17004: Fix setting properties on final collection

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index ec9c52c59aac69a5881cc25ccf0a4267e3e4e7ab..f3e122e603f8cd9cf9b768158132f28d7190b685 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -349,8 +349,8 @@ class ArvadosContainer(JobBase):
                 for pr in output_properties_req["outputProperties"]:
                     container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
             else:
                 for pr in output_properties_req["outputProperties"]:
                     container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
             else:

-                logger.warning("%s API server is too old to support setting properties on output collections.",
-                               self.arvrunner.label(self))
+                logger.warning("%s API revision is %s, revision %s is required to support setting properties on output collections.",
+                               self.arvrunner.label(self), self.arvrunner.api._rootDesc["revision"], "20220510")

 
         if runtimeContext.runnerjob.startswith("arvwf:"):
             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]
 
         if runtimeContext.runnerjob.startswith("arvwf:"):
             wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.index("#")]

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 7fdf07de254578af5b8778ceda2c10d0d8cf7561..fe078e32278738d5ebb2f1200199dad0a8771731 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -32,7 +32,7 @@ from arvados.errors import ApiError
 
 import arvados_cwl.util
 from .arvcontainer import RunnerContainer
 
 import arvados_cwl.util
 from .arvcontainer import RunnerContainer

-from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
+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
 from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
 from .arvworkflow import ArvadosWorkflow, upload_workflow
 from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache, pdh_size


@@ -795,8 +795,9 @@ The 'jobs' API is no longer supported.
             output_properties = {}
             output_properties_req, _ = tool.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
             if output_properties_req:
             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"]:
                 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,
 
             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, storage_classes,
                                                                                           self.output_tags, output_properties,