[ARVADOS] created: 6164f448f5828e1f4649fae4fe7866b8f082614c

[Git user]

        at  6164f448f5828e1f4649fae4fe7866b8f082614c (commit)


commit 6164f448f5828e1f4649fae4fe7866b8f082614c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 26 11:11:24 2017 -0400

    12037: Support CWL v1.0.1 spec.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curoverse.com>

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index e39c7d2..5a2d814 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -205,10 +205,20 @@ class ArvPathMapper(PathMapper):
 class StagingPathMapper(PathMapper):
     _follow_dirs = True
 
+    def __init__(self, referenced_files, basedir, stagedir, separateDirs=True):
+        self.targets = set()
+        super(StagingPathMapper, self).__init__(referenced_files, basedir, stagedir, separateDirs)
+
     def visit(self, obj, stagedir, basedir, copy=False, staged=False):
         # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
         loc = obj["location"]
         tgt = os.path.join(stagedir, obj["basename"])
+        basetgt, baseext = os.path.splitext(tgt)
+        n = 1
+        while tgt in self.targets:
+            n += 1
+            tgt = "%s_%i%s" % (basetgt, n, baseext)
+        self.targets.add(tgt)
         if obj["class"] == "Directory":
             self._pathmap[loc] = MapperEnt(loc, tgt, "Directory", staged)
             if loc.startswith("_:") or self._follow_dirs:
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index db11705..0823f89 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -51,8 +51,8 @@ setup(name='arvados-cwl-runner',
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to build.
       install_requires=[
-          'cwltool==1.0.20170707200431',
-          'schema-salad==2.6.20170630075932',
+          'cwltool==1.0.20170723124118',
+          'schema-salad==2.6.20170712194300',
           'typing==3.5.3.0',
           'ruamel.yaml==0.13.7',
           'arvados-python-client>=0.1.20170526013812',

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


hooks/post-receive
--