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  1. IGB
  2. IGBF-1417

Create new artifact with bigbed and bigwig parsing code from IGV codebase

    Details

    • Story Points:
      2
    • 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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            ann.loraine Ann Loraine created issue -
            ann.loraine Ann Loraine made changes -
            Field Original Value New Value
            Link This issue relates to IGBF-1098 [ IGBF-1098 ]
            ann.loraine Ann Loraine made changes -
            Status Open [ 1 ] Open [ 1 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Story Points 1 2
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            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.



            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-1418 [ IGBF-1418 ]
            kkorey Kiran Korey (Inactive) made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            kkorey Kiran Korey (Inactive) made changes -
            Assignee Kiran Korey [ kkorey ]
            kkorey Kiran Korey (Inactive) made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            kkorey Kiran Korey (Inactive) made changes -
            Assignee Kiran Korey [ kkorey ]
            ann.loraine Ann Loraine made changes -
            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.
            ]
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] Ready for Pull Request [ 10304 ]
            ann.loraine Ann Loraine made changes -
            Assignee Kiran Korey [ kkorey ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Fall 2018 Sprint 3 [ 53 ] Fall 2018 Sprint 3, Fall 2018 Sprint 4 [ 53, 54 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            kkorey Kiran Korey (Inactive) made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            kkorey Kiran Korey (Inactive) made changes -
            Assignee Kiran Korey [ kkorey ]
            ann.loraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Open [ 1 ]
            ann.loraine Ann Loraine made changes -
            Assignee Kiran Korey [ kkorey ]
            kkorey Kiran Korey (Inactive) made changes -
            Status Open [ 1 ] Pull Request Submitted [ 10101 ]
            kkorey Kiran Korey (Inactive) made changes -
            Assignee Kiran Korey [ kkorey ]
            ann.loraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Needs Testing [ 10002 ]
            ann.loraine Ann Loraine made changes -
            Comment [ Use this repo:

            * https://github.com/lorainelab/igv ]
            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-1446 [ IGBF-1446 ]
            stiwari8 Srishti Tiwari (Inactive) made changes -
            Assignee Srishti Tiwari [ stiwari8 ]
            stiwari8 Srishti Tiwari (Inactive) made changes -
            Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
            stiwari8 Srishti Tiwari (Inactive) made changes -
            Resolution Done [ 10000 ]
            Status Testing In Progress [ 10003 ] Closed [ 6 ]
            ann.loraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 18122 ] Fall 2019 Workflow Update [ 19949 ]
            ann.loraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 19949 ] Revised Fall 2019 Workflow Update [ 22070 ]
            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-2954 [ IGBF-2954 ]

              People

              • Assignee:
                stiwari8 Srishti Tiwari (Inactive)
                Reporter:
                ann.loraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: