[ARVADOS] updated: 4609a76d9b84e0f63233cdf6dcbef376b1686b69
git at public.curoverse.com
git at public.curoverse.com
Fri May 30 15:51:27 EDT 2014
Summary of changes:
.gitignore | 2 +
apps/admin/setup-new-user.rb | 168 ----
apps/workbench/.gitignore | 7 +
apps/workbench/Gemfile | 23 +-
apps/workbench/Gemfile.lock | 155 ++--
.../api_client_authorizations.js.coffee | 3 -
.../app/assets/javascripts/application.js | 1 -
.../assets/javascripts/authorized_keys.js.coffee | 3 -
.../app/assets/javascripts/collections.js | 1 -
apps/workbench/app/assets/javascripts/editable.js | 59 +-
apps/workbench/app/assets/javascripts/event_log.js | 45 ++
apps/workbench/app/assets/javascripts/folders.js | 12 +
.../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 | 31 +-
.../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 | 102 ++-
.../javascripts/pipeline_templates.js.coffee | 3 -
.../app/assets/javascripts/repositories.js.coffee | 3 -
.../app/assets/javascripts/select_modal.js | 39 +
apps/workbench/app/assets/javascripts/selection.js | 20 +-
.../app/assets/javascripts/sessions.js.coffee | 3 -
apps/workbench/app/assets/javascripts/sizing.js | 2 +-
.../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/application.css.scss | 72 +-
.../app/assets/stylesheets/cards.css.scss | 85 ++
.../app/assets/stylesheets/collections.css.scss | 48 ++
.../app/assets/stylesheets/folders.css.scss | 13 +
.../app/assets/stylesheets/keep_disks.css.scss | 8 +
.../app/assets/stylesheets/sb-admin.css.scss | 164 ++++
.../app/assets/stylesheets/select_modal.css.scss | 3 +
.../workbench/app/assets/stylesheets/selection.css | 22 +-
.../app/controllers/actions_controller.rb | 44 +-
.../api_client_authorizations_controller.rb | 13 -
.../app/controllers/application_controller.rb | 87 +-
.../app/controllers/collections_controller.rb | 176 ++--
.../app/controllers/folders_controller.rb | 118 +++
.../workbench/app/controllers/groups_controller.rb | 7 +-
apps/workbench/app/controllers/jobs_controller.rb | 7 +-
.../app/controllers/keep_disks_controller.rb | 47 ++
.../app/controllers/keep_services_controller.rb | 2 +
.../controllers/pipeline_instances_controller.rb | 8 +-
.../app/controllers/sessions_controller.rb | 2 +-
apps/workbench/app/controllers/users_controller.rb | 10 +-
apps/workbench/app/helpers/application_helper.rb | 38 +-
.../app/helpers/arvados_api_client_helper.rb | 13 +
apps/workbench/app/helpers/folders_helper.rb | 2 +
.../app/helpers/pipeline_instances_helper.rb | 21 +-
apps/workbench/app/models/arvados_api_client.rb | 51 +-
apps/workbench/app/models/arvados_base.rb | 117 ++-
apps/workbench/app/models/arvados_resource_list.rb | 13 +-
apps/workbench/app/models/collection.rb | 34 +-
apps/workbench/app/models/group.rb | 18 +-
apps/workbench/app/models/human.rb | 3 +
apps/workbench/app/models/job.rb | 8 +
.../app/models/{keep_disk.rb => keep_service.rb} | 2 +-
apps/workbench/app/models/log.rb | 5 +
apps/workbench/app/models/pipeline_instance.rb | 7 +-
apps/workbench/app/models/pipeline_template.rb | 4 +
apps/workbench/app/models/specimen.rb | 3 +
apps/workbench/app/models/trait.rb | 3 +
apps/workbench/app/models/user.rb | 26 +-
apps/workbench/app/models/user_agreement.rb | 8 +-
.../app/views/application/_content.html.erb | 2 +-
.../application/_delete_object_button.html.erb | 2 +-
.../application/_pipeline_status_label.html.erb | 6 +-
.../views/application/_selection_checkbox.html.erb | 2 +-
.../app/views/application/_show_metadata.html.erb | 4 +-
.../views/application/_show_object_button.html.erb | 3 +
.../app/views/application/_show_recent.html.erb | 27 +-
.../workbench/app/views/application/index.html.erb | 6 +-
.../app/views/collections/_sharing_button.html.erb | 21 +
.../app/views/collections/_show_files.html.erb | 116 ++-
.../app/views/collections/_show_jobs.html.erb | 64 --
.../views/collections/_show_provenance.html.erb | 84 --
.../views/collections/_show_source_data.html.erb | 44 -
.../app/views/collections/sharing_popup.js.erb | 1 +
apps/workbench/app/views/collections/show.html.erb | 111 +++
.../app/views/collections/show_file_links.html.erb | 82 ++
apps/workbench/app/views/folders/_choose.html.erb | 42 +
apps/workbench/app/views/folders/_choose.js.erb | 8 +
.../app/views/folders/_show_folders.html.erb | 29 +
.../workbench/app/views/folders/remove_item.js.erb | 5 +
apps/workbench/app/views/folders/show.html.erb | 214 +++++
.../workbench/app/views/jobs/_show_recent.html.erb | 6 +-
.../app/views/keep_disks/_content_layout.html.erb | 21 +
.../app/views/layouts/application.html.erb | 326 ++++----
apps/workbench/app/views/links/_recent.html.erb | 2 +-
apps/workbench/app/views/logs/show.html.erb | 1 -
.../pipeline_instances/_show_components.html.erb | 83 +-
.../_show_components_editable.html.erb | 4 +-
.../views/pipeline_instances/_show_inputs.html.erb | 50 ++
.../views/pipeline_instances/_show_recent.html.erb | 8 +-
.../app/views/pipeline_instances/show.js.erb | 6 +-
.../pipeline_templates/_show_components.html.erb | 2 +-
.../views/pipeline_templates/_show_recent.html.erb | 45 +-
.../app/views/user_agreements/index.html.erb | 2 +-
.../workbench/app/views/users/_show_admin.html.erb | 2 +-
apps/workbench/app/views/users/_tables.html.erb | 8 +-
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 | 21 +-
apps/workbench/public/robots.txt | 2 -
.../test/functional/collections_controller_test.rb | 80 +-
.../folders_controller_test.rb} | 2 +-
.../workbench/test/integration/collections_test.rb | 36 +-
apps/workbench/test/integration/folders_test.rb | 83 ++
.../test/integration/pipeline_instances_test.rb | 56 ++
apps/workbench/test/integration/smoke_test.rb | 6 +-
apps/workbench/test/integration/users_test.rb | 58 +-
.../test/integration/virtual_machines_test.rb | 4 +-
apps/workbench/test/integration_helper.rb | 47 ++
apps/workbench/test/test_helper.rb | 116 ++-
apps/workbench/test/unit/collection_test.rb | 27 +
.../test/unit/helpers/collections_helper_test.rb | 8 +
.../test/unit/helpers/folders_helper_test.rb | 4 +
doc/_config.yml | 7 +-
doc/api/index.html.textile.liquid | 2 -
doc/api/methods.html.textile.liquid | 39 +-
doc/api/methods/keep_services.html.textile.liquid | 75 ++
doc/api/methods/logs.html.textile.liquid | 22 +-
doc/api/schema/Collection.html.textile.liquid | 2 +-
doc/api/schema/Job.html.textile.liquid | 1 +
doc/api/schema/KeepDisk.html.textile.liquid | 4 +-
doc/api/schema/KeepService.html.textile.liquid | 24 +
doc/install/index.html.md.liquid | 18 -
doc/install/index.html.textile.liquid | 18 +
doc/install/install-api-server.html.textile.liquid | 5 +-
.../install-crunch-dispatch.html.textile.liquid | 44 +-
doc/install/install-sso.html.textile.liquid | 3 +-
.../install-workbench-app.html.textile.liquid | 41 +-
doc/sdk/index.html.textile.liquid | 3 +-
doc/sdk/java/index.html.textile.liquid | 140 ++++
doc/sdk/perl/index.html.textile.liquid | 2 +-
doc/sdk/python/sdk-python.html.textile.liquid | 11 +-
doc/sdk/ruby/index.html.textile.liquid | 2 +-
.../tutorial-firstscript.html.textile.liquid | 10 +-
docker/build_tools/Makefile | 10 +
docker/jobs/Dockerfile | 20 +
sdk/cli/arvados-cli.gemspec | 1 +
sdk/cli/bin/arv | 11 +-
sdk/cli/bin/arv-run-pipeline-instance | 93 ++-
sdk/cli/bin/crunch-job | 82 +-
sdk/cli/test/test_arv-run-pipeline-instance.rb | 33 +
sdk/go/go.sh | 17 +
sdk/go/src/arvados.org/keepclient/hashcheck.go | 77 ++
.../src/arvados.org/keepclient/hashcheck_test.go | 85 ++
sdk/go/src/arvados.org/keepclient/keepclient.go | 293 +++++++
.../src/arvados.org/keepclient/keepclient_test.go | 698 ++++++++++++++++
sdk/go/src/arvados.org/keepclient/support.go | 277 +++++++
sdk/go/src/arvados.org/streamer/streamer.go | 130 +++
sdk/go/src/arvados.org/streamer/streamer_test.go | 366 +++++++++
sdk/go/src/arvados.org/streamer/transfer.go | 308 +++++++
sdk/java/.classpath | 21 +
sdk/java/.project | 14 +
sdk/java/.settings/org.eclipse.jdt.core.prefs | 5 +
sdk/java/ArvadosSDKJavaExample.java | 80 ++
sdk/java/ArvadosSDKJavaExampleWithPrompt.java | 123 +++
sdk/java/README | 4 +
sdk/java/pom.xml | 106 +++
.../main/java/org/arvados/sdk/java/Arvados.java | 454 +++++++++++
.../java/org/arvados/sdk/java/MethodDetails.java | 22 +
sdk/java/src/main/resources/log4j.properties | 11 +
.../java/org/arvados/sdk/java/ArvadosTest.java | 464 +++++++++++
sdk/java/src/test/resources/first_pipeline.json | 16 +
sdk/perl/lib/Arvados.pm | 2 +-
sdk/perl/lib/Arvados/Request.pm | 9 +-
sdk/python/.gitignore | 1 -
sdk/python/arvados/api.py | 12 +-
sdk/python/arvados/collection.py | 237 +++++-
.../python/arvados/commands/__init__.py | 0
sdk/python/arvados/commands/put.py | 399 +++++++++
sdk/python/arvados/errors.py | 4 +
sdk/python/arvados/events.py | 33 +
sdk/python/arvados/fuse.py | 317 --------
sdk/python/arvados/keep.py | 221 ++++-
sdk/python/bin/arv-mount | 67 --
sdk/python/bin/arv-put | 215 +----
sdk/python/build.sh | 16 -
sdk/python/requirements.txt | 11 +-
sdk/python/{setup.py.src => setup.py} | 12 +-
sdk/python/test_cmdline.py | 81 ++
sdk/python/test_keep_client.py | 62 --
sdk/python/test_mount.py | 153 ----
sdk/python/tests/arvados_testutil.py | 61 ++
.../{testdata => tests/data}/1000G_ref_manifest | 0
sdk/python/{testdata => tests/data}/jlake_manifest | 0
sdk/python/tests/run_test_server.py | 287 +++++++
sdk/python/tests/test_arv-put.py | 352 ++++++++
sdk/python/{ => tests}/test_collections.py | 309 ++++---
sdk/python/tests/test_keep_client.py | 281 +++++++
