[ARVADOS] updated: 5bbd6abc7a32c6912db5f36f0af5a923ac4b7c79
git at public.curoverse.com
git at public.curoverse.com
Thu Aug 7 16:44:16 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 1 +
apps/workbench/Gemfile.lock | 2 +
.../app/assets/javascripts/application.js | 8 +-
.../workbench/app/assets/javascripts/filterable.js | 15 +-
.../app/assets/javascripts/infinite_scroll.js | 84 +-
.../app/assets/javascripts/select_modal.js | 81 +-
.../app/assets/stylesheets/application.css.scss | 4 +
.../app/assets/stylesheets/select_modal.css.scss | 3 +
.../app/controllers/actions_controller.rb | 13 +
.../app/controllers/application_controller.rb | 50 +-
.../app/controllers/collections_controller.rb | 14 +-
.../workbench/app/controllers/groups_controller.rb | 4 +-
.../app/controllers/projects_controller.rb | 26 +
.../workbench/app/controllers/search_controller.rb | 21 +
apps/workbench/app/controllers/users_controller.rb | 67 +
apps/workbench/app/helpers/application_helper.rb | 17 +-
apps/workbench/app/models/group.rb | 11 +-
apps/workbench/app/models/pipeline_instance.rb | 9 +-
apps/workbench/app/views/application/404.html.erb | 7 +-
.../app/views/application/_choose.html.erb | 74 +-
.../workbench/app/views/application/_choose.js.erb | 22 +-
.../app/views/application/_content_layout.html.erb | 2 +-
.../views/application/_projects_tree_menu.html.erb | 10 +-
.../workbench/app/views/application/index.html.erb | 2 +
.../app/views/collections/_choose_rows.html.erb | 4 +-
.../app/views/groups/_choose_rows.html.erb | 2 +-
apps/workbench/app/views/layouts/body.html.erb | 44 +-
.../views/pipeline_instances/_show_inputs.html.erb | 3 +-
.../views/pipeline_templates/_choose_rows.html.erb | 2 +-
.../app/views/projects/_show_sharing.html.erb | 6 +
.../app/views/projects/_show_tab_contents.html.erb | 13 +
.../app/views/search/_choose_rows.html.erb | 26 +
.../app/views/users/_add_ssh_key_popup.html.erb | 38 +
.../app/views/users/_choose_rows.html.erb | 4 +-
.../app/views/users/_manage_account.html.erb | 52 +
.../app/views/users/_manage_current_token.html.erb | 13 +
.../app/views/users/_manage_repositories.html.erb | 40 +
.../app/views/users/_manage_ssh_keys.html.erb | 55 +
.../views/users/_manage_virtual_machines.html.erb | 50 +
.../app/views/users/_setup_popup.html.erb | 2 +-
apps/workbench/app/views/users/add_ssh_key.js.erb | 2 +
.../app/views/users/add_ssh_key_popup.js.erb | 8 +
.../app/views/users/manage_account.html.erb | 1 +
apps/workbench/config/application.yml.example | 2 +-
apps/workbench/config/routes.rb | 8 +
.../search_controller_test.rb} | 2 +-
apps/workbench/test/helpers/search_helper_test.rb | 4 +
.../test/integration/pipeline_instances_test.rb | 2 +
.../test/integration/pipeline_templates_test.rb | 15 +
apps/workbench/test/integration/projects_test.rb | 28 +-
apps/workbench/test/integration/smoke_test.rb | 3 +
doc/_config.yml | 34 +-
doc/_includes/_alert_docker.liquid | 4 -
doc/_includes/_ssh_addkey.liquid | 10 +-
.../_tutorial_bwa_sortsam_pipeline.liquid | 65 +
doc/_includes/_tutorial_expectations.liquid | 2 +-
doc/_layouts/default.html.liquid | 6 +-
doc/api/schema/Group.html.textile.liquid | 2 +-
.../schema/PipelineTemplate.html.textile.liquid | 10 +-
doc/css/font-awesome.css | 1566 ++++++++++++++++++++
doc/css/nav-list.css | 7 +-
doc/fonts/FontAwesome.otf | Bin 0 -> 75188 bytes
doc/fonts/fontawesome-webfont.eot | Bin 0 -> 72449 bytes
doc/fonts/fontawesome-webfont.svg | 504 +++++++
doc/fonts/fontawesome-webfont.ttf | Bin 0 -> 141564 bytes
doc/fonts/fontawesome-webfont.woff | Bin 0 -> 83760 bytes
doc/images/ssh-adding-public-key.png | Bin 17463 -> 15117 bytes
doc/install/index.html.textile.liquid | 2 -
doc/install/install-api-server.html.textile.liquid | 6 +-
doc/install/install-docker.html.textile.liquid | 141 +-
doc/user/copying/copying.html.textile.liquid | 2 +-
.../examples/crunch-examples.html.textile.liquid | 2 +-
.../check-environment.html.textile.liquid | 6 +-
.../getting_started/workbench.html.textile.liquid | 10 +-
doc/user/index.html.textile.liquid | 29 +-
doc/user/reference/api-tokens.html.textile.liquid | 39 +-
