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Restore global logger state modified in main.py. #84

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Merged
merged 1 commit into from
May 15, 2016
Merged

Restore global logger state modified in main.py. #84

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250 changes: 127 additions & 123 deletions cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -436,151 +436,155 @@ def main(argsl=None,
# type: (List[str],Callable[...,Union[str,Dict[str,str]]],Callable[...,Process],Callable[[Dict[str,int]],Dict[str,int]],argparse.ArgumentParser,IO[Any],IO[Any],IO[Any],Callable[[],unicode]) -> int

_logger.removeHandler(defaultStreamHandler)
_logger.addHandler(logging.StreamHandler(stderr))

if argsl is None:
argsl = sys.argv[1:]
stderr_handler = logging.StreamHandler(stderr)
_logger.addHandler(stderr_handler)
try:
if argsl is None:
argsl = sys.argv[1:]

if parser is None:
parser = arg_parser()
if parser is None:
parser = arg_parser()

args = parser.parse_args(argsl)
args = parser.parse_args(argsl)

if args.quiet:
_logger.setLevel(logging.WARN)
if args.debug:
_logger.setLevel(logging.DEBUG)
if args.quiet:
_logger.setLevel(logging.WARN)
if args.debug:
_logger.setLevel(logging.DEBUG)

if args.version:
print versionfunc()
return 0
else:
_logger.info(versionfunc())
if args.version:
print versionfunc()
return 0
else:
_logger.info(versionfunc())

if not args.workflow:
parser.print_help()
_logger.error("")
_logger.error("CWL document required")
return 1
if not args.workflow:
parser.print_help()
_logger.error("")
_logger.error("CWL document required")
return 1

try:
document_loader, workflowobj, uri = fetch_document(args.workflow)
try:
document_loader, workflowobj, uri = fetch_document(args.workflow)

if args.print_deps:
printdeps(workflowobj, document_loader, stdout, args.relative_deps)
return 0
if args.print_deps:
printdeps(workflowobj, document_loader, stdout, args.relative_deps)
return 0

document_loader, avsc_names, processobj, metadata, uri \
= validate_document(document_loader, workflowobj, uri,
enable_dev=args.enable_dev, strict=args.strict,
preprocess_only=args.print_pre)
document_loader, avsc_names, processobj, metadata, uri \
= validate_document(document_loader, workflowobj, uri,
enable_dev=args.enable_dev, strict=args.strict,
preprocess_only=args.print_pre)

if args.print_pre:
stdout.write(json.dumps(processobj, indent=4))
return 0
if args.print_pre:
stdout.write(json.dumps(processobj, indent=4))
return 0

if args.print_rdf:
printrdf(uri, processobj, document_loader.ctx, args.rdf_serializer, stdout)
return 0
if args.print_rdf:
printrdf(uri, processobj, document_loader.ctx, args.rdf_serializer, stdout)
return 0

if args.print_dot:
printdot(uri, processobj, document_loader.ctx, stdout)
return 0
if args.print_dot:
printdot(uri, processobj, document_loader.ctx, stdout)
return 0

tool = make_tool(document_loader, avsc_names, processobj, metadata,
uri, makeTool, {})
except (validate.ValidationException) as exc:
_logger.error(u"Tool definition failed validation:\n%s", exc,
exc_info=(exc if args.debug else False))
return 1
except (RuntimeError, WorkflowException) as exc:
_logger.error(u"Tool definition failed initialization:\n%s", exc,
exc_info=(exc if args.debug else False))
return 1
except Exception as exc:
_logger.error(
u"I'm sorry, I couldn't load this CWL file%s",
", try again with --debug for more information.\nThe error was: "
"%s" % exc if not args.debug else ". The error was:",
exc_info=(exc if args.debug else False))
return 1
tool = make_tool(document_loader, avsc_names, processobj, metadata,
uri, makeTool, {})
except (validate.ValidationException) as exc:
_logger.error(u"Tool definition failed validation:\n%s", exc,
exc_info=(exc if args.debug else False))
return 1
except (RuntimeError, WorkflowException) as exc:
_logger.error(u"Tool definition failed initialization:\n%s", exc,
exc_info=(exc if args.debug else False))
return 1
except Exception as exc:
_logger.error(
u"I'm sorry, I couldn't load this CWL file%s",
", try again with --debug for more information.\nThe error was: "
"%s" % exc if not args.debug else ". The error was:",
exc_info=(exc if args.debug else False))
return 1

