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: 9.0.2 Minor Release
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Labels:
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Story Points:2
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Sprint:Fall 2018 Sprint 3, Fall 2018 Sprint 4
Description
IGV codebase has updated bigbed and bigwig parsing code.
We are currently using very old versions of this same code, packaged in artifact bigwig-1.0.jar.
This older artifact bigwig-1.0.jar uses SeekableStream and SeakableStreamReader classes from another very old artifact - tribble-0.1.jar, which is packaged into the bigwig-1.0.jar artifact.
However, elsewhere in the project we are now using an htsjdk artifact which contains SeekableStream and SeakableStreamReader classes that can replace same in tribble-0.1.jar. In addition, newer igv code is using these same classes.
To simplify the code base - and make the final packaged jar files smaller - we will build a new bundle containing IGV bigbed and bigwig parsing code that uses the htsjdk artifact, which will be provided as a bundle by the OSGi framework.
This new bundle should be as lightweight as possible - it should include just packages we need and include logging code used by the rest of the IGB code base.
To build the bundle, we will 1st fork the igv code base and add new scripts (or gradle/maven build configuration files) to build the bundle we want. We will also modify the igv code base as required to use our preferred logging framework. We will do this in such a way as to enable us to keep our fork up-to-date with the IGV code base.
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| Status | Open [ 1 ] | Open [ 1 ] |
| Rank | Ranked higher |
| Story Points | 1 | 2 |
| Rank | Ranked higher |
| Description |
IGV codebase has updated bigbed and bigwig parsing code.
We are currently using very old versions of this same code, packaged in artifact bigwig-1.0.jar. This older artifact bigwig-1.0.jar uses SeekableStream and SeakableStreamReader classes artifact tribble-0.1.jar packaged in the same bundle. We are now importing htsjdk artifact which contains SeekableStream and SeakableStreamReader classes that can replace same in tribble-0.1.jar. To simplify the code base - and make the final packaged jar files smaller - we should create a new bundle with IGV bigbed and bigwig parsing code that uses htsjdk artifact only. Our |
IGV codebase has updated bigbed and bigwig parsing code.
We are currently using very old versions of this same code, packaged in artifact bigwig-1.0.jar. This older artifact bigwig-1.0.jar uses SeekableStream and SeakableStreamReader classes from another very old artifact - tribble-0.1.jar, which is packaged into the bigwig-1.0.jar artifact. However, elsewhere in the project we are now using an htsjdk artifact which contains SeekableStream and SeakableStreamReader classes that can replace same in tribble-0.1.jar. In addition, newer igv code is using these same classes. To simplify the code base - and make the final packaged jar files smaller - we will build a *new* bundle containing IGV bigbed and bigwig parsing code that uses the htsjdk artifact, which will be provided as a bundle by the OSGi framework. This new bundle should be as lightweight as possible - it should include *just* packages we need and include logging code used by the rest of the IGB code base. To build the bundle, we will 1st fork the igv code base and add new scripts (or gradle/maven build configuration files) to build the bundle we want. We will also modify the igv code base as required to use our preferred logging framework. We will do this in such a way as to enable us to keep our fork up-to-date with the IGV code base. |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | Kiran Korey [ kkorey ] |
Made some code changes to use the new artifact, Please review the changes.
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1417-bigwig
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Comment |
[ I'm surprised that this can build under bitbucket pipelines because the project-level POM doesn't include the latest commit with https://nexus.bioviz.org repository added.
The artifact should be coming from there...but it cannot, because the repository is not added. Please take a look. ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 3 [ 53 ] | Fall 2018 Sprint 3, Fall 2018 Sprint 4 [ 53, 54 ] |
| Rank | Ranked higher |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Status | Pull Request Submitted [ 10101 ] | Open [ 1 ] |
Check for conflicts. Resolve & then please re-submit pull request.
| Assignee | Kiran Korey [ kkorey ] |
| Status | Open [ 1 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
bigwig artifact, plus sources, now deployed to
| Comment |
[ Use this repo:
* https://github.com/lorainelab/igv ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Tested on Windows. It works well. The new artifact gets downloaded from the Nexus repository. Bigbed and Bigwig files load properly in IGB.
Closing.
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 18122 ] | Fall 2019 Workflow Update [ 19949 ] |
| Workflow | Fall 2019 Workflow Update [ 19949 ] | Revised Fall 2019 Workflow Update [ 22070 ] |
Repository with revised bigwig / bigbed code is here: https://bitbucket.org/lorainelab/bigwig/src/master/
Note that the repo contains logic for uploading to maven repositories and packaging as an OSGi bundle.
Packages required:
org.broad.igv.bbfile
Package may be required - check in IGB code base to be sure:
org.broad.igv.bigwig