sdk/python/tests/test_keep_locator.py | 67 ++
sdk/python/{ => tests}/test_pipeline_template.py | 18 +-
sdk/python/{ => tests}/test_util.py | 0
sdk/python/tests/test_websockets.py | 32 +
sdk/ruby/.gitignore | 1 +
sdk/ruby/Gemfile.lock | 58 --
sdk/ruby/arvados.gemspec | 1 +
sdk/ruby/lib/arvados.rb | 7 +-
services/api/.gitignore | 6 +
services/api/Gemfile | 6 +-
services/api/Gemfile.lock | 20 +-
services/api/Rakefile | 6 +
.../api/app/controllers/application_controller.rb | 67 --
.../v1/api_client_authorizations_controller.rb | 2 +
.../arvados/v1/collections_controller.rb | 62 +-
.../controllers/arvados/v1/groups_controller.rb | 60 ++
.../app/controllers/arvados/v1/jobs_controller.rb | 4 +-
.../arvados/v1/keep_services_controller.rb | 21 +
.../app/controllers/arvados/v1/nodes_controller.rb | 2 +-
.../controllers/arvados/v1/schema_controller.rb | 15 +-
.../app/controllers/user_sessions_controller.rb | 3 +-
services/api/app/mailers/admin_notifier.rb | 14 +
services/api/app/models/api_client.rb | 2 +-
.../api/app/models/api_client_authorization.rb | 2 +-
services/api/app/models/arvados_model.rb | 87 +-
services/api/app/models/authorized_key.rb | 2 +-
services/api/app/models/collection.rb | 2 +-
services/api/app/models/group.rb | 22 +-
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 | 36 +-
services/api/app/models/pipeline_instance.rb | 93 ++-
services/api/app/models/pipeline_template.rb | 3 +-
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 | 22 +-
services/api/app/models/virtual_machine.rb | 2 +-
.../admin_notifier/new_inactive_user.text.erb | 6 +
.../api/app/views/admin_notifier/new_user.text.erb | 6 +
services/api/config/application.default.yml | 19 +-
services/api/config/application.yml.example | 28 +-
services/api/config/initializers/assign_uuid.rb | 1 -
services/api/config/initializers/eventbus.rb | 6 +-
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 ++
...152921_add_description_to_pipeline_templates.rb | 5 +
services/api/db/schema.rb | 24 +-
services/api/lib/assign_uuid.rb | 31 -
services/api/lib/can_be_an_owner.rb | 47 ++
services/api/lib/has_uuid.rb | 44 +
services/api/lib/record_filters.rb | 17 +-
services/api/script/crunch-dispatch.rb | 70 +-
services/api/script/import_commits.rb | 9 -
.../test/fixtures/api_client_authorizations.yml | 7 +
services/api/test/fixtures/collections.yml | 29 +-
services/api/test/fixtures/jobs.yml | 22 +-
services/api/test/fixtures/keep_disks.yml | 12 +-
services/api/test/fixtures/keep_services.yml | 23 +
services/api/test/fixtures/links.yml | 67 ++
services/api/test/fixtures/logs.yml | 5 +
services/api/test/fixtures/pipeline_instances.yml | 3 +
services/api/test/fixtures/pipeline_templates.yml | 4 +-
services/api/test/fixtures/specimens.yml | 18 +
.../arvados/v1/collections_controller_test.rb | 230 ++++++
.../api/test/functional/arvados/v1/filters_test.rb | 16 +
.../arvados/v1/groups_controller_test.rb | 37 +
.../functional/arvados/v1/jobs_controller_test.rb | 49 ++
.../arvados/v1/keep_disks_controller_test.rb | 34 +-
.../arvados/v1/keep_services_controller_test.rb | 23 +
.../functional/arvados/v1/users_controller_test.rb | 2 +
services/api/test/integration/keep_proxy_test.rb | 25 +
.../api/test/integration/user_sessions_test.rb | 28 +
services/api/test/integration/websocket_test.rb | 2 +-
services/api/test/test_helper.rb | 21 +
.../api/test/unit/api_client_authorization_test.rb | 16 +-
services/api/test/unit/arvados_model_test.rb | 78 ++
.../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/api/test/unit/permission_test.rb | 14 +
services/api/test/unit/pipeline_instance_test.rb | 26 +-
services/api/test/unit/user_test.rb | 235 ++----
services/datamanager/experimental/datamanager.py | 887 +++++++++++++++++++++
.../datamanager/experimental/datamanager_test.py | 41 +
services/fuse/.gitignore | 1 +
services/fuse/arvados_fuse/__init__.py | 588 ++++++++++++++
services/fuse/bin/arv-mount | 88 ++
{sdk/python => services/fuse}/readme.llfuse | 0
services/fuse/requirements.txt | 3 +
services/fuse/setup.py | 22 +
services/fuse/tests/run_test_server.py | 1 +
services/fuse/tests/test_mount.py | 332 ++++++++
services/keep/build.sh | 36 -
services/keep/go.sh | 17 +
.../keep/src/arvados.org/keepproxy/keepproxy.go | 424 ++++++++++
.../src/arvados.org/keepproxy/keepproxy_test.go | 276 +++++++
services/keep/src/keep/handler_test.go | 453 +++++++++++
services/keep/src/keep/keep.go | 375 ++++++++-
services/keep/src/keep/keep_test.go | 6 +-
services/keep/src/keep/perms.go | 13 +-
315 files changed, 14452 insertions(+), 3055 deletions(-)
delete mode 100755 apps/admin/setup-new-user.rb
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
