[ARVADOS] updated: cc8a6bcb59408c938c570e48bc9af0fa497cb48f

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvjob.py | 2 +-
 sdk/cwl/arvados_cwl/runner.py | 8 +++-----
 2 files changed, 4 insertions(+), 6 deletions(-)

       via  cc8a6bcb59408c938c570e48bc9af0fa497cb48f (commit)
      from  3bf898db1a6f0db043060cd601131b17bd6ef82d (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit cc8a6bcb59408c938c570e48bc9af0fa497cb48f
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Sep 15 10:27:12 2016 -0400

    Fix misake in arvados-cwl-runner upload_dependencies refactor. refs #9766

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 4ba19a6..a796b2a 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -207,7 +207,7 @@ class RunnerJob(Runner):
 
         workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
 
-        self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"])[1]
+        self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"]).target[5:]
         return {
             "script": "cwl-runner",
             "script_version": "master",
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 9f7b84a..72f347e 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -22,7 +22,7 @@ logger = logging.getLogger('arvados.cwl-runner')
 cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 
 def upload_dependencies(arvrunner, name, document_loader,
-                        workflowobj, uri, keepprefix, loadref_run):
+                        workflowobj, uri, loadref_run):
     loaded = set()
     def loadref(b, u):
         joined = urlparse.urljoin(b, u)
@@ -55,8 +55,8 @@ def upload_dependencies(arvrunner, name, document_loader,
         files.append({"class": "File", "location": workflowobj["id"]})
 
     mapper = ArvPathMapper(arvrunner, files, "",
-                           keepprefix+"%s",
-                           keepprefix+"%s/%s",
+                           "keep:%s",
+                           "keep:%s/%s",
                            name=name)
 
     def setloc(p):
@@ -99,7 +99,6 @@ class Runner(object):
                                              self.tool.doc_loader,
                                              self.tool.tool,
                                              self.tool.tool["id"],
-                                             kwargs.get("keepprefix", ""),
                                              True)
 
         jobmapper = upload_dependencies(self.arvrunner,
@@ -107,7 +106,6 @@ class Runner(object):
                                         self.tool.doc_loader,
                                         self.job_order,
                                         self.job_order.get("id", "#"),
-                                        kwargs.get("keepprefix", ""),
                                         False)
 
         if "id" in self.job_order:

-----------------------------------------------------------------------


hooks/post-receive
--