Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1.5
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Epic Link:
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Sprint:Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10
Description
Unpacking the jar finds there are many things getting included that probably are not needed, such as jars for libraries that IGB already includes:
- guava-19.0.jar
- log4j-api-2.5.jar
- log4j-core-2.5.jar
- log4j-slf4j-impl-2.5.jar
There also appear to be some transitive dependencies that might not be needed during operation of the App.
Here are the jar conrtents:
$ jar xvf biojava-igb-app-0.0.1.jar
inflated: META-INF/MANIFEST.MF
created: META-INF/
created: META-INF/maven/
created: META-INF/maven/igb-app-examples/
created: META-INF/maven/igb-app-examples/biojava-igb-app/
inflated: META-INF/maven/igb-app-examples/biojava-igb-app/pom.properties
inflated: META-INF/maven/igb-app-examples/biojava-igb-app/pom.xml
created: OSGI-INF/
inflated: OSGI-INF/org.lorainelab.igb.sequencereader.TwoBitReaderApp.xml
inflated: biojava-alignment-4.2.8.jar
inflated: biojava-core-4.2.8.jar
inflated: biojava-genome-4.2.8.jar
inflated: biojava-phylo-4.2.8.jar
inflated: forester-1.038.jar
inflated: guava-19.0.jar
inflated: log4j-api-2.5.jar
inflated: log4j-core-2.5.jar
inflated: log4j-slf4j-impl-2.5.jar
inflated: logo.png
created: org/
created: org/biojava/
created: org/biojava/nbio/
created: org/biojava/nbio/genome/
created: org/biojava/nbio/genome/parsers/
created: org/biojava/nbio/genome/parsers/twobit/
inflated: org/biojava/nbio/genome/parsers/twobit/TwoBitParser.class
created: org/lorainelab/
created: org/lorainelab/igb/
created: org/lorainelab/igb/sequencereader/
inflated: org/lorainelab/igb/sequencereader/TwoBitFileSummarizer.class
inflated: org/lorainelab/igb/sequencereader/TwoBitReaderApp.class
inflated: repository.xml
inflated: slf4j-api-1.7.14.jar
inflated: summarize.png
For this task, investigate maven-bundle-plugin configuration to ensure that only jars that are required by the App to run are included in the Bundle.
Attachments
Issue Links
Activity
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.
To get oriented, read this:
https://freecontent.manning.com/wp-content/uploads/demystifying-osgi-bundles.pdf