from cwltool.errors import WorkflowException def done(self, record, tmpdir, outdir, keepdir): colname = "Output %s of %s" % (record["output"][0:7], self.name) # check if collection already exists with same owner, name and content collection_exists = self.arvrunner.api.collections().list( filters=[["owner_uuid", "=", self.arvrunner.project_uuid], ['portable_data_hash', '=', record["output"]], ["name", "=", colname]] ).execute(num_retries=self.arvrunner.num_retries) if not collection_exists["items"]: # Create a collection located in the same project as the # pipeline with the contents of the output. # First, get output record. collections = self.arvrunner.api.collections().list( limit=1, filters=[['portable_data_hash', '=', record["output"]]], select=["manifest_text"] ).execute(num_retries=self.arvrunner.num_retries) if not collections["items"]: raise WorkflowException( "Job output '%s' cannot be found on API server" % ( record["output"])) # Create new collection in the parent project # with the output contents. self.arvrunner.api.collections().create(body={ "owner_uuid": self.arvrunner.project_uuid, "name": colname, "portable_data_hash": record["output"], "manifest_text": collections["items"][0]["manifest_text"] }, ensure_unique_name=True).execute( num_retries=self.arvrunner.num_retries) self.builder.outdir = outdir self.builder.pathmapper.keepdir = keepdir return self.collect_outputs("keep:" + record["output"])