Source Setup on OSX and Linux

This will tell you how to get the Geppetto source code and build it on a OSX and Linux machine (OSX? Linux? I’m on Windows!).

Note: if you just want to play with a sample Geppetto deployment you don’t need to install anything, just visit https://live.geppetto.org. If you want to install the latest released sample deployment just download it from here and run ./bin/startup.sh. The following instructions are if you want to setup Geppetto from sources.

Psst: If you get stuck at any point, you can join our Slack channel and we will assist you. Send an email to info@geppetto.org for an invite or if you just have a quick question. You can also send us screenshots and log files!

Prerequisite software

You need a bunch of other software to install Geppetto from sources. The good news: You probably have some of this on your machine already!

OSX and Linux

  • Java SE Development Kit 8

  • Python 2.7 or Python 3

  • Virgo Server for Apache Tomcat: ZIP file unpack it to your desired location by:

    gunzip -a virgo-tomcat-server-3.7.2.RELEASE.zip -d

  • As of Virgo 3.7.2, a couple of extra steps are needed to make it work with Geppetto.

    1. Once virgo has been unzipped, create folder named “usr” inside <virgo_directory>/repository
    2. Replace files “tomcat-server.xml” and “javar-server.profile” in <virgo_directory>/configuration with files of the same name found here tomcat-server.xml and java-server.profile

OSX

  • homebrew (see here): ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
  • Maven: brew install maven
  • git: brew install git
  • pip: Instructions
  • Apache Tomcat: brew install tomcat

Linux: Debian and variants (e.g. Ubuntu)

This should also work for alternative distributions, by substituting apt-get with the appropriate package manager, e.g. pacman for Arch, yum for Fedora and so forth.

  • homebrew (see here)
  • Maven: sudo apt-get install maven
  • git: sudo apt-get install git
  • pip: sudo apt-get install python-pip
  • Apache Tomcat: sudo apt-get install tomcat8

Environment Variables

Environment variables tell your operating system and other programs where you installed certain software.

Linux Variables

Create variables with the following names and values, or look if they already exist:

  • JAVA_HOME: path to Java SE Development Kit 8
  • SERVER_HOME: path to Virgo Server for Apache Tomcat
  • MVN_HOME: path to Maven

You can do this for example in .bashrc with:

export MVN_HOME="$(brew --prefix maven)/libexec"
export JAVA_HOME="$(/usr/libexec/java_home)"
export SERVER_HOME="/usr/local/Cellar/virgo/virgo-tomcat-server-3.7.2.RELEASE"

Maven needs to build with Java 8. If you want to point your JAVA_HOME variable to a different version, create a file .mavenrc in your home directory that contains:

export JAVA_HOME="/path/to/java8"

Note that if you are using Java 7, you still will need to install Java 8. You can have a conditional statement to switch between the two.

export JAVA_HOME="$(/usr/libexec/java_home -v 1.8)"
setjdk() 
    {export JAVA_HOME="$(/usr/libexec/java_home -v $1)"}
export SERVER_HOME="/usr/local/Cellar/virgo/virgo-tomcat-server.3.7.2.RELEASE"

When you close your terminal, it is possible that bashrc may reset SERVER_HOME. In order to reset SERVER_HOME, issue the following command from the terminal.

SERVER_HOME="/usr/local/Cellar/virgo/virgo-tomcat-server.3.7.2.RELEASE"

Mac OS X Variables

export MVN_HOME="$(brew --prefix maven)/libexec"
export JAVA_HOME="/usr/lib/jvm/java-1.8.0-openjdk"
export SERVER_HOME="/opt/virgo-tomcat-server-3.7.2.RELEASE"

The SERVER_HOME directory may be one of the directories that you are prompted to install to. Once you find where virgo tomcat is installed to, use that as your directory.

Also, following the guide above to installing homebrew on Linux, you made need to add extra details to your bashrc file.

OK, that was everything you need, let’s get the source code now.

Setup Geppetto Repositories

First, create a directory for the Geppetto source code (geppetto-sources from now on):

mkdir geppetto-sources
cd geppetto-sources

Once there, clone the org.geppetto repository from GitHub:

git clone https://github.com/openworm/org.geppetto.git

Navigate your shell to the source_setup directory:

cd org.geppetto/utilities/source_setup

Alternatively, copy the contents of source_setup to a convenient directory of your choice:

cp -r org.geppetto/utilities/source_setup/* <some other location>

Open the config.json file in a text editor and change the value of the sourcesdir field to the path of your source directory.

The source_setup folder contains some handy scripts. First, run the setup.py script:

./setup

or

python setup.py

Running this script will prompt you to enter the repositories you want copied to geppetto sources. At present, the repositories are:

org.geppetto
org.geppetto.core
org.geppetto.frontend
org.geppetto.model
org.geppetto.model.neuroml
org.geppetto.simulation

However, you will have the option to select other repositories from this list when you run the install script.

Make sure that your account has permission to write into geppetto-sources. If a repository is missing, check that the url for that repository is entered correctly in config.json and pom.xml.

Building Geppetto

Navigate back to the org.geppetto directory from utilities/source_setup:

cd ../..

Once there, run:

mvn -Dhttps.protocols=TLSv1.2 install

This will build all of the Geppetto modules at once. As you do development, you probably don’t want to re-build all modules if you only worked on a few. In this case, you can build the modules individually and then re-deploy. To build an individual module, just run the install command from its directory. To prevent problems caused by old build files, you may want to clean before reinstalling by:

mvn -Dhttps.protocols=TLSv1.2 clean install

Deploying Geppetto

To deploy Geppetto to the Virgo server, navigate your shell to the source_setup directory again by typing:

cd utilities/source_setup

Then run:

./update_server

or

python update_server.py

This will copy all of the built jars, wars and dependencies over to %SERVER_HOME%/repository/usr and the geppetto.plan file in org.geppetto to %SERVER_HOME%/pickup.

If you plan to start the server from the eclipse environment run the update_server script with the “eclipse” flag:

./update_server eclipse

This will copy only dependencies over to %SERVER_HOME%/repository/usr. Geppetto JARs and WARs will be copied by Eclipse in the Virgo stage folder upon deployment.

Starting and Stopping Virgo

The Virgo server is started and stopped via shell scripts in $SERVER_HOME/bin. To run these in the terminal, create a function in .bashrc that proxies commands to the scripts:

function virgo() {
        bash $SERVER_HOME/bin/$1
}

Then Virgo can be started using the command:

virgo startup.sh

Or shutdown using the command:

virgo shutdown.sh

For more info on Virgo’s control scripts, see here.

Note that when you are running on Linux, there may be other services that are using Port 8080.

Use:

netstat -plten | grep 8080

to find the process number on port 8080.

Then identify the process number and issue the following command to kill it:

sudo kill -9 <process number>

With that you are basically done! So, fire up the startup.bat file, wait until its output stops, cross your fingers and point your browser to:

http://localhost:8080/org.geppetto.frontend

You should now see Geppetto starting up. Good job!

Not quite there yet? Get in touch with us, we are there to help you! Send an email to info@geppetto.org for an invitation to our Slack channel or if you just have a quick question.

Using gitall.py

The gitall.py script allows you to perform git commands on all repositories at once. This makes it easier to maintain the state of the many repos required by Geppetto.

To use it, navigate your shell to the source_setup folder and type:

./gitall branches

to print the current branch of each repo

./gitall checkout <branch>

to checkout for each repo. Note the branch must exist on each repo.

./gitall fetch [remote] [branch]

to git fetch on each repo

./gitall pull [remote] [branch]

to git pull on each repo