Details
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Type: Bug
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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: 9.1.0 Major Release
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Labels:
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Story Points:2
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Epic Link:
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Sprint:Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10, Summer 2019 Sprint 11
Description
For details see:
Investigate bundle resolution error involving htsjdk-igb
https://jira.transvar.org/browse/IGBF-1627
This requires understanding OSGi and how bundle dependencies get resolved during bundle installation and activation.
Also, review how we made htsjdk-igb bundle in the first place by looking at linked Jira issues.
Probably we have to make some changes to how we generate that bundle?
Potentially useful resources:
- Wrapping libraries to OSGi bundles https://bnd.bndtools.org/chapters/390-wrapping.html
- Playing with Apache karaf - tool you can use to test installing bundles (note our bundle is a library and doesn't have an "activate" method, which is a bit like a "main" method in Java application) https://www.javaindeed.com/playing-with-apache-karaf-console/
Please add more as you work on this.
When done, please write up a short, plain English description of what you did to fix the problem. (This can be a useful case study to introduce devs to OSGi in IGB.)
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Attachments
Issue Links
Activity
Ann Loraine
created issue -
Ann Loraine
made changes -
Field | Original Value | New Value |
---|---|---|
Epic Link | IGBF-1531 [ 17617 ] |
Ann Loraine
made changes -
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | Open [ 1 ] | In Progress [ 3 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Attachment | jexl_Missing_Requirement.JPG [ 14335 ] | |
Attachment | MissingRequirements.JPG [ 14336 ] | |
Attachment | MissingRequirements_afterInstallingCompress.JPG [ 14337 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Attachment | htsjdk_success.JPG [ 14338 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Ann Loraine
made changes -
Sprint | Summer 2019 Sprint 8 [ 67 ] | Summer 2019 Sprint 8, Summer 2019 Sprint 9 [ 67, 68 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Status | Needs 1st Level Review [ 10005 ] | Open [ 1 ] |
Ann Loraine
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | Open [ 1 ] | Needs 1st Level Review [ 10005 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | Needs 1st Level Review [ 10005 ] | In Progress [ 3 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Story Points | 1 | 2 |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | Needs 1st Level Review [ 10005 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
made changes -
Status | Reviewing Pull Request [ 10303 ] | Reviewing [ 10301 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Attachment | htsjdktxt.txt [ 14347 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | Reviewing [ 10301 ] | In Progress [ 3 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | In Progress [ 3 ] | Reviewing [ 10301 ] |
Ann Loraine
made changes -
Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] | Sai Charan Reddy Vallapureddy [ svallapu ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Sai Charan Reddy Vallapureddy (Inactive)
made changes -
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Ann Loraine
made changes -
Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
Ann Loraine
made changes -
Sprint | Summer 2019 Sprint 8, Summer 2019 Sprint 9 [ 67, 68 ] | Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10 [ 67, 68, 69 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10 [ 67, 68, 69 ] | Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10, Summer 2019 Sprint 11 [ 67, 68, 69, 70 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Noor Zahara (Inactive)
made changes -
Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Noor Zahara (Inactive)
made changes -
Assignee | Noor Zahara [ noor91zahara ] |
Noor Zahara (Inactive)
made changes -
Assignee | Noor Zahara [ noor91zahara ] | Sai Charan Reddy Vallapureddy [ svallapu ] |
Noor Zahara (Inactive)
made changes -
Resolution | Done [ 10000 ] | |
Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
Ann Loraine
made changes -
Workflow | Loraine Lab Workflow [ 18489 ] | Fall 2019 Workflow Update [ 20191 ] |
Ann Loraine
made changes -
Workflow | Fall 2019 Workflow Update [ 20191 ] | Revised Fall 2019 Workflow Update [ 22328 ] |
[~aloraine]
Investigation Results:
htsjdk requires below jar to remove bundle resolution error. I manually downloaded this jar and copied them in /bundles.
1. commons-jexl-2.1.1.jar
jexl requires below jar to remove bundle resolution error. I manually downloaded this jar and copied them in /bundles.
1. commons-logging-1.2.jar
I manually copied these two jars in /bundles to remove bundle resolution error and now IGB runs without any error. These two jars should be downloaded from pom.xml (Maven). But for some reason maven is not downloading these jars even after providing dependencies.