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Testing external contributor PR #290 #300

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Merged
k-burt-uch merged 5 commits into from
May 4, 2026
Merged

Testing external contributor PR #290 #300

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ea416a8
fix: dbgap accession parser
WilsonnnTan Feb 9, 2026
8158a28
Merge branch 'master' into fix/dbgap-accession-parser
k-burt-uch Apr 24, 2026
1bf2e62
test: add test cases for get_dbgap_accession_as_parts util
WilsonnnTan Apr 25, 2026
a0d3551
Merge branch 'master' into fix/dbgap-accession-parser
k-burt-uch Apr 30, 2026
f95dc06
test: add test for unexpected order of `v`, `p`, and `c`
WilsonnnTan Apr 30, 2026
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2 changes: 1 addition & 1 deletion gen3/external/nih/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@
# For more details about this regex, see the function that uses it
DBGAP_ACCESSION_REGEX = (
"(?P<phsid>phs(?P<phsid_number>[0-9]+))"
"(.(?P<participant_set>p(?P<participant_set_number>[0-9]+))){0,1}"
"(.(?P<version>v(?P<version_number>[0-9]+))){0,1}"
"(.(?P<participant_set>p(?P<participant_set_number>[0-9]+))){0,1}"
"(.(?P<consent>c(?P<consent_number>[0-9]+)+)){0,1}"
)

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105 changes: 105 additions & 0 deletions tests/test_utils.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,105 @@
import pytest

from gen3.external.nih.utils import get_dbgap_accession_as_parts


@pytest.mark.parametrize("test_input, expected", [
(
'phs000123',
{
'phsid': 'phs000123',
'phsid_number': '000123',
'version': '',
'version_number': '',
'participant_set': '',
'participant_set_number': '',
'consent': '',
'consent_number': ''
}
),
(
'phs000123.p1.c3',
{
'phsid': 'phs000123',
'phsid_number': '000123',
'version': '',
'version_number': '',
'participant_set': 'p1',
'participant_set_number': '1',
'consent': 'c3',
'consent_number': '3'
}
),
(
'phs000123.v3.c3',
{
'phsid': 'phs000123',
'phsid_number': '000123',
'version': 'v3',
'version_number': '3',
'participant_set': '',
'participant_set_number': '',
'consent': 'c3',
'consent_number': '3'
}
),
(
'phs000123.v3.p1.c3',
{
'phsid': 'phs000123',
'phsid_number': '000123',
'version': 'v3',
'version_number': '3',
'participant_set': 'p1',
'participant_set_number': '1',
'consent': 'c3',
'consent_number': '3'
}
),
# Unexpected order of v, p, and c
(
'phs000123.p3.v1.c3',
{
'phsid': 'phs000123',
'phsid_number': '000123',
'version': '',
'version_number': '',
'participant_set': 'p3',
'participant_set_number': '3',
'consent': '',
'consent_number': ''
}
),
(
'phs000123.v3.c1.p3',
{
'phsid': 'phs000123',
'phsid_number': '000123',
'version': 'v3',
'version_number': '3',
'participant_set': '',
'participant_set_number': '',
'consent': 'c1',
'consent_number': '1'
}
),
(
'phs000123.p3.v1',
{
'phsid': 'phs000123',
'phsid_number': '000123',
'version': '',
'version_number': '',
'participant_set': 'p3',
'participant_set_number': '3',
'consent': '',
'consent_number': ''
}
),
])
def test_get_dbgap_accession_as_parts(test_input, expected):
"""
Test dbgap accession parsing works and outputs expected fields and values.
"""

assert get_dbgap_accession_as_parts(test_input) == expected
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