\",\n
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\ \"GRCh38.p3:1\",\n \"GRCh38.p3:chr1\",\n \"GRCh38.p4:1\",\n \"GRCh38.p4:chr1\",\n
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\ \"GRCh38.p5:1\",\n \"GRCh38.p5:chr1\",\n \"GRCh38.p6:1\",\n \"GRCh38.p6:chr1\",\n
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\ \"GRCh38.p7:1\",\n \"GRCh38.p7:chr1\",\n \"GRCh38.p8:1\",\n \"GRCh38.p8:chr1\",\n
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\ \"GRCh38.p9:1\",\n \"GRCh38.p9:chr1\",\n \"MD5:6aef897c3d6ff0c78aff06ac189178dd\",\n
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\ \"NCBI:NC_000001.11\",\n \"refseq:NC_000001.11\",\n \"SEGUID:FCUd6VJ6uikS/VWLbhGdVmj2rOA\",\n
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\ \"SHA1:14251de9527aba2912fd558b6e119d5668f6ace0\",\n \"VMC:GS_Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n
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\ \"sha512t24u:Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\"\n
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\ ],\n \"alphabet\": \"ACGMNRT\",\n \"length\": 248956422\n}\n"
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr1?start=160208880&end=160208881
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response:
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body:
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string: A
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO
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response:
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body:
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string: "{\n \"added\": \"2016-08-27T21:17:00Z\",\n \"aliases\": [\n \"GRCh38:1\",\n
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\ \"GRCh38:chr1\",\n \"GRCh38.p1:1\",\n \"GRCh38.p1:chr1\",\n \"GRCh38.p10:1\",\n
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\ \"GRCh38.p10:chr1\",\n \"GRCh38.p11:1\",\n \"GRCh38.p11:chr1\",\n
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\ \"GRCh38.p12:1\",\n \"GRCh38.p12:chr1\",\n \"GRCh38.p2:1\",\n \"GRCh38.p2:chr1\",\n
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\ \"GRCh38.p3:1\",\n \"GRCh38.p3:chr1\",\n \"GRCh38.p4:1\",\n \"GRCh38.p4:chr1\",\n
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\ \"GRCh38.p5:1\",\n \"GRCh38.p5:chr1\",\n \"GRCh38.p6:1\",\n \"GRCh38.p6:chr1\",\n
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\ \"GRCh38.p7:1\",\n \"GRCh38.p7:chr1\",\n \"GRCh38.p8:1\",\n \"GRCh38.p8:chr1\",\n
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\ \"GRCh38.p9:1\",\n \"GRCh38.p9:chr1\",\n \"MD5:6aef897c3d6ff0c78aff06ac189178dd\",\n
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\ \"NCBI:NC_000001.11\",\n \"refseq:NC_000001.11\",\n \"SEGUID:FCUd6VJ6uikS/VWLbhGdVmj2rOA\",\n
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\ \"SHA1:14251de9527aba2912fd558b6e119d5668f6ace0\",\n \"VMC:GS_Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n
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\ \"sha512t24u:Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\"\n
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\ ],\n \"alphabet\": \"ACGMNRT\",\n \"length\": 248956422\n}\n"
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=160208880&end=160208881
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response:
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body:
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string: A
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr1?start=160208934&end=160208935
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response:
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body:
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string: A
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=160208934&end=160208935
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response:
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body:
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string: A
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr1?start=160208970&end=160208971
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response:
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body:
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string: C
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=160208970&end=160208971
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response:
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body:
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string: C
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: '{"id": "ga4gh:VA.J3Hi64dkKFKdnKIwB2419Qz3STDB2sJq", "type": "Allele", "digest":
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"J3Hi64dkKFKdnKIwB2419Qz3STDB2sJq", "location": {"id": "ga4gh:SL._iSMSsX8LVlBhygQTF-qI8PIiPMvKyX1",
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"type": "SequenceLocation", "digest": "_iSMSsX8LVlBhygQTF-qI8PIiPMvKyX1", "sequenceReference":
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{"type": "SequenceReference", "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"},
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"start": 160208880, "end": 160208881}, "state": {"type": "LiteralSequenceExpression",
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"sequence": "C"}}'
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headers: {}
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method: PUT
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uri: http://localhost:8000/vrs_variation
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response:
