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  1. IGB
  2. IGBF-3433

Update protannot for new r6 annotations.

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          • Update Protannot to use new OSGi r6 annotations.
          • Update Maven Bundle plugin to 5.1.9.
          • Make a separate commit for each change above.

            Attachments

              Issue Links

              is blocked by

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3431 Update maven-bundle-plugin

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-3393 Investigate updating ProtAnnot to R6 annotations

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3518 Update ProtAnnot for JDK21

              • Major - Major loss of function.
              • Closed

                Activity

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                kgopu Kaushik Gopu added a comment - - edited
                • Updated protannot for new r6 annotations. pull this branch for testing.
                • The following changes includes: protannot now uses OSGI r6 declarative services and upgraded maven-bundle-plugin to 5.1.9
                • Ran protannot for a genome, no issues were encountered during and after the scan.
                • Moving to first level review
                Show
                kgopu Kaushik Gopu added a comment - - edited Updated protannot for new r6 annotations. pull this branch for testing. The following changes includes: protannot now uses OSGI r6 declarative services and upgraded maven-bundle-plugin to 5.1.9 Ran protannot for a genome, no issues were encountered during and after the scan. Moving to first level review
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                nfreese Nowlan Freese added a comment -

                This ticket is on hold while IGBF-3431 testing continues.

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                nfreese Nowlan Freese added a comment - This ticket is on hold while IGBF-3431 testing continues.
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                nfreese Nowlan Freese added a comment - - edited

                Tested on Mac
                Testing on main-JDK8 9.1.12

                Testing on IGB release 9.1.10

                • ProtAnnot from Kaushik's branch was not able to work on IGB release 9.1.10 as there was a resolver error.

                Conclusion:
                The current version of ProtAnnot (9.1.4) works on both main-JDK8 (IGB 9.1.12) and IGB release 9.1.10. Further investigation into the error observed on IGB 9.1.10 when installing the new version of ProtAnnot may be warranted as it could help us identify potential OSGI issues. However, at this time I don't see a reason to upgrade protannot to the new R6 annotations.

                This may be looking at in the future, but for the moment I am moving this ticket to the backlog.

                Show
                nfreese Nowlan Freese added a comment - - edited Tested on Mac Testing on main-JDK8 9.1.12 Downloaded Kaushik's IGBF-3433 branch . I changed the version to 9.1.5 as the current master branch version of ProtAnnot is at 9.1.4 . I was able to build Kaushik's branch, install it in IGB 9.1.12 (main-JDK8), and successfully run ProtAnnot. Testing on IGB release 9.1.10 ProtAnnot from Kaushik's branch was not able to work on IGB release 9.1.10 as there was a resolver error. Conclusion: The current version of ProtAnnot (9.1.4) works on both main-JDK8 (IGB 9.1.12) and IGB release 9.1.10. Further investigation into the error observed on IGB 9.1.10 when installing the new version of ProtAnnot may be warranted as it could help us identify potential OSGI issues. However, at this time I don't see a reason to upgrade protannot to the new R6 annotations. This may be looking at in the future, but for the moment I am moving this ticket to the backlog.
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                nfreese Nowlan Freese added a comment -

                This ticket has been superseded by IGBF-3518.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - This ticket has been superseded by IGBF-3518 . Closing ticket.

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    kgopu Kaushik Gopu
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                    Dates

                    • Created:
                      Updated:
                      Resolved: