[ARVADOS] updated: 6812b3350f48ed977ea2e3e788e49e1008a3b244
git at public.curoverse.com
git at public.curoverse.com
Sun Feb 16 06:06:44 EST 2014
Summary of changes:
.gitignore | 3 +-
apps/admin/list-inactive-users.rb | 24 -
.../app/assets/javascripts/application.js | 99 +-
apps/workbench/app/assets/javascripts/users.js | 11 +-
.../app/assets/stylesheets/application.css.scss | 50 +-
apps/workbench/app/assets/stylesheets/loading.css | 390 +-
.../app/controllers/application_controller.rb | 22 +-
.../app/controllers/collections_controller.rb | 6 +-
.../controllers/pipeline_instances_controller.rb | 2 +
apps/workbench/app/helpers/provenance_helper.rb | 107 +-
apps/workbench/app/models/pipeline_instance.rb | 4 +
apps/workbench/app/models/pipeline_template.rb | 3 +
.../app/views/application/_show_metadata.html.erb | 2 +-
.../app/views/collections/_index_tbody.html.erb | 24 +-
.../app/views/collections/_show_recent.html.erb | 10 +-
apps/workbench/app/views/collections/index.js.erb | 1 +
.../app/views/groups/_show_recent.html.erb | 2 +-
.../app/views/layouts/application.html.erb | 51 +-
...ext_compare.html.erb => _show_compare.html.erb} | 0
.../views/pipeline_instances/_show_graph.html.erb | 19 +-
.../views/pipeline_instances/_show_recent.html.erb | 19 +-
.../views/pipeline_templates/_show_recent.html.erb | 2 +-
.../app/views/user_agreements/index.html.erb | 2 +-
.../app/views/users/_notifications.html.erb | 93 -
apps/workbench/app/views/users/_tables.html.erb | 5 +-
apps/workbench/app/views/users/home.js.erb | 2 +-
doc/Gemfile | 4 +-
doc/Gemfile.lock | 63 +-
doc/README_FOR_APP | 2 -
doc/Rakefile | 25 +
doc/_config.yml | 100 +-
doc/_includes/{0-filter.py => _0_filter_py.liquid} | 0
...rt-incomplete.html => _alert-incomplete.liquid} | 0
.../{alert-stub.html => _alert_stub.liquid} | 0
doc/_includes/_navbar_left.liquid | 18 +
doc/_includes/_navbar_top.liquid | 23 +
.../{notebox-begin.html => _notebox_begin.liquid} | 0
.../{notebox-end.html => _notebox_end.liquid} | 0
...h_script.py => _parallel_hash_script_py.liquid} | 0
.../{run-md5sum.py => _run_md5sum_py.liquid} | 0
...h_script.py => _tutorial_hash_script_py.liquid} | 0
doc/_includes/navbar_left.html | 27 -
doc/_includes/navbar_top.html | 23 -
doc/_layouts/default.html | 120 -
doc/_layouts/default.html.liquid | 109 +
doc/admin/cheat_sheet.html.textile.liquid | 72 +
doc/admin/cheat_sheet.textile | 73 -
doc/admin/index.html.md.liquid | 14 +
doc/admin/index.md | 15 -
doc/api/authentication.html.textile.liquid | 40 +
doc/api/authentication.textile | 40 -
doc/api/crunch-scripts.html.textile.liquid | 46 +
doc/api/crunch-scripts.textile | 46 -
doc/api/index.html.textile.liquid | 52 +
doc/api/index.textile | 52 -
doc/api/methods.html.textile.liquid | 80 +
doc/api/methods.textile | 80 -
.../api_client_authorizations.html.textile.liquid | 109 +
doc/api/methods/api_client_authorizations.textile | 109 -
doc/api/methods/api_clients.html.textile.liquid | 98 +
doc/api/methods/api_clients.textile | 98 -
.../methods/authorized_keys.html.textile.liquid | 98 +
doc/api/methods/authorized_keys.textile | 98 -
doc/api/methods/collections.html.textile.liquid | 98 +
doc/api/methods/collections.textile | 98 -
doc/api/methods/groups.html.textile.liquid | 98 +
doc/api/methods/groups.textile | 98 -
doc/api/methods/humans.html.textile.liquid | 98 +
doc/api/methods/humans.textile | 98 -
doc/api/methods/job_tasks.html.textile.liquid | 98 +
doc/api/methods/job_tasks.textile | 98 -
doc/api/methods/jobs.html.textile.liquid | 130 +
doc/api/methods/jobs.textile | 130 -
doc/api/methods/keep_disks.html.textile.liquid | 114 +
doc/api/methods/keep_disks.textile | 114 -
doc/api/methods/links.html.textile.liquid | 109 +
doc/api/methods/links.textile | 109 -
doc/api/methods/logs.html.textile.liquid | 98 +
doc/api/methods/logs.textile | 98 -
doc/api/methods/nodes.html.textile.liquid | 109 +
doc/api/methods/nodes.textile | 109 -
.../methods/pipeline_instances.html.textile.liquid | 98 +
doc/api/methods/pipeline_instances.textile | 98 -
.../methods/pipeline_templates.html.textile.liquid | 98 +
doc/api/methods/pipeline_templates.textile | 98 -
doc/api/methods/repositories.html.textile.liquid | 107 +
doc/api/methods/repositories.textile | 107 -
doc/api/methods/specimens.html.textile.liquid | 98 +
doc/api/methods/specimens.textile | 98 -
doc/api/methods/traits.html.textile.liquid | 98 +
doc/api/methods/traits.textile | 98 -
doc/api/methods/users.html.textile.liquid | 126 +
doc/api/methods/users.textile | 126 -
.../methods/virtual_machines.html.textile.liquid | 117 +
doc/api/methods/virtual_machines.textile | 117 -
doc/api/permission-model.html.textile.liquid | 107 +
doc/api/permission-model.textile | 107 -
doc/api/resources.html.textile.liquid | 49 +
doc/api/resources.textile | 49 -
doc/api/schema/ApiClient.html.textile.liquid | 38 +
doc/api/schema/ApiClient.textile | 38 -
.../ApiClientAuthorization.html.textile.liquid | 44 +
doc/api/schema/ApiClientAuthorization.textile | 44 -