create mode 100644 apps/workbench/app/assets/javascripts/event_log.js
create mode 100644 apps/workbench/app/assets/javascripts/folders.js
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
create mode 100644 apps/workbench/app/assets/javascripts/select_modal.js
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/assets/stylesheets/cards.css.scss
create mode 100644 apps/workbench/app/assets/stylesheets/folders.css.scss
create mode 100644 apps/workbench/app/assets/stylesheets/sb-admin.css.scss
create mode 100644 apps/workbench/app/assets/stylesheets/select_modal.css.scss
create mode 100644 apps/workbench/app/controllers/folders_controller.rb
create mode 100644 apps/workbench/app/controllers/keep_services_controller.rb
create mode 100644 apps/workbench/app/helpers/arvados_api_client_helper.rb
create mode 100644 apps/workbench/app/helpers/folders_helper.rb
copy apps/workbench/app/models/{keep_disk.rb => keep_service.rb} (70%)
create mode 100644 apps/workbench/app/views/application/_show_object_button.html.erb
create mode 100644 apps/workbench/app/views/collections/_sharing_button.html.erb
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/sharing_popup.js.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
create mode 100644 apps/workbench/app/views/folders/_choose.html.erb
create mode 100644 apps/workbench/app/views/folders/_choose.js.erb
create mode 100644 apps/workbench/app/views/folders/_show_folders.html.erb
create mode 100644 apps/workbench/app/views/folders/remove_item.js.erb
create mode 100644 apps/workbench/app/views/folders/show.html.erb
create mode 100644 apps/workbench/app/views/keep_disks/_content_layout.html.erb
delete mode 100644 apps/workbench/app/views/logs/show.html.erb
create mode 100644 apps/workbench/app/views/pipeline_instances/_show_inputs.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%)
copy apps/workbench/test/{unit/job_test.rb => functional/folders_controller_test.rb} (57%)
create mode 100644 apps/workbench/test/integration/folders_test.rb
create mode 100644 apps/workbench/test/integration/pipeline_instances_test.rb
create mode 100644 apps/workbench/test/unit/helpers/folders_helper_test.rb
create mode 100644 doc/api/methods/keep_services.html.textile.liquid
create mode 100644 doc/api/schema/KeepService.html.textile.liquid
delete mode 100644 doc/install/index.html.md.liquid
create mode 100644 doc/install/index.html.textile.liquid
create mode 100644 doc/sdk/java/index.html.textile.liquid
create mode 100644 docker/jobs/Dockerfile
create mode 100644 sdk/cli/test/test_arv-run-pipeline-instance.rb
create mode 100755 sdk/go/go.sh
create mode 100644 sdk/go/src/arvados.org/keepclient/hashcheck.go
create mode 100644 sdk/go/src/arvados.org/keepclient/hashcheck_test.go
create mode 100644 sdk/go/src/arvados.org/keepclient/keepclient.go
create mode 100644 sdk/go/src/arvados.org/keepclient/keepclient_test.go
create mode 100644 sdk/go/src/arvados.org/keepclient/support.go
create mode 100644 sdk/go/src/arvados.org/streamer/streamer.go
create mode 100644 sdk/go/src/arvados.org/streamer/streamer_test.go
create mode 100644 sdk/go/src/arvados.org/streamer/transfer.go
create mode 100644 sdk/java/.classpath
create mode 100644 sdk/java/.project
create mode 100644 sdk/java/.settings/org.eclipse.jdt.core.prefs
create mode 100644 sdk/java/ArvadosSDKJavaExample.java
create mode 100644 sdk/java/ArvadosSDKJavaExampleWithPrompt.java
create mode 100644 sdk/java/README
create mode 100644 sdk/java/pom.xml
create mode 100644 sdk/java/src/main/java/org/arvados/sdk/java/Arvados.java
create mode 100644 sdk/java/src/main/java/org/arvados/sdk/java/MethodDetails.java
create mode 100644 sdk/java/src/main/resources/log4j.properties
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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 4609a76d9b84e0f63233cdf6dcbef376b1686b69
Merge: 0c1c7fa b6ea1fe
Author: Ward Vandewege <ward at curoverse.com>
Date: Fri May 30 15:50:59 2014 -0400
Merge branch 'master' into 2681-new-inactive-user-notification
commit 0c1c7fa2cba96aae542db0e6b6991c71d5ff578a
Author: Ward Vandewege <ward at curoverse.com>
Date: Fri May 30 15:49:44 2014 -0400
Refactor user notification tests
diff --git a/services/api/test/unit/user_test.rb b/services/api/test/unit/user_test.rb
index 235e5cb..0d55633 100644
--- a/services/api/test/unit/user_test.rb
+++ b/services/api/test/unit/user_test.rb
@@ -95,7 +95,9 @@ class UserTest < ActiveSupport::TestCase
user.save
# verify there is one extra user in the db now
- assert_equal @all_users.size+1, User.find(:all).size
+ # the API server also auto-creates the root system user after the first user
+ # is created, hence the test for the delta of 2.
