[ARVADOS] updated: ab58549b6249224decdb913097f1649e993b95a7
git at public.curoverse.com
git at public.curoverse.com
Wed Jul 30 15:22:31 EDT 2014
Summary of changes:
.../workbench/app/assets/javascripts/filterable.js | 2 +-
.../app/assets/javascripts/select_modal.js | 7 +-
.../workbench/app/controllers/search_controller.rb | 13 +-
.../app/views/search/_choose_rows.html.erb | 6 +-
doc/_config.yml | 1 +
doc/_includes/_alert_docker.liquid | 4 -
doc/install/index.html.textile.liquid | 2 -
doc/install/install-docker.html.textile.liquid | 94 ++++++------
.../check-environment.html.textile.liquid | 2 +-
docker/api/Dockerfile | 37 ++++-
docker/api/application.yml.in | 5 +
docker/api/apt.arvados.org.list | 2 +
docker/api/arvados-clients.yml.in | 5 +
docker/api/crunch-dispatch-run.sh | 24 +++
docker/api/keep_server_0.json | 6 +
docker/api/keep_server_1.json | 7 +
docker/api/munge.key | Bin 0 -> 1024 bytes
docker/api/setup-gitolite.sh.in | 77 ++++++++++
docker/api/setup.sh.in | 62 ++++++++
docker/api/slurm.conf.in | 60 ++++++++
docker/api/supervisor.conf | 29 ++++
docker/api/update-gitolite.rb | 162 +++++++++++++++++++++
docker/arvdock | 120 ++++++++++++---
docker/base/Dockerfile | 4 +
docker/base/apt.arvados.org.list | 2 +
docker/build.sh | 32 +++-
docker/build_tools/Makefile | 143 ++++++++++++++++--
docker/build_tools/build.rb | 28 +++-
docker/compute/Dockerfile | 28 ++++
docker/compute/fuse.conf | 10 ++
docker/compute/setup.sh.in | 20 +++
docker/{api => compute}/ssh.sh | 0
docker/compute/supervisor.conf | 29 ++++
docker/compute/wrapdocker | 90 ++++++++++++
docker/config.yml.example | 4 +
docker/shell/Dockerfile | 19 +++
docker/shell/fuse.conf | 10 ++
docker/shell/setup.sh.in | 21 +++
docker/{api => shell}/superuser_token.in | 0
docker/shell/supervisor.conf | 15 ++
docker/slurm/Dockerfile | 11 ++
docker/slurm/munge.key | Bin 0 -> 1024 bytes
docker/slurm/slurm.conf.in | 60 ++++++++
docker/slurm/supervisor.conf | 14 ++
docker/workbench/Dockerfile | 3 +
.../api/app/controllers/application_controller.rb | 1 +
.../controllers/arvados/v1/groups_controller.rb | 28 ++--
.../arvados/v1/groups_controller_test.rb | 34 +++--
48 files changed, 1204 insertions(+), 129 deletions(-)
delete mode 100644 doc/_includes/_alert_docker.liquid
create mode 100644 docker/api/apt.arvados.org.list
create mode 100644 docker/api/arvados-clients.yml.in
create mode 100755 docker/api/crunch-dispatch-run.sh
create mode 100644 docker/api/keep_server_0.json
create mode 100644 docker/api/keep_server_1.json
create mode 100644 docker/api/munge.key
create mode 100755 docker/api/setup-gitolite.sh.in
create mode 100755 docker/api/setup.sh.in
create mode 100644 docker/api/slurm.conf.in
create mode 100755 docker/api/update-gitolite.rb
create mode 100644 docker/base/apt.arvados.org.list
create mode 100644 docker/compute/Dockerfile
create mode 100644 docker/compute/fuse.conf
create mode 100755 docker/compute/setup.sh.in
copy docker/{api => compute}/ssh.sh (100%)
create mode 100644 docker/compute/supervisor.conf
create mode 100755 docker/compute/wrapdocker
create mode 100644 docker/shell/Dockerfile
create mode 100644 docker/shell/fuse.conf
create mode 100755 docker/shell/setup.sh.in
copy docker/{api => shell}/superuser_token.in (100%)
create mode 100644 docker/shell/supervisor.conf
create mode 100644 docker/slurm/Dockerfile
create mode 100644 docker/slurm/munge.key
create mode 100644 docker/slurm/slurm.conf.in
create mode 100644 docker/slurm/supervisor.conf
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commit ab58549b6249224decdb913097f1649e993b95a7
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 30 15:20:40 2014 -0400
3235: Accept group_class="folder" as a project.