doc/api/schema/AuthorizedKey.html.textile.liquid | 40 +
doc/api/schema/AuthorizedKey.textile | 40 -
doc/api/schema/Collection.html.textile.liquid | 45 +
doc/api/schema/Collection.textile | 45 -
doc/api/schema/Commit.html.textile.liquid | 38 +
doc/api/schema/Commit.textile | 38 -
doc/api/schema/CommitAncestor.html.textile.liquid | 39 +
doc/api/schema/CommitAncestor.textile | 39 -
doc/api/schema/Group.html.textile.liquid | 37 +
doc/api/schema/Group.textile | 37 -
doc/api/schema/Human.html.textile.liquid | 36 +
doc/api/schema/Human.textile | 36 -
doc/api/schema/Job.html.textile.liquid | 83 +
doc/api/schema/Job.textile | 83 -
doc/api/schema/JobTask.html.textile.liquid | 51 +
doc/api/schema/JobTask.textile | 51 -
doc/api/schema/KeepDisk.html.textile.liquid | 48 +
doc/api/schema/KeepDisk.textile | 48 -
doc/api/schema/Link.html.textile.liquid | 87 +
doc/api/schema/Link.textile | 87 -
doc/api/schema/Log.html.textile.liquid | 39 +
doc/api/schema/Log.textile | 39 -
doc/api/schema/Node.html.textile.liquid | 42 +
doc/api/schema/Node.textile | 42 -
.../schema/PipelineInstance.html.textile.liquid | 41 +
doc/api/schema/PipelineInstance.textile | 41 -
.../schema/PipelineTemplate.html.textile.liquid | 37 +
doc/api/schema/PipelineTemplate.textile | 37 -
doc/api/schema/Repository.html.textile.liquid | 38 +
doc/api/schema/Repository.textile | 38 -
doc/api/schema/Specimen.html.textile.liquid | 37 +
doc/api/schema/Specimen.textile | 37 -
doc/api/schema/Trait.html.textile.liquid | 37 +
doc/api/schema/Trait.textile | 37 -
doc/api/schema/User.html.textile.liquid | 43 +
doc/api/schema/User.textile | 43 -
doc/api/schema/VirtualMachine.html.textile.liquid | 36 +
doc/api/schema/VirtualMachine.textile | 36 -
.../badges.css.scss => doc/css/badges.css | 0
doc/css/bootstrap-responsive.min.css | 20 -
doc/css/bootstrap-theme.css | 347 +
doc/css/bootstrap-theme.css.map | 1 +
doc/css/bootstrap-theme.min.css | 7 +
doc/css/bootstrap.css | 9502 ++++++++++----------
doc/css/bootstrap.css.map | 1 +
doc/css/bootstrap.min.css | 7 +
doc/css/nav-list.css | 24 +
doc/fonts/glyphicons-halflings-regular.eot | Bin 0 -> 20290 bytes
doc/fonts/glyphicons-halflings-regular.svg | 229 +
doc/fonts/glyphicons-halflings-regular.ttf | Bin 0 -> 41236 bytes
doc/fonts/glyphicons-halflings-regular.woff | Bin 0 -> 23292 bytes
doc/gen_api_method_docs.py | 1 -
{apps/workbench/app/assets => doc}/images/dax.png | Bin 66943 -> 66943 bytes
doc/index.html | 46 -
doc/index.html.liquid | 45 +
doc/install/client.html.textile.liquid | 36 +
doc/install/client.textile | 36 -
.../create-standard-objects.html.textile.liquid | 60 +
doc/install/create-standard-objects.textile | 60 -
doc/install/index.html.md.liquid | 17 +
doc/install/index.md | 18 -
doc/install/install-api-server.html.md.liquid | 114 +
doc/install/install-api-server.md | 114 -
.../install-crunch-dispatch.html.textile.liquid | 102 +
doc/install/install-crunch-dispatch.textile | 102 -
doc/install/install-workbench-app.html.md.liquid | 63 +
doc/install/install-workbench-app.md | 63 -
doc/js/bootstrap.js | 1951 ++++
doc/js/bootstrap.min.js | 13 +-
doc/mkpydoc.sh | 5 -
doc/sdk/index.html.textile.liquid | 12 +
doc/sdk/index.textile | 12 -
.../crunch-utility-libraries.html.textile.liquid | 225 +
doc/sdk/python/crunch-utility-libraries.textile | 225 -
doc/sdk/python/python.html.textile.liquid | 10 +
doc/sdk/python/python.textile | 10 -
doc/sdk/python/sdk-python.html.textile.liquid | 120 +
doc/sdk/python/sdk-python.textile | 120 -
.../examples/crunch-examples.html.textile.liquid | 99 +
doc/user/examples/crunch-examples.textile | 98 -
.../check-environment.html.textile.liquid | 46 +
doc/user/getting_started/check-environment.textile | 54 -
.../getting_started/community.html.textile.liquid | 25 +
doc/user/getting_started/community.textile | 25 -
.../getting_started/ssh-access.html.textile.liquid | 217 +
doc/user/getting_started/ssh-access.textile | 217 -
.../getting_started/workbench.html.textile.liquid | 18 +
doc/user/getting_started/workbench.textile | 18 -
doc/user/index.html.textile.liquid | 52 +
doc/user/index.textile | 51 -
doc/user/reference/api-tokens.html.textile.liquid | 74 +
doc/user/reference/api-tokens.textile | 47 -
doc/user/reference/sdk-cli.html.textile.liquid | 47 +
doc/user/reference/sdk-cli.textile | 81 -
.../running-external-program.html.textile.liquid | 71 +
.../tutorials/running-external-program.textile | 67 -
.../tutorial-firstscript.html.textile.liquid | 124 +
doc/user/tutorials/tutorial-firstscript.textile | 124 -
...rial-gatk-variantfiltration.html.textile.liquid | 216 +
.../tutorial-gatk-variantfiltration.textile | 216 -
.../tutorial-job-debug.html.textile.liquid | 156 +
doc/user/tutorials/tutorial-job-debug.textile | 156 -
.../tutorials/tutorial-job1.html.textile.liquid | 235 +
doc/user/tutorials/tutorial-job1.textile | 233 -
.../tutorials/tutorial-keep.html.textile.liquid | 143 +
doc/user/tutorials/tutorial-keep.textile | 136 -
.../tutorial-new-pipeline.html.textile.liquid | 158 +
