X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/55e73facf08cc8651eb71529a2ab4e0657d3c870..9f42cb85807ebad098aaf6e0ab3218f763b712e2:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index e0ee7285a8..742906c616 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -17,7 +17,7 @@ import uuid
 import math
 
 import arvados_cwl.util
-import ruamel.yaml as yaml
+import ruamel.yaml
 
 from cwltool.errors import WorkflowException
 from cwltool.process import UnsupportedRequirement, shortname
@@ -250,11 +250,7 @@ class ArvadosContainer(JobBase):
         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
                                                                     docker_req,
                                                                     runtimeContext.pull_image,
-                                                                    runtimeContext.project_uuid,
-                                                                    runtimeContext.force_docker_pull,
-                                                                    runtimeContext.tmp_outdir_prefix,
-                                                                    runtimeContext.match_local_docker,
-                                                                    runtimeContext.copy_deps)
+                                                                    runtimeContext)
 
         network_req, _ = self.get_requirement("NetworkAccess")
         if network_req:
@@ -536,10 +532,11 @@ class RunnerContainer(Runner):
                 "portable_data_hash": "%s" % workflowcollection
             }
         elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
-            workflowpath = "/var/lib/cwl/workflow.json#main"
-            #record = self.arvrunner.api.workflows().get(uuid=self.embedded_tool.tool["id"][6:33]).execute(num_retries=self.arvrunner.num_retries)
-            #packed = yaml.safe_load(record["definition"])
-            packed = self.loadingContext.loader.idx[self.embedded_tool.tool["id"]]
+            uuid, frg = urllib.parse.urldefrag(self.embedded_tool.tool["id"])
+            workflowpath = "/var/lib/cwl/workflow.json#" + frg
+            packedtxt = self.loadingContext.loader.fetch_text(uuid)
+            yaml = ruamel.yaml.YAML(typ='safe', pure=True)
+            packed = yaml.load(packedtxt)
             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
                 "kind": "json",
                 "content": packed
@@ -547,6 +544,8 @@ class RunnerContainer(Runner):
             container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
         else:
             main = self.loadingContext.loader.idx["_:main"]
+            if main.get("id") == "_:main":
+                del main["id"]
             workflowpath = "/var/lib/cwl/workflow.json#main"
             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
                 "kind": "json",