[Debian-med-packaging] Bug#1025014: ncbi-acc-download: (autopkgtest) needs update for python3.11: Asked for extended validation, but Biopython not available
Paul Gevers
elbrus at debian.org
Mon Nov 28 20:14:03 GMT 2022
Source: ncbi-acc-download
Version: 0.2.8-1
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: needs-update
User: debian-python at lists.debian.org
Usertags: python3.11
Control: affects -1 src:python3-defaults
Dear maintainer(s),
We are in the transition of adding python3.11 as a supported Python
version [0]. With a recent upload of python3-defaults the autopkgtest of
ncbi-acc-download fails in testing when that autopkgtest is run with the
binary packages of python3-defaults from unstable. It passes when run
with only packages from testing. In tabular form:
pass fail
python3-defaults from testing 3.10.6-3
ncbi-acc-download from testing 0.2.8-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of python3-defaults
to testing [1]. https://docs.python.org/3/whatsnew/3.11.html lists
what's new in Python3.11, it may help to identify what needs to be updated.
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[0] https://bugs.debian.org/1021984
[1] https://qa.debian.org/excuses.php?package=python3-defaults
https://ci.debian.net/data/autopkgtest/testing/amd64/n/ncbi-acc-download/28727754/log.gz
=================================== FAILURES
===================================
__________________________ test_config_have_biopython
__________________________
def test_config_have_biopython():
"""Test we detect Biopython."""
> assert core.HAVE_BIOPYTHON
E assert False
E + where False = core.HAVE_BIOPYTHON
test_core.py:46: AssertionError
_________________ test_validate_and_write_extended_validation
__________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58de410>
def test_validate_and_write_extended_validation(req):
"""Test extended validation before writing."""
handle = StringIO()
req.get('http://fake/', text=u'>foo\nMAGIC')
r = requests.get('http://fake/')
> config = core.Config(extended_validation='loads', molecule='protein')
test_core.py:226: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/ncbi_acc_download/core.py:64: in __init__
self.extended_validation = extended_validation
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _ _
self = <ncbi_acc_download.core.Config object at 0x7f09f5d73ec0>, value =
'loads'
@extended_validation.setter
def extended_validation(self, value):
if value != 'none' and not HAVE_BIOPYTHON:
> raise ValueError("Asked for extended validation, but Biopython not available")
E ValueError: Asked for extended validation, but Biopython not
available
/usr/lib/python3/dist-packages/ncbi_acc_download/core.py:96: ValueError
____________________ test_download_and_validate_partial_wgs
____________________
req = <requests_mock.mocker.Mocker object at 0x7f09f5933610>
def test_download_and_validate_partial_wgs(req):
handle = StringIO(open(full_path('partialcontig.gbk'), 'r').read())
> assert validate.run_extended_validation(handle, 'genbank', 'loads')
E AssertionError: assert False
E + where False = <function run_extended_validation at
0x7f09f5882c00>(<_io.StringIO object at 0x7f09f5a3e710>, 'genbank', 'loads')
E + where <function run_extended_validation at 0x7f09f5882c00>
= validate.run_extended_validation
test_correct.py:15: AssertionError
_____________________ test_run_extended_validation_raises
______________________
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7f09f5767850>
mocker = <pytest_mock.plugin.MockerFixture object at 0x7f09f5767910>
def test_run_extended_validation_raises(monkeypatch, mocker):
"""Test the "seqence loads" validator catches exceptions in
SeqIO.parse()."""
seqio_mock = mocker.MagicMock()
seqio_mock.parse = mocker.MagicMock(side_effect=ValueError)
> monkeypatch.setattr(validate, 'SeqIO', seqio_mock)
E AttributeError: <module 'ncbi_acc_download.validate' from
'/usr/lib/python3/dist-packages/ncbi_acc_download/validate.py'> has no
attribute 'SeqIO'
test_validate.py:19: AttributeError
______________________ test_run_extended_validation_loads
______________________
def test_run_extended_validation_loads():
"""Test the "sequence loads" validator."""
