[ARVADOS] updated: 7b5729d984a9c516920270250f050bf72f1896d1

git at public.curoverse.com git at public.curoverse.com
Tue Jan 6 09:10:29 EST 2015


Summary of changes:
 apps/workbench/Gemfile                             |  19 +-
 apps/workbench/Gemfile.lock                        | 172 ++++----
 .../app/assets/javascripts/angular_shim.js         |  12 +
 .../app/assets/javascripts/application.js          |  10 +-
 .../app/assets/javascripts/arvados_client.js       | 101 +++++
 apps/workbench/app/assets/javascripts/event_log.js | 312 ++++++++++++++
 .../app/assets/javascripts/pipeline_instances.js   |  43 +-
 .../app/assets/javascripts/report_issue.js         |   4 +-
 .../app/assets/javascripts/selection.js.erb        | 189 +-------
 apps/workbench/app/assets/javascripts/tab_panes.js |   2 +-
 .../app/assets/javascripts/upload_to_collection.js | 476 +++++++++++++++++++++
 .../app/assets/stylesheets/application.css.scss    |  13 +-
 .../workbench/app/assets/stylesheets/jobs.css.scss |   5 +
 .../workbench/app/assets/stylesheets/selection.css |  17 -
 .../app/controllers/application_controller.rb      |  15 +-
 .../app/controllers/collections_controller.rb      |  20 +-
 apps/workbench/app/controllers/jobs_controller.rb  |  15 +
 .../controllers/pipeline_instances_controller.rb   |  22 +-
 .../workbench/app/controllers/search_controller.rb |   4 +-
 .../app/controllers/virtual_machines_controller.rb |   3 -
 .../helpers/api_client_authorizations_helper.rb    |   2 -
 apps/workbench/app/helpers/application_helper.rb   |  69 +--
 .../app/helpers/authorized_keys_helper.rb          |   2 -
 apps/workbench/app/helpers/groups_helper.rb        |   2 -
 apps/workbench/app/helpers/humans_helper.rb        |   2 -
 apps/workbench/app/helpers/job_tasks_helper.rb     |   2 -
 apps/workbench/app/helpers/keep_disks_helper.rb    |   2 -
 apps/workbench/app/helpers/links_helper.rb         |   2 -
 apps/workbench/app/helpers/logs_helper.rb          |   2 -
 apps/workbench/app/helpers/nodes_helper.rb         |   2 -
 apps/workbench/app/helpers/projects_helper.rb      |   2 -
 apps/workbench/app/helpers/provenance_helper.rb    |   5 +-
 apps/workbench/app/helpers/repositories_helper.rb  |   2 -
 apps/workbench/app/helpers/sessions_helper.rb      |   2 -
 apps/workbench/app/helpers/specimens_helper.rb     |   2 -
 apps/workbench/app/helpers/traits_helper.rb        |   2 -
 .../app/helpers/user_agreements_helper.rb          |   2 -
 apps/workbench/app/helpers/users_helper.rb         |   2 -
 apps/workbench/app/helpers/vcf_pipeline_helper.rb  | 234 ----------
 apps/workbench/app/helpers/version_helper.rb       |  30 ++
 .../app/helpers/virtual_machines_helper.rb         |   2 -
 apps/workbench/app/models/collection.rb            |  14 +-
 .../views/application/_projects_tree_menu.html.erb |  50 +--
 .../views/application/_report_issue_popup.html.erb |  14 +-
 .../views/application/report_issue_popup.js.erb    |   8 +-
 .../app/views/authorized_keys/_show_help.html.erb  |  10 -
 .../app/views/collections/_index_tbody.html.erb    |  15 +-
 .../app/views/collections/_sharing_button.html.erb |  36 +-
 .../app/views/collections/_show_files.html.erb     |  21 +-
 .../app/views/collections/_show_recent.html.erb    |   2 +-
 .../app/views/collections/_show_upload.html.erb    |  66 +++
 apps/workbench/app/views/jobs/_show_log.html.erb   |   8 +-
 .../app/views/keep_disks/_content_layout.html.erb  |   3 -
 .../app/views/layouts/application.html.erb         |   4 +-
 apps/workbench/app/views/layouts/body.html.erb     |  20 +-
 .../notifications/_ssh_key_notification.html.erb   |  22 +-
 .../pipeline_instances/_running_component.html.erb |   4 +-
 .../views/pipeline_instances/_show_recent.html.erb |   2 +-
 .../app/views/pipeline_instances/index.html.erb    |   3 +-
 .../views/pipeline_templates/_show_recent.html.erb |   2 +-
 .../app/views/pipeline_templates/show.html.erb     |   2 +-
 .../views/projects/_compute_node_status.html.erb   |   2 +-
 .../app/views/projects/_show_dashboard.html.erb    |  14 +-
 .../app/views/projects/_show_sharing.html.erb      |   2 +-
 .../app/views/projects/_show_tab_contents.html.erb |  12 +-
 apps/workbench/app/views/projects/show.html.erb    |  52 ++-
 .../app/views/user_agreements/index.html.erb       |   2 +-
 .../app/views/users/_add_ssh_key_popup.html.erb    |   6 +-
 .../app/views/users/_manage_ssh_keys.html.erb      |   8 +-
 .../workbench/app/views/users/_show_admin.html.erb |   2 +-
 apps/workbench/app/views/users/_tables.html.erb    |   6 +-
 apps/workbench/app/views/users/setup_popup.js.erb  |   6 +-
 apps/workbench/app/views/users/welcome.html.erb    |  21 +-
 apps/workbench/config/application.default.yml      |  11 +-
 apps/workbench/config/database.yml                 |   7 +
 apps/workbench/config/routes.rb                    |   1 +
 .../actions_controller_test.rb                     |   0
 .../api_client_authorizations_controller_test.rb   |   0
 .../application_controller_test.rb                 |   4 +
 .../authorized_keys_controller_test.rb             |   0
 .../controllers/collections_controller_test.rb     | 247 +++++++++++
 .../groups_controller_test.rb                      |   0
 .../humans_controller_test.rb                      |   0
 .../job_tasks_controller_test.rb                   |   0
 .../jobs_controller_test.rb                        |   0
 .../keep_disks_controller_test.rb                  |   0
 .../links_controller_test.rb                       |   0
 .../logs_controller_test.rb                        |   0
 .../nodes_controller_test.rb                       |   0
 .../pipeline_instances_controller_test.rb          | 171 ++++++--
 .../pipeline_templates_controller_test.rb          |   0
 .../projects_controller_test.rb                    |   0
 .../repositories_controller_test.rb                |   0
 .../test/controllers/search_controller_test.rb     |  41 +-
 .../sessions_controller_test.rb                    |   0
 .../specimens_controller_test.rb                   |   0
 .../traits_controller_test.rb                      |   0
 .../user_agreements_controller_test.rb             |   0
 .../users_controller_test.rb                       |   2 +-
 .../virtual_machines_controller_test.rb            |   0
 apps/workbench/test/diagnostics_test_helper.rb     |   3 +
 apps/workbench/test/functional/.gitkeep            |   0
 .../test/functional/collections_controller_test.rb | 229 ----------
 .../pipeline_instances_controller_test.rb          | 157 -------
 .../test/helpers/pipeline_instances_helper_test.rb |  38 ++
 .../test/integration/application_layout_test.rb    |   5 +
 .../test/integration/collection_upload_test.rb     | 100 +++++
 .../workbench/test/integration/collections_test.rb |  33 +-
 .../test/integration/pipeline_instances_test.rb    | 114 +++--
 apps/workbench/test/integration/projects_test.rb   | 206 ++++++---
 .../test/integration/report_issue_test.rb          |   6 +
 .../test/integration/user_manage_account_test.rb   |  46 +-
 apps/workbench/test/integration/websockets_test.rb |  41 ++
 apps/workbench/test/performance/browsing_test.rb   |  49 ++-
 apps/workbench/test/performance_test_helper.rb     |  32 ++
 apps/workbench/test/test_helper.rb                 |  92 +++-
 .../test/unit/api_client_authorization_test.rb     |   7 -
 apps/workbench/test/unit/authorized_key_test.rb    |   7 -
 apps/workbench/test/unit/human_test.rb             |   7 -
 apps/workbench/test/unit/job_task_test.rb          |   7 -
 apps/workbench/test/unit/keep_disk_test.rb         |   4 -
 apps/workbench/test/unit/log_test.rb               |   7 -
 apps/workbench/test/unit/node_test.rb              |   7 -
 apps/workbench/test/unit/pipeline_template_test.rb |   7 -
 apps/workbench/test/unit/repository_test.rb        |   7 -
 apps/workbench/test/unit/specimen_test.rb          |   7 -
 apps/workbench/test/unit/trait_test.rb             |   7 -
 apps/workbench/test/unit/user_agreement_test.rb    |   7 -
 apps/workbench/test/unit/virtual_machine_test.rb   |   7 -
 .../vendor/assets/javascripts/jquery.number.min.js |   2 +
 crunch_scripts/run-command                         |   6 +-
 doc/_config.yml                                    |   2 +-
 doc/_includes/_0_filter_py.liquid                  |  29 +-
 doc/_includes/_concurrent_hash_script_py.liquid    |  33 +-
 doc/_includes/_run_md5sum_py.liquid                |   7 +-
 doc/_includes/_tutorial_expectations.liquid        |   4 +-
 doc/_includes/_tutorial_hash_script_py.liquid      |  44 +-
 doc/api/schema/Job.html.textile.liquid             |   2 +-
 doc/css/bootstrap.css                              |   6 +-
 .../create-standard-objects.html.textile.liquid    |  22 +-
 doc/install/install-keepproxy.html.textile.liquid  |   9 +-
 doc/install/install-keepstore.html.textile.liquid  |   9 +-
 .../install-shell-server.html.textile.liquid       |   2 +-
 doc/install/install-sso.html.textile.liquid        |  20 +-
 doc/sdk/cli/index.html.textile.liquid              |   6 +-
 doc/sdk/cli/install.html.textile.liquid            |   4 +-
 doc/sdk/cli/reference.html.textile.liquid          |  80 ++++
 doc/sdk/cli/subcommands.html.textile.liquid        | 152 ++++++-
 doc/sdk/python/sdk-python.html.textile.liquid      |  21 +-
 .../check-environment.html.textile.liquid          |   2 +-
 doc/user/reference/sdk-cli.html.textile.liquid     |  46 --
 doc/user/topics/arv-run.html.textile.liquid        |   4 +-
 .../tutorial-firstscript.html.textile.liquid       |  15 +-
 .../tutorials/tutorial-keep.html.textile.liquid    |  54 +--
 docker/api/Dockerfile                              |   3 +-
 docker/api/arvados-clients.yml.in                  |   1 +
 docker/api/setup.sh.in                             |   9 -
 docker/api/ssh.sh                                  |  10 -
 docker/api/supervisor.conf                         |   5 +-
 docker/api/update-gitolite.rb                      |   6 +
 docker/arvdock                                     |  23 +-
 docker/base/Dockerfile                             |   6 +-
 docker/build_tools/Makefile                        |   5 +-
 docker/build_tools/build.rb                        |  17 -
 docker/build_tools/config.rb                       |   9 -
 docker/compute/Dockerfile                          |   1 -
 docker/compute/ssh.sh                              |  10 -
 docker/compute/supervisor.conf                     |   5 -
 docker/config.yml.example                          |   6 -
 docker/doc/apache2_foreground.sh                   |   5 -
 docker/java-bwa-samtools/Dockerfile                |   4 +-
 docker/jobs/Dockerfile                             |   3 +-
 docker/passenger/Dockerfile                        |   2 +-
 docker/shell/Dockerfile                            |   2 +-
 docker/shell/setup.sh.in                           |   2 -
 docker/slurm/supervisor.conf                       |   7 -
 docker/sso/apache2_foreground.sh                   |   5 -
 docker/workbench/apache2_foreground.sh             |   7 +-
 sdk/cli/.gitignore                                 |   1 +
 sdk/cli/Gemfile.lock                               |  72 ----
 sdk/cli/bin/crunch-job                             | 384 +++++++++++------
 sdk/cli/test/test_arv-collection-create.rb         |   5 +-
 sdk/cli/test/test_arv-get.rb                       |  50 ++-
 sdk/cli/test/test_arv-put.rb                       |  41 +-
 sdk/cli/test/test_arv-run-pipeline-instance.rb     |   2 +
 sdk/cli/test/test_arv-tag.rb                       |   6 +
 sdk/go/keepclient/keepclient.go                    |  22 +-
 sdk/go/keepclient/keepclient_test.go               |  91 ++--
 sdk/go/keepclient/support.go                       | 119 ++++--
 sdk/python/.gitignore                              |   6 +-
 sdk/python/arvados/__init__.py                     |   1 +
 sdk/python/arvados/collection.py                   |  36 +-
