11162: Fix tests.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index fea6adfacc323539d7c2cd595f66d441859893b8..2d15610a5fe934120f157951b0364e7d146bd296 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -12,6 +12,8 @@ class ArvadosCommandTool(CommandLineTool):
 
     def __init__(self, arvrunner, toolpath_object, **kwargs):
         super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
+        if "cwlVersion" not in self.metadata:
+            raise Exception("missing")
         self.arvrunner = arvrunner
         self.work_api = kwargs["work_api"]
 

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 6f731fd6877b18fc6bc434bd8110fe2b44775196..f675fb10e80811e92e90b209f073c806c9777afb 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -277,6 +277,7 @@ class ArvadosWorkflow(Workflow):
             })
             kwargs["loader"] = self.doc_loader
             kwargs["avsc_names"] = self.doc_schema
+            kwargs["metadata"]  = self.metadata
             return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder_resolved, output_callback, **kwargs)
         else:
             return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)

diff --git a/sdk/cwl/arvados_cwl/http.py b/sdk/cwl/arvados_cwl/http.py
index ea77786c4c1806ba6e522bc4ac0eecaaf32655f5..1ee1607466eb3d0f594e3d7eba144548b04b8663 100644 (file)
--- a/sdk/cwl/arvados_cwl/http.py
+++ b/sdk/cwl/arvados_cwl/http.py
@@ -18,7 +18,7 @@ def my_parsedate(text):
     if parsed:
         return datetime.datetime(*parsed[:6])
     else:
-        datetime.datetime(1970, 1, 1)
+        return datetime.datetime(1970, 1, 1)
 
 def fresh_cache(url, properties):
     pr = properties[url]
@@ -89,7 +89,7 @@ def http_to_keep(api, project_uuid, url):
     req = requests.get(url, stream=True, allow_redirects=True)
 
     if req.status_code != 200:
-        raise Exception("Failed to download '%s' got status %s " % (req.status_code, url))
+        raise Exception("Failed to download '%s' got status %s " % (url, req.status_code))
 
     remember_headers(url, properties, req.headers)
 

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 35610e2882d9d0b4268f38d1bcafc3ef83561f07..625f27518d8d5076a23bc2ac3f63263d90fb21d8 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -33,7 +33,7 @@ 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==1.0.20180523203033',
+          'cwltool==1.0.20180524215209',
           'schema-salad==2.7.20180501211602',
           'typing >= 3.5.3',
           'ruamel.yaml >=0.13.11, <0.15',

diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index 522946a4f49ee2acd68588c6100d45bcb097cbe8..2295e934ac77de76182d04749715a57f730874b4 100644 (file)
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -53,7 +53,8 @@ class TestContainer(unittest.TestCase):
             make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
             arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
-                                                     basedir="", make_fs_access=make_fs_access, loader=Loader({}))
+                                                     basedir="", make_fs_access=make_fs_access, loader=Loader({}),
+                                                     metadata={"cwlVersion": "v1.0"})
             arvtool.formatgraph = None
             for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run_"+str(enable_reuse),
                                  make_fs_access=make_fs_access, tmpdir="/tmp"):
@@ -139,7 +140,7 @@ class TestContainer(unittest.TestCase):
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers",
                                                  avsc_names=avsc_names, make_fs_access=make_fs_access,
-                                                 loader=Loader({}))
+                                                 loader=Loader({}), metadata={"cwlVersion": "v1.0"})
         arvtool.formatgraph = None
         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_resource_requirements",
                              make_fs_access=make_fs_access, tmpdir="/tmp"):
@@ -251,7 +252,7 @@ class TestContainer(unittest.TestCase):
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers",
                                                  avsc_names=avsc_names, make_fs_access=make_fs_access,
-                                                 loader=Loader({}))
+                                                 loader=Loader({}), metadata={"cwlVersion": "v1.0"})
         arvtool.formatgraph = None
         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_initial_work_dir",
                              make_fs_access=make_fs_access, tmpdir="/tmp"):
@@ -352,7 +353,8 @@ class TestContainer(unittest.TestCase):
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
-                                                 basedir="", make_fs_access=make_fs_access, loader=Loader({}))
+                                                 basedir="", make_fs_access=make_fs_access, loader=Loader({}),
+                                                 metadata={"cwlVersion": "v1.0"})
         arvtool.formatgraph = None
         for j in arvtool.job({}, mock.MagicMock(), basedir="", name="test_run_redirect",
                              make_fs_access=make_fs_access, tmpdir="/tmp"):
@@ -477,7 +479,8 @@ class TestContainer(unittest.TestCase):
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                      collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
-                                                 basedir="", make_fs_access=make_fs_access, loader=Loader({}))
+                                                 basedir="", make_fs_access=make_fs_access, loader=Loader({}),
+                                                 metadata={"cwlVersion": "v1.0"})
         arvtool.formatgraph = None
         job_order = {
             "p1": {
@@ -584,7 +587,8 @@ class TestContainer(unittest.TestCase):
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                      collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="containers", avsc_names=avsc_names,
-                                                 basedir="", make_fs_access=make_fs_access, loader=Loader({}))
+                                                 basedir="", make_fs_access=make_fs_access, loader=Loader({}),
+                                                 metadata={"cwlVersion": "v1.0"})
         arvtool.formatgraph = None
 
