[ARVADOS] created: 1.1.3-117-gb0a3fa7
Git user
git at public.curoverse.com
Fri Mar 2 15:09:50 EST 2018
at b0a3fa7167c604792de4683d5827b972ce608cd1 (commit)
commit b0a3fa7167c604792de4683d5827b972ce608cd1
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Mar 2 14:18:10 2018 -0500
13140: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/tests/test_container.py b/sdk/cwl/tests/test_container.py
index c206934..fea21e9 100644
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@ -45,7 +45,8 @@ class TestContainer(unittest.TestCase):
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#"
+ "id": "#",
+ "class": "CommandLineTool"
})
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -126,7 +127,8 @@ class TestContainer(unittest.TestCase):
"enableReuse": False
}],
"baseCommand": "ls",
- "id": "#"
+ "id": "#",
+ "class": "CommandLineTool"
})
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -234,7 +236,8 @@ class TestContainer(unittest.TestCase):
} ]
}],
"baseCommand": "ls",
- "id": "#"
+ "id": "#",
+ "class": "CommandLineTool"
})
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -333,7 +336,8 @@ class TestContainer(unittest.TestCase):
"stderr": "stderr.txt",
"stdin": "/keep/99999999999999999999999999999996+99/file.txt",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#"
+ "id": "#",
+ "class": "CommandLineTool"
})
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -454,7 +458,8 @@ class TestContainer(unittest.TestCase):
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#"
+ "id": "#",
+ "class": "CommandLineTool"
})
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
diff --git a/sdk/cwl/tests/test_job.py b/sdk/cwl/tests/test_job.py
index 5a6e6dc..1dfd86b 100644
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@ -53,7 +53,8 @@ class TestJob(unittest.TestCase):
"outputs": [],
"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}],
- "id": "#"
+ "id": "#",
+ "class": "CommandLineTool"
})
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
@@ -144,7 +145,8 @@ class TestJob(unittest.TestCase):
"enableReuse": False
}],
"baseCommand": "ls",
- "id": "#"
+ "id": "#",
+ "class": "CommandLineTool"
}
make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index 4ab5fb5..c0b74fe 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -982,7 +982,7 @@ class TestSubmit(unittest.TestCase):
@mock.patch("arvados.commands.keepdocker.find_one_image_hash")
- @mock.patch("cwltool.docker.get_image")
+ @mock.patch("cwltool.docker.DockerCommandLineJob.get_image")
@mock.patch("arvados.api")
def test_arvados_jobs_image(self, api, get_image, find_one_image_hash):
arvrunner = mock.MagicMock()
commit cd4c51ffcf09f28cf13605e97260f5a00641527c
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Mar 2 10:00:12 2018 -0500
13140: Bump cwltool version
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 4701b4d..628b6ae 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -42,7 +42,7 @@ from ._version import __version__
from cwltool.pack import pack
from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
-from cwltool.draft2tool import compute_checksums
+from cwltool.command_line_tool import compute_checksums
from arvados.api import OrderedJsonModel
logger = logging.getLogger('arvados.cwl-runner')
@@ -677,8 +677,8 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
return parser
def add_arv_hints():
- cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
- cwltool.draft2tool.ACCEPTLIST_RE = cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE
+ cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
+ cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
res.close()
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 2731b26..88155b5 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -10,7 +10,7 @@ import time
from cwltool.process import get_feature, shortname, UnsupportedRequirement
from cwltool.errors import WorkflowException
-from cwltool.draft2tool import revmap_file, CommandLineTool
+from cwltool.command_line_tool import revmap_file, CommandLineTool
from cwltool.load_tool import fetch_document
from cwltool.builder import Builder
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 81faff4..de32979 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -2,7 +2,7 @@
#
# SPDX-License-Identifier: Apache-2.0
-from cwltool.draft2tool import CommandLineTool
+from cwltool.command_line_tool import CommandLineTool
from .arvjob import ArvadosJob
from .arvcontainer import ArvadosContainer
from .pathmapper import ArvPathMapper
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index fb5d036..9b79d45 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -13,8 +13,7 @@ from StringIO import StringIO
from schema_salad.sourceline import SourceLine
-import cwltool.draft2tool
-from cwltool.draft2tool import CommandLineTool
+from cwltool.command_line_tool import CommandLineTool
import cwltool.workflow
from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname
from cwltool.load_tool import fetch_document
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index e548465..5b1d737 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -41,7 +41,7 @@ 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==1.0.20180130110340',
+ 'cwltool==1.0.20180225105849',
'schema-salad==2.6.20171201034858',
'typing==3.5.3.0',
'ruamel.yaml==0.13.7',
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