source 'https://rubygems.org'
gem 'rails', '~> 4.1.0'
-gem 'arvados', '>= 0.1.20150413172135'
+gem 'arvados', '>= 0.1.20150421171838'
gem 'sqlite3'
andand (1.3.3)
angularjs-rails (1.3.8)
arel (5.0.1.20140414130214)
- arvados (0.1.20150413172135)
+ arvados (0.1.20150421171838)
activesupport (>= 3.2.13)
andand (~> 1.3, >= 1.3.3)
google-api-client (~> 0.6.3, >= 0.6.3)
RedCloth
andand
angularjs-rails
- arvados (>= 0.1.20150413172135)
+ arvados (>= 0.1.20150421171838)
bootstrap-sass (~> 3.1.0)
bootstrap-tab-history-rails
bootstrap-x-editable-rails
{
:name => 'Subprojects',
:filters => [%w(uuid is_a arvados#group)]
- } if current_user
+ }
pane_list <<
{
:name => 'Other_objects',
if opts[:no_link] or (resource_class == User && !current_user)
raw(link_name)
else
- (link_to raw(link_name), { controller: resource_class.to_s.tableize, action: 'show', id: ((opts[:name_link].andand.uuid) || link_uuid) }, style_opts) + raw(tags)
+ controller_class = resource_class.to_s.tableize
+ if controller_class.eql?('groups') and object.andand.group_class.eql?('project')
+ controller_class = 'projects'
+ end
+ (link_to raw(link_name), { controller: controller_class, action: 'show', id: ((opts[:name_link].andand.uuid) || link_uuid) }, style_opts) + raw(tags)
end
else
# just return attrvalue if it is not recognizable as an Arvados object or uuid.
</div>
<div class="modal-footer">
- <button class="btn btn-default" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">Cancel</button>
+ <button type="button" class="btn btn-default" onClick="reset_form()" data-dismiss="modal" aria-hidden="true">Cancel</button>
<button type="submit" class="btn btn-primary" autofocus>Submit</button>
</div>
assert_selector 'a', text: 'Data collections'
assert_selector 'a', text: 'Jobs and pipelines'
assert_selector 'a', text: 'Pipeline templates'
+ assert_selector 'a', text: 'Subprojects'
assert_selector 'a', text: 'Advanced'
- assert_no_selector 'a', text: 'Subprojects'
assert_no_selector 'a', text: 'Other objects'
assert_no_selector 'button', text: 'Add data'
assert_no_selector 'a', text: 'Run this pipeline'
end
+ test "anonymous user accesses subprojects tab in shared project" do
+ visit PUBLIC_PROJECT + '#Subprojects'
+
+ assert_text 'Subproject in anonymous accessible project'
+
+ within first('tr[data-kind="arvados#group"]') do
+ click_link 'Show'
+ end
+
+ # in subproject
+ assert_text 'Description for subproject in anonymous accessible project'
+ end
+
[
['pipeline_in_publicly_accessible_project', true],
['pipeline_in_publicly_accessible_project_but_other_objects_elsewhere', false],
<div class="container-fluid">
<div class="row">
- <div class="col-sm-5">
+ <div class="col-sm-6">
+ <p><strong>What is Arvados</strong>
<p><a href="https://arvados.org/">Arvados</a> enables you to quickly begin using cloud computing resources in your data science work. It allows you to track your methods and datasets, share them securely, and easily re-run analyses.
</p>
- <p><strong>News</strong>: Read our <a href="https://arvados.org/projects/arvados/blogs">blog updates</a> or look through our <a href="https://arvados.org/projects/arvados/activity">recent developer activity</a>.
+ <p><strong>News</strong>
+ <p>Read our <a href="https://arvados.org/projects/arvados/blogs">blog updates</a> or look through our <a href="https://arvados.org/projects/arvados/activity">recent developer activity</a>.
</p>
- <p><strong>Questions?</strong> Email <a href="http://lists.arvados.org/mailman/listinfo/arvados">the mailing list</a>, or chat with us on IRC: <a href="irc://irc.oftc.net:6667/#arvados">#arvados</a> @ OFTC (you can <a href="https://webchat.oftc.net/?channels=arvados">join in your browser</a>).
+ <p><strong>Questions?</strong></p>
+ <p>Email <a href="http://lists.arvados.org/mailman/listinfo/arvados">the mailing list</a>, or chat with us on IRC: <a href="irc://irc.oftc.net:6667/#arvados">#arvados</a> @ OFTC (you can <a href="https://webchat.oftc.net/?channels=arvados">join in your browser</a>).
</p>
- <p><strong>Want to contribute?</strong> Check out our <a href="https://arvados.org/projects/arvados">developer site</a>. We're open source, check out our code on <a href="https://github.com/curoverse/arvados">github</a>.
+ <p><strong>Want to contribute?</strong></p>
+ <p>Check out our <a href="https://arvados.org/projects/arvados">developer site</a>. We're open source, check out our code on <a href="https://github.com/curoverse/arvados">github</a>.
</p>
- <p><strong>License</strong>: Arvados is under the copyleft <a href="{{ site.baseurl }}/user/copying/agpl-3.0.html">GNU AGPL v3</a>, with our SDKs under <a href="{{ site.baseurl }}/user/copying/LICENSE-2.0.html">Apache License 2.0</a> (so that you can incorporate proprietary toolchains into your pipelines).
+ <p><strong>License</strong></p>
+ <p>Arvados is under the copyleft <a href="{{ site.baseurl }}/user/copying/agpl-3.0.html">GNU AGPL v3</a>, with our SDKs under <a href="{{ site.baseurl }}/user/copying/LICENSE-2.0.html">Apache License 2.0</a> (so that you can incorporate proprietary toolchains into your pipelines).
</p>
</div>
- <div class="col-sm-7" style="border-left: solid; border-width: 1px">
+ <div class="col-sm-6" style="border-left: solid; border-width: 1px">
<p><strong>Quickstart</strong>
<p>
Try any pipeline from the <a href="https://arvados.org/projects/arvados/wiki/Public_Pipelines_and_Datasets">list of public pipelines</a>. For instance, the <a href="http://curover.se/pathomap">Pathomap Pipeline</a> links to these <a href="https://arvados.org/projects/arvados/wiki/pathomap_tutorial/">step-by-step instructions</a> for trying Arvados out right in your browser using Curoverse's <a href="http://lp.curoverse.com/beta-signup/">public Arvados instance</a>.
<p>
Want to port your pipeline to Arvados? Check out the step-by-step <a href="https://arvados.org/projects/arvados/wiki/Port_a_Pipeline">Port-a-Pipeline</a> guide on the Arvados wiki.
</p>
- <p><strong>Below you can also find more in-depth guides for using Arvados.
+ <p><strong>More in-depth guides
</strong></p>
<!--<p>-->
<!--<a href="{{ site.baseurl }}/start/index.html">Getting Started</a> — Start here if you're new to Arvados.-->
Generate a new secret token for signing cookies:
<notextile>
-<pre><code>~/arvados/services/api$ <span class="userinput">rake secret</span>
+<pre><code>~/arvados/services/api$ <span class="userinput">ruby -e 'puts rand(2**400).to_s(36)'</span>
zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
</code></pre></notextile>
<notextile>
<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">cp -i config/initializers/secret_token.rb.example config/initializers/secret_token.rb</span>
-~/sso-devise-omniauth-provider$ <span class="userinput">rake secret</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">ruby -e 'puts rand(2**400).to_s(36)'</span>
zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
</code></pre>
</notextile>
-Edit @config/initializers/secret_token.rb@ to set @config.secret_token@ to the string produced by @rake secret@.