doc/user/reference/sdk-cli.html.textile.liquid | 2 +-
doc/user/topics/keep.html.textile.liquid | 8 +-
...nning-pipeline-command-line.html.textile.liquid | 117 +-
.../topics/tutorial-job-debug.html.textile.liquid | 27 +-
.../topics/tutorial-parallel.html.textile.liquid | 24 +-
.../tutorials/intro-crunch.html.textile.liquid | 17 +-
.../running-external-program.html.textile.liquid | 79 +-
.../tutorial-firstscript.html.textile.liquid | 61 +-
.../tutorial-keep-get.html.textile.liquid | 47 +
.../tutorial-keep-mount.html.textile.liquid | 32 +
.../tutorials/tutorial-keep.html.textile.liquid | 161 +-
.../tutorial-new-pipeline.html.textile.liquid | 63 +-
...tutorial-pipeline-workbench.html.textile.liquid | 40 +-
docker/api/Dockerfile | 37 +-
docker/api/application.yml.in | 5 +
docker/api/apt.arvados.org.list | 2 +
docker/api/arvados-clients.yml.in | 5 +
docker/api/crunch-dispatch-run.sh | 24 +
docker/api/keep_server_0.json | 6 +
docker/api/keep_server_1.json | 7 +
docker/api/munge.key | Bin 0 -> 1024 bytes
docker/api/omniauth.rb.in | 6 +-
docker/api/setup-gitolite.sh.in | 77 +
docker/api/setup.sh.in | 62 +
docker/api/slurm.conf.in | 60 +
docker/api/supervisor.conf | 29 +
docker/api/update-gitolite.rb | 162 ++
docker/arvdock | 128 +-
docker/base/Dockerfile | 4 +
docker/base/apt.arvados.org.list | 2 +
docker/build.sh | 41 +-
docker/build_tools/Makefile | 203 ++-
docker/build_tools/build.rb | 36 +-
docker/build_tools/config.rb | 20 +-
docker/compute/Dockerfile | 28 +
docker/compute/fuse.conf | 10 +
docker/compute/setup.sh.in | 20 +
docker/{api => compute}/ssh.sh | 0
docker/compute/supervisor.conf | 29 +
docker/compute/wrapdocker | 90 ++
docker/config.yml.example | 19 +-
docker/keep/Dockerfile | 9 +-
docker/keep/keep_signing_secret.in | 1 +
docker/keep/run-keep.in | 11 +
docker/shell/Dockerfile | 19 +
docker/shell/fuse.conf | 10 +
docker/shell/setup.sh.in | 21 +
docker/{api => shell}/superuser_token.in | 0
docker/shell/supervisor.conf | 15 +
docker/slurm/Dockerfile | 11 +
docker/slurm/munge.key | Bin 0 -> 1024 bytes
docker/slurm/slurm.conf.in | 60 +
docker/slurm/supervisor.conf | 14 +
docker/workbench/Dockerfile | 15 +-
docker/workbench/workbench_rails_env.in | 1 +
sdk/cli/bin/crunch-job | 37 +-
sdk/python/arvados/api.py | 82 +-
sdk/python/arvados/commands/put.py | 20 +-
sdk/python/arvados/errors.py | 11 +
sdk/python/arvados/keep.py | 139 +-
sdk/python/arvados/stream.py | 2 +-
sdk/python/bin/arv-ls | 2 +-
sdk/python/tests/test_api.py | 76 +
sdk/python/tests/test_collections.py | 20 +
services/api/Gemfile | 1 +
services/api/Gemfile.lock | 2 +
.../api/app/controllers/application_controller.rb | 1 +
.../controllers/arvados/v1/groups_controller.rb | 92 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 20 +-
services/api/app/models/arvados_model.rb | 6 +
services/api/app/models/authorized_key.rb | 9 +-
services/api/app/models/collection.rb | 4 +-
services/api/app/models/link.rb | 2 +-
services/api/app/models/user.rb | 2 +-
services/api/config/application.default.yml | 24 +-
services/api/config/application.yml.example | 39 +-
services/api/config/routes.rb | 1 +
... => 20140607150616_rename_folder_to_project.rb} | 0
.../db/migrate/20140714184006_empty_collection.rb | 4 +-
services/api/db/structure.sql | 3 +
services/api/lib/current_api_client.rb | 2 +-
.../test/fixtures/api_client_authorizations.yml | 6 +
services/api/test/fixtures/groups.yml | 2 +-
services/api/test/fixtures/links.yml | 46 +
services/api/test/fixtures/users.yml | 11 +
.../arvados/v1/groups_controller_test.rb | 64 +-
.../arvados/v1/job_reuse_controller_test.rb | 21 +
services/fuse/arvados_fuse/__init__.py | 3 +-
services/fuse/tests/test_mount.py | 1 +
services/keep/src/keep/handler_test.go | 144 +-
services/keep/src/keep/handlers.go | 97 ++
services/keep/src/keep/volume.go | 11 +-
services/keep/src/keep/volume_unix.go | 37 +-
169 files changed, 5352 insertions(+), 1092 deletions(-)
create mode 100644 apps/workbench/app/controllers/search_controller.rb
create mode 100644 apps/workbench/app/views/search/_choose_rows.html.erb
