[ARVADOS] updated: 34173202861e94dee58ccd5b189983918813d870
git at public.curoverse.com
git at public.curoverse.com
Tue Aug 26 20:25:51 EDT 2014
Summary of changes:
.../app/assets/javascripts/application.js | 4 +-
.../workbench/app/assets/javascripts/filterable.js | 43 +-
.../app/assets/javascripts/infinite_scroll.js | 70 ++-
.../app/assets/javascripts/permission_toggle.js | 55 ++
.../app/assets/javascripts/pipeline_instances.js | 33 +-
.../app/assets/javascripts/report_issue.js | 30 +
.../app/assets/javascripts/select_modal.js | 10 +-
apps/workbench/app/assets/javascripts/tab_panes.js | 1 +
.../app/assets/javascripts/user_agreements.js | 16 +-
.../app/assets/stylesheets/application.css.scss | 6 +-
.../workbench/app/assets/stylesheets/jobs.css.scss | 2 +-
.../assets/stylesheets/pipeline_instances.css.scss | 20 +
.../app/assets/stylesheets/select_modal.css.scss | 4 +
.../app/controllers/actions_controller.rb | 65 ++-
.../app/controllers/application_controller.rb | 7 +-
.../app/controllers/collections_controller.rb | 25 +-
.../controllers/pipeline_instances_controller.rb | 4 +-
.../app/controllers/projects_controller.rb | 6 +-
.../app/controllers/user_agreements_controller.rb | 6 +
apps/workbench/app/helpers/application_helper.rb | 23 +-
apps/workbench/app/helpers/jobs_helper.rb | 19 +
.../app/helpers/pipeline_instances_helper.rb | 35 +-
apps/workbench/app/mailers/issue_reporter.rb | 12 +
apps/workbench/app/models/arvados_base.rb | 2 +-
apps/workbench/app/models/collection.rb | 30 +-
apps/workbench/app/models/group.rb | 6 -
apps/workbench/app/models/pipeline_instance.rb | 6 +-
apps/workbench/app/views/application/404.html.erb | 4 +
.../views/application/_arvados_attr_value.html.erb | 6 +-
.../application/_arvados_object_attr.html.erb | 2 +-
.../app/views/application/_choose.html.erb | 23 +-
.../app/views/application/_content.html.erb | 2 +-
.../app/views/application/_report_error.html.erb | 21 +
.../views/application/_report_issue_popup.html.erb | 147 +++++
.../app/views/application/_show_recent.html.erb | 14 +-
.../app/views/application/api_error.html.erb | 2 +
.../views/application/report_issue_popup.js.erb | 2 +
apps/workbench/app/views/application/show.html.erb | 4 +-
.../app/views/collections/_choose_rows.html.erb | 25 +
.../app/views/collections/_index_tbody.html.erb | 4 -
.../app/views/collections/_show_files.html.erb | 4 +-
.../app/views/collections/_show_recent.html.erb | 10 +-
.../app/views/collections/_toggle_persist.html.erb | 3 -
apps/workbench/app/views/collections/show.html.erb | 34 +-
.../app/views/issue_reporter/send_report.text.erb | 12 +
apps/workbench/app/views/jobs/_show_log.html.erb | 25 +-
apps/workbench/app/views/layouts/body.html.erb | 192 ++++---
apps/workbench/app/views/links/_recent.html.erb | 57 --
.../pipeline_instances/_show_compare.html.erb | 17 +-
.../pipeline_instances/_show_components.html.erb | 16 +-
.../_show_components_running.html.erb | 63 +--
.../views/pipeline_instances/_show_graph.html.erb | 11 -
.../views/pipeline_instances/_show_log.html.erb | 6 +
apps/workbench/app/views/projects/_choose.html.erb | 10 +-
.../app/views/projects/_index_projects.html.erb | 4 +-
.../app/views/projects/_show_sharing.html.erb | 2 +-
.../app/views/projects/_show_tab_contents.html.erb | 5 +-
apps/workbench/app/views/projects/show.html.erb | 3 +-
.../app/views/user_agreements/index.html.erb | 14 +-
.../workbench/app/views/users/_show_admin.html.erb | 115 +++-
