[ARVADOS] updated: 6284bed37f6b2bb3c0671b401aa0d99d5ef7a5b7
Git user
git at public.curoverse.com
Wed Sep 14 11:38:17 EDT 2016
Summary of changes:
.../app/controllers/work_units_controller.rb | 8 +--
apps/workbench/app/models/pipeline_instance.rb | 2 +-
.../test/controllers/workflows_controller_test.rb | 2 +-
build/run-build-docker-jobs-image.sh | 6 +-
build/run-build-packages.sh | 2 +-
doc/_config.yml | 6 ++
.../_container_runtime_constraints.liquid | 9 +++
doc/_includes/_mount_types.liquid | 63 ++++++++++++++++++
.../methods/container_requests.html.textile.liquid | 74 ++++++++++++++++++++++
...xtile.liquid => containers.html.textile.liquid} | 48 +++++++-------
...extile.liquid => workflows.html.textile.liquid} | 30 ++++-----
doc/api/schema/Container.html.textile.liquid | 59 +++++++++++++++++
.../schema/ContainerRequest.html.textile.liquid | 50 +++++++++++++++
doc/api/schema/Workflow.html.textile.liquid | 23 +++++++
sdk/cli/bin/crunch-job | 42 +++++++++++-
sdk/cwl/arvados_cwl/__init__.py | 4 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 4 +-
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/test_submit.py | 2 +-
sdk/go/dispatch/dispatch.go | 20 +++++-
.../arvados/v1/containers_controller.rb | 10 +++
services/api/app/models/arvados_model.rb | 8 ++-
services/api/app/models/container.rb | 20 ++++++
services/api/app/models/workflow.rb | 14 ++--
services/api/config/routes.rb | 2 +
...20160909181442_rename_workflow_to_definition.rb | 10 +++
services/api/db/structure.sql | 8 ++-
services/api/test/fixtures/container_requests.yml | 5 +-
services/api/test/fixtures/containers.yml | 1 +
services/api/test/fixtures/jobs.yml | 6 +-
services/api/test/fixtures/workflows.yml | 16 ++---
.../arvados/v1/containers_controller_test.rb | 44 ++++++++++++-
.../functional/arvados/v1/jobs_controller_test.rb | 2 +-
services/api/test/unit/container_test.rb | 24 +++----
services/api/test/unit/job_test.rb | 22 +++++++
services/api/test/unit/workflow_test.rb | 66 +++++++++----------
.../crunch-dispatch-local_test.go | 8 ++-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 21 +++---
services/keep-balance/balance.go | 19 +++---
39 files changed, 611 insertions(+), 151 deletions(-)
create mode 100644 doc/_includes/_container_runtime_constraints.liquid
create mode 100644 doc/_includes/_mount_types.liquid
create mode 100644 doc/api/methods/container_requests.html.textile.liquid
copy doc/api/methods/{nodes.html.textile.liquid => containers.html.textile.liquid} (51%)
copy doc/api/methods/{specimens.html.textile.liquid => workflows.html.textile.liquid} (59%)
create mode 100644 doc/api/schema/Container.html.textile.liquid
create mode 100644 doc/api/schema/ContainerRequest.html.textile.liquid
create mode 100644 doc/api/schema/Workflow.html.textile.liquid
create mode 100644 services/api/db/migrate/20160909181442_rename_workflow_to_definition.rb
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commit 6284bed37f6b2bb3c0671b401aa0d99d5ef7a5b7
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Sep 14 11:38:13 2016 -0400
9766: Rename metavar. Post packed yaml text instead of json. Adjust fixture
to have similar form as posted by --create-workflow. Fix fixture to be a
string instead of structured text.
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index b11ca54..309e941 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -329,7 +329,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
default=True, dest="enable_reuse",
help="")
- parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs, if not provided, will go to home project.")
+ parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
parser.add_argument("--ignore-docker-for-reuse", action="store_true",
help="Ignore Docker image version when deciding whether to reuse past jobs.",
default=False)
@@ -341,7 +341,7 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
default=True, dest="submit")
exgroup.add_argument("--create-template", action="store_true", help="Create an Arvados pipeline template.")
exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow.")
- exgroup.add_argument("--update-workflow", type=str, help="Update Arvados workflow.")
+ exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update existing Arvados workflow with uuid.")
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index fb14ab4..37a0540 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -6,6 +6,8 @@ from cwltool.pack import pack
from cwltool.load_tool import fetch_document
from cwltool.process import shortname
+import ruamel.yaml as yaml
+
from .runner import upload_docker, upload_dependencies
def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
@@ -30,7 +32,7 @@ def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
"owner_uuid": project_uuid,
"name": tool.tool.get("label", name),
"description": tool.tool.get("doc", ""),
- "workflow":json.dumps(packed, sort_keys=True, indent=4, separators=(',',': '))
+ "definition":yaml.safe_dump(packed)
}}
if update_uuid:
diff --git a/sdk/cwl/tests/test_submit.py b/sdk/cwl/tests/test_submit.py
index ddb9e46..b8d2a55 100644
--- a/sdk/cwl/tests/test_submit.py
+++ b/sdk/cwl/tests/test_submit.py
@@ -306,7 +306,7 @@ class TestCreateWorkflow(unittest.TestCase):
"owner_uuid": project_uuid,
"name": "submit_wf.cwl",
"description": "",
- "workflow": expect_workflow
+ "definition": expect_workflow
}
}
stubs.api.workflows().create.assert_called_with(
diff --git a/services/api/test/fixtures/container_requests.yml b/services/api/test/fixtures/container_requests.yml
index dcaf657..49a1fae 100644
--- a/services/api/test/fixtures/container_requests.yml
+++ b/services/api/test/fixtures/container_requests.yml
@@ -209,6 +209,8 @@ uncommitted:
"kind": "json",
"content": {
"cwlVersion": "v1.0",
+ "$graph": [{
+ "id": "#main",
"class": "CommandLineTool",
"baseCommand": ["echo"],
"inputs": [
@@ -289,7 +291,8 @@ uncommitted:
}
],
"outputs": []
- }
+ }]
+ }
},
"/var/lib/cwl/cwl.input.json": {
"kind": "json",
diff --git a/services/api/test/fixtures/workflows.yml b/services/api/test/fixtures/workflows.yml
index 4e1f4af..4badf9e 100644
--- a/services/api/test/fixtures/workflows.yml
+++ b/services/api/test/fixtures/workflows.yml
@@ -25,7 +25,7 @@ workflow_with_input_specifications:
name: Workflow with input specifications
description: this workflow has inputs specified
created_at: <%= 1.minute.ago.to_s(:db) %>
- definition:
+ definition: |
cwlVersion: v1.0
class: CommandLineTool
baseCommand:
commit 1a87c77a5cfe200921a9d09e995383bc675e7370
Merge: 2b50a58 05428b7
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Sep 14 08:35:15 2016 -0400
Merge branch 'master' into 9766-register-workflow
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