[ARVADOS] updated: ddce4f6de6f0a77b45e9f3358eb6f0c1f1870fba
Git user
git at public.curoverse.com
Wed Nov 16 11:41:53 EST 2016
Summary of changes:
.gitignore | 3 +
doc/_config.yml | 83 +++--
doc/_layouts/default.html.liquid | 2 +-
doc/api/authentication.html.textile.liquid | 40 ---
doc/api/crunch-scripts.html.textile.liquid | 5 +-
doc/api/execution.html.textile.liquid | 27 ++
doc/api/index.html.textile.liquid | 44 +--
doc/api/methods.html.textile.liquid | 120 +++----
.../api_client_authorizations.html.textile.liquid | 54 +++-
doc/api/methods/api_clients.html.textile.liquid | 40 ++-
.../methods/authorized_keys.html.textile.liquid | 43 ++-
doc/api/methods/collections.html.textile.liquid | 55 +++-
.../methods/container_requests.html.textile.liquid | 100 ++++--
doc/api/methods/containers.html.textile.liquid | 76 ++++-
doc/api/methods/groups.html.textile.liquid | 47 +--
doc/api/methods/humans.html.textile.liquid | 39 ++-
doc/api/methods/job_tasks.html.textile.liquid | 55 +++-
doc/api/methods/jobs.html.textile.liquid | 101 ++++--
doc/api/methods/keep_disks.html.textile.liquid | 52 ++-
doc/api/methods/keep_services.html.textile.liquid | 52 +--
doc/api/methods/links.html.textile.liquid | 69 ++--
doc/api/methods/logs.html.textile.liquid | 49 ++-
doc/api/methods/nodes.html.textile.liquid | 50 ++-
.../methods/pipeline_instances.html.textile.liquid | 44 ++-
.../methods/pipeline_templates.html.textile.liquid | 182 ++++++++++-
doc/api/methods/repositories.html.textile.liquid | 45 ++-
doc/api/methods/specimens.html.textile.liquid | 41 ++-
doc/api/methods/traits.html.textile.liquid | 40 ++-
doc/api/methods/users.html.textile.liquid | 67 ++--
.../methods/virtual_machines.html.textile.liquid | 52 +--
doc/api/methods/workflows.html.textile.liquid | 44 ++-
doc/api/permission-model.html.textile.liquid | 143 +++------
doc/api/requests.html.textile.liquid | 349 +++++++++++++++++++++
doc/api/resources.html.textile.liquid | 46 ++-
doc/api/schema/ApiClient.html.textile.liquid | 24 --
.../ApiClientAuthorization.html.textile.liquid | 29 --
doc/api/schema/AuthorizedKey.html.textile.liquid | 24 --
doc/api/schema/Collection.html.textile.liquid | 39 ---
doc/api/schema/Container.html.textile.liquid | 59 ----
.../schema/ContainerRequest.html.textile.liquid | 70 -----
doc/api/schema/Group.html.textile.liquid | 25 --
doc/api/schema/Human.html.textile.liquid | 19 --
doc/api/schema/Job.html.textile.liquid | 69 ----
doc/api/schema/JobTask.html.textile.liquid | 47 ---
doc/api/schema/KeepDisk.html.textile.liquid | 31 --
doc/api/schema/KeepService.html.textile.liquid | 24 --
doc/api/schema/Link.html.textile.liquid | 83 -----
doc/api/schema/Log.html.textile.liquid | 33 --
doc/api/schema/Node.html.textile.liquid | 28 --
.../schema/PipelineInstance.html.textile.liquid | 26 --
.../schema/PipelineTemplate.html.textile.liquid | 161 ----------
doc/api/schema/Repository.html.textile.liquid | 25 --
doc/api/schema/Specimen.html.textile.liquid | 22 --
doc/api/schema/Trait.html.textile.liquid | 22 --
doc/api/schema/User.html.textile.liquid | 30 --
doc/api/schema/VirtualMachine.html.textile.liquid | 21 --
doc/api/schema/Workflow.html.textile.liquid | 23 --
doc/api/storage.html.textile.liquid | 170 ++++++++++
doc/api/tokens.html.textile.liquid | 63 ++++
doc/images/Arvados_Permissions.svg | 4 +
doc/images/Crunch_dispatch.svg | 4 +
doc/images/Keep_manifests.svg | 4 +
doc/images/Keep_reading_writing_block.svg | 4 +
doc/images/Keep_rendezvous_hashing.svg | 4 +
doc/images/Session_Establishment.svg | 4 +
.../install-prerequisites.html.textile.liquid | 4 +-
doc/sdk/cli/install.html.textile.liquid | 1 -
doc/sdk/go/example.html.textile.liquid | 76 +++++
doc/sdk/go/index.html.textile.liquid | 15 +-
doc/sdk/index.html.textile.liquid | 13 +-
doc/sdk/java/example.html.textile.liquid | 78 +++++
doc/sdk/java/index.html.textile.liquid | 11 +-
doc/sdk/perl/example.html.textile.liquid | 81 +++++
doc/sdk/perl/index.html.textile.liquid | 59 +---
doc/sdk/python/events.html.textile.liquid | 2 +-
doc/sdk/python/example.html.textile.liquid | 51 +++
doc/sdk/python/sdk-python.html.textile.liquid | 3 +-
doc/sdk/ruby/example.html.textile.liquid | 75 +++++
doc/sdk/ruby/index.html.textile.liquid | 74 +----
doc/user/cwl/cwl-runner.html.textile.liquid | 1 +
.../reference/job-pipeline-ref.html.textile.liquid | 2 +-
.../running-external-program.html.textile.liquid | 4 +-
.../tutorial-submit-job.html.textile.liquid | 4 +-
sdk/cli/bin/arv-run-pipeline-instance | 2 +
sdk/cwl/arvados_cwl/__init__.py | 23 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 3 +
sdk/cwl/arvados_cwl/arvjob.py | 6 +-
sdk/cwl/arvados_cwl/crunch_script.py | 7 +-
sdk/cwl/arvados_cwl/runner.py | 3 +-
sdk/cwl/tests/test_make_output.py | 9 +-
sdk/cwl/tests/test_submit.py | 88 ++++++
.../arvados/v1/collections_controller.rb | 2 +-
.../arvados/v1/container_requests_controller.rb | 1 +
.../arvados/v1/collections_controller_test.rb | 43 +++
.../v1/container_requests_controller_test.rb | 22 ++
services/arv-git-httpd/main.go | 2 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 2 +-
services/keep-web/main.go | 2 +-
services/keepproxy/keepproxy.go | 2 +-
services/keepstore/keepstore.go | 2 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 48 ++-
tools/arvbox/lib/arvbox/docker/common.sh | 6 +-
.../lib/arvbox/docker/service/ready/run-service | 4 +-
103 files changed, 2423 insertions(+), 1858 deletions(-)
delete mode 100644 doc/api/authentication.html.textile.liquid
create mode 100644 doc/api/execution.html.textile.liquid
create mode 100644 doc/api/requests.html.textile.liquid
delete mode 100644 doc/api/schema/ApiClient.html.textile.liquid
delete mode 100644 doc/api/schema/ApiClientAuthorization.html.textile.liquid
delete mode 100644 doc/api/schema/AuthorizedKey.html.textile.liquid
delete mode 100644 doc/api/schema/Collection.html.textile.liquid
delete mode 100644 doc/api/schema/Container.html.textile.liquid
delete mode 100644 doc/api/schema/ContainerRequest.html.textile.liquid
delete mode 100644 doc/api/schema/Group.html.textile.liquid
delete mode 100644 doc/api/schema/Human.html.textile.liquid
delete mode 100644 doc/api/schema/Job.html.textile.liquid
delete mode 100644 doc/api/schema/JobTask.html.textile.liquid
delete mode 100644 doc/api/schema/KeepDisk.html.textile.liquid
delete mode 100644 doc/api/schema/KeepService.html.textile.liquid
delete mode 100644 doc/api/schema/Link.html.textile.liquid
delete mode 100644 doc/api/schema/Log.html.textile.liquid
delete mode 100644 doc/api/schema/Node.html.textile.liquid
delete mode 100644 doc/api/schema/PipelineInstance.html.textile.liquid
delete mode 100644 doc/api/schema/PipelineTemplate.html.textile.liquid
delete mode 100644 doc/api/schema/Repository.html.textile.liquid
delete mode 100644 doc/api/schema/Specimen.html.textile.liquid
delete mode 100644 doc/api/schema/Trait.html.textile.liquid
delete mode 100644 doc/api/schema/User.html.textile.liquid
delete mode 100644 doc/api/schema/VirtualMachine.html.textile.liquid
delete mode 100644 doc/api/schema/Workflow.html.textile.liquid
create mode 100644 doc/api/storage.html.textile.liquid
create mode 100644 doc/api/tokens.html.textile.liquid
create mode 100644 doc/images/Arvados_Permissions.svg
create mode 100644 doc/images/Crunch_dispatch.svg
create mode 100644 doc/images/Keep_manifests.svg
create mode 100644 doc/images/Keep_reading_writing_block.svg
create mode 100644 doc/images/Keep_rendezvous_hashing.svg
create mode 100644 doc/images/Session_Establishment.svg
create mode 100644 doc/sdk/go/example.html.textile.liquid
create mode 100644 doc/sdk/java/example.html.textile.liquid
create mode 100644 doc/sdk/perl/example.html.textile.liquid
create mode 100644 doc/sdk/python/example.html.textile.liquid
create mode 100644 doc/sdk/ruby/example.html.textile.liquid
create mode 100644 services/api/test/functional/arvados/v1/container_requests_controller_test.rb
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commit ddce4f6de6f0a77b45e9f3358eb6f0c1f1870fba
Author: radhika <radhika at curoverse.com>
Date: Wed Nov 16 11:40:55 2016 -0500
10290: scheduling_parameters added to container_requests controller.
diff --git a/services/api/app/controllers/arvados/v1/container_requests_controller.rb b/services/api/app/controllers/arvados/v1/container_requests_controller.rb
index 6e2848c..ed04a4b 100644
--- a/services/api/app/controllers/arvados/v1/container_requests_controller.rb
+++ b/services/api/app/controllers/arvados/v1/container_requests_controller.rb
@@ -4,4 +4,5 @@ class Arvados::V1::ContainerRequestsController < ApplicationController
accept_attribute_as_json :runtime_constraints, Hash
accept_attribute_as_json :command, Array
accept_attribute_as_json :filters, Array
+ accept_attribute_as_json :scheduling_parameters, Hash
end
diff --git a/services/api/test/functional/arvados/v1/container_requests_controller_test.rb b/services/api/test/functional/arvados/v1/container_requests_controller_test.rb
new file mode 100644
index 0000000..e54e15d
--- /dev/null
+++ b/services/api/test/functional/arvados/v1/container_requests_controller_test.rb
@@ -0,0 +1,22 @@
+require 'test_helper'
+
+class Arvados::V1::ContainerRequestsControllerTest < ActionController::TestCase
+ test 'create with scheduling parameters' do
+ authorize_with :system_user
+
+ sp = {'partitions' => ['test1', 'test2']}
+ post :create, {
+ container_request: {
+ command: ['echo', 'hello'],
+ container_image: 'test',
+ output_path: 'test',
+ scheduling_parameters: sp,
+ },
+ }
+ assert_response :success
+
+ cr = JSON.parse(@response.body)
+ assert_not_nil cr, 'Expected container request'
+ assert_equal sp, cr['scheduling_parameters']
+ end
+end
commit e7a865275a832420b9d63c0ab3ebf87eaca57d26
Merge: d8db04f d2f9e78
Author: radhika <radhika at curoverse.com>
Date: Wed Nov 16 11:24:00 2016 -0500
Merge branch 'master' into 10290-container-partitions
commit d8db04f0165e57ab8021f2c1e4ff7061e494ceba
Merge: 82fa37a b21e623
Author: radhika <radhika at curoverse.com>
Date: Wed Nov 16 11:23:40 2016 -0500
Merge branch '10290-container-partitions' of git.curoverse.com:arvados into 10290-container-partitions
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