[ARVADOS] updated: 5bb11227e0d7d37cc6cf574b5d5f289afd1a43b1
git at public.curoverse.com
git at public.curoverse.com
Mon Feb 2 09:31:18 EST 2015
Summary of changes:
apps/workbench/Gemfile | 24 +-
apps/workbench/Gemfile.lock | 126 ++++----
.../app/assets/javascripts/selection.js.erb | 50 +--
.../app/controllers/application_controller.rb | 79 +++--
.../app/controllers/projects_controller.rb | 54 +---
.../app/controllers/repositories_controller.rb | 14 +
apps/workbench/app/controllers/users_controller.rb | 3 +-
apps/workbench/app/models/repository.rb | 7 +
.../app/views/application/_choose.html.erb | 7 +-
.../_show_sharing.html.erb | 12 +-
.../jobs/_rerun_job_with_options_popup.html.erb | 48 +++
.../app/views/jobs/_show_job_buttons.html.erb | 30 +-
apps/workbench/app/views/jobs/show.html.erb | 3 +-
apps/workbench/app/views/layouts/body.html.erb | 7 +-
.../views/projects/_show_contents_rows.html.erb | 2 +-
.../app/views/projects/_show_tab_contents.html.erb | 11 +-
.../app/views/users/_manage_repositories.html.erb | 6 +
apps/workbench/app/views/users/profile.html.erb | 6 +-
.../config/initializers/rack_mini_profile.rb | 5 +
apps/workbench/config/routes.rb | 4 +-
.../test/controllers/projects_controller_test.rb | 54 ++--
.../controllers/repositories_controller_test.rb | 61 ++++
apps/workbench/test/helpers/share_object_helper.rb | 78 +++++
apps/workbench/test/integration/jobs_test.rb | 41 +++
.../test/integration/pipeline_instances_test.rb | 27 +-
apps/workbench/test/integration/projects_test.rb | 84 +----
.../test/integration/repositories_test.rb | 46 +++
.../test/integration/user_manage_account_test.rb | 25 ++
.../test/integration/user_profile_test.rb | 10 +-
apps/workbench/test/integration/websockets_test.rb | 4 +-
apps/workbench/test/performance/browsing_test.rb | 15 +-
apps/workbench/test/test_helper.rb | 9 +-
apps/workbench/test/unit/repository_test.rb | 18 ++
doc/_config.yml | 9 +
doc/_includes/_arv_run_redirection.liquid | 19 ++
doc/_includes/_navbar_top.liquid | 1 +
doc/_layouts/default.html.liquid | 1 +
doc/css/carousel-override.css | 25 ++
doc/images/download-shared-collection.png | Bin 0 -> 39610 bytes
doc/images/files-uploaded.png | Bin 0 -> 53926 bytes
doc/images/keyfeatures/chooseinputs.png | Bin 0 -> 76641 bytes
doc/images/keyfeatures/collectionpage.png | Bin 0 -> 84533 bytes
doc/images/keyfeatures/dashboard2.png | Bin 0 -> 44396 bytes
doc/images/keyfeatures/graph.png | Bin 0 -> 49127 bytes
doc/images/keyfeatures/log.png | Bin 0 -> 135214 bytes
doc/images/keyfeatures/provenance.png | Bin 0 -> 67060 bytes
doc/images/keyfeatures/rerun.png | Bin 0 -> 73314 bytes
doc/images/keyfeatures/running2.png | Bin 0 -> 56959 bytes
doc/images/keyfeatures/shared.png | Bin 0 -> 62395 bytes
doc/images/keyfeatures/webupload.png | Bin 0 -> 88061 bytes
doc/images/quickstart/1.png | Bin 0 -> 47239 bytes
doc/images/quickstart/2.png | Bin 0 -> 74431 bytes
doc/images/quickstart/3.png | Bin 0 -> 80668 bytes
doc/images/quickstart/4.png | Bin 0 -> 66686 bytes
doc/images/quickstart/5.png | Bin 0 -> 83038 bytes
doc/images/quickstart/6.png | Bin 0 -> 98604 bytes
doc/images/quickstart/7.png | Bin 0 -> 77820 bytes
doc/images/shared-collection.png | Bin 0 -> 31833 bytes
doc/images/upload-tab-in-new-collection.png | Bin 0 -> 77537 bytes
doc/images/upload-using-workbench.png | Bin 0 -> 49690 bytes
doc/images/uses/choosefiles.png | Bin 0 -> 75434 bytes
doc/images/uses/gotohome.png | Bin 0 -> 76218 bytes
doc/images/uses/rename.png | Bin 0 -> 77738 bytes
doc/images/uses/share.png | Bin 0 -> 85695 bytes
doc/images/uses/shared.png | Bin 0 -> 57235 bytes
doc/images/uses/sharedsubdirs.png | Bin 0 -> 67642 bytes
doc/images/uses/uploaddata.png | Bin 0 -> 85535 bytes
doc/images/uses/uploading.png | Bin 0 -> 74365 bytes
doc/index.html.liquid | 12 +-
.../firstpipeline.html.textile.liquid | 89 +++++
.../getting_started/sharedata.html.textile.liquid | 97 ++++++
doc/start/index.html.textile.liquid | 128 ++++++++
doc/start/index.html.textile.liquid.bkup | 50 +++
doc/user/topics/arv-run.html.textile.liquid | 20 +-
.../crunch-tools-overview.html.textile.liquid | 63 ++++
.../tutorial-keep-get.html.textile.liquid | 36 ++-
.../tutorials/tutorial-keep.html.textile.liquid | 33 +-
sdk/cli/arvados-cli.gemspec | 2 +-
sdk/cli/bin/arv | 32 +-
sdk/cli/bin/crunch-job | 30 +-
sdk/python/arvados/api.py | 16 +-
sdk/python/arvados/arvfile.py | 359 ++++++++++++---------
sdk/python/arvados/collection.py | 211 ++++++------
sdk/python/arvados/commands/arv_copy.py | 3 +-
sdk/python/arvados/commands/ws.py | 4 +-
sdk/python/arvados/events.py | 21 +-
sdk/python/tests/test_api.py | 10 +-
sdk/python/tests/test_arv_put.py | 4 +-
sdk/python/tests/test_pipeline_template.py | 10 +-
sdk/python/tests/test_websockets.py | 33 +-
sdk/ruby/arvados.gemspec | 3 +-
sdk/ruby/lib/arvados.rb | 31 +-
sdk/ruby/lib/arvados/google_api_client.rb | 55 ++++
sdk/ruby/lib/arvados/keep.rb | 73 +++--
services/api/Gemfile | 3 +-
services/api/Gemfile.lock | 6 +-
.../api/app/controllers/application_controller.rb | 15 +-
.../arvados/v1/collections_controller.rb | 6 +-
.../controllers/arvados/v1/groups_controller.rb | 2 +-
.../arvados/v1/keep_disks_controller.rb | 2 +-
.../app/controllers/arvados/v1/nodes_controller.rb | 2 +-
.../arvados/v1/repositories_controller.rb | 8 +-
.../controllers/arvados/v1/schema_controller.rb | 2 +-
.../app/controllers/arvados/v1/users_controller.rb | 2 +-
.../arvados/v1/virtual_machines_controller.rb | 2 +-
.../api/app/controllers/database_controller.rb | 2 +-
services/api/app/models/arvados_model.rb | 10 +-
.../api/db/migrate/20141208185217_search_index.rb | 10 +-
...0150122175935_no_description_in_search_index.rb | 30 ++
services/api/db/structure.sql | 14 +-
services/api/lib/josh_id.rb | 2 +-
services/api/lib/kind_and_etag.rb | 4 +-
services/api/test/fixtures/jobs.yml | 30 ++
services/api/test/fixtures/links.yml | 14 +
services/api/test/fixtures/pipeline_instances.yml | 31 ++
services/api/test/fixtures/repositories.yml | 5 +
.../arvados/v1/collections_controller_test.rb | 3 +
services/api/test/performance/browsing_test.rb | 12 -
services/api/test/performance/links_index_test.rb | 14 +
services/api/test/test_helper.rb | 2 +-
services/api/test/unit/arvados_model_test.rb | 2 +-
services/api/test/unit/log_test.rb | 14 +
services/crunchstat/crunchstat.go | 13 +-
services/crunchstat/crunchstat_test.go | 29 ++
services/fuse/arvados_fuse/__init__.py | 2 +
125 files changed, 1912 insertions(+), 831 deletions(-)
rename apps/workbench/app/views/{projects => application}/_show_sharing.html.erb (88%)
create mode 100644 apps/workbench/app/views/jobs/_rerun_job_with_options_popup.html.erb
create mode 100644 apps/workbench/config/initializers/rack_mini_profile.rb
create mode 100644 apps/workbench/test/helpers/share_object_helper.rb
create mode 100644 apps/workbench/test/integration/repositories_test.rb
create mode 100644 apps/workbench/test/unit/repository_test.rb
create mode 100644 doc/_includes/_arv_run_redirection.liquid
create mode 100644 doc/css/carousel-override.css
create mode 100644 doc/images/download-shared-collection.png
create mode 100644 doc/images/files-uploaded.png
create mode 100644 doc/images/keyfeatures/chooseinputs.png
create mode 100644 doc/images/keyfeatures/collectionpage.png
create mode 100644 doc/images/keyfeatures/dashboard2.png
create mode 100644 doc/images/keyfeatures/graph.png
create mode 100644 doc/images/keyfeatures/log.png
create mode 100644 doc/images/keyfeatures/provenance.png
create mode 100644 doc/images/keyfeatures/rerun.png
create mode 100644 doc/images/keyfeatures/running2.png
create mode 100644 doc/images/keyfeatures/shared.png
create mode 100644 doc/images/keyfeatures/webupload.png
create mode 100644 doc/images/quickstart/1.png
create mode 100644 doc/images/quickstart/2.png
create mode 100644 doc/images/quickstart/3.png
create mode 100644 doc/images/quickstart/4.png
create mode 100644 doc/images/quickstart/5.png
create mode 100644 doc/images/quickstart/6.png
create mode 100644 doc/images/quickstart/7.png
create mode 100644 doc/images/shared-collection.png
create mode 100644 doc/images/upload-tab-in-new-collection.png
create mode 100644 doc/images/upload-using-workbench.png
create mode 100644 doc/images/uses/choosefiles.png
create mode 100644 doc/images/uses/gotohome.png
create mode 100644 doc/images/uses/rename.png
create mode 100644 doc/images/uses/share.png
create mode 100644 doc/images/uses/shared.png
create mode 100644 doc/images/uses/sharedsubdirs.png
create mode 100644 doc/images/uses/uploaddata.png
create mode 100644 doc/images/uses/uploading.png
create mode 100644 doc/start/getting_started/firstpipeline.html.textile.liquid
create mode 100644 doc/start/getting_started/sharedata.html.textile.liquid
create mode 100644 doc/start/index.html.textile.liquid
create mode 100644 doc/start/index.html.textile.liquid.bkup
create mode 100644 doc/user/topics/crunch-tools-overview.html.textile.liquid
create mode 100644 sdk/ruby/lib/arvados/google_api_client.rb
create mode 100644 services/api/db/migrate/20150122175935_no_description_in_search_index.rb
delete mode 100644 services/api/test/performance/browsing_test.rb
create mode 100644 services/api/test/performance/links_index_test.rb
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commit 5bb11227e0d7d37cc6cf574b5d5f289afd1a43b1
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Feb 2 09:33:28 2015 -0500
4823: Adding @_synchronized to protect arvfile and block manager. Updated
docstrings to PEP 257 and PEP 287.
commit facbf48de90f600a42363b72bcb2b4929f78c73d
Merge: 2b60134 9af0808
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Jan 30 16:40:18 2015 -0500
Merge branch 'master' into 4823-python-sdk-writable-collection-api
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