diff --git a/services/api/app/controllers/arvados/v1/groups_controller.rb b/services/api/app/controllers/arvados/v1/groups_controller.rb
index 4dc5c9b..e7d5530 100644
--- a/services/api/app/controllers/arvados/v1/groups_controller.rb
+++ b/services/api/app/controllers/arvados/v1/groups_controller.rb
@@ -64,7 +64,7 @@ class Arvados::V1::GroupsController < ApplicationController
Human, Specimen, Trait].each do |klass|
@objects = klass.readable_by(*@read_users)
if klass == Group
- @objects = @objects.where('group_class = ?', 'project')
+ @objects = @objects.where('group_class in (?)', ['project', 'folder'])
end
if opts[:owner_uuid]
conds = []
commit 45dd2c3f3db472132974aeb4fe3f0e0f4e57dd13
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 30 15:11:53 2014 -0400
3235: Show names of named collections instead of their uuids, but support searching by uuid.
diff --git a/apps/workbench/app/views/search/_choose_rows.html.erb b/apps/workbench/app/views/search/_choose_rows.html.erb
index 81d1f68..0a73a41 100644
--- a/apps/workbench/app/views/search/_choose_rows.html.erb
+++ b/apps/workbench/app/views/search/_choose_rows.html.erb
@@ -12,8 +12,12 @@
<div class="row filterable selectable" data-section-name="<%= object.class.to_s %>" data-object-uuid="<%= object.uuid %>" data-preview-href="<%= chooser_preview_url_for object %>">
<div class="col-sm-12" style="overflow-x:hidden; white-space: nowrap">
<i class="fa fa-fw <%= icon_class %>"></i>
- <% if object.respond_to?(:name) and object.name and object.name.length > 0 %>
+ <% if (name_link = @objects.links_for(object, 'name').first) %>
+ <%= name_link.name %>
+ <span style="display:none"><%= object.uuid %></span>
+ <% elsif object.respond_to?(:name) and object.name and object.name.length > 0 %>
<%= object.name %>
+ <span style="display:none"><%= object.uuid %></span>
<% else %>
unnamed - <span class="arvados-uuid"><%= object.uuid %></span>
<% end %>
commit 04cdd8c9292523aaca50ff6f41791ea54ee91e3b
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 30 15:01:33 2014 -0400
3235: Make collections show up in search results.
diff --git a/apps/workbench/app/assets/javascripts/select_modal.js b/apps/workbench/app/assets/javascripts/select_modal.js
index ee33b54..1fec3dc 100644
--- a/apps/workbench/app/assets/javascripts/select_modal.js
+++ b/apps/workbench/app/assets/javascripts/select_modal.js
@@ -72,11 +72,14 @@ $(document).on('click', '.selectable', function() {
});
}).on('click', '.chooser-show-project', function() {
var params = {};
+ var project_uuid = $(this).attr('data-project-uuid');
$(this).attr('href', '#'); // Skip normal click handler
- if ($(this).attr('data-project-uuid')) {
+ if (project_uuid) {
params = {'filters[]': JSON.stringify(['owner_uuid',
'=',
- $(this).attr('data-project-uuid')])};
+ project_uuid]),
+ project_uuid: project_uuid
+ };
}
// Use current selection as dropdown button label
$(this).
diff --git a/apps/workbench/app/controllers/search_controller.rb b/apps/workbench/app/controllers/search_controller.rb
index 2b0ad7e..31c6663 100644
--- a/apps/workbench/app/controllers/search_controller.rb
+++ b/apps/workbench/app/controllers/search_controller.rb
@@ -1,6 +1,17 @@
class SearchController < ApplicationController
def find_objects_for_index
- @objects = Group.contents(limit: @limit, offset: @offset, filters: @filters)
+ search_what = Group
+ if params[:project_uuid]
+ # Special case for "search all things in project":
+ @filters = @filters.select do |attr, operator, operand|
+ not (attr == 'owner_uuid' and operator == '=')
+ end
+ search_what = Group.find(params[:project_uuid])
+ end
+ @objects = search_what.contents(limit: @limit,
+ offset: @offset,
+ filters: @filters,
+ include_linked: true)
super
end
diff --git a/services/api/app/controllers/arvados/v1/groups_controller.rb b/services/api/app/controllers/arvados/v1/groups_controller.rb
index 6b21403..4dc5c9b 100644
--- a/services/api/app/controllers/arvados/v1/groups_controller.rb
+++ b/services/api/app/controllers/arvados/v1/groups_controller.rb
@@ -23,8 +23,8 @@ class Arvados::V1::GroupsController < ApplicationController
def contents
# Set @objects:
- load_searchable_objects(owner_uuid: @object.andand.uuid, include_linked: params[:include_linked])
-
+ load_searchable_objects(owner_uuid: @object.andand.uuid,
+ include_linked: params[:include_linked])
sql = 'link_class=? and head_uuid in (?)'
