19280: Add metrics checkpoints

[arvados.git] / sdk / cwl / arvados_cwl / executor.py

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 0bb17e99a296f00da1db725706945840295a89d4..3e8115ddb13d21716639746aa39cf5a096f9e83b 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -31,8 +31,8 @@ from arvados.keep import KeepClient
 from arvados.errors import ApiError
 
 import arvados_cwl.util
-from .arvcontainer import RunnerContainer
-from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
+from .arvcontainer import RunnerContainer, cleanup_name_for_collection
+from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder
 from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
 from .arvworkflow import ArvadosWorkflow, upload_workflow
 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size
@@ -581,6 +581,7 @@ The 'jobs' API is no longer supported.
 
         loadingContext = self.loadingContext.copy()
         loadingContext.do_validate = False
+        loadingContext.disable_js_validation = True
         if submitting:
             loadingContext.do_update = False
             # Document may have been auto-updated. Reload the original
@@ -593,6 +594,7 @@ The 'jobs' API is no longer supported.
 
         # Upload direct dependencies of workflow steps, get back mapping of files to keep references.
         # Also uploads docker images.
+        logger.info("Uploading workflow dependencies")
         merged_map = upload_workflow_deps(self, tool, runtimeContext)
 
         # Recreate process object (ArvadosWorkflow or
@@ -627,6 +629,11 @@ The 'jobs' API is no longer supported.
         runtimeContext.tmpdir_prefix = "tmp"
         runtimeContext.work_api = self.work_api
 
+        if not self.output_name:
+             self.output_name = "Output from workflow %s" % runtimeContext.name
+
+        self.output_name  = cleanup_name_for_collection(self.output_name)
+
         if self.work_api == "containers":
             if self.ignore_docker_for_reuse:
                 raise Exception("--ignore-docker-for-reuse not supported with containers API.")
@@ -779,8 +786,6 @@ The 'jobs' API is no longer supported.
             if workbench2 or workbench1:
                 logger.info("Output at %scollections/%s", workbench2 or workbench1, tool.final_output)
         else:
-            if self.output_name is None:
-                self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
             if self.output_tags is None:
                 self.output_tags = ""
 
@@ -794,8 +799,9 @@ The 'jobs' API is no longer supported.
             output_properties = {}
             output_properties_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
             if output_properties_req:
+                builder = make_builder(job_order, tool.hints, tool.requirements, runtimeContext, tool.metadata)
                 for pr in output_properties_req["outputProperties"]:
-                    output_properties[pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
+                    output_properties[pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
 
             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes,
                                                                                           self.output_tags, output_properties,