[ARVADOS] updated: 91a77b7ce2abca7d4297b2dfa5eca54fc78a1425
git at public.curoverse.com
git at public.curoverse.com
Tue Jul 21 10:30:23 EDT 2015
Summary of changes:
.../app/controllers/application_controller.rb | 1 +
.../app/views/users/_manage_repositories.html.erb | 1 +
.../views/users/_manage_virtual_machines.html.erb | 9 +-
apps/workbench/config/load_config.rb | 12 ++-
.../controllers/application_controller_test.rb | 16 +++
.../controllers/collections_controller_test.rb | 53 ++++++++++
.../test/controllers/projects_controller_test.rb | 64 ++++++++++++
.../test/controllers/users_controller_test.rb | 45 +++++++++
.../test/integration/anonymous_access_test.rb | 10 --
.../test/integration/application_layout_test.rb | 8 ++
.../test/integration/collection_upload_test.rb | 7 --
.../workbench/test/integration/collections_test.rb | 45 ---------
apps/workbench/test/integration/projects_test.rb | 109 ---------------------
.../test/integration/user_manage_account_test.rb | 2 +
apps/workbench/test/integration/users_test.rb | 40 --------
doc/_config.yml | 1 +
doc/_includes/_tutorial_expectations.liquid | 2 +-
doc/images/add-new-repository.png | Bin 10026 -> 9575 bytes
doc/images/added-new-repository.png | Bin 0 -> 14210 bytes
doc/images/vm-access-with-webshell.png | Bin 0 -> 61121 bytes
doc/install/install-api-server.html.textile.liquid | 24 +++--
.../install-arv-git-httpd.html.textile.liquid | 24 ++---
.../install-shell-server.html.textile.liquid | 13 +++
doc/install/install-sso.html.textile.liquid | 6 +-
.../check-environment.html.textile.liquid | 2 +-
.../ssh-access-unix.html.textile.liquid | 2 +-
.../ssh-access-windows.html.textile.liquid | 2 +-
.../vm-login-with-webshell.html.textile.liquid | 19 ++++
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
.../add-new-repository.html.textile.liquid | 10 +-
.../tutorial-submit-job.html.textile.liquid | 13 ++-
sdk/python/arvados/util.py | 18 ++--
sdk/python/tests/run_test_server.py | 7 +-
sdk/python/tests/test_util.py | 18 +++-
34 files changed, 312 insertions(+), 273 deletions(-)
create mode 100644 doc/images/added-new-repository.png
create mode 100644 doc/images/vm-access-with-webshell.png
create mode 100644 doc/user/getting_started/vm-login-with-webshell.html.textile.liquid
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commit 91a77b7ce2abca7d4297b2dfa5eca54fc78a1425
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jul 21 10:26:10 2015 -0400
6438: Make puma run script relocatable, set ARVADOS_WEBSOCKETS.
diff --git a/doc/install/install-api-server.html.textile.liquid b/doc/install/install-api-server.html.textile.liquid
index f0f2cde..f2e868f 100644
--- a/doc/install/install-api-server.html.textile.liquid
+++ b/doc/install/install-api-server.html.textile.liquid
@@ -173,18 +173,21 @@ For best performance, we recommend you use Nginx as your Web server front-end, w
<pre><code>#!/bin/bash
set -e
+exec 2>&1
+
# Uncomment the line below if you're using RVM.
#source /etc/profile.d/rvm.sh
-envdir="/etc/sv/puma/env"
-root=/etc/sv/puma
-echo "Starting puma from ${root}"
-cd $root
-mkdir -p "${envdir}"
-exec 2>&1
+envdir="`pwd`/env"
+mkdir -p "$envdir"
+echo ws-only > "$envdir/ARVADOS_WEBSOCKETS"
+
cd /var/www/arvados-api/current
+echo "Starting puma in `pwd`"
+
# You may need to change arguments below to match your deployment, especially -u.
-exec chpst -e "${envdir}" -m 1073741824 -u www-data:www-data bundle exec puma -t 0:512 -e production -b tcp://127.0.0.1:8100
+exec chpst -m 1073741824 -u www-data:www-data -e "$envdir" \
+ bundle exec puma -t 0:512 -e production -b tcp://127.0.0.1:8100
</code></pre>
</li>
commit 1794be475e5bb94d8dd6764329731bacc2a67f2b
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Jul 16 16:17:44 2015 -0400
6438: Back out dependency on lsb_release command.
diff --git a/doc/install/install-manual-prerequisites.html.textile.liquid b/doc/install/install-manual-prerequisites.html.textile.liquid
index 13b875d..96d3082 100644
--- a/doc/install/install-manual-prerequisites.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites.html.textile.liquid
@@ -48,12 +48,12 @@ First, register the Curoverse signing key in apt's database:
{% include 'install_debian_key' %}
-Configure apt to retrieve packages from the Arvados package repository:
+Configure apt to retrieve packages from the Arvados package repository. This command depends on your OS vendor and version:
-<notextile>
-<pre><code>~$ <span class="userinput">echo "deb http://apt.arvados.org/ $(lsb_release -cs) main" | sudo tee /etc/apt/sources.list.d/arvados.list</span>
-</code></pre>
-</notextile>
+table(table table-bordered table-condensed).
+|OS version|Command|
+|Debian 7 ("wheezy")|<notextile><code><span class="userinput">echo "deb http://apt.arvados.org/ wheezy main" | sudo tee /etc/apt/sources.list.d/arvados.list</span></code></notextile>|
+|Ubuntu 12.04 ("precise")|<notextile><code><span class="userinput">echo "deb http://apt.arvados.org/ precise main" | sudo tee /etc/apt/sources.list.d/arvados.list</span></code></notextile>|
Retrieve the package list:
commit 8c1a3773b9ae07e8f37e3567a9e7c225e47d2ea5
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Jul 16 15:03:36 2015 -0400
6438: Add missing steps to SSO installation.
diff --git a/doc/install/install-sso.html.textile.liquid b/doc/install/install-sso.html.textile.liquid
index c078e46..d07fc3f 100644
--- a/doc/install/install-sso.html.textile.liquid
+++ b/doc/install/install-sso.html.textile.liquid
@@ -8,6 +8,24 @@ h2(#dependencies). Install dependencies
Make sure you have "Ruby and Bundler":install-manual-prerequisites-ruby.html installed.
+On a Debian-based system, install the following packages:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo apt-get install git libpq-dev postgresql</span>
+</code></pre>
+</notextile>
+
+On a Red Hat-based system, install the following packages:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo yum install git postgresql postgresql-devel</span>
+</code></pre>
+</notextile>
+
+{% include 'notebox_begin' %}
+If your distribution offers PostgreSQL 8, consider using Software Collections to install postgresql92 and postgresql92-postgresql-devel instead, as described on the "API server installation page":install-api-server.html.
+{% include 'notebox_end' %}
+
h2(#install). Install SSO server
h3. Get SSO server code and run bundle
@@ -16,7 +34,7 @@ h3. Get SSO server code and run bundle
<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
~$ <span class="userinput">git clone https://github.com/curoverse/sso-devise-omniauth-provider.git</span>
~$ <span class="userinput">cd sso-devise-omniauth-provider</span>
-~/sso-devise-omniauth-provider$ <span class="userinput">bundle install</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">bundle</span>
</code></pre></notextile>
h2. Configure the SSO server
@@ -48,28 +66,35 @@ Then put that value in the @secret_token@ field.
h3(#authentication_methods). Authentication methods
-Three authentication methods are supported: google OAuth2, ldap, local accounts.
+Three authentication methods are supported: Google+, LDAP, and local accounts.
-h3(#google_oauth2). google_oauth2 authentication
+h3(#google). Google+ authentication
-Google OAuth2 authentication can be configured with these options.
+In order to use Google+ authentication, you must use the "Google Developers Console":https://console.developers.google.com to create a set of client credentials. In short:
-<pre>
+* Enable the Contacts and Google+ APIs.
+* Create an OAuth Client ID for a web application.
+** JavaScript origins: @https://sso.example.com/@
+** Redirect URIs: @https://sso.example.com/auth/google_oauth2/callback@
+
+Copy the "Client ID" and "Client secret" values from the Google Developers Console into the Google section of @config/application.yml@, like this:
+
+<notextile>
+<pre><code>
# Google API tokens required for OAuth2 login.
#
# See https://github.com/zquestz/omniauth-google-oauth2
#
# and https://developers.google.com/accounts/docs/OAuth2
- google_oauth2_client_id: false
- google_oauth2_client_secret: false
+ google_oauth2_client_id: "<span class="userinput">---YOUR---CLIENT---ID---HERE---</span>"
+ google_oauth2_client_secret: "<span class="userinput">---YOUR---CLIENT---SECRET---HERE---</span>"
# Set this to your OpenId 2.0 realm to enable migration from Google OpenId
# 2.0 to Google OAuth2 OpenId Connect (Google will provide OpenId 2.0 user
# identifiers via the openid.realm parameter in the OAuth2 flow until 2017).
- google_openid_realm: false
-</pre>
+ google_openid_realm: <span class="userinput">false</span></code></pre></notextile>
-h3(#ldap). ldap authentication
+h3(#ldap). LDAP authentication
LDAP authentication can be configured with these options. Make sure to preserve the indentation of the fields beyond @use_ldap at .
@@ -92,7 +117,7 @@ LDAP authentication can be configured with these options. Make sure to preserve
use_ldap: false
</pre>
-h3(#local_accounts). local account authentication
+h3(#local_accounts). Local account authentication
If neither Google OAuth2 nor LDAP are enabled, the SSO server automatically
falls back to local accounts. There are two configuration options for local
@@ -121,7 +146,7 @@ You can also create local accounts on the SSO server from the rails console:
h2. Set up the database
-Generate a new database password. Nobody ever needs to memorize it or type it, so we'll make a strong one:
+Generate a new database password. Nobody ever needs to memorize it or type it, so make a strong one:
<notextile>
<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">ruby -e 'puts rand(2**128).to_s(36)'</span>
@@ -153,7 +178,7 @@ Alternatively, if the database user you intend to use for the SSO server is not
<notextile>
<pre><code>~/sso-devise-omniauth-provider$ <span class="userinput">su postgres createdb arvados_sso_production -E UTF8 -O arvados_sso</span>
-~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rake db:structure:load</span>
+~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rake db:schema:load</span>
~/sso-devise-omniauth-provider$ <span class="userinput">RAILS_ENV=production bundle exec rake db:seed</span>
</code></pre></notextile>
commit 9e4957c362c398c4276833075f54b19fa4050041
Author: Tom Clegg <tom at curoverse.com>
Date: Mon Jul 13 10:08:20 2015 -0400
6438: Use uuid_prefix (more) consistently.
diff --git a/doc/install/install-api-server.html.textile.liquid b/doc/install/install-api-server.html.textile.liquid
index bdd9379..f0f2cde 100644
--- a/doc/install/install-api-server.html.textile.liquid
+++ b/doc/install/install-api-server.html.textile.liquid
@@ -127,7 +127,7 @@ h3. workbench_address
Fill in the url of your workbench application in @workbench_address@, for example
- https://workbench.@prefix_uuid@.your.domain
+ https://workbench.@uuid_prefix@.your.domain
h3(#omniauth). sso_app_id, sso_app_secret, sso_provider_url
@@ -215,7 +215,7 @@ proxy_http_version 1.1;
server {
listen <span class="userinput">[your public IP address]</span>:443 ssl;
- server_name <span class="userinput">uuid-prefix.your.domain</span>;
+ server_name <span class="userinput">uuid_prefix.your.domain</span>;
ssl on;
@@ -235,7 +235,7 @@ server {
server {
listen <span class="userinput">[your public IP address]</span>:443 ssl;
- server_name ws.<span class="userinput">uuid-prefix.your.domain</span>;
+ server_name ws.<span class="userinput">uuid_prefix.your.domain</span>;
ssl on;
commit 8c8b6b67c412633c762af1769c71af56c2310f5c
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Jul 10 11:07:50 2015 -0400
6438: Merge debian and ubuntu sections. The same recipe works for both.
diff --git a/doc/install/install-manual-prerequisites.html.textile.liquid b/doc/install/install-manual-prerequisites.html.textile.liquid
index de8f8cb..13b875d 100644
--- a/doc/install/install-manual-prerequisites.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites.html.textile.liquid
@@ -40,28 +40,11 @@ baseurl=http://rpm.arvados.org/CentOS/$releasever/os/$basearch/
</code></pre>
</notextile>
-h3. Debian
+h3. Debian and Ubuntu
-Packages are available for Debian 7 ("wheezy"). First, register the Curoverse signing key in apt's database:
+Packages are available for Debian 7 ("wheezy") and Ubuntu 12.04 ("precise").
-{% include 'install_debian_key' %}
-
-Then save the configuration line listed for your version of Debian in @/etc/apt/sources.list.d/arvados.list@:
-
-table(table table-bordered table-condensed).
-|*Debian version*|*@/etc/apt/sources.list.d/arvados.list@*|
-|7 ("wheezy")|@deb http://apt.arvados.org/ wheezy main@|
-
-Finally, add this new repository to apt's database:
-
-<notextile>
-<pre><code>~$ <span class="userinput">sudo /usr/bin/apt-get update</span>
-</code></pre>
-</notextile>
-
-h3. Ubuntu
-
-Packages are available for Ubuntu 12.04 ("precise"). First, register the Curoverse signing key in apt's database:
+First, register the Curoverse signing key in apt's database:
{% include 'install_debian_key' %}
commit 0bb9d575d4c9609693d71fa47f8958af10f40d2b
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Jul 10 11:02:22 2015 -0400
6438: Use urandom instead of md5(hostname) for UUID. Avoid using Ruby at this stage.
diff --git a/doc/install/install-manual-prerequisites.html.textile.liquid b/doc/install/install-manual-prerequisites.html.textile.liquid
index 420c12a..de8f8cb 100644
--- a/doc/install/install-manual-prerequisites.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites.html.textile.liquid
@@ -81,11 +81,12 @@ Retrieve the package list:
h2. A unique identifier
-Each Arvados installation should have a globally unique identifier, which is a unique 5-character alphanumeric string. Here is a snippet of ruby that generates such a string based on the hostname of your computer:
+Each Arvados installation should have a globally unique identifier, which is a unique 5-character lowercase alphanumeric string. For testing purposes, here is one way to make a random 5-character string:
-<pre>
-Digest::MD5.hexdigest(`hostname`).to_i(16).to_s(36)[0..4]
-</pre>
+<notextile>
+<pre><code>~$ <span class="userinput">tr -dc 0-9a-z </dev/urandom | head -c5; echo</span>
+</code></pre>
+</notextile>
You may also use a different method to pick the unique identifier. The unique identifier will be part of the hostname of the services in your Arvados cluster. The rest of this documentation will refer to it as your @uuid_prefix at .
commit e6e3409439ef6d72a701e409b1c079900e006913
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Jul 10 11:00:46 2015 -0400
6438: Add missing "apt-get update". Give a command to add the package repo.
Replace version table with $(lsb_release -cs).
diff --git a/doc/install/install-manual-prerequisites.html.textile.liquid b/doc/install/install-manual-prerequisites.html.textile.liquid
index afe2830..420c12a 100644
--- a/doc/install/install-manual-prerequisites.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites.html.textile.liquid
@@ -65,11 +65,19 @@ Packages are available for Ubuntu 12.04 ("precise"). First, register the Curove
{% include 'install_debian_key' %}
-Then save the configuration line listed for your version of Ubuntu in @/etc/apt/sources.list.d/arvados.list@:
+Configure apt to retrieve packages from the Arvados package repository:
-table(table table-bordered table-condensed).
-|*Ubuntu version*|*@/etc/apt/sources.list.d/arvados.list@*|
-|12.04 ("precise")|@deb http://apt.arvados.org/ precise main@|
+<notextile>
+<pre><code>~$ <span class="userinput">echo "deb http://apt.arvados.org/ $(lsb_release -cs) main" | sudo tee /etc/apt/sources.list.d/arvados.list</span>
+</code></pre>
+</notextile>
+
+Retrieve the package list:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo apt-get update</span>
+</code></pre>
+</notextile>
h2. A unique identifier
commit 847f47a1a86d40dc6ae5d13f62039e55d1afa36d
Author: Tom Clegg <tom at curoverse.com>
Date: Fri Jul 10 10:58:29 2015 -0400
6438: Add specific commands for nginx16 and postgresql92 Software Collections.
diff --git a/doc/install/install-api-server.html.textile.liquid b/doc/install/install-api-server.html.textile.liquid
index 77a90e0..bdd9379 100644
--- a/doc/install/install-api-server.html.textile.liquid
+++ b/doc/install/install-api-server.html.textile.liquid
@@ -31,7 +31,10 @@ On a Red Hat-based system, install the following packages:
{% include 'notebox_begin' %}
-If you intend to use specific versions of these packages from Software Collections, you may have to adapt some of the package names to match; e.g., @postgresql92-postgresql-server postgresql92-postgresql-devel nginx16 at .
+If you intend to use specific versions of these packages from Software Collections, you may have to adapt some of the package names to match. For example:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo yum install postgresql92 postgresql92-postgresql-devel nginx16</span></code></pre></notextile>
{% include 'notebox_end' %}
commit d591acbac423d324cf00e5930851fff6957a19d9
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Jul 9 13:46:30 2015 -0400
6438: Add some missing steps to rvm recipe. Install rvm as root.
diff --git a/doc/install/install-manual-prerequisites-ruby.html.textile.liquid b/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
index 07f1ff2..fa6f24f 100644
--- a/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
@@ -9,9 +9,16 @@ Currently, only Ruby 2.1 is supported.
h2(#rvm). Option 1: Install with rvm
<notextile>
-<pre><code>~$ <span class="userinput">gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3</span>
-~$ <span class="userinput">\curl -sSL https://get.rvm.io | bash -s stable --ruby=2.1</span>
-~$ <span class="userinput">gem install bundler
+<pre><code><span class="userinput">sudo gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3
+\curl -sSL https://get.rvm.io | sudo bash -s stable --ruby=2.1
+sudo -i gem install bundler
+sudo adduser "$USER" rvm
+</span></code></pre></notextile>
+
+Either log out and log back in to activate RVM, or explicitly load it in all open shells like this:
+
+<notextile>
+<pre><code><span class="userinput">source /usr/local/rvm/scripts/rvm
</span></code></pre></notextile>
h2(#fromsource). Option 2: Install from source
commit 2b41829bf0a889558c320121710ef3fd2e90ef7e
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Jul 9 11:45:02 2015 -0400
6438: Bring back package dependencies for "build Ruby from source" option.
These used to be documented earlier in the process, but were removed.
diff --git a/doc/install/install-manual-prerequisites-ruby.html.textile.liquid b/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
index f1bb5f2..07f1ff2 100644
--- a/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
@@ -16,6 +16,35 @@ h2(#rvm). Option 1: Install with rvm
h2(#fromsource). Option 2: Install from source
+Install prerequisites for Debian 7 or 8:
+
+<notextile>
+<pre><code><span class="userinput">sudo apt-get install \
+ bison build-essential gettext libcurl3 libcurl3-gnutls \
+ libcurl4-openssl-dev libpcre3-dev libreadline-dev \
+ libssl-dev libxslt1.1 zlib1g-dev
+</span></code></pre></notextile>
+
+Install prerequisites for CentOS 6:
+
+<notextile>
+<pre><code><span class="userinput">sudo yum install \
+ libyaml-devel glibc-headers autoconf gcc-c++ glibc-devel \
+ patch readline-devel zlib-devel libffi-devel openssl-devel \
+ automake libtool bison sqlite-devel
+</span></code></pre></notextile>
+
+Install prerequisites for Ubuntu 12.04:
+
+<notextile>
+<pre><code><span class="userinput">sudo apt-get install \
+ gawk g++ gcc make libc6-dev libreadline6-dev zlib1g-dev libssl-dev \
+ libyaml-dev libsqlite3-dev sqlite3 autoconf libgdbm-dev \
+ libncurses5-dev automake libtool bison pkg-config libffi-dev
+</span></code></pre></notextile>
+
+Build and install Ruby:
+
<notextile>
<pre><code><span class="userinput">mkdir -p ~/src
cd ~/src
commit 623be7f83c1a88dd2eeae5ee6028daac47ad0e1c
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Jul 9 11:38:13 2015 -0400
6438: Drop wget dependency. Update ./configure flags for Ruby 2.1.6.
diff --git a/doc/install/install-manual-prerequisites-ruby.html.textile.liquid b/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
index 2142aca..f1bb5f2 100644
--- a/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
+++ b/doc/install/install-manual-prerequisites-ruby.html.textile.liquid
@@ -19,10 +19,9 @@ h2(#fromsource). Option 2: Install from source
<notextile>
<pre><code><span class="userinput">mkdir -p ~/src
cd ~/src
-wget http://cache.ruby-lang.org/pub/ruby/2.1/ruby-2.1.6.tar.gz
-tar xzf ruby-2.1.6.tar.gz
+curl http://cache.ruby-lang.org/pub/ruby/2.1/ruby-2.1.6.tar.gz | tar xz
cd ruby-2.1.6
-./configure --no-rdoc --no-ri
+./configure --no-install-rdoc
make
sudo make install
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