[ARVADOS] updated: 12d990a6590e5f23a5998d29a2d8efdb0f733688
git at public.curoverse.com
git at public.curoverse.com
Fri Sep 19 11:34:55 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 2 +-
apps/workbench/Gemfile.lock | 4 +-
.../javascripts/{selection.js => selection.js.erb} | 17 ++-
apps/workbench/app/assets/javascripts/tab_panes.js | 8 ++
.../app/controllers/actions_controller.rb | 8 +-
.../app/controllers/projects_controller.rb | 75 ++++++++--
.../app/controllers/user_agreements_controller.rb | 2 +-
apps/workbench/app/models/arvados_base.rb | 6 +
apps/workbench/app/models/collection.rb | 4 +
apps/workbench/app/models/group.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 +-
.../app/views/application/_content.html.erb | 58 ++++----
.../application/_name_and_description.html.erb | 12 ++
.../workbench/app/views/application/destroy.js.erb | 1 +
apps/workbench/app/views/application/show.html.erb | 42 ++++++
.../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 | 21 +--
.../app/views/pipeline_instances/show.html.erb | 22 +--
.../views/pipeline_templates/_show_recent.html.erb | 3 +-
.../app/views/pipeline_templates/show.html.erb | 3 +-
.../app/views/projects/_show_tab_contents.html.erb | 12 +-
.../app/views/projects/remove_items.js.erb | 7 +-
apps/workbench/app/views/projects/show.html.erb | 28 +---
.../workbench/app/views/projects/tab_counts.js.erb | 3 +
apps/workbench/config/application.default.yml | 29 ++++
apps/workbench/config/database.yml | 7 +
apps/workbench/config/routes.rb | 2 +
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 | 89 +++++++++++-
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 | 36 ++++-
apps/workbench/test/integration_helper.rb | 6 +-
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 | 41 ++++--
sdk/python/arvados/collection.py | 154 ++++++++++++--------
sdk/python/arvados/commands/_util.py | 12 ++
sdk/python/arvados/commands/keepdocker.py | 55 ++++---
sdk/python/arvados/commands/put.py | 45 +++---
sdk/python/arvados/keep.py | 156 +++++++++++---------
sdk/python/arvados/retry.py | 18 +++
sdk/python/arvados/stream.py | 68 +++++----
sdk/python/arvados/util.py | 4 +-
sdk/python/bin/arv-get | 46 +++---
sdk/python/bin/arv-ls | 21 +--
sdk/python/setup.py | 2 +-
sdk/python/tests/arvados_testutil.py | 11 ++
sdk/python/tests/test_arv_put.py | 8 +-
sdk/python/tests/test_collections.py | 143 +++++++++++++++++-
sdk/python/tests/test_keep_client.py | 69 ++++-----
sdk/python/tests/test_retry.py | 27 ++++
sdk/python/tests/test_stream.py | 117 +++++++++++++++
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 | 12 ++
.../20140918153541_add_properties_to_node.rb | 9 ++
services/api/db/structure.sql | 24 +++-
services/api/lib/tasks/config_check.rake | 4 +
services/api/script/crunch-dispatch.rb | 82 ++++++-----
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 | 122 ++++++++++------
services/fuse/bin/arv-mount | 66 +++++----
services/fuse/setup.py | 2 +-
services/fuse/tests/test_mount.py | 13 +-
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 -----------
102 files changed, 2376 insertions(+), 753 deletions(-)
rename apps/workbench/app/assets/javascripts/{selection.js => selection.js.erb} (93%)
create mode 100644 apps/workbench/app/views/application/_name_and_description.html.erb
create mode 100644 apps/workbench/app/views/projects/tab_counts.js.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 sdk/python/tests/test_stream.py
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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Those revisions listed above that are new to this repository have
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commit 12d990a6590e5f23a5998d29a2d8efdb0f733688
Merge: ab7c978 5bb258b
Author: Tim Pierce <twp at curoverse.com>
Date: Fri Sep 19 11:34:46 2014 -0400
Merge branch 'master' into 3699-arv-copy
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