bibiserv / bibiserv_dev

Develop environment for the BiBiServ framework.

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

bibiserv_dev's Issues

Wizard crashes when loading existing XML description

Wizard crashes (OutOfMemory Exception -> ViewExpiredException: viewId:/loadXML.xhtml - View /loadXML.xhtml could not be restored) when loaded an existing and valid xml description file.

Configuration : OSX 10.11.6, Java 1.8.0_112, Glassfish 4.1 (unpatched), Domain is limited to max. 1 GB RAM

Clean up and update documentation

Since the Wizard comes with a full manual we have to check if everything is up-to-date (in fact this is currently not the case) and fix it. We should concentrate on the Markup based version and remove the Tex variant.

Wizard unit test could fail due to encoding problems ...

We detect that under some circumstances the units could fail with an (UTF-8) encoding problem. The error occurs when an UTF-8 encoded XML file (with german umlaute) is read, encoded as base64 stream, decoded as string and then compared against original content. We have to check what are the surrounding conditions for this problem ...

Enhance Wizard to support latest tool description schema.

Remove webstart submodule

WebStart is an outdated way to start Java programs directly from a web browser. The CodeGen process doesn't generate webstart pages per default anymore - it must be explity enabled using a Java system property. For backward compatibility the xml schema must contain an optional webstart section, but the wizard should not support this any more.

CMDline interface of CodGen lacks of some features

Missing features :

• specification of a target directory (where to generate the tool projects)
• specification of a project dir (instead of target + tool[id] directory)
• example usage

CodeGen has many unnecessary 3rd party dependencies

The CodeGen subproject has many unnecessary 3rd part dependencies that blows up the shaded jar . We have to clean up the pom and add some exclusions.

• aws-java-sdk
• spring-security-core
• spring-web
• ...