apps/workbench/config/application.default.yml | 10 +
apps/workbench/config/routes.rb | 2 +
.../test/functional/actions_controller_test.rb | 19 +
.../test/functional/collections_controller_test.rb | 4 +-
.../functional/user_agreements_controller_test.rb | 12 +
.../test/integration/application_layout_test.rb | 274 ++-------
.../workbench/test/integration/collections_test.rb | 40 +-
apps/workbench/test/integration/errors_test.rb | 55 ++
apps/workbench/test/integration/logins_test.rb | 4 +
.../test/integration/pipeline_instances_test.rb | 10 +-
apps/workbench/test/integration/projects_test.rb | 6 +-
.../test/integration/report_issue_test.rb | 96 ++++
apps/workbench/test/integration/search_box_test.rb | 103 ++++
.../test/integration/user_agreements_test.rb | 29 +
.../test/integration/user_manage_account_test.rb | 76 +++
.../test/integration/user_profile_test.rb | 148 +++++
.../test/unit/arvados_resource_list_test.rb | 17 +-
apps/workbench/test/unit/group_test.rb | 11 +-
crunch_scripts/crunchutil/robust_put.py | 1 +
doc/api/methods.html.textile.liquid | 4 +-
doc/api/permission-model.html.textile.liquid | 4 +-
doc/images/workbench-move-selected.png | Bin 0 -> 11267 bytes
.../create-standard-objects.html.textile.liquid | 25 +-
doc/install/install-api-server.html.textile.liquid | 8 +-
.../getting_started/workbench.html.textile.liquid | 2 +-
doc/user/reference/api-tokens.html.textile.liquid | 8 +-
...nning-pipeline-command-line.html.textile.liquid | 2 +-
doc/user/topics/tutorial-job1.html.textile.liquid | 4 +-
.../tutorial-firstscript.html.textile.liquid | 2 +-
.../tutorials/tutorial-keep.html.textile.liquid | 8 +-
...tutorial-pipeline-workbench.html.textile.liquid | 28 +-
sdk/cli/bin/crunch-job | 36 +-
sdk/python/arvados/api.py | 6 +-
sdk/python/arvados/collection.py | 45 +-
sdk/python/arvados/commands/keepdocker.py | 1 -
sdk/python/arvados/commands/put.py | 33 +-
sdk/python/arvados/config.py | 3 +
sdk/python/arvados/errors.py | 6 +-
sdk/python/arvados/events.py | 1 -
sdk/python/arvados/keep.py | 620 +++++++++++++--------
sdk/python/arvados/retry.py | 140 +++++
sdk/python/arvados/stream.py | 7 +-
sdk/python/arvados/util.py | 5 +-
sdk/python/bin/arv-get | 7 +-
sdk/python/setup.py | 2 +-
sdk/python/tests/arvados_testutil.py | 21 +-
sdk/python/tests/run_test_server.py | 102 +++-
sdk/python/tests/test_api.py | 15 +-
sdk/python/tests/test_arv_put.py | 104 ++--
sdk/python/tests/test_collections.py | 99 ++--
sdk/python/tests/test_keep_client.py | 333 ++++++-----
sdk/python/tests/test_keep_locator.py | 32 +-
sdk/python/tests/test_retry.py | 198 +++++++
sdk/python/tests/test_websockets.py | 8 +-
services/api/Gemfile | 1 +
services/api/Gemfile.lock | 12 +-
.../api/app/controllers/application_controller.rb | 52 +-
.../arvados/v1/collections_controller.rb | 311 ++++-------
.../controllers/arvados/v1/groups_controller.rb | 12 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 8 +-
.../controllers/arvados/v1/schema_controller.rb | 1 +
.../app/controllers/arvados/v1/users_controller.rb | 19 +-
.../app/controllers/user_sessions_controller.rb | 3 +
services/api/app/mailers/admin_notifier.rb | 8 +-
services/api/app/models/arvados_model.rb | 171 +++---
services/api/app/models/collection.rb | 169 ++++--
services/api/app/models/commit.rb | 15 +-
services/api/app/models/group.rb | 9 +
services/api/app/models/job.rb | 2 +-
services/api/app/models/link.rb | 32 +-
services/api/app/models/locator.rb | 15 +-
services/api/app/models/user.rb | 51 +-
.../api/app/views/admin_notifier/new_user.text.erb | 9 +-
.../views/api_client_authorizations/index.html.erb | 36 --
services/api/app/views/collections/index.html.erb | 47 --
services/api/app/views/nodes/index.html.erb | 66 ---
.../app/views/pipeline_instances/index.html.erb | 63 ---
services/api/config/application.default.yml | 17 +
.../20140811184643_collection_use_regular_uuids.rb | 180 ++++++
.../20140817035914_add_unique_name_constraints.rb | 30 +
...125735_add_not_null_constraint_to_group_name.rb | 6 +
services/api/db/structure.sql | 62 ++-
services/api/lib/current_api_client.rb | 24 +-
services/api/lib/eventbus.rb | 4 +-
services/api/lib/has_uuid.rb | 38 +-
services/api/lib/record_filters.rb | 143 ++---
services/api/script/crunch-dispatch.rb | 27 +-
services/api/test/factories/api_client.rb | 10 +
.../api/test/factories/api_client_authorization.rb | 19 +
services/api/test/factories/group.rb | 4 +
services/api/test/factories/link.rb | 7 +
services/api/test/factories/user.rb | 44 ++
services/api/test/fixtures/collections.yml | 87 ++-
services/api/test/fixtures/groups.yml | 25 +-
services/api/test/fixtures/links.yml | 215 +++----
services/api/test/fixtures/logs.yml | 4 +-
services/api/test/fixtures/repositories.yml | 5 +
services/api/test/fixtures/specimens.yml | 12 -
services/api/test/fixtures/traits.yml | 5 +
.../arvados/v1/collections_controller_test.rb | 95 ++--
.../arvados/v1/groups_controller_test.rb | 191 +++----
.../functional/arvados/v1/links_controller_test.rb | 38 +-
.../functional/arvados/v1/users_controller_test.rb | 104 ++--
.../api/test/integration/collections_api_test.rb | 53 +-
services/api/test/integration/select_test.rb | 3 +-
.../api/test/integration/user_sessions_test.rb | 86 ++-
services/api/test/test_helper.rb | 18 +-
services/api/test/unit/arvados_model_test.rb | 19 +-
services/api/test/unit/group_test.rb | 13 +-
services/api/test/unit/job_test.rb | 18 +-
services/api/test/unit/link_test.rb | 46 +-
services/api/test/unit/owner_test.rb | 16 +-
services/api/test/unit/permission_test.rb | 192 +++++++
services/api/test/unit/user_test.rb | 223 +++++++-
services/fuse/arvados_fuse/__init__.py | 2 +-
services/fuse/tests/test_mount.py | 268 ++++-----
services/keepstore/handler_test.go | 28 +
services/keepstore/handlers.go | 46 +-
services/keepstore/keepstore_test.go | 62 ++-
services/keepstore/volume.go | 52 +-
services/keepstore/volume_unix.go | 57 +-
services/keepstore/volume_unix_test.go | 39 ++
182 files changed, 5283 insertions(+), 2701 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/permission_toggle.js
create mode 100644 apps/workbench/app/assets/javascripts/report_issue.js
create mode 100644 apps/workbench/app/mailers/issue_reporter.rb
create mode 100644 apps/workbench/app/views/application/_report_error.html.erb
create mode 100644 apps/workbench/app/views/application/_report_issue_popup.html.erb
create mode 100644 apps/workbench/app/views/application/report_issue_popup.js.erb
delete mode 100644 apps/workbench/app/views/collections/_toggle_persist.html.erb
create mode 100644 apps/workbench/app/views/issue_reporter/send_report.text.erb
delete mode 100644 apps/workbench/app/views/links/_recent.html.erb
create mode 100644 apps/workbench/app/views/pipeline_instances/_show_log.html.erb
create mode 100644 apps/workbench/test/functional/actions_controller_test.rb
create mode 100644 apps/workbench/test/integration/report_issue_test.rb
create mode 100644 apps/workbench/test/integration/search_box_test.rb
create mode 100644 apps/workbench/test/integration/user_agreements_test.rb
create mode 100644 apps/workbench/test/integration/user_manage_account_test.rb
create mode 100644 apps/workbench/test/integration/user_profile_test.rb
create mode 100644 doc/images/workbench-move-selected.png
create mode 100644 sdk/python/arvados/retry.py
create mode 100644 sdk/python/tests/test_retry.py
delete mode 100644 services/api/app/views/api_client_authorizations/index.html.erb
delete mode 100644 services/api/app/views/collections/index.html.erb
delete mode 100644 services/api/app/views/nodes/index.html.erb
delete mode 100644 services/api/app/views/pipeline_instances/index.html.erb
create mode 100644 services/api/db/migrate/20140811184643_collection_use_regular_uuids.rb
create mode 100644 services/api/db/migrate/20140817035914_add_unique_name_constraints.rb
create mode 100644 services/api/db/migrate/20140818125735_add_not_null_constraint_to_group_name.rb
create mode 100644 services/api/test/factories/api_client.rb
create mode 100644 services/api/test/factories/api_client_authorization.rb
create mode 100644 services/api/test/factories/group.rb
create mode 100644 services/api/test/factories/link.rb
create mode 100644 services/api/test/factories/user.rb
create mode 100644 services/api/test/fixtures/traits.yml
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commit 34173202861e94dee58ccd5b189983918813d870
Merge: c28604e ff742a8
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Aug 26 20:13:41 2014 -0400
3354: Merge branch 'master' into 3354-render-textile
Conflicts:
apps/workbench/app/assets/stylesheets/application.css.scss
apps/workbench/app/helpers/application_helper.rb
apps/workbench/app/models/group.rb
diff --cc apps/workbench/app/assets/stylesheets/application.css.scss
index 7d87dc3,5d6acf3..bfb57e9
--- a/apps/workbench/app/assets/stylesheets/application.css.scss
+++ b/apps/workbench/app/assets/stylesheets/application.css.scss
@@@ -244,7 -244,9 +244,11 @@@ div.pane-content iframe
width: 100%;
border: none;
}
--
+span.editable-textile {
+ display: inline-block;
+}
+ .text-overflow-ellipsis {
+ white-space: nowrap;
+ overflow: hidden;
+ text-overflow: ellipsis;
+ }
diff --cc apps/workbench/app/helpers/application_helper.rb
index de7fd17,1f0e5e2..edcb7fb
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@@ -180,11 -186,11 +190,11 @@@ module ApplicationHelpe
@unique_id ||= (Time.now.to_f*1000000).to_i
span_id = object.uuid.to_s + '-' + attr.to_s + '-' + (@unique_id += 1).to_s
- span_tag = content_tag 'span', attrvalue.to_s, {
- "data-emptytext" => ('(none)'),
+ span_tag = content_tag 'span', rendervalue, {
- "data-emptytext" => (object.andand.default_name || 'none'),
++ "data-emptytext" => '(none)',
"data-placement" => "bottom",
"data-type" => input_type,
- "data-title" => "Edit #{attr.gsub '_', ' '}",
+ "data-title" => "Edit #{attr.to_s.gsub '_', ' '}",
"data-name" => attr,
"data-object-uuid" => object.uuid,
"data-toggle" => "manual",
diff --cc apps/workbench/app/models/group.rb
index a91b729,b7ffd63..d478198
--- a/apps/workbench/app/models/group.rb
+++ b/apps/workbench/app/models/group.rb
@@@ -24,14 -24,4 +24,8 @@@ class Group < ArvadosBas
def class_for_display
group_class == 'project' ? 'Project' : super
end
+
- def editable?
- respond_to?(:writable_by) and
- writable_by and
- writable_by.index(current_user.uuid)
- end
-
+ def textile_attributes
+ [ 'description' ]
+ end
end
diff --cc apps/workbench/test/integration/projects_test.rb
index b420260,8a80bc2..07a7b10
--- a/apps/workbench/test/integration/projects_test.rb
+++ b/apps/workbench/test/integration/projects_test.rb
@@@ -25,80 -25,9 +25,80 @@@ class ProjectsTest < ActionDispatch::In
"Description update did not survive page refresh")
end
+ test 'Find a project and edit description to textile description' do
+ visit page_with_token 'active', '/'
+ find('.arv-project-list a,button', text: 'A Project').
+ click
+ within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
+ find('span', text: api_fixture('groups')['aproject']['name']).click
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('*Textile description for A project* - "take me home":/')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+ end
+ visit current_path
+ assert(find?('.container-fluid', text: 'Textile description for A project'),
+ "Description update did not survive page refresh")
+ assert(!find?('.container-fluid', text: '*Textile description for A project*'),
+ "Textile description is displayed with uninterpreted formatting characters")
+ assert(page.has_link?("take me home"), "link not found in description")
+ click_link 'take me home'
+ assert page.has_text?('My projects')
+ assert page.has_text?('Projects shared with me')
+ end
+
+ test 'Find a project and edit description to html description' do
+ visit page_with_token 'active', '/'
+ find('.arv-project-list a,button', text: 'A Project').
+ click
+ within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
+ find('span', text: api_fixture('groups')['aproject']['name']).click
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('<br>Textile description for A project</br> - <a href="/">take me home</a>')
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+ end
+ visit current_path
+ assert(find?('.container-fluid', text: 'Textile description for A project'),
+ "Description update did not survive page refresh")
+ assert(!find?('.container-fluid', text: '<br>Textile description for A project</br>'),
+ "Textile description is displayed with uninterpreted formatting characters")
+ assert(page.has_link?("take me home"),"link not found in description")
+ click_link 'take me home'
+ assert page.has_text?('My projects')
+ assert page.has_text?('Projects shared with me')
+ end
+
+ test 'Find a project and edit description to textile description with link to object' do
+ visit page_with_token 'active', '/'
+ find('.arv-project-list a,button', text: 'A Project').
+ click
+ within('.container-fluid', text: api_fixture('groups')['aproject']['name']) do
+ find('span', text: api_fixture('groups')['aproject']['name']).click
+ within('.arv-description-as-subtitle') do
+ find('.fa-pencil').click
+ find('.editable-input textarea').set('*Textile description for A project* - "go to sub-project":' + api_fixture('groups')['asubproject']['uuid'] + "'")
+ find('.editable-submit').click
+ end
+ wait_for_ajax
+ end
+ visit current_path
+ assert(find?('.container-fluid', text: 'Textile description for A project'),
+ "Description update did not survive page refresh")
+ assert(!find?('.container-fluid', text: '*Textile description for A project*'),
+ "Textile description is displayed with uninterpreted formatting characters")
+ assert(page.has_link?("go to sub-project"), "link not found in description")
+ click_link 'go to sub-project'
+ assert(page.has_text?(api_fixture('groups')['asubproject']['name']), 'sub-project name not found after clicking link')
+ end
+
test 'Add a new name, then edit it, without creating a duplicate' do
project_uuid = api_fixture('groups')['aproject']['uuid']
- specimen_uuid = api_fixture('specimens')['owned_by_aproject_with_no_name_link']['uuid']
+ specimen_uuid = api_fixture('traits')['owned_by_aproject_with_no_name']['uuid']
visit page_with_token 'active', '/projects/' + project_uuid
click_link 'Other objects'
within '.selection-action-container' do
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