[ARVADOS] updated: 406dd530310ee83a70550c9d541e4e951ce5c546

git at public.curoverse.com git at public.curoverse.com
Wed Aug 6 10:10:02 EDT 2014


Summary of changes:
 apps/workbench/Gemfile                             |    1 +
 apps/workbench/Gemfile.lock                        |    2 +
 .../app/assets/stylesheets/collections.css.scss    |    7 +-
 .../app/controllers/application_controller.rb      |    4 +-
 .../app/controllers/projects_controller.rb         |   26 +
 apps/workbench/app/controllers/users_controller.rb |   67 +
 apps/workbench/app/helpers/application_helper.rb   |    1 +
 apps/workbench/app/views/application/404.html.erb  |    7 +-
 .../app/views/application/_choose.html.erb         |    2 +-
 .../workbench/app/views/application/_choose.js.erb |    1 +
 .../workbench/app/views/application/index.html.erb |    2 +
 .../app/views/collections/_show_files.html.erb     |    7 +-
 apps/workbench/app/views/layouts/body.html.erb     |   23 +-
 .../app/views/projects/_show_tab_contents.html.erb |   13 +
 .../app/views/search/_choose_rows.html.erb         |    2 +-
 .../app/views/users/_add_ssh_key_popup.html.erb    |   38 +
 .../app/views/users/_manage_account.html.erb       |   52 +
 .../app/views/users/_manage_current_token.html.erb |   13 +
 .../app/views/users/_manage_repositories.html.erb  |   40 +
 .../app/views/users/_manage_ssh_keys.html.erb      |   55 +
 .../views/users/_manage_virtual_machines.html.erb  |   50 +
 .../app/views/users/_setup_popup.html.erb          |    2 +-
 apps/workbench/app/views/users/add_ssh_key.js.erb  |    2 +
 .../app/views/users/add_ssh_key_popup.js.erb       |    8 +
 .../app/views/users/manage_account.html.erb        |    1 +
 apps/workbench/config/application.yml.example      |    2 +-
 apps/workbench/config/routes.rb                    |    4 +
 .../test/integration/pipeline_templates_test.rb    |   15 +
 doc/_config.yml                                    |   33 +-
 doc/_includes/_ssh_addkey.liquid                   |   10 +-
 .../_tutorial_bwa_sortsam_pipeline.liquid          |   65 +
 doc/_includes/_tutorial_expectations.liquid        |    2 +-
 doc/_layouts/default.html.liquid                   |    6 +-
 .../schema/PipelineTemplate.html.textile.liquid    |    6 +-
 doc/css/font-awesome.css                           | 1566 ++++++++++++++++++++
 doc/css/nav-list.css                               |    7 +-
 doc/fonts/FontAwesome.otf                          |  Bin 0 -> 75188 bytes
 doc/fonts/fontawesome-webfont.eot                  |  Bin 0 -> 72449 bytes
 doc/fonts/fontawesome-webfont.svg                  |  504 +++++++
 doc/fonts/fontawesome-webfont.ttf                  |  Bin 0 -> 141564 bytes
 doc/fonts/fontawesome-webfont.woff                 |  Bin 0 -> 83760 bytes
 doc/images/ssh-adding-public-key.png               |  Bin 17463 -> 15117 bytes
 doc/install/install-api-server.html.textile.liquid |    6 +-
 doc/install/install-docker.html.textile.liquid     |   49 +-
 doc/user/copying/copying.html.textile.liquid       |    2 +-
 .../examples/crunch-examples.html.textile.liquid   |    2 +-
 .../check-environment.html.textile.liquid          |    4 +-
 .../getting_started/workbench.html.textile.liquid  |   10 +-
 doc/user/index.html.textile.liquid                 |   29 +-
 doc/user/reference/api-tokens.html.textile.liquid  |   39 +-
 doc/user/reference/sdk-cli.html.textile.liquid     |    2 +-
 doc/user/topics/keep.html.textile.liquid           |    8 +-
 ...nning-pipeline-command-line.html.textile.liquid |  117 +-
 .../topics/tutorial-job-debug.html.textile.liquid  |   27 +-
 .../topics/tutorial-parallel.html.textile.liquid   |   24 +-
 .../tutorials/intro-crunch.html.textile.liquid     |   17 +-
 .../running-external-program.html.textile.liquid   |   79 +-
 .../tutorial-firstscript.html.textile.liquid       |   61 +-
 .../tutorial-keep-get.html.textile.liquid          |   47 +
 .../tutorial-keep-mount.html.textile.liquid        |   32 +
