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
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1908 [ 17998 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 3 : 17 Feb to 28 Feb [ 87 ] | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 87, 89 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | 2-bit reader 1.JPG [ 14660 ] | |
| Attachment | 2-bit reader 2.JPG [ 14661 ] | |
| Attachment | manifest - 1.JPG [ 14662 ] | |
| Attachment | manifest - 2.JPG [ 14663 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Comment |
[ Prof. [~aloraine]
1) When I remove the <Embed-Dependency> tag, the jars which were getting included in the target jar, are not embedded now. The app works fine even without embedding the dependencies separately. I have attached the screenshots for the target jar and manifest in both the cases. Case 1 - when <Embed-Dependency> tag is present, and case 2 - when it has been removed. 2) 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. Thank you for pointing it out. 3) I have removed the export statement and the changes are present here: https://bitbucket.org/skulka2710/shamika-2bit-reader/branch/IGBF-2264#diff Should we create a separate ticket for the errors, and its investigation and fix? ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Attachment | After_making_embed_transitive_false.JPG [ 14679 ] | |
| Attachment | Original_jar.JPG [ 14680 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 87, 89 ] | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 87, 89, 90 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Sprint | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 87, 89, 90 ] | 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 [ 87, 89, 90, 91 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |