[ARVADOS] updated: d6d7788c4e6b1d3da88833329b326fd7a3891503
git at public.curoverse.com
git at public.curoverse.com
Fri Aug 1 14:18:41 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 2 +
apps/workbench/Gemfile.lock | 4 +
.../app/assets/javascripts/application.js | 34 ++++-
apps/workbench/app/assets/javascripts/editable.js | 11 +-
.../workbench/app/assets/javascripts/filterable.js | 15 +-
.../app/assets/javascripts/infinite_scroll.js | 84 ++++++++---
.../app/assets/javascripts/select_modal.js | 81 +++++++++-
apps/workbench/app/assets/javascripts/tab_panes.js | 38 +++++
.../app/assets/stylesheets/application.css.scss | 9 ++
.../app/assets/stylesheets/select_modal.css.scss | 3 +
.../app/controllers/actions_controller.rb | 13 ++
.../app/controllers/application_controller.rb | 47 +++---
.../app/controllers/collections_controller.rb | 14 +-
.../controllers/pipeline_instances_controller.rb | 3 +-
.../controllers/pipeline_templates_controller.rb | 3 +-
.../app/controllers/projects_controller.rb | 26 ++++
.../workbench/app/controllers/search_controller.rb | 21 +++
apps/workbench/app/controllers/users_controller.rb | 67 +++++++++
apps/workbench/app/helpers/application_helper.rb | 10 ++
.../app/helpers/pipeline_components_helper.rb | 13 ++
.../app/helpers/pipeline_instances_helper.rb | 4 +
apps/workbench/app/models/arvados_api_client.rb | 7 +-
apps/workbench/app/models/group.rb | 9 ++
apps/workbench/app/views/application/404.html.erb | 7 +-
.../app/views/application/_choose.html.erb | 68 +++++----
.../workbench/app/views/application/_choose.js.erb | 22 +--
.../views/application/_pipeline_progress.html.erb | 2 +-
.../application/_pipeline_status_label.html.erb | 2 +-
.../views/application/_projects_tree_menu.html.erb | 17 +--
.../workbench/app/views/application/index.html.erb | 2 +
.../app/views/collections/_choose_rows.html.erb | 4 +-
.../app/views/groups/_choose_rows.html.erb | 2 +-
.../app/views/layouts/application.html.erb | 167 +--------------------
.../{application.html.erb => body.html.erb} | 112 ++++++--------
.../pipeline_instances/_show_components.html.erb | 79 +---------
.../_show_components_json.html.erb | 16 ++
....html.erb => _show_components_running.html.erb} | 34 -----
.../views/pipeline_instances/_show_recent.html.erb | 4 +-
.../views/pipeline_templates/_choose_rows.html.erb | 2 +-
.../pipeline_templates/_show_components.html.erb | 4 +-
.../app/views/projects/_show_tab_contents.html.erb | 13 ++
.../app/views/search/_choose_rows.html.erb | 26 ++++
.../app/views/users/_add_ssh_key_popup.html.erb | 38 +++++
.../app/views/users/_choose_rows.html.erb | 2 +-
.../app/views/users/_manage_account.html.erb | 52 +++++++
.../app/views/users/_manage_current_token.html.erb | 13 ++
.../app/views/users/_manage_repositories.html.erb | 40 +++++
.../app/views/users/_manage_ssh_keys.html.erb | 49 ++++++
.../views/users/_manage_virtual_machines.html.erb | 50 ++++++
.../app/views/users/_setup_popup.html.erb | 2 +-
apps/workbench/app/views/users/add_ssh_key.js.erb | 2 +
.../app/views/users/add_ssh_key_popup.js.erb | 8 +
.../app/views/users/manage_account.html.erb | 1 +
apps/workbench/config/application.yml.example | 2 +-
apps/workbench/config/routes.rb | 8 +
.../search_controller_test.rb} | 2 +-
.../pipeline_instances_controller_test.rb | 7 +
.../pipeline_templates_controller_test.rb | 6 +
apps/workbench/test/helpers/search_helper_test.rb | 4 +
.../test/integration/pipeline_instances_test.rb | 12 +-
apps/workbench/test/integration/smoke_test.rb | 3 +
doc/_config.yml | 1 +
doc/_includes/_alert_docker.liquid | 4 -
doc/_includes/_ssh_addkey.liquid | 10 +-
.../schema/PipelineTemplate.html.textile.liquid | 6 +-
doc/images/ssh-adding-public-key.png | Bin 17463 -> 15117 bytes
doc/install/index.html.textile.liquid | 4 +-
doc/install/install-api-server.html.textile.liquid | 6 +-
doc/install/install-docker.html.textile.liquid | 94 ++++++------
doc/install/install-keep.html.textile.liquid | 52 +++++++
.../check-environment.html.textile.liquid | 2 +-
doc/user/reference/api-tokens.html.textile.liquid | 39 +----
docker/api/Dockerfile | 37 ++++-
docker/api/application.yml.in | 5 +
docker/api/apt.arvados.org.list | 2 +
docker/api/arvados-clients.yml.in | 5 +
docker/api/crunch-dispatch-run.sh | 24 +++
docker/api/keep_server_0.json | 6 +
docker/api/keep_server_1.json | 7 +
docker/api/munge.key | Bin 0 -> 1024 bytes
docker/api/setup-gitolite.sh.in | 77 ++++++++++
docker/api/setup.sh.in | 62 ++++++++
docker/api/slurm.conf.in | 60 ++++++++
docker/api/supervisor.conf | 29 ++++
docker/api/update-gitolite.rb | 162 ++++++++++++++++++++
docker/arvdock | 120 ++++++++++++---
docker/base/Dockerfile | 4 +
docker/base/apt.arvados.org.list | 2 +
docker/build.sh | 32 +++-
docker/build_tools/Makefile | 143 ++++++++++++++++--
docker/build_tools/build.rb | 28 +++-
docker/compute/Dockerfile | 28 ++++
docker/compute/fuse.conf | 10 ++
