[ARVADOS] updated: 1fdb31ed54f690d6a14a55aa7d50559697421fb6
git at public.curoverse.com
git at public.curoverse.com
Fri Jul 10 11:02:38 EDT 2015
Summary of changes:
apps/workbench/Gemfile | 2 +-
apps/workbench/Gemfile.lock | 78 ++++++------
.../app/controllers/projects_controller.rb | 2 +-
apps/workbench/app/views/layouts/body.html.erb | 4 +-
apps/workbench/config/application.default.yml | 3 +
.../test/controllers/projects_controller_test.rb | 26 ++++
doc/install/install-api-server.html.textile.liquid | 42 ++++---
...l-manual-prerequisites-ruby.html.textile.liquid | 53 ++++++--
...nstall-manual-prerequisites.html.textile.liquid | 25 ++--
.../tutorial-keep-mount.html.textile.liquid | 2 +-
sdk/pam/arvados_pam.py | 99 +++++++++++++++
sdk/pam/debian/arvados_pam | 10 ++
sdk/pam/debian/shellinabox | 136 +++++++++++++++++++++
sdk/python/tests/run_test_server.py | 9 +-
sdk/python/tests/test_arv_put.py | 2 +-
services/api/Rakefile | 31 +++++
.../arvados/v1/repositories_controller.rb | 19 ++-
.../app/controllers/user_sessions_controller.rb | 4 +-
.../api/app/views/static/login_failure.html.erb | 2 +-
services/api/config/application.default.yml | 9 ++
services/api/config/application.yml.example | 3 +
services/api/config/database.yml.sample | 3 +
services/api/config/initializers/load_config.rb | 16 +++
.../api/config/initializers/omniauth.rb.example | 13 --
services/api/config/initializers/omniauth_init.rb | 19 +++
services/api/db/structure.sql | 2 +-
.../arvados/v1/repositories_controller_test.rb | 11 ++
27 files changed, 516 insertions(+), 109 deletions(-)
create mode 100644 sdk/pam/arvados_pam.py
create mode 100644 sdk/pam/debian/arvados_pam
create mode 100644 sdk/pam/debian/shellinabox
delete mode 100644 services/api/config/initializers/omniauth.rb.example
create mode 100644 services/api/config/initializers/omniauth_init.rb
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commit 1fdb31ed54f690d6a14a55aa7d50559697421fb6
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 6c38124b71b62927e880224f3a4f01874109cb08
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 453cdbc12b93d666995f5d955f174ae8a4d6b378
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 eecabf2..3790766 100644
--- a/doc/install/install-api-server.html.textile.liquid
+++ b/doc/install/install-api-server.html.textile.liquid
@@ -13,7 +13,12 @@ The Arvados package repository includes an API server package that can help auto
* Build tools and the curl and PostgreSQL development libraries, to build gem dependencies
* Nginx
-On older distributions, you may need to use a backports repository to satisfy these requirements. For example, on older Red Hat-based systems, consider using the "postgresql92":https://www.softwarecollections.org/en/scls/rhscl/postgresql92/ and "nginx16":https://www.softwarecollections.org/en/scls/rhscl/nginx16/ Software Collections.
+On older distributions, you may need to use a backports repository to satisfy these requirements. For example, on older Red Hat-based systems, consider using the "postgresql92":https://www.softwarecollections.org/en/scls/rhscl/postgresql92/ and "nginx16":https://www.softwarecollections.org/en/scls/rhscl/nginx16/ Software Collections. For example, on CentOS 6:
+
+<notextile>
+<pre><code>~$ <span class="userinput">sudo yum install scl-utils</span>
+~$ <span class="userinput">sudo yum install https://www.softwarecollections.org/en/scls/rhscl/postgresql92/epel-6-x86_64/download/rhscl-postgresql92-epel-6-x86_64.noarch.rpm</span>
+~$ <span class="userinput">sudo yum install https://www.softwarecollections.org/en/scls/rhscl/nginx16/epel-6-x86_64/download/rhscl-nginx16-epel-6-x86_64.noarch.rpm</span></code></pre></notextile>
On a Debian-based system, install the following packages:
@@ -31,7 +36,10 @@ 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 896855457f5966f3130bba4176c1c0b9f160114d
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 2fed32a4c6bcc086a90037733052cb572a2f0a37
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 e39a5e062b86e677a1d990066670efb512c7fe72
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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