[ARVADOS] updated: 1dec6cc7093bcc565bed2baba17c8a892b7e2633
git at public.curoverse.com
git at public.curoverse.com
Fri Mar 14 10:31:12 EDT 2014
Summary of changes:
COPYING | 11 +
LICENSE-2.0.txt | 202 ++++++
README | 21 +
agpl-3.0.txt | 661 +++++++++++++++++++
apps/workbench/.gitignore | 1 +
apps/workbench/Gemfile | 3 +-
apps/workbench/Gemfile.lock | 2 +
.../app/assets/javascripts/application.js | 3 +-
apps/workbench/app/assets/javascripts/editable.js | 17 +-
.../app/assets/javascripts/pipeline_instances.js | 46 ++
.../javascripts/pipeline_instances.js.coffee | 3 -
apps/workbench/app/assets/javascripts/selection.js | 172 +++++
apps/workbench/app/assets/javascripts/sizing.js | 4 +-
.../app/assets/stylesheets/application.css.scss | 11 +-
.../assets/stylesheets/pipeline_templates.css.scss | 27 +
.../workbench/app/assets/stylesheets/selection.css | 29 +
.../app/controllers/actions_controller.rb | 99 +++
.../app/controllers/application_controller.rb | 18 +-
.../app/controllers/collections_controller.rb | 12 +-
apps/workbench/app/controllers/jobs_controller.rb | 5 +-
.../app/controllers/keep_disks_controller.rb | 5 +
.../controllers/pipeline_instances_controller.rb | 48 ++
.../controllers/pipeline_templates_controller.rb | 13 +
apps/workbench/app/controllers/users_controller.rb | 18 +
apps/workbench/app/helpers/application_helper.rb | 125 ++++-
apps/workbench/app/helpers/collections_helper.rb | 4 +
.../app/helpers/pipeline_instances_helper.rb | 53 +-
.../app/helpers/pipeline_templates_helper.rb | 22 +
apps/workbench/app/helpers/provenance_helper.rb | 56 ++-
apps/workbench/app/models/arvados_base.rb | 25 +
apps/workbench/app/models/collection.rb | 2 +
apps/workbench/app/models/pipeline_instance.rb | 4 +-
.../app/views/application/_content.html.erb | 5 +-
.../app/views/application/_job_progress.html.erb | 20 +
.../views/application/_job_status_label.html.erb | 11 +
.../views/application/_pipeline_progress.html.erb | 8 +
.../application/_pipeline_status_label.html.erb | 13 +
.../views/application/_selection_checkbox.html.erb | 8 +
.../app/views/application/_show_recent.html.erb | 9 +
.../app/views/collections/_index_tbody.html.erb | 3 +
.../app/views/collections/_show_files.html.erb | 48 +-
.../app/views/collections/_show_recent.html.erb | 7 +
.../workbench/app/views/jobs/_show_recent.html.erb | 18 +-
.../app/views/layouts/application.html.erb | 27 +-
.../notifications/_pipelines_notification.html.erb | 2 +-
.../pipeline_instances/_show_components.html.erb | 74 ++-
.../views/pipeline_instances/_show_recent.html.erb | 38 +-
.../app/views/pipeline_instances/show.js.erb | 1 +
.../pipeline_templates/_show_attributes.html.erb | 38 +-
.../pipeline_templates/_show_components.html.erb | 8 +
.../_show_components_template.html.erb | 54 ++
.../pipeline_templates/_show_pipelines.html.erb | 2 +
.../views/pipeline_templates/_show_recent.html.erb | 22 +
.../workbench/app/views/users/_show_admin.html.erb | 7 +
apps/workbench/app/views/users/_tables.html.erb | 74 +--
apps/workbench/config/application.default.yml | 66 ++
apps/workbench/config/application.yml.example | 20 +
.../config/initializers/zz_load_config.rb | 46 ++
apps/workbench/config/routes.rb | 10 +-
apps/workbench/lib/tasks/config_check.rake | 8 +
by-sa-3.0.txt | 297 +++++++++
doc/Gemfile | 2 +-
doc/README | 28 +
doc/Rakefile | 9 +
doc/_config.yml | 32 +-
doc/_includes/_run_md5sum_py.liquid | 33 +-
doc/_includes/_tutorial_hash_script_py.liquid | 72 +--
doc/_includes/_webring.liquid | 29 +
doc/_layouts/default.html.liquid | 18 +-
doc/admin/cheat_sheet.html.textile.liquid | 2 +-
doc/api/authentication.html.textile.liquid | 2 +-
doc/api/index.html.textile.liquid | 2 +-
doc/api/methods.html.textile.liquid | 2 +-
.../api_client_authorizations.html.textile.liquid | 2 +-
doc/api/methods/api_clients.html.textile.liquid | 2 +-
.../methods/authorized_keys.html.textile.liquid | 2 +-
doc/api/methods/collections.html.textile.liquid | 2 +-
