def _match(self, collection, patternsegments, parent):
ret = []
- for i in collection:
- if fnmatch.fnmatch(i, patternsegments[0]):
- cur = os.path.join(parent, i)
+ for filename in collection:
+ if fnmatch.fnmatch(filename, patternsegments[0]):
+ cur = os.path.join(parent, filename)
if len(patternsegments) == 1:
ret.append(cur)
else:
- ret.extend(self._match(collection[i], patternsegments[1:], cur))
+ ret.extend(self._match(collection[filename], patternsegments[1:], cur))
return ret
def glob(self, pattern):
script_parameters["task.env"] = {"TMPDIR": "$(task.tmpdir)"}
if self.environment:
- for k,v in self.environment.items():
- script_parameters["task.env"][k] = v
+ script_parameters["task.env"].update(self.environment)
if self.stdin:
script_parameters["task.stdin"] = self.pathmapper.mapper(self.stdin)[1]
self._pathmap = {}
uploadfiles = []
- pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+/(.*)')
+ pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+/.+')
for src in referenced_files:
if isinstance(src, basestring) and pdh_path.match(src):
finally:
self.cond.release()
- def arvExecutor(self, t, job_order, input_basedir, args, **kwargs):
+ def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
self.fs_access = CollectionFsAccess(input_basedir)
kwargs["enable_reuse"] = args.enable_reuse
if kwargs.get("conformance_test"):
- return cwltool.main.single_job_executor(t, job_order, input_basedir, args, **kwargs)
+ return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
else:
- jobiter = t.job(job_order,
+ jobiter = tool.job(job_order,
input_basedir,
self.output_callback,
**kwargs)
- for r in jobiter:
- if r:
+ for runnable in jobiter:
+ if runnable:
with self.lock:
- r.run(**kwargs)
+ runnable.run(**kwargs)
else:
if self.jobs:
try: