In addition to bundled gems, running the integration tests requires "PhantomJS":http://phantomjs.org/download.html to test JavaScript elements. The simplest way to get started is to download one of the binary builds provided, and install the executable into one of the directories in your @$PATH@.
+If you install the Workbench Bundle in deployment mode, you must also install the API server Bundle in deployment mode, and vice versa. If your Bundle installs have mismatched modes, the integration tests will fail with "Gem not found" errors.
+
h2. Writing tests
Integration tests are written with Capybara, which drives a fully-featured Web browser to interact with Workbench exactly as a user would.
class UsersController < ApplicationController
skip_before_filter :find_object_by_uuid, :only => [:welcome, :activity]
skip_around_filter :thread_with_mandatory_api_token, :only => :welcome
- before_filter :ensure_current_user_is_admin, only: :sudo
+ before_filter :ensure_current_user_is_admin, only: [:sudo, :unsetup]
def welcome
if current_user
f.html { render template: 'users/home' }
end
end
+
+ def unsetup
+ if current_user.andand.is_admin
+ @object.unsetup
+ end
+ show
+ end
+
end
def friendly_link_name
[self.first_name, self.last_name].compact.join ' '
end
+
+ def unsetup
+ self.private_reload($arvados_api_client.api(self.class,
+ "/#{self.uuid}/unsetup",
+ {}))
+ end
+
end
-->
<li class="dropdown notification-menu">
- <a href="#" class="dropdown-toggle" data-toggle="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="collections-menu">
<span class="glyphicon glyphicon-paperclip"></span>
<span class="badge" id="persistent-selection-count"></span>
<span class="caret"></span>
<% if current_user.is_active %>
<li class="dropdown notification-menu">
- <a href="#" class="dropdown-toggle" data-toggle="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" id="notifications-menu">
<span class="glyphicon glyphicon-envelope"></span>
<span class="badge badge-alert notification-count"><%= @notification_count %></span>
<span class="caret"></span>
<% content_for :js do %>
setInterval(function(){$('a.refresh').click()}, 15000);
<% end %>
+
+<% content_for :tab_line_buttons do %>
+ <%= form_tag @object, :method => :put do |f| %>
+
+ <%= hidden_field @object.class.to_s.underscore.singularize.to_sym, :active, :value => false %>
+
+ <%= button_tag "Stop pipeline", {class: 'btn btn-primary pull-right', id: "run-pipeline-button"} %>
+ <% end %>
+<% end %>
+
<% end %>
<% else %>
<blockquote>
<%= button_to "Log in as #{@object.full_name}", sudo_user_url(id: @object.uuid), class: 'btn btn-primary' %>
</blockquote>
+
+<p>As an admin, you can deactivate and reset this user. This will remove all repository/VM permissions for the user. If you "setup" the user again, the user will have to sign the user agreement again.</p>
+
+<blockquote>
+<%= button_to "Deactivate #{@object.full_name}", unsetup_user_url(id: @object.uuid), class: 'btn btn-primary', confirm: "Are you sure you want to deactivate #{@object.full_name}?"%>
+</blockquote>
<td>
<small>
- <% if j.success %>
+ <% if j.success and j.output %>
<a href="<%= collection_path(j.output) %>">
<% Collection.limit(1).where(uuid: j.output).each do |c| %>
<span class="glyphicon glyphicon-search"></span>
<% end %>
</span>
- </div>
+ </div>
<% end %>
</div>
<% if not current_user.andand.is_active or @my_collections.empty? %>
<p>
Your account must be activated by an Arvados administrator. If this
is your first time accessing Arvados and would like to request
- access, or you believe you are seeing the page in error, please
- <%= link_to "contact us", Rails.configuration.activation_contact_link %>.
+ access, or you believe you are seeing the page in error, please
+ <%= link_to "contact us", Rails.configuration.activation_contact_link %>.
You should receive an email at the address you used to log in when
- your account is activated. In the mean time, you can
+ your account is activated. In the mean time, you can
<%= link_to "learn more about Arvados", "https://arvados.org/projects/arvados/wiki/Introduction_to_Arvados" %>,
and <%= link_to "read the Arvados user guide", "http://doc.arvados.org/user" %>.
</p>
get 'welcome', :on => :collection
get 'activity', :on => :collection
post 'sudo', :on => :member
+ post 'unsetup', :on => :member
end
resources :logs
resources :factory_jobs
+++ /dev/null
-Use this README file to introduce your application and point to useful places in the API for learning more.
-Run "rake doc:app" to generate API documentation for your models, controllers, helpers, and libraries.
+++ /dev/null
-require 'integration_helper'
-
-class ApiClientAuthorizationsTest < ActionDispatch::IntegrationTest
- test "try loading Manage API tokens page" do
- Capybara.current_driver = Capybara.javascript_driver
- visit page_with_token('admin_trustedclient')
- click_link 'user-menu'
- click_link 'Manage API tokens'
- assert_equal 200, status_code
- end
-end
class LoginsTest < ActionDispatch::IntegrationTest
test "login with api_token works after redirect" do
visit page_with_token('active_trustedclient')
- assert page.has_text? 'Recent jobs'
+ assert page.has_text?('Recent jobs'), "Missing 'Recent jobs' from page"
assert_no_match(/\bapi_token=/, current_path)
end
--- /dev/null
+require 'integration_helper'
+require 'uri'
+
+class SmokeTest < ActionDispatch::IntegrationTest
+ def assert_visit_success(allowed=[200])
+ assert_includes(allowed, status_code,
+ "#{current_url} returned #{status_code}, not one of " +
+ allowed.inspect)
+ end
+
+ def all_links_in(find_spec, text_regexp=//)
+ find(find_spec).all('a').collect { |tag|
+ if tag[:href].nil? or tag[:href].empty? or (tag.text !~ text_regexp)
+ nil
+ else
+ url = URI(tag[:href])
+ url.host.nil? ? url.path : nil
+ end
+ }.compact
+ end
+
+ test "all first-level links succeed" do
+ visit page_with_token('active_trustedclient', '/')
+ assert_visit_success
+ click_link 'user-menu'
+ urls = [all_links_in('.arvados-nav'),
+ all_links_in('.navbar', /^Manage /)].flatten
+ seen_urls = ['/']
+ while not (url = urls.shift).nil?
+ next if seen_urls.include? url
+ visit url
+ seen_urls << url
+ assert_visit_success
+ # Uncommenting the line below lets you crawl the entire site for a
+ # more thorough test.
+ # urls += all_links_in('body')
+ end
+ end
+end
_system('bundle', 'exec', 'rake', 'db:test:load')
_system('bundle', 'exec', 'rake', 'db:fixtures:load')
_system('bundle', 'exec', 'rails', 'server', '-d')
- timeout = Time.now.tv_sec + 5
- while (not File.exists? SERVER_PID_PATH) and (Time.now.tv_sec < timeout)
+ timeout = Time.now.tv_sec + 10
+ begin
sleep 0.2
+ begin
+ server_pid = IO.read(SERVER_PID_PATH).to_i
+ good_pid = (server_pid > 0) and (Process.kill(0, pid) rescue false)
+ rescue Errno::ENOENT
+ good_pid = false
+ end
+ end while (not good_pid) and (Time.now.tv_sec < timeout)
+ if not good_pid
+ raise RuntimeError, "could not find API server Rails pid"
end
- IO.read(SERVER_PID_PATH).to_i
+ server_pid
end
begin
super(args)
arvados/doc$ rake
</pre>
+Alternately, to make the documentation browsable on the local filesystem:
+
+<pre>
+arvados/doc$ rake generate baseurl=$PWD/.site
+</pre>
+
h2. 2. Preview HTML pages
<pre>
- Reference:
- user/reference/api-tokens.html.textile.liquid
- user/reference/sdk-cli.html.textile.liquid
+ - user/reference/job-and-pipeline-reference.html.textile.liquid
- Arvados License:
- user/copying/copying.html.textile.liquid
- user/copying/agpl-3.0.html
- sdk/python/sdk-python.html.textile.liquid
- sdk/python/python.html.textile.liquid
- sdk/python/crunch-utility-libraries.html.textile.liquid
+ - Perl:
+ - sdk/perl/index.html.textile.liquid
+ - Ruby:
+ - sdk/ruby/index.html.textile.liquid
+ - CLI:
+ - sdk/cli/index.html.textile.liquid
api:
- Concepts:
- api/index.html.textile.liquid
{% if nx == 1 %}
<hr>
{% if prev != "" %}
- <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a></li>
+ <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a>
{% endif %}
- <a href="{{ site.baseurl }}{{ p.url }}" class="pull-right">Next: {{ p.title }}</a></li>
+ <a href="{{ site.baseurl }}{{ p.url }}" class="pull-right">Next: {{ p.title }}</a>
{% assign nx = 0 %}
{% assign n = 1 %}
{% endif %}
{% endfor %}
{% if n == 0 && prev != "" %}
<hr>
- <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a></li>
+ <a href="{{ site.baseurl }}{{ prev.url }}" class="pull-left">Previous: {{ prev.title }}</a>
{% assign n = 1 %}
{% endif %}
\ No newline at end of file
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_clients@
h2. Resources
-Each ApiClient has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each ApiClient has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/api_client_authorizations@
navsection: api
navmenu: Schema
title: AuthorizedKey
-
...
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/authorized_keys@
h2. Resources
-Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each AuthorizedKey has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
-This resource concerns metadata, usage accounting, and integrity checks for data stored on the cloud. Reading and writing the data _per se_ is achieved by the "Keep":/user/tutorials/tutorial-keep.html storage system.
+This resource concerns metadata, usage accounting, and integrity checks for data stored on the cloud. Reading and writing the data _per se_ is achieved by the "Keep":{{site.baseurl}}/user/tutorials/tutorial-keep.html storage system.
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/links@
h2. Resource
-Each collection has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each collection has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commits@
h2. Resources
-Each Commit has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Commit has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/commit_ancestors@
h2. Resources
-Each CommitAncestor has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each CommitAncestor has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/groups@
h2. Resources
-Each Group has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Group has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/humans@
h2. Resources
-Each Human has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Human has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/jobs@
→ Job resource list
-This method is equivalent to the "index method":/api/methods.html#index, except that the results are restricted to queued jobs (i.e., jobs that have not yet been started or cancelled) and order defaults to queue priority.
+This method is equivalent to the "index method":{{site.baseurl}}/api/methods.html#index, except that the results are restricted to queued jobs (i.e., jobs that have not yet been started or cancelled) and order defaults to queue priority.
h2. Resource
-Each job has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each job has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Notes|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/job_tasks@
h2. Resources
-Each JobTask has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each JobTask has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/keep_disks@
h2. Resources
-Each KeepDisk has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each KeepDisk has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/links@
h2. Resource
-Each link has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each link has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/logs@
h2. Resources
-Each Log has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Log has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/nodes@
h2. Resources
-Each Node has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Node has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_instances@
h2. Resources
-Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each PipelineInstance has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/pipeline_templates@
h2. Resources
-Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each PipelineTemplate has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/repositories@
h2. Resources
-Each Repository has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Repository has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/specimens@
h2. Resources
-Each Specimen has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Specimen has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/traits@
h2. Resources
-Each Trait has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each Trait has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/users@
h2. Resources
-Each User has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each User has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+See "REST methods for working with Arvados resources":{{site.baseurl}}/api/methods.html
API endpoint base: @https://{{ site.arvados_api_host }}/arvados/v1/virtual_machines@
h2. Resources
-Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":/api/resources.html:
+Each VirtualMachine has, in addition to the usual "attributes of Arvados resources":{{site.baseurl}}/api/resources.html:
table(table table-bordered table-condensed).
|_. Attribute|_. Type|_. Description|_. Example|
navsection: api
navmenu: Schema
title: {resource}
-navorder: {navorder}
---
h1. {resource}
h2. Methods
-See "REST methods for working with Arvados resources":/api/methods.html
+ See "REST methods for working with Arvados resources":{{{{site.baseurl}}}}/api/methods.html
API endpoint base: @https://{{{{ site.arvados_api_host }}}}/arvados/v1/{res_api_endpoint}@
<p>manuals, guides, and references</p>
</div>
<div class="col-sm-6">
- <img src="images/dax.png" style="max-height: 10em"></img>
+ <img src="images/dax-reading-book.png" style="max-height: 10em" alt="Dax reading a book" />
</div>
</div>
</div>
</p>
<p>
<a href="{{ site.baseurl }}/install/index.html">Install Guide</a> — How to install Arvados on a cloud platform.
- </p>
+ </p>
</div>
</div>
</div>
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: CLI
+title: "Command line SDK"
+
+...
+
+The @arv@ CLI tool provides a generic set of wrappers so you can make API calls easily. It performs some validation before connecting to the API server: for example, it refuses to do an API call if a required parameter is missing.
+
+It also provides access to Keep storage services with the @arv keep@ subcommand.
+
+h3. Usage
+
+See the "command line interface":{{site.baseurl}}/user/reference/sdk-cli.html page in the user guide.
+
+h3. Installation
+
+If you are logged in to an Arvados VM, the @arv@ should be installed.
+
+To use @arv@ elsewhere, you can either install the @arvados-cli@ gem via RubyGems or build and install the package using the arvados source tree.
+
+h4. Prerequisites: Ruby >= 2.0.0 and curl libraries
+
+You can use "RVM":http://rvm.io/rvm/install to install and manage Ruby versions.
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo apt-get install curl</code>
+$ <code class="userinput">sudo sh -c 'curl -sSL https://get.rvm.io | bash -s stable'</code>
+$ <code class="userinput">source /etc/profile.d/rvm.sh</code>
+</pre>
+</notextile>
+
+Install curl libraries with your system's package manager. For example, with Debian or Ubuntu:
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo apt-get install libcurl3 libcurl3-gnutls libcurl4-openssl-dev</code>
+</pre>
+</notextile>
+
+h4. Option 1: install with RubyGems
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo gem install arvados-cli</code>
+</pre>
+</notextile>
+
+h4. Option 2: build and install from source
+
+<notextile>
+<pre>
+$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">cd arvados/sdk/cli</code>
+$ <code class="userinput">gem build arvados-cli.gemspec</code>
+$ <code class="userinput">sudo gem install arvados-cli-*.gem</code>
+</pre>
+</notextile>
+
This section documents how to access the Arvados API and Keep using various programming languages.
-* "Python SDK":python/sdk-python.html
+* "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html
+* "Perl SDK":{{site.baseurl}}/sdk/perl/index.html
+* "Ruby SDK":{{site.baseurl}}/sdk/ruby/index.html
+* "Command line SDK":{{site.baseurl}}/sdk/cli/index.html ("arv")
+
+SDKs not yet implemented:
+
+* Rails SDK: Workbench uses an ActiveRecord-like interface to Arvados. This hasn't yet been extracted from Workbench and packaged as a gem.
+* R and Java: We plan to support these, but they have not been implemented yet.
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Perl
+title: "Perl SDK"
+
+...
+
+The Perl SDK provides a generic set of wrappers so you can make API calls easily.
+
+It should be treated as alpha/experimental. Currently, limitations include:
+* Verbose syntax.
+* No native Keep client.
+* No CPAN package.
+
+h3. Installation
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo apt-get install libjson-perl libio-socket-ssl-perl libwww-perl</code>
+$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">cd arvados/sdk/perl</code>
+$ <code class="userinput">perl Makefile.PL</code>
+$ <code class="userinput">sudo make install</code>
+</pre>
+</notextile>
+
+h4. Test installation
+
+If the SDK is installed, @perl -MArvados -e ''@ should produce no errors.
+
+If your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ environment variables are set up correctly (see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for details), the following test script should work:
+
+<notextile>
+<pre>$ <code class="userinput">perl <<'EOF'
+use Arvados;
+my $arv = Arvados->new('apiVersion' => 'v1');
+my $me = $arv->{'users'}->{'current'}->execute;
+print ("arvados.v1.users.current.full_name = '", $me->{'full_name'}, "'\n");
+EOF</code>
+arvados.v1.users.current.full_name = 'Your Name'
+</pre>
+</notextile>
+
+h3. Examples
+
+Set up an API client user agent:
+
+<notextile>
+<pre><code class="userinput">my $arv = Arvados->new('apiVersion' => 'v1');
+</code></pre>
+</notextile>
+
+Get the User object for the current user:
+
+<notextile>
+<pre><code class="userinput">my $current_user = $arv->{'users'}->{'current'}->execute;
+</code></pre>
+</notextile>
+
+Get the UUID of an object that was retrieved using the SDK:
+
+<notextile>
+<pre><code class="userinput">my $current_user_uuid = $current_user->{'uuid'}
+</code></pre>
+</notextile>
+
+Retrieve an object by ID:
+
+<notextile>
+<pre><code class="userinput">my $some_user = $arv->{'users'}->{'get'}->execute('uuid' => $current_user_uuid);
+</code></pre>
+</notextile>
+
+Create an object:
+
+<notextile>
+<pre><code class="userinput">my $test_link = $arv->{'links'}->{'create'}->execute('link' => { 'link_class' => 'test', 'name' => 'test' });
+</code></pre>
+</notextile>
+
+Update an object:
+
+<notextile>
+<pre><code class="userinput">my $test_link = $arv->{'links'}->{'update'}->execute(
+ 'uuid' => $test_link->{'uuid'},
+ 'link' => { 'properties' => { 'foo' => 'bar' } });
+</code></pre>
+</notextile>
+
+Get a list of objects:
+
+<notextile>
+<pre><code class="userinput">my $repos = $arv->{'repositories'}->{'list'}->execute;
+print ("UUID of first repo returned is ", $repos->{'items'}->[0], "\n");
+</code></pre>
+</notextile>
+
+The SDK retrieves the list of API methods from the server at run time. Therefore, the set of available methods is determined by the server version rather than the SDK version.
--- /dev/null
+---
+layout: default
+navsection: sdk
+navmenu: Ruby
+title: "Ruby SDK"
+
+...
+
+The Ruby SDK provides a generic set of wrappers so you can make API calls easily.
+
+h3. Installation
+
+If you are logged in to an Arvados VM, the Ruby SDK should be installed.
+
+To use it elsewhere, you can either install the @arvados@ gem via RubyGems or build and install the package using the arvados source tree.
+
+h4. Prerequisites: Ruby >= 2.0.0
+
+You can use "RVM":http://rvm.io/rvm/install to install and manage Ruby versions.
+
+h4. Option 1: install with RubyGems
+
+<notextile>
+<pre>
+$ <code class="userinput">sudo gem install arvados</code>
+</pre>
+</notextile>
+
+h4. Option 2: build and install from source
+
+<notextile>
+<pre>
+$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+$ <code class="userinput">cd arvados/sdk/cli</code>
+$ <code class="userinput">gem build arvados.gemspec</code>
+$ <code class="userinput">sudo gem install arvados-*.gem</code>
+</pre>
+</notextile>
+
+h4. Test installation
+
+If the SDK is installed, @ruby -r arvados -e 'puts "OK!"'@ should produce no errors.
+
+If your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ environment variables are set up correctly (see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for details), the following test script should work:
+
+<notextile>
+<pre>$ <code class="userinput">ruby -r arvados <<'EOF'
+arv = Arvados.new api_version: 'v1'
+my_full_name = arv.user.current[:full_name]
+puts "arvados.v1.users.current.full_name = '#{my_full_name}'"
+EOF</code>
+arvados.v1.users.current.full_name = 'Your Name'
+</pre>
+</notextile>
+
+h3. Examples
+
+Import the module (we skipped this step above by using "ruby -r arvados"):
+
+<notextile>
+<pre><code class="userinput">require 'arvados'
+</code></pre>
+</notextile>
+
+Set up an API client user agent:
+
+<notextile>
+<pre><code class="userinput">arv = Arvados.new(apiVersion: 'v1')
+</code></pre>
+</notextile>
+
+Get the User object for the current user:
+
+<notextile>
+<pre><code class="userinput">current_user = arv.user.current
+</code></pre>
+</notextile>
+
+Get the UUID of an object that was retrieved using the SDK:
+
+<notextile>
+<pre><code class="userinput">current_user_uuid = current_user[:uuid]
+</code></pre>
+</notextile>
+
+Retrieve an object by ID:
+
+<notextile>
+<pre><code class="userinput">some_user = arv.user.get(uuid: current_user_uuid)
+</code></pre>
+</notextile>
+
+Create an object:
+
+<notextile>
+<pre><code class="userinput">new_link = arv.link.create(link: {link_class: 'test', name: 'test'})
+</code></pre>
+</notextile>
+
+Update an object:
+
+<notextile>
+<pre><code class="userinput">updated_link = arv.link.update(uuid: new_link[:uuid],
+ link: {properties: {foo: 'bar'}})
+</code></pre>
+</notextile>
+
+Delete an object:
+
+<notextile>
+<pre><code class="userinput">arv.link.delete(uuid: new_link[:uuid])
+</code></pre>
+</notextile>
+
+Get a list of objects:
+
+<notextile>
+<pre><code class="userinput">repos = arv.repository.list
+first_repo = repos[:items][0]
+puts "UUID of first repo returned is #{first_repo[:uuid]}"</code>
+UUID of first repo returned is qr1hi-s0uqq-b1bnybpx3u5temz
+</pre>
+</notextile>
+
+The SDK retrieves the list of API methods from the server at run time. Therefore, the set of available methods is determined by the server version rather than the SDK version.
<p style="text-align: center;">Version 3, 19 November 2007</p>
<p>Copyright © 2007 Free Software Foundation,
-Inc. <<a href="http://fsf.org/">http://fsf.org/</a>>
+Inc. <<a href="http://www.fsf.org/">http://fsf.org/</a>>
<br />
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.</p>
--- /dev/null
+---
+layout: default
+navsection: userguide
+title: "Job and Pipeline Reference"
+...
+
+h2. Submitting jobs
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type|_. Accepted values |_. Required|_. Description|
+|script |string |filename |yes |The actual script that will be run by crunch. Must be the name of an executable file in the crunch_scripts/ directory at the git revision specified by script_version.|
+|script_version |string |git branch, tag, or version hash |yes |The code version to run, which is available in the specified repository. May be a git hash or tag to specify an exact version, or a branch. If it is a branch, use the branch head.|
+|repository |string |name of git repository hosted by Arvados |yes |The repository to search for script_version.|
+|script_parameters |object |any JSON object |yes |The input parameters for the job, with the parameter names as keys mapping to parameter values.|
+|minimum_script_version |string |git branch, tag, or version hash |no |The minimum acceptable script version when deciding whether to re-use a past job.|
+|exclude_script_versions|array of strings|git branch, tag, or version hash|no |Script versions to exclude when deciding whether to re-use a past job.|
+|nondeterministic |boolean | |no |If true, never re-use a past job, and flag this job so it will never be considered for re-use.|
+|no_reuse |boolean | |no |If true, do not re-use a past job, but this job may be re-used.|
+
+When a job is executed, the 'script_version' field is resolved to an exact git revision and the git hash for that revision is recorded in 'script_version'. If 'script_version' can't be resolved, the job submission will be rejected.
+
+h3. Reusing jobs
+
+Because Arvados records the exact version of the script, input parameters, and runtime environment [1] that was used to run the job, if the script is deterministic (meaning that the same code version is guaranteed to produce the same outputs from the same inputs) then it is possible to re-use the results of past jobs, and avoid re-running the computation to save time. Arvados uses the following algorithm to determine if a past job can be re-used:
+
+notextile. <div class="spaced-out">
+
+# If 'nondeterministic' or 'no_reuse' are true, always create a new job.
+# Find a list of acceptable values for 'script_version'. If 'minimum_script_version' is specified, this is the set of all revisions in the git commit graph between 'minimum_script_version' and 'script_version' (inclusive) [2]. If 'minimum_script_version' is not specified, only 'script_version' is added to the list. If 'exclude_script_versions' is specified, the listed versions are excluded from the list.
+# Select jobs have the same 'script' and 'script_parameters' attributes, and where the 'script_version' attribute is in the list of acceptable versions. Exclude failed jobs or where 'nondeterministic' is true.
+# If there is more than one candidate job, check that all selected past jobs actually did produce the same output.
+# If everything passed, re-use one of the selected past jobs (if there is more than one match, which job will be returned is undefined). Otherwise create a new job.
+
+fn1. As of this writing, versioning the runtime environment is still under development.
+
+fn2. This may include parallel branches if there is more than one path between 'minimum_script_version' and 'script_version' in the git commit graph. Use 'exclude_script_versions' to blacklist specific versions.
+
+</div>
+
+h3. Examples
+
+Run the script "crunch_scripts/hash.py" in the repository "you" using the "master" branch head. Arvados is allowed to re-use a previous job if the script_version of the past job is the same as the "master" branch head (i.e. there have not been any subsequent commits to "master").
+
+<pre>
+{
+ "script": "hash.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+</pre>
+
+Run using exactly the version "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5". Arvados is allowed to re-use a previous job if the script_version of that job is also "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5".
+
+<pre>
+{
+ "script": "hash.py",
+ "repository": "you",
+ "script_version": "d00220fb38d4b85ca8fc28a8151702a2b9d1dec5",
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+</pre>
+
+Arvados is allowed to re-use a previous job if the script_version of the past job is between "earlier_version_tag" and the head of the "master" branch (inclusive), but not "blacklisted_version_tag". If there are no previous jobs, run the job using the head of the "master" branch as specified in "script_version".
+
+<pre>
+{
+ "script": "hash.py",
+ "repository": "you",
+ "minimum_script_version": "earlier_version_tag",
+ "script_version": "master",
+ "exclude_script_versions", ["blacklisted_version_tag"],
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+</pre>
+
+Run the script "crunch_scripts/monte-carlo.py" in the repository "you" using the "master" branch head. Because it is marked as "nondeterministic", never re-use previous jobs, and never re-use this job.
+
+<pre>
+{
+ "script": "monte-carlo.py",
+ "repository": "you",
+ "script_version": "master",
+ "nondeterministic": true,
+ "script_parameters": {
+ "input": "c1bad4b39ca5a924e481008009d94e32+210"
+ }
+}
+</pre>
+
+h2. Pipelines
+
+Pipelines consist of a set of "components". Each component is an Arvados job submission, so when a component job is submitted, Arvados may re-use past jobs based on the rules described above.
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type |_. Accepted values |_. Required|_. Description|
+|name |string |any |yes |The human-readable name of the pipeline template.|
+|components |object |JSON object containing job submission objects|yes |The component jobs that make up the pipeline, with the component name as the key. |
+
+h3. Script parameters
+
+When used in a pipeline, each parameter in the 'script_parameters' attribute of a component job can specify that the input parameter must be supplied by the user, or the input parameter should be linked to the output of another component. To do this, the value of the parameter should be JSON object containing one of the following attributes:
+
+table(table table-bordered table-condensed).
+|_. Attribute |_. Type |_. Accepted values |_. Description|
+|default |any |any |The default value for this parameter.|
+|required |boolean |true or false |Specifies whether the parameter is required to have a value or not.|
+|dataclass |string |One of 'Collection', 'File' [3], 'number', or 'text' |Data type of this parameter.|
+|output_of |string |the name of another component in the pipeline |Specifies that the value of this parameter should be set to the 'output' attribute of the job that corresponds to the specified component.|
+
+The 'output_of' parameter is especially important, as this is how components are actually linked together to form a pipeline. Component jobs that depend on the output of other components do not run until the parent job completes and has produced output. If the parent job fails, the entire pipeline fails.
+
+fn3. The 'File' type refers to a specific file within a Keep collection in the form 'collection_hash/filename', for example '887cd41e9c613463eab2f0d885c6dd96+83/bob.txt'.
+
+h3. Examples
+
+This a pipeline named "Filter md5 hash values" with two components, "do_hash" and "filter". The "input" script parameter of the "do_hash" component is required to be filled in by the user, and the expected data type is "Collection". This also specifies that the "input" script parameter of the "filter" component is the output of "do_hash", so "filter" will not run until "do_hash" completes successfully. When the pipeline runs, past jobs that meet the criteria described above may be substituted for either or both components to avoid redundant computation.
+
+<pre>
+{
+ "name": "Filter md5 hash values",
+ "components": {
+ "do_hash": {
+ "script": "hash.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "required": true,
+ "dataclass": "Collection"
+ }
+ },
+ },
+ "filter": {
+ "script": "0-filter.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "do_hash"
+ }
+ },
+ }
+ }
+}
+</pre>
+
+This pipeline consists of three components. The components "thing1" and "thing2" both depend on "cat_in_the_hat". Once the "cat_in_the_hat" job is complete, both "thing1" and "thing2" can run in parallel, because they do not depend on each other.
+
+<pre>
+{
+ "name": "Wreck the house",
+ "components": {
+ "cat_in_the_hat": {
+ "script": "cat.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "thing1": {
+ "script": "thing1.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "cat_in_the_hat"
+ }
+ },
+ },
+ "thing2": {
+ "script": "thing2.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "input": {
+ "output_of": "cat_in_the_hat"
+ }
+ },
+ },
+ }
+}
+</pre>
+
+This pipeline consists of three components. The component "cleanup" depends on "thing1" and "thing2". Both "thing1" and "thing2" are started immediately and can run in parallel, because they do not depend on each other, but "cleanup" cannot begin until both "thing1" and "thing2" have completed.
+
+<pre>
+{
+ "name": "Clean the house",
+ "components": {
+ "thing1": {
+ "script": "thing1.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "thing2": {
+ "script": "thing2.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": { }
+ },
+ "cleanup": {
+ "script": "cleanup.py",
+ "repository": "you",
+ "script_version": "master",
+ "script_parameters": {
+ "mess1": {
+ "output_of": "thing1"
+ },
+ "mess2": {
+ "output_of": "thing2"
+ }
+ }
+ }
+ }
+}
+</pre>
In order to reassemble the file, Keep stores a *collection* data block which lists in sequence the data blocks that make up the original file. A collection data block may store the information for multiple files, including a directory structure.
-In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@ which we added to Keep in "the first Keep tutorial":{{ site.baseurl }}/users/tutorial/tutorial-keep.html. First let us examine the contents of this collection using @arv keep get@:
+In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@ which we added to Keep in "the first Keep tutorial":{{ site.baseurl }}/user/tutorials/tutorial-keep.html. First let us examine the contents of this collection using @arv keep get@:
<notextile>
<pre><code>~$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210</span>
"script_parameters":{
"input": "887cd41e9c613463eab2f0d885c6dd96+83"
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
},
"filter":{
"script":"0-filter.py",
"output_of":"do_hash"
}
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
}
}
}
<pre><code>~$ <span class="userinput">arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt</span>
44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
~$ <span class="userinput">arv keep get 490cd451c8108824b8a17e3723e1f236+19/0-filter.txt</span>
-~$
</code></pre>
</notextile>
~$ <span class="userinput">cat >the_job <<EOF
{
"script":"GATK2-VariantFiltration",
+ "repository":"arvados",
"script_version":"$src_version",
"script_parameters":
{
<pre><code>~$ <span class="userinput">cat >the_job <<EOF
{
"script": "hash",
- "script_version": "arvados:master",
- "script_parameters":
- {
+ "repository": "arvados",
+ "script_version": "master",
+ "script_parameters": {
"input": "c1bad4b39ca5a924e481008009d94e32+210"
}
}
* @<<EOF@ tells the shell to direct the following lines into the standard input for @cat@ up until it sees the line @EOF@
* @>the_job@ redirects standard output to a file called @the_job@
* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories .
+* @"repository"@ is the git repository to search for the script version. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}//repositories .
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, a tag, or a branch (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
* @"script_parameters"@ are provided to the script. In this case, the input is the locator for the collection that we inspected in the previous section.
Use @arv job create@ to actually submit the job. It should print out a JSON object which describes the newly created job:
h2. Monitor job progress
-Go to the "Workbench dashboard":http://{{site.arvados_workbench_host}}. Your job should be at the top of the "Recent jobs" table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
+Go to the "Workbench dashboard":https://{{site.arvados_workbench_host}}. Your job should be at the top of the "Recent jobs" table. This table refreshes automatically. When the job has completed successfully, it will show <span class="label label-success">finished</span> in the *Status* column.
On the command line, you can access log messages while the job runs using @arv job log_tail_follow@:
h2. Inspect the job output
-On the "Workbench dashboard":http://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *files* column to view a file, or click on the download icon <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
+On the "Workbench dashboard":https://{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table. Click on the link under *Output* for your job to go to the files page with the job output. The files page lists all the files that were output by the job. Click on the link under the *files* column to view a file, or click on the download icon <span class="glyphicon glyphicon-download-alt"></span> to download the output file.
On the command line, you can use @arv job get@ to access a JSON object describing the output:
2013-12-16_20:44:38 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 0 done, 1 running, 0 todo
2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 child 7681 on compute13.1 exit 0 signal 0 success=true
2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 success in 1 seconds
-2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 output
+2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 0 output
2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 wait for last 0 children to finish
2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 status: 1 done, 0 running, 1 todo
2013-12-16_20:44:39 qr1hi-8i9sb-1pm1t02dezhupss 7575 start level 1
<pre><code>~/<b>you</b>/crunch_scripts$ <span class="userinput">cat >~/the_job <<EOF
{
"script": "parallel-hash.py",
- "script_version": "<b>you</b>:master",
+ "repository": "<b>you</b>",
+ "script_version": "master",
"script_parameters":
{
"input": "887cd41e9c613463eab2f0d885c6dd96+83"
"dataclass": "Collection"
}
},
- "script_version":"<b>you</b>:master"
+ "repository":"<b>you</b>",
+ "script_version":"master"
}
}
}
</code></pre>
</notextile>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
~$ <span class="userinput">git config --global user.email <b>you</b>@example.com</span></code></pre>
</notextile>
-On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}/repositories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
+On the Arvados Workbench, navigate to "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}/repositories . You should see a repository with your user name listed in the *name* column. Next to *name* is the column *push_url*. Copy the *push_url* value associated with your repository. This should look like <notextile><code>git@git.{{ site.arvados_api_host }}:<b>you</b>.git</code></notextile>.
Next, on the Arvados virtual machine, clone your git repository:
"dataclass": "Collection"
}
},
- "script_version":"<b>you</b>:master",
+ "repository":"<b>you</b>",
+ "script_version":"master",
"output_is_persistent":true
}
}
* @"components"@ is a set of scripts that make up the pipeline
* The component is listed with a human-readable name (@"do_hash"@ in this example)
* @"script"@ specifies the name of the script to run. The script is searched for in the "crunch_scripts/" subdirectory of the @git@ checkout specified by @"script_version"@.
-* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, or in the form "repository:branch" (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":http://{{site.arvados_workbench_host}}//repositories .
+* @"repository"@ is the git repository to search for the script version. You can access a list of available @git@ repositories on the Arvados workbench under "Compute %(rarr)→% Code repositories":https://{{site.arvados_workbench_host}}//repositories .
+* @"script_version"@ specifies the version of the script that you wish to run. This can be in the form of an explicit @git@ revision hash, a tag, or a branch (in which case it will take the HEAD of the specified branch). Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
* @"script_parameters"@ describes the parameters for the script. In this example, there is one parameter called @input@ which is @required@ and is a @Collection@.
* @"output_is_persistent"@ indicates whether the output of the job is considered valuable. If this value is false (or not given), the output will be treated as intermediate data and eventually deleted to reclaim disk space.
</code></pre>
</notextile>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page. You can run the "pipeline using workbench":tutorial-pipeline-workbench.html
"dataclass": "Collection"
}
},
- "script_version":"<b>you</b>:master",
+ "repository":"<b>you</b>",
+ "script_version":"master",
"output_is_persistent":false
},
"filter":{
"output_of":"do_hash"
}
},
- "script_version":"<b>you</b>:master",
+ "repository":"<b>you</b>",
+ "script_version":"master",
"output_is_persistent":true
}
}
</code></pre>
</notextile>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_templates page.
-
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page.
notextile. <div class="spaced-out">
-# Go to "Collections":http://{{ site.arvados_workbench_host }}/collections .
+# Go to "Collections":https://{{ site.arvados_workbench_host }}/collections .
# On the collections page, go to the search box <span class="glyphicon glyphicon-search"></span> and search for "tutorial".
# This should yield a collection with the contents "var-GS000016015-ASM.tsv.bz2"
# Click on the check box to the left of "var-GS000016015-ASM.tsv.bz2". This puts the collection in your persistent selection list. Click on the paperclip <span class="glyphicon glyphicon-paperclip"></span> in the upper right to get a dropdown menu listing your current selections.
-# Go to "Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_templates .
+# Go to "Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates .
# Look for a pipeline named "Tutorial pipeline".
# Click on the play button <span class="glyphicon glyphicon-play"></span> to the left of "Tutorial pipeline". This will take you to a new page to configure the pipeline.
# Under *parameter* look for "input". Set the value of "input" by clicking on on "none" to get a editing popup. At the top of the selection list in the editing popup will be the collection that you selected in step 4.
rescue LoadError
abort <<-EOS
-Please install all required gems:
+Please install all required gems:
gem install activesupport andand curb google-api-client json oj trollop
end
end
-client = ArvadosClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0')
-arvados = client.discovered_api('arvados', ENV['ARVADOS_API_VERSION'])
+begin
+ client = ArvadosClient.new(:host => ENV['ARVADOS_API_HOST'], :application_name => 'arvados-cli', :application_version => '1.0')
+ arvados = client.discovered_api('arvados', ENV['ARVADOS_API_VERSION'])
+rescue Exception => e
+ puts "Failed to connect to Arvados API server: #{e}"
+ exit 1
+end
def to_boolean(s)
!!(s =~ /^(true|t|yes|y|1)$/i)
end
banner += "\n"
STDERR.puts banner
-
- if not method.nil? and method != '--help' then
+
+ if not method.nil? and method != '--help' then
Trollop::die ("Unknown method #{method.inspect} " +
"for resource #{resource.inspect}")
end
banner += "\n"
STDERR.puts banner
- if not resource.nil? and resource != '--help' then
+ if not resource.nil? and resource != '--help' then
Trollop::die "Unknown resource type #{resource.inspect}"
end
exit 255
curl.headers['Accept'] = 'text/plain'
curl.headers['Authorization'] = "OAuth2 #{ENV['ARVADOS_API_TOKEN']}"
if ENV['ARVADOS_API_HOST_INSECURE']
- curl.ssl_verify_peer = false
+ curl.ssl_verify_peer = false
curl.ssl_verify_host = false
end
if global_opts[:verbose]
puts results['uuid']
end
end
-
-
# [--no-wait] Make only as much progress as possible without entering
# a sleep/poll loop.
#
-# [--no-reuse-finished] Do not reuse existing outputs to satisfy
-# pipeline components. Always submit a new job
-# or use an existing job which has not yet
-# finished.
-#
# [--no-reuse] Do not reuse existing jobs to satisfy pipeline
# components. Submit a new job for every component.
#
"Do not wait for jobs to finish. Just look up status, submit new jobs if needed, and exit.",
:short => :none,
:type => :boolean)
- opt(:no_reuse_finished,
- "Do not reuse existing outputs to satisfy pipeline components. Always submit a new job or use an existing job which has not yet finished.",
- :short => :none,
- :type => :boolean)
opt(:no_reuse,
"Do not reuse existing jobs to satisfy pipeline components. Submit a new job for every component.",
:short => :none,
if j.is_a? Hash and j[:uuid]
@cache[j[:uuid]] = j
else
- debuglog "create job: #{j[:errors] rescue nil}", 0
+ debuglog "create job: #{j[:errors] rescue nil} with attribute #{attributes}", 0
nil
end
end
c[:job][:uuid] &&
!c[:job][:success].nil?)
if !c[:job] and
- c[:script_parameters].select { |pname, p| p.is_a? Hash }.empty?
- # Job is fully specified (all parameter values are present) but
- # no particular job has been found.
-
- debuglog "component #{cname} ready to satisfy."
-
- c.delete :wait
- second_place_job = nil # satisfies component, but not finished yet
-
- (@options[:no_reuse] ? [] : JobCache.
- where(script: c[:script],
- script_parameters: c[:script_parameters],
- script_version_descends_from: c[:script_version])
- ).each do |candidate_job|
- candidate_params_downcase = Hash[candidate_job[:script_parameters].
- map { |k,v| [k.downcase,v] }]
- c_params_downcase = Hash[c[:script_parameters].
- map { |k,v| [k.downcase,v] }]
-
- debuglog "component #{cname} considering job #{candidate_job[:uuid]} version #{candidate_job[:script_version]} parameters #{candidate_params_downcase.inspect}", 3
-
- unless candidate_params_downcase == c_params_downcase
- next
- end
-
- if c[:script_version] !=
- candidate_job[:script_version][0,c[:script_version].length]
- debuglog "component #{cname} would be satisfied by job #{candidate_job[:uuid]} if script_version matched.", 2
- next
- end
-
- unless candidate_job[:success] || candidate_job[:running] ||
- (!candidate_job[:started_at] && !candidate_job[:cancelled_at])
- debuglog "component #{cname} would be satisfied by job #{candidate_job[:uuid]} if it were running or successful.", 2
- next
- end
-
- if candidate_job[:success]
- unless @options[:no_reuse_finished]
- job = candidate_job
- $stderr.puts "using #{job[:uuid]} (finished at #{job[:finished_at]}) for component #{cname}"
- c[:job] = job
- end
- else
- second_place_job ||= candidate_job
- end
- break
- end
- if not c[:job] and second_place_job
- job = second_place_job
- $stderr.puts "using #{job[:uuid]} (running since #{job[:started_at]}) for component #{cname}"
+ c[:script_parameters].select { |pname, p| p.is_a? Hash and p[:output_of]}.empty?
+ # No job yet associated with this component and is component inputs
+ # are fully specified (any output_of script_parameters are resolved
+ # to real value)
+ job = JobCache.create({:script => c[:script],
+ :script_parameters => c[:script_parameters],
+ :script_version => c[:script_version],
+ :repository => c[:repository],
+ :minimum_script_version => c[:minimum_script_version],
+ :exclude_script_versions => c[:exclude_minimum_script_versions],
+ :nondeterministic => c[:nondeterministic],
+ :no_reuse => @options[:no_reuse],
+ :output_is_persistent => c[:output_is_persistent] || false})
+ if job
+ debuglog "component #{cname} new job #{job[:uuid]}"
c[:job] = job
+ else
+ debuglog "component #{cname} new job failed"
end
- if not c[:job]
- debuglog "component #{cname} not satisfied by any existing job."
- if !@options[:dry_run]
- debuglog "component #{cname} new job."
- job = JobCache.create(:script => c[:script],
- :script_parameters => c[:script_parameters],
- :runtime_constraints => c[:runtime_constraints] || {},
- :script_version => c[:script_version] || 'master',
- :output_is_persistent => c[:output_is_persistent] || false)
- if job
- debuglog "component #{cname} new job #{job[:uuid]}"
- c[:job] = job
- else
- debuglog "component #{cname} new job failed"
- end
- end
- end
- else
- c[:wait] = true
end
+
if c[:job] and c[:job][:uuid]
if (c[:job][:running] or
not (c[:job][:finished_at] or c[:job][:cancelled_at]))
- c[:job] = JobCache.get(c[:job][:uuid])
+ # Job is running so update copy of job record
+ c[:job] = JobCache.get(c[:job][:uuid])
end
+
if c[:job][:success]
# Populate script_parameters of other components waiting for
# this job
end
elsif c[:job][:running] ||
(!c[:job][:started_at] && !c[:job][:cancelled_at])
+ # Job is still running
moretodo = true
elsif c[:job][:cancelled_at]
debuglog "component #{cname} job #{c[:job][:uuid]} cancelled."
}
$ENV{"TASK_SLOT_NODE"} = $slot[$childslot]->{node}->{name};
$ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
- $ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/".$slot[$childslot]->{cpu};
+ $ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/$id.$$";
$ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}."/keep";
$ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
$ENV{"CRUNCH_NODE_SLOTS"} = $slot[$childslot]->{node}->{ncpus};
skip_before_filter :find_object_by_uuid, :only => :queue
skip_before_filter :render_404_if_no_object, :only => :queue
- def index
- return super unless @where.is_a? Hash
- want_ancestor = @where[:script_version_descends_from]
- if want_ancestor
- # Check for missing commit_ancestor rows, and create them if
- # possible.
- @objects.
- dup.
- includes(:commit_ancestors). # I wish Rails would let me
- # specify here which
- # commit_ancestors I am
- # interested in.
- each do |o|
- if o.commit_ancestors.
- select { |ca| ca.ancestor == want_ancestor }.
- empty? and !o.script_version.nil?
- begin
- o.commit_ancestors << CommitAncestor.find_or_create_by_descendant_and_ancestor(o.script_version, want_ancestor)
- rescue
+ def create
+ [:repository, :script, :script_version, :script_parameters].each do |r|
+ if !resource_attrs[r]
+ return render json: {
+ :error => "#{r} attribute must be specified"
+ }, status: :unprocessable_entity
+ end
+ end
+
+ r = Commit.find_commit_range(current_user,
+ resource_attrs[:repository],
+ resource_attrs[:minimum_script_version],
+ resource_attrs[:script_version],
+ resource_attrs[:exclude_script_versions])
+ if !resource_attrs[:nondeterministic] and !resource_attrs[:no_reuse]
+ # Search for jobs where the script_version is in the list of commits
+ # returned by find_commit_range
+ @object = nil
+ Job.readable_by(current_user).where(script: resource_attrs[:script],
+ script_version: r).
+ each do |j|
+ if j.nondeterministic != true and
+ j.success != false and
+ j.script_parameters == resource_attrs[:script_parameters]
+ # Record the first job in the list
+ if !@object
+ @object = j
+ end
+ # Ensure that all candidate jobs actually did produce the same output
+ if @object.output != j.output
+ @object = nil
+ break
end
end
- o.commit_ancestors.
- select { |ca| ca.ancestor == want_ancestor }.
- select(&:is).
- first
+ if @object
+ return show
+ end
end
- # Now it is safe to do an .includes().where() because we are no
- # longer interested in jobs that have other ancestors but not
- # want_ancestor.
- @objects = @objects.
- includes(:commit_ancestors).
- where('commit_ancestors.ancestor = ? and commit_ancestors.is = ?',
- want_ancestor, true)
end
+ if r
+ resource_attrs[:script_version] = r[0]
+ end
+
+ # Don't pass these on to activerecord
+ resource_attrs.delete(:minimum_script_version)
+ resource_attrs.delete(:exclude_script_versions)
+ resource_attrs.delete(:no_reuse)
super
end
class Arvados::V1::SchemaController < ApplicationController
+ skip_before_filter :find_objects_for_index
skip_before_filter :find_object_by_uuid
skip_before_filter :render_404_if_no_object
skip_before_filter :require_auth_scope_all
- def show
- classes = Rails.cache.fetch 'arvados_v1_schema' do
- Rails.application.eager_load!
- classes = {}
- ActiveRecord::Base.descendants.reject(&:abstract_class?).each do |k|
- classes[k] = k.columns.collect do |col|
- if k.serialized_attributes.has_key? col.name
- { name: col.name,
- type: k.serialized_attributes[col.name].object_class.to_s }
- else
- { name: col.name,
- type: col.type }
- end
- end
- end
- classes
- end
- render json: classes
- end
-
- def discovery_rest_description
+ def index
expires_in 24.hours, public: true
discovery = Rails.cache.fetch 'arvados_v1_rest_discovery' do
Rails.application.eager_load!
generatedAt: Time.now.iso8601,
title: "Arvados API",
description: "The API to interact with Arvados.",
- documentationLink: "https://redmine.clinicalfuture.com/projects/arvados/",
+ documentationLink: "http://doc.arvados.org/api/index.html",
protocol: "rest",
baseUrl: root_url + "/arvados/v1/",
basePath: "/arvados/v1/",
class Arvados::V1::UsersController < ApplicationController
skip_before_filter :find_object_by_uuid, only:
- [:activate, :event_stream, :current, :system]
+ [:activate, :event_stream, :current, :system, :setup]
skip_before_filter :render_404_if_no_object, only:
- [:activate, :event_stream, :current, :system]
-
+ [:activate, :event_stream, :current, :system, :setup]
+ before_filter :admin_required, only: [:setup, :unsetup]
+
def current
@object = current_user
show
end
show
end
+
+ # create user object and all the needed links
+ def setup
+ @object = nil
+ if params[:uuid]
+ @object = User.find_by_uuid params[:uuid]
+ if !@object
+ return render_404_if_no_object
+ end
+ object_found = true
+ else
+ if !params[:user]
+ raise ArgumentError.new "Required uuid or user"
+ else
+ if params[:user]['uuid']
+ @object = User.find_by_uuid params[:user]['uuid']
+ if @object
+ object_found = true
+ end
+ end
+
+ if !@object
+ if !params[:user]['email']
+ raise ArgumentError.new "Require user email"
+ end
+
+ if !params[:openid_prefix]
+ raise ArgumentError.new "Required openid_prefix parameter is missing."
+ end
+
+ @object = model_class.create! resource_attrs
+ end
+ end
+ end
+
+ if object_found
+ @response = @object.setup_repo_vm_links params[:repo_name], params[:vm_uuid]
+ else
+ @response = User.setup @object, params[:openid_prefix],
+ params[:repo_name], params[:vm_uuid]
+ end
+
+ render json: { kind: "arvados#HashList", items: @response }
+ end
+
+ # delete user agreements, vm, repository, login links; set state to inactive
+ def unsetup
+ reload_object_before_update
+ @object.unsetup
+ show
+ end
+
end
class Commit < ActiveRecord::Base
require 'shellwords'
- # Make sure the specified commit really exists, and return the full
- # sha1 commit hash.
- #
- # Accepts anything "git rev-list" accepts, optionally (and
- # preferably) preceded by "repo_name:".
- #
- # Examples: "1234567", "master", "apps:1234567", "apps:master",
- # "apps:HEAD"
-
- def self.find_by_commit_ish(commit_ish)
- want_repo = nil
- if commit_ish.index(':')
- want_repo, commit_ish = commit_ish.split(':',2)
+ def self.git_check_ref_format(e)
+ if !e or e.empty? or e[0] == '-' or e[0] == '$'
+ # definitely not valid
+ false
+ else
+ `git check-ref-format --allow-onelevel #{e.shellescape}`
+ $?.success?
end
- repositories.each do |repo_name, repo|
- next if want_repo and want_repo != repo_name
- ENV['GIT_DIR'] = repo[:git_dir]
- IO.foreach("|git rev-list --max-count=1 --format=oneline 'origin/'#{commit_ish.shellescape} 2>/dev/null || git rev-list --max-count=1 --format=oneline ''#{commit_ish.shellescape}") do |line|
- sha1, message = line.strip.split " ", 2
- next if sha1.length != 40
- begin
- Commit.find_or_create_by_repository_name_and_sha1_and_message(repo_name, sha1, message[0..254])
- rescue
- logger.warn "find_or_create failed: repo_name #{repo_name} sha1 #{sha1} message #{message[0..254]}"
- # Ignore cache failure. Commit is real. We should proceed.
+ end
+
+ def self.find_commit_range(current_user, repository, minimum, maximum, exclude)
+ if (minimum and !git_check_ref_format(minimum)) or !git_check_ref_format(maximum)
+ logger.warn "find_commit_range called with invalid minimum or maximum: '#{minimum}', '#{maximum}'"
+ return nil
+ end
+
+ if minimum and minimum.empty?
+ minimum = nil
+ end
+
+ if !maximum
+ maximum = "HEAD"
+ end
+
+ # Get list of actual repository directories under management
+ on_disk_repos = repositories
+
+ # Get list of repository objects readable by user
+ readable = Repository.readable_by(current_user)
+
+ # filter repository objects on requested repository name
+ if repository
+ readable = readable.where(name: repository)
+ end
+
+ commits = []
+ readable.each do |r|
+ if on_disk_repos[r.name]
+ ENV['GIT_DIR'] = on_disk_repos[r.name][:git_dir]
+
+ # We've filtered for invalid characters, so we can pass the contents of
+ # minimum and maximum safely on the command line
+
+ # Get the commit hash for the upper bound
+ max_hash = nil
+ IO.foreach("|git rev-list --max-count=1 #{maximum.shellescape}") do |line|
+ max_hash = line.strip
+ end
+
+ # If not found or string is invalid, nothing else to do
+ next if !max_hash or !git_check_ref_format(max_hash)
+
+ resolved_exclude = nil
+ if exclude
+ resolved_exclude = []
+ exclude.each do |e|
+ if git_check_ref_format(e)
+ IO.foreach("|git rev-list --max-count=1 #{e.shellescape}") do |line|
+ resolved_exclude.push(line.strip)
+ end
+ else
+ logger.warn "find_commit_range called with invalid exclude invalid characters: '#{exclude}'"
+ return nil
+ end
+ end
+ end
+
+ if minimum
+ # Get the commit hash for the lower bound
+ min_hash = nil
+ IO.foreach("|git rev-list --max-count=1 #{minimum.shellescape}") do |line|
+ min_hash = line.strip
+ end
+
+ # If not found or string is invalid, nothing else to do
+ next if !min_hash or !git_check_ref_format(min_hash)
+
+ # Now find all commits between them
+ IO.foreach("|git rev-list #{min_hash.shellescape}..#{max_hash.shellescape}") do |line|
+ hash = line.strip
+ commits.push(hash) if !resolved_exclude or !resolved_exclude.include? hash
+ end
+
+ commits.push(min_hash) if !resolved_exclude or !resolved_exclude.include? min_hash
+ else
+ commits.push(max_hash) if !resolved_exclude or !resolved_exclude.include? max_hash
end
- return sha1
end
end
- nil
+
+ if !commits or commits.empty?
+ nil
+ else
+ commits
+ end
end
# Import all commits from configured git directory into the commits
end
end
+ def self.refresh_repositories
+ @repositories = nil
+ end
+
protected
def self.repositories
next if repo.match /^\./
git_dir = File.join(@gitdirbase,
repo.match(/\.git$/) ? repo : File.join(repo, '.git'))
+ next if git_dir == Rails.configuration.git_internal_dir
repo_name = repo.sub(/\.git$/, '')
@repositories[repo_name] = {git_dir: git_dir}
end
t.add :dependencies
t.add :log_stream_href
t.add :log_buffer
+ t.add :nondeterministic
+ t.add :repository
end
def assert_finished
order('priority desc, created_at')
end
+ def self.running
+ self.where('running = ?', true).
+ order('priority desc, created_at')
+ end
+
protected
def foreign_key_attributes
return true
end
if new_record? or script_version_changed?
- sha1 = Commit.find_by_commit_ish(self.script_version) rescue nil
+ sha1 = Commit.find_commit_range(current_user, nil, nil, self.script_version, nil)[0] rescue nil
if sha1
self.script_version = sha1
else
end
end
+ def self.setup(user, openid_prefix, repo_name=nil, vm_uuid=nil)
+ login_perm_props = {identity_url_prefix: openid_prefix}
+
+ # Check oid_login_perm
+ oid_login_perms = Link.where(tail_uuid: user.email,
+ head_kind: 'arvados#user',
+ link_class: 'permission',
+ name: 'can_login')
+
+ if !oid_login_perms.any?
+ # create openid login permission
+ oid_login_perm = Link.create(link_class: 'permission',
+ name: 'can_login',
+ tail_kind: 'email',
+ tail_uuid: user.email,
+ head_kind: 'arvados#user',
+ head_uuid: user.uuid,
+ properties: login_perm_props
+ )
+ logger.info { "openid login permission: " + oid_login_perm[:uuid] }
+ else
+ oid_login_perm = oid_login_perms.first
+ end
+
+ return [oid_login_perm] + user.setup_repo_vm_links(repo_name, vm_uuid)
+ end
+
+ # create links
+ def setup_repo_vm_links(repo_name, vm_uuid)
+ repo_perm = create_user_repo_link repo_name
+ vm_login_perm = create_vm_login_permission_link vm_uuid, repo_name
+ group_perm = create_user_group_link
+
+ return [repo_perm, vm_login_perm, group_perm, self].compact
+ end
+
+ # delete user signatures, login, repo, and vm perms, and mark as inactive
+ def unsetup
+ # delete oid_login_perms for this user
+ oid_login_perms = Link.where(tail_uuid: self.email,
+ head_kind: 'arvados#user',
+ link_class: 'permission',
+ name: 'can_login')
+ oid_login_perms.each do |perm|
+ Link.delete perm
+ end
+
+ # delete repo_perms for this user
+ repo_perms = Link.where(tail_uuid: self.uuid,
+ head_kind: 'arvados#repository',
+ link_class: 'permission',
+ name: 'can_write')
+ repo_perms.each do |perm|
+ Link.delete perm
+ end
+
+ # delete vm_login_perms for this user
+ vm_login_perms = Link.where(tail_uuid: self.uuid,
+ head_kind: 'arvados#virtualMachine',
+ link_class: 'permission',
+ name: 'can_login')
+ vm_login_perms.each do |perm|
+ Link.delete perm
+ end
+
+ # delete any signatures by this user
+ signed_uuids = Link.where(link_class: 'signature',
+ tail_kind: 'arvados#user',
+ tail_uuid: self.uuid)
+ signed_uuids.each do |sign|
+ Link.delete sign
+ end
+
+ # mark the user as inactive
+ self.is_active = false
+ self.save!
+ end
+
protected
def permission_to_update
upstream_path.delete start
merged
end
+
+ def create_user_repo_link(repo_name)
+ # repo_name is optional
+ if not repo_name
+ logger.warn ("Repository name not given for #{self.uuid}.")
+ return
+ end
+
+ # Check for an existing repository with the same name we're about to use.
+ repo = Repository.where(name: repo_name).first
+
+ if repo
+ logger.warn "Repository exists for #{repo_name}: #{repo[:uuid]}."
+
+ # Look for existing repository access for this repo
+ repo_perms = Link.where(tail_uuid: self.uuid,
+ head_kind: 'arvados#repository',
+ head_uuid: repo[:uuid],
+ link_class: 'permission',
+ name: 'can_write')
+ if repo_perms.any?
+ logger.warn "User already has repository access " +
+ repo_perms.collect { |p| p[:uuid] }.inspect
+ return repo_perms.first
+ end
+ end
+
+ # create repo, if does not already exist
+ repo ||= Repository.create(name: repo_name)
+ logger.info { "repo uuid: " + repo[:uuid] }
+
+ repo_perm = Link.create(tail_kind: 'arvados#user',
+ tail_uuid: self.uuid,
+ head_kind: 'arvados#repository',
+ head_uuid: repo[:uuid],
+ link_class: 'permission',
+ name: 'can_write')
+ logger.info { "repo permission: " + repo_perm[:uuid] }
+ return repo_perm
+ end
+
+ # create login permission for the given vm_uuid, if it does not already exist
+ def create_vm_login_permission_link(vm_uuid, repo_name)
+ begin
+
+ # vm uuid is optional
+ if vm_uuid
+ vm = VirtualMachine.where(uuid: vm_uuid).first
+
+ if not vm
+ logger.warn "Could not find virtual machine for #{vm_uuid.inspect}"
+ raise "No vm found for #{vm_uuid}"
+ end
+ else
+ return
+ end
+
+ logger.info { "vm uuid: " + vm[:uuid] }
+
+ login_perms = Link.where(tail_uuid: self.uuid,
+ head_uuid: vm[:uuid],
+ head_kind: 'arvados#virtualMachine',
+ link_class: 'permission',
+ name: 'can_login')
+ if !login_perms.any?
+ login_perm = Link.create(tail_kind: 'arvados#user',
+ tail_uuid: self.uuid,
+ head_kind: 'arvados#virtualMachine',
+ head_uuid: vm[:uuid],
+ link_class: 'permission',
+ name: 'can_login',
+ properties: {username: repo_name})
+ logger.info { "login permission: " + login_perm[:uuid] }
+ else
+ login_perm = login_perms.first
+ end
+
+ return login_perm
+ end
+ end
+
+ # add the user to the 'All users' group
+ def create_user_group_link
+ # Look up the "All users" group (we expect uuid *-*-fffffffffffffff).
+ group = Group.where(name: 'All users').select do |g|
+ g[:uuid].match /-f+$/
+ end.first
+
+ if not group
+ logger.warn "No 'All users' group with uuid '*-*-fffffffffffffff'."
+ raise "No 'All users' group with uuid '*-*-fffffffffffffff' is found"
+ else
+ logger.info { "\"All users\" group uuid: " + group[:uuid] }
+
+ group_perms = Link.where(tail_uuid: self.uuid,
+ head_uuid: group[:uuid],
+ head_kind: 'arvados#group',
+ link_class: 'permission',
+ name: 'can_read')
+
+ if !group_perms.any?
+ group_perm = Link.create(tail_kind: 'arvados#user',
+ tail_uuid: self.uuid,
+ head_kind: 'arvados#group',
+ head_uuid: group[:uuid],
+ link_class: 'permission',
+ name: 'can_read')
+ logger.info { "group permission: " + group_perm[:uuid] }
+ else
+ group_perm = group_perms.first
+ end
+
+ return group_perm
+ end
+ end
+
end
secret_token: ~
uuid_prefix: <%= Digest::MD5.hexdigest(`hostname`).to_i(16).to_s(36)[0..4] %>
- git_repositories_dir: /var/cache/git
+ # Git repositories must be readable by api server, or you won't be
+ # able to submit crunch jobs. To pass the test suites, put a clone
+ # of the arvados tree in {git_repositories_dir}/arvados.git or
+ # {git_repositories_dir}/arvados/.git
+ git_repositories_dir: /var/lib/arvados/git
+
+ # This is a (bare) repository that stores commits used in jobs. When a job
+ # runs, the source commits are first fetched into this repository, then this
+ # repository is used to deploy to compute nodes. This should NOT be a
+ # subdirectory of {git_repositiories_dir}.
+ git_internal_dir: /var/lib/arvados/internal.git
# :none or :slurm_immediate
crunch_job_wrapper: :none
secret_token: <%= rand(2**512).to_s(36) %>
common:
-
- # Git repositories must be readable by api server, or you won't be
- # able to submit crunch jobs. To pass the test suites, put a clone
- # of the arvados tree in {git_repositories_dir}/arvados.git or
- # {git_repositories_dir}/arvados/.git
- #
#git_repositories_dir: /var/cache/git
+ #git_internal_dir: /var/cache/arvados/internal.git
# Initialize the rails application
Server::Application.initialize!
+begin
+ Rails.cache.clear
+rescue Errno::ENOENT => e
+ # Cache directory does not exist? Then cache is clear, proceed.
+ Rails.logger.warn "In Rails.cache.clear, ignoring #{e.inspect}"
+end
namespace :arvados do
namespace :v1 do
- match '/schema' => 'schema#show'
match '/nodes/:uuid/ping' => 'nodes#ping', :as => :ping_node
match '/keep_disks/ping' => 'keep_disks#ping', :as => :ping_keep_disk
match '/links/from/:tail_uuid' => 'links#index', :as => :arvados_v1_links_from
post '/jobs/:uuid/cancel' => 'jobs#cancel'
match '/users/:uuid/event_stream' => 'users#event_stream'
post '/users/:uuid/activate' => 'users#activate'
+ post '/users/setup' => 'users#setup'
+ post '/users/:uuid/unsetup' => 'users#unsetup'
match '/virtual_machines/get_all_logins' => 'virtual_machines#get_all_logins'
match '/virtual_machines/:uuid/logins' => 'virtual_machines#logins'
post '/api_client_authorizations/create_system_auth' => 'api_client_authorizations#create_system_auth'
match '/login', :to => 'user_sessions#login'
match '/logout', :to => 'user_sessions#logout'
- match '/discovery/v1/apis/arvados/v1/rest', :to => 'arvados/v1/schema#discovery_rest_description'
+ match '/discovery/v1/apis/arvados/v1/rest', :to => 'arvados/v1/schema#index'
match '/static/login_failure', :to => 'static#login_failure', :as => :login_failure
--- /dev/null
+class AddNondeterministicColumnToJob < ActiveRecord::Migration
+ def up
+ add_column :jobs, :nondeterministic, :boolean
+ end
+
+ def down
+ remove_column :jobs, :nondeterministic
+ end
+end
--- /dev/null
+class SeparateRepositoryFromScriptVersion < ActiveRecord::Migration
+ include CurrentApiClient
+
+ def fixup pt
+ c = pt.components
+ c.each do |k, v|
+ commit_ish = v["script_version"]
+ if commit_ish.andand.index(':')
+ want_repo, commit_ish = commit_ish.split(':',2)
+ v[:repository] = want_repo
+ v[:script_version] = commit_ish
+ end
+ end
+ pt.save!
+ end
+
+ def up
+ act_as_system_user do
+ PipelineTemplate.all.each do |pt|
+ fixup pt
+ end
+ PipelineInstance.all.each do |pt|
+ fixup pt
+ end
+ end
+ end
+
+ def down
+ raise ActiveRecord::IrreversibleMigration
+ end
+end
--- /dev/null
+class AddRepositoryColumnToJob < ActiveRecord::Migration
+ def up
+ add_column :jobs, :repository, :string
+ end
+
+ def down
+ remove_column :jobs, :repository
+ end
+end
create_table "collections", :force => true do |t|
t.string "locator"
t.string "owner_uuid"
- t.datetime "created_at", :null => false
+ t.datetime "created_at"
t.string "modified_by_client_uuid"
t.string "modified_by_user_uuid"
t.datetime "modified_at"
t.string "redundancy_confirmed_by_client_uuid"
t.datetime "redundancy_confirmed_at"
t.integer "redundancy_confirmed_as"
- t.datetime "updated_at", :null => false
+ t.datetime "updated_at"
t.string "uuid"
t.text "manifest_text"
end
t.string "repository_name"
t.string "sha1"
t.string "message"
- t.datetime "created_at", :null => false
- t.datetime "updated_at", :null => false
+ t.datetime "created_at"
+ t.datetime "updated_at"
end
add_index "commits", ["repository_name", "sha1"], :name => "index_commits_on_repository_name_and_sha1", :unique => true
t.string "modified_by_user_uuid"
t.datetime "modified_at"
t.text "properties"
- t.datetime "created_at", :null => false
- t.datetime "updated_at", :null => false
+ t.datetime "created_at"
+ t.datetime "updated_at"
end
add_index "humans", ["uuid"], :name => "index_humans_on_uuid", :unique => true
t.string "log"
t.text "tasks_summary"
t.text "runtime_constraints"
+ t.boolean "nondeterministic"
+ t.string "repository"
t.boolean "output_is_persistent", :default => false, :null => false
end
create_table "links", :force => true do |t|
t.string "uuid"
t.string "owner_uuid"
- t.datetime "created_at", :null => false
+ t.datetime "created_at"
t.string "modified_by_client_uuid"
t.string "modified_by_user_uuid"
t.datetime "modified_at"
t.string "name"
t.string "head_uuid"
t.text "properties"
- t.datetime "updated_at", :null => false
+ t.datetime "updated_at"
t.string "head_kind"
end
create_table "pipeline_instances", :force => true do |t|
t.string "uuid"
t.string "owner_uuid"
- t.datetime "created_at", :null => false
+ t.datetime "created_at"
t.string "modified_by_client_uuid"
t.string "modified_by_user_uuid"
t.datetime "modified_at"
t.text "components"
t.boolean "success"
t.boolean "active", :default => false
- t.datetime "updated_at", :null => false
+ t.datetime "updated_at"
t.text "properties"
end
raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
end
+ require 'shellwords'
+
+ arvados_internal = Rails.configuration.git_internal_dir
+ if not File.exists? arvados_internal
+ $stderr.puts `mkdir -p #{arvados_internal.shellescape} && cd #{arvados_internal.shellescape} && git init --bare`
+ end
+
+ src_repo = File.join(Rails.configuration.git_repositories_dir, job.repository + '.git')
+ src_repo = File.join(Rails.configuration.git_repositories_dir, job.repository, '.git') unless File.exists? src_repo
+
+ unless src_repo
+ $stderr.puts "dispatch: #{File.join Rails.configuration.git_repositories_dir, job.repository} doesn't exist"
+ sleep 1
+ untake(job)
+ next
+ end
+
+ $stderr.puts `cd #{arvados_internal.shellescape} && git fetch --no-tags #{src_repo.shellescape} && git tag #{job.uuid.shellescape} #{job.script_version.shellescape}`
+
cmd_args << crunch_job_bin
cmd_args << '--job-api-token'
cmd_args << job_auth.api_token
cmd_args << '--job'
cmd_args << job.uuid
-
- commit = Commit.where(sha1: job.script_version).first
- if commit
- cmd_args << '--git-dir'
- if File.exists?(File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name + '.git'))
- cmd_args << File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name + '.git')
- else
- cmd_args << File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name, '.git')
- end
- end
+ cmd_args << '--git-dir'
+ cmd_args << arvados_internal
$stderr.puts "dispatch: #{cmd_args.join ' '}"
end
def update_pipelines
+ expire_tokens = @pipe_auth_tokens.dup
@todo_pipelines.each do |p|
- pipe_auth = ApiClientAuthorization.
- new(user: User.where('uuid=?', p.modified_by_user_uuid).first,
- api_client_id: 0)
- pipe_auth.save
-
+ pipe_auth = (@pipe_auth_tokens[p.uuid] ||= ApiClientAuthorization.
+ create(user: User.where('uuid=?', p.modified_by_user_uuid).first,
+ api_client_id: 0))
puts `export ARVADOS_API_TOKEN=#{pipe_auth.api_token} && arv-run-pipeline-instance --run-here --no-wait --instance #{p.uuid}`
+ expire_tokens.delete p.uuid
+ end
+
+ expire_tokens.each do |k, v|
+ v.update_attributes expires_at: Time.now
+ @pipe_auth_tokens.delete k
end
end
def run
act_as_system_user
@running ||= {}
+ @pipe_auth_tokens ||= { }
$stderr.puts "dispatch: ready"
while !$signal[:term] or @running.size > 0
read_pipes
unless @todo.empty? or did_recently(:start_jobs, 1.0) or $signal[:term]
start_jobs
end
- unless @todo_pipelines.empty? or did_recently(:update_pipelines, 5.0)
+ unless (@todo_pipelines.empty? and @pipe_auth_tokens.empty?) or did_recently(:update_pipelines, 5.0)
update_pipelines
end
end
:config => File.expand_path("config.ru"),
:SSLEnable => true,
:SSLVerifyClient => OpenSSL::SSL::VERIFY_NONE,
- :SSLCertName => [["CN", WEBrick::Utils::getservername]]
+ :SSLCertName => [["CN", "#{WEBrick::Utils::getservername} #{Time.now().to_s}"]]
})
end
end
-end
+end
######### /SSL
--- /dev/null
+#!/usr/bin/env ruby
+
+abort 'Error: Ruby >= 1.9.3 required.' if RUBY_VERSION < '1.9.3'
+
+require 'logger'
+require 'trollop'
+
+log = Logger.new STDERR
+log.progname = $0.split('/').last
+
+opts = Trollop::options do
+ banner ''
+ banner "Usage: #{log.progname} " +
+ "{user_uuid_or_email} {user_and_repo_name} {vm_uuid}"
+ banner ''
+ opt :debug, <<-eos
+Show debug messages.
+ eos
+ opt :openid_prefix, <<-eos, default: 'https://www.google.com/accounts/o8/id'
+If creating a new user record, require authentication from an OpenID \
+with this OpenID prefix *and* a matching email address in order to \
+claim the account.
+ eos
+end
+
+log.level = (ENV['DEBUG'] || opts.debug) ? Logger::DEBUG : Logger::WARN
+
+if ARGV.count != 3
+ Trollop::die "required arguments are missing"
+end
+
+user_arg, user_repo_name, vm_uuid = ARGV
+
+require 'arvados'
+arv = Arvados.new(api_version: 'v1')
+
+# Look up the given user by uuid or, failing that, email address.
+begin
+ found_user = arv.user.get(uuid: user_arg)
+rescue Arvados::TransactionFailedError
+ found = arv.user.list(where: {email: user_arg})[:items]
+
+ if found.count == 0
+ if !user_arg.match(/\w\@\w+\.\w+/)
+ abort "About to create new user, but #{user_arg.inspect} " +
+ "does not look like an email address. Stop."
+ end
+ elsif found.count != 1
+ abort "Found #{found.count} users with email. Stop."
+ else
+ found_user = found.first
+ end
+end
+
+# Invoke user setup method
+if (found_user)
+ user = arv.user.setup uuid: found_user[:uuid], repo_name: user_repo_name,
+ vm_uuid: vm_uuid, openid_prefix: opts.openid_prefix
+else
+ user = arv.user.setup user: {email: user_arg}, repo_name: user_repo_name,
+ vm_uuid: vm_uuid, openid_prefix: opts.openid_prefix
+end
+
+log.info {"user uuid: " + user[:uuid]}
+
+puts user.inspect
user_agreement:
- uuid: b519d9cb706a29fc7ea24dbea2f05851
+ uuid: b519d9cb706a29fc7ea24dbea2f05851+249025
owner_uuid: qr1hi-tpzed-tpj2ff66551eyym
created_at: 2013-12-26T19:22:54Z
modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
running: 0
done: 1
runtime_constraints: {}
+
+previous_job_run:
+ uuid: zzzzz-8i9sb-cjs4pklxxjykqqq
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ script: hash
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: "1"
+ success: true
+
+nondeterminisic_job_run:
+ uuid: zzzzz-8i9sb-cjs4pklxxjykyyy
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ script: hash2
+ script_version: 4fe459abe02d9b365932b8f5dc419439ab4e2577
+ script_parameters:
+ input: fa7aeb5140e2848d39b416daeef4ffc5+45
+ an_integer: "1"
+ success: true
+ nondeterministic: true
\ No newline at end of file
link_class: signature
name: require
head_kind: arvados#collection
- head_uuid: b519d9cb706a29fc7ea24dbea2f05851
+ head_uuid: b519d9cb706a29fc7ea24dbea2f05851+249025
properties: {}
user_agreement_readable:
link_class: permission
name: can_read
head_kind: arvados#collection
- head_uuid: b519d9cb706a29fc7ea24dbea2f05851
+ head_uuid: b519d9cb706a29fc7ea24dbea2f05851+249025
properties: {}
active_user_member_of_all_users_group:
link_class: signature
name: click
head_kind: arvados#collection
- head_uuid: b519d9cb706a29fc7ea24dbea2f05851
+ head_uuid: b519d9cb706a29fc7ea24dbea2f05851+249025
properties: {}
user_agreement_signed_by_inactive:
link_class: signature
name: click
head_kind: arvados#collection
- head_uuid: b519d9cb706a29fc7ea24dbea2f05851
+ head_uuid: b519d9cb706a29fc7ea24dbea2f05851+249025
properties: {}
spectator_user_member_of_all_users_group:
head_uuid: zzzzz-8i9sb-cjs4pklxxjykyuq
properties: {}
+foo_repository_readable_by_spectator:
+ uuid: zzzzz-o0j2j-cpy7p41hpk5xxx
+ owner_uuid: zzzzz-tpzed-000000000000000
+ created_at: 2014-01-24 20:42:26 -0800
+ modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+ modified_by_user_uuid: zzzzz-tpzed-000000000000000
+ modified_at: 2014-01-24 20:42:26 -0800
+ updated_at: 2014-01-24 20:42:26 -0800
+ tail_kind: arvados#user
+ tail_uuid: zzzzz-tpzed-l1s2piq4t4mps8r
+ link_class: permission
+ name: can_read
+ head_kind: arvados#repository
+ head_uuid: zzzzz-2x53u-382brsig8rp3666
+ properties: {}
--- /dev/null
+foo:
+ uuid: zzzzz-2x53u-382brsig8rp3666
+ owner_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+ name: foo
--- /dev/null
+require 'test_helper'
+load 'test/functional/arvados/v1/git_setup.rb'
+
+class Arvados::V1::CommitsControllerTest < ActionController::TestCase
+ fixtures :repositories, :users
+
+ # See git_setup.rb for the commit log for test.git.tar
+ include GitSetup
+
+ test "test_find_commit_range" do
+ authorize_with :active
+
+ # single
+ a = Commit.find_commit_range(users(:active), nil, nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', nil)
+ assert_equal ['31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+
+ #test "test_branch1" do
+ a = Commit.find_commit_range(users(:active), nil, nil, 'master', nil)
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57'], a
+
+ #test "test_branch2" do
+ a = Commit.find_commit_range(users(:active), 'foo', nil, 'b1', nil)
+ assert_equal ['1de84a854e2b440dc53bf42f8548afa4c17da332'], a
+
+ #test "test_branch3" do
+ a = Commit.find_commit_range(users(:active), 'foo', nil, 'HEAD', nil)
+ assert_equal ['1de84a854e2b440dc53bf42f8548afa4c17da332'], a
+
+ #test "test_single_revision_repo" do
+ a = Commit.find_commit_range(users(:active), "foo", nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', nil)
+ assert_equal ['31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+ a = Commit.find_commit_range(users(:active), "bar", nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', nil)
+ assert_equal nil, a
+
+ #test "test_multi_revision" do
+ a = Commit.find_commit_range(users(:active), nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', '077ba2ad3ea24a929091a9e6ce545c93199b8e57', nil)
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57', '4fe459abe02d9b365932b8f5dc419439ab4e2577', '31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+
+ #test "test_tag" do
+ a = Commit.find_commit_range(users(:active), nil, 'tag1', 'master', nil)
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57', '4fe459abe02d9b365932b8f5dc419439ab4e2577'], a
+
+ #test "test_multi_revision_exclude" do
+ a = Commit.find_commit_range(users(:active), nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', '077ba2ad3ea24a929091a9e6ce545c93199b8e57', ['4fe459abe02d9b365932b8f5dc419439ab4e2577'])
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57', '31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+
+ #test "test_multi_revision_tagged_exclude" do
+ a = Commit.find_commit_range(users(:active), nil, '31ce37fe365b3dc204300a3e4c396ad333ed0556', '077ba2ad3ea24a929091a9e6ce545c93199b8e57', ['tag1'])
+ assert_equal ['077ba2ad3ea24a929091a9e6ce545c93199b8e57', '31ce37fe365b3dc204300a3e4c396ad333ed0556'], a
+
+ Dir.mktmpdir do |touchdir|
+ # invalid input to maximum
+ a = Commit.find_commit_range(users(:active), nil, nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556 ; touch #{touchdir}/uh_oh", nil)
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to maximum
+ a = Commit.find_commit_range(users(:active), nil, nil, "$(uname>#{touchdir}/uh_oh)", nil)
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'maximum' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to minimum
+ a = Commit.find_commit_range(users(:active), nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556 ; touch #{touchdir}/uh_oh", "31ce37fe365b3dc204300a3e4c396ad333ed0556", nil)
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'minimum' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to minimum
+ a = Commit.find_commit_range(users(:active), nil, "$(uname>#{touchdir}/uh_oh)", "31ce37fe365b3dc204300a3e4c396ad333ed0556", nil)
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'minimum' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to 'excludes'
+ a = Commit.find_commit_range(users(:active), nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556", "077ba2ad3ea24a929091a9e6ce545c93199b8e57", ["4fe459abe02d9b365932b8f5dc419439ab4e2577 ; touch #{touchdir}/uh_oh"])
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'excludes' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ # invalid input to 'excludes'
+ a = Commit.find_commit_range(users(:active), nil, "31ce37fe365b3dc204300a3e4c396ad333ed0556", "077ba2ad3ea24a929091a9e6ce545c93199b8e57", ["$(uname>#{touchdir}/uh_oh)"])
+ assert !File.exists?("#{touchdir}/uh_oh"), "#{touchdir}/uh_oh should not exist, 'excludes' parameter of find_commit_range is exploitable"
+ assert_equal nil, a
+
+ end
+
+ end
+
+end
--- /dev/null
+require 'fileutils'
+require 'tmpdir'
+
+# Commit log for test.git.tar
+# master is the main branch
+# b1 is a branch off of master
+# tag1 is a tag
+#
+# 1de84a8 * b1
+# 077ba2a * master
+# 4fe459a * tag1
+# 31ce37f * foo
+
+module GitSetup
+ def setup
+ @tmpdir = Dir.mktmpdir()
+ #puts "setup #{@tmpdir}"
+ `cp test/test.git.tar #{@tmpdir} && cd #{@tmpdir} && tar xf test.git.tar`
+ Rails.configuration.git_repositories_dir = "#{@tmpdir}/test"
+ Commit.refresh_repositories
+ end
+
+ def teardown
+ #puts "teardown #{@tmpdir}"
+ FileUtils.remove_entry @tmpdir, true
+ end
+end
--- /dev/null
+require 'test_helper'
+load 'test/functional/arvados/v1/git_setup.rb'
+
+class Arvados::V1::JobReuseControllerTest < ActionController::TestCase
+ fixtures :repositories, :users, :jobs, :links
+
+ # See git_setup.rb for the commit log for test.git.tar
+ include GitSetup
+
+ test "test_reuse_job" do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_reuse_job_range" do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ minimum_script_version: "tag1",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_different_input" do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '2'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_different_version" do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ script_version: "master",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '2'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '077ba2ad3ea24a929091a9e6ce545c93199b8e57', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_submitted_nondeterministic" do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ },
+ nondeterministic: true
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_past_nondeterministic" do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :active
+ post :create, job: {
+ script: "hash2",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykyyy', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_no_permission" do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :spectator
+ post :create, job: {
+ script: "hash",
+ script_version: "4fe459abe02d9b365932b8f5dc419439ab4e2577",
+ repository: "foo",
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '4fe459abe02d9b365932b8f5dc419439ab4e2577', new_job['script_version']
+ end
+
+ test "test_cannot_reuse_job_excluded" do
+ @controller = Arvados::V1::JobsController.new
+ authorize_with :active
+ post :create, job: {
+ script: "hash",
+ minimum_script_version: "31ce37fe365b3dc204300a3e4c396ad333ed0556",
+ script_version: "master",
+ repository: "foo",
+ exclude_script_versions: ["tag1"],
+ script_parameters: {
+ input: 'fa7aeb5140e2848d39b416daeef4ffc5+45',
+ an_integer: '1'
+ }
+ }
+ assert_response :success
+ assert_not_nil assigns(:object)
+ new_job = JSON.parse(@response.body)
+ assert_not_equal 'zzzzz-8i9sb-cjs4pklxxjykqqq', new_job['uuid']
+ assert_equal '077ba2ad3ea24a929091a9e6ce545c93199b8e57', new_job['script_version']
+ end
+
+
+end
require 'test_helper'
+load 'test/functional/arvados/v1/git_setup.rb'
class Arvados::V1::JobsControllerTest < ActionController::TestCase
+ include GitSetup
+
test "submit a job" do
authorize_with :active
post :create, job: {
script: "hash",
script_version: "master",
+ repository: "foo",
script_parameters: {}
}
assert_response :success
script: "hash",
script_version: "master",
script_parameters: {},
+ repository: "foo",
started_at: Time.now,
finished_at: Time.now,
running: false,
}
assert_response 422
end
+
+
end
test "should get fresh discovery document" do
MAX_SCHEMA_AGE = 60
- get :discovery_rest_description
+ get :index
assert_response :success
discovery_doc = JSON.parse(@response.body)
assert_equal 'discovery#restDescription', discovery_doc['kind']
class Arvados::V1::UsersControllerTest < ActionController::TestCase
+ setup do
+ @all_links_at_start = Link.all
+ @vm_uuid = virtual_machines(:testvm).uuid
+ end
+
test "activate a user after signing UA" do
authorize_with :inactive_but_signed_user_agreement
get :current
assert_equal true, me['is_active']
end
+ test "create new user with user as input" do
+ authorize_with :admin
+ post :create, user: {
+ first_name: "test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ assert_response :success
+ created = JSON.parse(@response.body)
+ assert_equal 'test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected uuid for the newly created user'
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+ end
+
+ test "create user with user, vm and repo as input" do
+ authorize_with :admin
+ repo_name = 'test_repo'
+
+ post :setup, {
+ repo_name: repo_name,
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ user: {
+ uuid: "this_is_agreeable",
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+
+ created = find_obj_in_resp response_items, 'User', nil
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected non-null uuid for the new user'
+ assert_equal 'this_is_agreeable', created['uuid']
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # arvados#user, repo link and link add user to 'All users' group
+ verify_num_links @all_links_at_start, 3
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_write',
+ repo_name, created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ # invoke setup again with the same data
+ post :setup, {
+ repo_name: repo_name,
+ vm_uuid: @vm_uuid,
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ user: {
+ uuid: "this_is_agreeable",
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }
+
+ response_items = JSON.parse(@response.body)['items']
+
+ created = find_obj_in_resp response_items, 'User', nil
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected non-null uuid for the new user'
+ assert_equal 'this_is_agreeable', created['uuid']
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # arvados#user, repo link and link add user to 'All users' group
+ verify_num_links @all_links_at_start, 4
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_write',
+ repo_name, created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ @vm_uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "setup user with bogus uuid and expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ uuid: 'bogus_uuid',
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid
+ }
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'Path not found'), 'Expected 404'
+ end
+
+ test "setup user with bogus uuid in user and expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ user: {uuid: 'bogus_uuid'},
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'ArgumentError: Require user email'),
+ 'Expected RuntimeError'
+ end
+
+ test "setup user with no uuid and user, expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'Required uuid or user'),
+ 'Expected ArgumentError'
+ end
+
+ test "setup user with no uuid and email, expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ user: {},
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? '<ArgumentError: Require user email'),
+ 'Expected ArgumentError'
+ end
+
+ test "invoke setup with existing uuid, vm and repo and verify links" do
+ authorize_with :inactive
+ get :current
+ assert_response :success
+ inactive_user = JSON.parse(@response.body)
+
+ authorize_with :admin
+
+ post :setup, {
+ uuid: inactive_user['uuid'],
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ resp_obj = find_obj_in_resp response_items, 'User', nil
+
+ assert_not_nil resp_obj['uuid'], 'expected uuid for the new user'
+ assert_equal inactive_user['uuid'], resp_obj['uuid']
+ assert_equal inactive_user['email'], resp_obj['email'],
+ 'expecting inactive user email'
+
+ # expect repo and vm links
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_write',
+ 'test_repo', resp_obj['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ @vm_uuid, resp_obj['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "invoke setup with existing uuid in user, verify response" do
+ authorize_with :inactive
+ get :current
+ assert_response :success
+ inactive_user = JSON.parse(@response.body)
+
+ authorize_with :admin
+
+ post :setup, {
+ user: {uuid: inactive_user['uuid']},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ resp_obj = find_obj_in_resp response_items, 'User', nil
+
+ assert_not_nil resp_obj['uuid'], 'expected uuid for the new user'
+ assert_equal inactive_user['uuid'], resp_obj['uuid']
+ assert_equal inactive_user['email'], resp_obj['email'],
+ 'expecting inactive user email'
+ end
+
+ test "invoke setup with existing uuid but different email, expect original email" do
+ authorize_with :inactive
+ get :current
+ assert_response :success
+ inactive_user = JSON.parse(@response.body)
+
+ authorize_with :admin
+
+ post :setup, {
+ uuid: inactive_user['uuid'],
+ user: {email: 'junk_email'}
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ resp_obj = find_obj_in_resp response_items, 'User', nil
+
+ assert_not_nil resp_obj['uuid'], 'expected uuid for the new user'
+ assert_equal inactive_user['uuid'], resp_obj['uuid']
+ assert_equal inactive_user['email'], resp_obj['email'],
+ 'expecting inactive user email'
+ end
+
+ test "setup user with valid email and repo as input" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for the new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+
+ # three extra links; login link, group link and repo link
+ verify_num_links @all_links_at_start, 3
+ end
+
+ test "setup user with fake vm and expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ vm_uuid: 'no_such_vm',
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? "No vm found for no_such_vm"),
+ 'Expected RuntimeError: No vm found for no_such_vm'
+ end
+
+ test "setup user with valid email, repo and real vm as input" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ vm_uuid: @vm_uuid,
+ user: {email: 'foo@example.com'}
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for the new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+
+ # three extra links; login link, group link and repo link
+ verify_num_links @all_links_at_start, 4
+ end
+
+ test "setup user with valid email, no vm and repo as input" do
+ authorize_with :admin
+
+ post :setup, {
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+
+ # two extra links; login link and group link
+ verify_num_links @all_links_at_start, 2
+ end
+
+ test "setup user with email, first name, repo name and vm uuid" do
+ authorize_with :admin
+
+ post :setup, {
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ user: {
+ first_name: 'test_first_name',
+ email: 'foo@example.com'
+ }
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+ assert_equal 'test_first_name', response_object['first_name'],
+ 'expecting first name'
+
+ # four extra links; login link, group link, repo link and vm link
+ verify_num_links @all_links_at_start, 4
+ end
+
+ test "setup user twice with email and check two different objects created" do
+ authorize_with :admin
+
+ post :setup, {
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ repo_name: 'test_repo',
+ user: {
+ email: 'foo@example.com'
+ }
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil response_object['uuid'], 'expected uuid for new user'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+ verify_num_links @all_links_at_start, 3 # openid, group, and repo. no vm
+
+ # create again
+ post :setup, {
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ response_object2 = find_obj_in_resp response_items, 'User', nil
+ assert_not_equal response_object['uuid'], response_object2['uuid'],
+ 'expected same uuid as first create operation'
+ assert_equal response_object['email'], 'foo@example.com', 'expected given email'
+
+ # extra login link only
+ verify_num_links @all_links_at_start, 4
+ end
+
+ test "setup user with openid prefix" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ openid_prefix: 'http://www.example.com/account',
+ user: {
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected uuid for new user'
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # verify links
+ # 3 new links: arvados#user, repo, and 'All users' group.
+ verify_num_links @all_links_at_start, 3
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_write',
+ 'test_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "invoke setup with no openid prefix, expect error" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ user: {
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ }
+ }
+
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'openid_prefix parameter is missing'),
+ 'Expected ArgumentError'
+ end
+
+ test "setup user with user, vm and repo and verify links" do
+ authorize_with :admin
+
+ post :setup, {
+ user: {
+ first_name: "in_create_test_first_name",
+ last_name: "test_last_name",
+ email: "foo@example.com"
+ },
+ vm_uuid: @vm_uuid,
+ repo_name: 'test_repo',
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal 'in_create_test_first_name', created['first_name']
+ assert_not_nil created['uuid'], 'expected uuid for new user'
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_nil created['identity_url'], 'expected no identity_url'
+
+ # expect 4 new links: arvados#user, repo, vm and 'All users' group link
+ verify_num_links @all_links_at_start, 4
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_write',
+ 'test_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ @vm_uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "create user as non admin user and expect error" do
+ authorize_with :active
+
+ post :create, {
+ user: {email: 'foo@example.com'}
+ }
+
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'PermissionDenied'),
+ 'Expected PermissionDeniedError'
+ end
+
+ test "setup user as non admin user and expect error" do
+ authorize_with :active
+
+ post :setup, {
+ openid_prefix: 'https://www.google.com/accounts/o8/id',
+ user: {email: 'foo@example.com'}
+ }
+
+ response_body = JSON.parse(@response.body)
+ response_errors = response_body['errors']
+ assert_not_nil response_errors, 'Expected error in response'
+ assert (response_errors.first.include? 'Forbidden'),
+ 'Expected Forbidden error'
+ end
+
+ test "setup user in multiple steps and verify response" do
+ authorize_with :admin
+
+ post :setup, {
+ openid_prefix: 'http://www.example.com/account',
+ user: {
+ email: "foo@example.com"
+ }
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_not_nil created['uuid'], 'expected uuid for new user'
+ assert_not_nil created['email'], 'expected non-nil email'
+ assert_equal created['email'], 'foo@example.com', 'expected input email'
+
+ # verify links; 2 new links: arvados#user, and 'All users' group.
+ verify_num_links @all_links_at_start, 2
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', false, 'permission', 'can_write',
+ 'test_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ # invoke setup with a repository
+ post :setup, {
+ openid_prefix: 'http://www.example.com/account',
+ repo_name: 'new_repo',
+ uuid: created['uuid']
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal 'foo@example.com', created['email'], 'expected input email'
+
+ # verify links
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_write',
+ 'new_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', false, 'permission', 'can_login',
+ nil, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ # invoke setup with a vm_uuid
+ post :setup, {
+ vm_uuid: @vm_uuid,
+ openid_prefix: 'http://www.example.com/account',
+ user: {
+ email: 'junk_email'
+ },
+ uuid: created['uuid']
+ }
+
+ assert_response :success
+
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+
+ assert_equal created['email'], 'foo@example.com', 'expected original email'
+
+ # verify links
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ # since no repo name in input, we won't get any; even though user has one
+ verify_link response_items, 'arvados#repository', false, 'permission', 'can_write',
+ 'new_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ @vm_uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+ end
+
+ test "setup and unsetup user" do
+ authorize_with :admin
+
+ post :setup, {
+ repo_name: 'test_repo',
+ vm_uuid: @vm_uuid,
+ user: {email: 'foo@example.com'},
+ openid_prefix: 'https://www.google.com/accounts/o8/id'
+ }
+
+ assert_response :success
+ response_items = JSON.parse(@response.body)['items']
+ created = find_obj_in_resp response_items, 'User', nil
+ assert_not_nil created['uuid'], 'expected uuid for the new user'
+ assert_equal created['email'], 'foo@example.com', 'expected given email'
+
+ # 4 extra links: login, group, repo and vm
+ verify_num_links @all_links_at_start, 4
+
+ verify_link response_items, 'arvados#user', true, 'permission', 'can_login',
+ created['uuid'], created['email'], 'arvados#user', false, 'User'
+
+ verify_link response_items, 'arvados#group', true, 'permission', 'can_read',
+ 'All users', created['uuid'], 'arvados#group', true, 'Group'
+
+ verify_link response_items, 'arvados#repository', true, 'permission', 'can_write',
+ 'test_repo', created['uuid'], 'arvados#repository', true, 'Repository'
+
+ verify_link response_items, 'arvados#virtualMachine', true, 'permission', 'can_login',
+ @vm_uuid, created['uuid'], 'arvados#virtualMachine', false, 'VirtualMachine'
+
+ verify_link_existence created['uuid'], created['email'], true, true, true, false
+
+ # now unsetup this user
+ post :unsetup, uuid: created['uuid']
+ assert_response :success
+
+ created2 = JSON.parse(@response.body)
+ assert_not_nil created2['uuid'], 'expected uuid for the newly created user'
+ assert_equal created['uuid'], created2['uuid'], 'expected uuid not found'
+
+ verify_link_existence created['uuid'], created['email'], false, false, false, false
+ end
+
+ test "unsetup active user" do
+ authorize_with :active
+ get :current
+ assert_response :success
+ active_user = JSON.parse(@response.body)
+ assert_not_nil active_user['uuid'], 'expected uuid for the active user'
+ assert active_user['is_active'], 'expected is_active for active user'
+
+ verify_link_existence active_user['uuid'], active_user['email'],
+ false, false, false, true
+
+ authorize_with :admin
+
+ # now unsetup this user
+ post :unsetup, uuid: active_user['uuid']
+ assert_response :success
+
+ response_user = JSON.parse(@response.body)
+ assert_not_nil response_user['uuid'], 'expected uuid for the upsetup user'
+ assert_equal active_user['uuid'], response_user['uuid'], 'expected uuid not found'
+ assert !response_user['is_active'], 'expected user to be inactive'
+
+ verify_link_existence response_user['uuid'], response_user['email'],
+ false, false, false, false
+ end
+
+ def verify_num_links (original_links, expected_additional_links)
+ links_now = Link.all
+ assert_equal original_links.size+expected_additional_links, Link.all.size,
+ "Expected #{expected_additional_links.inspect} more links"
+ end
+
+ def find_obj_in_resp (response_items, object_type, head_kind=nil)
+ return_obj = nil
+ response_items.each { |x|
+ if !x
+ next
+ end
+
+ if object_type == 'User'
+ if !x['head_kind']
+ return_obj = x
+ break
+ end
+ else # looking for a link
+ if x['head_kind'] == head_kind
+ return_obj = x
+ break
+ end
+ end
+ }
+ return return_obj
+ end
+
+ def verify_link(response_items, link_object_name, expect_link, link_class,
+ link_name, head_uuid, tail_uuid, head_kind, fetch_object, class_name)
+
+ link = find_obj_in_resp response_items, 'Link', link_object_name
+
+ if !expect_link
+ assert_nil link, "Expected no link for #{link_object_name}"
+ return
+ end
+
+ assert_not_nil link, "Expected link for #{link_object_name}"
+
+ if fetch_object
+ object = Object.const_get(class_name).where(name: head_uuid)
+ assert [] != object, "expected #{class_name} with name #{head_uuid}"
+ head_uuid = object.first[:uuid]
+ end
+ assert_equal link['link_class'], link_class,
+ "did not find expected link_class for #{link_object_name}"
+
+ assert_equal link['name'], link_name,
+ "did not find expected link_name for #{link_object_name}"
+
+ assert_equal link['tail_uuid'], tail_uuid,
+ "did not find expected tail_uuid for #{link_object_name}"
+
+ assert_equal link['head_kind'], head_kind,
+ "did not find expected head_kind for #{link_object_name}"
+
+ assert_equal link['head_uuid'], head_uuid,
+ "did not find expected head_uuid for #{link_object_name}"
+ end
+
+ def verify_link_existence uuid, email, expect_oid_login_perms,
+ expect_repo_perms, expect_vm_perms, expect_signatures
+ # verify that all links are deleted for the user
+ oid_login_perms = Link.where(tail_uuid: email,
+ head_kind: 'arvados#user',
+ link_class: 'permission',
+ name: 'can_login')
+ if expect_oid_login_perms
+ assert oid_login_perms.any?, "expected oid_login_perms"
+ else
+ assert !oid_login_perms.any?, "expected all oid_login_perms deleted"
+ end
+
+ repo_perms = Link.where(tail_uuid: uuid,
+ head_kind: 'arvados#repository',
+ link_class: 'permission',
+ name: 'can_write')
+ if expect_repo_perms
+ assert repo_perms.any?, "expected repo_perms"
+ else
+ assert !repo_perms.any?, "expected all repo_perms deleted"
+ end
+
+ vm_login_perms = Link.where(tail_uuid: uuid,
+ head_kind: 'arvados#virtualMachine',
+ link_class: 'permission',
+ name: 'can_login')
+ if expect_vm_perms
+ assert vm_login_perms.any?, "expected vm_login_perms"
+ else
+ assert !vm_login_perms.any?, "expected all vm_login_perms deleted"
+ end
+
+ signed_uuids = Link.where(link_class: 'signature',
+ tail_kind: 'arvados#user',
+ tail_uuid: uuid)
+
+ if expect_signatures
+ assert signed_uuids.any?, "expected singnatures"
+ else
+ assert !signed_uuids.any?, "expected all singnatures deleted"
+ end
+
+ end
end
--- /dev/null
+package main
+
+import (
+ "bufio"
+ "crypto/md5"
+ "errors"
+ "fmt"
+ "github.com/gorilla/mux"
+ "log"
+ "net/http"
+ "os"
+ "strings"
+)
+
+const DEFAULT_PORT = 25107
+const BLOCKSIZE = 64 * 1024 * 1024
+
+var KeepVolumes []string
+
+func main() {
+ // Look for local keep volumes.
+ KeepVolumes = FindKeepVolumes()
+ if len(KeepVolumes) == 0 {
+ log.Fatal("could not find any keep volumes")
+ }
+ for _, v := range KeepVolumes {
+ log.Println("keep volume:", v)
+ }
+
+ // Set up REST handlers.
+ //
+ // Start with a router that will route each URL path to an
+ // appropriate handler.
+ //
+ rest := mux.NewRouter()
+ rest.HandleFunc("/{hash:[0-9a-f]{32}}", GetBlockHandler).Methods("GET")
+
+ // Tell the built-in HTTP server to direct all requests to the REST
+ // router.
+ http.Handle("/", rest)
+
+ // Start listening for requests.
+ port := fmt.Sprintf(":%d", DEFAULT_PORT)
+ http.ListenAndServe(port, nil)
+}
+
+// FindKeepVolumes
+// Returns a list of Keep volumes mounted on this system.
+//
+// A Keep volume is a normal or tmpfs volume with a /keep
+// directory at the top level of the mount point.
+//
+func FindKeepVolumes() []string {
+ vols := make([]string, 0)
+
+ if f, err := os.Open("/proc/mounts"); err != nil {
+ log.Fatal("could not read /proc/mounts: ", err)
+ } else {
+ scanner := bufio.NewScanner(f)
+ for scanner.Scan() {
+ args := strings.Fields(scanner.Text())
+ dev, mount := args[0], args[1]
+ if (dev == "tmpfs" || strings.HasPrefix(dev, "/dev/")) && mount != "/" {
+ keep := mount + "/keep"
+ if st, err := os.Stat(keep); err == nil && st.IsDir() {
+ vols = append(vols, keep)
+ }
+ }
+ }
+ if err := scanner.Err(); err != nil {
+ log.Fatal(err)
+ }
+ }
+ return vols
+}
+
+func GetBlockHandler(w http.ResponseWriter, req *http.Request) {
+ hash := mux.Vars(req)["hash"]
+
+ block, err := GetBlock(hash)
+ if err != nil {
+ http.Error(w, err.Error(), 404)
+ return
+ }
+
+ _, err = w.Write(block)
+ if err != nil {
+ log.Printf("GetBlockHandler: writing response: %s", err)
+ }
+
+ return
+}
+
+func GetBlock(hash string) ([]byte, error) {
+ var buf = make([]byte, BLOCKSIZE)
+
+ // Attempt to read the requested hash from a keep volume.
+ for _, vol := range KeepVolumes {
+ var f *os.File
+ var err error
+ var nread int
+
+ path := fmt.Sprintf("%s/%s/%s", vol, hash[0:3], hash)
+
+ f, err = os.Open(path)
+ if err != nil {
+ log.Printf("%s: opening %s: %s\n", vol, path, err)
+ continue
+ }
+
+ nread, err = f.Read(buf)
+ if err != nil {
+ log.Printf("%s: reading %s: %s\n", vol, path, err)
+ continue
+ }
+
+ // Double check the file checksum.
+ //
+ filehash := fmt.Sprintf("%x", md5.Sum(buf[:nread]))
+ if filehash != hash {
+ // TODO(twp): this condition probably represents a bad disk and
+ // should raise major alarm bells for an administrator: e.g.
+ // they should be sent directly to an event manager at high
+ // priority or logged as urgent problems.
+ //
+ log.Printf("%s: checksum mismatch: %s (actual hash %s)\n",
+ vol, path, filehash)
+ continue
+ }
+
+ // Success!
+ return buf[:nread], nil
+ }
+
+ log.Printf("%s: not found on any volumes, giving up\n", hash)
+ return buf, errors.New("not found: " + hash)
+}
--- /dev/null
+package main
+
+import (
+ "fmt"
+ "io/ioutil"
+ "os"
+ "path"
+ "testing"
+)
+
+var TEST_BLOCK = []byte("The quick brown fox jumps over the lazy dog.")
+var TEST_HASH = "e4d909c290d0fb1ca068ffaddf22cbd0"
+var BAD_BLOCK = []byte("The magic words are squeamish ossifrage.")
+
+// Test simple block reads.
+func TestGetBlockOK(t *testing.T) {
+ defer teardown()
+
+ // Create two test Keep volumes and store a block in each of them.
+ setup(t, 2)
+ for _, vol := range KeepVolumes {
+ store(t, vol, TEST_HASH, TEST_BLOCK)
+ }
+
+ // Check that GetBlock returns success.
+ result, err := GetBlock(TEST_HASH)
+ if err != nil {
+ t.Errorf("GetBlock error: %s", err)
+ }
+ if fmt.Sprint(result) != fmt.Sprint(TEST_BLOCK) {
+ t.Errorf("expected %s, got %s", TEST_BLOCK, result)
+ }
+}
+
+// Test block reads when one Keep volume is missing.
+func TestGetBlockOneKeepOK(t *testing.T) {
+ defer teardown()
+
+ // Two test Keep volumes, only the second has a block.
+ setup(t, 2)
+ store(t, KeepVolumes[1], TEST_HASH, TEST_BLOCK)
+
+ // Check that GetBlock returns success.
+ result, err := GetBlock(TEST_HASH)
+ if err != nil {
+ t.Errorf("GetBlock error: %s", err)
+ }
+ if fmt.Sprint(result) != fmt.Sprint(TEST_BLOCK) {
+ t.Errorf("expected %s, got %s", TEST_BLOCK, result)
+ }
+}
+
+// Test block read failure.
+func TestGetBlockFail(t *testing.T) {
+ defer teardown()
+
+ // Create two empty test Keep volumes.
+ setup(t, 2)
+
+ // Check that GetBlock returns failure.
+ result, err := GetBlock(TEST_HASH)
+ if err == nil {
+ t.Errorf("GetBlock incorrectly returned success: ", result)
+ }
+}
+
+// Test reading a corrupt block.
+func TestGetBlockCorrupt(t *testing.T) {
+ defer teardown()
+
+ // Create two test Keep volumes and store a block in each of them,
+ // but the hash of the block does not match the filename.
+ setup(t, 2)
+ for _, vol := range KeepVolumes {
+ store(t, vol, TEST_HASH, BAD_BLOCK)
+ }
+
+ // Check that GetBlock returns failure.
+ result, err := GetBlock(TEST_HASH)
+ if err == nil {
+ t.Errorf("GetBlock incorrectly returned success: %s", result)
+ }
+}
+
+// setup
+// Create KeepVolumes for testing.
+//
+func setup(t *testing.T, num_volumes int) {
+ KeepVolumes = make([]string, num_volumes)
+ for i := range KeepVolumes {
+ if dir, err := ioutil.TempDir(os.TempDir(), "keeptest"); err == nil {
+ KeepVolumes[i] = dir + "/keep"
+ } else {
+ t.Fatal(err)
+ }
+ }
+}
+
+// teardown
+// Cleanup to perform after each test.
+//
+func teardown() {
+ for _, vol := range KeepVolumes {
+ os.RemoveAll(path.Dir(vol))
+ }
+}
+
+// store
+//
+func store(t *testing.T, keepdir string, filename string, block []byte) error {
+ blockdir := fmt.Sprintf("%s/%s", keepdir, filename[:3])
+ if err := os.MkdirAll(blockdir, 0755); err != nil {
+ t.Fatal(err)
+ }
+
+ blockpath := fmt.Sprintf("%s/%s", blockdir, filename)
+ if f, err := os.Create(blockpath); err == nil {
+ f.Write(block)
+ f.Close()
+ } else {
+ t.Fatal(err)
+ }
+
+ return nil
+}
projects / arvados.git / commitdiff
