[ARVADOS] updated: dc45eea849bb9371b778c7401bc522c82ee84021
git at public.curoverse.com
git at public.curoverse.com
Thu Jul 3 20:50:41 EDT 2014
Summary of changes:
.../app/controllers/projects_controller.rb | 2 +-
.../app/views/application/_content_layout.html.erb | 15 ++-
.../_show_advanced_cli_example.html.erb | 4 +
.../_show_advanced_curl_example.html.erb | 1 +
.../_show_advanced_python_example.html.erb | 1 +
.../app/views/projects/_index_projects.html.erb | 11 +-
.../app/views/projects/_show_contents.html.erb | 122 ---------------------
.../views/projects/_show_data_collections.html.erb | 57 ++++++++++
.../projects/_show_jobs_and_pipelines.html.erb | 1 +
.../views/projects/_show_other_objects.html.erb | 1 +
.../projects/_show_pipeline_templates.html.erb | 1 +
.../app/views/projects/_show_subprojects.html.erb | 1 +
.../app/views/projects/_show_tab_contents.html.erb | 58 ++++++++++
doc/api/methods/jobs.html.textile.liquid | 20 ++++
doc/install/install-docker.html.textile.liquid | 47 +++++++-
docker/mkimage-debootstrap.sh | 2 +
sdk/cli/bin/arv-run-pipeline-instance | 16 +--
sdk/python/bin/arv-ls | 3 +-
sdk/python/tests/test_arv_put.py | 5 +-
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 8 +-
.../app/controllers/arvados/v1/links_controller.rb | 26 +++++
services/api/app/models/arvados_model.rb | 19 ++++
services/api/app/models/job.rb | 4 +
services/api/app/models/link.rb | 36 +++---
services/api/app/models/user.rb | 11 ++
services/api/config/routes.rb | 1 +
services/api/test/integration/permissions_test.rb | 89 +++++++++++++++
services/api/test/unit/link_test.rb | 4 +
services/api/test/unit/permission_test.rb | 103 +++++++++++++++++
30 files changed, 506 insertions(+), 165 deletions(-)
delete mode 100644 apps/workbench/app/views/projects/_show_contents.html.erb
create mode 100644 apps/workbench/app/views/projects/_show_data_collections.html.erb
create mode 100644 apps/workbench/app/views/projects/_show_jobs_and_pipelines.html.erb
create mode 100644 apps/workbench/app/views/projects/_show_other_objects.html.erb
create mode 100644 apps/workbench/app/views/projects/_show_pipeline_templates.html.erb
create mode 100644 apps/workbench/app/views/projects/_show_subprojects.html.erb
create mode 100644 apps/workbench/app/views/projects/_show_tab_contents.html.erb
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commit dc45eea849bb9371b778c7401bc522c82ee84021
Author: radhika <radhika at curoverse.com>
Date: Thu Jul 3 20:18:36 2014 -0400
3140: add partials for all the content tabs
diff --git a/apps/workbench/app/views/projects/_show_contents.html.erb b/apps/workbench/app/views/projects/_show_data_collections.html.erb
similarity index 56%
rename from apps/workbench/app/views/projects/_show_contents.html.erb
rename to apps/workbench/app/views/projects/_show_data_collections.html.erb
index d6114ef..a8b58b8 100644
--- a/apps/workbench/app/views/projects/_show_contents.html.erb
+++ b/apps/workbench/app/views/projects/_show_data_collections.html.erb
@@ -54,49 +54,4 @@
<% end %>
<% end %>
-<div class="selection-action-container">
- <div class="row">
- <div class="col-sm-5">
- <div class="btn-group btn-group-sm">
- <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">Selection... <i class="fa fa-fw fa-long-arrow-down "></i></button>
- <ul class="dropdown-menu" role="menu">
- <li><%= link_to "Compare selected", '#',
- 'data-href' => compare_pipeline_instances_path,
- 'data-selection-param-name' => 'uuids[]',
- 'data-selection-action' => 'compare'
- %></li>
- <li><%= link_to "Remove selected", '#',
- 'data-href' => url_for(action: :remove_items),
- 'data-selection-param-name' => 'item_uuids[]',
- 'data-selection-action' => 'remove',
- 'data-remote' => true,
- 'method' => 'delete'
- %></li>
- </ul>
- </div>
- </div>
- <div class="col-sm-4 pull-right">
- <input type="text" class="form-control filterable-control" placeholder="Search project contents" data-filterable-target="table.arv-index.arv-project-contents tbody"/>
- </div>
- </div>
-
- <table class="table table-condensed table-fixedlayout arv-index arv-project-contents" style="overflow-x: hidden">
- <colgroup>
- <col width="40%" />
- <col width="60%" />
- </colgroup>
- <tbody data-infinite-scroller="#Contents-scroll" data-infinite-content-href="<%= url_for(format: :json, partial: :contents_rows, offset: next_page_offset) if next_page_offset %>">
- <%= render partial: 'show_contents_rows', locals: {project: @object, objects_and_names: @objects_and_names} %>
- </tbody>
- <thead>
- <tr>
- <th>
- </th>
- <th>
- description
- </th>
- </tr>
- </thead>
- </table>
-
-</div>
+<%= render partial: 'show_tab_contents', locals: {project: @object, objects_and_names: @objects_and_names, data_kind: ['arvados#collection']} %>
diff --git a/apps/workbench/app/views/projects/_show_jobs_and_pipelines.html.erb b/apps/workbench/app/views/projects/_show_jobs_and_pipelines.html.erb
new file mode 100644
index 0000000..619e51b
--- /dev/null
+++ b/apps/workbench/app/views/projects/_show_jobs_and_pipelines.html.erb
@@ -0,0 +1 @@
+<%= render partial: 'show_tab_contents', locals: {project: @object, objects_and_names: @objects_and_names, data_kind: ['arvados#job', 'arvados#pipelineInstance']} %>
diff --git a/apps/workbench/app/views/projects/_show_other_objects.html.erb b/apps/workbench/app/views/projects/_show_other_objects.html.erb
new file mode 100644
index 0000000..7a87413
--- /dev/null
+++ b/apps/workbench/app/views/projects/_show_other_objects.html.erb
@@ -0,0 +1 @@
+<%= render partial: 'show_tab_contents', locals: {project: @object, objects_and_names: @objects_and_names, data_kind: []} %>
diff --git a/apps/workbench/app/views/projects/_show_pipeline_templates.html.erb b/apps/workbench/app/views/projects/_show_pipeline_templates.html.erb
new file mode 100644
index 0000000..26082c0
--- /dev/null
+++ b/apps/workbench/app/views/projects/_show_pipeline_templates.html.erb
@@ -0,0 +1 @@
+<%= render partial: 'show_tab_contents', locals: {project: @object, objects_and_names: @objects_and_names, data_kind: ['arvados#pipelineTemplate']} %>
diff --git a/apps/workbench/app/views/projects/_show_subprojects.html.erb b/apps/workbench/app/views/projects/_show_subprojects.html.erb
new file mode 100644
index 0000000..cd9c3e6
--- /dev/null
+++ b/apps/workbench/app/views/projects/_show_subprojects.html.erb
@@ -0,0 +1 @@
+<%= render partial: 'show_tab_contents', locals: {project: @object, objects_and_names: @objects_and_names, data_kind: ['arvados#group']} %>
diff --git a/apps/workbench/app/views/projects/_show_tab_contents.html.erb b/apps/workbench/app/views/projects/_show_tab_contents.html.erb
new file mode 100644
index 0000000..e95ba72
--- /dev/null
+++ b/apps/workbench/app/views/projects/_show_tab_contents.html.erb
@@ -0,0 +1,58 @@
+<div class="selection-action-container">
+ <div class="row">
+ <div class="col-sm-5">
+ <div class="btn-group btn-group-sm">
+ <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">Selection... <i class="fa fa-fw fa-long-arrow-down "></i></button>
+ <ul class="dropdown-menu" role="menu">
+ <li><%= link_to "Compare selected", '#',
+ 'data-href' => compare_pipeline_instances_path,
+ 'data-selection-param-name' => 'uuids[]',
+ 'data-selection-action' => 'compare'
+ %></li>
+ <li><%= link_to "Remove selected", '#',
+ 'data-href' => url_for(action: :remove_items),
+ 'data-selection-param-name' => 'item_uuids[]',
+ 'data-selection-action' => 'remove',
+ 'data-remote' => true,
+ 'method' => 'delete'
+ %></li>
+ </ul>
+ </div>
+ </div>
+ <div class="col-sm-4 pull-right">
+ <input type="text" class="form-control filterable-control" placeholder="Search project contents" data-filterable-target="table.arv-index.arv-project-contents tbody"/>
+ </div>
+ </div>
+
+ <%
+ selected_objects_and_names = []
+ specific_data_kinds = ['arvados#collection', 'arvados#group', 'arvados#job', 'arvados#pipelineInstance', 'arvados#pipelineTemplate']
+ @objects_and_names.each do |object, name_link|
+ if !data_kind.any? && !specific_data_kinds.include?(object.kind)
