[ARVADOS] updated: 1.2.0-315-gaebcdea92
Git user
git at public.curoverse.com
Mon Nov 5 11:44:18 EST 2018
Summary of changes:
sdk/cwl/arvados_cwl/__init__.py | 4 ++-
sdk/cwl/arvados_cwl/arvjob.py | 1 +
sdk/cwl/arvados_cwl/arvworkflow.py | 2 +-
sdk/cwl/tests/test_submit.py | 66 ++++++++++++++++++++------------------
4 files changed, 39 insertions(+), 34 deletions(-)
via aebcdea9212191671cbdce9b89f96b4ea0b53d5e (commit)
via 58a92afe9affebe3c832a53736c75cac87e8f94b (commit)
from 27a4a8c459b156b0bd7d046aaa0cb3c5145915da (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 aebcdea9212191671cbdce9b89f96b4ea0b53d5e
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Mon Nov 5 10:16:48 2018 -0500
14198: Unit tests pass again
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 141c74de4..a29bafb22 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -36,10 +36,12 @@ from .executor import ArvCwlExecutor
# These arn't used directly in this file but
# other code expects to import them from here
from .arvcontainer import ArvadosContainer
+from .arvjob import ArvadosJob
from .arvtool import ArvadosCommandTool
-from .fsaccess import CollectionFsAccess, CollectionCache
+from .fsaccess import CollectionFsAccess, CollectionCache, CollectionFetcher
from .util import get_current_container
from .executor import RuntimeStatusLoggingHandler, DEFAULT_PRIORITY
+from .arvworkflow import ArvadosWorkflow
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 189282ec2..9a03372d3 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -30,6 +30,7 @@ from .pathmapper import VwdPathMapper, trim_listing
from .perf import Perf
from . import done
from ._version import __version__
+from .util import get_intermediate_collection_info
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index b689e94ef..72ef8fd4f 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -22,7 +22,7 @@ import ruamel.yaml as yaml
from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection,
trim_anonymous_location, remove_redundant_fields, discover_secondary_files)
from .pathmapper import ArvPathMapper, trim_listing
-from .arvtool import ArvadosCommandTool
+from .arvtool import ArvadosCommandTool, check_cluster_target
from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
commit 58a92afe9affebe3c832a53736c75cac87e8f94b
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Nov 2 17:05:20 2018 -0400
14198: test_submit passes
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 53a4a17ee..0fd824fbe 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -1216,43 +1216,45 @@ class TestSubmit(unittest.TestCase):
self.assertEqual(capture_stdout.getvalue(),
stubs.expect_container_request_uuid + '\n')
+ def tearDown(self):
+ arvados_cwl.arvdocker.arv_docker_clear_cache()
@mock.patch("arvados.commands.keepdocker.find_one_image_hash")
@mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
@mock.patch("arvados.api")
def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
- try:
- arvrunner = mock.MagicMock()
- arvrunner.project_uuid = ""
- api.return_value = mock.MagicMock()
- arvrunner.api = api.return_value
- arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
- "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "link_class": "docker_image_repo+tag",
- "name": "arvados/jobs:"+arvados_cwl.__version__,
- "owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
- {"items": [{"created_at": "",
- "head_uuid": "",
- "link_class": "docker_image_hash",
- "name": "123456",
- "owner_uuid": "",
- "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
- )
- find_one_image_hash.return_value = "123456"
-
- arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "owner_uuid": "",
- "manifest_text": "",
- "properties": ""
- }], "items_available": 1, "offset": 0},)
- arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
- arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
- "portable_data_hash": "9999999999999999999999999999999b+99"}
- self.assertEqual("9999999999999999999999999999999b+99",
- arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
- finally:
- arvados_cwl.arvdocker.arv_docker_clear_cache()
+ arvados_cwl.arvdocker.arv_docker_clear_cache()
+
+ arvrunner = mock.MagicMock()
+ arvrunner.project_uuid = ""
+ api.return_value = mock.MagicMock()
+ arvrunner.api = api.return_value
+ arvrunner.api.links().list().execute.side_effect = ({"items": [{"created_at": "",
+ "head_uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "link_class": "docker_image_repo+tag",
+ "name": "arvados/jobs:"+arvados_cwl.__version__,
+ "owner_uuid": "",
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0},
+ {"items": [{"created_at": "",
+ "head_uuid": "",
+ "link_class": "docker_image_hash",
+ "name": "123456",
+ "owner_uuid": "",
+ "properties": {"image_timestamp": ""}}], "items_available": 1, "offset": 0}
+ )
+ find_one_image_hash.return_value = "123456"
+
+ arvrunner.api.collections().list().execute.side_effect = ({"items": [{"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "owner_uuid": "",
+ "manifest_text": "",
+ "properties": ""
+ }], "items_available": 1, "offset": 0},)
+ arvrunner.api.collections().create().execute.return_value = {"uuid": ""}
+ arvrunner.api.collections().get().execute.return_value = {"uuid": "zzzzz-4zz18-zzzzzzzzzzzzzzb",
+ "portable_data_hash": "9999999999999999999999999999999b+99"}
+ self.assertEqual("9999999999999999999999999999999b+99",
+ arvados_cwl.runner.arvados_jobs_image(arvrunner, "arvados/jobs:"+arvados_cwl.__version__))
+
@stubs
def test_submit_secrets(self, stubs):
-----------------------------------------------------------------------
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