 .../tutorials/tutorial-keep.html.textile.liquid    |  161 +-
 .../tutorial-new-pipeline.html.textile.liquid      |   63 +-
 ...tutorial-pipeline-workbench.html.textile.liquid |   40 +-
 docker/api/omniauth.rb.in                          |    6 +-
 docker/arvdock                                     |   10 +-
 docker/build.sh                                    |   11 +-
 docker/build_tools/Makefile                        |  136 +-
 docker/build_tools/build.rb                        |    8 +-
 docker/build_tools/config.rb                       |   20 +-
 docker/config.yml.example                          |   15 +-
 docker/keep/Dockerfile                             |    9 +-
 docker/keep/keep_signing_secret.in                 |    1 +
 docker/keep/run-keep.in                            |   11 +
 docker/workbench/Dockerfile                        |   12 +-
 docker/workbench/workbench_rails_env.in            |    1 +
 sdk/cli/bin/crunch-job                             |   15 +-
 sdk/python/arvados/api.py                          |   82 +-
 sdk/python/arvados/errors.py                       |   11 +
 sdk/python/arvados/stream.py                       |    2 +-
 sdk/python/tests/test_api.py                       |   76 +
 sdk/python/tests/test_collections.py               |   20 +
 services/api/Gemfile                               |    1 +
 services/api/Gemfile.lock                          |    2 +
 .../app/controllers/arvados/v1/jobs_controller.rb  |   20 +-
 services/api/app/models/arvados_model.rb           |    6 +
 services/api/app/models/authorized_key.rb          |    9 +-
 services/api/config/application.default.yml        |   24 +-
 services/api/config/application.yml.example        |   39 +-
 .../test/fixtures/api_client_authorizations.yml    |    6 +
 services/api/test/fixtures/links.yml               |   46 +
 services/api/test/fixtures/users.yml               |   11 +
 .../arvados/v1/groups_controller_test.rb           |   33 +-
 .../arvados/v1/job_reuse_controller_test.rb        |   21 +
 services/fuse/tests/test_mount.py                  |    1 +
 services/keep/src/keep/handler_test.go             |  144 +-
 services/keep/src/keep/handlers.go                 |   97 ++
 services/keep/src/keep/volume.go                   |   11 +-
 services/keep/src/keep/volume_unix.go              |   37 +-
 98 files changed, 3646 insertions(+), 773 deletions(-)
 create mode 100644 apps/workbench/app/views/users/_add_ssh_key_popup.html.erb
 create mode 100644 apps/workbench/app/views/users/_manage_account.html.erb
 create mode 100644 apps/workbench/app/views/users/_manage_current_token.html.erb
 create mode 100644 apps/workbench/app/views/users/_manage_repositories.html.erb
 create mode 100644 apps/workbench/app/views/users/_manage_ssh_keys.html.erb
 create mode 100644 apps/workbench/app/views/users/_manage_virtual_machines.html.erb
 create mode 100644 apps/workbench/app/views/users/add_ssh_key.js.erb
 create mode 100644 apps/workbench/app/views/users/add_ssh_key_popup.js.erb
 create mode 100644 apps/workbench/app/views/users/manage_account.html.erb
 create mode 100644 apps/workbench/test/integration/pipeline_templates_test.rb
 create mode 100644 doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
 create mode 100644 doc/css/font-awesome.css
 create mode 100644 doc/fonts/FontAwesome.otf
 create mode 100755 doc/fonts/fontawesome-webfont.eot
 create mode 100755 doc/fonts/fontawesome-webfont.svg
 create mode 100755 doc/fonts/fontawesome-webfont.ttf
 create mode 100755 doc/fonts/fontawesome-webfont.woff
 create mode 100644 doc/user/tutorials/tutorial-keep-get.html.textile.liquid
 create mode 100644 doc/user/tutorials/tutorial-keep-mount.html.textile.liquid
 create mode 100644 docker/keep/keep_signing_secret.in
 create mode 100755 docker/keep/run-keep.in
 create mode 100644 docker/workbench/workbench_rails_env.in
 create mode 100644 sdk/python/tests/test_api.py

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commit 406dd530310ee83a70550c9d541e4e951ce5c546
Author: Tom Clegg <tom at curoverse.com>
Date:   Wed Aug 6 10:09:54 2014 -0400

    3235: Do not highlight file rows in preview pane. Tone down indentation.

diff --git a/apps/workbench/app/assets/stylesheets/collections.css.scss b/apps/workbench/app/assets/stylesheets/collections.css.scss
index 35c2249..f717203 100644
--- a/apps/workbench/app/assets/stylesheets/collections.css.scss
+++ b/apps/workbench/app/assets/stylesheets/collections.css.scss
@@ -18,7 +18,7 @@ ul.collection_files li {
   padding: 1px;  /* Replaced by border for :hover */
 }
 
-.collection_files_row:hover {
+.hover-highlight .collection_files_row:hover {
   background-color: #D9EDF7;
   padding: 0px;
   border: 1px solid #BCE8F1;
@@ -46,6 +46,11 @@ ul.collection_files li {
   width: 1.6em;
 }
 
+/* indent less inside preview pane */
+.modal-dialog-preview-pane ul.collection_files {
+    padding-left: 0.5em;
+}
+
 /*
   "active" and "inactive" colors are too similar for a toggle switch
   in the default bootstrap theme.
diff --git a/apps/workbench/app/views/collections/_show_files.html.erb b/apps/workbench/app/views/collections/_show_files.html.erb
index 8576d40..ef99394 100644
--- a/apps/workbench/app/views/collections/_show_files.html.erb
+++ b/apps/workbench/app/views/collections/_show_files.html.erb
@@ -1,3 +1,5 @@
+<% if !defined? no_checkboxes then no_checkboxes = false end %>
+
 <% content_for :tab_line_buttons do %>
 <span style="padding-left: 1em">Collection storage status:</span>
 <%= render partial: 'toggle_persist', locals: { uuid: @object.uuid, current_state: (@is_persistent ? 'persistent' : 'cache') } %>
@@ -7,7 +9,8 @@
 <% if file_tree.nil? or file_tree.empty? %>
   <p>This collection is empty.</p>
 <% else %>
-  <ul id="collection_files" class="collection_files">
+  <ul id="collection_files"
+      class="collection_files <%= 'hover-highlight' unless no_checkboxes %>">
   <% dirstack = [file_tree.first.first] %>
   <% file_tree.each_with_index do |(dirname, filename, size), index| %>
     <% file_path = CollectionsHelper::file_path([dirname, filename]) %>
@@ -27,7 +30,7 @@
        <div class="collection_files_row">
         <div class="collection_files_buttons pull-right">
           <%= raw(human_readable_bytes_html(size)) %>
-          <% if !defined? no_checkboxes or !no_checkboxes %>
+          <% unless no_checkboxes %>
           <%= check_box_tag 'uuids[]', "#{@object.uuid}/#{file_path}", false, {
                 :class => 'persistent-selection',
                 :friendly_type => "File",

-----------------------------------------------------------------------


hooks/post-receive
-- 




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