+ selected_objects_and_names << [object, name_link]
+ elsif data_kind.include?(object.kind)
+ selected_objects_and_names << [object, name_link]
+ end
+ end
+ %>
+
+ <table class="table table-condensed table-fixedlayout arv-index arv-project-contents" style="overflow-x: hidden">
+ <colgroup>
+ <col width="40%" />
+ <col width="60%" />
+ </colgroup>
+ <tbody data-infinite-scroller="#Contents-scroll" data-infinite-content-href="<%= url_for(format: :json, partial: :contents_rows, offset: next_page_offset) if next_page_offset %>">
+ <%= render partial: 'show_contents_rows', locals: {project: @object, objects_and_names: selected_objects_and_names} %>
+ </tbody>
+ <thead>
+ <tr>
+ <th>
+ </th>
+ <th>
+ description
+ </th>
+ </tr>
+ </thead>
+ </table>
+
+</div>
commit 01af85ef744203ffb1d8b81df78b9db910b0b2da
Author: radhika <radhika at curoverse.com>
Date: Thu Jul 3 20:03:37 2014 -0400
oops
diff --git a/apps/workbench/app/views/projects/_show_contents.html.erb b/apps/workbench/app/views/projects/_show_contents.html.erb
index fdc972d..d6114ef 100644
--- a/apps/workbench/app/views/projects/_show_contents.html.erb
+++ b/apps/workbench/app/views/projects/_show_contents.html.erb
@@ -86,7 +86,6 @@
<col width="60%" />
</colgroup>
<tbody data-infinite-scroller="#Contents-scroll" data-infinite-content-href="<%= url_for(format: :json, partial: :contents_rows, offset: next_page_offset) if next_page_offset %>">
-<% puts "\n**********objects_and_names in contents page = #{@objects_and_names}" %>
<%= render partial: 'show_contents_rows', locals: {project: @object, objects_and_names: @objects_and_names} %>
</tbody>
<thead>
diff --git a/apps/workbench/app/views/projects/_show_contents_rows.html.erb b/apps/workbench/app/views/projects/_show_contents_rows.html.erb
index 863a57e..b690a1b 100644
--- a/apps/workbench/app/views/projects/_show_contents_rows.html.erb
+++ b/apps/workbench/app/views/projects/_show_contents_rows.html.erb
@@ -1,4 +1,3 @@
-<% puts "\n***************** IN SHOW CONTENT ROWS objects_and_names = #{objects_and_names.inspect} " %>
<% objects_and_names.each do |object, name_link| %>
<% name_object = (object.respond_to?(:name) || !name_link) ? object : name_link %>
<tr class="filterable"
commit 68f12bfd1ca6612338ff65106f404019a28d0cd3
Merge: b7931c2 f88096f
Author: radhika <radhika at curoverse.com>
Date: Thu Jul 3 16:55:43 2014 -0400
Merge branch 'master' into 3140-project-content-tabs
commit b7931c244d591af71c8e631e0b15752f652ae11c
Author: radhika <radhika at curoverse.com>
Date: Thu Jul 3 16:43:38 2014 -0400
3140: add Other_objects to pane list
diff --git a/apps/workbench/app/controllers/projects_controller.rb b/apps/workbench/app/controllers/projects_controller.rb
index 1a062f2..01ab89b 100644
--- a/apps/workbench/app/controllers/projects_controller.rb
+++ b/apps/workbench/app/controllers/projects_controller.rb
@@ -8,7 +8,7 @@ class ProjectsController < ApplicationController
end
def show_pane_list
- %w(Data_collections Jobs_and_pipelines Pipeline_templates Subprojects Permissions Advanced)
+ %w(Data_collections Jobs_and_pipelines Pipeline_templates Subprojects Other_objects Permissions Advanced)
end
def remove_item
commit 81efb09c62d3289b8be5f7268ee6caab8e7fecb8
Author: radhika <radhika at curoverse.com>
Date: Thu Jul 3 10:16:34 2014 -0400
3140: add additional content tabs to pane list
diff --git a/apps/workbench/app/controllers/projects_controller.rb b/apps/workbench/app/controllers/projects_controller.rb
index 91d6e8a..1a062f2 100644
--- a/apps/workbench/app/controllers/projects_controller.rb
+++ b/apps/workbench/app/controllers/projects_controller.rb
@@ -8,7 +8,7 @@ class ProjectsController < ApplicationController
end
def show_pane_list
- %w(Contents Permissions Advanced)
+ %w(Data_collections Jobs_and_pipelines Pipeline_templates Subprojects Permissions Advanced)
end
def remove_item
diff --git a/apps/workbench/app/views/projects/_show_contents.html.erb b/apps/workbench/app/views/projects/_show_contents.html.erb
index d6114ef..fdc972d 100644
