[ARVADOS] updated: 8f237f88d58d9634814010e00ffe55e2cdde2334

[git at public.curoverse.com]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

       via  8f237f88d58d9634814010e00ffe55e2cdde2334 (commit)
       via  a0b3480b644c79a44f3ad03030b573d40111fbaf (commit)
      from  001e1ecfddb4f1d0cc26cdb415395ff47cde4914 (commit)

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commit 8f237f88d58d9634814010e00ffe55e2cdde2334
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Oct 28 11:08:53 2015 -0400

    7593: Generate files replaces $(task.keep)/ with keep: notation to reference
    keep files.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 1c118b9..5000b97 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -107,7 +107,7 @@ class ArvadosJob(object):
             script_parameters["task.vwd"] = {}
             for t in self.generatefiles:
                 if isinstance(self.generatefiles[t], dict):
-                    src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"][13:])
+                    src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"].replace("$(task.keep)/", "keep:"))
                     vwd.copy(rest, t, source_collection=src)
                 else:
                     with vwd.open(t, "w") as f:

commit a0b3480b644c79a44f3ad03030b573d40111fbaf
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Oct 27 16:54:30 2015 -0400

    7593: Fixup to use keep: URI scheme globbing for outputs.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 0fdf753..1c118b9 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -41,6 +41,7 @@ def arv_docker_get_image(api_client, dockerRequirement, pull_image):
 
     return dockerRequirement["dockerImageId"]
 
+
 class CollectionFsAccess(cwltool.process.StdFsAccess):
     def __init__(self, basedir):
         self.collections = {}
@@ -48,10 +49,11 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
 
     def get_collection(self, path):
         p = path.split("/")
-        if arvados.util.keep_locator_pattern.match(p[0]):
-            if p[0] not in self.collections:
-                self.collections[p[0]] = arvados.collection.CollectionReader(p[0])
-            return (self.collections[p[0]], "/".join(p[1:]))
+        if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
+            pdh = p[0][5:]
+            if pdh not in self.collections:
+                self.collections[pdh] = arvados.collection.CollectionReader(pdh)
+            return (self.collections[pdh], "/".join(p[1:]))
         else:
             return (None, path)
 
@@ -157,7 +159,7 @@ class ArvadosJob(object):
 
             try:
                 outputs = {}
-                outputs = self.collect_outputs(record["output"])
+                outputs = self.collect_outputs("keep:" + record["output"])
             except Exception as e:
                 logger.exception("Got exception while collecting job outputs:")
                 processStatus = "permanentFail"

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