doc/api/methods/groups.html.textile.liquid | 2 +-
doc/api/methods/humans.html.textile.liquid | 2 +-
doc/api/methods/job_tasks.html.textile.liquid | 2 +-
doc/api/methods/jobs.html.textile.liquid | 2 +-
doc/api/methods/keep_disks.html.textile.liquid | 2 +-
doc/api/methods/links.html.textile.liquid | 2 +-
doc/api/methods/logs.html.textile.liquid | 2 +-
doc/api/methods/nodes.html.textile.liquid | 2 +-
.../methods/pipeline_instances.html.textile.liquid | 2 +-
.../methods/pipeline_templates.html.textile.liquid | 2 +-
doc/api/methods/repositories.html.textile.liquid | 2 +-
doc/api/methods/specimens.html.textile.liquid | 2 +-
doc/api/methods/traits.html.textile.liquid | 2 +-
doc/api/methods/users.html.textile.liquid | 2 +-
.../methods/virtual_machines.html.textile.liquid | 2 +-
doc/api/permission-model.html.textile.liquid | 2 +-
doc/api/resources.html.textile.liquid | 2 +-
doc/api/schema/ApiClient.html.textile.liquid | 2 +-
.../ApiClientAuthorization.html.textile.liquid | 4 +-
doc/api/schema/AuthorizedKey.html.textile.liquid | 4 +-
doc/api/schema/Collection.html.textile.liquid | 2 +-
doc/api/schema/Commit.html.textile.liquid | 4 +-
doc/api/schema/CommitAncestor.html.textile.liquid | 4 +-
doc/api/schema/Group.html.textile.liquid | 4 +-
doc/api/schema/Human.html.textile.liquid | 4 +-
doc/api/schema/Job.html.textile.liquid | 2 +-
doc/api/schema/JobTask.html.textile.liquid | 2 +-
doc/api/schema/KeepDisk.html.textile.liquid | 4 +-
doc/api/schema/Link.html.textile.liquid | 2 +-
doc/api/schema/Log.html.textile.liquid | 4 +-
doc/api/schema/Node.html.textile.liquid | 4 +-
.../schema/PipelineInstance.html.textile.liquid | 4 +-
.../schema/PipelineTemplate.html.textile.liquid | 4 +-
doc/api/schema/Repository.html.textile.liquid | 4 +-
doc/api/schema/Specimen.html.textile.liquid | 4 +-
doc/api/schema/Trait.html.textile.liquid | 4 +-
doc/api/schema/User.html.textile.liquid | 4 +-
doc/api/schema/VirtualMachine.html.textile.liquid | 4 +-
doc/css/code.css | 27 +
doc/css/nav-list.css | 4 +
.../pipeline_templates/gatk-exome-fq-snp.json | 85 ++-
doc/index.html.liquid | 10 +-
doc/install/client.html.textile.liquid | 2 +-
.../create-standard-objects.html.textile.liquid | 2 +-
doc/install/index.html.md.liquid | 1 +
doc/install/install-api-server.html.md.liquid | 116 ----
doc/install/install-api-server.html.textile.liquid | 128 ++++
.../install-crunch-dispatch.html.textile.liquid | 2 +-
doc/install/install-sso.html.textile.liquid | 24 +
doc/install/install-workbench-app.html.md.liquid | 63 --
.../install-workbench-app.html.textile.liquid | 54 ++
doc/sdk/index.html.textile.liquid | 5 +-
.../crunch-utility-libraries.html.textile.liquid | 2 -
doc/sdk/python/sdk-python.html.textile.liquid | 12 +-
doc/user/copying/LICENSE-2.0.html | 182 ++++++
doc/user/copying/agpl-3.0.html | 684 ++++++++++++++++++++
doc/user/copying/by-sa-3.0.html | 418 ++++++++++++
doc/user/copying/copying.html.textile.liquid | 11 +
.../examples/crunch-examples.html.textile.liquid | 4 -
.../check-environment.html.textile.liquid | 6 -
.../getting_started/community.html.textile.liquid | 4 -
.../getting_started/ssh-access.html.textile.liquid | 9 +-
.../getting_started/workbench.html.textile.liquid | 7 +-
doc/user/index.html.textile.liquid | 18 +-
doc/user/reference/api-tokens.html.textile.liquid | 6 +-
doc/user/reference/sdk-cli.html.textile.liquid | 3 -
doc/user/topics/keep.html.textile.liquid | 48 ++
...nning-pipeline-command-line.html.textile.liquid | 119 ++++
...rial-gatk-variantfiltration.html.textile.liquid | 212 ++++++
.../topics/tutorial-job-debug.html.textile.liquid | 151 +++++
doc/user/topics/tutorial-job1.html.textile.liquid | 221 +++++++
.../topics/tutorial-parallel.html.textile.liquid | 79 +++
.../tutorial-trait-search.html.textile.liquid | 269 ++++++++
.../tutorials/intro-crunch.html.textile.liquid | 17 +
.../running-external-program.html.textile.liquid | 46 +-
.../tutorial-firstscript.html.textile.liquid | 72 ++-
...rial-gatk-variantfiltration.html.textile.liquid | 216 ------
.../tutorial-job-debug.html.textile.liquid | 156 -----
.../tutorials/tutorial-job1.html.textile.liquid | 235 -------
.../tutorials/tutorial-keep.html.textile.liquid | 95 ++-
.../tutorial-new-pipeline.html.textile.liquid | 129 +---
.../tutorial-parallel.html.textile.liquid | 88 ---
...tutorial-pipeline-workbench.html.textile.liquid | 25 +
.../tutorial-trait-search.html.textile.liquid | 273 --------
doc/zenweb-liquid.rb | 33 +-
docker/README.md | 27 +-
sdk/cli/bin/arv-run-pipeline-instance | 75 ++-
sdk/cli/bin/crunch-job | 4 -
sdk/python/arvados/collection.py | 8 +-
sdk/python/arvados/errors.py | 2 +
sdk/python/bin/arv-mount | 8 +-
sdk/python/bin/arv-normalize | 17 +-
sdk/python/setup.py.src | 1 +
sdk/python/test_collections.py | 2 +-
services/api/.gitignore | 1 +
services/api/Gemfile | 13 +-
services/api/Gemfile.lock | 39 ++
.../api/app/controllers/application_controller.rb | 32 +-
.../v1/api_client_authorizations_controller.rb | 1 +
.../app/controllers/user_sessions_controller.rb | 3 +-
services/api/app/models/arvados_model.rb | 4 +-
services/api/app/models/blob.rb | 96 +++
services/api/app/models/node.rb | 12 +-
services/api/app/models/pipeline_instance.rb | 4 +
services/api/app/models/user.rb | 2 +-
services/api/config/application.default.yml | 101 +++
services/api/config/application.rb | 26 -
services/api/config/application.yml.example | 41 ++
services/api/config/database.yml.sample | 12 +-
services/api/config/environments/test.rb.example | 7 +
.../api/config/initializers/omniauth.rb.example | 2 +-
services/api/config/initializers/zz_load_config.rb | 46 ++
...load_all_models.rb => zz_preload_all_models.rb} | 0
services/api/lib/tasks/config_check.rake | 8 +
services/api/script/crunch-dispatch.rb | 28 +-
.../functional/arvados/v1/jobs_controller_test.rb | 49 ++
.../arvados/v1/keep_disks_controller_test.rb | 28 +
.../api_client_authorizations_api_test.rb | 36 +
services/api/test/unit/blob_test.rb | 94 +++
196 files changed, 6251 insertions(+), 1964 deletions(-)
create mode 100644 COPYING
create mode 100644 LICENSE-2.0.txt
create mode 100644 README
create mode 100644 agpl-3.0.txt
create mode 100644 apps/workbench/app/assets/javascripts/pipeline_instances.js
delete mode 100644 apps/workbench/app/assets/javascripts/pipeline_instances.js.coffee
create mode 100644 apps/workbench/app/assets/javascripts/selection.js
create mode 100644 apps/workbench/app/assets/stylesheets/selection.css
create mode 100644 apps/workbench/app/controllers/actions_controller.rb
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create mode 100644 apps/workbench/app/views/application/_job_status_label.html.erb
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create mode 100644 apps/workbench/app/views/application/_pipeline_status_label.html.erb
create mode 100644 apps/workbench/app/views/application/_selection_checkbox.html.erb
create mode 100644 apps/workbench/app/views/pipeline_templates/_show_components.html.erb
create mode 100644 apps/workbench/app/views/pipeline_templates/_show_components_template.html.erb
create mode 100644 apps/workbench/app/views/pipeline_templates/_show_pipelines.html.erb
create mode 100644 apps/workbench/app/views/users/_show_admin.html.erb
create mode 100644 apps/workbench/config/application.default.yml
create mode 100644 apps/workbench/config/application.yml.example
create mode 100644 apps/workbench/config/initializers/zz_load_config.rb
create mode 100644 apps/workbench/lib/tasks/config_check.rake
create mode 100644 by-sa-3.0.txt
create mode 100644 doc/README
create mode 100644 doc/_includes/_webring.liquid
create mode 100644 doc/css/code.css
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commit 1dec6cc7093bcc565bed2baba17c8a892b7e2633
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Mar 14 10:31:03 2014 -0400
Make integer attributes searchable, add test cases.
diff --git a/services/api/app/controllers/application_controller.rb b/services/api/app/controllers/application_controller.rb
index 2d37dc1..a47bfb5 100644
--- a/services/api/app/controllers/application_controller.rb
+++ b/services/api/app/controllers/application_controller.rb
@@ -153,8 +153,10 @@ class ApplicationController < ActionController::Base
when '=', '<', '<=', '>', '>=', 'like'
if operand.is_a? String
cond_out << "#{table_name}.#{attr} #{operator} ?"
- if operator.match(/[<=>]/) and
- model_class.attribute_column(attr).type == :datetime
+ if (# any operator that operates on value rather than
+ # representation:
+ operator.match(/[<=>]/) and
+ model_class.attribute_column(attr).type == :datetime)
operand = Time.parse operand
end
param_out << operand
diff --git a/services/api/app/models/arvados_model.rb b/services/api/app/models/arvados_model.rb
index 84bdf95..8e37898 100644
--- a/services/api/app/models/arvados_model.rb
+++ b/services/api/app/models/arvados_model.rb
@@ -40,7 +40,7 @@ class ArvadosModel < ActiveRecord::Base
def self.searchable_columns
self.columns.collect do |col|
- if [:string, :text, :datetime].index(col.type) && col.name != 'owner_uuid'
+ if [:string, :text, :datetime, :integer].index(col.type) && col.name != 'owner_uuid'
col.name
end
end.compact
diff --git a/services/api/test/functional/arvados/v1/jobs_controller_test.rb b/services/api/test/functional/arvados/v1/jobs_controller_test.rb
index 91f867a..f68cbc2 100644
--- a/services/api/test/functional/arvados/v1/jobs_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/jobs_controller_test.rb
@@ -170,6 +170,55 @@ class Arvados::V1::JobsControllerTest < ActionController::TestCase
'zzzzz-8i9sb-pshmckwoma9plh7']
end
+ test "search jobs by started_at with < query" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '<', Time.now.to_s]]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs by started_at with > query" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>', Time.now.to_s]]
+ }
+ assert_response :success
+ assert_equal 0, assigns(:objects).count
+ end
+
+ test "search jobs by started_at with >= query on metric date" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>=', '2014-01-01']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs by started_at with >= query on metric date and time" do
+ authorize_with :active
+ get :index, {
+ filters: [['started_at', '>=', '2014-01-01 01:23:45']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
+ test "search jobs with 'any' operator" do
+ authorize_with :active
+ get :index, {
+ where: { any: ['contains', 'pshmckw'] }
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-8i9sb-pshmckwoma9plh7')
+ end
+
test "search jobs by nonexistent column with < query" do
authorize_with :active
get :index, {
diff --git a/services/api/test/functional/arvados/v1/keep_disks_controller_test.rb b/services/api/test/functional/arvados/v1/keep_disks_controller_test.rb
index 3ccfa05..385710e 100644
--- a/services/api/test/functional/arvados/v1/keep_disks_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/keep_disks_controller_test.rb
@@ -94,4 +94,32 @@ class Arvados::V1::KeepDisksControllerTest < ActionController::TestCase
end
end
+ test "search keep_disks by service_port with >= query" do
+ authorize_with :active
+ get :index, {
+ filters: [['service_port', '>=', 25107]]
+ }
+ assert_response :success
+ assert_equal true, assigns(:objects).any?
+ end
+
+ test "search keep_disks by service_port with < query" do
+ authorize_with :active
+ get :index, {
+ filters: [['service_port', '<', 25107]]
+ }
+ assert_response :success
+ assert_equal false, assigns(:objects).any?
+ end
+
+ test "search keep_disks with 'any' operator" do
+ authorize_with :active
+ get :index, {
+ where: { any: ['contains', 'o2t1q5w'] }
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_equal true, !!found.index('zzzzz-penuu-5w2o2t1q5wy7fhn')
+ end
+
end
commit 35336cd73e444534cb2eda20e3730464cc4e6553
Merge: 63e8f77 113d3f9
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Mar 14 10:17:46 2014 -0400
Merge branch 'master' into 2257-inequality-conditions
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