[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
delete mode 100644 services/api/app/assets/javascripts/commits.js.coffee
delete mode 100644 services/api/app/assets/javascripts/groups.js.coffee
delete mode 100644 services/api/app/assets/javascripts/humans.js.coffee
delete mode 100644 services/api/app/assets/javascripts/job_tasks.js.coffee
delete mode 100644 services/api/app/assets/javascripts/jobs.js.coffee
delete mode 100644 services/api/app/assets/javascripts/keep_disks.js.coffee
delete mode 100644 services/api/app/assets/javascripts/links.js.coffee
delete mode 100644 services/api/app/assets/javascripts/logs.js.coffee
delete mode 100644 services/api/app/assets/javascripts/nodes.js
delete mode 100644 services/api/app/assets/javascripts/nodes.js.coffee
delete mode 100644 services/api/app/assets/javascripts/pipeline_instances.js.coffee
delete mode 100644 services/api/app/assets/javascripts/pipeline_templates.js.coffee
delete mode 100644 services/api/app/assets/javascripts/repositories.js.coffee
delete mode 100644 services/api/app/assets/javascripts/specimens.js.coffee
delete mode 100644 services/api/app/assets/javascripts/traits.js.coffee
delete mode 100644 services/api/app/assets/javascripts/virtual_machines.js.coffee
create mode 100644 services/api/app/controllers/database_controller.rb
create mode 100644 services/api/app/models/database_seeds.rb
create mode 100644 services/api/db/migrate/20141208164553_owner_uuid_index.rb
create mode 100644 services/api/lib/simulate_job_log.rb
create mode 100644 services/api/lib/tasks/replay_job_log.rake
create mode 100644 services/api/test/functional/database_controller_test.rb
create mode 100644 services/api/test/integration/cross_origin_test.rb
create mode 100644 services/api/test/integration/database_reset_test.rb
create mode 100644 services/api/test/job_logs/crunchstatshort.log
mode change 100644 => 120000 services/nodemanager/.gitignore
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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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