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Merge branch '8784-dir-listings'
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
runner.py
diff --git
a/sdk/cwl/arvados_cwl/runner.py
b/sdk/cwl/arvados_cwl/runner.py
index 69e4f5bd7b628e89349822e45ae01a587320c605..683f548c48cc835cd5ff7664cd0306cb0ea7f17e 100644
(file)
--- a/
sdk/cwl/arvados_cwl/runner.py
+++ b/
sdk/cwl/arvados_cwl/runner.py
@@
-1,3
+1,7
@@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import os
import urlparse
from functools import partial
import os
import urlparse
from functools import partial
@@
-100,7
+104,8
@@
def upload_dependencies(arvrunner, name, document_loader,
mapper = ArvPathMapper(arvrunner, sc, "",
"keep:%s",
"keep:%s/%s",
mapper = ArvPathMapper(arvrunner, sc, "",
"keep:%s",
"keep:%s/%s",
- name=name)
+ name=name,
+ single_collection=True)
def setloc(p):
if "location" in p and (not p["location"].startswith("_:")) and (not p["location"].startswith("keep:")):
def setloc(p):
if "location" in p and (not p["location"].startswith("_:")) and (not p["location"].startswith("keep:")):
@@
-186,7
+191,7
@@
def upload_job_order(arvrunner, name, tool, job_order):
return job_order
return job_order
-def upload_workflow_deps(arvrunner, tool):
+def upload_workflow_deps(arvrunner, tool
, override_tools
):
# Ensure that Docker images needed by this workflow are available
upload_docker(arvrunner, tool)
# Ensure that Docker images needed by this workflow are available
upload_docker(arvrunner, tool)
@@
-203,6
+208,7
@@
def upload_workflow_deps(arvrunner, tool):
False,
include_primary=False)
document_loader.idx[deptool["id"]] = deptool
False,
include_primary=False)
document_loader.idx[deptool["id"]] = deptool
+ override_tools[deptool["id"]] = json.dumps(deptool)
tool.visit(upload_tool_deps)
tool.visit(upload_tool_deps)
@@
-246,7
+252,8
@@
class Runner(object):
def __init__(self, runner, tool, job_order, enable_reuse,
output_name, output_tags, submit_runner_ram=0,
def __init__(self, runner, tool, job_order, enable_reuse,
output_name, output_tags, submit_runner_ram=0,
- name=None, on_error=None, submit_runner_image=None):
+ name=None, on_error=None, submit_runner_image=None,
+ intermediate_output_ttl=0):
self.arvrunner = runner
self.tool = tool
self.job_order = job_order
self.arvrunner = runner
self.tool = tool
self.job_order = job_order
@@
-259,6
+266,7
@@
class Runner(object):
self.name = name
self.on_error = on_error
self.jobs_image = submit_runner_image or "arvados/jobs:"+__version__
self.name = name
self.on_error = on_error
self.jobs_image = submit_runner_image or "arvados/jobs:"+__version__
+ self.intermediate_output_ttl = intermediate_output_ttl
if submit_runner_ram:
self.submit_runner_ram = submit_runner_ram
if submit_runner_ram:
self.submit_runner_ram = submit_runner_ram