X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/cc095ef1f8c86b05a8e58f15c4086a2caa861ec5..083b86a4e748900bcc285cac8bfd2ecdd36679f6:/sdk/cwl/arvados_cwl/executor.py diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py index e481a5f10b..ef84dd4983 100644 --- a/sdk/cwl/arvados_cwl/executor.py +++ b/sdk/cwl/arvados_cwl/executor.py @@ -34,9 +34,9 @@ from arvados.errors import ApiError import arvados_cwl.util from .arvcontainer import RunnerContainer, cleanup_name_for_collection -from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder +from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder, update_from_merged_map from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool -from .arvworkflow import ArvadosWorkflow, upload_workflow, new_upload_workflow, make_workflow_record +from .arvworkflow import ArvadosWorkflow, upload_workflow, make_workflow_record from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size from .perf import Perf from .pathmapper import NoFollowPathMapper @@ -657,9 +657,11 @@ The 'jobs' API is no longer supported. # Upload local file references in the job order. with Perf(metrics, "upload_job_order"): - job_order = upload_job_order(self, "%s input" % runtimeContext.name, + job_order, jobmapper = upload_job_order(self, "%s input" % runtimeContext.name, updated_tool, job_order, runtimeContext) + # determine if we are submitting or directly executing the workflow. + # # the last clause means: if it is a command line tool, and we # are going to wait for the result, and always_submit_runner # is false, then we don't submit a runner process. @@ -674,15 +676,6 @@ The 'jobs' API is no longer supported. loadingContext = self.loadingContext.copy() loadingContext.do_validate = False loadingContext.disable_js_validation = True - # if submitting and not self.fast_submit: - # loadingContext.do_update = False - # # Document may have been auto-updated. Reload the original - # # document with updating disabled because we want to - # # submit the document with its original CWL version, not - # # the auto-updated one. - # with Perf(metrics, "load_tool original"): - # tool = load_tool(updated_tool.tool["id"], loadingContext) - # else: tool = updated_tool # Upload direct dependencies of workflow steps, get back mapping of files to keep references. @@ -692,57 +685,59 @@ The 'jobs' API is no longer supported. with Perf(metrics, "upload_workflow_deps"): merged_map = upload_workflow_deps(self, tool, runtimeContext) else: + # in the fast submit case, we are running a workflow that + # has already been uploaded to Arvados, so we assume all + # the dependencies have been pinned to keep references and + # there is nothing to do. merged_map = {} - # Recreate process object (ArvadosWorkflow or - # ArvadosCommandTool) because tool document may have been - # updated by upload_workflow_deps in ways that modify - # hints or requirements. loadingContext.loader = tool.doc_loader loadingContext.avsc_names = tool.doc_schema loadingContext.metadata = tool.metadata loadingContext.skip_resolve_all = True - #with Perf(metrics, "load_tool"): - # tool = load_tool(tool.tool, loadingContext) workflow_wrapper = None if submitting and not self.fast_submit: # upload workflow and get back the workflow wrapper - workflow_wrapper = new_upload_workflow(self, tool, job_order, - runtimeContext.project_uuid, - runtimeContext, - uuid=runtimeContext.update_workflow, - submit_runner_ram=runtimeContext.submit_runner_ram, - name=runtimeContext.name, - merged_map=merged_map, - submit_runner_image=runtimeContext.submit_runner_image, - git_info=git_info, - set_defaults=(runtimeContext.update_workflow or runtimeContext.create_workflow)) + workflow_wrapper = upload_workflow(self, tool, job_order, + runtimeContext.project_uuid, + runtimeContext, + uuid=runtimeContext.update_workflow, + submit_runner_ram=runtimeContext.submit_runner_ram, + name=runtimeContext.name, + merged_map=merged_map, + submit_runner_image=runtimeContext.submit_runner_image, + git_info=git_info, + set_defaults=(runtimeContext.update_workflow or runtimeContext.create_workflow), + jobmapper=jobmapper) if runtimeContext.update_workflow or runtimeContext.create_workflow: - # Now create a workflow record and exit. + # We're registering the workflow, so create or update + # the workflow record and then exit. uuid = make_workflow_record(self, workflow_wrapper, runtimeContext.name, tool, runtimeContext.project_uuid, runtimeContext.update_workflow) self.stdout.write(uuid + "\n") return (None, "success") + # Did not register a workflow, we're going to submit + # it instead. loadingContext.loader.idx.clear() loadingContext.loader.idx["_:main"] = workflow_wrapper workflow_wrapper["id"] = "_:main" - # Reload just the wrapper workflow. + # Reload the minimal wrapper workflow. self.fast_submit = True - #print("bah bah", loadingContext.requirements) - #workflow_wrapper, _ = loadingContext.loader.resolve_all(cmap(workflow_wrapper), "_:main", checklinks=True) - - #tool = load_tool(workflow_wrapper[0], loadingContext) - #print("AAA", json.dumps(loadingContext.loader.idx["_:main"], indent=2)) tool = load_tool(workflow_wrapper, loadingContext) - loadingContext.loader.idx["_:main"] = workflow_wrapper - #print("BBB", json.dumps(loadingContext.loader.idx["_:main"], indent=2)) + if not submitting: + # If we are going to run the workflow now (rather than + # submit it), we need to update the workflow document + # replacing file references with keep references. If we + # are just going to construct a run submission, we don't + # need to do this. + update_from_merged_map(tool, merged_map) self.apply_reqs(job_order, tool) @@ -786,7 +781,10 @@ The 'jobs' API is no longer supported. runnerjob = None if runtimeContext.submit: - # Submit a runner job to run the workflow for us. + # We are submitting instead of running immediately. + # + # Create a "Runner job" that when run() is invoked, + # creates the container request to run the workflow. if self.work_api == "containers": if submitting: loadingContext.metadata = updated_tool.metadata.copy() @@ -815,11 +813,16 @@ The 'jobs' API is no longer supported. runtimeContext) if runtimeContext.submit and not runtimeContext.wait: + # User provided --no-wait so submit the container request, + # get the container request uuid, print it out, and exit. runnerjob = next(jobiter) runnerjob.run(runtimeContext) self.stdout.write(runnerjob.uuid+"\n") return (None, "success") + # We either running the workflow directly, or submitting it + # and will wait for a final result. + current_container = arvados_cwl.util.get_current_container(self.api, self.num_retries, logger) if current_container: logger.info("Running inside container %s", current_container.get("uuid"))