[ARVADOS] updated: 1.3.0-231-g1e8da3c17

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvworkflow.py   | 3 ++-
 sdk/cwl/arvados_cwl/crunch_script.py | 3 ++-
 sdk/cwl/arvados_cwl/executor.py      | 3 ++-
 sdk/cwl/arvados_cwl/fsaccess.py      | 3 ++-
 4 files changed, 8 insertions(+), 4 deletions(-)

       via  1e8da3c17b221eba0288ec3b6fd5769df2598531 (commit)
       via  dd98e9fb19b413e649a2656513714e1bda81bfa0 (commit)
      from  77d847ff11736567d67c91cb89aea9c9f3c0c83e (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 1e8da3c17b221eba0288ec3b6fd5769df2598531
Author: Eric Biagiotti <ebiagiotti at veritasgenetcs.com>
Date:   Fri Feb 1 13:45:25 2019 -0500

    13306: Improved py2/3 str compatibility
    
    Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti at gmail.com>

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index eab12efaa..535cfd758 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -5,6 +5,7 @@
 from __future__ import division
 from builtins import next
 from builtins import object
+from builtins import str
 from future.utils import viewvalues
 
 import argparse
@@ -467,7 +468,7 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
         adjustFileObjs(outputObj, rewrite)
 
         with final.open("cwl.output.json", "w") as f:
-            res = json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False).encode('utf-8').decode()
+            res = str(json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False))
             f.write(res)           
 
         final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True)
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index fc0bbb80b..fc7cc42d1 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -5,6 +5,7 @@
 from future import standard_library
 standard_library.install_aliases()
 from builtins import object
+from builtins import str
 from future.utils import viewvalues
 
 import fnmatch
@@ -288,7 +289,7 @@ pipeline_template_uuid_pattern = re.compile(r'[a-z0-9]{5}-p5p6p-[a-z0-9]{15}')
 
 def collectionResolver(api_client, document_loader, uri, num_retries=4):
     if uri.startswith("keep:") or uri.startswith("arvwf:"):
-        return uri.encode("utf-8").decode()
+        return str(uri)
 
     if workflow_uuid_pattern.match(uri):
         return u"arvwf:%s#main" % (uri)

commit dd98e9fb19b413e649a2656513714e1bda81bfa0
Author: Eric Biagiotti <ebiagiotti at veritasgenetcs.com>
Date:   Fri Feb 1 13:33:14 2019 -0500

    13306: Additional dict item iteration improvements
    
    Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti at gmail.com>

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index ff9504177..8e6bff4f0 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: Apache-2.0
 
 from past.builtins import basestring
+from future.utils import viewitems
 
 import os
 import json
@@ -137,7 +138,7 @@ class ArvadosWorkflowStep(WorkflowStep):
         runtimeContext = runtimeContext.copy()
         runtimeContext.toplevel = True  # Preserve behavior for #13365
 
-        builder = make_builder({shortname(k): v for k,v in list(joborder.items())}, self.hints, self.requirements, runtimeContext)
+        builder = make_builder({shortname(k): v for k,v in viewitems(joborder)}, self.hints, self.requirements, runtimeContext)
         runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
         return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext)
 
diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index d9a986663..c886550d4 100644
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -11,6 +11,7 @@
 # collection for this runner job.
 
 from past.builtins import basestring
+from future.utils import viewitems
 
 import arvados
 import arvados_cwl
@@ -63,7 +64,7 @@ def run():
             if "location" in v:
                 v["location"] = keeppath(v["location"])
 
-        for k,v in list(job_order_object.items()):
+        for k,v in viewitems(job_order_object):
             if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
                 job_order_object[k] = {
                     "class": "File",

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