Arvados

{{>toc}}

h1. Hacking prerequisites

The Arvados test suite can run in a Docker container, a VM, or your workstation -- provided a few prerequisites are satisfied.

h2. Host options

h3. Starting on your workstation

If your workstation is a debian stretch system -- and you don't mind installing a bunch of packages on your workstation, some of them without apt -- the easiest way to get running is to run tests on bare metal. Skip to "Dependencies".

Other linux distributions should work too with some modifications, but it's probably easier to use a VM.

h3. Starting on a VM

Another option is to create a virtual machine using something like Xen or VirtualBox, and run debian stretch on it. The instructions below assume you have just a few basic requirements:

* SSH server

* sudo (@apt-get install sudo@)

* A user account with sudo privileges

h3. Starting in a docker container

_[[Arvbox]] provides a preinstalled Docker-based dev environment.  The following instructions are for creating a dev environment inside Docker from scratch._

This can get you started quickly, but (unlike the above options) you'll need to remember to use something like @docker commit@ to save your state before shutting down your container.

See http://docker.io for more about installing docker. On debian it looks something like this.

<pre>

sudo apt-get install docker-ce

sudo adduser $USER docker

# {log out & log back in}

groups

# {should include "docker"}

</pre>

Start up a new container with debian 9 (stretch), make a new user and log in as that user:

<pre>

docker run -it --privileged debian:9 bash

apt-get update

apt-get -y install sudo

adduser me

adduser me sudo

sudo -u me -i

</pre>

The "--privileged" is required in order for /dev/fuse to be accessible (without it, no tests that require FUSE will work).

h2. Install dev environment

<pre>

# only on debian 9 (stretch), to permit ruby 2.3 compilation (see https://github.com/rbenv/ruby-build/wiki#openssl-usrincludeopensslasn1_mach102-error-error-this-file-is-obsolete-please-update-your-software):

sudo apt-get install --no-install-recommends libssl1.0-dev

# other systems:

sudo apt-get install --no-install-recommends libssl-dev

# all systems:

sudo apt-get install --no-install-recommends \

    bison build-essential cadaver fuse gettext git gitolite3 graphviz \

    iceweasel libattr1-dev libfuse-dev libcrypt-ssleay-perl libjson-perl \

    libcrypt-ssleay-perl libcurl3 libcurl3-gnutls libcurl4-openssl-dev curl \

    libjson-perl libpcre3-dev libpq-dev libpython2.7-dev libreadline-dev \

    libxslt1.1 libwww-perl linkchecker lsof nginx perl-modules \

    postgresql python python-epydoc pkg-config sudo virtualenv \

    wget xvfb zlib1g-dev libgnutls28-dev python3-dev \

    r-base r-cran-testthat libxml2-dev pandoc cython bsdmainutils

# ruby 2.5

(

 set -e

 mkdir -p ~/src

 cd ~/src

 wget https://cache.ruby-lang.org/pub/ruby/2.5/ruby-2.5.5.tar.gz

 tar xzf ruby-2.5.5.tar.gz

 cd ruby-2.5.5

 ./configure --disable-install-doc

 make

 sudo make install

 sudo gem install bundler

)

# go >= 1.12

sudo apt-get install golang-1.12 || \

(

 set -e

 wget https://storage.googleapis.com/golang/go1.12.5.linux-amd64.tar.gz

 sudo tar -C /usr/local -xzf go1.12.5.linux-amd64.tar.gz

 cd /usr/local/bin

 sudo ln -s ../go/bin/* .

)

# phantomjs 1.9.8

(

 set -e

 PJS=phantomjs-1.9.8-linux-x86_64

 wget -P /tmp https://bitbucket.org/ariya/phantomjs/downloads/$PJS.tar.bz2

 sudo tar -C /usr/local -xjf /tmp/$PJS.tar.bz2

 sudo ln -s ../$PJS/bin/phantomjs /usr/local/bin/

)

# geckodriver

(

 set -e

 GD=v0.24.0

 wget -P /tmp https://github.com/mozilla/geckodriver/releases/download/$GD/geckodriver-$GD-linux64.tar.gz

 sudo tar -C /usr/local/bin -xzf /tmp/geckodriver-$GD-linux64.tar.gz geckodriver

)

# npm

(

 set -e

 wget -O- https://nodejs.org/dist/v6.11.2/node-v6.11.2-linux-x64.tar.xz | sudo tar -C /usr/local -xJf -

 sudo ln -s ../node-v6.11.2-linux-x64/bin/{node,npm} /usr/local/bin/

)

</pre>

Note: For ubuntu, virtualenv is python-virtualenv

h2. Get the arvados source tree and test scripts

<pre>

cd

git clone https://github.com/curoverse/arvados.git

</pre>

...or, if you're a committer with your public key on our git server:

<pre>

cd

git clone git@git.curoverse.com:arvados.git

</pre>

h2. Start Postgres

_If you're running in a docker container_ you'll need to start Postgres manually:

<pre>

sudo /etc/init.d/postgresql start

</pre>

(If you're on a regular workstation/server/VM, startup scripts have already taken care of that for you.)

h2. Ensure entropy

If you're running in a VM, you might run out of entropy, which will make some tests run very slowly. The easiest solution is to install haveged.

<pre>

sudo apt-get install haveged

</pre>

h2. Setup groups

Make sure the fuse and docker groups exist (create them if necessary) and that the user who will run the tests is a member of them.

h2. Create a Postgres user

Create an "arvados" user with "create database" privileges. The test suite will create and drop the arvados_test database as needed.

<pre>

newpw=`tr -cd a-zA-Z </dev/urandom |head -c32`

sudo -u postgres psql -c "create user arvados with createdb encrypted password '$newpw'"

cp -i ~/arvados/services/api/config/database.yml{.example,}

newpw="$newpw" perl -pi~ -e 's/xxxxxxxx/$ENV{newpw}/' ~/arvados/services/api/config/database.yml

</pre>

h2. Run tests

<pre>

time ~/arvados/build/run-tests.sh WORKSPACE=~/arvados

</pre>

During development, you'll probably want something more like this. It reuses the given temp directory, which avoids a lot of repetitive downloading of dependencies, and allows you to save time with @--skip-install@ or @--only-install sdk/ruby@ and so on.

<pre>

mkdir -p ~/.cache/arvados-build

time ~/arvados/build/run-tests.sh WORKSPACE=~/arvados --temp ~/.cache/arvados-build

</pre>