12934: Tweak output of directories to pass conformance tests

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index a55db8d53ebeab4cc0567700945bf124f4d9158b..71ddd172214c4dac1b20907c8cf5a18bce6c37b2 100644 (file)
--- 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 bb95ba9ee4636ff273cd93455f901a2123a62995..998890a31c50acac0513479d0fad9675fd790647 100644 (file)
--- 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"):