sql_params = ['name', @objects.collect(&:uuid)]
if @object
@@ -66,19 +66,23 @@ class Arvados::V1::GroupsController < ApplicationController
if klass == Group
@objects = @objects.where('group_class = ?', 'project')
end
- conds = []
- cond_params = []
if opts[:owner_uuid]
+ conds = []
+ cond_params = []
conds << "#{klass.table_name}.owner_uuid = ?"
cond_params << opts[:owner_uuid]
+ if opts[:include_linked]
+ haslink = "#{klass.table_name}.uuid IN (SELECT head_uuid FROM links WHERE link_class=#{klass.sanitize 'name'}"
+ haslink += " AND links.tail_uuid=#{klass.sanitize opts[:owner_uuid]}"
+ haslink += ")"
+ conds << haslink
+ end
+ if conds.any?
+ cond_sql = '(' + conds.join(') OR (') + ')'
+ @objects = @objects.where(cond_sql, *cond_params)
+ end
end
- if opts[:include_linked]
- conds << "#{klass.table_name}.uuid IN (SELECT head_uuid FROM links WHERE link_class=#{klass.sanitize 'name'} AND links.tail_uuid=#{klass.sanitize @object.uuid})"
- end
- if conds.any?
- cond_sql = '(' + conds.join(') OR (') + ')'
- @objects = @objects.where(cond_sql, *cond_params)
- end
+
@objects = @objects.order("#{klass.table_name}.uuid")
@limit = limit_all - all_objects.count
apply_where_limit_order_params
diff --git a/services/api/test/functional/arvados/v1/groups_controller_test.rb b/services/api/test/functional/arvados/v1/groups_controller_test.rb
index d6ac3ce..0110e65 100644
--- a/services/api/test/functional/arvados/v1/groups_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/groups_controller_test.rb
@@ -90,22 +90,24 @@ class Arvados::V1::GroupsControllerTest < ActionController::TestCase
check_project_contents_response
end
- test 'list objects across multiple projects' do
- authorize_with :project_viewer
- get :contents, {
- format: :json,
- include_linked: false,
- filters: [['uuid', 'is_a', 'arvados#specimen']]
- }
- assert_response :success
- found_uuids = json_response['items'].collect { |i| i['uuid'] }
- [[:in_aproject, true],
- [:in_asubproject, true],
- [:owned_by_private_group, false]].each do |specimen_fixture, should_find|
- if should_find
- assert_includes found_uuids, specimens(specimen_fixture).uuid, "did not find specimen fixture '#{specimen_fixture}'"
- else
- refute_includes found_uuids, specimens(specimen_fixture).uuid, "found specimen fixture '#{specimen_fixture}'"
+ [false, true].each do |include_linked|
+ test 'list objects across multiple projects' do
+ authorize_with :project_viewer
+ get :contents, {
+ format: :json,
+ include_linked: include_linked,
+ filters: [['uuid', 'is_a', 'arvados#specimen']]
+ }
+ assert_response :success
+ found_uuids = json_response['items'].collect { |i| i['uuid'] }
+ [[:in_aproject, true],
+ [:in_asubproject, true],
+ [:owned_by_private_group, false]].each do |specimen_fixture, should_find|
+ if should_find
+ assert_includes found_uuids, specimens(specimen_fixture).uuid, "did not find specimen fixture '#{specimen_fixture}'"
+ else
+ refute_includes found_uuids, specimens(specimen_fixture).uuid, "found specimen fixture '#{specimen_fixture}'"
+ end
end
end
end
commit 4b007d7c702987f3b65d0c3fec5b21dcf6ac647c
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 30 13:54:20 2014 -0400
3235: Update results as soon as search modal opens.
diff --git a/apps/workbench/app/assets/javascripts/filterable.js b/apps/workbench/app/assets/javascripts/filterable.js
index 0e9e9cb..7da461e 100644
--- a/apps/workbench/app/assets/javascripts/filterable.js
+++ b/apps/workbench/app/assets/javascripts/filterable.js
@@ -49,5 +49,5 @@ $(document).
data('filters', filters).
trigger('refresh');
}).on('ajax:complete', function() {
- $('.filterable-control').trigger('change');
+ $('.filterable-control').trigger('input');
});
commit 6790e24febd872dcf98b1356ad1d06fc69fc2915
Merge: 4aae929 20f944b
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Jul 30 13:48:52 2014 -0400
3235: Merge branch 'master' into 3235-top-nav-site-search
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