Details
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Sub-task
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Status: Resolved
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P3
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Resolution: Fixed
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None
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None
Description
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)
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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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Attachments
Issue Links
- blocks
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BEAM-5315 Finish Python 3 porting for io module
- Resolved
- links to