doc/user/tutorials/tutorial-new-pipeline.textile | 158 -
.../tutorial-parallel.html.textile.liquid | 85 +
doc/user/tutorials/tutorial-parallel.textile | 81 -
.../tutorial-trait-search.html.textile.liquid | 273 +
doc/user/tutorials/tutorial-trait-search.textile | 273 -
doc/zenweb-liquid.rb | 41 +
doc/zenweb-textile.rb | 17 +
docker/Makefile | 2 +-
docker/README.md | 12 +-
docker/api/Dockerfile | 2 +-
docker/api/apache2_vhost.in | 4 +-
docker/api/production.rb.in | 4 +
docker/arvdock | 354 +
docker/base/Dockerfile | 4 +-
docker/config.rb | 2 +
docker/config.yml.example | 2 +-
docker/doc/Dockerfile | 4 +-
docker/doc/apache2_vhost | 4 +-
docker/passenger/Dockerfile | 2 +-
docker/postgresql/Dockerfile | 2 +-
docker/run.sh | 303 -
docker/sso/Dockerfile | 4 +-
docker/sso/apache2_vhost.in | 4 +-
docker/warehouse/Dockerfile | 4 +-
docker/workbench/Dockerfile | 2 +-
docker/workbench/apache2_vhost.in | 2 +-
docker/workbench/production.rb.in | 9 +-
sdk/cli/Gemfile | 2 +-
sdk/cli/Gemfile.lock | 24 +-
sdk/cli/arvados-cli.gemspec | 2 +-
sdk/cli/bin/arv | 2 +-
sdk/cli/bin/arv-run-pipeline-instance | 6 +-
sdk/perl/lib/Arvados/ResourceMethod.pm | 17 +-
sdk/python/arvados/collection.py | 9 +-
sdk/python/arvados/keep.py | 40 +-
sdk/python/bin/arv-get | 11 +-
.../v1/api_client_authorizations_controller.rb | 1 +
.../arvados/v1/collections_controller.rb | 33 +-
services/api/app/controllers/static_controller.rb | 8 +-
.../app/controllers/user_sessions_controller.rb | 2 +-
services/api/app/models/arvados_model.rb | 19 +
services/api/app/models/collection.rb | 26 +-
services/api/app/models/commit_ancestor.rb | 4 +-
services/api/app/models/job.rb | 14 +-
services/api/app/models/user.rb | 6 +-
services/api/test/fixtures/jobs.yml | 1 +
.../api_client_authorizations_controller_test.rb | 18 +
.../arvados/v1/collections_controller_test.rb | 18 +-
.../functional/arvados/v1/jobs_controller_test.rb | 32 +
.../api_client_authorizations_api_test.rb | 11 +
260 files changed, 14628 insertions(+), 12513 deletions(-)
delete mode 100755 apps/admin/list-inactive-users.rb
rename apps/workbench/app/views/pipeline_instances/{_show_text_compare.html.erb => _show_compare.html.erb} (100%)
delete mode 100644 apps/workbench/app/views/users/_notifications.html.erb
delete mode 100644 doc/README_FOR_APP
create mode 100644 doc/Rakefile
rename doc/_includes/{0-filter.py => _0_filter_py.liquid} (100%)
rename doc/_includes/{alert-incomplete.html => _alert-incomplete.liquid} (100%)
rename doc/_includes/{alert-stub.html => _alert_stub.liquid} (100%)
create mode 100644 doc/_includes/_navbar_left.liquid
create mode 100644 doc/_includes/_navbar_top.liquid
rename doc/_includes/{notebox-begin.html => _notebox_begin.liquid} (100%)
rename doc/_includes/{notebox-end.html => _notebox_end.liquid} (100%)
rename doc/_includes/{parallel_hash_script.py => _parallel_hash_script_py.liquid} (100%)
rename doc/_includes/{run-md5sum.py => _run_md5sum_py.liquid} (100%)
rename doc/_includes/{tutorial_hash_script.py => _tutorial_hash_script_py.liquid} (100%)
delete mode 100644 doc/_includes/navbar_left.html
delete mode 100644 doc/_includes/navbar_top.html
delete mode 100644 doc/_layouts/default.html
create mode 100644 doc/_layouts/default.html.liquid
create mode 100644 doc/admin/cheat_sheet.html.textile.liquid
delete mode 100644 doc/admin/cheat_sheet.textile
create mode 100644 doc/admin/index.html.md.liquid
delete mode 100644 doc/admin/index.md
create mode 100644 doc/api/authentication.html.textile.liquid
delete mode 100644 doc/api/authentication.textile
create mode 100644 doc/api/crunch-scripts.html.textile.liquid
delete mode 100644 doc/api/crunch-scripts.textile
create mode 100644 doc/api/index.html.textile.liquid
delete mode 100644 doc/api/index.textile
create mode 100644 doc/api/methods.html.textile.liquid
delete mode 100644 doc/api/methods.textile
create mode 100644 doc/api/methods/api_client_authorizations.html.textile.liquid
delete mode 100644 doc/api/methods/api_client_authorizations.textile
create mode 100644 doc/api/methods/api_clients.html.textile.liquid
delete mode 100644 doc/api/methods/api_clients.textile
create mode 100644 doc/api/methods/authorized_keys.html.textile.liquid
delete mode 100644 doc/api/methods/authorized_keys.textile
create mode 100644 doc/api/methods/collections.html.textile.liquid
delete mode 100644 doc/api/methods/collections.textile
create mode 100644 doc/api/methods/groups.html.textile.liquid
delete mode 100644 doc/api/methods/groups.textile
create mode 100644 doc/api/methods/humans.html.textile.liquid
delete mode 100644 doc/api/methods/humans.textile
create mode 100644 doc/api/methods/job_tasks.html.textile.liquid
delete mode 100644 doc/api/methods/job_tasks.textile
create mode 100644 doc/api/methods/jobs.html.textile.liquid
delete mode 100644 doc/api/methods/jobs.textile
create mode 100644 doc/api/methods/keep_disks.html.textile.liquid
delete mode 100644 doc/api/methods/keep_disks.textile
create mode 100644 doc/api/methods/links.html.textile.liquid
delete mode 100644 doc/api/methods/links.textile
create mode 100644 doc/api/methods/logs.html.textile.liquid
delete mode 100644 doc/api/methods/logs.textile
create mode 100644 doc/api/methods/nodes.html.textile.liquid
delete mode 100644 doc/api/methods/nodes.textile
create mode 100644 doc/api/methods/pipeline_instances.html.textile.liquid
delete mode 100644 doc/api/methods/pipeline_instances.textile
create mode 100644 doc/api/methods/pipeline_templates.html.textile.liquid
delete mode 100644 doc/api/methods/pipeline_templates.textile
create mode 100644 doc/api/methods/repositories.html.textile.liquid
delete mode 100644 doc/api/methods/repositories.textile
create mode 100644 doc/api/methods/specimens.html.textile.liquid
delete mode 100644 doc/api/methods/specimens.textile
create mode 100644 doc/api/methods/traits.html.textile.liquid
delete mode 100644 doc/api/methods/traits.textile
create mode 100644 doc/api/methods/users.html.textile.liquid
delete mode 100644 doc/api/methods/users.textile
create mode 100644 doc/api/methods/virtual_machines.html.textile.liquid
delete mode 100644 doc/api/methods/virtual_machines.textile
create mode 100644 doc/api/permission-model.html.textile.liquid
delete mode 100644 doc/api/permission-model.textile
create mode 100644 doc/api/resources.html.textile.liquid
delete mode 100644 doc/api/resources.textile
create mode 100644 doc/api/schema/ApiClient.html.textile.liquid
delete mode 100644 doc/api/schema/ApiClient.textile
create mode 100644 doc/api/schema/ApiClientAuthorization.html.textile.liquid
delete mode 100644 doc/api/schema/ApiClientAuthorization.textile
create mode 100644 doc/api/schema/AuthorizedKey.html.textile.liquid
delete mode 100644 doc/api/schema/AuthorizedKey.textile
create mode 100644 doc/api/schema/Collection.html.textile.liquid
delete mode 100644 doc/api/schema/Collection.textile
create mode 100644 doc/api/schema/Commit.html.textile.liquid
delete mode 100644 doc/api/schema/Commit.textile
create mode 100644 doc/api/schema/CommitAncestor.html.textile.liquid
delete mode 100644 doc/api/schema/CommitAncestor.textile
create mode 100644 doc/api/schema/Group.html.textile.liquid
delete mode 100644 doc/api/schema/Group.textile
create mode 100644 doc/api/schema/Human.html.textile.liquid
delete mode 100644 doc/api/schema/Human.textile
create mode 100644 doc/api/schema/Job.html.textile.liquid
delete mode 100644 doc/api/schema/Job.textile
create mode 100644 doc/api/schema/JobTask.html.textile.liquid
delete mode 100644 doc/api/schema/JobTask.textile
create mode 100644 doc/api/schema/KeepDisk.html.textile.liquid
delete mode 100644 doc/api/schema/KeepDisk.textile
create mode 100644 doc/api/schema/Link.html.textile.liquid
delete mode 100644 doc/api/schema/Link.textile
create mode 100644 doc/api/schema/Log.html.textile.liquid
delete mode 100644 doc/api/schema/Log.textile
create mode 100644 doc/api/schema/Node.html.textile.liquid
delete mode 100644 doc/api/schema/Node.textile
create mode 100644 doc/api/schema/PipelineInstance.html.textile.liquid
delete mode 100644 doc/api/schema/PipelineInstance.textile
create mode 100644 doc/api/schema/PipelineTemplate.html.textile.liquid
delete mode 100644 doc/api/schema/PipelineTemplate.textile
create mode 100644 doc/api/schema/Repository.html.textile.liquid
delete mode 100644 doc/api/schema/Repository.textile
create mode 100644 doc/api/schema/Specimen.html.textile.liquid
delete mode 100644 doc/api/schema/Specimen.textile
create mode 100644 doc/api/schema/Trait.html.textile.liquid
delete mode 100644 doc/api/schema/Trait.textile
create mode 100644 doc/api/schema/User.html.textile.liquid
delete mode 100644 doc/api/schema/User.textile
create mode 100644 doc/api/schema/VirtualMachine.html.textile.liquid
delete mode 100644 doc/api/schema/VirtualMachine.textile
copy apps/workbench/app/assets/stylesheets/badges.css.scss => doc/css/badges.css (100%)
delete mode 100644 doc/css/bootstrap-responsive.min.css
create mode 100644 doc/css/bootstrap-theme.css
create mode 100644 doc/css/bootstrap-theme.css.map
create mode 100644 doc/css/bootstrap-theme.min.css
create mode 100644 doc/css/bootstrap.css.map
create mode 100644 doc/css/bootstrap.min.css
create mode 100644 doc/css/nav-list.css
create mode 100644 doc/fonts/glyphicons-halflings-regular.eot
create mode 100644 doc/fonts/glyphicons-halflings-regular.svg
create mode 100644 doc/fonts/glyphicons-halflings-regular.ttf
create mode 100644 doc/fonts/glyphicons-halflings-regular.woff
copy {apps/workbench/app/assets => doc}/images/dax.png (100%)
delete mode 100644 doc/index.html
create mode 100644 doc/index.html.liquid
create mode 100644 doc/install/client.html.textile.liquid
delete mode 100644 doc/install/client.textile
create mode 100644 doc/install/create-standard-objects.html.textile.liquid
delete mode 100644 doc/install/create-standard-objects.textile
create mode 100644 doc/install/index.html.md.liquid
delete mode 100644 doc/install/index.md
create mode 100644 doc/install/install-api-server.html.md.liquid
delete mode 100644 doc/install/install-api-server.md
create mode 100644 doc/install/install-crunch-dispatch.html.textile.liquid
delete mode 100644 doc/install/install-crunch-dispatch.textile
create mode 100644 doc/install/install-workbench-app.html.md.liquid
delete mode 100644 doc/install/install-workbench-app.md
create mode 100644 doc/js/bootstrap.js
delete mode 100755 doc/mkpydoc.sh
create mode 100644 doc/sdk/index.html.textile.liquid
delete mode 100644 doc/sdk/index.textile
create mode 100644 doc/sdk/python/crunch-utility-libraries.html.textile.liquid
delete mode 100644 doc/sdk/python/crunch-utility-libraries.textile
create mode 100644 doc/sdk/python/python.html.textile.liquid
delete mode 100644 doc/sdk/python/python.textile
create mode 100644 doc/sdk/python/sdk-python.html.textile.liquid
delete mode 100644 doc/sdk/python/sdk-python.textile
create mode 100644 doc/user/examples/crunch-examples.html.textile.liquid
delete mode 100644 doc/user/examples/crunch-examples.textile
create mode 100644 doc/user/getting_started/check-environment.html.textile.liquid
delete mode 100644 doc/user/getting_started/check-environment.textile
create mode 100644 doc/user/getting_started/community.html.textile.liquid
delete mode 100644 doc/user/getting_started/community.textile
create mode 100644 doc/user/getting_started/ssh-access.html.textile.liquid
delete mode 100644 doc/user/getting_started/ssh-access.textile
create mode 100644 doc/user/getting_started/workbench.html.textile.liquid
delete mode 100644 doc/user/getting_started/workbench.textile
create mode 100644 doc/user/index.html.textile.liquid
delete mode 100644 doc/user/index.textile
create mode 100644 doc/user/reference/api-tokens.html.textile.liquid
delete mode 100644 doc/user/reference/api-tokens.textile
create mode 100644 doc/user/reference/sdk-cli.html.textile.liquid
delete mode 100644 doc/user/reference/sdk-cli.textile
create mode 100644 doc/user/tutorials/running-external-program.html.textile.liquid
delete mode 100644 doc/user/tutorials/running-external-program.textile
create mode 100644 doc/user/tutorials/tutorial-firstscript.html.textile.liquid
delete mode 100644 doc/user/tutorials/tutorial-firstscript.textile
create mode 100644 doc/user/tutorials/tutorial-gatk-variantfiltration.html.textile.liquid
delete mode 100644 doc/user/tutorials/tutorial-gatk-variantfiltration.textile
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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 6812b3350f48ed977ea2e3e788e49e1008a3b244
Merge: 78a1683 4290ebf
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Feb 16 03:05:35 2014 -0800
Merge branch 'master' into 2060-edit-tags-in-workbench
commit 78a1683680177da480dc3ffaea2d4f2b79ab793d
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Feb 16 02:58:28 2014 -0800
Lighten and add tooltips to "delete tag" buttons.
diff --git a/apps/workbench/app/assets/javascripts/application.js b/apps/workbench/app/assets/javascripts/application.js
index cb20b32..dc71770 100644
--- a/apps/workbench/app/assets/javascripts/application.js
+++ b/apps/workbench/app/assets/javascripts/application.js
@@ -78,7 +78,7 @@ jQuery(function($){
attr('data-tag-link-uuid', new_tag_uuid).
text(new_tag).
css('opacity', '0.2').
- append(' <a><i class="glyphicon glyphicon-trash"></i></a> ');
+ append(' <a title="Delete tag"><i class="glyphicon glyphicon-trash"></i></a> ');
$(this).
parent().
find('>span').
diff --git a/apps/workbench/app/assets/stylesheets/application.css.scss b/apps/workbench/app/assets/stylesheets/application.css.scss
index 5ee9508..7d241ad 100644
--- a/apps/workbench/app/assets/stylesheets/application.css.scss
+++ b/apps/workbench/app/assets/stylesheets/application.css.scss
@@ -140,6 +140,7 @@ td.add-tag-button .add-tag-button:hover {
margin-top: .2em;
}
.label.removable-tag a {
+ color: #fff;
cursor: pointer;
}
diff --git a/apps/workbench/app/views/collections/_index_tbody.html.erb b/apps/workbench/app/views/collections/_index_tbody.html.erb
index 19a13ed..258b00b 100644
--- a/apps/workbench/app/views/collections/_index_tbody.html.erb
+++ b/apps/workbench/app/views/collections/_index_tbody.html.erb
@@ -36,7 +36,7 @@
<% @collection_info[c.uuid][:tag_links].each do |tag_link| %>
<span class="label label-info removable-tag" data-tag-link-uuid="<%= tag_link.uuid %>"><%= tag_link.name %>
<% if tag_link.owner_uuid == current_user.uuid %>
- <a><i class="glyphicon glyphicon-trash"></i></a>
+ <a title="Delete tag"><i class="glyphicon glyphicon-trash"></i></a>
<% end %>
</span>
<% end %>
commit 50567a15ccfdc5e73289227e343bfce946974ecd
Merge: 603517c 3d3f6b1
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Feb 16 02:36:57 2014 -0800
Merge branch 'master' into 2060-edit-tags-in-workbench
commit 603517c58cb2a57961de70c7b67f9856206515da
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Feb 16 02:23:07 2014 -0800
Light up "add tag" buttons on button hover, not cell hover.
diff --git a/apps/workbench/app/assets/stylesheets/application.css.scss b/apps/workbench/app/assets/stylesheets/application.css.scss
index 1ea67d2..5ee9508 100644
--- a/apps/workbench/app/assets/stylesheets/application.css.scss
+++ b/apps/workbench/app/assets/stylesheets/application.css.scss
@@ -133,7 +133,7 @@ td.add-tag-button .add-tag-button {
margin-right: 4px;
opacity: 0.2;
}
-td.add-tag-button:hover .add-tag-button {
+td.add-tag-button .add-tag-button:hover {
opacity: 1;
}
.label.removable-tag {
commit a23b909256ae2ee222036d91d6e46faccfe13542
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Feb 16 02:23:02 2014 -0800
Do not show "delete tag" button unless current user owns tag.
diff --git a/apps/workbench/app/views/collections/_index_tbody.html.erb b/apps/workbench/app/views/collections/_index_tbody.html.erb
index fad520e..19a13ed 100644
--- a/apps/workbench/app/views/collections/_index_tbody.html.erb
+++ b/apps/workbench/app/views/collections/_index_tbody.html.erb
@@ -34,7 +34,11 @@
<span>
<% if @collection_info[c.uuid] %>
<% @collection_info[c.uuid][:tag_links].each do |tag_link| %>
- <span class="label label-info removable-tag" data-tag-link-uuid="<%= tag_link.uuid %>"><%= tag_link.name %> <a><i class="glyphicon glyphicon-trash"></i></a></span>
+ <span class="label label-info removable-tag" data-tag-link-uuid="<%= tag_link.uuid %>"><%= tag_link.name %>
+ <% if tag_link.owner_uuid == current_user.uuid %>
+ <a><i class="glyphicon glyphicon-trash"></i></a>
+ <% end %>
+ </span>
<% end %>
<% end %>
</span>
commit 3c6f8001fb5d63ef92da36e662ac58396f18a9d0
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Feb 16 02:17:15 2014 -0800
Add and remove collection tags with ajax.
diff --git a/apps/workbench/app/assets/javascripts/application.js b/apps/workbench/app/assets/javascripts/application.js
index 2f3b094..92cce3e 100644
--- a/apps/workbench/app/assets/javascripts/application.js
+++ b/apps/workbench/app/assets/javascripts/application.js
@@ -49,24 +49,58 @@ jQuery(function($){
$('.loading').fadeOut('fast', 0);
}).
on('click', '.removable-tag a', function(e) {
- $(this).parents('[data-tag-link-uuid]').eq(0).remove();
+ var tag_span = $(this).parents('[data-tag-link-uuid]').eq(0)
+ tag_span.fadeTo('fast', 0.2);
+ $.ajax('/links/' + tag_span.attr('data-tag-link-uuid'),
+ {dataType: 'json',
+ type: 'POST',
+ data: { '_method': 'DELETE' },
+ context: tag_span}).
+ done(function(data, status, jqxhr) {
+ this.remove();
+ }).
+ fail(function(jqxhr, status, error) {
+ this.addClass('label-danger').fadeTo('fast', '1');
+ });
return false;
}).
on('click', 'a.add-tag-button', function(e) {
- new_tag = window.prompt("Add tag for collection "+
- $(this).parents('tr').attr('data-object-uuid'),
+ var jqxhr;
+ var new_tag_uuid = 'new-tag-' + Math.random();
+ var tag_head_uuid = $(this).parents('tr').attr('data-object-uuid');
+ var new_tag = window.prompt("Add tag for collection "+
+ tag_head_uuid,
"");
- if (new_tag != null) {
- new_tag_uuid = 'xxx';
- $(this).
- parent().
- find('>span').
- append($('<span class="label label-info removable-tag" data-tag-link-uuid=""></span>').
- attr('data-tag-link-uuid', new_tag_uuid).
- text(new_tag).
- append(' <a><i class="glyphicon glyphicon-trash"></i></a> ')).
- append(' ');
- }
+ if (new_tag == null)
+ return false;
+ var new_tag_span =
+ $('<span class="label label-info removable-tag"></span>').
+ attr('data-tag-link-uuid', new_tag_uuid).
+ text(new_tag).
+ css('opacity', '0.2').
+ append(' <a><i class="glyphicon glyphicon-trash"></i></a> ');
+ $(this).
+ parent().
+ find('>span').
+ append(new_tag_span).
+ append(' ');
+ $.ajax($(this).attr('data-remote-href'),
+ {dataType: 'json',
+ type: $(this).attr('data-remote-method'),
+ data: {
+ 'link[head_kind]': 'arvados#collection',
+ 'link[head_uuid]': tag_head_uuid,
+ 'link[link_class]': 'tag',
+ 'link[name]': new_tag
+ },
+ context: new_tag_span}).
+ done(function(data, status, jqxhr) {
+ this.attr('data-tag-link-uuid', data.uuid).
+ fadeTo('fast', '1');
+ }).