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body:
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string: '{"messages":[],"object":{"id":"ga4gh:VA.J3Hi64dkKFKdnKIwB2419Qz3STDB2sJq","type":"Allele","digest":"J3Hi64dkKFKdnKIwB2419Qz3STDB2sJq","location":{"id":"ga4gh:SL._iSMSsX8LVlBhygQTF-qI8PIiPMvKyX1","type":"SequenceLocation","digest":"_iSMSsX8LVlBhygQTF-qI8PIiPMvKyX1","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"},"start":160208880,"end":160208881},"state":{"type":"LiteralSequenceExpression","sequence":"C"}},"object_id":"ga4gh:VA.J3Hi64dkKFKdnKIwB2419Qz3STDB2sJq"}'
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: '{"id": "ga4gh:VA.cBM4F57wcT0WN7lZ5iJ8RrYooERbb_qr", "type": "Allele", "digest":
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"cBM4F57wcT0WN7lZ5iJ8RrYooERbb_qr", "location": {"id": "ga4gh:SL.ukxL6Ds27MlHSPN9c7FuKtue7fix0mg2",
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"type": "SequenceLocation", "digest": "ukxL6Ds27MlHSPN9c7FuKtue7fix0mg2", "sequenceReference":
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{"type": "SequenceReference", "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"},
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"start": 160208934, "end": 160208935}, "state": {"type": "LiteralSequenceExpression",
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"sequence": "C"}}'
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headers: {}
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method: PUT
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uri: http://localhost:8000/vrs_variation
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response:
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body:
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string: '{"messages":[],"object":{"id":"ga4gh:VA.cBM4F57wcT0WN7lZ5iJ8RrYooERbb_qr","type":"Allele","digest":"cBM4F57wcT0WN7lZ5iJ8RrYooERbb_qr","location":{"id":"ga4gh:SL.ukxL6Ds27MlHSPN9c7FuKtue7fix0mg2","type":"SequenceLocation","digest":"ukxL6Ds27MlHSPN9c7FuKtue7fix0mg2","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"},"start":160208934,"end":160208935},"state":{"type":"LiteralSequenceExpression","sequence":"C"}},"object_id":"ga4gh:VA.cBM4F57wcT0WN7lZ5iJ8RrYooERbb_qr"}'
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headers: {}
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status:
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code: 200
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message: OK
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- request:
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body: '{"id": "ga4gh:VA.Tx1gJiL1oQdOBdD07KK95VxR8NbUcg21", "type": "Allele", "digest":
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"Tx1gJiL1oQdOBdD07KK95VxR8NbUcg21", "location": {"id": "ga4gh:SL.y2nvzxXsN3yEY_xhT6bjYOYH6SzHuQQ9",
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"type": "SequenceLocation", "digest": "y2nvzxXsN3yEY_xhT6bjYOYH6SzHuQQ9", "sequenceReference":
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{"type": "SequenceReference", "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"},
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"start": 160208970, "end": 160208971}, "state": {"type": "LiteralSequenceExpression",
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"sequence": "T"}}'
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headers: {}
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method: PUT
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uri: http://localhost:8000/vrs_variation
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response:
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body:
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string: '{"messages":[],"object":{"id":"ga4gh:VA.Tx1gJiL1oQdOBdD07KK95VxR8NbUcg21","type":"Allele","digest":"Tx1gJiL1oQdOBdD07KK95VxR8NbUcg21","location":{"id":"ga4gh:SL.y2nvzxXsN3yEY_xhT6bjYOYH6SzHuQQ9","type":"SequenceLocation","digest":"y2nvzxXsN3yEY_xhT6bjYOYH6SzHuQQ9","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO"},"start":160208970,"end":160208971},"state":{"type":"LiteralSequenceExpression","sequence":"T"}},"object_id":"ga4gh:VA.Tx1gJiL1oQdOBdD07KK95VxR8NbUcg21"}'
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headers: {}
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status:
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code: 200
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message: OK
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version: 1

‎tests/unit/functions/test_ingest_vcf.py‎

Lines changed: 3 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -11,10 +11,6 @@ def input_vcf_path(test_data_dir: Path) -> Path:
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return test_data_dir / "vcf.vcf"
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@pytest.fixture
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def client() -> HttpAnyVarClient:
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return HttpAnyVarClient()
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def test_ingest_vcf(input_vcf_path: Path, client: HttpAnyVarClient):
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ingest_vcf(input_vcf_path, client)
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@pytest.mark.vcr
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def test_ingest_vcf(input_vcf_path: Path, anyvar_client: HttpAnyVarClient):
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ingest_vcf(input_vcf_path, anyvar_client)

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