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  1. IGB
  2. IGBF-1418

Import htsjdk as OSGi bundle

        Details

        • Type: Improvement
        • Status: Closed (View Workflow)
        • Priority: Critical
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1
        • Sprint:
          Fall 2018 Sprint 3, Fall 2018 Sprint 4

          Description

          We are now using packages from htsjdk artifact in the IGB project. However, there is a problem. It is not an OSGi bundle. To handle this, we are now importing the htsjdk into the "shared-lib-wrapper" module of IGB project. The pom.xml file of this module uses the BND-tool maven plug-in to packages htsjdk along with many other completely unrelated artifacts into one large bundle, which then gets loaded into the OSGi run-time along with all the other bundles that make up the IGB application.

          This is not ideal. Maintaining the "shared-lib-wrapper" module is made extra complicated by this approach. For example, if some of these libraries rely on different versions of the same artifact, the approach won't work.

          To simplify our codebase, we should transform these 3rd-party jar artifacts into proper OSGi bundles.

          To do this, let's "fork" the htsjdk library and modify/enhance their build process to create a proper OSGi bundle.

          Following this, we should add it to our nexus maven repository (https://nexus.bioviz.org) so that the new htsjdk OSGi bundle is available to IGB developers.

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1457 Startup Error in Console (ERROR com.affymetrix.main.OSGiHandler)

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1419 Add new Nexus repository to top-level POM.xml

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1098 Update BAM, tabix reader libraries

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-1417 Create new artifact with bigbed and bigwig parsing code from IGV codebase

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3464 Deploy htsjdk-igb

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Sprint Fall 2018 Sprint 3 [ 53 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1417 [ IGBF-1417 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1098 [ IGBF-1098 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status In Progress [ 3 ] Pull Request Submitted [ 10101 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Pull Request Submitted [ 10101 ] In Progress [ 3 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status In Progress [ 3 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                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 -
                Assignee Kiran Korey [ kkorey ]
                kkorey Kiran Korey (Inactive) made changes -
                Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Status Testing In Progress [ 10003 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1419 [ IGBF-1419 ]
                ann.loraine Ann Loraine made changes -
                Assignee Kiran Korey [ kkorey ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                kkorey Kiran Korey (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] Reviewing [ 10301 ]
                kkorey Kiran Korey (Inactive) made changes -
                Status Reviewing [ 10301 ] Ready for Pull Request [ 10304 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Needs 1st Level Review [ 10005 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1457 [ IGBF-1457 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18124 ] Fall 2019 Workflow Update [ 19950 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19950 ] Revised Fall 2019 Workflow Update [ 22071 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3464 [ IGBF-3464 ]

                  People

                  • Assignee:
                    stiwari8 Srishti Tiwari (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: