def executor(self, tool, job_order, **kwargs):
final_output = []
final_status = []
def output_callback(out, processStatus):
final_status.append(processStatus)
final_output.append(out)
if "basedir" not in kwargs:
raise WorkflowException("Must provide 'basedir' in kwargs")
output_dirs = set()
if kwargs.get("outdir"):
finaloutdir = os.path.abspath(kwargs.get("outdir"))
else:
finaloutdir = None
if kwargs.get("tmp_outdir_prefix"):
kwargs["outdir"] = tempfile.mkdtemp(
prefix=kwargs["tmp_outdir_prefix"])
else:
kwargs["outdir"] = tempfile.mkdtemp()
output_dirs.add(kwargs["outdir"])
kwargs["mutation_manager"] = MutationManager()
jobReqs = None
if "cwl:requirements" in job_order:
jobReqs = job_order["cwl:requirements"]
elif ("cwl:defaults" in tool.metadata
and "cwl:requirements" in tool.metadata["cwl:defaults"]):
jobReqs = tool.metadata["cwl:defaults"]["cwl:requirements"]
if jobReqs:
for req in jobReqs:
tool.requirements.append(req)
if kwargs.get("default_container"):
tool.requirements.insert(
0, {
"class": "DockerRequirement",
"dockerPull": kwargs["default_container"]
})
jobs = tool.job(job_order, output_callback, **kwargs)
try:
for runnable in jobs:
if runnable:
builder = kwargs.get("builder", None)
if builder is not None:
runnable.builder = builder
if runnable.outdir:
output_dirs.add(runnable.outdir)
runnable.run(**kwargs)
else:
time.sleep(1)
except WorkflowException as e:
raise e
except Exception as e:
log.error("Got exception")
raise WorkflowException(str(e))
# wait for all processes to finish
self.wait()
if final_output and final_output[0] and finaloutdir:
final_output[0] = relocateOutputs(final_output[0], finaloutdir,
output_dirs,
kwargs.get("move_outputs"),
kwargs["make_fs_access"](""))
if kwargs.get("rm_tmpdir"):
cleanIntermediate(output_dirs)
if final_output and final_status:
return (final_output[0], final_status[0])
else:
return (None, "permanentFail")
def executor(self, tool, job_order, runtimeContext, **kwargs):
"""Executor method."""
final_output = []
final_status = []
def output_callback(out, processStatus):
final_status.append(processStatus)
final_output.append(out)
if not runtimeContext.basedir:
raise WorkflowException('`runtimeContext` should contain a '
'`basedir`')
output_dirs = set()
if runtimeContext.outdir:
finaloutdir = os.path.abspath(runtimeContext.outdir)
else:
finaloutdir = None
if runtimeContext.tmp_outdir_prefix:
runtimeContext.outdir = tempfile.mkdtemp(
prefix=runtimeContext.tmp_outdir_prefix)
else:
runtimeContext.outdir = tempfile.mkdtemp()
output_dirs.add(runtimeContext.outdir)
runtimeContext.mutation_manager = MutationManager()
jobReqs = None
if "cwl:requirements" in job_order:
jobReqs = job_order["cwl:requirements"]
elif ("cwl:defaults" in tool.metadata
and "cwl:requirements" in tool.metadata["cwl:defaults"]):
jobReqs = tool.metadata["cwl:defaults"]["cwl:requirements"]
if jobReqs:
for req in jobReqs:
tool.requirements.append(req)
if not runtimeContext.default_container:
runtimeContext.default_container = 'frolvlad/alpine-bash'
runtimeContext.docker_outdir = os.path.join(runtimeContext.working_dir,
"cwl/docker_outdir")
runtimeContext.docker_tmpdir = os.path.join(runtimeContext.working_dir,
"cwl/docker_tmpdir")
runtimeContext.docker_stagedir = os.path.join(
runtimeContext.working_dir, "cwl/docker_stagedir")
jobs = tool.job(job_order, output_callback, runtimeContext)
try:
for runnable in jobs:
if runnable:
if runtimeContext.builder:
runnable.builder = runtimeContext.builder
if runnable.outdir:
output_dirs.add(runnable.outdir)
runnable.run(runtimeContext)
else:
# log.error(
# "Workflow cannot make any more progress"
# )
# break
time.sleep(1)
except WorkflowException as e:
traceback.print_exc()
raise e
except Exception as e:
traceback.print_exc()
raise WorkflowException(str(e))
# wait for all processes to finish
self.wait()
if final_output and final_output[0] and finaloutdir:
final_output[0] = relocateOutputs(
final_output[0], finaloutdir, output_dirs,
runtimeContext.move_outputs, runtimeContext.make_fs_access(""))
if runtimeContext.rm_tmpdir:
cleanIntermediate(output_dirs)
if final_output and final_status:
return str(final_output[0]), str(final_status[0])
else:
return None, "permanentFail"
