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October 2024 release #339

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merged 19 commits into from
Oct 2, 2024
Merged

October 2024 release #339

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dc2f1dc
style: update ruff and drop black (#283)
jsstevenson Jul 16, 2024
575baad
cicd: allow missing credentials (#291)
jsstevenson Jul 16, 2024
e44ae67
chore: update ebextensions for downloading latest seqrepo instance (#…
korikuzma Jul 29, 2024
133aad9
cicd: pin exact ruff version (#297)
jsstevenson Aug 3, 2024
e66d981
refactor: address config deprecation (#299)
jsstevenson Aug 5, 2024
4becc20
feat: use latest fastapi event management api (#298)
jsstevenson Aug 5, 2024
2848394
fix: update deprecated pytest async features (#300)
jsstevenson Aug 5, 2024
195b860
docs: remove docstring types and clean up formatting (#301)
jsstevenson Aug 5, 2024
381bd22
fix: handle unnecessary checks for build files (#309)
jsstevenson Aug 7, 2024
265c80f
feat!: use latest object schemas and dependency releases (#293)
katiestahl Aug 12, 2024
ba2699b
cicd(fix): fix curfu path (#312)
korikuzma Aug 12, 2024
527dc5c
refactor: remove unused seqrepo configuration (#308)
jsstevenson Aug 12, 2024
1a25af3
build(deps): bump webpack-dev-middleware from 5.3.3 to 5.3.4 in /clie…
dependabot[bot] Sep 17, 2024
e0785dc
merge main
katiestahl Oct 2, 2024
7682da0
revert conftest
katiestahl Oct 2, 2024
cdd267b
fix tests from merge
katiestahl Oct 2, 2024
dabdae2
update requirements
katiestahl Oct 2, 2024
4951706
remove debug code
katiestahl Oct 2, 2024
d824f3d
use staging requirements.txt
katiestahl Oct 2, 2024
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7 changes: 4 additions & 3 deletions client/yarn.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -2232,6 +2232,7 @@
"@types/react-is" "^16.7.1 || ^17.0.0"
prop-types "^15.8.1"
react-is "^18.2.0"

"@nicolo-ribaudo/[email protected]":
version "5.1.1-v1"
resolved "https://registry.yarnpkg.com/@nicolo-ribaudo/eslint-scope-5-internals/-/eslint-scope-5-internals-5.1.1-v1.tgz#dbf733a965ca47b1973177dc0bb6c889edcfb129"
Expand Down Expand Up @@ -11025,9 +11026,9 @@ webidl-conversions@^6.1.0:
integrity sha512-qBIvFLGiBpLjfwmYAaHPXsn+ho5xZnGvyGvsarywGNc8VyQJUMHJ8OBKGGrPER0okBeMDaan4mNBlgBROxuI8w==

webpack-dev-middleware@^5.3.1:
version "5.3.3"
resolved "https://registry.yarnpkg.com/webpack-dev-middleware/-/webpack-dev-middleware-5.3.3.tgz#efae67c2793908e7311f1d9b06f2a08dcc97e51f"
integrity sha512-hj5CYrY0bZLB+eTO+x/j67Pkrquiy7kWepMHmUMoPsmcUaeEnQJqFzHJOyxgWlq746/wUuA64p9ta34Kyb01pA==
version "5.3.4"
resolved "https://registry.yarnpkg.com/webpack-dev-middleware/-/webpack-dev-middleware-5.3.4.tgz#eb7b39281cbce10e104eb2b8bf2b63fce49a3517"
integrity sha512-BVdTqhhs+0IfoeAf7EoH5WE+exCmqGerHfDM0IL096Px60Tq2Mn9MAbnaGUe6HiMa41KMCYF19gyzZmBcq/o4Q==
dependencies:
colorette "^2.0.10"
memfs "^3.4.3"
Expand Down
28 changes: 9 additions & 19 deletions server/tests/integration/test_constructors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -148,41 +148,31 @@ async def test_build_tx_segment_ec(

# test handle invalid transcript
await check_response(
"/api/construct/structural_element/tx_segment_ect?transcript=NM_0012529.3&exon_start=3",
"/api/construct/structural_element/tx_segment_ec?transcript=NM_0012529.3&exon_start=3",
{"warnings": ["No exons found given NM_0012529.3"]},
check_tx_element_response,
)


@pytest.mark.asyncio()
async def test_build_segment_gct(
check_response, check_tx_element_response, tpm3_tx_t_element
async def test_build_segment_gc(
check_response, check_tx_element_response, tpm3_tx_g_element, tpm3_tx_t_element
):
"""Test correct functioning of transcript segment element construction using
genomic coordinates and transcript.
genomic coordinates and gene name.
"""
await check_response(
"/api/construct/structural_element/tx_segment_gct?transcript=NM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417",
{"element": tpm3_tx_t_element},
check_tx_element_response,
)
await check_response(
"/api/construct/structural_element/tx_segment_gct?transcript=refseq%3ANM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417",
{"element": tpm3_tx_t_element},
"/api/construct/structural_element/tx_segment_gc?gene=TPM3&chromosome=NC_000001.11&start=154171416&end=154171417",
{"element": tpm3_tx_g_element},
check_tx_element_response,
)


@pytest.mark.asyncio()
async def test_build_segment_gc(
check_response, check_tx_element_response, tpm3_tx_g_element
):
"""Test correct functioning of transcript segment element construction using
genomic coordinates and gene name.
genomic coordinates and transcript.
"""
await check_response(
"/api/construct/structural_element/tx_segment_gc?gene=TPM3&chromosome=NC_000001.11&start=154171416&end=154171417",
{"element": tpm3_tx_g_element},
"/api/construct/structural_element/tx_segment_gc?transcript=NM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417",
{"element": tpm3_tx_t_element},
check_tx_element_response,
)

Expand Down