+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import re
from cwltool.errors import WorkflowException
from collections import deque
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)
+ cols = [
+ ("output", "Output %s of %s" % (record["output"][0:7], self.name), record["output"]),
+ ("log", "Log of %s" % (record["uuid"]), record["log"])
+ ]
- 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"]
+ for coltype, colname, colpdh in cols:
+ # 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', '=', colpdh],
+ ["name", "=", colname]]
).execute(num_retries=self.arvrunner.num_retries)
- if not collections["items"]:
- raise WorkflowException(
- "[job %s] output '%s' cannot be found on API server" % (
- self.name, record["output"]))
+ if not collection_exists["items"]:
+ # Create a collection located in the same project as the
+ # pipeline with the contents of the output/log.
+ # First, get output/log record.
+ collections = self.arvrunner.api.collections().list(
+ limit=1,
+ filters=[['portable_data_hash', '=', colpdh]],
+ select=["manifest_text"]
+ ).execute(num_retries=self.arvrunner.num_retries)
+
+ if not collections["items"]:
+ raise WorkflowException(
+ "[job %s] %s '%s' cannot be found on API server" % (
+ self.name, coltype, colpdh))
- # 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)
+ # Create new collection in the parent project
+ # with the output/log contents.
+ self.arvrunner.api.collections().create(body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "name": colname,
+ "portable_data_hash": colpdh,
+ "manifest_text": collections["items"][0]["manifest_text"]
+ }, ensure_unique_name=True).execute(
+ num_retries=self.arvrunner.num_retries)
return done_outputs(self, record, tmpdir, outdir, keepdir)