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Posted to issues@beam.apache.org by "Valentyn Tymofieiev (Jira)" <ji...@apache.org> on 2019/10/28 16:17:00 UTC
[jira] [Updated] (BEAM-5628) VcfIO is not Python3-compatible and
there are no plans to make it compatible.
[ https://issues.apache.org/jira/browse/BEAM-5628?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Valentyn Tymofieiev updated BEAM-5628:
--------------------------------------
Summary: VcfIO is not Python3-compatible and there are no plans to make it compatible. (was: Several VcfIO tests fail in Python 3 with TypeError: cannot use a string pattern on a bytes-like object)
> VcfIO is not Python3-compatible and there are no plans to make it compatible.
> -----------------------------------------------------------------------------
>
> Key: BEAM-5628
> URL: https://issues.apache.org/jira/browse/BEAM-5628
> Project: Beam
> Issue Type: Sub-task
> Components: sdk-py-core
> Reporter: Valentyn Tymofieiev
> Priority: Minor
>
> Several VcfIO tests fail in Python 3 with TypeError: cannot use a string pattern on a bytes-like object
>
> ERROR: test_read_after_splitting (apache_beam.io.vcfio_test.VcfSourceTest)
> "
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/apache_beam/io/vcfio_test.py"", line 336, in test_read_after_splitting
> ] split_records.extend(source_test_utils.read_from_source(*source_info))
> ] File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/apache_beam/io/source_test_utils.py"", line 101, in read_from_source
> for value in reader:
> File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/apache_beam/io/vcfio.py"", line 264, in read_records
> for line in record_iterator:
> File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/apache_beam/io/vcfio.py"", line 330, in __next__
> record = next(self._vcf_reader)
> File ""/usr/local/google/home/valentyn/projects/beam/clean_head/beam/sdks/python/target/.tox/py3/lib/python3.5/site-packages/vcf/parser.py"", line 543, in __next__
> row = self._row_pattern.split(line.rstrip())
> TypeError: cannot use a string pattern on a bytes-like object
> "
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