Details
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Type:
Improvement
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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: 10.0.0 Major Release
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7
Description
Situation: The BigWigHandler and BigBedHandler have a dependency on the artifact bigWigHandler (https://bitbucket.org/lorainelab/bigwig/src/master/). The bigWigHandler dependency has a dependency on htsjdk-igb version 2.16.2 which makes it a blocker for IGBF-3464.
Task: Fork the bigwig repo and create a new branch with htsjdk-igb updated to a newer version (most likely >= 3). You will need to build and test the dependency locally to make sure that IGB works. See this documentation on adding local jars to local m2 repository.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1531 [ 17617 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Story Points | 3 |
Discussed strategy for using newer htsjdk code in IGB. Made a diagram showing the strategy on a whiteboard and took a picture of it. Picture is attached for reference.
| Attachment | IMG_3751.jpg [ 18056 ] |
I was able to get IGB to build and run using htsjdk 2.24.1. After updating the pom.xml files for htsjdk (instead of htsjdk-igb), I added the following to the pom.xml for shared-lib-wrapper:
Under the section "Dependencies which need to be "wrapped" into OSGI bundles"
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
Then within the maven-bundle-plugin <Export-Package> I added
htsjdk.*
There is one error with BaiFileSymLoader and BaiSymLoader for samReaderFactory.open - this may be due to a change for visualizing the bai data by itself in IGB, though I'm not sure.
I commented out the BigBedHandler, BigWigHandler, and bai modules to get around the errors. Everything else seems to be working in IGB.
However, at this time I recommend Kaushik continue his work on updating htsjdk-igb to use the newer version of the htsjdk.
| Sprint | Fall 3 2023 Oct 2 [ 179 ] | Fall 3 2023 Oct 2, Fall 4 2023 Oct 16 [ 179, 180 ] |
| Rank | Ranked higher |
- Forked htsjdk 3.0.0 into my GitHub and made necessary changes to use it as a OSGi bundle
- Both IGB and BigWig are now pulling htsjdk 3.0.0 from my local maven repository
- Ran the application and no issues were found during compile time or runtime
My concerns:
- Cherry-picking commits can be time-consuming and often leads to dealing with merge conflicts. As a result, I manually incorporated the changes made by the IGB developers into my repository instead of using the cherry-picking process.
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 3 2023 Oct 2, Fall 4 2023 Oct 16 [ 179, 180 ] | Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5 [ 179, 180, 181 ] |
| Rank | Ranked higher |
| Sprint | Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5 [ 179, 180, 181 ] | Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6 [ 179, 180, 181, 182 ] |
| Rank | Ranked higher |
- Updated htsjdk-igb and bigwig to version 3.0.5 (previously 2.16.2) and 2.0.1 (previously 2.0.0) respectively
- Submitted PR for the same.
Note: This PR cannot be merged until htsjdk-3.0.5 is deployed. COMPLETED
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Kaushik Gopu [ kgopu ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6 [ 179, 180, 181, 182 ] | Fall 3 2023 Oct 2, Fall 4 2023 Oct 16, Fall 5, Fall 6, Fall 7 [ 179, 180, 181, 182, 183 ] |
Tested on Mac using strategy described in IGBF-3464. Everything is working correctly. Closing ticket.
| Assignee | Kaushik Gopu [ kgopu ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 10.0.0 Major Release [ 10900 ] |
| Issue Type | Task [ 3 ] | Improvement [ 4 ] |
Our BigWig/BigBed code currently declares a dependency on https://github.com/lorainelab/htsjdk-igb