 sdk/python/arvados/commands/ls.py                  |  52 +++
 sdk/python/bin/arv-get                             |   2 +-
 sdk/python/bin/arv-ls                              |  23 +-
 sdk/python/setup.py                                |  32 +-
 sdk/python/tests/test_arv_ls.py                    |  80 ++++
 sdk/python/tests/test_collections.py               |  14 +
 sdk/python/tests/test_sdk.py                       |  43 ++
 services/api/Gemfile                               |   4 +-
 services/api/Gemfile.lock                          |  18 +-
 .../api_client_authorizations.js.coffee            |   3 -
 .../app/assets/javascripts/api_clients.js.coffee   |   3 -
 services/api/app/assets/javascripts/application.js |   9 -
 .../assets/javascripts/authorized_keys.js.coffee   |   3 -
 .../app/assets/javascripts/collections.js.coffee   |   3 -
 .../assets/javascripts/commit_ancestors.js.coffee  |   3 -
 .../api/app/assets/javascripts/commits.js.coffee   |   3 -
 .../api/app/assets/javascripts/groups.js.coffee    |   3 -
 .../api/app/assets/javascripts/humans.js.coffee    |   3 -
 .../api/app/assets/javascripts/job_tasks.js.coffee |   3 -
 services/api/app/assets/javascripts/jobs.js.coffee |   3 -
 .../app/assets/javascripts/keep_disks.js.coffee    |   3 -
 .../api/app/assets/javascripts/links.js.coffee     |   3 -
 services/api/app/assets/javascripts/logs.js.coffee |   3 -
 services/api/app/assets/javascripts/nodes.js       |  17 -
 .../api/app/assets/javascripts/nodes.js.coffee     |   3 -
 .../javascripts/pipeline_instances.js.coffee       |   3 -
 .../javascripts/pipeline_templates.js.coffee       |   3 -
 .../app/assets/javascripts/repositories.js.coffee  |   3 -
 .../api/app/assets/javascripts/specimens.js.coffee |   3 -
 .../api/app/assets/javascripts/traits.js.coffee    |   3 -
 .../assets/javascripts/virtual_machines.js.coffee  |   3 -
 .../api/app/controllers/application_controller.rb  |  43 ++
 .../arvados/v1/collections_controller.rb           |   2 +-
 .../arvados/v1/keep_disks_controller.rb            |  14 +-
 .../app/controllers/arvados/v1/nodes_controller.rb |  15 +-
 .../controllers/arvados/v1/schema_controller.rb    |   8 +-
 .../api/app/controllers/database_controller.rb     |  73 ++++
 services/api/app/controllers/static_controller.rb  |   6 +-
 .../app/controllers/user_sessions_controller.rb    |   5 +
 services/api/app/models/arvados_model.rb           |   4 +
 services/api/app/models/database_seeds.rb          |  11 +
 services/api/app/models/job.rb                     |  41 +-
 services/api/app/models/node.rb                    |  18 +-
 services/api/app/models/user.rb                    |  36 +-
 services/api/config/application.default.yml        |   4 +-
 services/api/config/routes.rb                      |  14 +
 .../20140422011506_pipeline_instance_state.rb      |   9 +-
 .../db/migrate/20141208164553_owner_uuid_index.rb  |  20 +
 services/api/db/seeds.rb                           |   9 +-
 services/api/db/structure.sql                      | 137 +++++-
 services/api/lib/current_api_client.rb             |  22 +
 services/api/lib/eventbus.rb                       |  27 +-
 services/api/lib/simulate_job_log.rb               |  49 +++
 services/api/lib/tasks/replay_job_log.rake         |   7 +
 services/api/script/crunch-dispatch.rb             | 250 ++++++-----
 .../test/fixtures/api_client_authorizations.yml    |   6 +
 services/api/test/fixtures/collections.yml         |  30 ++
 services/api/test/fixtures/groups.yml              |  16 +-
 services/api/test/fixtures/users.yml               |  21 +-
 .../test/functional/application_controller_test.rb |  44 ++
 .../arvados/v1/collections_controller_test.rb      |   6 +-
 .../arvados/v1/job_reuse_controller_test.rb        |  43 +-
 .../arvados/v1/keep_disks_controller_test.rb       |  31 +-
 .../functional/arvados/v1/links_controller_test.rb |  17 +-
 .../functional/arvados/v1/logs_controller_test.rb  |   4 +-
 .../functional/arvados/v1/nodes_controller_test.rb |   8 +
 .../test/functional/database_controller_test.rb    |  47 ++
 services/api/test/integration/cross_origin_test.rb |  76 ++++
 .../api/test/integration/database_reset_test.rb    |  75 ++++
 services/api/test/integration/errors_test.rb       |   2 +-
 services/api/test/job_logs/crunchstatshort.log     |   1 +
 services/api/test/test_helper.rb                   |   4 +
 services/api/test/unit/arvados_model_test.rb       |  23 +
 services/api/test/unit/job_test.rb                 |  54 ++-
 services/fuse/arvados_fuse/__init__.py             |  99 +++--
 services/fuse/setup.py                             |  33 +-
 services/fuse/tests/test_mount.py                  | 178 ++++----
 services/keepproxy/keepproxy.go                    |  88 +++-
 services/keepproxy/keepproxy_test.go               |  89 +++-
 services/keepstore/handler_test.go                 |  18 +-
 services/keepstore/handlers.go                     |   2 +-
 services/keepstore/logging_router.go               |  14 +-
 services/nodemanager/.gitignore                    |   6 +-
 services/nodemanager/arvnodeman/clientactor.py     |  13 +-
 .../arvnodeman/computenode/dispatch/__init__.py    |  63 ++-
 .../arvnodeman/computenode/dispatch/slurm.py       |   4 +-
 .../arvnodeman/computenode/driver/__init__.py      |  20 +
 .../arvnodeman/computenode/driver/ec2.py           |  12 +-
 services/nodemanager/arvnodeman/config.py          |   4 +-
 services/nodemanager/arvnodeman/daemon.py          |  61 ++-
 services/nodemanager/arvnodeman/jobqueue.py        |  13 +-
 services/nodemanager/arvnodeman/launcher.py        |  22 +-
 services/nodemanager/arvnodeman/nodelist.py        |  10 +-
 services/nodemanager/doc/ec2.example.cfg           |   6 +
 services/nodemanager/setup.py                      |  32 +-
 .../nodemanager/tests/test_computenode_dispatch.py |  36 +-
 .../tests/test_computenode_dispatch_slurm.py       |  20 +-
 .../tests/test_computenode_driver_ec2.py           |  52 ++-
 services/nodemanager/tests/test_daemon.py          | 124 ++++--
 services/nodemanager/tests/test_jobqueue.py        |  22 +-
 services/nodemanager/tests/testutil.py             |  18 +-
 293 files changed, 5408 insertions(+), 2895 deletions(-)
 create mode 100644 apps/workbench/app/assets/javascripts/angular_shim.js
 create mode 100644 apps/workbench/app/assets/javascripts/arvados_client.js
 create mode 100644 apps/workbench/app/assets/javascripts/upload_to_collection.js
 delete mode 100644 apps/workbench/app/assets/stylesheets/selection.css
 delete mode 100644 apps/workbench/app/helpers/api_client_authorizations_helper.rb
 delete mode 100644 apps/workbench/app/helpers/authorized_keys_helper.rb
 delete mode 100644 apps/workbench/app/helpers/groups_helper.rb
 delete mode 100644 apps/workbench/app/helpers/humans_helper.rb
 delete mode 100644 apps/workbench/app/helpers/job_tasks_helper.rb
 delete mode 100644 apps/workbench/app/helpers/keep_disks_helper.rb
 delete mode 100644 apps/workbench/app/helpers/links_helper.rb
 delete mode 100644 apps/workbench/app/helpers/logs_helper.rb
 delete mode 100644 apps/workbench/app/helpers/nodes_helper.rb
 delete mode 100644 apps/workbench/app/helpers/projects_helper.rb
 delete mode 100644 apps/workbench/app/helpers/repositories_helper.rb
 delete mode 100644 apps/workbench/app/helpers/sessions_helper.rb
 delete mode 100644 apps/workbench/app/helpers/specimens_helper.rb
 delete mode 100644 apps/workbench/app/helpers/traits_helper.rb
 delete mode 100644 apps/workbench/app/helpers/user_agreements_helper.rb
 delete mode 100644 apps/workbench/app/helpers/users_helper.rb
 delete mode 100644 apps/workbench/app/helpers/vcf_pipeline_helper.rb
 create mode 100644 apps/workbench/app/helpers/version_helper.rb
 delete mode 100644 apps/workbench/app/helpers/virtual_machines_helper.rb
 delete mode 100644 apps/workbench/app/views/authorized_keys/_show_help.html.erb
 create mode 100644 apps/workbench/app/views/collections/_show_upload.html.erb
