from .arvcontainer import ArvadosContainer, RunnerContainer
from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
-from. runner import Runner, upload_instance
+from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
from .arvtool import ArvadosCommandTool
from .arvworkflow import ArvadosWorkflow, upload_workflow
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver
for p in proc_states["items"]:
self.on_message({
- "object_uuid": p["uuid"],
+ "object_uuid": p["uuid"],
"event_type": "update",
"properties": {
"new_attributes": p
keep_client=self.keep_client)
self.fs_access = make_fs_access(kwargs["basedir"])
+ if not kwargs.get("name"):
+ kwargs["name"] = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
+
+ # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
+ # Also uploads docker images.
+ upload_workflow_deps(self, tool)
+
+ # Reload tool object which may have been updated by
+ # upload_workflow_deps
+ tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]],
+ makeTool=self.arv_make_tool,
+ loader=tool.doc_loader,
+ avsc_names=tool.doc_schema,
+ metadata=tool.metadata)
+
+ # Upload local file references in the job order.
+ job_order = upload_job_order(self, "%s input" % kwargs["name"],
+ tool, job_order)
+
existing_uuid = kwargs.get("update_workflow")
if existing_uuid or kwargs.get("create_workflow"):
+ # Create a pipeline template or workflow record and exit.
if self.work_api == "jobs":
tmpl = RunnerTemplate(self, tool, job_order,
kwargs.get("enable_reuse"),
uuid=existing_uuid,
submit_runner_ram=kwargs.get("submit_runner_ram"),
- name=kwargs.get("name"))
+ name=kwargs["name"])
tmpl.save()
# cwltool.main will write our return value to stdout.
return (tmpl.uuid, "success")
- else:
+ elif self.work_api == "containers":
return (upload_workflow(self, tool, job_order,
- self.project_uuid,
- uuid=existing_uuid,
- submit_runner_ram=kwargs.get("submit_runner_ram"),
- name=kwargs.get("name")), "success")
+ self.project_uuid,
+ uuid=existing_uuid,
+ submit_runner_ram=kwargs.get("submit_runner_ram"),
+ name=kwargs["name"]),
+ "success")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
kwargs["tmpdir_prefix"] = "tmp"
kwargs["compute_checksum"] = kwargs.get("compute_checksum")
- if not kwargs["name"]:
- del kwargs["name"]
-
if self.work_api == "containers":
kwargs["outdir"] = "/var/spool/cwl"
kwargs["docker_outdir"] = "/var/spool/cwl"
kwargs["docker_outdir"] = "$(task.outdir)"
kwargs["tmpdir"] = "$(task.tmpdir)"
- upload_instance(self, shortname(tool.tool["id"]), tool, job_order)
-
runnerjob = None
if kwargs.get("submit"):
+ # Submit a runner job to run the workflow for us.
if self.work_api == "containers":
if tool.tool["class"] == "CommandLineTool":
kwargs["runnerjob"] = tool.tool["id"]
+ upload_dependencies(self,
+ kwargs["name"],
+ tool.doc_loader,
+ tool.tool,
+ tool.tool["id"],
+ False)
runnerjob = tool.job(job_order,
self.output_callback,
**kwargs).next()
else:
- runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name,
- self.output_tags, submit_runner_ram=kwargs.get("submit_runner_ram"),
- name=kwargs.get("name"), on_error=kwargs.get("on_error"))
- else:
- runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"), self.output_name,
- self.output_tags, submit_runner_ram=kwargs.get("submit_runner_ram"),
- name=kwargs.get("name"), on_error=kwargs.get("on_error"))
+ runnerjob = RunnerContainer(self, tool, job_order, kwargs.get("enable_reuse"),
+ self.output_name,
+ self.output_tags,
+ submit_runner_ram=kwargs.get("submit_runner_ram"),
+ name=kwargs.get("name"),
+ on_error=kwargs.get("on_error"),
+ submit_runner_image=kwargs.get("submit_runner_image"))
+ elif self.work_api == "jobs":
+ runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"),
+ self.output_name,
+ self.output_tags,
+ submit_runner_ram=kwargs.get("submit_runner_ram"),
+ name=kwargs.get("name"),
+ on_error=kwargs.get("on_error"),
+ submit_runner_image=kwargs.get("submit_runner_image"))
- if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
+ if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and self.work_api == "jobs":
# Create pipeline for local run
self.pipeline = self.api.pipeline_instances().create(
body={
help="RAM (in MiB) required for the workflow runner job (default 1024)",
default=1024)
+ parser.add_argument("--submit-runner-image", type=str,
+ help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
+ default=None)
+
parser.add_argument("--name", type=str,
help="Name to use for workflow execution instance.",
default=None)
projects / arvados.git / blobdiff