[ARVADOS] updated: de98daba898ad2dfa58c9e810d98dadf4d208b95
git at public.curoverse.com
git at public.curoverse.com
Wed Jul 8 11:40:42 EDT 2015
Summary of changes:
.gitignore | 2 +
.../app/assets/javascripts/select_modal.js | 5 +-
apps/workbench/app/assets/javascripts/users.js | 2 +-
.../app/controllers/actions_controller.rb | 3 +-
.../app/controllers/projects_controller.rb | 20 +-
apps/workbench/app/controllers/users_controller.rb | 9 +-
.../app/views/application/_show_recent.html.erb | 16 +-
apps/workbench/app/views/layouts/body.html.erb | 4 +-
.../app/views/users/_setup_popup.html.erb | 7 +-
.../workbench/app/views/users/_show_admin.html.erb | 8 +-
apps/workbench/config/application.default.yml | 3 +
.../controllers/collections_controller_test.rb | 3 +
.../test/controllers/projects_controller_test.rb | 71 ++
apps/workbench/test/integration/projects_test.rb | 75 --
apps/workbench/test/integration/search_box_test.rb | 13 +-
apps/workbench/test/integration/users_test.rb | 72 +-
crunch_scripts/crunchutil/vwd.py | 6 +
crunch_scripts/run-command | 9 +-
doc/_includes/_install_debian_key.liquid | 4 +
doc/_includes/_install_redhat_key.liquid | 6 +
doc/_includes/_note_python27_sc.liquid | 5 +
doc/install/install-api-server.html.textile.liquid | 255 ++++---
.../install-arv-git-httpd.html.textile.liquid | 20 +-
.../install-compute-node.html.textile.liquid | 44 +-
.../install-crunch-dispatch.html.textile.liquid | 34 +-
doc/install/install-keepproxy.html.textile.liquid | 18 +-
doc/install/install-keepstore.html.textile.liquid | 19 +-
...l-manual-prerequisites-ruby.html.textile.liquid | 6 +-
...nstall-manual-prerequisites.html.textile.liquid | 52 +-
.../install-shell-server.html.textile.liquid | 38 +-
.../install-workbench-app.html.textile.liquid | 165 +++--
doc/sdk/perl/index.html.textile.liquid | 40 +-
doc/sdk/python/sdk-python.html.textile.liquid | 61 +-
doc/user/topics/run-command.html.textile.liquid | 13 +
.../tutorial-keep-mount.html.textile.liquid | 22 +-
docker/api/Dockerfile | 4 +-
docker/api/update-gitolite.rb | 11 +-
docker/base/Dockerfile | 14 +-
docker/compute/Dockerfile | 6 +-
docker/doc/Dockerfile | 4 +-
docker/java-bwa-samtools/Dockerfile | 4 +-
docker/keepproxy/Dockerfile | 4 +-
docker/passenger/Dockerfile | 4 +-
docker/postgresql/Dockerfile | 2 +-
docker/shell/Dockerfile | 4 +-
docker/slurm/Dockerfile | 4 +-
docker/workbench/Dockerfile | 4 +-
sdk/cli/bin/crunch-job | 154 ++--
sdk/python/arvados/_ranges.py | 22 +-
sdk/python/arvados/api.py | 6 +-
sdk/python/arvados/arvfile.py | 399 +++++++----
sdk/python/arvados/collection.py | 327 ++++++---
sdk/python/arvados/commands/put.py | 5 +-
sdk/python/arvados/events.py | 6 +-
sdk/python/arvados/keep.py | 4 +-
sdk/python/arvados/util.py | 18 +
sdk/python/setup.py | 2 -
.../python/tests/performance}/__init__.py | 0
.../tests/performance/performance_profiler.py | 49 ++
sdk/python/tests/performance/test_a_sample.py | 15 +
sdk/python/tests/test_arv_put.py | 14 +
sdk/python/tests/test_arvfile.py | 178 ++---
sdk/python/tests/test_collections.py | 38 +-
services/api/Rakefile | 31 +
.../arvados/v1/repositories_controller.rb | 19 +-
services/api/app/mailers/user_notifier.rb | 2 +-
.../views/user_notifier/account_is_setup.text.erb | 7 +-
services/api/db/structure.sql | 2 +-
services/api/script/crunch-dispatch.rb | 69 +-
.../arvados/v1/repositories_controller_test.rb | 11 +
.../functional/arvados/v1/users_controller_test.rb | 8 +-
services/api/test/unit/user_notifier_test.rb | 8 +-
services/fuse/README.rst | 4 +
services/fuse/arvados_fuse/__init__.py | 432 ++++++++++--
services/fuse/arvados_fuse/fresh.py | 52 +-
services/fuse/arvados_fuse/fusedir.py | 457 +++++++++---
services/fuse/arvados_fuse/fusefile.py | 54 +-
services/fuse/bin/arv-mount | 23 +-
services/fuse/setup.py | 2 +-
services/fuse/tests/fstest.py | 133 ++++
services/fuse/tests/{ => performance}/__init__.py | 0
.../fuse/tests/performance/performance_profiler.py | 1 +
services/fuse/tests/prof.py | 17 +
services/fuse/tests/test_inodes.py | 5 +-
services/fuse/tests/test_mount.py | 781 ++++++++++++++++++++-
85 files changed, 3460 insertions(+), 1090 deletions(-)
create mode 100644 doc/_includes/_install_debian_key.liquid
create mode 100644 doc/_includes/_install_redhat_key.liquid
create mode 100644 doc/_includes/_note_python27_sc.liquid
copy {services/fuse/tests => sdk/python/tests/performance}/__init__.py (100%)
create mode 100644 sdk/python/tests/performance/performance_profiler.py
create mode 100644 sdk/python/tests/performance/test_a_sample.py
create mode 100644 services/fuse/tests/fstest.py
copy services/fuse/tests/{ => performance}/__init__.py (100%)
create mode 120000 services/fuse/tests/performance/performance_profiler.py
create mode 100644 services/fuse/tests/prof.py
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commit de98daba898ad2dfa58c9e810d98dadf4d208b95
Merge: fc2dc01 76e03ae
Author: Manoj <jonam33 at gmail.com>
Date: Wed Jul 8 11:40:16 2015 -0400
Merge branch 'master' into 6465-optimize-workbench-integration-tests
commit fc2dc01f5e98b3c1d663e78f882eed20962de9d7
Author: Manoj <jonam33 at gmail.com>
Date: Wed Jul 8 11:34:13 2015 -0400
6465-Removed two description based tests in projects integration test and added four tests in projects controller test.
Kept one description test in projects integration test to check if the edit description button works.
diff --git a/apps/workbench/test/controllers/projects_controller_test.rb b/apps/workbench/test/controllers/projects_controller_test.rb
index 62a93a1..c695bd5 100644
--- a/apps/workbench/test/controllers/projects_controller_test.rb
+++ b/apps/workbench/test/controllers/projects_controller_test.rb
@@ -306,4 +306,49 @@ class ProjectsControllerTest < ActionController::TestCase
assert_match /\/users\/welcome/, @response.redirect_url
assert_empty css_select('[href="/projects/public"]')
end
+
+ test "find a project and edit its description" do
+ project = api_fixture('groups')['aproject']
+ use_token :active
+ found = Group.find(project['uuid'])
+ found.description = 'test description update'
+ found.save!
+ get(:show, {id: project['uuid']}, session_for(:active))
+ assert_includes @response.body, 'test description update'
+ end
+
+ test "find a project and edit description to textile description" do
+ project = api_fixture('groups')['aproject']
+ use_token :active
+ found = Group.find(project['uuid'])
+ found.description = '*test bold description for textile formatting*'
+ found.save!
+ get(:show, {id: project['uuid']}, session_for(:active))
+ assert_includes @response.body, '<strong>test bold description for textile formatting</strong>'
+ end
+
+ test "find a project and edit description to html description" do
+ project = api_fixture('groups')['aproject']
+ use_token :active
+ found = Group.find(project['uuid'])
+ found.description = 'Textile description with link to home page <a href="/">take me home</a>.'
