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tests: use updated method name and re-run cassettes #684

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Merged
korikuzma merged 1 commit into from
Nov 6, 2026
Merged

tests: use updated method name and re-run cassettes #684

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17 changes: 0 additions & 17 deletions tests/extras/cassettes/test_from_hgvs_coding_coordinates.yaml
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Original file line number Diff line number Diff line change
@@ -1,21 +1,4 @@
interactions:
- request:
body: null
headers: {}
method: GET
uri: http://localhost:5000/seqrepo/1/metadata/refseq:NM_001331029.1
response:
body:
string: "{\n \"added\": \"2016-08-24T05:03:40Z\",\n \"aliases\": [\n \"MD5:a8d7243ffeea4ade1dbc33613887693b\",\n
\ \"NCBI:NM_001331029.1\",\n \"refseq:NM_001331029.1\",\n \"NCBI:XM_017001344.1\",\n
\ \"refseq:XM_017001344.1\",\n \"SEGUID:qw9iIJ9BPdGZfypwQH7S3L2f9gI\",\n
\ \"SHA1:ab0f62209f413dd1997f2a70407ed2dcbd9ff602\",\n \"VMC:GS_MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\",\n
\ \"sha512t24u:MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\",\n \"ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\"\n
\ ],\n \"alphabet\": \"ACGT\",\n \"length\": 11291\n}\n"
headers: {}
status:
code: 200
message: OK
- request:
body: null
headers: {}
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25 changes: 0 additions & 25 deletions ...gvs_uncertain_range[NC_000002.12:g.(202377551_202464808)_(202559947_?)del-expected2].yaml
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This file was deleted.

16 changes: 8 additions & 8 deletions tests/extras/cassettes/test_hgvs[NM_181798.1:c.1007G>T-expected7].yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -67,13 +67,13 @@ interactions:
body: null
headers: {}
method: GET
uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NR_040711.1&rettype=fasta&seq_start=1263&seq_stop=1263&tool=bioutils&email=biocommons-dev@googlegroups.com
uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_181798.1&rettype=fasta&seq_start=1263&seq_stop=1268&tool=bioutils&email=biocommons-dev@googlegroups.com
response:
body:
string: '>NR_040711.1:1263-1263 Homo sapiens potassium voltage-gated channel,
KQT-like subfamily, member 1 (KCNQ1), transcript variant 2, non-coding RNA
string: '>NM_181798.1:1263-1268 Homo sapiens potassium voltage-gated channel
subfamily Q member 1 (KCNQ1), transcript variant 2, mRNA

G
GTTCTG


'
Expand All @@ -85,13 +85,13 @@ interactions:
body: null
headers: {}
method: GET
uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_181798.1&rettype=fasta&seq_start=1263&seq_stop=1268&tool=bioutils&email=biocommons-dev@googlegroups.com
uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NR_040711.1&rettype=fasta&seq_start=1263&seq_stop=1263&tool=bioutils&email=biocommons-dev@googlegroups.com
response:
body:
string: '>NM_181798.1:1263-1268 Homo sapiens potassium voltage-gated channel
subfamily Q member 1 (KCNQ1), transcript variant 2, mRNA
string: '>NR_040711.1:1263-1263 Homo sapiens potassium voltage-gated channel,
KQT-like subfamily, member 1 (KCNQ1), transcript variant 2, non-coding RNA

GTTCTG
G


'
Expand Down
6 changes: 3 additions & 3 deletions tests/extras/test_location_bounds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,7 @@ def _bounds_msg(sequence_id: str, detail: str, seq_len: int) -> str:
def test_out_of_bounds(request: pytest.FixtureRequest, case: dict) -> None:
tlr = request.getfixturevalue(case["tlr_fixture"])
with pytest.raises(DataProxyValidationError, match=f"^{re.escape(case['msg'])}$"):
tlr.translate_from(case["var"], fmt=case["fmt"], **case.get("kwargs", {}))
tlr.to_vrs(case["var"], fmt=case["fmt"], **case.get("kwargs", {}))


@pytest.mark.parametrize("case", start_after_end_cases, ids=lambda c: c["id"])
Expand All @@ -176,13 +176,13 @@ def test_start_after_end(request: pytest.FixtureRequest, case: dict) -> None:
with pytest.raises(
DataProxyValidationError, match=f"^{re.escape(START_AFTER_END_MSG)}$"
):
tlr.translate_from(case["var"], fmt="hgvs")
tlr.to_vrs(case["var"], fmt="hgvs")


@pytest.mark.parametrize("case", in_bounds_cases, ids=lambda c: c["id"])
@pytest.mark.vcr
def test_in_bounds(request: pytest.FixtureRequest, case: dict) -> None:
tlr = request.getfixturevalue(case["tlr_fixture"])
location = tlr.translate_from(case["var"], fmt=case["fmt"]).location.model_dump()
location = tlr.to_vrs(case["var"], fmt=case["fmt"]).location.model_dump()
expected_location = case["expected_location"]
assert {k: location[k] for k in expected_location} == expected_location
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