[ARVADOS] updated: 0274800af0b90207c64b6982a5b78384c9f04bf5
git at public.curoverse.com
git at public.curoverse.com
Wed May 21 11:38:42 EDT 2014
Summary of changes:
.../app/controllers/collections_controller.rb | 87 ++++++-----------
apps/workbench/app/helpers/application_helper.rb | 12 +++
.../app/views/collections/_show_jobs.html.erb | 64 -------------
.../views/collections/_show_provenance.html.erb | 84 -----------------
.../views/collections/_show_source_data.html.erb | 44 ---------
apps/workbench/app/views/collections/show.html.erb | 105 +++++++++++++++++++++
.../app/views/collections/show_file_links.html.erb | 45 ++++++---
apps/workbench/app/views/folders/show.html.erb | 60 ++++++------
.../test/functional/collections_controller_test.rb | 47 ++++++++-
services/api/test/fixtures/jobs.yml | 2 +-
services/api/test/fixtures/logs.yml | 5 +
11 files changed, 260 insertions(+), 295 deletions(-)
delete mode 100644 apps/workbench/app/views/collections/_show_jobs.html.erb
delete mode 100644 apps/workbench/app/views/collections/_show_provenance.html.erb
delete mode 100644 apps/workbench/app/views/collections/_show_source_data.html.erb
create mode 100644 apps/workbench/app/views/collections/show.html.erb
via 0274800af0b90207c64b6982a5b78384c9f04bf5 (commit)
via 22f1aef9b47f6d8eb190cfada1878d499c031625 (commit)
via 2768b056f5d99952d2d2c4ba8cd1dfbb898901e3 (commit)
via c965f26c02b0f358eccf6989e49703d173206486 (commit)
via f1a04b3e3c61cc92501d18863ccf0abb162f9855 (commit)
via 6d1b822d5a168166deb44d4256bf0abcfd618c67 (commit)
via 9cdf7a2f51489403a488c3d06cf252a36b8e4198 (commit)
from ee73fe1721723da22514b60bd639b72c059fe05b (commit)
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commit 0274800af0b90207c64b6982a5b78384c9f04bf5
Merge: 22f1aef 2768b05
Author: Brett Smith <brett at curoverse.com>
Date: Wed May 21 11:35:00 2014 -0400
Merge branch 'master' into 2764-wget-collections-wip
Conflicts:
apps/workbench/test/functional/collections_controller_test.rb
diff --cc apps/workbench/app/controllers/collections_controller.rb
index 501484f,656c063..180e1d0
--- a/apps/workbench/app/controllers/collections_controller.rb
+++ b/apps/workbench/app/controllers/collections_controller.rb
@@@ -1,9 -1,10 +1,11 @@@
class CollectionsController < ApplicationController
- skip_around_filter :thread_with_mandatory_api_token, only: [:show_file]
- skip_before_filter :find_object_by_uuid, only: [:provenance, :show_file]
- skip_before_filter :check_user_agreements, only: [:show_file]
+ skip_around_filter(:thread_with_mandatory_api_token,
+ only: [:show_file, :show_file_links])
+ skip_before_filter(:find_object_by_uuid,
+ only: [:provenance, :show_file, :show_file_links])
+ RELATION_LIMIT = 5
+
def show_pane_list
%w(Files Attributes Metadata Provenance_graph Used_by JSON API)
end
diff --cc apps/workbench/test/functional/collections_controller_test.rb
index 5fc2780,7a15161..f4e7a30
--- a/apps/workbench/test/functional/collections_controller_test.rb
+++ b/apps/workbench/test/functional/collections_controller_test.rb
@@@ -49,16 -53,66 +53,51 @@@ class CollectionsControllerTest < Actio
assert_equal([['.', 'foo', 3]], assigns(:object).files)
end
+ test "viewing collection files with a reader token" do
+ params = collection_params(:foo_file)
+ params[:reader_token] =
+ api_fixture('api_client_authorizations')['active']['api_token']
+ get(:show_file_links, params)
+ assert_response :success
+ assert_equal([['.', 'foo', 3]], assigns(:object).files)
+ assert_no_session
+ end
+
+ test "viewing a collection fetches related folders" do
+ show_collection(:foo_file, :active)
+ assert_includes(assigns(:folders).map(&:uuid),
+ api_fixture('groups')['afolder']['uuid'],
+ "controller did not find linked folder")
+ end
+
+ test "viewing a collection fetches related permissions" do
+ show_collection(:bar_file, :active)
+ assert_includes(assigns(:permissions).map(&:uuid),
+ api_fixture('links')['bar_file_readable_by_active']['uuid'],
+ "controller did not find permission link")
+ end
+
+ test "viewing a collection fetches jobs that output it" do
+ show_collection(:bar_file, :active)
+ assert_includes(assigns(:output_of).map(&:uuid),
+ api_fixture('jobs')['foobar']['uuid'],
+ "controller did not find output job")
+ end
+
+ test "viewing a collection fetches jobs that logged it" do
+ show_collection(:baz_file, :active)
+ assert_includes(assigns(:log_of).map(&:uuid),
+ api_fixture('jobs')['foobar']['uuid'],
+ "controller did not find logger job")
+ end
+
+ test "viewing a collection fetches logs about it" do
+ show_collection(:foo_file, :active)
+ assert_includes(assigns(:logs).map(&:uuid),
+ api_fixture('logs')['log4']['uuid'],
+ "controller did not find related log")
+ end
+
- test "viewing a collection with a reader token" do
- params = collection_params(:foo_file)
- params[:reader_tokens] =
- [api_fixture('api_client_authorizations')['active']['api_token']]
- show_collection(params)
- assert_equal([['.', 'foo', 3]], assigns(:object).files)
- assert_no_session
- end
-
- test "viewing the index with a reader token" do
- params = {reader_tokens:
- [api_fixture('api_client_authorizations')['spectator']['api_token']]
- }
- get(:index, params)
- assert_response :success
- assert_no_session
- listed_collections = assigns(:collections).map { |c| c.uuid }
- assert_includes(listed_collections,
- api_fixture('collections')['bar_file']['uuid'],
- "spectator reader token didn't list bar file")
- refute_includes(listed_collections,
- api_fixture('collections')['foo_file']['uuid'],
- "spectator reader token listed foo file")
- end
-
test "getting a file from Keep" do
params = collection_params(:foo_file, 'foo')
sess = session_for(:active)
commit 22f1aef9b47f6d8eb190cfada1878d499c031625
Author: Brett Smith <brett at curoverse.com>
Date: Wed May 21 11:30:44 2014 -0400
2764: Add information to the Collection download page.
diff --git a/apps/workbench/app/views/collections/show_file_links.html.erb b/apps/workbench/app/views/collections/show_file_links.html.erb
index 9d61a6a..efc1d01 100644
--- a/apps/workbench/app/views/collections/show_file_links.html.erb
+++ b/apps/workbench/app/views/collections/show_file_links.html.erb
@@ -1,27 +1,43 @@
<!DOCTYPE html>
<html>
+<% coll_name = (@object.name =~ /\S/) ? @object.name : "Collection #{@object.uuid}" %>
+<% link_opts = {controller: 'collections', action: 'show_file',
+ uuid: @object.uuid, reader_token: params[:reader_token]} %>
<head>
<meta charset="utf-8">
<title>
- <% if content_for? :page_title %>
- <%= yield :page_title %> / <%= Rails.configuration.site_name %>
- <% else %>
- <%= Rails.configuration.site_name %>
- <% end %>
+ <%= coll_name %> / <%= Rails.configuration.site_name %>
</title>
<meta name="description" content="">
<meta name="author" content="">
<meta name="robots" content="NOINDEX">
+ <style type="text/css">
+body {
+ margin: 1.5em;
+}
+pre {
+ background-color: #D9EDF7;
+ border-radius: .25em;
+ padding: .75em;
+ overflow: auto;
+}
+ </style>
</head>
<body>
-<% content_for :page_title do %>
- <%= (@object.respond_to?(:properties) ? @object.properties[:page_title] : nil) ||
- @object.friendly_link_name %>
-<% end %>
+
+<h1><%= coll_name %></h1>
+
+<p>This collection of data files is being shared with you through
+Arvados. You can download individual files listed below. To download
+the entire collection with wget, try:</p>
+
+<pre>$ wget -m -np -nH --cut-dirs=3 <%=
+ url_for(link_opts.merge(action: 'show_file_links', only_path: false))
+ %></pre>
+
+<h2>File Listing</h2>
<% if @object.andand.files.andand.any? %>
- <% link_opts = {controller: 'collections', action: 'show_file',
- uuid: @object.uuid, reader_token: params[:reader_token]} %>
<ul>
<% @object.files.map { |spec|
CollectionsHelper::file_path(spec)
@@ -32,5 +48,12 @@
<% else %>
<p>No files in this collection.</p>
<% end %>
+
+<h2>About Arvados</h2>
+
+<p>Arvados is a free and open source software bioinformatics platform.
+To learn more, visit arvados.org.
+Arvados is not responsible for the files listed on this page.</p>
+
</body>
</html>
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