18947: Remove errant uses of runsu.sh.

[arvados.git] / sdk / cwl / arvados_cwl / pathmapper.py

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 4cd204f7df83ba49197f2cdb6ab2a61673a40b28..4a91a7a836f3a289e4088619eaffc7e058eaeed2 100644 (file)
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -21,7 +21,9 @@ import arvados.collection
 from schema_salad.sourceline import SourceLine
 
 from arvados.errors import ApiError
-from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
+from cwltool.pathmapper import PathMapper, MapperEnt
+from cwltool.utils import adjustFileObjs, adjustDirObjs
+from cwltool.stdfsaccess import abspath
 from cwltool.workflow import WorkflowException
 
 from .http import http_to_keep
@@ -99,9 +101,12 @@ class ArvPathMapper(PathMapper):
                 if srcobj["class"] == "Directory" and "listing" not in srcobj:
                     raise WorkflowException("Directory literal '%s' is missing `listing`" % src)
             elif src.startswith("http:") or src.startswith("https:"):
-                keepref = http_to_keep(self.arvrunner.api, self.arvrunner.project_uuid, src)
-                logger.info("%s is %s", src, keepref)
-                self._pathmap[src] = MapperEnt(keepref, keepref, srcobj["class"], True)
+                try:
+                    keepref = http_to_keep(self.arvrunner.api, self.arvrunner.project_uuid, src)
+                    logger.info("%s is %s", src, keepref)
+                    self._pathmap[src] = MapperEnt(keepref, keepref, srcobj["class"], True)
+                except Exception as e:
+                    logger.warning(str(e))
             else:
                 self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True)
 
@@ -285,6 +290,7 @@ class StagingPathMapper(PathMapper):
     def visit(self, obj, stagedir, basedir, copy=False, staged=False):
         # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
         loc = obj["location"]
+        stagedir = obj.get("dirname") or stagedir
         tgt = os.path.join(stagedir, obj["basename"])
         basetgt, baseext = os.path.splitext(tgt)