[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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