 rename apps/workbench/test/{functional => controllers}/actions_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/api_client_authorizations_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/application_controller_test.rb (98%)
 rename apps/workbench/test/{functional => controllers}/authorized_keys_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/groups_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/humans_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/job_tasks_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/jobs_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/keep_disks_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/links_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/logs_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/nodes_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/pipeline_templates_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/projects_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/repositories_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/sessions_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/specimens_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/traits_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/user_agreements_controller_test.rb (100%)
 rename apps/workbench/test/{functional => controllers}/users_controller_test.rb (96%)
 rename apps/workbench/test/{functional => controllers}/virtual_machines_controller_test.rb (100%)
 delete mode 100644 apps/workbench/test/functional/.gitkeep
 delete mode 100644 apps/workbench/test/functional/collections_controller_test.rb
 delete mode 100644 apps/workbench/test/functional/pipeline_instances_controller_test.rb
 create mode 100644 apps/workbench/test/helpers/pipeline_instances_helper_test.rb
 create mode 100644 apps/workbench/test/integration/collection_upload_test.rb
 create mode 100644 apps/workbench/test/performance_test_helper.rb
 delete mode 100644 apps/workbench/test/unit/api_client_authorization_test.rb
 delete mode 100644 apps/workbench/test/unit/authorized_key_test.rb
 delete mode 100644 apps/workbench/test/unit/human_test.rb
 delete mode 100644 apps/workbench/test/unit/job_task_test.rb
 delete mode 100644 apps/workbench/test/unit/keep_disk_test.rb
 delete mode 100644 apps/workbench/test/unit/log_test.rb
 delete mode 100644 apps/workbench/test/unit/node_test.rb
 delete mode 100644 apps/workbench/test/unit/pipeline_template_test.rb
 delete mode 100644 apps/workbench/test/unit/repository_test.rb
 delete mode 100644 apps/workbench/test/unit/specimen_test.rb
 delete mode 100644 apps/workbench/test/unit/trait_test.rb
 delete mode 100644 apps/workbench/test/unit/user_agreement_test.rb
 delete mode 100644 apps/workbench/test/unit/virtual_machine_test.rb
 create mode 100644 apps/workbench/vendor/assets/javascripts/jquery.number.min.js
 create mode 100644 doc/sdk/cli/reference.html.textile.liquid
 delete mode 100644 doc/user/reference/sdk-cli.html.textile.liquid
 delete mode 100755 docker/api/ssh.sh
 delete mode 100755 docker/compute/ssh.sh
 delete mode 100644 sdk/cli/Gemfile.lock
 create mode 100755 sdk/python/arvados/commands/ls.py
 create mode 100644 sdk/python/tests/test_arv_ls.py
 create mode 100644 sdk/python/tests/test_sdk.py
 delete mode 100644 services/api/app/assets/javascripts/api_client_authorizations.js.coffee
 delete mode 100644 services/api/app/assets/javascripts/api_clients.js.coffee
 delete mode 100644 services/api/app/assets/javascripts/application.js
 delete mode 100644 services/api/app/assets/javascripts/authorized_keys.js.coffee
 delete mode 100644 services/api/app/assets/javascripts/collections.js.coffee
 delete mode 100644 services/api/app/assets/javascripts/commit_ancestors.js.coffee
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commit 7b5729d984a9c516920270250f050bf72f1896d1
Merge: b4b8bac 9013faf
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jan 6 08:45:08 2015 -0500

