[ARVADOS] updated: 80eb8b1ed6da790a2a94e7f791cca9eeae91b6f8

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvjob.py | 14 +++++++++-----
 sdk/cwl/arvados_cwl/runner.py | 17 +++++++++--------
 sdk/cwl/setup.py              |  4 ++--
 3 files changed, 20 insertions(+), 15 deletions(-)

       via  80eb8b1ed6da790a2a94e7f791cca9eeae91b6f8 (commit)
       via  cc36bdd54001b561fe1ad7c866049f960242aa90 (commit)
       via  41c2220404f82803f927b84209b3a0b19346996f (commit)
      from  b379ee48f1d7a8ff05bcbc9ec9993949029376c6 (commit)

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commit 80eb8b1ed6da790a2a94e7f791cca9eeae91b6f8
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jan 11 16:33:11 2017 -0500

    10812: Improve check that already packed workflow collection exists with same
    PDH and similar name.  Don't crash when registering pipeline template that has
    array inputs.

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index b7a6eb0..f68d99e 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -241,9 +241,11 @@ class RunnerJob(Runner):
         with collection.open("workflow.cwl", "w") as f:
             f.write(yaml.round_trip_dump(packed))
 
-        exists = self.arvrunner.api.collections().list(filters=[["owner_uuid", "=", self.arvrunner.project_uuid],
-                                                 ["portable_data_hash", "=", collection.portable_data_hash()],
-                                                 ["name", "like", self.name+"%"]]).execute(num_retries=self.arvrunner.num_retries)
+        filters = [["portable_data_hash", "=", collection.portable_data_hash()],
+                   ["name", "like", self.name+"%"]]
+        if self.arvrunner.project_uuid:
+            filters.append(["owner_uuid", "=", self.arvrunner.project_uuid])
+        exists = self.arvrunner.api.collections().list(filters=filters).execute(num_retries=self.arvrunner.num_retries)
 
         if exists["items"]:
             logger.info("Using collection %s", exists["items"][0]["uuid"])
@@ -385,10 +387,12 @@ class RunnerTemplate(object):
             if not isinstance(types, list):
                 types = [types]
             param['required'] = 'null' not in types
-            non_null_types = set(types) - set(['null'])
+            non_null_types = [t for t in types if t != "null"]
             if len(non_null_types) == 1:
                 the_type = [c for c in non_null_types][0]
-                dataclass = self.type_to_dataclass.get(the_type)
+                dataclass = None
+                if isinstance(the_type, basestring):
+                    dataclass = self.type_to_dataclass.get(the_type)
                 if dataclass:
                     param['dataclass'] = dataclass
             # Note: If we didn't figure out a single appropriate

commit cc36bdd54001b561fe1ad7c866049f960242aa90
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jan 11 15:51:54 2017 -0500

    10812: Don't try to upload embedded tools separately unless they have an
    identifier.

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 5306e90..5d2a2d9 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -184,14 +184,15 @@ def upload_workflow_deps(arvrunner, tool):
     document_loader = tool.doc_loader
 
     def upload_tool_deps(deptool):
-        upload_dependencies(arvrunner,
-                            "%s dependencies" % (shortname(deptool["id"])),
-                            document_loader,
-                            deptool,
-                            deptool["id"],
-                            False,
-                            include_primary=False)
-        document_loader.idx[deptool["id"]] = deptool
+        if "id" in deptool:
+            upload_dependencies(arvrunner,
+                                "%s dependencies" % (shortname(deptool["id"])),
+                                document_loader,
+                                deptool,
+                                deptool["id"],
+                                False,
+                                include_primary=False)
+            document_loader.idx[deptool["id"]] = deptool
 
     tool.visit(upload_tool_deps)
 

commit 41c2220404f82803f927b84209b3a0b19346996f
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jan 11 14:46:25 2017 -0500

    10812: Bump cwltool and schema-salad versions.

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 61b8f0b..34a8dec 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -48,8 +48,8 @@ setup(name='arvados-cwl-runner',
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to build.
       install_requires=[
-          'cwltool==1.0.20170105144051',
-          'schema-salad==2.1.20161227191302',
+          'cwltool==1.0.20170111193653',
+          'schema-salad==2.2.20170111180227',
           'ruamel.yaml==0.13.7',
           'arvados-python-client>=0.1.20160826210445',
           'setuptools'

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