[ARVADOS] updated: 1.1.2-152-gc5795cc

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py   | 2 +-
 sdk/cwl/arvados_cwl/pathmapper.py | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

       via  c5795cc6f73d5affc55a332fcddc37fa56636f9a (commit)
       via  f64238be677ff7f67cb5ac71ecac534d0c4aa488 (commit)
      from  69b7576df3796887ebe754a71437f6dc3032f119 (commit)

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commit c5795cc6f73d5affc55a332fcddc37fa56636f9a
Merge: 69b7576 f64238b
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Jan 31 10:51:44 2018 -0500

    Merge branch '12934-cwl-dir-output' refs #12934
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>


commit f64238be677ff7f67cb5ac71ecac534d0c4aa488
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Jan 31 09:23:57 2018 -0500

    12934: Tweak output of directories to pass conformance tests
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index a55db8d..71ddd17 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -282,7 +282,7 @@ class ArvCwlRunner(object):
 
         def rewrite(fileobj):
             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
-            for k in ("basename", "listing", "contents", "nameext", "nameroot", "dirname"):
+            for k in ("listing", "contents", "nameext", "nameroot", "dirname"):
                 if k in fileobj:
                     del fileobj[k]
 
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index bb95ba9..998890a 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -225,9 +225,10 @@ class StagingPathMapper(PathMapper):
         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)
+        if tgt in self.targets and (self.reversemap(tgt)[0] != loc):
+            while tgt in self.targets:
+                n += 1
+                tgt = "%s_%i%s" % (basetgt, n, baseext)
         self.targets.add(tgt)
         if obj["class"] == "Directory":
             if obj.get("writable"):

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