We made some pretty good progress here but are not sure how to enable developers to see the source code for IGB bundles. Moving to the backlog for us to work on later.

Thank you Pooja Nikhare and Shamika Gajanan Kulkarni for the progress made thus far!

Prof. [~aloraine] I have tried the first and second methods mentioned above. The second method seems to include the source code as a separate jar called sources [for example, for affymetrix-common, one more jar will be included in the target folder called 'affymetrix-common-9.1.4-sources']. The java files are not packaged in the installer released to users.
However, I haven't been able to find a specific profile in maven to force the bundles to be updated in .m2, I am working on finding it. Also, I am not sure I completely understand what is the requirement there. Can you please elaborate it to me so that it helps me understand if what I am working on is right? Also, can you please check if this is what we want? I have pushed the above changes to my fork on a new branch. The link is as follows.
https://bitbucket.org/skulka2710/shamika_igb/branch/IGBF-2235#diff

For now, I have commented the test files for 'das' since I was facing build failures. Also, I noticed there is a conflict in one of the test class and I shall fix it later.

To test:

• Build using the new method (to package java files with the jar)
• Run mvn clean install with a specific profile to force the bundles to be added to your local .m2 (maven) repository
• Then, check that when you use "view source" in Netbeans, you can see the actual source brought in from the jar file

Note: We do NOT want to package the java files with the installer released to users.

This can be done in 3 ways. By adding build properties in maven profile - release-to-nexus.bioviz.org
1. add resources
<resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>*/.java</include>
</includes>
</resource>
</resources>
Command : mvn -P release-to-nexus.bioviz.org clean
creates igb_exe.jar. On extracting .java files can be found with .class files

2. Maven source plugin
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.0</version>
<inherited>true</inherited>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
command : mvn -P release-to-nexus.bioviz.org clean source:aggregate
creates igb-project-source.jar inside target folder
3. maven assembly plugin
https://maven.apache.org/plugins/maven-assembly-plugin/examples/multimodule/module-source-inclusion-simple.html

Suggestion for how to do this:

The Genoviz SDK POM.xml contains directive to include *.java files in the jar file:
snip
<build>
<resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>*/.java</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
snip

We could include the above, or something similar, in the release to nexus profile in the top-level parent POM of the Integrated Genome Browser project. We probably want the jar files released to Nexus to contain the source code, but we do not want the jar files packaged with the installer to include the source code.