Uploaded image for project: 'Beam'
  1. Beam
  2. BEAM-1251 Python 3 Support
  3. BEAM-5628

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

    XMLWordPrintableJSON

    Details

    • Type: Sub-task
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: sdk-py-core
    • Labels:
      None

      Description

      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
      "

        Attachments

          Issue Links

            Activity

              People

              • Assignee:
                splovyt Simon
                Reporter:
                tvalentyn Valentyn Tymofieiev
              • Votes:
                0 Vote for this issue
                Watchers:
                5 Start watching this issue

                Dates

                • Created:
                  Updated: