[ARVADOS] updated: 01b5da8f2cd7f88dba7be836673c22579b465422

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py     |  2 +-
 sdk/cwl/arvados_cwl/arvcontainer.py |  2 --
 sdk/cwl/arvados_cwl/pathmapper.py   | 25 +++++++++++++------------
 3 files changed, 14 insertions(+), 15 deletions(-)

       via  01b5da8f2cd7f88dba7be836673c22579b465422 (commit)
      from  328f506a294619694b84cf123332f7c2694552e1 (commit)

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commit 01b5da8f2cd7f88dba7be836673c22579b465422
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Dec 21 10:34:53 2016 -0500

    10497: Use SourceLine in context manager in PathMapper.  Remove unnecessary import.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 85156db..d4af0f9 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -208,7 +208,7 @@ class ArvCwlRunner(object):
                         raise SourceLine(obj, "stderr", UnsupportedRequirement).makeError("Stderr redirection currently not suppported with --api=containers")
             for v in obj.itervalues():
                 self.check_features(v)
-        if isinstance(obj, list):
+        elif isinstance(obj, list):
             for i,v in enumerate(obj):
                 with SourceLine(obj, i, UnsupportedRequirement):
                     self.check_features(v)
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 25a8ffa..dbbd83d 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -4,8 +4,6 @@ import os
 
 import ruamel.yaml as yaml
 
-from schema_salad.sourceline import SourceLine
-
 from cwltool.errors import WorkflowException
 from cwltool.process import get_feature, UnsupportedRequirement, shortname
 from cwltool.pathmapper import adjustFiles
diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index e63161d..a6b3d15 100644
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -40,19 +40,20 @@ class ArvPathMapper(PathMapper):
                 # mount.
                 ab = abspath(src, self.input_basedir)
                 st = arvados.commands.run.statfile("", ab, fnPattern="keep:%s/%s")
-                if isinstance(st, arvados.commands.run.UploadFile):
-                    uploadfiles.add((src, ab, st))
-                elif isinstance(st, arvados.commands.run.ArvFile):
-                    self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File")
-                elif src.startswith("_:"):
-                    if "contents" in srcobj:
-                        pass
+                with SourceLine(srcobj, "location", WorkflowException):
+                    if isinstance(st, arvados.commands.run.UploadFile):
+                        uploadfiles.add((src, ab, st))
+                    elif isinstance(st, arvados.commands.run.ArvFile):
+                        self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File")
+                    elif src.startswith("_:"):
+                        if "contents" in srcobj:
+                            pass
+                        else:
+                            raise WorkflowException("File literal '%s' is missing contents" % src)
+                    elif src.startswith("arvwf:"):
+                        self._pathmap[src] = MapperEnt(src, src, "File")
                     else:
-                        raise SourceLine(srcobj, "location", WorkflowException).makeError("File literal '%s' is missing contents" % src)
-                elif src.startswith("arvwf:"):
-                    self._pathmap[src] = MapperEnt(src, src, "File")
-                else:
-                    raise SourceLine(srcobj, "location", WorkflowException).makeError("Input file path '%s' is invalid" % st)
+                        raise WorkflowException("Input file path '%s' is invalid" % st)
             if "secondaryFiles" in srcobj:
                 for l in srcobj["secondaryFiles"]:
                     self.visit(l, uploadfiles)

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