Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2063

Add maven resources variable to all IGB App pom.xml files

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          0.5
        • Epic Link:
        • Sprint:
          Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec

          Description

          We recently discovered that our use of the BundleResources tag in our demonstration IGB App pom.xml's was blocking inclusion of everything under main/resources in the jar file.

          This came up when we noticed that the "Get Average Score" App was no longer getting installed when we included the repository.xml file in the jar file.

          We now know why this was happening!

          (Spoiler alert: It's a maven thing.)

          For details, see:

          For the next step, we need to implement and of course test the fix recommended in the above ticket.

          For this task, update all the pom.xml files for each of the IGB demonstration Apps in our lorainelab bitbucket account. Make forks and submit PRs from there.

          Please note: All IGB demonstration App's are in the project "IGB Apps" which you can find by visiting the Loraine Lab bitbucket page https://bitbucket.org/lorainelab/. Just click the link labeled "Projects" on the left of the page.

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              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2041 Investigate and fix errors in functionality of Get Average Score App

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment - - edited

                Also please update bitbucket_pipelines.yml:

                • update the Docker image
                • change mvn command to "mvn package" instead of "mvn clean install"

                Installation does not make sense because "mvn install" typically means: copy the jar to the user's local .m2 directory.
                This should never happen for an App because Apps should never be used for compiling projects.
                Also, this does not make sense for our Docker image.

                The IGB project mvn command is running "mvn install" only because the project pom's are organized in a weird way.

                Show
                ann.loraine Ann Loraine added a comment - - edited Also please update bitbucket_pipelines.yml: update the Docker image change mvn command to "mvn package" instead of "mvn clean install" Installation does not make sense because "mvn install" typically means: copy the jar to the user's local .m2 directory. This should never happen for an App because Apps should never be used for compiling projects. Also, this does not make sense for our Docker image. The IGB project mvn command is running "mvn install" only because the project pom's are organized in a weird way.
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                shamika Shamika Gajanan Kulkarni (Inactive) added a comment - - edited

                Prof. [~aloraine], could you please let me know the name of the docker image so that I can update the pipeline configuration accordingly?

                Show
                shamika Shamika Gajanan Kulkarni (Inactive) added a comment - - edited Prof. [~aloraine] , could you please let me know the name of the docker image so that I can update the pipeline configuration accordingly?
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                ann.loraine Ann Loraine added a comment -

                See IGB project pipeline config file:
                lorainelab/igb-maven-install4j:jre-1.8.0-212-mvn-deploy

                To save time, I will edit the files directly using the bitbucket UI.

                Show
                ann.loraine Ann Loraine added a comment - See IGB project pipeline config file: lorainelab/igb-maven-install4j:jre-1.8.0-212-mvn-deploy To save time, I will edit the files directly using the bitbucket UI.
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                shamika Shamika Gajanan Kulkarni (Inactive) added a comment -

                I have made the changes in the bitbucket configurations. Kindly check if this helps you. I am sorry for the delay, since me and Prutha were working on the same thing I had to revert the changes and my laptop crashed so had to do this again on LoraineLabs laptop. Also, I am not sure whether to change the command from 'mvn clean install' to 'mvn package' for development apps as well. The changes are present for the rest of the apps.

                https://bitbucket.org/skulka2710/23andme-snp-converter-shamika/branch/IGBF-2063#diff
                https://bitbucket.org/skulka2710/command-socket-sgk-fork/branch/IGBF-2063#diff
                https://bitbucket.org/skulka2710/geometric-mean-operator-shamika/branch/IGBF-2063#diff
                https://bitbucket.org/skulka2710/get-average-score-shamika/branch/IGBF-2063#diff
                https://bitbucket.org/skulka2710/sgk-merge-annotation-operator/branch/IGBF-2063#diff
                https://bitbucket.org/skulka2710/protannot-shamika/branch/IGBF-2063#diff
                https://bitbucket.org/skulka2710/shamika-super-simple-igb-app/branch/IGBF-2063#diff

                Thank you.

                Show
                shamika Shamika Gajanan Kulkarni (Inactive) added a comment - I have made the changes in the bitbucket configurations. Kindly check if this helps you. I am sorry for the delay, since me and Prutha were working on the same thing I had to revert the changes and my laptop crashed so had to do this again on LoraineLabs laptop. Also, I am not sure whether to change the command from 'mvn clean install' to 'mvn package' for development apps as well. The changes are present for the rest of the apps. https://bitbucket.org/skulka2710/23andme-snp-converter-shamika/branch/IGBF-2063#diff https://bitbucket.org/skulka2710/command-socket-sgk-fork/branch/IGBF-2063#diff https://bitbucket.org/skulka2710/geometric-mean-operator-shamika/branch/IGBF-2063#diff https://bitbucket.org/skulka2710/get-average-score-shamika/branch/IGBF-2063#diff https://bitbucket.org/skulka2710/sgk-merge-annotation-operator/branch/IGBF-2063#diff https://bitbucket.org/skulka2710/protannot-shamika/branch/IGBF-2063#diff https://bitbucket.org/skulka2710/shamika-super-simple-igb-app/branch/IGBF-2063#diff Thank you.
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                ann.loraine Ann Loraine added a comment -

                These changes are fine. Proceed when you are ready.

                Show
                ann.loraine Ann Loraine added a comment - These changes are fine. Proceed when you are ready.

                  People

                  • Assignee:
                    shamika Shamika Gajanan Kulkarni (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: