floratos-lab / geworkbench Goto Github PK

When I do an ant clean, the following files are removed. It is not expected.

    deleted:    components/anova/test/org/geworkbench/service/AnovaServiceTest.java
    deleted:    components/anova/test/org/geworkbench/service/AnovaTest.java
    deleted:    components/aracne-java/test/org/geworkbench/aracne/service/client/AracneClient.java
    deleted:    components/aracne-java/test/org/geworkbench/components/aracne/test/PerformanceTest.java
    deleted:    components/hierarchicalclustering/test/org/geworkbench/hierarchicalclustering/service/client/HierClusterTest.java
    deleted:    components/ttest/test/log4j.properties
    deleted:    components/ttest/test/org/geworkbench/service/TTestTest.java

System/tool parameters:

• Apache Ant(TM) version 1.10.7 compiled on October 24 2019
• openjdk version "11.0.11" 2021-04-20
  OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04)
  OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing)
• Linux DESKTOP-VJR0I6H 4.19.104-microsoft-standard #1 SMP Wed Feb 19 06:37:35 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

"In March 2011, the NCI published an extensive review of CaBIG, the NCI CBIIT program that funded the caGrid software development, which included a long list of problems with the program, and recommended that most of the software development projects should be discontinued. "

see:

• https://deainfo.nci.nih.gov/advisory/bsa/archive/bsa0311/caBIGfinalReport.pdf
• https://en.wikipedia.org/wiki/CaBIG

This issue is entered as a 'meta-issue' to describe the goal of the planned new release.

There are basically two things we need to do for the new release:

1. The project (and maybe code as well when necessary) needs to be updated to make it readily build-able, and after building, readily executable with Java 11. By 'readily', we mean that the users (or the developers in the former part), do not need anything beyond the most common tools on common systems.
2. The list of components should be reviewed and those no longer supported should be removed from the project and eventually from the release package.

A component directory can contain more than one actual components.

A 'type' column is added to the list, where 'general support' means that we must keep them as part of geworkbench platform although they are technically components.

When I do ant run, the application does not launch. The following error is displayed:

run:
     [java] -Xbootclasspath/p is no longer a supported option.
     [java] OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
     [java] Error: Could not create the Java Virtual Machine.
     [java] Error: A fatal exception has occurred. Program will exit.
     [java] Java Result: 1

BUILD SUCCESSFUL
Total time: 0 seconds