X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/3fa6aa4043286ad61e5f29c136d3cc2942e8750d..8032cee83c73d333a6b20c400e86f0d17b8da273:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index f3e122e603..e9b58bc83b 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -37,6 +37,9 @@ from ._version import __version__
 logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
 
+def cleanup_name_for_collection(name):
+    return name.replace("/", " ")
+
 class ArvadosContainer(JobBase):
     """Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
 
@@ -320,7 +323,7 @@ class ArvadosContainer(JobBase):
         if runtimeContext.submit_runner_cluster:
             extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
 
-        container_request["output_name"] = "Output from step %s" % (self.name)
+        container_request["output_name"] = cleanup_name_for_collection("Output from step %s" % (self.name))
         container_request["output_ttl"] = self.output_ttl
         container_request["mounts"] = mounts
         container_request["secret_mounts"] = secret_mounts
@@ -450,7 +453,7 @@ class ArvadosContainer(JobBase):
 class RunnerContainer(Runner):
     """Submit and manage a container that runs arvados-cwl-runner."""
 
-    def arvados_job_spec(self, runtimeContext):
+    def arvados_job_spec(self, runtimeContext, git_info):
         """Create an Arvados container request for this workflow.
 
         The returned dict can be used to create a container passed as
@@ -512,7 +515,7 @@ class RunnerContainer(Runner):
                 "portable_data_hash": "%s" % workflowcollection
             }
         else:
-            packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext)
+            packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext, git_info)
             workflowpath = "/var/lib/cwl/workflow.json#main"
             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
                 "kind": "json",
@@ -521,6 +524,8 @@ class RunnerContainer(Runner):
             if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
                 container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
 
+        container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})
+
         properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
         if properties_req:
             builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
@@ -592,7 +597,7 @@ class RunnerContainer(Runner):
 
     def run(self, runtimeContext):
         runtimeContext.keepprefix = "keep:"
-        job_spec = self.arvados_job_spec(runtimeContext)
+        job_spec = self.arvados_job_spec(runtimeContext, self.git_info)
         if runtimeContext.project_uuid:
             job_spec["owner_uuid"] = runtimeContext.project_uuid