handle = StringIO(u'>foo\nATGC\n>bar\nATGTGA\n')
> assert validate.run_extended_validation(handle, 'fasta', 'loads')
E AssertionError: assert False
E + where False = <function run_extended_validation at
0x7f09f5882c00>(<_io.StringIO object at 0x7f09f5a3ecb0>, 'fasta', 'loads')
E + where <function run_extended_validation at 0x7f09f5882c00>
= validate.run_extended_validation
test_validate.py:29: AssertionError
_________________________ test_download_wgs_parts_wgs
__________________________
req = <requests_mock.mocker.Mocker object at 0x7f09f5761990>
def test_download_wgs_parts_wgs(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs.gbk'), 'rt')
req.get(ENTREZ_URL, body=open(full_path('wgs_full.gbk'), 'rt'))
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
wgs_full = open(full_path('wgs_full.gbk'), 'rt')
> assert outhandle.getvalue() == wgs_full.read()
E AttributeError: '_io.TextIOWrapper' object has no attribute
'getvalue'
test_wgs.py:91: AttributeError
______________________ test_download_wgs_parts_wgs_retry
_______________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58fee90>
def test_download_wgs_parts_wgs_retry(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs.gbk'), 'rt')
req.get(ENTREZ_URL, response_list=[
{"text": u'Whoa, slow down', "status_code": 429, "headers":
{"Retry-After": "0"}},
{"body": open(full_path('wgs_full.gbk'), 'rt')},
])
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
wgs_full = open(full_path('wgs_full.gbk'), 'rt')
> assert outhandle.getvalue() == wgs_full.read()
E AttributeError: '_io.TextIOWrapper' object has no attribute
'getvalue'
test_wgs.py:106: AttributeError
______________________ test_download_wgs_parts_wgs_scafld
______________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58aad10>
def test_download_wgs_parts_wgs_scafld(req):
cfg = Config(format="genbank")
wgs_contig = open(full_path('wgs_scafld.gbk'), 'rt')
with open(full_path('wgs_full.gbk'), 'rt') as handle:
full_file = handle.read()
req.get(ENTREZ_URL, text=full_file)
outhandle = wgs.download_wgs_parts(wgs_contig, cfg)
> assert outhandle.getvalue() == full_file
E AttributeError: '_io.TextIOWrapper' object has no attribute
'getvalue'
test_wgs.py:119: AttributeError
_____________________ test_download_wgs_parts_supercontig
______________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58f1990>
def test_download_wgs_parts_supercontig(req):
cfg = Config(format="genbank")
supercontig = open(full_path('supercontig.gbk'), 'rt')
req.get(ENTREZ_URL,
body=open(full_path('supercontig_full.gbk'), 'rt'))
outhandle = wgs.download_wgs_parts(supercontig, cfg)
supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
> assert outhandle.getvalue() == supercontig_full.read()
E AttributeError: '_io.TextIOWrapper' object has no attribute
'getvalue'
test_wgs.py:130: AttributeError
__________________ test_download_wgs_parts_supercontig_retry
___________________
req = <requests_mock.mocker.Mocker object at 0x7f09f5933110>
def test_download_wgs_parts_supercontig_retry(req):
cfg = Config(format="genbank")
supercontig = open(full_path('supercontig.gbk'), 'rt')
req.get(ENTREZ_URL, response_list=[
{"text": u'Whoa, slow down', "status_code": 429, "headers":
{"Retry-After": "0"}},
{"body": open(full_path('supercontig_full.gbk'), 'rt')}
])
outhandle = wgs.download_wgs_parts(supercontig, cfg)
supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
> assert outhandle.getvalue() == supercontig_full.read()
E AttributeError: '_io.TextIOWrapper' object has no attribute
'getvalue'
test_wgs.py:145: AttributeError
__________________________ test_download_wgs_no_parts
__________________________
req = <requests_mock.mocker.Mocker object at 0x7f09f58791d0>
def test_download_wgs_no_parts(req):
cfg = Config(format="genbank")
supercontig = open(full_path('supercontig_full.gbk'), 'rt')
req.get(ENTREZ_URL, status_code=404)
outhandle = wgs.download_wgs_parts(supercontig, cfg)
supercontig_full = open(full_path('supercontig_full.gbk'), 'rt')
> assert outhandle.getvalue() == supercontig_full.read()
E AttributeError: '_io.TextIOWrapper' object has no attribute
'getvalue'
test_wgs.py:157: AttributeError
=========================== short test summary info
============================
FAILED test_core.py::test_config_have_biopython - assert False
FAILED test_core.py::test_validate_and_write_extended_validation -
ValueError...
FAILED test_correct.py::test_download_and_validate_partial_wgs -
AssertionErr...
FAILED test_validate.py::test_run_extended_validation_raises -
AttributeError...
FAILED test_validate.py::test_run_extended_validation_loads -
AssertionError:...
FAILED test_wgs.py::test_download_wgs_parts_wgs - AttributeError:
'_io.TextIO...
FAILED test_wgs.py::test_download_wgs_parts_wgs_retry - AttributeError:
'_io....
FAILED test_wgs.py::test_download_wgs_parts_wgs_scafld - AttributeError:
'_io...
FAILED test_wgs.py::test_download_wgs_parts_supercontig -
AttributeError: '_i...
FAILED test_wgs.py::test_download_wgs_parts_supercontig_retry -
AttributeErro...
FAILED test_wgs.py::test_download_wgs_no_parts - AttributeError:
'_io.TextIOW...
=================== 11 failed, 20 passed, 1 xfailed in 0.15s
===================
autopkgtest [20:14:21]: test run-param-test
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