    Merge branch 'master' into 4570-multi-auth-method


commit b4b8bac5eb19bdfd792014250a65fbc1f7cfd007
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jan 6 08:44:49 2015 -0500

    4570: Revert to links on log in page instead of form.  Fixup documentation to
    to describe a production setup.

diff --git a/apps/workbench/app/views/users/welcome.html.erb b/apps/workbench/app/views/users/welcome.html.erb
index 4541d5b..f4fb4d1 100644
--- a/apps/workbench/app/views/users/welcome.html.erb
+++ b/apps/workbench/app/views/users/welcome.html.erb
@@ -28,22 +28,15 @@
 
       </p>
       <p>
-        <!-- <%= arvados_api_client.arvados_login_url %> -->
-        <%= form_tag(arvados_api_client.arvados_login_url(), :method => :get, :authenticity_token => false) do %>
-          <%= hidden_field_tag 'return_to', request.url %>
-          <div class="row pull-right">
-
-            <%# Todo: add list of external authentications providers to
-            discovery document, then generate the option list on the fly. Right
-            now, don't provide 'auth_provider' and hope that the default one is
-            the one we want. %>
-
-            <%#= select_tag "auth_provider", "<option value='google'>Google OpenID</option><option value='google_oauth2'>Google OAuth2</option>".html_safe, class: "form-control", style: "width: 15em; display: inline" %>
-	    <%= button_tag type: 'submit', name: nil, class: "btn btn-primary" do %>
-            Log in to <%= Rails.configuration.site_name %> <i class="fa fa-fw fa-arrow-circle-right"></i>
+        <%# Todo: add list of external authentications providers to
+            discovery document, then generate the option list here. Right
+            now, don't provide 'auth_provider' to get the default one. %>
+        <div class="row pull-right">
+	  <%= link_to arvados_api_client.arvados_login_url(return_to: request.url), class: "pull-right btn btn-primary" do %>
+          Log in to <%= Rails.configuration.site_name %>
+          <i class="fa fa-fw fa-arrow-circle-right"></i>
           <% end %>
         </div>
-        <% end %>
       </p>
     </div>
   </div>
diff --git a/doc/install/install-sso.html.textile.liquid b/doc/install/install-sso.html.textile.liquid
index 646cb3b..f272d85 100644
--- a/doc/install/install-sso.html.textile.liquid
+++ b/doc/install/install-sso.html.textile.liquid
@@ -6,7 +6,7 @@ title: Install Single Sign On (SSO) server
 
 h2(#dependencies). Install dependencies
 
-Make sure you have "Ruby and bundler":install-manual-prerequisites-ruby.html installed.
+Make sure you have "Ruby and Bundler":install-manual-prerequisites-ruby.html installed.
 