+ found.save!
+ get(:show, {id: project['uuid']}, session_for(:active))
+ assert_not_includes 'Textile description with link to home page <a href="/">take me home</a>.', @response.body
+ assert_match /Textile description with link to home page .*a href=.*take me home.*\/a.*./, @response.body
+ end
+
+ test "find a project and edit description to textile description with link to object" do
+ project = api_fixture('groups')['aproject']
+ use_token :active
+ found = Group.find(project['uuid'])
+ found.description = '"Link to object":' + api_fixture('groups')['asubproject']['uuid']
+ found.save!
+ get(:show, {id: project['uuid']}, session_for(:active))
+ puts @response.body
+ assert_not_includes '"Link to object"', @response.body
+ assert_match /href=.*Link to object.*\/a./, @response.body
+ refute_empty css_select('[href="/groups/zzzzz-j7d0g-axqo7eu9pwvna1x"]')
+ end
+
end
diff --git a/apps/workbench/test/integration/projects_test.rb b/apps/workbench/test/integration/projects_test.rb
index 9c2842f..366b1d3 100644
--- a/apps/workbench/test/integration/projects_test.rb
+++ b/apps/workbench/test/integration/projects_test.rb
@@ -36,81 +36,6 @@ class ProjectsTest < ActionDispatch::IntegrationTest
"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("#projects-menu").click
- find(".dropdown-menu a", 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('<p>*Textile description for A project* - "take me home":/ </p><p>And a new paragraph in description.</p>')
- find('.editable-submit').click
- end
- wait_for_ajax
- end
-
- # visit project page
- visit current_path
- assert_no_text '*Textile description for A project*'
- assert(find?('.container-fluid', text: 'Textile description for A project'),
- "Description update did not survive page refresh")
- assert(find?('.container-fluid', text: 'And a new paragraph in description'),
- "Description did not contain the expected new paragraph")
- assert(page.has_link?("take me home"), "link not found in description")
-
- click_link 'take me home'
-
- # now in dashboard
- assert(page.has_text?('Active pipelines'), 'Active pipelines - not found on dashboard')
- end
-
- test 'Find a project and edit description to html description' do
- visit page_with_token 'active', '/'
- find("#projects-menu").click
- find(".dropdown-menu a", 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?('Active pipelines')
- end
-
- test 'Find a project and edit description to textile description with link to object' do
- visit page_with_token 'active', '/'
- find("#projects-menu").click
- find(".dropdown-menu a", 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('traits')['owned_by_aproject_with_no_name']['uuid']
commit cfcfa1c48d95a07bb961baeef8d7658ddecce41e
Merge: b67167e fdb63be
Author: Manoj <jonam33 at gmail.com>
Date: Tue Jul 7 09:15:30 2015 -0400
Merge branch 'master' into 6465-optimize-workbench-integration-tests
commit b67167e763608af2909ce4e4e25c03d0e7db8b84
Author: Manoj <jonam33 at gmail.com>
Date: Mon Jul 6 09:28:35 2015 -0400
6465 - Moved test for anonymous user accessing collection in a shared project from integration
to controller.
diff --git a/apps/workbench/test/controllers/collections_controller_test.rb b/apps/workbench/test/controllers/collections_controller_test.rb
index dd9aefc..d046d88 100644
--- a/apps/workbench/test/controllers/collections_controller_test.rb
+++ b/apps/workbench/test/controllers/collections_controller_test.rb
@@ -471,5 +471,8 @@ class CollectionsControllerTest < ActionController::TestCase
response_object = assigns(:object)
assert_equal collection['name'], response_object['name']
assert_equal collection['uuid'], response_object['uuid']
+ assert_includes @response.body, 'Hello world'
+ assert_includes @response.body, 'Content address'
+ refute_nil css_select('[href="#Advanced"]')
end
end
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