--- a/apps/workbench/app/views/projects/_show_contents.html.erb
+++ b/apps/workbench/app/views/projects/_show_contents.html.erb
@@ -86,6 +86,7 @@
<col width="60%" />
</colgroup>
<tbody data-infinite-scroller="#Contents-scroll" data-infinite-content-href="<%= url_for(format: :json, partial: :contents_rows, offset: next_page_offset) if next_page_offset %>">
+<% puts "\n**********objects_and_names in contents page = #{@objects_and_names}" %>
<%= render partial: 'show_contents_rows', locals: {project: @object, objects_and_names: @objects_and_names} %>
</tbody>
<thead>
diff --git a/apps/workbench/app/views/projects/_show_contents_rows.html.erb b/apps/workbench/app/views/projects/_show_contents_rows.html.erb
index b690a1b..863a57e 100644
--- a/apps/workbench/app/views/projects/_show_contents_rows.html.erb
+++ b/apps/workbench/app/views/projects/_show_contents_rows.html.erb
@@ -1,3 +1,4 @@
+<% puts "\n***************** IN SHOW CONTENT ROWS objects_and_names = #{objects_and_names.inspect} " %>
<% objects_and_names.each do |object, name_link| %>
<% name_object = (object.respond_to?(:name) || !name_link) ? object : name_link %>
<tr class="filterable"
commit 257119b9ef8e3d3fdd27dbabe65fac422ae97b95
Author: radhika <radhika at curoverse.com>
Date: Thu Jul 3 08:53:48 2014 -0400
3140: Move tab line buttons, remove show filtering widget
diff --git a/apps/workbench/app/views/application/_content_layout.html.erb b/apps/workbench/app/views/application/_content_layout.html.erb
index 426a497..c8e3827 100644
--- a/apps/workbench/app/views/application/_content_layout.html.erb
+++ b/apps/workbench/app/views/application/_content_layout.html.erb
@@ -1,6 +1,13 @@
<%= content_for :content_top %>
-<br clear="all" />
-<div class="pull-right">
- <%= content_for :tab_line_buttons %>
-</div>
+ <% if @object and @object.is_a?(Group) and @object.group_class.in?(['project','folder']) %>
+ <div class="pull-right">
+ <%= content_for :tab_line_buttons %>
+ </div>
+ <br clear="all" />
+<% else %>
+ <br clear="all" />
+ <div class="pull-right">
+ <%= content_for :tab_line_buttons %>
+ </div>
+<% end %>
<%= content_for :tab_panes %>
diff --git a/apps/workbench/app/views/projects/_show_contents.html.erb b/apps/workbench/app/views/projects/_show_contents.html.erb
index c3d509f..d6114ef 100644
--- a/apps/workbench/app/views/projects/_show_contents.html.erb
+++ b/apps/workbench/app/views/projects/_show_contents.html.erb
@@ -58,11 +58,7 @@
<div class="row">
<div class="col-sm-5">
<div class="btn-group btn-group-sm">
- <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">Selection...</button>
- <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">
- <span class="caret"></span>
- <span class="sr-only">Toggle Dropdown</span>
- </button>
+ <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">Selection... <i class="fa fa-fw fa-long-arrow-down "></i></button>
<ul class="dropdown-menu" role="menu">
<li><%= link_to "Compare selected", '#',
'data-href' => compare_pipeline_instances_path,
@@ -79,23 +75,7 @@
</ul>
</div>
</div>
- <div class="col-sm-3">
- <form class="form-inline" role="form">
- Show:
- <select class="form-control form-control-sm filterable-control" data-filterable-attribute="data-kind" data-filterable-target="table.arv-index.arv-project-contents tbody">
- <option value="">Everything</option>
- <option value="arvados#collection">Data</option>
- <option value="arvados#pipelineInstance arvados#job">Compute jobs</option>
- <option value="arvados#pipelineTemplate">Pipelines</option>
- <!--
- <option value="arvados#specimen">Specimens</option>
- <option value="arvados#human">Humans</option>
- <option value="arvados#trait">Traits</option>
- -->
- </select>
- </form>
- </div>
- <div class="col-sm-4">
+ <div class="col-sm-4 pull-right">
<input type="text" class="form-control filterable-control" placeholder="Search project contents" data-filterable-target="table.arv-index.arv-project-contents tbody"/>
</div>
</div>
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