[jira] [Comment Edited] (BEAM-5628) Several VcfIO tests fail in Python 3 with TypeError: cannot use a string pattern on a bytes-like object

["Valentyn Tymofieiev (JIRA)" <ji...@apache.org>]

    [ https://issues.apache.org/jira/browse/BEAM-5628?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16648694#comment-16648694 ] 

Valentyn Tymofieiev edited comment on BEAM-5628 at 10/13/18 2:20 AM:
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Looks like VCF IO is using another package (PyVCF). We need to understand whether the issue is because we don't use PyVCF correctly (VCF IO issue), or because PyVCF itself is not Python3-compatible as it claims to be.


was (Author: tvalentyn):
Looks like VCF IO is using another package (PyVCF). We need to understand whether the issue is because we don't use PyVCF correctly (VCF IO issue), or because PyVCF itself is not Python3-compatible.

> Several VcfIO tests fail in Python 3 with  TypeError: cannot use a string pattern on a bytes-like object
> --------------------------------------------------------------------------------------------------------
>
>                 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
>            Assignee: Simon
>            Priority: Major
>
> 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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