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  1. IGB
  2. IGBF-3394

Refactor SNP file converter plugin

        Details

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

          Description

          Situation: The SNP file converter plugin does not appear in the IGB main-JDK8 app manager. Most likely this is due to a dependence on Google Guava 16.0.1 similar to IGBF-3349.

          Task: Refactor the app so that it appears in the IGB main-JDK8 app manager.

          Link: https://bitbucket.org/lorainelab/snp-file-converter/src/master/

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3400 Deploy SNP File Converter version 9.1.1 to App Store

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

              Task - A task that needs to be done. IGBF-3349 Remove guava (google) upper bound version requirement for ProtAnnot

              • Blocker - Blocks development and/or testing work, production could not run.
              • Closed

                Activity

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                kgopu Kaushik Gopu added a comment -

                The SNP-file-converter-plugin is coming up after upgrading guava dependency. However, I would like to perform run time testing so that I can conclude that application is working fine.

                Show
                kgopu Kaushik Gopu added a comment - The SNP-file-converter-plugin is coming up after upgrading guava dependency. However, I would like to perform run time testing so that I can conclude that application is working fine.
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                kgopu Kaushik Gopu added a comment - - edited

                Tested the application by using sample file and it is working fine. moving to first level review.

                Show
                kgopu Kaushik Gopu added a comment - - edited Tested the application by using sample file and it is working fine. moving to first level review. branch
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                nfreese Nowlan Freese added a comment - - edited

                Testing Kaushik's branch locally on Mac.

                IGB release-9.1.10
                Installed version 9.1.0 of SNP File Converter through the App Manager. After adding Kaushik's SNP File Converter as a new repository the app manager showed that I could update SNP File Converter from 9.1.0 to 9.1.1. SNP File Converter worked correctly on the attached example data.

                IGB main-JDK8
                With the default app manager repositories SNP File Converter is not available. After adding Kaushik's SNP File Converter as a new local repository the app manager showed that I could install SNP File Converter version 9.1.1. SNP File Converter worked correctly.

                Note: The name of the app was changed in this commit along with a change from version 9.1.0 to 9.1.1. However, the 9.1.1 version of the app was never released on the app store. In Kaushik's branch the app version is 9.1.1 which I think should work, since 9.1.1 was never released.

                2nd note: Please make sure your IDE is not auto formatting tabs/spaces as they make commits more difficult to read.

                Ready for pull request.

                Show
                nfreese Nowlan Freese added a comment - - edited Testing Kaushik's branch locally on Mac. IGB release-9.1.10 Installed version 9.1.0 of SNP File Converter through the App Manager. After adding Kaushik's SNP File Converter as a new repository the app manager showed that I could update SNP File Converter from 9.1.0 to 9.1.1. SNP File Converter worked correctly on the attached example data. IGB main-JDK8 With the default app manager repositories SNP File Converter is not available. After adding Kaushik's SNP File Converter as a new local repository the app manager showed that I could install SNP File Converter version 9.1.1. SNP File Converter worked correctly. Note: The name of the app was changed in this commit along with a change from version 9.1.0 to 9.1.1. However, the 9.1.1 version of the app was never released on the app store. In Kaushik's branch the app version is 9.1.1 which I think should work, since 9.1.1 was never released. 2nd note: Please make sure your IDE is not auto formatting tabs/spaces as they make commits more difficult to read. Ready for pull request.
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                kgopu Kaushik Gopu added a comment - - edited

                Pull request submitted:https://bitbucket.org/lorainelab/snp-file-converter/pull-requests/10

                Show
                kgopu Kaushik Gopu added a comment - - edited Pull request submitted: https://bitbucket.org/lorainelab/snp-file-converter/pull-requests/10
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                nfreese Nowlan Freese added a comment -

                Tested on Mac using https://bitbucket.org/lorainelab/snp-file-converter/downloads/ and the testing strategy outlined above.

                Everything is working correctly.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested on Mac using https://bitbucket.org/lorainelab/snp-file-converter/downloads/ and the testing strategy outlined above. Everything is working correctly. Closing ticket.

                  People

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

                    Dates

                    • Created:
                      Updated:
                      Resolved: