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Merge pull request #10225 from mvdbeek/decrease_pysam_verbository

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[20.05] Decrease pysam verbosity
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Dannon
2020-09-15 13:23:49 -04:00
committed by GitHub
parent b47daef47a f31b071112
commit 38ca1293a5
2 changed files with 8 additions and 2 deletions
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lib/galaxy/datatypes/binary.py
+5 -2
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@@ -33,6 +33,9 @@ from galaxy.util.checkers import is_bz2, is_gzip
from . import data, dataproviders
log = logging.getLogger(__name__)
# pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
# Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
pysam.set_verbosity(0)
# Currently these supported binary data types must be manually set on upload
@@ -489,9 +492,9 @@ class Bam(BamNative):
# we start another process and discard stderr.
if index_flag == '-b':
# IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
cmd = ['python', '-c', "import pysam; pysam.index('%s', '%s')" % (file_name, index_name)]
cmd = ['python', '-c', "import pysam; pysam.set_verbosity(0); pysam.index('{}', '{}')".format(file_name, index_name)]
else:
cmd = ['python', '-c', "import pysam; pysam.index('%s', '%s', '%s')" % (index_flag, file_name, index_name)]
cmd = ['python', '-c', "import pysam; pysam.set_verbosity(0); pysam.index('{}', '{}', '{}')".format(index_flag, file_name, index_name)]
with open(os.devnull, 'w') as devnull:
subprocess.check_call(cmd, stderr=devnull, shell=False)
needs_sorting = False
lib/galaxy/visualization/data_providers/genome.py
+3
View File
@@ -27,6 +27,9 @@ from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and
# Utility functions.
#
# pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
# Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
pysam.set_verbosity(0)
PYSAM_INDEX_SYMLINK_NECESSARY = packaging.version.parse(pysam.__version__) <= packaging.version.parse('0.13.0')