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[WIP] Move pysam index to external process #11558

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[WIP] Move pysam index to external process #11558

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18 changes: 5 additions & 13 deletions lib/galaxy/datatypes/binary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
)
from galaxy.datatypes.metadata import DictParameter, ListParameter, MetadataElement, MetadataParameter
from galaxy.datatypes.sniff import build_sniff_from_prefix
from galaxy.datatypes.util.generic_util import call_pysam_index
from galaxy.util import nice_size, sqlite
from galaxy.util.checkers import is_bz2, is_gzip
from . import data, dataproviders
Expand Down Expand Up @@ -488,13 +489,8 @@ def dataset_content_needs_grooming(self, file_name):
# If pysam fails to index a file it will write to stderr,
# and this causes the set_meta script to fail. So instead
# 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', f"import pysam; pysam.set_verbosity(0); pysam.index('{file_name}', '{index_name}')"]
else:
cmd = ['python', '-c', f"import pysam; pysam.set_verbosity(0); pysam.index('{index_flag}', '{file_name}', '{index_name}')"]
with open(os.devnull, 'w') as devnull:
subprocess.check_call(cmd, stderr=devnull, shell=False)
call_pysam_index(file_name, index_name, index_flag=index_flag,
stderr=os.devnull)
needs_sorting = False
except subprocess.CalledProcessError:
needs_sorting = True
Expand All @@ -516,11 +512,7 @@ def set_meta(self, dataset, overwrite=True, **kwd):
index_file = dataset.metadata.bam_csi_index
if not index_file:
index_file = dataset.metadata.spec[spec_key].param.new_file(dataset=dataset)
if index_flag == '-b':
# IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
pysam.index(dataset.file_name, index_file.file_name)
else:
pysam.index(index_flag, dataset.file_name, index_file.file_name)
call_pysam_index(dataset.file_name, index_file.file_name, index_flag=index_flag)
dataset.metadata.bam_index = index_file

def sniff(self, file_name):
Expand Down Expand Up @@ -691,7 +683,7 @@ def get_cram_version(self, filename):

def set_index_file(self, dataset, index_file):
try:
pysam.index(dataset.file_name, index_file.file_name)
call_pysam_index(dataset.file_name, index_file.file_name)
return True
except Exception as exc:
log.warning('%s, set_index_file Exception: %s', self, exc)
Expand Down
18 changes: 18 additions & 0 deletions lib/galaxy/datatypes/util/generic_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,3 +16,21 @@ def count_special_lines(word, filename, invert=False):
except commands.CommandLineException:
return 0
return int(out)


def call_pysam_index(self, file_name, index_name, index_flag=None, stderr=None):
"""
The pysam.index call can block the GIL, which can pause all threads, including
the heartbeat thread. Therefore, start it as an external process.
"""
if index_flag == '-b' or not index_flag:
# IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
cmd = ['python', '-c', f"import pysam; pysam.set_verbosity(0); pysam.index('{file_name}', '{index_name}')"]
else:
cmd = ['python', '-c',
f"import pysam; pysam.set_verbosity(0); pysam.index('{index_flag}', '{file_name}', '{index_name}')"]
if stderr:
with open(stderr, 'w') as stderr:
subprocess.check_call(cmd, stderr=stderr, shell=False)
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Can you use

galaxy/lib/galaxy/util/commands.py

Line 88 in ca44259

def execute(cmds, input=None):
?

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@nuwang nuwang Mar 6, 2021 •
edited
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Thanks for reviewing. The original code has a specific comment saying that stderr needs to be discarded:

galaxy/lib/galaxy/datatypes/binary.py

Line 490 in e5a9524

# we start another process and discard stderr.

and execute doesn't seem to support stderr redirection?

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@mvdbeek mvdbeek Mar 6, 2021 •
edited
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That's what stderr=subprocess.PIPE does (not exactly, but this good enough. the only important thing is that stderr of the externalize pysam call doesn't end up in the outer stderr, which was? a failure reason for the metadata script)

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Aah I see, the piped stderr is being ignored. Sure, seems fine, can do.

else:
subprocess.check_call(cmd, shell=False)