[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
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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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