docker/compute/setup.sh.in | 20 +++
docker/{api => compute}/ssh.sh | 0
docker/compute/supervisor.conf | 29 ++++
docker/compute/wrapdocker | 90 +++++++++++
docker/config.yml.example | 4 +
docker/shell/Dockerfile | 19 +++
docker/shell/fuse.conf | 10 ++
docker/shell/setup.sh.in | 21 +++
docker/{api => shell}/superuser_token.in | 0
docker/shell/supervisor.conf | 15 ++
docker/slurm/Dockerfile | 11 ++
docker/slurm/munge.key | Bin 0 -> 1024 bytes
docker/slurm/slurm.conf.in | 60 ++++++++
docker/slurm/supervisor.conf | 14 ++
docker/workbench/Dockerfile | 3 +
sdk/cli/bin/crunch-job | 26 +++-
sdk/python/arvados/commands/put.py | 21 +--
sdk/python/arvados/keep.py | 139 ++++++++++-------
sdk/python/bin/arv-get | 2 +-
sdk/python/bin/arv-ls | 2 +-
services/api/Gemfile | 1 +
services/api/Gemfile.lock | 2 +
.../api/app/controllers/application_controller.rb | 1 +
.../controllers/arvados/v1/groups_controller.rb | 92 ++++++++----
services/api/app/models/authorized_key.rb | 9 +-
services/api/app/models/user.rb | 2 +-
services/api/config/application.default.yml | 24 ++-
services/api/config/application.yml.example | 39 +----
services/api/config/routes.rb | 1 +
... => 20140607150616_rename_folder_to_project.rb} | 0
.../db/migrate/20140714184006_empty_collection.rb | 4 +-
services/api/db/structure.sql | 2 +
services/api/lib/current_api_client.rb | 2 +-
services/api/test/fixtures/groups.yml | 2 +-
services/api/test/fixtures/pipeline_instances.yml | 22 ++-
services/api/test/fixtures/pipeline_templates.yml | 21 +++
.../arvados/v1/groups_controller_test.rb | 29 ++++
services/fuse/arvados_fuse/__init__.py | 3 +-
131 files changed, 2439 insertions(+), 766 deletions(-)
create mode 100644 apps/workbench/app/controllers/search_controller.rb
create mode 100644 apps/workbench/app/helpers/pipeline_components_helper.rb
copy apps/workbench/app/views/layouts/{application.html.erb => body.html.erb} (70%)
create mode 100644 apps/workbench/app/views/pipeline_instances/_show_components_json.html.erb
copy apps/workbench/app/views/pipeline_instances/{_show_components.html.erb => _show_components_running.html.erb} (63%)
create mode 100644 apps/workbench/app/views/search/_choose_rows.html.erb
create mode 100644 apps/workbench/app/views/users/_add_ssh_key_popup.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_account.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_current_token.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_repositories.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_ssh_keys.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_virtual_machines.html.erb
create mode 100644 apps/workbench/app/views/users/add_ssh_key.js.erb
create mode 100644 apps/workbench/app/views/users/add_ssh_key_popup.js.erb
create mode 100644 apps/workbench/app/views/users/manage_account.html.erb
copy apps/workbench/test/{unit/job_test.rb => controllers/search_controller_test.rb} (57%)
create mode 100644 apps/workbench/test/helpers/search_helper_test.rb
delete mode 100644 doc/_includes/_alert_docker.liquid
create mode 100644 doc/install/install-keep.html.textile.liquid
create mode 100644 docker/api/apt.arvados.org.list
create mode 100644 docker/api/arvados-clients.yml.in
create mode 100755 docker/api/crunch-dispatch-run.sh
create mode 100644 docker/api/keep_server_0.json
create mode 100644 docker/api/keep_server_1.json
create mode 100644 docker/api/munge.key
create mode 100755 docker/api/setup-gitolite.sh.in
create mode 100755 docker/api/setup.sh.in
create mode 100644 docker/api/slurm.conf.in
create mode 100755 docker/api/update-gitolite.rb
create mode 100644 docker/base/apt.arvados.org.list
create mode 100644 docker/compute/Dockerfile
create mode 100644 docker/compute/fuse.conf
create mode 100755 docker/compute/setup.sh.in
copy docker/{api => compute}/ssh.sh (100%)
create mode 100644 docker/compute/supervisor.conf
create mode 100755 docker/compute/wrapdocker
create mode 100644 docker/shell/Dockerfile
create mode 100644 docker/shell/fuse.conf
create mode 100755 docker/shell/setup.sh.in
copy docker/{api => shell}/superuser_token.in (100%)
create mode 100644 docker/shell/supervisor.conf
create mode 100644 docker/slurm/Dockerfile
create mode 100644 docker/slurm/munge.key
create mode 100644 docker/slurm/slurm.conf.in
create mode 100644 docker/slurm/supervisor.conf
rename services/api/db/migrate/{20140607150616_rename_folder_to_project.rb_deferred => 20140607150616_rename_folder_to_project.rb} (100%)
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Those revisions listed above that are new to this repository have
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commit d6d7788c4e6b1d3da88833329b326fd7a3891503
Merge: 62fd09a 42d84bd
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Aug 1 14:18:35 2014 -0400
Merge branch 'master' into 3232-user-guide-updates
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