Introduction

The Virtual Imaging Platform is a web portal for pipeline execution on distributed systems. An instance of this portal deployed on the European Grid Infrastructure is accessible at https://vip.creatis.insa-lyon.fr.

Credits

The VIP logo was designed by Max Langer under the CC BY-NC-SA license.

Development guidelines

0. Your Git username and email should be set to your First-Last name and actual email:

git config --global user.name "Jeanne Tartempion"                  # not "tartempion" or "jtartempion" or "root"
git config --global user.email "[email protected]"   # not "root@localhost"

1. Developments are made in forks from the base repository. Developments lead to pull-requests that are merged by the owner(s) of the base repository.
2. Starting from release 1.15, we adopt the branching model described here.
3. When working on a new feature:

• In your fork, create a new feature branch from the development branch:

git checkout -b new_feature develop

You may name your branch anything except master, develop, release-, or hotfix- 3. When feature development is finished:

• Push your commits to Github (your fork).
• Make a pull request to merge feature branch (in your fork) to development branch (in the base repository).

Production installation instructions

You can follow the instruction here

You can contact us at [email protected] for precisions.

Local test installation instructions

It is possible to launch a local vip instance in a tomcat on a linux machine. This is only useful for testing purposes as most of the features are simulated and many are still to be implemented and do not work yet. Here are the instructions to configure a local vip instance :

• create a empty folder that will contain all the configuration files and simulated data. /path/to/vip/local/folder will be its path used in the next instructions
• unzip the local-config.zip archive available in vip-local/src/main/resources in /path/to/vip/local/folder. This should contain 3 .conf files
• create a $HOME/.vip directory and a $HOME/.vip/local-config-folder.properties file
• put vipConfigFolder = /path/to/vip/local/folder in the $HOME/.vip/local-config-folder.properties file

Then, install vip in your local tomcat :

1. Build the vip-local war with mvn clean package at the root of the VIP-portal project.
2. Put the vip-portal/target/vip-portal-[...]-local.war file in the $TOMCAT_HOME/webapps directory
3. Add the folowing lines in $TOMCAT_HOME/conf/context.xml (database jndi configuration), and edit path/to/vip/local/folder/vip to the real path in url

<Resource name="jdbc/vip" auth="Container"  type="javax.sql.DataSource" 
       username="sa"     
       password="" 
       driverClassName="org.h2.Driver" 
       description="VIP local h2 Connection" 
       url="jdbc:h2:/path/to/vip/local/folder/vip" 
       maxActive="100" 
       maxIdle="50" />

4. Create or adapt the $TOMCAT_HOME/bin/setenv.sh file with these lines (edit path/to/vip/local/folder/vip to the real path) :

export CATALINA_OPTS="$CATALINA_OPTS -Dspring.profiles.active=local,config-file,jndi-db"
export CATALINA_OPTS="$CATALINA_OPTS -DvipConfigFolder=/path/to/vip/local/folder"

5. That's it, start tomcat (bin/startup.sh). Access vip on localhost:8080/vip-portal-[...]-local (adapt with the war name and your tomcat host/port configuration)

Local instance notes

• The default admin email/password is [email protected]/localAdminPassword.
• all is not working perfectly yet, expect to see some error messages. The home page, files transfers and execution launchs shoud work, but application imports and the page with execution details are not implemented at the moment.
• vip do not send email but logs them
• at the moment, logging is done in the $HOME/.vip/vip.log file

Keycloak Server

VIP API can be secured with keycloak by adding keycloak.json in the vip config folder after updating the parameters it should look like :

{
  "realm": "<name-of-realm>",
  "auth-server-url": "http://localhost:8180/auth/",
  "ssl-required": "none",
  "use-resource-role-mappings" : true,
  "bearer-only" : true,
  "resource": "<client ID>",
  "public-client": true,
  "disable-trust-manager": true,
  "credentials" : {
      "secret" : "<credential-secret>"
   }
}

Testing VIP with keycloak

• Boot the keycloak server and run it on port 8180, because by default it runs on 8080

$ cd keycloak/bin
$ ./standalone.sh -Djboss.socket.bidning.port-offset=100
or in windows :
> standalone.bat -Djboss.socket.bidning.port-offset=100

• Create a realm it's a good practice to use another realm other the master realm (default)
• Create a client ,
• Add roles specific to the client here we have ADVANCED, ADMINISTRATOR
• Add a realm Role and map it to the client roles
• Create a user and give it the realm role

Import the collection vip-keycloak.postman_collection.json to postman, this collection is an example that can test the following endpoints:

• get access token from keycloak
• /rest/pipelines to test the VipUser compatibility with keycloak
• /rest/statistics/users to test roles