bibiserv / instantbibi

Bibiserv

Web application framework mainly for bioinformatic developers to publish their tools with an user-friendly web interface.

Development-Guidelines

https://github.com/BiBiServ/Development-Guidelines

How to build the project?

dependency: >= Maven 3.3.9

Run

mvn package

How to version the project?

We decided that all modules should have the same version as the parent module. By using the below command in the project root you can update all child modules at once.

mvn  versions:set -DnewVersion=<version>

where

• version = 2.1.0.alpha.2

instantbibi's Issues

Readme section for proxy settings

We should extend the readme for using instantbibi behind the proxy:

ant -autoproxy instant -Dbase.dir=/local/bibiserv

Stop/Undeploy

Add to the readme a description for stopping and undeploying the bibiserv.

Test default configuration

The bibiserv default setup should be tested on circle ci (ant instant, ant instant.dev, etc....).

asadmin proxy setting

Add jobproxy parameter for using proxy:

Something like this before running the other asadmin commands:

  
      <target name="deploy" depends=".config.setting" description="(re)deploys bibimainapp">
 
 
 	<exec executable="${basedir}/glassfish/bin/asadmin" failifexecutionfails="true"
 	    failonerror="true">
 	    <arg value="--user=admin"/>
 	    <arg value="--passwordfile=appserver_config/local.passwordfile"/>
 	    <arg value="--port=${admin.port}"/>
 	    <arg value="--host=localhost"/>
 	    <arg value="create-jvm-options"/>
 	    <arg value="-Dhttp.proxyHost=rzproxy.helmholtz-hzi.de"/>
 	</exec>
 	<exec executable="${basedir}/glassfish/bin/asadmin" failifexecutionfails="true"
 	    failonerror="true">
 	    <arg value="--user=admin"/>
 	    <arg value="--passwordfile=appserver_config/local.passwordfile"/>
 	    <arg value="--port=${admin.port}"/>
 	    <arg value="--host=localhost"/>
 	    <arg value="create-jvm-options"/>
 	    <arg value="-Dhttp.proxyPort=3128"/>
 	</exec>

version

If we distribute the instantbibi to developers and maybe users it should report its version number . That way a user/developer could for example tell us the instantbibi version that does not work.

instantbibi does not start with openjdk 8

while calling

ant instant.environment && ant install.wizard

it throws:

BUILD FAILED
/home/ubuntu/instantbibi/build.xml:155: The following error occurred while executing this line:
/home/ubuntu/instantbibi/build.xml:680: The following error occurred while executing this line:
/home/ubuntu/instantbibi/appserver_config/build.xml:221: The following error occurred while executing this line:
/home/ubuntu/instantbibi/appserver_config/build.xml:672: Unable to find a javac compiler;
com.sun.tools.javac.Main is not on the classpath.
Perhaps JAVA_HOME does not point to the JDK.
It is currently set to "/usr/lib/jvm/java-8-openjdk-amd64/jre"

Total time: 6 minutes 55 seconds

It seems that oracle Java is required.

I've tested the installation with both – openJDK 8 and Oracle JDK 8 – it works only with the last one.

portbase=>8000

The readme does not tell that the default portbase is 8000.