Source Setup on OSX and Linux¶

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!

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="/usr/share/maven"
export JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64"
export SERVER_HOME="/path/to/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.

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

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

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¶

For development¶

Clone geppetto-client inside geppetto-application,

cd ../../../org.geppetto.frontend/src/main/webapp
git checkout development
git clone -b development https://github.com/openworm/geppetto-client.git

¶

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

cd ../../../../org.geppetto

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:

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.

How to Update¶

JS/HTML code can be found inside org.geppetto.frontend/src/main/webapp/. The code needs to be rebuilt with webpack every time there is a change. The recommended way is to run in org.geppetto.frontend/src/main/webapp this command:

npm run start

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