[ARVADOS] updated: 4c8ec1b2166a81b05b2b6cf5a6fae5b839876802
git at public.curoverse.com
git at public.curoverse.com
Thu Sep 18 17:18:23 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 2 +-
apps/workbench/Gemfile.lock | 4 +-
apps/workbench/app/assets/javascripts/selection.js | 9 +-
.../app/controllers/actions_controller.rb | 8 +-
.../app/controllers/user_agreements_controller.rb | 2 +-
apps/workbench/app/models/collection.rb | 4 +
apps/workbench/app/models/job.rb | 10 +-
apps/workbench/app/models/pipeline_instance.rb | 6 +-
apps/workbench/app/models/pipeline_template.rb | 4 +
.../views/application/_arvados_attr_value.html.erb | 2 +-
.../application/_name_and_description.html.erb | 12 ++
apps/workbench/app/views/application/show.html.erb | 3 +
.../app/views/collections/_show_files.html.erb | 45 ++++--
.../app/views/collections/_show_recent.html.erb | 21 +++
.../collections/_show_source_summary.html.erb | 5 +-
apps/workbench/app/views/collections/show.html.erb | 3 +
.../app/views/pipeline_instances/show.html.erb | 22 +--
.../views/pipeline_templates/_show_recent.html.erb | 3 +-
.../app/views/pipeline_templates/show.html.erb | 1 +
.../app/views/projects/_show_tab_contents.html.erb | 12 +-
apps/workbench/app/views/projects/show.html.erb | 10 +-
apps/workbench/config/application.default.yml | 29 ++++
apps/workbench/config/database.yml | 7 +
apps/workbench/config/routes.rb | 1 +
apps/workbench/test/diagnostics/pipeline_test.rb | 93 ++++++++++++
apps/workbench/test/diagnostics_test_helper.rb | 29 ++++
.../test/functional/actions_controller_test.rb | 30 ++++
.../workbench/test/integration/collections_test.rb | 70 +++++++++
apps/workbench/test/integration/jobs_test.rb | 29 ++++
.../test/integration/pipeline_instances_test.rb | 22 ++-
.../test/integration/pipeline_templates_test.rb | 31 ++++
apps/workbench/test/integration/projects_test.rb | 27 ++++
apps/workbench/test/test_helper.rb | 7 +-
crunch_scripts/split-fastq.py | 7 +-
doc/_includes/_example_sdk_go.liquid | 109 ++++++++++++++
doc/_includes/_example_sdk_go_imports.liquid | 4 +
doc/sdk/go/index.html.textile.liquid | 52 +------
...nning-pipeline-command-line.html.textile.liquid | 12 +-
docker/java-bwa-samtools/Dockerfile | 5 +-
sdk/cli/bin/arv-run-pipeline-instance | 115 ++++++++++-----
sdk/cli/bin/crunch-job | 19 ++-
sdk/python/arvados/collection.py | 12 +-
sdk/python/arvados/keep.py | 130 +++++++++--------
services/api/Gemfile | 4 +-
services/api/Gemfile.lock | 8 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 10 +-
.../controllers/arvados/v1/schema_controller.rb | 1 +
services/api/app/models/collection.rb | 3 +
services/api/app/models/job.rb | 12 ++
services/api/app/models/job_task.rb | 2 +
services/api/app/models/node.rb | 11 +-
services/api/app/models/pipeline_instance.rb | 3 +
services/api/config/application.default.yml | 3 +
services/api/config/routes.rb | 1 +
...add_start_finish_time_to_tasks_and_pipelines.rb | 15 ++
...d_description_to_pipeline_instances_and_jobs.rb | 11 ++
...140918141529_change_user_owner_uuid_not_null.rb | 10 ++
.../20140918153541_add_properties_to_node.rb | 9 ++
services/api/db/structure.sql | 25 +++-
services/api/lib/tasks/config_check.rake | 4 +
services/api/script/crunch-dispatch.rb | 60 ++++----
services/api/test/fixtures/collections.yml | 26 ++++
services/api/test/fixtures/users.yml | 1 +
.../arvados/v1/collections_controller_test.rb | 57 ++++++++
.../functional/arvados/v1/jobs_controller_test.rb | 28 +++-
.../functional/arvados/v1/nodes_controller_test.rb | 8 +-
.../arvados/v1/schema_controller_test.rb | 7 +
services/api/test/unit/node_test.rb | 8 +-
services/fuse/arvados_fuse/__init__.py | 18 ++-
services/fuse/tests/test_mount.py | 1 +
services/keepstore/block_work_list.go | 160 +++++++++++++++++++++
services/keepstore/block_work_list_test.go | 149 +++++++++++++++++++
services/keepstore/handler_test.go | 13 +-
services/keepstore/handlers.go | 24 +++-
services/keepstore/keepstore.go | 3 +-
services/keepstore/pull_list/pull_list.go | 81 -----------
76 files changed, 1441 insertions(+), 363 deletions(-)
create mode 100644 apps/workbench/app/views/application/_name_and_description.html.erb
create mode 100644 apps/workbench/test/diagnostics/pipeline_test.rb
create mode 100644 apps/workbench/test/diagnostics_test_helper.rb
create mode 100644 apps/workbench/test/integration/jobs_test.rb
create mode 100644 doc/_includes/_example_sdk_go.liquid
create mode 100644 doc/_includes/_example_sdk_go_imports.liquid
create mode 100644 services/api/db/migrate/20140909183946_add_start_finish_time_to_tasks_and_pipelines.rb
create mode 100644 services/api/db/migrate/20140911221252_add_description_to_pipeline_instances_and_jobs.rb
create mode 100644 services/api/db/migrate/20140918141529_change_user_owner_uuid_not_null.rb
create mode 100644 services/api/db/migrate/20140918153541_add_properties_to_node.rb
create mode 100644 services/keepstore/block_work_list.go
create mode 100644 services/keepstore/block_work_list_test.go
delete mode 100644 services/keepstore/pull_list/pull_list.go
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