+ assert_equal @all_users.size+2, User.find(:all).size
user = User.find(user.id) # get the user back
assert_equal(user.first_name, 'first_name_for_newly_created_user')
@@ -109,134 +111,17 @@ class UserTest < ActiveSupport::TestCase
assert_equal(user.first_name, 'first_name_for_newly_created_user_updated')
end
- test "create new inactive user with new_inactive_user_notification_recipients empty" do
+ test "create new user with notifications" do
set_user_from_auth :admin
- Rails.configuration.new_inactive_user_notification_recipients = ''
-
- ActionMailer::Base.deliveries = []
-
- user = User.new
- user.first_name = "first_name_for_newly_created_user"
- user.is_active = false
- user.save
-
- assert_equal '', Rails.configuration.new_inactive_user_notification_recipients
-
- ActionMailer::Base.deliveries.each do |d|
- assert_not_equal "#{Rails.configuration.email_subject_prefix}New inactive user notification", setup_email.subject
- end
-
+ user_notification_helper true, 'active-notify-address at example.com', 'inactive-notify-address at example.com'
+ user_notification_helper true, 'active-notify-address at example.com', []
+ user_notification_helper true, [], []
+ user_notification_helper false, 'active-notify-address at example.com', 'inactive-notify-address at example.com'
+ user_notification_helper false, [], 'inactive-notify-address at example.com'
+ user_notification_helper false, [], []
end
- test "create new inactive user with new_user_notification_recipients empty" do
- set_user_from_auth :admin
-
- Rails.configuration.new_user_notification_recipients = ''
-
- ActionMailer::Base.deliveries = []
-
- user = User.new
- user.first_name = "first_name_for_newly_created_user"
- user.is_active = false
- user.save
-
- assert_equal '', Rails.configuration.new_user_notification_recipients
-
- ActionMailer::Base.deliveries.each do |d|
- assert_not_equal "#{Rails.configuration.email_subject_prefix}New user notification", d.subject
- end
-
- end
-
- test "create new inactive user with new_user_notification_recipients and new_inactive_user_notification_recipients set" do
- set_user_from_auth :admin
-
- Rails.configuration.new_user_notification_recipients = 'foo_new at example.com'
- Rails.configuration.new_inactive_user_notification_recipients = 'foo_new_inactive at example.com'
-
- ActionMailer::Base.deliveries = []
-
- user = User.new
- user.first_name = "first_name_for_newly_created_user"
- user.is_active = false
- user.save
-
- new_user_email = nil
- new_inactive_user_email = nil
- ActionMailer::Base.deliveries.each do |d|
- if d.subject == "#{Rails.configuration.email_subject_prefix}New inactive user notification" then
- new_inactive_user_email = d
- end
- if d.subject == "#{Rails.configuration.email_subject_prefix}New user notification" then
- new_user_email = d
- end
- end
-
- assert_not_nil new_inactive_user_email, 'Expected new inactive user email after setup'
- assert_not_nil new_user_email, 'Expected new user email after setup'
-
- assert_equal 'foo_new at example.com', Rails.configuration.new_user_notification_recipients
- assert_equal 'foo_new_inactive at example.com', Rails.configuration.new_inactive_user_notification_recipients
-
- assert_equal Rails.configuration.user_notifier_email_from, new_inactive_user_email.from[0]
- assert_equal 'foo_new_inactive at example.com', new_inactive_user_email.to[0]
- assert_equal "#{Rails.configuration.email_subject_prefix}New inactive user notification", new_inactive_user_email.subject
-
- assert_equal Rails.configuration.user_notifier_email_from, new_user_email.from[0]
- assert_equal 'foo_new at example.com', new_user_email.to[0]
- assert_equal "#{Rails.configuration.email_subject_prefix}New user notification", new_user_email.subject
- end
-
- test "create new inactive user with new_user_notification_recipients set" do
- set_user_from_auth :admin
-
