self.uploaded[src] = pair
def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
- try:
- self.api.collections().get(uuid=crunchrunner_pdh).execute()
- except arvados.errors.ApiError as e:
- import httplib2
- h = httplib2.Http(ca_certs=arvados.util.ca_certs_path())
- resp, content = h.request(crunchrunner_download, "GET")
- resp2, content2 = h.request(certs_download, "GET")
- with arvados.collection.Collection() as col:
- with col.open("crunchrunner", "w") as f:
- f.write(content)
- with col.open("ca-certificates.crt", "w") as f:
- f.write(content2)
-
- col.save_new("crunchrunner binary", ensure_unique_name=True)
-
+ self.debug = args.debug
+
+ if args.quiet:
+ logger.setLevel(logging.WARN)
+ logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
+
+ useruuid = self.api.users().current().execute()["uuid"]
+ self.project_uuid = args.project_uuid if args.project_uuid else useruuid
+ self.pipeline = None
+
+ if args.submit:
+ runnerjob = RunnerJob(self, tool, job_order, args.enable_reuse)
+ if not args.wait:
+ runnerjob.run()
+ return
+
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
- self.debug = args.debug
self.fs_access = CollectionFsAccess(input_basedir)
kwargs["fs_access"] = self.fs_access