+ fail(function(jqxhr, status, error) {
+ this.addClass('label-danger').fadeTo('fast', '1');
+ });
return false;
});
diff --git a/apps/workbench/app/controllers/application_controller.rb b/apps/workbench/app/controllers/application_controller.rb
index 02ebc8b..e94428e 100644
--- a/apps/workbench/app/controllers/application_controller.rb
+++ b/apps/workbench/app/controllers/application_controller.rb
@@ -107,9 +107,10 @@ class ApplicationController < ActionController::Base
end
def create
- @object ||= model_class.new params[model_class.to_s.singularize.to_sym]
+ @object ||= model_class.new params[model_class.to_s.underscore.singularize]
@object.save!
respond_to do |f|
+ f.json { render json: @object }
f.html {
redirect_to(params[:return_to] || @object)
}
@@ -120,6 +121,7 @@ class ApplicationController < ActionController::Base
def destroy
if @object.destroy
respond_to do |f|
+ f.json { render json: @object }
f.html {
redirect_to(params[:return_to] || :back)
}
diff --git a/apps/workbench/app/controllers/collections_controller.rb b/apps/workbench/app/controllers/collections_controller.rb
index f8895da..b6997b9 100644
--- a/apps/workbench/app/controllers/collections_controller.rb
+++ b/apps/workbench/app/controllers/collections_controller.rb
@@ -19,7 +19,7 @@ class CollectionsController < ApplicationController
@collection_info = {}
@collections.each do |c|
@collection_info[c.uuid] = {
- tags: [],
+ tag_links: [],
wanted: false,
wanted_by_me: false,
provenance: [],
@@ -31,7 +31,7 @@ class CollectionsController < ApplicationController
info = @collection_info[link.head_uuid]
case link.link_class
when 'tag'
- info[:tags] << link.name
+ info[:tag_links] << link
when 'resources'
info[:wanted] = true
info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
diff --git a/apps/workbench/app/views/collections/_index_tbody.html.erb b/apps/workbench/app/views/collections/_index_tbody.html.erb
index f7209ee..fad520e 100644
--- a/apps/workbench/app/views/collections/_index_tbody.html.erb
+++ b/apps/workbench/app/views/collections/_index_tbody.html.erb
@@ -30,11 +30,11 @@
<% end %>
</td>
<td class="add-tag-button">
- <a class="btn btn-xs btn-info add-tag-button pull-right"><i class="glyphicon glyphicon-plus"></i> Add</a>
+ <a class="btn btn-xs btn-info add-tag-button pull-right" data-remote-href="<%= url_for(controller: 'links', action: 'create') %>" data-remote-method="post"><i class="glyphicon glyphicon-plus"></i> Add</a>
<span>
<% if @collection_info[c.uuid] %>
- <% @collection_info[c.uuid][:tags].uniq.each do |tag| %>
- <span class="label label-info removable-tag" data-tag-link-uuid=""><%= tag %> <a><i class="glyphicon glyphicon-trash"></i></a></span>
+ <% @collection_info[c.uuid][:tag_links].each do |tag_link| %>
+ <span class="label label-info removable-tag" data-tag-link-uuid="<%= tag_link.uuid %>"><%= tag_link.name %> <a><i class="glyphicon glyphicon-trash"></i></a></span>
<% end %>
<% end %>
</span>
commit 6ecd3b6f76a1dbb39a56fc81d306969dc0a3f6af
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Feb 16 01:04:30 2014 -0800
Fix up tag and "add tag" button display.
diff --git a/apps/workbench/app/assets/javascripts/application.js b/apps/workbench/app/assets/javascripts/application.js
index 4d9c1b8..2f3b094 100644
--- a/apps/workbench/app/assets/javascripts/application.js
+++ b/apps/workbench/app/assets/javascripts/application.js
@@ -49,18 +49,23 @@ jQuery(function($){
$('.loading').fadeOut('fast', 0);
}).
on('click', '.removable-tag a', function(e) {
- $(this).parents('[data-tag-link-uuid]').eq(0).next().andSelf().remove();
+ $(this).parents('[data-tag-link-uuid]').eq(0).remove();
+ return false;
}).
on('click', 'a.add-tag-button', function(e) {
new_tag = window.prompt("Add tag for collection "+
$(this).parents('tr').attr('data-object-uuid'),
"");
if (new_tag != null) {
+ new_tag_uuid = 'xxx';
$(this).
parent().
find('>span').
- append($('<span class="label label-info removable-tag" data-tag-link-uuid=""></span>').text(new_tag).append(' <a>×</a>')).
- append('<br/>');
+ append($('<span class="label label-info removable-tag" data-tag-link-uuid=""></span>').
+ attr('data-tag-link-uuid', new_tag_uuid).
+ text(new_tag).
+ append(' <a><i class="glyphicon glyphicon-trash"></i></a> ')).
