X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c40389e0f064d4ea379d5f5471116936239a467a..60d986b8908487c086eb4e402ac69669cb26108b:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index a3a26aae0a..14513c7c32 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -6,14 +6,14 @@ import ruamel.yaml as yaml
 
 from cwltool.errors import WorkflowException
 from cwltool.process import get_feature, UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFiles
+from cwltool.pathmapper import adjustFiles, adjustDirObjs
 from cwltool.utils import aslist
 
 import arvados.collection
 
 from .arvdocker import arv_docker_get_image
 from . import done
-from .runner import Runner, arvados_jobs_image
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_listing
 from .fsaccess import CollectionFetcher
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -190,7 +190,9 @@ class RunnerContainer(Runner):
         the +body+ argument to container_requests().create().
         """
 
-        workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
+        packed = packed_workflow(self.arvrunner, self.tool)
+
+        adjustDirObjs(self.job_order, trim_listing)
 
         container_req = {
             "owner_uuid": self.arvrunner.project_uuid,
@@ -222,27 +224,13 @@ class RunnerContainer(Runner):
             "properties": {}
         }
 
-        workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
-        if workflowcollection.startswith("keep:"):
-            workflowcollection = workflowcollection[5:workflowcollection.index('/')]
-            workflowname = os.path.basename(self.tool.tool["id"])
-            workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
-            container_req["mounts"]["/var/lib/cwl/workflow"] = {
-                "kind": "collection",
-                "portable_data_hash": "%s" % workflowcollection
-                }
-        elif workflowcollection.startswith("arvwf:"):
-            workflowpath = "/var/lib/cwl/workflow.json#main"
-            wfuuid = workflowcollection[6:workflowcollection.index("#")]
-            wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
-            wfobj = yaml.safe_load(wfrecord["definition"])
-            if container_req["name"].startswith("arvwf:"):
-                container_req["name"] = wfrecord["name"]
-            container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
-                "kind": "json",
-                "json": wfobj
-            }
-            container_req["properties"]["template_uuid"] = wfuuid
+        workflowpath = "/var/lib/cwl/workflow.json#main"
+        container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
+            "kind": "json",
+            "json": packed
+        }
+        if self.tool.tool.get("id", "").startswith("arvwf:"):
+            container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33]
 
         command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps"]
         if self.output_name: