[ARVADOS] updated: 87143451d4c6535576fe7232729ae9ce93a26d30

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py | 11 +++++------
 sdk/cwl/arvados_cwl/runner.py   |  7 ++++---
 2 files changed, 9 insertions(+), 9 deletions(-)

       via  87143451d4c6535576fe7232729ae9ce93a26d30 (commit)
       via  5f38e62616773fcc97d795d1dd707c7fce801f2a (commit)
      from  1a8d456e6e8b7026dfe1c1b1176e8d46f9f374e7 (commit)

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commit 87143451d4c6535576fe7232729ae9ce93a26d30
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Dec 1 13:11:24 2016 -0500

    10293: Fix error message when wrong --api provided.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index bd65252..4fb240f 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -73,7 +73,9 @@ class ArvCwlRunner(object):
         else:
             self.keep_client = arvados.keep.KeepClient(api_client=self.api, num_retries=self.num_retries)
 
-        for api in ["jobs", "containers"]:
+        self.work_api = None
+        expected_api = ["jobs", "containers"]
+        for api in expected_api:
             try:
                 methods = self.api._rootDesc.get('resources')[api]['methods']
                 if ('httpMethod' in methods['create'] and
@@ -82,11 +84,12 @@ class ArvCwlRunner(object):
                     break
             except KeyError:
                 pass
+
         if not self.work_api:
             if work_api is None:
                 raise Exception("No supported APIs")
             else:
-                raise Exception("Unsupported API '%s'" % work_api)
+                raise Exception("Unsupported API '%s', expected one of %s" % (work_api, expected_api))
 
     def arv_make_tool(self, toolpath_object, **kwargs):
         kwargs["work_api"] = self.work_api
@@ -567,10 +570,6 @@ def main(args, stdout, stderr, api_client=None, keep_client=None):
             return 1
         arvargs.work_api = want_api
 
-    if arvargs.work_api not in ("jobs", "containers"):
-        logger.error("Unknown --api '%s' expected one of 'jobs' or 'containers'", arvargs.work_api)
-        return 1
-
     if (arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
         job_order_object = ({}, "")
 

commit 5f38e62616773fcc97d795d1dd707c7fce801f2a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Nov 30 17:12:42 2016 -0500

    10293: Avoid noisy and unhelpful error when cwl.output.json is missing.

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 178285d..4854a06 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -203,9 +203,10 @@ class Runner(object):
                                                            api_client=self.arvrunner.api,
                                                            keep_client=self.arvrunner.keep_client,
                                                            num_retries=self.arvrunner.num_retries)
-                with outc.open("cwl.output.json") as f:
-                    if f.size() > 0:
-                        outputs = json.load(f)
+                if "cwl.output.json" in outc:
+                    with outc.open("cwl.output.json") as f:
+                        if f.size() > 0:
+                            outputs = json.load(f)
                 def keepify(fileobj):
                     path = fileobj["location"]
                     if not path.startswith("keep:"):

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