From 68c8dada2c0ebf9e7d9faf61780aacae0d566440 Mon Sep 17 00:00:00 2001 From: John Han Date: Mon, 13 May 2019 02:53:11 -0700 Subject: [PATCH] Make final fixes to PR --- gcp_variant_transforms/beam_io/vcf_file_size_io.py | 14 +++++++------- gcp_variant_transforms/beam_io/vcfio.py | 6 +++--- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/gcp_variant_transforms/beam_io/vcf_file_size_io.py b/gcp_variant_transforms/beam_io/vcf_file_size_io.py index a26e58391..826ad65d3 100644 --- a/gcp_variant_transforms/beam_io/vcf_file_size_io.py +++ b/gcp_variant_transforms/beam_io/vcf_file_size_io.py @@ -17,29 +17,29 @@ from __future__ import absolute_import from typing import Iterable, List, Tuple # pylint: disable=unused-import -import itertools import logging +import itertools import apache_beam as beam from apache_beam import coders from apache_beam import transforms from apache_beam.io import filebasedsource -from apache_beam.io import range_trackers # pylint: disable=unused-import from apache_beam.io import filesystem from apache_beam.io import filesystems from apache_beam.io import iobase +from apache_beam.io import range_trackers # pylint: disable=unused-import from gcp_variant_transforms.beam_io import vcfio def _get_file_size(file_name): # type: (str) -> List[FileSizeInfo] - match_result = filesystems.FileSystems.match([file_name])[0] - if len(match_result.metadata_list) != 1: + matched_files = filesystems.FileSystems.match([file_name])[0].metadata_list + if len(matched_files) != 1: raise IOError("File name {} did not correspond to exactly 1 result. " - "Instead, got {}.".format(file_name, - len(match_result.metadata_list))) - file_metadata = match_result.metadata_list[0] + "Instead, got {} matches.".format(file_name, + len(matched_files))) + file_metadata = matched_files[0] compression_type = filesystem.CompressionTypes.detect_compression_type( file_metadata.path) diff --git a/gcp_variant_transforms/beam_io/vcfio.py b/gcp_variant_transforms/beam_io/vcfio.py index d633b42d5..04b9eb729 100644 --- a/gcp_variant_transforms/beam_io/vcfio.py +++ b/gcp_variant_transforms/beam_io/vcfio.py @@ -24,14 +24,14 @@ import enum import apache_beam as beam +from apache_beam import transforms from apache_beam.coders import coders from apache_beam.io import filebasedsource +from apache_beam.io import filesystem from apache_beam.io import filesystems +from apache_beam.io import iobase from apache_beam.io import range_trackers # pylint: disable=unused-import from apache_beam.io import textio -from apache_beam.io import filesystem -from apache_beam.io import iobase -from apache_beam import transforms from gcp_variant_transforms.beam_io import vcf_parser