- Rails.configuration.new_user_notification_recipients = 'foo at example.com'
-
- user = User.new
- user.first_name = "first_name_for_newly_created_user"
- user.is_active = false
- user.save
-
- new_user_email = nil
-
- ActionMailer::Base.deliveries.each do |d|
- if d.subject == "#{Rails.configuration.email_subject_prefix}New user notification" then
- new_user_email = d
- break
- end
- end
-
- assert_not_nil new_user_email, 'Expected email after setup'
-
- assert_equal 'foo at example.com', Rails.configuration.new_user_notification_recipients
-
- assert_equal Rails.configuration.user_notifier_email_from, new_user_email.from[0]
- assert_equal 'foo at example.com', new_user_email.to[0]
- assert_equal "#{Rails.configuration.email_subject_prefix}New user notification", new_user_email.subject
- end
-
- test "create new active user with new_inactive_user_notification_recipients set" do
- set_user_from_auth :admin
-
- Rails.configuration.new_inactive_user_notification_recipients = 'foo at example.com'
-
- ActionMailer::Base.deliveries = []
-
- user = User.new
- user.first_name = "first_name_for_newly_created_user"
- user.is_active = true
- user.save
-
- assert_equal 'foo at example.com', Rails.configuration.new_inactive_user_notification_recipients
-
- ActionMailer::Base.deliveries.each do |d|
- assert_not_equal "#{Rails.configuration.email_subject_prefix}New inactive user notification", setup_email.subject
- end
-
- end
-
-
test "update existing user" do
set_user_from_auth :active # set active user as current user
@@ -462,4 +347,55 @@ class UserTest < ActiveSupport::TestCase
end
end
+ def user_notification_helper (active, active_recipients, inactive_recipients)
+ Rails.configuration.new_user_notification_recipients = active_recipients
+ Rails.configuration.new_inactive_user_notification_recipients = inactive_recipients
+
+ assert_equal active_recipients, Rails.configuration.new_user_notification_recipients
+ assert_equal inactive_recipients, Rails.configuration.new_inactive_user_notification_recipients
+
+ ActionMailer::Base.deliveries = []
+
+ user = User.new
+ user.first_name = "first_name_for_newly_created_user"
+ user.is_active = active
+ user.save
+
+ new_user_email = nil
+ new_inactive_user_email = nil
+
+ ActionMailer::Base.deliveries.each do |d|
+ if d.subject == "#{Rails.configuration.email_subject_prefix}New user notification" then
+ new_user_email = d
+ elsif d.subject == "#{Rails.configuration.email_subject_prefix}New inactive user notification" then
+ new_inactive_user_email = d
+ end
+ end
+
+ if not active
+ if not inactive_recipients.empty? then
+ assert_not_nil new_inactive_user_email, 'Expected new inactive user email after setup'
+ assert_equal Rails.configuration.user_notifier_email_from, new_inactive_user_email.from[0]
+ assert_equal inactive_recipients, new_inactive_user_email.to[0]
+ assert_equal "#{Rails.configuration.email_subject_prefix}New inactive user notification", new_inactive_user_email.subject
+ else
+ assert_nil new_inactive_user_email, 'Did not expect new inactive user email after setup'
+ end
+ end
+
+ if active
+ assert_nil new_inactive_user_email, 'Expected email after setup'
+ if not active_recipients.empty? then
+ assert_not_nil new_user_email, 'Expected new user email after setup'
+ assert_equal Rails.configuration.user_notifier_email_from, new_user_email.from[0]
+ assert_equal active_recipients, new_user_email.to[0]
+ assert_equal "#{Rails.configuration.email_subject_prefix}New user notification", new_user_email.subject
+ else
+ assert_nil new_user_email, 'Did not expect new user email after setup'
+ end
+ end
+ ActionMailer::Base.deliveries = []
+
+ end
+
end
commit e9fc734bb270a5648c923ed0419ff745e283419c
Author: Ward Vandewege <ward at curoverse.com>
Date: Thu May 29 14:17:23 2014 -0400
Switch to using auth helpers instead of messing with Thread.current in the user tests.
diff --git a/services/api/test/unit/user_test.rb b/services/api/test/unit/user_test.rb
index e5352bf..235e5cb 100644
--- a/services/api/test/unit/user_test.rb
+++ b/services/api/test/unit/user_test.rb
@@ -3,27 +3,8 @@ require 'test_helper'
class UserTest < ActiveSupport::TestCase
include CurrentApiClient
- # The fixture services/api/test/fixtures/users.yml serves as the input for this test case
- setup do
- # Make sure system_user exists before making "pre-test users" list
- system_user
-
- @all_users = User.find(:all)
-
- @all_users.each do |user|
- if user.uuid == system_user_uuid
- @system_user = user
- elsif user.is_admin && user.is_active
- @admin_user = user
- elsif user.is_active && !user.is_admin
- @active_user = user
- elsif !user.is_active && !user.is_invited
- @uninvited_user = user
- end
- end
- end
-
test "check non-admin active user properties" do
+ @active_user = users(:active) # get the active user
assert !@active_user.is_admin, 'is_admin should not be set for a non-admin user'
assert @active_user.is_active, 'user should be active'
assert @active_user.is_invited, 'is_invited should be set'
@@ -35,12 +16,14 @@ class UserTest < ActiveSupport::TestCase
assert @active_user.groups_i_can(:read).size > 0, "active user should be able read at least one group"
# non-admin user cannot manage or write other user objects
+ @uninvited_user = users(:inactive_uninvited) # get the uninvited user
assert !(@active_user.can? :read=>"#{@uninvited_user.uuid}")
assert !(@active_user.can? :write=>"#{@uninvited_user.uuid}")
assert !(@active_user.can? :manage=>"#{@uninvited_user.uuid}")
end
test "check admin user properties" do
+ @admin_user = users(:admin) # get the admin user
assert @admin_user.is_admin, 'is_admin should be set for admin user'
assert @admin_user.is_active, 'admin user cannot be inactive'
assert @admin_user.is_invited, 'is_invited should be set'
@@ -56,12 +39,14 @@ class UserTest < ActiveSupport::TestCase
assert @admin_user.groups_i_can(:manage).size > 0, "admin active user should be able manage at least one group"
# admin user can also write or manage other users
+ @uninvited_user = users(:inactive_uninvited) # get the uninvited user
assert @admin_user.can? :read=>"#{@uninvited_user.uuid}"
assert @admin_user.can? :write=>"#{@uninvited_user.uuid}"
assert @admin_user.can? :manage=>"#{@uninvited_user.uuid}"
end
test "check inactive and uninvited user properties" do
+ @uninvited_user = users(:inactive_uninvited) # get the uninvited user
assert !@uninvited_user.is_admin, 'is_admin should not be set for a non-admin user'
assert !@uninvited_user.is_active, 'user should be inactive'
assert !@uninvited_user.is_invited, 'is_invited should not be set'
@@ -88,7 +73,7 @@ class UserTest < ActiveSupport::TestCase
end
test "full name should not contain spurious whitespace" do
- Thread.current[:user] = @admin_user # set admin user as the current user
+ set_user_from_auth :admin
user = User.create ({uuid: 'zzzzz-tpzed-abcdefghijklmno', email: 'foo at example.com' })
@@ -101,7 +86,9 @@ class UserTest < ActiveSupport::TestCase
end
test "create new user" do
- Thread.current[:user] = @admin_user # set admin user as the current user
+ set_user_from_auth :admin
+
+ @all_users = User.find(:all)
user = User.new
user.first_name = "first_name_for_newly_created_user"
@@ -123,7 +110,7 @@ class UserTest < ActiveSupport::TestCase
end
test "create new inactive user with new_inactive_user_notification_recipients empty" do
- Thread.current[:user] = @admin_user # set admin user as the current user
+ set_user_from_auth :admin
Rails.configuration.new_inactive_user_notification_recipients = ''
@@ -143,7 +130,7 @@ class UserTest < ActiveSupport::TestCase
end
test "create new inactive user with new_user_notification_recipients empty" do
- Thread.current[:user] = @admin_user # set admin user as the current user
+ set_user_from_auth :admin
Rails.configuration.new_user_notification_recipients = ''
@@ -163,7 +150,7 @@ class UserTest < ActiveSupport::TestCase
end
test "create new inactive user with new_user_notification_recipients and new_inactive_user_notification_recipients set" do
- Thread.current[:user] = @admin_user # set admin user as the current user
+ set_user_from_auth :admin
Rails.configuration.new_user_notification_recipients = 'foo_new at example.com'
Rails.configuration.new_inactive_user_notification_recipients = 'foo_new_inactive at example.com'
@@ -202,7 +189,7 @@ class UserTest < ActiveSupport::TestCase
end
test "create new inactive user with new_user_notification_recipients set" do
- Thread.current[:user] = @admin_user # set admin user as the current user
+ set_user_from_auth :admin
Rails.configuration.new_user_notification_recipients = 'foo at example.com'
@@ -230,7 +217,7 @@ class UserTest < ActiveSupport::TestCase
end
test "create new active user with new_inactive_user_notification_recipients set" do
- Thread.current[:user] = @admin_user # set admin user as the current user
+ set_user_from_auth :admin
Rails.configuration.new_inactive_user_notification_recipients = 'foo at example.com'
@@ -251,7 +238,10 @@ class UserTest < ActiveSupport::TestCase
test "update existing user" do
- Thread.current[:user] = @active_user # set active user as current user
+ set_user_from_auth :active # set active user as current user
+
+ @active_user = users(:active) # get the active user
+
@active_user.first_name = "first_name_changed"
@active_user.save
@@ -259,7 +249,7 @@ class UserTest < ActiveSupport::TestCase
assert_equal(@active_user.first_name, 'first_name_changed')
# admin user also should be able to update the "active" user info
- Thread.current[:user] = @admin_user # set admin user as current user
+ set_user_from_auth :admin # set admin user as current user
@active_user.first_name = "first_name_changed_by_admin_for_active_user"
@active_user.save
@@ -268,9 +258,10 @@ class UserTest < ActiveSupport::TestCase
end
test "delete a user and verify" do
+ @active_user = users(:active) # get the active user
active_user_uuid = @active_user.uuid
- Thread.current[:user] = @admin_user
+ set_user_from_auth :admin
@active_user.delete
found_deleted_user = false
@@ -285,7 +276,7 @@ class UserTest < ActiveSupport::TestCase
end
test "create new user as non-admin user" do
- Thread.current[:user] = @active_user
+ set_user_from_auth :active
begin
user = User.new
@@ -297,7 +288,7 @@ class UserTest < ActiveSupport::TestCase
end
test "setup new user" do
- Thread.current[:user] = @admin_user
+ set_user_from_auth :admin
email = 'foo at example.com'
openid_prefix = 'http://openid/prefix'
@@ -330,7 +321,7 @@ class UserTest < ActiveSupport::TestCase
end
test "setup new user with junk in database" do
- Thread.current[:user] = @admin_user
+ set_user_from_auth :admin
email = 'foo at example.com'
openid_prefix = 'http://openid/prefix'
@@ -374,7 +365,7 @@ class UserTest < ActiveSupport::TestCase
test "setup new user in multiple steps" do
- Thread.current[:user] = @admin_user
+ set_user_from_auth :admin
email = 'foo at example.com'
openid_prefix = 'http://openid/prefix'
commit e1868aea69f51b3fb3d281a0dcca66b9de239cfa
Author: Ward Vandewege <ward at curoverse.com>
Date: Thu May 29 13:32:59 2014 -0400
Provide link to users page in notification e-mails.
diff --git a/services/api/app/mailers/admin_notifier.rb b/services/api/app/mailers/admin_notifier.rb
index 871c901..e17f4a1 100644
--- a/services/api/app/mailers/admin_notifier.rb
+++ b/services/api/app/mailers/admin_notifier.rb
@@ -1,5 +1,8 @@
class AdminNotifier < ActionMailer::Base
+ include AbstractController::Callbacks
+
default from: Rails.configuration.admin_notifier_email_from
+ before_filter :load_variables
def new_user(user)
@user = user
@@ -23,4 +26,15 @@ class AdminNotifier < ActionMailer::Base
end
end
+private
+ def load_variables
+ if Rails.configuration.respond_to?('workbench_address') and
+ not Rails.configuration.workbench_address.nil? and
+ not Rails.configuration.workbench_address.empty? then
+ @wb_address = Rails.configuration.workbench_address.sub(/\/$/,'') + '/users'
+ else
+ @wb_address = ''
+ end
+ end
+
end
diff --git a/services/api/app/views/admin_notifier/new_inactive_user.text.erb b/services/api/app/views/admin_notifier/new_inactive_user.text.erb
index 98c7037..f5c9a07 100644
--- a/services/api/app/views/admin_notifier/new_inactive_user.text.erb
+++ b/services/api/app/views/admin_notifier/new_inactive_user.text.erb
@@ -3,5 +3,11 @@ A new user landed on the inactive user page:
<%= @user.full_name %> <<%= @user.email %>>
+<% if not @wb_address.empty? -%>
+Please see workbench for more information:
+
+ <%= not @wb_address %>
+
+<% end -%>
Thanks,
Your friendly Arvados robot.
diff --git a/services/api/app/views/admin_notifier/new_user.text.erb b/services/api/app/views/admin_notifier/new_user.text.erb
index 8858a62..374e46e 100644
--- a/services/api/app/views/admin_notifier/new_user.text.erb
+++ b/services/api/app/views/admin_notifier/new_user.text.erb
@@ -5,6 +5,12 @@ A new user has been created:
This user is <%= @user.is_active ? '' : 'NOT ' %>active.
+<% if not @wb_address.empty? -%>
+Please see workbench for more information:
+
+ <%= @wb_address %>
+
+<% end -%>
Thanks,
Your friendly Arvados robot.
commit c811cb98bce53f775a865a04ea0f01635dbe75f3
Author: Ward Vandewege <ward at curoverse.com>
Date: Thu May 29 11:16:21 2014 -0400
Change default for
new_user_notification_recipients
new_inactive_user_notification_recipients
in config/application.default.yml to an empty array, so that it is
obvious how to specify multiple recipients.
diff --git a/services/api/config/application.default.yml b/services/api/config/application.default.yml
index 88a8aee..848675c 100644
--- a/services/api/config/application.default.yml
+++ b/services/api/config/application.default.yml
@@ -87,8 +87,8 @@ common:
admin_notifier_email_from: arvados at example.com
email_subject_prefix: "[ARVADOS] "
user_notifier_email_from: arvados at example.com
- new_user_notification_recipients: ''
- new_inactive_user_notification_recipients: ''
+ new_user_notification_recipients: [ ]
+ new_inactive_user_notification_recipients: [ ]
# Visitors to the API server will be redirected to the workbench
workbench_address: https://workbench.local:3001/
commit ebb166d65eb37f89edeccfc5be97014f3f2a73e2
Merge: 1eee45c 40b6a69
Author: Ward Vandewege <ward at curoverse.com>
Date: Wed May 28 20:29:12 2014 -0400
Merge branch 'master' into 2681-new-inactive-user-notification
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