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  1. IGB
  2. IGBF-3543

Rebase cram changes on main-JDK21-with-javafx-no-theme

        Details

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

          Description

          Situation: We would like to include the cram implementation in the JDK21 release of IGB.

          Task: Rebase the cram implementation onto the JDK21 branch: main-JDK21-with-javafx-no-theme

            Attachments

              Issue Links

              relates to

              New Feature - A new feature of the product, which has yet to be developed. IGBF-3478 Add CRAM support to IGB

              • Major - Major loss of function.
              • Closed

                Activity

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                kgopu Kaushik Gopu added a comment -

                PR has been submitted.

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                kgopu Kaushik Gopu added a comment - PR has been submitted.
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                ann.loraine Ann Loraine added a comment - - edited

                A request:

                (Note that doing the above could be tricky because the source branch in the above PR looks like it's already JDK21-with-javafx-no-theme, as it exists on your fork.)

                • Apply the new CRAM feature commit(s) to that branch, and send a PR to lorainelab/integrated-genome-browser : main-JDK21-with-javafx-no-theme

                Doing this should make it possible to build an installer with the new feature in it, due to some recent updates in our continuous integration / continuous release infrastructure.

                I'm not sure how difficult or easy doing the above would be, however.

                Nowlan Freese may want to comment.

                Show
                ann.loraine Ann Loraine added a comment - - edited A request: Please make a new topic branch from the current tip of main-JDK21-with-javafx-no-theme at https://bitbucket.org/lorainelab/integrated-genome-browser/branch/main-JDK21-with-javafx-no-theme (Note that doing the above could be tricky because the source branch in the above PR looks like it's already JDK21-with-javafx-no-theme, as it exists on your fork.) Apply the new CRAM feature commit(s) to that branch, and send a PR to lorainelab/integrated-genome-browser : main-JDK21-with-javafx-no-theme Doing this should make it possible to build an installer with the new feature in it, due to some recent updates in our continuous integration / continuous release infrastructure. I'm not sure how difficult or easy doing the above would be, however. Nowlan Freese may want to comment.
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                nfreese Nowlan Freese added a comment - - edited

                Kaushik's approach was to clone main-JDK21-with-javafx-no-theme and then apply his cram commits to that branch. I built his branch on my Mac and it ran and I was able to load cram files. It looks like his bitbucket pipeline build was also successful, though I did not test the installer. The only commits that are missing are the two recent commits changing the version and pipeline as well as a merge. There are no merge conflicts so it shouldn't have an effect on merging them.

                I meant to add these comments earlier. Kaushik and I had a discussion through Meet and we tested that his changes worked and IGB ran.

                Show
                nfreese Nowlan Freese added a comment - - edited Kaushik's approach was to clone main-JDK21-with-javafx-no-theme and then apply his cram commits to that branch. I built his branch on my Mac and it ran and I was able to load cram files. It looks like his bitbucket pipeline build was also successful, though I did not test the installer. The only commits that are missing are the two recent commits changing the version and pipeline as well as a merge. There are no merge conflicts so it shouldn't have an effect on merging them. I meant to add these comments earlier. Kaushik and I had a discussion through Meet and we tested that his changes worked and IGB ran.
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                ann.loraine Ann Loraine added a comment -

                Sounds like I should go ahead and accept (merge) the PR. Let me know if yes Nowlan Freese. Thank you!

                Show
                ann.loraine Ann Loraine added a comment - Sounds like I should go ahead and accept (merge) the PR. Let me know if yes Nowlan Freese . Thank you!
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                nfreese Nowlan Freese added a comment -

                I think it can be merged.

                Show
                nfreese Nowlan Freese added a comment - I think it can be merged.
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                ann.loraine Ann Loraine added a comment -

                Merged. Bitbucket pipelines completed and installers are now ready for testing.

                See:

                IGB-[ mac, windows, unix, etc ]-main-JDK21-with-javafx-no-theme.[sh,dmg,exe]

                In:

                https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/

                Ready for testing

                Show
                ann.loraine Ann Loraine added a comment - Merged. Bitbucket pipelines completed and installers are now ready for testing. See: IGB-[ mac, windows, unix, etc ]-main-JDK21-with-javafx-no-theme. [sh,dmg,exe] In: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/ Ready for testing
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                nfreese Nowlan Freese added a comment -

                Tested installer on Mac.
                Able to load cram files locally and via URL, and able to see the MD5 error when there is an issue with the cram.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested installer on Mac. Able to load cram files locally and via URL, and able to see the MD5 error when there is an issue with the cram. Closing ticket.

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
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                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: