def run_cwltool(ctx, path, job_path, **kwds):
"""Translate planemo kwds to cwltool kwds and run cwltool main function."""
ensure_cwltool_available()
args = []
conformance_test = kwds.get("conformance_test", False)
if conformance_test:
args.append("--conformance-test")
if ctx.verbose:
args.append("--verbose")
output_directory = kwds.get("output_directory", None)
if output_directory:
args.append("--outdir")
args.append(output_directory)
if kwds.get("no_container", False):
args.append("--no-container")
args.extend([path, job_path])
ctx.vlog("Calling cwltool with arguments %s" % args)
with tempfile.NamedTemporaryFile() as tmp_stdout, \
tempfile.NamedTemporaryFile() as tmp_stderr:
# cwltool passes sys.stderr to subprocess.Popen - ensure it has
# and actual fileno.
with real_io():
ret_code = main.main(
args,
stdout=tmp_stdout,
stderr=tmp_stderr
)
tmp_stdout.flush()
tmp_stderr.flush()
with open(tmp_stderr.name, "r") as stderr_f:
log = stderr_f.read()
ctx.vlog("cwltool log output [%s]" % log)
with open(tmp_stdout.name, "r") as stdout_f:
try:
result = json.load(stdout_f)
except ValueError:
message = JSON_PARSE_ERROR_MESSAGE % (
open(tmp_stdout.name, "r").read(),
tmp_stdout.name,
log
)
error(message)
raise Exception(message)
if ret_code != 0:
return ErrorRunResponse("Error running cwltool", log=log)
if conformance_test:
cwl_command_state = result
outputs = None
else:
cwl_command_state = None
outputs = result
return CwlToolRunResponse(
log,
cwl_command_state=cwl_command_state,
outputs=outputs,
)
def run_cwltool(ctx, path, job_path, **kwds):
"""Translate planemo kwds to cwltool kwds and run cwltool main function."""
ensure_cwltool_available()
args = []
if ctx.verbose:
args.append("--verbose")
output_directory = kwds.get("output_directory", None)
if output_directory:
args.append("--outdir")
args.append(output_directory)
if kwds.get("no_container", False):
args.append("--no-container")
ensure_dependency_resolvers_conf_configured(ctx, kwds)
args.append("--beta-dependency-resolvers-configuration")
args.append(kwds["dependency_resolvers_config_file"])
if kwds.get("mulled_containers"):
args.append("--beta-use-biocontainers")
if kwds.get("non_strict_cwl", False):
args.append("--non-strict")
args.extend([path, job_path])
ctx.vlog("Calling cwltool with arguments %s" % args)
with tempfile.NamedTemporaryFile("w") as tmp_stdout, \
tempfile.NamedTemporaryFile("w") as tmp_stderr:
# cwltool passes sys.stderr to subprocess.Popen - ensure it has
# and actual fileno.
with real_io():
ret_code = main.main(
args,
stdout=tmp_stdout,
stderr=tmp_stderr,
)
tmp_stdout.flush()
tmp_stderr.flush()
with open(tmp_stderr.name, "r") as stderr_f:
log = stderr_f.read()
ctx.vlog("cwltool log output [%s]" % log)
with open(tmp_stdout.name, "r") as stdout_f:
try:
result = json.load(stdout_f)
except ValueError:
message = JSON_PARSE_ERROR_MESSAGE % (
open(tmp_stdout.name, "r").read(),
tmp_stdout.name,
log
)
error(message)
raise Exception(message)
if ret_code != 0:
return ErrorRunResponse("Error running cwltool", log=log)
outputs = result
return CwlToolRunResponse(
log,
outputs=outputs,
)
def execute(ctx, config, runnable, job_path, **kwds):
"""Execute a Galaxy activity."""
try:
return _execute(ctx, config, runnable, job_path, **kwds)
except Exception as e:
if ctx.verbose:
ctx.vlog("Failed to execute Galaxy activity, throwing ErrorRunResponse")
traceback.print_exc(file=sys.stdout)
return ErrorRunResponse(unicodify(e))
def execute(ctx, config, runnable, job_path, **kwds):
"""Execute a Galaxy activity."""
try:
start_datetime = datetime.now()
return _execute(ctx, config, runnable, job_path, **kwds)
except Exception as e:
end_datetime = datetime.now()
ctx.log("Failed to execute Galaxy activity, throwing ErrorRunResponse")
traceback.print_exc(file=sys.stdout)
return ErrorRunResponse(unicodify(e), start_datetime=start_datetime, end_datetime=end_datetime)
def execute(ctx, config, runnable, job_path, **kwds):
"""Execute a Galaxy activity."""
try:
return _execute(ctx, config, runnable, job_path, **kwds)
except Exception as e:
return ErrorRunResponse(str(e))