+Edit @config/initializers/secret_token.rb@ to set @config.secret_token@ to the string produced by @rand@ above.
h3. Configure upstream authentication provider
Use @rails console@ to create a @Client@ record that will be used by the Arvados API server. The values of @app_id@ and @app_secret@ correspond to the @APP_ID@ and @APP_SECRET@ that must be set in in "Setting up Omniauth in the API server.":install-api-server.html#omniauth
<notextile>
-<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">rake secret</span>
+<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">ruby -e 'puts rand(2**400).to_s(36)'</span>
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rails console</span>
:001 > <span class="userinput">c = Client.new</span>
This application needs a secret token. Generate a new secret:
<notextile>
-<pre><code>~/arvados/apps/workbench$ <span class="userinput">rake secret</span>
+<pre><code>~/arvados/apps/workbench$ <span class="userinput">ruby -e 'puts rand(2**400).to_s(36)'</span>
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
</code></pre>
</notextile>
if @files.nil?
file_sizes = Hash.new(0)
each_file_spec do |streamname, _, filesize, filename|
+ if filename.include?('/')
+ parts = filename.rpartition('/')
+ streamname = streamname + parts[1] + parts[0] # ./dir_parts
+ filename = parts[2]
+ end
file_sizes[[streamname, filename]] += filesize
end
@files = file_sizes.each_pair.map do |(streamname, filename), size|
NONNORMALIZED_MANIFEST =
["./dir2 #{random_block} 0:0:z 0:0:y 0:0:x",
"./dir1 #{random_block} 0:0:p 0:0:o 0:0:n\n"].join("\n")
+ MANIFEST_WITH_DIRS_IN_FILENAMES =
+ [". #{random_block(10)} 0:3:file1 3:3:dir1/file1 6:3:dir1/dir2/file1\n"].join("")
+ MULTILEVEL_MANIFEST_WITH_DIRS_IN_FILENAMES =
+ [". #{random_block(10)} 0:3:file1 3:3:dir1/file1 6:4:dir1/dir2/file1\n",
+ "./dir1 #{random_block(10)} 0:3:file1 3:7:dir2/file1\n"].join("")
### Non-tree manifests
# These manifests follow the spec, but they express a structure that can't
assert !file_name.empty?, "empty file_name in #{name} fixture"
end
end
+
+ def test_collection_with_dirs_in_filenames
+ manifest = Keep::Manifest.new(MANIFEST_WITH_DIRS_IN_FILENAMES)
+
+ seen = Hash.new { |this, key| this[key] = [] }
+
+ manifest.files.each do |stream, basename, size|
+ refute(seen[stream].include?(basename), "each_file repeated #{stream}/#{basename}")
+ assert_equal(3, size, "wrong size for #{stream}/#{basename}")
+ seen[stream] << basename
+ end
+
+ assert_equal(%w(. ./dir1 ./dir1/dir2), seen.keys)
+
+ seen.each_pair do |stream, basenames|
+ assert_equal(%w(file1), basenames.sort, "wrong file list for #{stream}")
+ end
+ end
+
+ def test_multilevel_collection_with_dirs_in_filenames
+ manifest = Keep::Manifest.new(MULTILEVEL_MANIFEST_WITH_DIRS_IN_FILENAMES)
+
+ seen = Hash.new { |this, key| this[key] = [] }
+ expected_sizes = {'.' => 3, './dir1' => 6, './dir1/dir2' => 11}
+
+ manifest.files.each do |stream, basename, size|
+ refute(seen[stream].include?(basename), "each_file repeated #{stream}/#{basename}")
+ assert_equal(expected_sizes[stream], size, "wrong size for #{stream}/#{basename}")
+ seen[stream] << basename
+ end
+
+ assert_equal(%w(. ./dir1 ./dir1/dir2), seen.keys)
+
+ seen.each_pair do |stream, basenames|
+ assert_equal(%w(file1), basenames.sort, "wrong file list for #{stream}")
+ end
+ end
end
group_class: project
description: An anonymously accessible project
+subproject_in_anonymous_accessible_project:
+ uuid: zzzzz-j7d0g-mhtfesvgmkolpyf
+ owner_uuid: zzzzz-j7d0g-zhxawtyetzwc5f0
+ created_at: 2014-04-21 15:37:48 -0400
+ name: Subproject in anonymous accessible project
+ description: Description for subproject in anonymous accessible project
+ group_class: project
+
active_user_has_can_manage:
uuid: zzzzz-j7d0g-ptt1ou6a9lxrv07
owner_uuid: zzzzz-tpzed-d9tiejq69daie8f
projects / arvados.git / commitdiff