[ARVADOS] updated: 3ba5aa15ea0156a4fce63dcb43b7f972b4c760df

git at public.curoverse.com git at public.curoverse.com
Wed May 21 16:00:51 EDT 2014


Summary of changes:
 apps/workbench/Gemfile                             |  18 +-
 apps/workbench/Gemfile.lock                        | 147 +++++++-------
 .../api_client_authorizations.js.coffee            |   3 -
 .../assets/javascripts/authorized_keys.js.coffee   |   3 -
 .../app/assets/javascripts/collections.js          |   1 -
 .../app/assets/javascripts/folders.js.coffee       |   3 -
 .../app/assets/javascripts/groups.js.coffee        |   3 -
 .../app/assets/javascripts/humans.js.coffee        |   3 -
 .../app/assets/javascripts/job_tasks.js.coffee     |   3 -
 .../app/assets/javascripts/jobs.js.coffee          |   3 -
 .../app/assets/javascripts/keep_disks.js.coffee    |   4 -
 .../app/assets/javascripts/links.js.coffee         |   3 -
 .../app/assets/javascripts/logs.js.coffee          |   3 -
 .../app/assets/javascripts/nodes.js.coffee         |   3 -
 .../app/assets/javascripts/pipeline_instances.js   |   1 -
 .../javascripts/pipeline_templates.js.coffee       |   3 -
 .../app/assets/javascripts/repositories.js.coffee  |   3 -
 .../app/assets/javascripts/sessions.js.coffee      |   3 -
 .../app/assets/javascripts/specimens.js.coffee     |   3 -
 .../app/assets/javascripts/traits.js.coffee        |   3 -
 .../assets/javascripts/user_agreements.js.coffee   |   3 -
 .../app/assets/javascripts/users.js.coffee         |   3 -
 .../assets/javascripts/virtual_machines.js.coffee  |   3 -
 .../app/assets/stylesheets/collections.css.scss    |  46 +++++
 .../app/controllers/actions_controller.rb          |   2 +-
 .../app/controllers/application_controller.rb      |  25 +--
 .../app/controllers/collections_controller.rb      | 143 ++++++--------
 .../app/controllers/keep_services_controller.rb    |   2 +
 .../app/controllers/sessions_controller.rb         |   2 +-
 apps/workbench/app/controllers/users_controller.rb |  10 +-
 apps/workbench/app/helpers/application_helper.rb   |  13 ++
 .../app/helpers/arvados_api_client_helper.rb       |  13 ++
 apps/workbench/app/models/arvados_api_client.rb    |  41 ++--
 apps/workbench/app/models/arvados_base.rb          |  60 ++++--
 apps/workbench/app/models/arvados_resource_list.rb |   7 +-
 apps/workbench/app/models/collection.rb            |  25 ++-
 apps/workbench/app/models/group.rb                 |   4 +-
 .../app/models/{keep_disk.rb => keep_service.rb}   |   2 +-
 apps/workbench/app/models/user.rb                  |  26 +--
 apps/workbench/app/models/user_agreement.rb        |   8 +-
 .../app/views/collections/_show_files.html.erb     | 111 +++++------
 .../app/views/collections/_show_jobs.html.erb      |  64 ------
 .../views/collections/_show_provenance.html.erb    |  84 --------
 .../views/collections/_show_source_data.html.erb   |  44 -----
 apps/workbench/app/views/collections/show.html.erb | 105 ++++++++++
 .../app/views/collections/show_file_links.html.erb |  82 ++++++++
 apps/workbench/app/views/folders/show.html.erb     |  60 +++---
 .../app/views/layouts/application.html.erb         |   8 +-
 apps/workbench/app/views/links/_recent.html.erb    |   2 +-
 .../pipeline_instances/_show_components.html.erb   |   5 +-
 .../app/views/pipeline_instances/show.js.erb       |   6 +-
 .../workbench/app/views/users/_show_admin.html.erb |   2 +-
 apps/workbench/app/views/users/welcome.html.erb    |   2 +-
 apps/workbench/app/views/websocket/index.html.erb  |   2 +-
 apps/workbench/config/application.default.yml      |  14 +-
 apps/workbench/config/application.rb               |  15 +-
 .../config/environments/development.rb.example     |  12 +-
 .../config/environments/production.rb.example      |   6 +-
 apps/workbench/config/environments/test.rb.example |   6 -
 .../config/initializers/zzz_arvados_api_client.rb  |   8 -
 .../zza_load_config.rb => load_config.rb}          |   0
 apps/workbench/config/routes.rb                    |  12 +-
 apps/workbench/public/robots.txt                   |   2 -
 .../test/functional/collections_controller_test.rb |  80 +++++---
 .../workbench/test/integration/collections_test.rb |  27 ++-
 apps/workbench/test/integration/users_test.rb      |   7 +-
 apps/workbench/test/integration_helper.rb          |   5 +
 apps/workbench/test/test_helper.rb                 |  79 +++++---
 apps/workbench/test/unit/collection_test.rb        |  27 +++
 .../test/unit/helpers/collections_helper_test.rb   |   8 +
 doc/_config.yml                                    |   2 +
 doc/api/methods/keep_services.html.textile.liquid  |  75 +++++++
 doc/api/schema/KeepDisk.html.textile.liquid        |   4 +-
 doc/api/schema/KeepService.html.textile.liquid     |  24 +++
 .../install-workbench-app.html.textile.liquid      |  11 ++
 sdk/python/run_test_server.py                      |   9 +-
 .../arvados/v1/collections_controller.rb           |  62 +++++-
 .../arvados/v1/keep_services_controller.rb         |  21 ++
 services/api/app/models/api_client.rb              |   2 +-
 .../api/app/models/api_client_authorization.rb     |   2 +-
 services/api/app/models/arvados_model.rb           |  10 +-
 services/api/app/models/authorized_key.rb          |   2 +-
 services/api/app/models/collection.rb              |   2 +-
 services/api/app/models/group.rb                   |   5 +-
 services/api/app/models/human.rb                   |   2 +-
 services/api/app/models/job.rb                     |   2 +-
 services/api/app/models/job_task.rb                |   2 +-
 services/api/app/models/keep_disk.rb               |  20 +-
 services/api/app/models/keep_service.rb            |  15 ++
 services/api/app/models/link.rb                    |   2 +-
 services/api/app/models/locator.rb                 |  84 ++++++++
 services/api/app/models/log.rb                     |   2 +-
 services/api/app/models/node.rb                    |   2 +-
 services/api/app/models/pipeline_instance.rb       |   2 +-
 services/api/app/models/pipeline_template.rb       |   2 +-
 services/api/app/models/repository.rb              |   2 +-
 services/api/app/models/specimen.rb                |   2 +-
 services/api/app/models/trait.rb                   |   2 +-
 services/api/app/models/user.rb                    |   6 +-
 services/api/app/models/virtual_machine.rb         |   2 +-
 services/api/config/application.default.yml        |   5 +
 services/api/config/application.yml.example        |  13 ++
 services/api/config/initializers/assign_uuid.rb    |   1 -
 services/api/config/initializers/secret_token.rb   |   7 -
 services/api/config/routes.rb                      |   3 +
 .../20140422011506_pipeline_instance_state.rb      |   2 +
 .../migrate/20140519205916_create_keep_services.rb |  51 +++++
 services/api/db/schema.rb                          |  23 ++-
 services/api/lib/assign_uuid.rb                    |  31 ---
 services/api/lib/can_be_an_owner.rb                |  47 +++++
 services/api/lib/has_uuid.rb                       |  42 ++++
 .../test/fixtures/api_client_authorizations.yml    |   7 +
 services/api/test/fixtures/collections.yml         |  21 ++
 services/api/test/fixtures/jobs.yml                |   2 +-
 services/api/test/fixtures/keep_disks.yml          |  12 +-
 services/api/test/fixtures/keep_services.yml       |  23 +++
 services/api/test/fixtures/links.yml               |  14 ++
 services/api/test/fixtures/logs.yml                |   5 +
 .../arvados/v1/collections_controller_test.rb      | 216 +++++++++++++++++++++
 .../arvados/v1/keep_disks_controller_test.rb       |  34 +---
 .../arvados/v1/keep_services_controller_test.rb    |  23 +++
 services/api/test/integration/keep_proxy_test.rb   |  25 +++
 services/api/test/unit/arvados_model_test.rb       |  34 ++++
 .../api/test/unit/keep_service_test.rb             |   2 +-
 services/api/test/unit/link_test.rb                |  14 +-
 services/api/test/unit/owner_test.rb               | 126 ++++++++++++
 services/fuse/arvados_fuse/__init__.py             |  27 +--
 services/fuse/bin/arv-mount                        |   4 +-
 services/keep/src/keep/keep.go                     |  30 ++-
 129 files changed, 1928 insertions(+), 835 deletions(-)
