[ARVADOS] updated: 1.1.4-2-g95cf046

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvtool.py  |  7 +++++++
 sdk/cwl/arvados_cwl/fsaccess.py | 10 +++++++++-
 2 files changed, 16 insertions(+), 1 deletion(-)

       via  95cf0469411e73c279037822e4cfc1d98a36cdaa (commit)
      from  672b0c1254891cfba38a7c00f2ae2c93e526c37b (commit)

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commit 95cf0469411e73c279037822e4cfc1d98a36cdaa
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Tue May 1 16:09:38 2018 -0400

    13365: Reintroduce secondaryFile discovery.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index de32979..ddc270d 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -35,6 +35,13 @@ class ArvadosCommandTool(CommandLineTool):
                                  **kwargs)
 
     def job(self, joborder, output_callback, **kwargs):
+
+        # Workaround for #13365
+        builderargs = kwargs.copy()
+        builderargs["toplevel"] = True
+        builder = self._init_job(joborder, **builderargs)
+        joborder = builder.job
+
         if self.work_api == "containers":
             dockerReq, is_req = self.get_requirement("DockerRequirement")
             if dockerReq and dockerReq.get("dockerOutputDirectory"):
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 0b577b0..15689a9 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -22,6 +22,8 @@ import arvados.collection
 import arvados.arvfile
 import arvados.errors
 
+from googleapiclient.errors import HttpError
+
 from schema_salad.ref_resolver import DefaultFetcher
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -122,7 +124,13 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
             return super(CollectionFsAccess, self).open(self._abs(fn), mode)
 
     def exists(self, fn):
-        collection, rest = self.get_collection(fn)
+        try:
+            collection, rest = self.get_collection(fn)
+        except HttpError as err:
+            if err.resp.status == 404:
+                return False
+            else:
+                raise
         if collection is not None:
             if rest:
                 return collection.exists(rest)

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