class ArvPathMapper(cwltool.pathmapper.PathMapper):
- def __init__(self, arvrunner, referenced_files, basedir, **kwargs):
+ def __init__(self, arvrunner, referenced_files, basedir,
+ collection_pattern, file_pattern, **kwargs):
self._pathmap = arvrunner.get_uploaded()
uploadfiles = []
for src in referenced_files:
if isinstance(src, basestring) and pdh_path.match(src):
- self._pathmap[src] = (src, "$(task.keep)/%s" % src[5:])
+ self._pathmap[src] = (src, collection_pattern % src[5:])
if src not in self._pathmap:
ab = cwltool.pathmapper.abspath(src, basedir)
- st = arvados.commands.run.statfile("", ab, fnPattern="$(task.keep)/%s/%s")
+ st = arvados.commands.run.statfile("", ab, fnPattern=file_pattern)
if kwargs.get("conformance_test"):
self._pathmap[src] = (src, ab)
elif isinstance(st, arvados.commands.run.UploadFile):
arvrunner.api,
dry_run=kwargs.get("dry_run"),
num_retries=3,
- fnPattern="$(task.keep)/%s/%s",
+ fnPattern=file_pattern,
project=arvrunner.project_uuid)
for src, ab, st in uploadfiles:
return ArvadosJob(self.arvrunner)
def makePathMapper(self, reffiles, input_basedir, **kwargs):
- return ArvPathMapper(self.arvrunner, reffiles, input_basedir, **kwargs)
+ return ArvPathMapper(self.arvrunner, reffiles, input_basedir,
+ "$(task.keep)/%s",
+ "$(task.keep)/%s/%s",
+ **kwargs)
class ArvCwlRunner(object):
def add_uploaded(self, src, pair):
self.uploaded[src] = pair
+ def upload_docker(self, tool):
+ pass
+
+ def submit(self, tool, job_order, input_basedir, args, **kwargs):
+ files = set()
+ def visitFiles(self, path):
+ files.add(path)
+
+ adjustFiles(process.scandeps("", tool.tool,
+ set(("run")),
+ set(("$schemas", "path"))),
+ visitFiles)
+ adjustFiles(job_order, visitFiles)
+
+ mapper = ArvPathMapper(self, files, "",
+ "$(task.keep)/%s",
+ "$(task.keep)/%s/%s",
+ **kwargs)
+
+ job_order = adjustFiles(job_order, lambda p: mapper.mapper(p))
+
+ response = self.api.jobs().create(body={
+ "script": "cwl-runner",
+ "script_version": "8654-arv-jobs-cwl-runner",
+ "repository": "arvados",
+ "script_parameters": job_order,
+ "runtime_constraints": {
+ "docker_image": "arvados/jobs"
+ }
+ }, find_or_create=args.enable_reuse).execute(num_retries=self.num_retries)
+ print response["uuid"]
+ return None
+
+
def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
+ if args.submit:
+ self.submit(tool, job_order, input_basedir, args, **kwargs)
+ return
+
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
self.debug = args.debug
default=True, dest="enable_reuse",
help="")
parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
+ parser.add_argument("--submit", type=str, help="Submit job and print job uuid.")
try:
runner = ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))