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19070: Prefer to use the passed-in runtimeContext
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
arvcontainer.py
diff --git
a/sdk/cwl/arvados_cwl/arvcontainer.py
b/sdk/cwl/arvados_cwl/arvcontainer.py
index f75bde81e6cebd655a8378fbd382f18b3bf18d2f..5082cc2f4b57eacd0934019099509c2f42c7493b 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/
sdk/cwl/arvados_cwl/arvcontainer.py
@@
-247,7
+247,8
@@
class ArvadosContainer(JobBase):
runtimeContext.project_uuid,
runtimeContext.force_docker_pull,
runtimeContext.tmp_outdir_prefix,
runtimeContext.project_uuid,
runtimeContext.force_docker_pull,
runtimeContext.tmp_outdir_prefix,
- runtimeContext.match_local_docker)
+ runtimeContext.match_local_docker,
+ runtimeContext.copy_deps)
network_req, _ = self.get_requirement("NetworkAccess")
if network_req:
network_req, _ = self.get_requirement("NetworkAccess")
if network_req:
@@
-465,7
+466,7
@@
class RunnerContainer(Runner):
"cwd": "/var/spool/cwl",
"priority": self.priority,
"state": "Committed",
"cwd": "/var/spool/cwl",
"priority": self.priority,
"state": "Committed",
- "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
+ "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image
, runtimeContext
),
"mounts": {
"/var/lib/cwl/cwl.input.json": {
"kind": "json",
"mounts": {
"/var/lib/cwl/cwl.input.json": {
"kind": "json",
@@
-500,7
+501,7
@@
class RunnerContainer(Runner):
"portable_data_hash": "%s" % workflowcollection
}
else:
"portable_data_hash": "%s" % workflowcollection
}
else:
- packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
+ packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map
, runtimeContext
)
workflowpath = "/var/lib/cwl/workflow.json#main"
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
workflowpath = "/var/lib/cwl/workflow.json#main"
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
@@
-550,17
+551,17
@@
class RunnerContainer(Runner):
if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
- if
self
.on_error:
+ if
runtimeContext
.on_error:
command.append("--on-error=" + self.on_error)
command.append("--on-error=" + self.on_error)
- if
self
.intermediate_output_ttl:
- command.append("--intermediate-output-ttl=%d" %
self
.intermediate_output_ttl)
+ if
runtimeContext
.intermediate_output_ttl:
+ command.append("--intermediate-output-ttl=%d" %
runtimeContext
.intermediate_output_ttl)
- if
self.arvrunner
.trash_intermediate:
+ if
runtimeContext
.trash_intermediate:
command.append("--trash-intermediate")
command.append("--trash-intermediate")
- if
self.arvrunner
.project_uuid:
- command.append("--project-uuid="+
self.arvrunner
.project_uuid)
+ if
runtimeContext
.project_uuid:
+ command.append("--project-uuid="+
runtimeContext
.project_uuid)
if self.enable_dev:
command.append("--enable-dev")
if self.enable_dev:
command.append("--enable-dev")
@@
-581,8
+582,8
@@
class RunnerContainer(Runner):
def run(self, runtimeContext):
runtimeContext.keepprefix = "keep:"
job_spec = self.arvados_job_spec(runtimeContext)
def run(self, runtimeContext):
runtimeContext.keepprefix = "keep:"
job_spec = self.arvados_job_spec(runtimeContext)
- if
self.arvrunner
.project_uuid:
- job_spec["owner_uuid"] =
self.arvrunner
.project_uuid
+ if
runtimeContext
.project_uuid:
+ job_spec["owner_uuid"] =
runtimeContext
.project_uuid
extra_submit_params = {}
if runtimeContext.submit_runner_cluster:
extra_submit_params = {}
if runtimeContext.submit_runner_cluster: