[ARVADOS] updated: 9d035125ea1f8b6bd32fa6f862b32ba9308ebc66
Git user
git at public.curoverse.com
Thu Mar 31 11:00:19 EDT 2016
Summary of changes:
apps/workbench/test/test_helper.rb | 6 +-
build/run-build-packages.sh | 2 +
crunch_scripts/crunchrunner | 7 +-
doc/api/schema/Job.html.textile.liquid | 1 +
sdk/cwl/arvados_cwl/__init__.py | 17 +++--
sdk/cwl/tests/{inp => input}/blorp.txt | 0
sdk/cwl/tests/submit_test_job.json | 2 +-
sdk/cwl/tests/test_job.py | 8 +--
sdk/cwl/tests/test_submit.py | 36 ++++++-----
sdk/cwl/tests/tool/submit_tool.cwl | 5 ++
sdk/cwl/tests/wf/submit_wf.cwl | 5 ++
.../app/controllers/arvados/v1/jobs_controller.rb | 1 +
services/api/app/models/job.rb | 5 +-
.../20160324144017_add_components_to_job.rb | 11 ++++
services/api/db/structure.sql | 7 +-
services/api/test/fixtures/jobs.yml | 29 +++++++++
.../arvados/v1/groups_controller_test.rb | 6 +-
.../functional/arvados/v1/jobs_controller_test.rb | 75 ++++++++++++++++++++++
services/api/test/test_helper.rb | 6 +-
19 files changed, 185 insertions(+), 44 deletions(-)
rename sdk/cwl/tests/{inp => input}/blorp.txt (100%)
create mode 100644 services/api/db/migrate/20160324144017_add_components_to_job.rb
via 9d035125ea1f8b6bd32fa6f862b32ba9308ebc66 (commit)
via c980683a243903babe9cc09cabc71e1c6229fef1 (commit)
via 057a218324fd68bf5b9d034240d225b539b393a6 (commit)
via e68d56d2d033c7be04294fd30cd0edb424f291fb (commit)
via cf5af834e8fb31720b459127394f6bf4e2c0158e (commit)
via a3f2cb186e437bfce0031b024b2157b73ed2717d (commit)
via dbafab756158fa8bbd374a9938f0f4cb21e02818 (commit)
via a7d819f660840767df3e393a30a775f445db266e (commit)
via 4743b2e8f9587146f24359f98b648e92d5b04e38 (commit)
via 98036435a54261258faadedeef0675eecfe4ff39 (commit)
via f2f5c6aa8117b51e9fed1a59a41b97b18ac713a8 (commit)
via 7a6612d56b719165d3aff84754521c9a38d9912a (commit)
from f7e07c3a28d4f4e1adbd957749bd825e44a2e523 (commit)
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commit 9d035125ea1f8b6bd32fa6f862b32ba9308ebc66
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 31 11:00:15 2016 -0400
8654: Fix versionstring(). Improve help text / comments / style tweaks.
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 5958100..511f173 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -612,14 +612,13 @@ class ArvCwlRunner(object):
def versionstring():
"""Print version string of key packages for provenance and debugging."""
- cwlpkg = pkg_resources.require("cwltool")
- arvpkg = pkg_resources.require("arvados-python-client")
arvcwlpkg = pkg_resources.require("arvados-cwl-runner")
+ arvpkg = pkg_resources.require("arvados-python-client")
+ cwlpkg = pkg_resources.require("cwltool")
- return "%s %s, %s %s, %s %s" % (sys.argv[0],
- arvcwlpkg[0].version,
- "arvados-python-client", cwlpkg[0].version,
- "cwltool", arvpkg[0].version)
+ return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
+ "arvados-python-client", arvpkg[0].version,
+ "cwltool", cwlpkg[0].version)
def main(args, stdout, stderr, api_client=None):
args.insert(0, "--leave-outputs")
@@ -636,15 +635,15 @@ def main(args, stdout, stderr, api_client=None):
parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
exgroup = parser.add_mutually_exclusive_group()
- exgroup.add_argument("--submit", action="store_true", help="Submit runner job so workflow can run unattended.",
+ exgroup.add_argument("--submit", action="store_true", help="Submit workflow to run on Arvados.",
default=True, dest="submit")
- exgroup.add_argument("--local", action="store_false", help="Workflow runner runs on local host and submits jobs.",
+ exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
default=True, dest="submit")
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
default=True, dest="wait")
- exgroup.add_argument("--no-wait", action="store_false", help="Exit after submitting workflow runner job.",
+ exgroup.add_argument("--no-wait", action="store_false", help="Submit workflow runner job and exit.",
default=True, dest="wait")
try:
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index d383a48..c9da6bc 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -31,19 +31,21 @@ class TestSubmit(unittest.TestCase):
api.collections().create.assert_has_calls([
mock.call(),
mock.call(body={'manifest_text': './tool b0fa9cffda3d37ba401bc338bb0b54a6+257 0:16:blub.txt 16:241:submit_tool.cwl\n./wf 888e237b758adf86ca66c36f7bd88a24+175 0:175:submit_wf.cwl\n',
- 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
- 'name': 'submit_wf.cwl'
- }, ensure_unique_name=True),
- mock.call().execute(),
- mock.call(body={'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
- 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
- 'name': 'submit_test_job.json'
- }, ensure_unique_name=True),
- mock.call().execute()])
- api.jobs().create.assert_called_with(body={
- 'runtime_constraints': {
- 'docker_image': 'arvados/jobs'
- },
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': 'submit_wf.cwl'
+ }, ensure_unique_name=True),
+ mock.call().execute(),
+ mock.call(body={'manifest_text': '. 979af1245a12a1fed634d4222473bfdc+16 0:16:blorp.txt\n',
+ 'owner_uuid': 'zzzzz-tpzed-zzzzzzzzzzzzzzz',
+ 'name': '#'
+ }, ensure_unique_name=True),
+ mock.call().execute()])
+
+ api.jobs().create.assert_called_with(
+ body={
+ 'runtime_constraints': {
+ 'docker_image': 'arvados/jobs'
+ },
'script_parameters': {
'x': {
'path': '99999999999999999999999999999992+99/blorp.txt',
@@ -52,7 +54,7 @@ class TestSubmit(unittest.TestCase):
'cwl:tool': '99999999999999999999999999999991+99/wf/submit_wf.cwl'
},
'repository': 'arvados',
- 'script_version': 'master',
- 'script': 'cwl-runner'
- },
- find_or_create=True)
+ 'script_version': 'master',
+ 'script': 'cwl-runner'
+ },
+ find_or_create=True)
diff --git a/sdk/cwl/tests/tool/submit_tool.cwl b/sdk/cwl/tests/tool/submit_tool.cwl
index 4bdb235..28fecff 100644
--- a/sdk/cwl/tests/tool/submit_tool.cwl
+++ b/sdk/cwl/tests/tool/submit_tool.cwl
@@ -1,3 +1,8 @@
+# Test case for arvados-cwl-runner
+#
+# Used to test whether scanning a tool file for dependencies (e.g. default
+# value blub.txt) and uploading to Keep works as intended.
+
class: CommandLineTool
requirements:
- class: DockerRequirement
diff --git a/sdk/cwl/tests/wf/submit_wf.cwl b/sdk/cwl/tests/wf/submit_wf.cwl
index 104203b..e1ff188 100644
--- a/sdk/cwl/tests/wf/submit_wf.cwl
+++ b/sdk/cwl/tests/wf/submit_wf.cwl
@@ -1,3 +1,8 @@
+# Test case for arvados-cwl-runner
+#
+# Used to test whether scanning a workflow file for dependencies
+# (e.g. submit_tool.cwl) and uploading to Keep works as intended.
+
class: Workflow
inputs:
- id: x
commit c980683a243903babe9cc09cabc71e1c6229fef1
Merge: 057a218 e68d56d
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 31 10:32:09 2016 -0400
Merge branch 'master' into 8654-arv-jobs-cwl-runner
commit 057a218324fd68bf5b9d034240d225b539b393a6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 31 10:31:59 2016 -0400
8654: Rename tests/inp/ to test/input/
diff --git a/sdk/cwl/tests/inp/blorp.txt b/sdk/cwl/tests/input/blorp.txt
similarity index 100%
rename from sdk/cwl/tests/inp/blorp.txt
rename to sdk/cwl/tests/input/blorp.txt
diff --git a/sdk/cwl/tests/submit_test_job.json b/sdk/cwl/tests/submit_test_job.json
index e453f42..95ff0ff 100644
--- a/sdk/cwl/tests/submit_test_job.json
+++ b/sdk/cwl/tests/submit_test_job.json
@@ -1,6 +1,6 @@
{
"x": {
"class": "File",
- "path": "inp/blorp.txt"
+ "path": "input/blorp.txt"
}
}
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