+ append(' ');
}
return false;
});
diff --git a/apps/workbench/app/assets/stylesheets/application.css.scss b/apps/workbench/app/assets/stylesheets/application.css.scss
index a4163f8..1ea67d2 100644
--- a/apps/workbench/app/assets/stylesheets/application.css.scss
+++ b/apps/workbench/app/assets/stylesheets/application.css.scss
@@ -126,14 +126,20 @@ ul.arvados-nav li ul li {
display:inline-block;
}
+td.add-tag-button {
+ white-space: normal;
+}
td.add-tag-button .add-tag-button {
- margin-top: 2px;
- opacity: 0;
+ margin-right: 4px;
+ opacity: 0.2;
}
td.add-tag-button:hover .add-tag-button {
opacity: 1;
}
-.removable-tag a {
+.label.removable-tag {
+ margin-top: .2em;
+}
+.label.removable-tag a {
cursor: pointer;
}
diff --git a/apps/workbench/app/views/collections/_index_tbody.html.erb b/apps/workbench/app/views/collections/_index_tbody.html.erb
index a34b213..f7209ee 100644
--- a/apps/workbench/app/views/collections/_index_tbody.html.erb
+++ b/apps/workbench/app/views/collections/_index_tbody.html.erb
@@ -20,16 +20,6 @@
<td>
<%= raw(distance_of_time_in_words(c.created_at, Time.now).sub('about ','~').sub(' ',' ')) if c.created_at %>
</td>
- <td class="add-tag-button">
- <span>
- <% if @collection_info[c.uuid] %>
- <% @collection_info[c.uuid][:tags].uniq.each do |tag| %>
- <span class="label label-info removable-tag" data-tag-link-uuid=""><%= tag %> <a>×</a></span><br/>
- <% end %>
- <% end %>
- </span>
- <a class="btn btn-xs btn-info add-tag-button"><i class="glyphicon glyphicon-plus"></i> Add</a>
- </td>
<td>
<% if @collection_info[c.uuid][:wanted_by_me] %>
<span class="label label-info">2×</span>
@@ -39,6 +29,16 @@
<span class="label">cache</span>
<% end %>
</td>
+ <td class="add-tag-button">
+ <a class="btn btn-xs btn-info add-tag-button pull-right"><i class="glyphicon glyphicon-plus"></i> Add</a>
+ <span>
+ <% if @collection_info[c.uuid] %>
+ <% @collection_info[c.uuid][:tags].uniq.each do |tag| %>
+ <span class="label label-info removable-tag" data-tag-link-uuid=""><%= tag %> <a><i class="glyphicon glyphicon-trash"></i></a></span>
+ <% end %>
+ <% end %>
+ </span>
+ </td>
</tr>
<% end %>
diff --git a/apps/workbench/app/views/collections/_show_recent.html.erb b/apps/workbench/app/views/collections/_show_recent.html.erb
index 125f413..3cedb57 100644
--- a/apps/workbench/app/views/collections/_show_recent.html.erb
+++ b/apps/workbench/app/views/collections/_show_recent.html.erb
@@ -19,10 +19,10 @@
<colgroup>
<col width="10%" />
<col width="36%" />
- <col width="22%" />
+ <col width="15%" />
<col width="8%" />
- <col width="16%" />
<col width="8%" />
+ <col width="23%" />
</colgroup>
<thead>
<tr class="contain-align-left">
@@ -30,8 +30,8 @@
<th>contents</th>
<th>owner</th>
<th>age</th>
- <th>tags</th>
<th>storage</th>
+ <th>tags</th>
</tr>
</thead>
<tbody>
commit 7024cc159936593350aaf7939d700102f6510787
Merge: 5793004 ccf75b9
Author: Tom Clegg <tom at curoverse.com>
Date: Sun Feb 16 00:26:54 2014 -0800
Merge branch 'master' into 2060-edit-tags-in-workbench
Conflicts:
apps/workbench/app/assets/javascripts/application.js
apps/workbench/app/assets/stylesheets/application.css.scss
diff --cc apps/workbench/app/assets/javascripts/application.js
index 3d2914b,927e7ae..4d9c1b8
--- a/apps/workbench/app/assets/javascripts/application.js
+++ b/apps/workbench/app/assets/javascripts/application.js
@@@ -43,25 -43,35 +43,51 @@@ jQuery(function($)
});
$(document).
on('ajax:send', function(e, xhr) {
- $('.loading').show();
+ $('.loading').fadeTo('fast', 1);
}).
on('ajax:complete', function(e, status) {
- $('.loading').hide();
+ $('.loading').fadeOut('fast', 0);
+ }).
+ on('click', '.removable-tag a', function(e) {
+ $(this).parents('[data-tag-link-uuid]').eq(0).next().andSelf().remove();
+ }).
+ on('click', 'a.add-tag-button', function(e) {
+ new_tag = window.prompt("Add tag for collection "+
+ $(this).parents('tr').attr('data-object-uuid'),
+ "");
+ if (new_tag != null) {
+ $(this).
+ parent().
+ find('>span').
+ append($('<span class="label label-info removable-tag" data-tag-link-uuid=""></span>').text(new_tag).append(' <a>×</a>')).
+ append('<br/>');
+ }
+ return false;
});
+
+ HeaderRowFixer = function(selector) {
+ var tables = $(selector);
+ this.duplicateTheadTr = function() {
+ $('>tbody', tables).each(function(){
+ $(this).prepend($('thead>tr', this).clone().css('opacity:0'));
+ });
+ }
+ this.fixThead = function() {
+ tables.each(function() {
+ var widths = [];
+ $('> tbody > tr:eq(1) > td', this).each( function(i,v){
+ widths.push($(v).width());
+ });
+ for(i=0;i<widths.length;i++) {
+ $('thead th:eq('+i+')', this).width(widths[i]);
+ }
+ });
+ }
+ }
+ var fixer = new HeaderRowFixer('.table-fixed-header-row');
+ fixer.fixThead();
+ fixer.duplicateTheadTr();
+ $(window).resize(function(){
+ fixer.fixThead();
+ });
})(jQuery);
diff --cc apps/workbench/app/assets/stylesheets/application.css.scss
index c992959,5ada51a..a4163f8
--- a/apps/workbench/app/assets/stylesheets/application.css.scss
+++ b/apps/workbench/app/assets/stylesheets/application.css.scss
@@@ -126,15 -126,35 +126,46 @@@ ul.arvados-nav li ul li
display:inline-block;
}
+td.add-tag-button .add-tag-button {
+ margin-top: 2px;
+ opacity: 0;
+}
-
+td.add-tag-button:hover .add-tag-button {
+ opacity: 1;
+}
-
+.removable-tag a {
+ cursor: pointer;
+}
++
+ li.notification {
+ padding: 10px;
+ }
+ .arvados-nav-container {
+ top: 70px;
+ height: calc(100% - 70px);
+ overflow: auto;
+ z-index: 2;
+ }
+
+ .arvados-nav-active {
+ background: rgb(66, 139, 202);
+ }
+
+ .arvados-nav-active a {
+ color: white;
+ }
+
+ // See HeaderRowFixer in application.js
+ table.table-fixed-header-row {
+ width: 100%;
+ border-spacing: 0px;
+ margin:0;
+ }
+ table.table-fixed-header-row thead {
+ position:fixed;
+ background: #fff;
+ }
+ table.table-fixed-header-row tbody {
+ position:relative;
+ top:1.5em;
+ }
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