8442: Debugging container --submit with crunch2

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 136d5aec152bb53b60458942357a6562c915befe..ba26816c219bc871dfb85e6bfc6290916390d395 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -19,6 +19,7 @@ import arvados.events
 from .arvcontainer import ArvadosContainer, RunnerContainer
 from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
 from .arvtool import ArvadosCommandTool
+from .fsaccess import CollectionFsAccess
 
 from cwltool.process import shortname, UnsupportedRequirement
 from arvados.api import OrderedJsonModel
@@ -184,6 +185,9 @@ class ArvCwlRunner(object):
             if self.pipeline:
                 self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
                                                      body={"state": "Failed"}).execute(num_retries=self.num_retries)
+            if runnerjob and self.crunch2:
+                self.api.container_requests().update(uuid=runnerjob.uuid,
+                                                     body={"priority": "0"}).execute(num_retries=self.num_retries)
         finally:
             self.cond.release()
 

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index be1140469ade22369f5ae51fac6da24a4826ddcd..4c80896fbe8e019a05dfb04f6dab17cdd876d285 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -152,7 +152,7 @@ class RunnerContainer(Runner):
         workflowname = os.path.basename(self.tool.tool["id"])
         workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
         workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
-        workflowcollection = workflowcollection[5:workflowcollection.index('/')]
+        workflowcollection = workflowcollection[workflowcollection.index('/')]
         jobpath = "/var/lib/cwl/job/cwl.input.json"
 
         container_image = arv_docker_get_image(self.arvrunner.api,
@@ -181,11 +181,16 @@ class RunnerContainer(Runner):
                 "stdout": {
                     "kind": "file",
                     "path": "/var/spool/cwl/cwl.output.json"
+                },
+                "/var/spool/cwl": {
+                    "kind": "collection",
+                    "writable": True
                 }
             },
             "runtime_constraints": {
                 "vcpus": 1,
-                "ram": 1024*1024*256
+                "ram": 1024*1024*256,
+                "API": True
             }
         }
 

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index c911895fa22a90b395ed63ec8f04d1ff788c2740..d48c93a14a9b6c27fb1c943efb06c9010420508f 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -1,4 +1,5 @@
 import fnmatch
+import cwltool.process
 
 class CollectionFsAccess(cwltool.process.StdFsAccess):
     """Implement the cwltool FsAccess interface for Arvados Collections."""