         job_order = {"pw": "blorp"}

diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index abf96947eb1b40f21207e0fc9171f66482a0bd47..30930dd49abb1a91fe371cc291cd916feac735df 100644 (file)
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -59,7 +59,8 @@ class TestJob(unittest.TestCase):
             make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
             arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
-                                                     basedir="", make_fs_access=make_fs_access, loader=Loader({}))
+                                                     basedir="", make_fs_access=make_fs_access, loader=Loader({}),
+                                                     metadata={"cwlVersion": "v1.0"})
             arvtool.formatgraph = None
             for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
                 j.run(enable_reuse=enable_reuse)
@@ -150,7 +151,8 @@ class TestJob(unittest.TestCase):
         make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
                                          collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
         arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
-                                                 make_fs_access=make_fs_access, loader=Loader({}))
+                                                 make_fs_access=make_fs_access, loader=Loader({}),
+                                                 metadata={"cwlVersion": "v1.0"})
         arvtool.formatgraph = None
         for j in arvtool.job({}, mock.MagicMock(), basedir="", make_fs_access=make_fs_access):
             j.run(enable_reuse=True)

diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 77bef075fa97903e96bcc18e5f6c2c11dc4f5654..ce20aba6026c6b102e2eef70a6b45af58e3c41c6 100644 (file)
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -234,7 +234,6 @@ def stubs(func):
             },
             'secret_mounts': {},
             'state': 'Committed',
-            'owner_uuid': None,
             'command': ['arvados-cwl-runner', '--local', '--api=containers',
                         '--no-log-timestamps', '--disable-validate',
                         '--eval-timeout=20', '--thread-count=4',
@@ -751,7 +750,6 @@ class TestSubmit(unittest.TestCase):
                     'kind': 'json'
                 }
             }, 'state': 'Committed',
-            'owner_uuid': None,
             'output_path': '/var/spool/cwl',
             'name': 'expect_arvworkflow.cwl#main',
             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
@@ -870,7 +868,6 @@ class TestSubmit(unittest.TestCase):
                     'kind': 'json'
                 }
             }, 'state': 'Committed',
-            'owner_uuid': None,
             'output_path': '/var/spool/cwl',
             'name': 'a test workflow',
             'container_image': 'arvados/jobs:'+arvados_cwl.__version__,
@@ -1236,7 +1233,6 @@ class TestSubmit(unittest.TestCase):
             },
             "name": "secret_wf.cwl",
             "output_path": "/var/spool/cwl",
-            "owner_uuid": None,
             "priority": 500,
             "properties": {},
             "runtime_constraints": {