if isinstance(tool, int):
return tool
if isinstance(tool, int):
return tool

if args.tmp_outdir_prefix != 'tmp':
# Use user defined temp directory (if it exists)
args.tmp_outdir_prefix = os.path.abspath(args.tmp_outdir_prefix)
if not os.path.exists(args.tmp_outdir_prefix):
_logger.error("Intermediate output directory prefix doesn't exist, reverting to default")
return 1
if args.tmp_outdir_prefix != 'tmp':
# Use user defined temp directory (if it exists)
args.tmp_outdir_prefix = os.path.abspath(args.tmp_outdir_prefix)
if not os.path.exists(args.tmp_outdir_prefix):
_logger.error("Intermediate output directory prefix doesn't exist, reverting to default")
return 1

if args.tmpdir_prefix != 'tmp':
# Use user defined prefix (if the folder exists)
args.tmpdir_prefix = os.path.abspath(args.tmpdir_prefix)
if not os.path.exists(args.tmpdir_prefix):
_logger.error("Temporary directory prefix doesn't exist.")
return 1
if args.tmpdir_prefix != 'tmp':
# Use user defined prefix (if the folder exists)
args.tmpdir_prefix = os.path.abspath(args.tmpdir_prefix)
if not os.path.exists(args.tmpdir_prefix):
_logger.error("Temporary directory prefix doesn't exist.")
return 1

job_order_object = load_job_order(args, tool, parser, stdin,
print_input_deps=args.print_input_deps,
relative_deps=args.relative_deps,
stdout=stdout)
job_order_object = load_job_order(args, tool, parser, stdin,
print_input_deps=args.print_input_deps,
relative_deps=args.relative_deps,
stdout=stdout)

if isinstance(job_order_object, int):
return job_order_object
if isinstance(job_order_object, int):
return job_order_object

if args.cachedir:
args.cachedir = os.path.abspath(args.cachedir)
args.move_outputs = False
if args.cachedir:
args.cachedir = os.path.abspath(args.cachedir)
args.move_outputs = False

try:
out = executor(tool, job_order_object[0],
job_order_object[1], args,
conformance_test=args.conformance_test,
dry_run=args.dry_run,
outdir=args.outdir,
tmp_outdir_prefix=args.cachedir if args.cachedir else args.tmp_outdir_prefix,
use_container=args.use_container,
preserve_environment=args.preserve_environment,
pull_image=args.enable_pull,
rm_container=args.rm_container,
tmpdir_prefix=args.tmpdir_prefix,
enable_net=args.enable_net,
rm_tmpdir=args.rm_tmpdir,
makeTool=makeTool,
move_outputs=args.move_outputs,
select_resources=selectResources,
eval_timeout=args.eval_timeout,
cachedir=args.cachedir
)
# This is the workflow output, it needs to be written
if out is not None:
if isinstance(out, basestring):
stdout.write(out)
try:
out = executor(tool, job_order_object[0],
job_order_object[1], args,
conformance_test=args.conformance_test,
dry_run=args.dry_run,
outdir=args.outdir,
tmp_outdir_prefix=args.cachedir if args.cachedir else args.tmp_outdir_prefix,
use_container=args.use_container,
preserve_environment=args.preserve_environment,
pull_image=args.enable_pull,
rm_container=args.rm_container,
tmpdir_prefix=args.tmpdir_prefix,
enable_net=args.enable_net,
rm_tmpdir=args.rm_tmpdir,
makeTool=makeTool,
move_outputs=args.move_outputs,
select_resources=selectResources,
eval_timeout=args.eval_timeout,
cachedir=args.cachedir
)
# This is the workflow output, it needs to be written
if out is not None:
if isinstance(out, basestring):
stdout.write(out)
else:
stdout.write(json.dumps(out, indent=4))
stdout.write("\n")
stdout.flush()
else:
stdout.write(json.dumps(out, indent=4))
stdout.write("\n")
stdout.flush()
else:
return 1
except (validate.ValidationException) as exc:
_logger.error(
u"Input object failed validation:\n%s", exc,
exc_info=(exc if args.debug else False))
return 1
except WorkflowException as exc:
_logger.error(
u"Workflow error, try again with --debug for more "
"information:\n %s", exc, exc_info=(exc if args.debug else False))
return 1
except Exception as exc:
_logger.error(
u"Unhandled error, try again with --debug for more information:\n"
" %s", exc, exc_info=(exc if args.debug else False))
return 1
except (validate.ValidationException) as exc:
_logger.error(
u"Input object failed validation:\n%s", exc,
exc_info=(exc if args.debug else False))
return 1
except WorkflowException as exc:
_logger.error(
u"Workflow error, try again with --debug for more "
"information:\n %s", exc, exc_info=(exc if args.debug else False))
return 1
except Exception as exc:
_logger.error(
u"Unhandled error, try again with --debug for more information:\n"
" %s", exc, exc_info=(exc if args.debug else False))
return 1

return 0
return 0
finally:
_logger.removeHandler(stderr_handler)
_logger.addHandler(defaultStreamHandler)

if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))