To get oriented, read this:
https://freecontent.manning.com/wp-content/uploads/demystifying-osgi-bundles.pdf

Prof. [~aloraine] can you please provide me with a 2bit sequence file to test this app, so that I can be sure that the changes I make to remove the unnecessary jars won't affect the working of the app?

Sure! See genome sub-directories in IGB quickload site http://igbquickload.org/quickload for many 2bit files.

Yes. Thank you Professor

The <Embed-Dependency> tag in maven-bundle-plugin is embedding the jars in target jar. I have commented this tag and <Embed-Transitive> as I suppose we do not need transitive dependency. The app works fine after commenting these tags. Checked the working with different 2bit files.
The changes are present in https://bitbucket.org/skulka2710/shamika-2bit-reader/branch/IGBF-2264#diff
Kindly review.

Shamika Gajanan Kulkarni - please report in the comments:

• When you remove the <Embed-Dependency>, how does the "jar" file change?
• When you install the bundle and when you run it, do you observe any errors printed to the Console?

Also, please do this:

• Remove the Export statement. Nothing should be exported from the bundle as it is providing a service only, not providing any packages for other bundles to import and use. Please confirm that when you remove the Export statement, the bundle still functions as it should.

Regarding observation and question from Shamika Gajanan Kulkarni

"The errors printed to the console are null-pointer exceptions. These errors occur irrespective of the presence of <Embed-Dependency> tag and are seen whenever this app repository is included in App manager, and continue to appear even after the repo has been removed. My guess is that some events continue to have null values. This will need some digging into...Should we create a separate ticket for the errors, and its investigation and fix?"

Reply:

Yes, please create a new Jira issue to investigate and (possibly) fix the observed NPEs.

Yes. I also saw that there was a NoClassDefinitionFound error along with the NPEs. I shall create a separate ticket for the same. I am still trying to be sure if its because of <Embed-Dependency> or something else.

Question:

When you remove the <Embed-Dependency> tag, it looks like no "jar" files are getting included on the bundle classpath, which is fine. However, I am confused about what is in "org"
Are the required biojava classes getting extracted from a biojava jar file and included there?

The new MANIFEST is showing that dependencies are now all optional, which only is true for packages that are not actually going to be used by the bundle. However, the biojava twobit parser is going to be needed. So I am confused as to how the bundle is actually working.

Yes. I initially thought that the bundle needed is mentioned as a dependency in the pom.xml. I believe that the biojava-genome jar will be needed and its okay to not include the complete set of transitive dependencies. This can be done by setting the value of <Embed-Transitive> to false. The app works as needed, and the NoClassDefinitionFound exception also doesn't occur. I am still working on NPEs. So, for now this is one solution. Once I figure out the cause of NPE I will make the code changes. Is that alright Prof. [~aloraine]?

I was setting up the environment on my personal laptop so took some time to get this done. Setting the <Embed-Transitive> to false solves the purpose to not include the other unnecessary jars. It will only embed the dependencies we are directly dependent on.

"Normally the plugin only checks direct dependencies, but this can be changed to include the complete set of transitive dependencies with the following option:
<Embed-Transitive>true</Embed-Transitive>"
-http://felix.apache.org/documentation/subprojects/apache-felix-maven-bundle-plugin-bnd.html#ApacheFelixMavenBundlePlugin%28BND%29-Embeddingdependencies

The changes are present in
https://bitbucket.org/skulka2710/shamika-2bit-reader/branch/IGBF-2264#diff

Also, the <Export-package> tag has been removed from pom.xml
Kindly review and let me know if this works fine.
Prof. [~aloraine]

Another way to do this would be by using the following instead.
This will embed all compile and runtime scope dependencies, except those with artifactIds mentioned in the list
<Embed-Dependency>*;scope=compile|runtime;inline=false;artifactId=!cli|lang|runtime|tidy|jsch</Embed-Dependency>

Shamika Gajanan Kulkarni - Please make a note here:
What gets included in the jar when using the above <Embed-Dependency> tag?
Please report the full contents, e.g., output from "jar tf" (see: https://stackoverflow.com/questions/320510/viewing-contents-of-a-jar-file)

With the <Embed-Dependency> tag, all the dependency jars are embedded in the bundle.
I have attached screenshots for the jar -tf command to compare the cases when <Embed-Transitive> was set to true and after I have changed it to false.
Names of the screenshot - 'Original-jar.jpg' and 'After_making_embed_transitive_false.jpg'

The dependencies our app needs [let's call them A] will be included in the jar. But by using the <Embed-Transitive> tag set to true, it will also include all the dependencies A needs [B and C]. By setting it to false, we can only include A.
But if a need arises that we would want B but not C, that can be done using the following option:
<Embed-Dependency>*;scope=compile|runtime;inline=false;artifactId=!cli|lang|runtime|tidy|jsch</Embed-Dependency>
where we can mention the artifact ID of C so that we do not include it.

This is my understanding of this concept. Please let me know if this helps and if I am missing out on something.
Prof. [~aloraine]

I had a question about

• "<Embed-Dependency>*;scope=compile|runtime"

This looks like it would trigger inclusion of IGB API bundles, since they are required at compile time. But the POM also indicates that their scope is "provided." This is enough to tell the maven-bundle-plugin to *not* include the IGB API bundles, since they will be provided by the OSGi framework during run-time?

For next step: Just make sure the bundle can properly run inside IGB with this new Embed-Dependency tag.

Be sure to check things like:

• 2bit file is named "2bit" but is not really a 2bit file

The TwoBit reader code may rely on reporting (logging) bundles that are only used when there is an error, for example. Also, do please inspect the BioJava code the bundle is actually using for possible imports that might need to be provided.

For total awesomeness, include a test case for this type of thing. Or, we can make that a separate ticket.

Yes, I am looking into this currently. Thank you for your insights.

Prof. [~aloraine], today I tried implementing the <Embed-Dependency> tag in the following manner.
<Embed-Dependency>*;scope=compile|runtime;inline=false;artifactId=!guava|slf4j-api|log4j-slf4j-impl|log4j-api|log4j-core</Embed-Dependency>
This excludes the jars for which the artifactId is mentioned. The bundle runs properly except for the NullPointerExceptions occurring otherwise too.
I checked for files which contained no 2bit data but were stored with a .2bit extension. Your point was right, it does require the other jars to display the error message. Using the above <Embed-Dependency> the message was displayed properly.

Ok - I think it is ready for a PR. Thank you for all your work on this Shamika Gajanan Kulkarni

I enjoyed working on it Prof. [~aloraine]. Thank you for appreciating it.
I have submitted the PR.
https://bitbucket.org/lorainelab/2bit-reader/pull-requests/3/igbf-2264-modify-embed-dependency-tag-to/diff

Merged, ready for testing.