 h2(#install). Install SSO server
 
@@ -17,8 +17,8 @@ h3. Get SSO server code and create database
 ~$ <span class="userinput">git clone https://github.com/curoverse/sso-devise-omniauth-provider.git</span>
 ~$ <span class="userinput">cd sso-devise-omniauth-provider</span>
 ~/sso-devise-omniauth-provider$ <span class="userinput">bundle install</span>
-~/sso-devise-omniauth-provider$ <span class="userinput">rake db:create</span>
-~/sso-devise-omniauth-provider$ <span class="userinput">rake db:migrate</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rake db:create</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rake db:migrate</span>
 </code></pre>
 </notextile>
 
@@ -38,11 +38,11 @@ Edit @config/initializers/secret_token.rb@ to set @config.secret_token@ to the s
 h3. Configure upstream authentication provider
 
 <notextile>
-<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">cp -i config/environment.rb.example config/environment.rb</span>
+<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">cp -i config/environments/production.rb.example config/environments/production.rb</span>
 </code></pre>
 </notextile>
 
-Edit @config/environment.rb@ to set @config.google_client_id@ and @config.google_client_secret at .  See "Omniauth Google OAuth2 gem documentation":https://github.com/zquestz/omniauth-google-oauth2 and "Using OAuth 2.0 to Access Google APIs":https://developers.google.com/accounts/docs/OAuth2 for information about using the "Google Developers Console":https://console.developers.google.com to get a Google client id and client secret.
+Edit @config/environments/production.rb@ to set @config.google_oauth2_client_id@ and @config.google_oauth2_client_secret at .  See "Omniauth Google OAuth2 gem documentation":https://github.com/zquestz/omniauth-google-oauth2 and "Using OAuth 2.0 to Access Google APIs":https://developers.google.com/accounts/docs/OAuth2 for information about using the "Google Developers Console":https://console.developers.google.com to get a Google client id and client secret.
 
 h3(#client). Create arvados-server client
 
@@ -51,7 +51,7 @@ Use @rails console@ to create a @Client@ record that will be used by the Arvados
 <notextile>
 <pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">rake secret</span>
 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-~/sso-devise-omniauth-provider$ <span class="userinput">rails console</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rails console</span>
 irb(main):001:0> <span class="userinput">c = Client.new</span>
 irb(main):002:0> <span class="userinput">c.name = "joshid"</span>
 irb(main):003:0> <span class="userinput">c.app_id = "arvados-server"</span>
@@ -63,15 +63,15 @@ irb(main):006:0> <span class="userinput">quit</span>
 
 h2. Start the SSO server
 
-h3. Development environment
+h3. Run a simple standalone server
 
-To run in development mode, you can now run the development server this way:
+You can use the Webrick server that is bundled with Ruby to quickly verify that your installation is functioning:
 
 <notextile>
-<pre><code>~/arvados/services/api$ <span class="userinput">bundle exec rails server</span>
+<pre><code>~/arvados/services/api$ <span class="userinput">RAILS_ENV=production bundle exec rails server</span>
 </code></pre>
 </notextile>
 
 h3. Production environment
 
-As a Ruby on Rails application, the SSO server should be compatible with any Ruby application server that supports Rack applications.
+As a Ruby on Rails application, the SSO server should be compatible with any Ruby application server that supports Rack applications.  We recommend "Passenger":https://www.phusionpassenger.com/ to run the SSO server in production.

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