create mode 100644 apps/workbench/app/views/users/_add_ssh_key_popup.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_account.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_current_token.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_repositories.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_ssh_keys.html.erb
create mode 100644 apps/workbench/app/views/users/_manage_virtual_machines.html.erb
create mode 100644 apps/workbench/app/views/users/add_ssh_key.js.erb
create mode 100644 apps/workbench/app/views/users/add_ssh_key_popup.js.erb
create mode 100644 apps/workbench/app/views/users/manage_account.html.erb
copy apps/workbench/test/{unit/job_test.rb => controllers/search_controller_test.rb} (57%)
create mode 100644 apps/workbench/test/helpers/search_helper_test.rb
create mode 100644 apps/workbench/test/integration/pipeline_templates_test.rb
delete mode 100644 doc/_includes/_alert_docker.liquid
create mode 100644 doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
create mode 100644 doc/css/font-awesome.css
create mode 100644 doc/fonts/FontAwesome.otf
create mode 100755 doc/fonts/fontawesome-webfont.eot
create mode 100755 doc/fonts/fontawesome-webfont.svg
create mode 100755 doc/fonts/fontawesome-webfont.ttf
create mode 100755 doc/fonts/fontawesome-webfont.woff
create mode 100644 doc/user/tutorials/tutorial-keep-get.html.textile.liquid
create mode 100644 doc/user/tutorials/tutorial-keep-mount.html.textile.liquid
create mode 100644 docker/api/apt.arvados.org.list
create mode 100644 docker/api/arvados-clients.yml.in
create mode 100755 docker/api/crunch-dispatch-run.sh
create mode 100644 docker/api/keep_server_0.json
create mode 100644 docker/api/keep_server_1.json
create mode 100644 docker/api/munge.key
create mode 100755 docker/api/setup-gitolite.sh.in
create mode 100755 docker/api/setup.sh.in
create mode 100644 docker/api/slurm.conf.in
create mode 100755 docker/api/update-gitolite.rb
create mode 100644 docker/base/apt.arvados.org.list
create mode 100644 docker/compute/Dockerfile
create mode 100644 docker/compute/fuse.conf
create mode 100755 docker/compute/setup.sh.in
copy docker/{api => compute}/ssh.sh (100%)
create mode 100644 docker/compute/supervisor.conf
create mode 100755 docker/compute/wrapdocker
create mode 100644 docker/keep/keep_signing_secret.in
create mode 100755 docker/keep/run-keep.in
create mode 100644 docker/shell/Dockerfile
create mode 100644 docker/shell/fuse.conf
create mode 100755 docker/shell/setup.sh.in
copy docker/{api => shell}/superuser_token.in (100%)
create mode 100644 docker/shell/supervisor.conf
create mode 100644 docker/slurm/Dockerfile
create mode 100644 docker/slurm/munge.key
create mode 100644 docker/slurm/slurm.conf.in
create mode 100644 docker/slurm/supervisor.conf
create mode 100644 docker/workbench/workbench_rails_env.in
create mode 100644 sdk/python/tests/test_api.py
rename services/api/db/migrate/{20140607150616_rename_folder_to_project.rb_deferred => 20140607150616_rename_folder_to_project.rb} (100%)
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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
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commit 5bbd6abc7a32c6912db5f36f0af5a923ac4b7c79
Merge: b1ea822 1d10696
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Aug 7 16:32:59 2014 -0400
3036: Merge branch 'master' into 3036-mutable-collections
commit b1ea8228cf8b891a94deb09a619294315a0f1901
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Aug 7 16:32:25 2014 -0400
3036: Remove unnecessary code path.
diff --git a/services/api/app/models/collection.rb b/services/api/app/models/collection.rb
index 59aef67..a50c47b 100644
--- a/services/api/app/models/collection.rb
+++ b/services/api/app/models/collection.rb
@@ -29,9 +29,7 @@ class Collection < ArvadosModel
end
def assign_uuid
- if self.manifest_text.nil? and self.uuid.nil?
- return super
- elsif not self.manifest_text
+ if not self.manifest_text
errors.add :manifest_text, 'not supplied'
return false
end
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