[ARVADOS] updated: c5f94a44dbbcf13976ae0ac6ffafce7b04c90389
git at public.curoverse.com
git at public.curoverse.com
Wed Jul 2 16:17:49 EDT 2014
Summary of changes:
.../images/{ajax-loader.gif => spinner_32px.gif} | Bin
.../app/assets/javascripts/infinite_scroll.js | 21 +-
.../app/assets/javascripts/select_modal.js | 2 +-
.../{loading.css => loading.css.scss.erb} | 21 ++
.../app/controllers/application_controller.rb | 195 ++++++------
.../app/controllers/collections_controller.rb | 16 +-
apps/workbench/app/helpers/application_helper.rb | 2 +-
apps/workbench/app/models/arvados_api_client.rb | 83 +++--
apps/workbench/app/models/arvados_base.rb | 2 +-
apps/workbench/app/views/application/404.html.erb | 21 ++
.../application/{error.json.erb => 404.json.erb} | 0
.../workbench/app/views/application/_choose.js.erb | 2 +-
.../app/views/application/_content.html.erb | 2 +-
.../app/views/application/api_error.html.erb | 23 ++
.../{error.json.erb => api_error.json.erb} | 0
.../app/views/collections/_index_tbody.html.erb | 2 +-
.../app/views/collections/_show_recent.html.erb | 2 +-
apps/workbench/app/views/jobs/_show_log.html.erb | 22 +-
.../app/views/layouts/application.html.erb | 15 +-
.../views/pipeline_instances/_show_recent.html.erb | 4 +-
.../pipeline_templates/_show_components.html.erb | 18 +-
.../views/pipeline_templates/_show_recent.html.erb | 20 +-
apps/workbench/app/views/users/_tables.html.erb | 10 +-
.../test/functional/application_controller_test.rb | 7 +
.../test/functional/collections_controller_test.rb | 7 +
.../test/functional/users_controller_test.rb | 2 +-
apps/workbench/test/integration/errors_test.rb | 61 +++-
.../test/integration/pipeline_instances_test.rb | 13 +-
crunch_scripts/collection-merge | 58 +++-
crunch_scripts/run-command | 73 +++++
crunch_scripts/subst.py | 71 +++++
doc/Rakefile | 2 +-
doc/_config.yml | 5 +-
doc/_includes/_alert_docker.liquid | 4 +
doc/install/index.html.textile.liquid | 18 +-
doc/install/install-docker.html.textile.liquid | 114 +++++++
docker/api/Dockerfile | 4 +-
.../api/application.yml.in | 13 +-
docker/api/passenger.conf | 4 +-
docker/api/production.rb.in | 100 ------
docker/api/secret_token.rb.in | 12 -
docker/arvdock | 336 +++++++++++----------
docker/build_tools/Makefile | 40 +--
docker/build_tools/build.rb | 29 +-
docker/bwa-samtools/Dockerfile | 21 ++
docker/keep/Dockerfile | 14 +
docker/mkimage-debootstrap.sh | 18 +-
docker/sso/passenger.conf | 4 +-
docker/warehouse/Dockerfile | 28 --
docker/warehouse/supervisor.conf | 3 -
docker/warehouse/warehouse.conf.in | 12 -
docker/workbench/Dockerfile | 5 +-
docker/workbench/apache2_foreground.sh | 5 +
.../workbench/application.yml.in | 15 +-
docker/workbench/passenger.conf | 4 +-
sdk/cli/arvados-cli.gemspec | 1 +
sdk/cli/bin/arv | 20 +-
sdk/cli/bin/crunch-job | 2 +
sdk/ruby/arvados.gemspec | 1 +
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 6 +-
.../api/app/controllers/application_controller.rb | 60 ++--
.../v1/api_client_authorizations_controller.rb | 3 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 5 +-
.../app/controllers/arvados/v1/links_controller.rb | 3 +-
services/api/app/models/blob.rb | 2 +-
services/api/app/models/user.rb | 6 +-
.../db/migrate/20140627210837_anonymous_group.rb | 17 ++
services/api/db/schema.rb | 2 +-
services/api/db/seeds.rb | 6 +-
services/api/lib/current_api_client.rb | 59 ++++
services/api/script/crunch-dispatch.rb | 2 +-
services/api/script/get_anonymous_user_token.rb | 50 +++
.../test/fixtures/api_client_authorizations.yml | 14 +
services/api/test/fixtures/groups.yml | 13 +
services/api/test/fixtures/links.yml | 39 +++
services/api/test/fixtures/users.yml | 8 +
.../test/functional/application_controller_test.rb | 49 +++
services/api/test/unit/user_test.rb | 3 +-
services/fuse/bin/arv-mount | 26 +-
services/keep/src/keep/keep.go | 2 +-
81 files changed, 1368 insertions(+), 618 deletions(-)
rename apps/workbench/app/assets/images/{ajax-loader.gif => spinner_32px.gif} (100%)
rename apps/workbench/app/assets/stylesheets/{loading.css => loading.css.scss.erb} (78%)
create mode 100644 apps/workbench/app/views/application/404.html.erb
copy apps/workbench/app/views/application/{error.json.erb => 404.json.erb} (100%)
create mode 100644 apps/workbench/app/views/application/api_error.html.erb
copy apps/workbench/app/views/application/{error.json.erb => api_error.json.erb} (100%)
mode change 100644 => 100755 crunch_scripts/collection-merge
create mode 100755 crunch_scripts/run-command
create mode 100644 crunch_scripts/subst.py
create mode 100644 doc/_includes/_alert_docker.liquid
create mode 100644 doc/install/install-docker.html.textile.liquid
copy services/api/config/application.yml.example => docker/api/application.yml.in (78%)
delete mode 100644 docker/api/production.rb.in
delete mode 100644 docker/api/secret_token.rb.in
create mode 100644 docker/bwa-samtools/Dockerfile
create mode 100644 docker/keep/Dockerfile
delete mode 100644 docker/warehouse/Dockerfile
delete mode 100644 docker/warehouse/supervisor.conf
delete mode 100644 docker/warehouse/warehouse.conf.in
copy apps/workbench/config/application.yml.example => docker/workbench/application.yml.in (60%)
create mode 100644 services/api/db/migrate/20140627210837_anonymous_group.rb
create mode 100755 services/api/script/get_anonymous_user_token.rb
create mode 100644 services/api/test/functional/application_controller_test.rb
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit c5f94a44dbbcf13976ae0ac6ffafce7b04c90389
Merge: 892e6e0 678f9f5
Author: Tim Pierce <twp at curoverse.com>
Date: Wed Jul 2 16:16:31 2014 -0400
Merge branch 'master' into 2985-workbench-ui
Refs #2985
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