 delete mode 100644 apps/workbench/app/assets/javascripts/api_client_authorizations.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/authorized_keys.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/folders.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/groups.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/humans.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/job_tasks.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/jobs.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/links.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/logs.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/nodes.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/pipeline_templates.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/repositories.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/sessions.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/specimens.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/traits.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/user_agreements.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/users.js.coffee
 delete mode 100644 apps/workbench/app/assets/javascripts/virtual_machines.js.coffee
 create mode 100644 apps/workbench/app/controllers/keep_services_controller.rb
 create mode 100644 apps/workbench/app/helpers/arvados_api_client_helper.rb
 copy apps/workbench/app/models/{keep_disk.rb => keep_service.rb} (70%)
 delete mode 100644 apps/workbench/app/views/collections/_show_jobs.html.erb
 delete mode 100644 apps/workbench/app/views/collections/_show_provenance.html.erb
 delete mode 100644 apps/workbench/app/views/collections/_show_source_data.html.erb
 create mode 100644 apps/workbench/app/views/collections/show.html.erb
 create mode 100644 apps/workbench/app/views/collections/show_file_links.html.erb
 delete mode 100644 apps/workbench/config/initializers/zzz_arvados_api_client.rb
 rename apps/workbench/config/{initializers/zza_load_config.rb => load_config.rb} (100%)
 create mode 100644 doc/api/methods/keep_services.html.textile.liquid
 create mode 100644 doc/api/schema/KeepService.html.textile.liquid
 create mode 100644 services/api/app/controllers/arvados/v1/keep_services_controller.rb
 create mode 100644 services/api/app/models/keep_service.rb
 create mode 100644 services/api/app/models/locator.rb
 delete mode 100644 services/api/config/initializers/assign_uuid.rb
 delete mode 100644 services/api/config/initializers/secret_token.rb
 create mode 100644 services/api/db/migrate/20140519205916_create_keep_services.rb
 delete mode 100644 services/api/lib/assign_uuid.rb
 create mode 100644 services/api/lib/can_be_an_owner.rb
 create mode 100644 services/api/lib/has_uuid.rb
 create mode 100644 services/api/test/fixtures/keep_services.yml
 create mode 100644 services/api/test/functional/arvados/v1/keep_services_controller_test.rb
 create mode 100644 services/api/test/integration/keep_proxy_test.rb
 create mode 100644 services/api/test/unit/arvados_model_test.rb
 copy apps/workbench/test/unit/job_task_test.rb => services/api/test/unit/keep_service_test.rb (61%)
 create mode 100644 services/api/test/unit/owner_test.rb

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commit 3ba5aa15ea0156a4fce63dcb43b7f972b4c760df
Merge: d54a48f 1b3750c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 21 16:00:47 2014 -0400

    Merge branch 'master' into 2798-go-keep-client

diff --cc sdk/python/run_test_server.py
index 9901e14,ba1df86..dbb4ff0
--- a/sdk/python/run_test_server.py
+++ b/sdk/python/run_test_server.py
@@@ -149,13 -149,10 +149,14 @@@ def run_keep()
      _start_keep(0)
      _start_keep(1)
  
 +
 +    os.environ["ARVADOS_API_HOST"] = "127.0.0.1:3001"
 +    os.environ["ARVADOS_API_HOST_INSECURE"] = "true"
 +
      authorize_with("admin")
      api = arvados.api('v1', cache=False)
-     a = api.keep_disks().list().execute()
+     for d in api.keep_services().list().execute()['items']:
+         api.keep_services().delete(uuid=d['uuid']).execute()
      for d in api.keep_disks().list().execute()['items']:
          api.keep_disks().delete(uuid=d['uuid']).execute()
  

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