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  1. IGB
  2. IGBF-4039

Few IGB Apps are not showing in App Manager when added

    Details

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

      Description

      When going through the documentation (https://wiki.bioviz.org/confluence/display/igbdevelopers/Hello+World+IGB+App) to create a new plugin IGB App, came across this sample IGB app https://bitbucket.org/lorainelab/hello-world-igb-app/src/master/ which isn't working as expected now, same case with ncbi-primer, https://bitbucket.org/lorainelab/ncbi-primer/src/master/ both when added as repositories in Manage repositories tab isn't getting added as a new App in the App Manager.

      Steps to reproduce:

      1. Clone a copy of the Hello World App source code from Bitbucket - https://bitbucket.org/lorainelab/hello-world-igb-app
      2. Build the app using mvn clean install command, it generates a target folder.
      3. Start IGB
      4. Select Tools > Open App Manager
      5. Click Manage Repositories... button (opens Plug-in Repositories tab in Preferences window)
      6. Click Add... button (opens Plugin Repository dialog)
      7. Enter a name for your repository (can be anything)
      8. Click Choose local folder button
      9. Select the "target" folder in your igb-app-hello-world project folder.
      10. Once you add "target" as a new local App repository, you should see the Hello World App added as a new App in the IGB App Manager window but this isn't working as expected.

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            jsirigin Jaya Sravani Sirigineedi created issue -
            jsirigin Jaya Sravani Sirigineedi made changes -
            Field Original Value New Value
            Epic Link IGBF-1531 [ 17617 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Link This issue relates to IGBF-4032 [ IGBF-4032 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            Hide
            jsirigin Jaya Sravani Sirigineedi added a comment - - edited

            Investigated the issue, the reason is the igb version when importing the igb dependencies in the project, found related past issues: https://jira.bioviz.org/browse/IGBF-3595 and https://jira.bioviz.org/browse/IGBF-1906. When made changes according to these, it works as expected. Here is the updated code: https://bitbucket.org/jaya-sravani/hello-world-igb-app/branch/IGBF-4039.

            To Test: Follow the same steps in the ticket description but clone this branch and see whether it's working.

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - - edited Investigated the issue, the reason is the igb version when importing the igb dependencies in the project, found related past issues: https://jira.bioviz.org/browse/IGBF-3595 and https://jira.bioviz.org/browse/IGBF-1906 . When made changes according to these, it works as expected. Here is the updated code: https://bitbucket.org/jaya-sravani/hello-world-igb-app/branch/IGBF-4039 . To Test: Follow the same steps in the ticket description but clone this branch and see whether it's working.
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Assignee Jaya Sravani Sirigineedi [ jsirigin ] Paige Kulzer [ pkulzer ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Assignee Paige Kulzer [ pkulzer ] Jaya Sravani Sirigineedi [ jsirigin ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Assignee Jaya Sravani Sirigineedi [ jsirigin ] Paige Kulzer [ pkulzer ]
            pkulzer Paige Kulzer made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            Hide
            pkulzer Paige Kulzer added a comment -

            Following the steps outlined in the Description of this ticket, I observed the issue of the Hello World app not appearing in the IGB App Manager after it had been added. I then tested Sravani's changes by cloning her branch and following those same steps. Now, the Hello World app is appearing in the IGB App Manager as it should and the app is working as expected.

            Tasks for Jaya Sravani Sirigineedi:

            • Update your commit message to include the "IGBF-4039" string.
            • Link the tickets mentioned in your comment above to this ticket as related issues.
            • Implement the same code changes for the ncbi-primer app, then move this ticket back to Needs First Level Review once you're done.
            Show
            pkulzer Paige Kulzer added a comment - Following the steps outlined in the Description of this ticket, I observed the issue of the Hello World app not appearing in the IGB App Manager after it had been added. I then tested Sravani's changes by cloning her branch and following those same steps. Now, the Hello World app is appearing in the IGB App Manager as it should and the app is working as expected. Tasks for Jaya Sravani Sirigineedi : Update your commit message to include the " IGBF-4039 " string. Link the tickets mentioned in your comment above to this ticket as related issues. Implement the same code changes for the ncbi-primer app, then move this ticket back to Needs First Level Review once you're done.
            pkulzer Paige Kulzer made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            pkulzer Paige Kulzer made changes -
            Assignee Paige Kulzer [ pkulzer ] Jaya Sravani Sirigineedi [ jsirigin ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Link This issue relates to IGBF-3595 [ IGBF-3595 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Link This issue relates to IGBF-1906 [ IGBF-1906 ]
            Hide
            jsirigin Jaya Sravani Sirigineedi added a comment -

            Updated the commit message to include the Jira ticket number and linked the related issues to this ticket as well. Implemented the same changes to the ncbi-primer code as well: https://bitbucket.org/jaya-sravani/ncbi-primer/branch/IGBF-4039

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - Updated the commit message to include the Jira ticket number and linked the related issues to this ticket as well. Implemented the same changes to the ncbi-primer code as well: https://bitbucket.org/jaya-sravani/ncbi-primer/branch/IGBF-4039
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Assignee Jaya Sravani Sirigineedi [ jsirigin ]
            pkulzer Paige Kulzer made changes -
            Assignee Paige Kulzer [ pkulzer ]
            pkulzer Paige Kulzer made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            pkulzer Paige Kulzer made changes -
            Assignee Paige Kulzer [ pkulzer ] Nowlan Freese [ nfreese ]
            pkulzer Paige Kulzer made changes -
            Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
            Hide
            nfreese Nowlan Freese added a comment - - edited

            Testing Sravani's branch for ncbi-primer on Mac on IGB 10.1.0.

            The ncbi-primer app is not showing in the IGB 10.1.0 app manager due to the inclusion of <Import-Package> within the project pom. You can remove the <Import-Package> from the <instructions> of the pom.xml as it will by default import whatever packages it needs. I think by specifying version=10.0.0 for the import-packages the app will only work/show up in IGB 10.0.0.

            Update - What I said above is not correct, see IGBF-3518 for a detailed explanation of our strategy on versioning of IGB apps.

            Briefly:

            By declaring an import-package in the maven-bundle-plugin for the IGB dependencies with just a single version(i.e. 10.0.0), it sets the manifest's import-package version for those IGB dependencies to anything 10.0.0 or greater. Compare this to the normal convention of not passing anything in to the import-package as part of maven-bundle-plugin, which leads to the manifest giving an upper bound of version="[10.0,11)". It would be more "correct" to have the upper bound, as the assumption is that by changing to a new major version we are indicating that there are new changes that would break backwards compatibility. However, it would mean that anytime we changed the major version of IGB, we would need to re-release all apps, whether or not they were compatible.

            Show
            nfreese Nowlan Freese added a comment - - edited Testing Sravani's branch for ncbi-primer on Mac on IGB 10.1.0. The ncbi-primer app is not showing in the IGB 10.1.0 app manager due to the inclusion of <Import-Package> within the project pom. You can remove the <Import-Package> from the <instructions> of the pom.xml as it will by default import whatever packages it needs. I think by specifying version=10.0.0 for the import-packages the app will only work/show up in IGB 10.0.0. Update - What I said above is not correct, see IGBF-3518 for a detailed explanation of our strategy on versioning of IGB apps. Briefly: By declaring an import-package in the maven-bundle-plugin for the IGB dependencies with just a single version(i.e. 10.0.0), it sets the manifest's import-package version for those IGB dependencies to anything 10.0.0 or greater. Compare this to the normal convention of not passing anything in to the import-package as part of maven-bundle-plugin, which leads to the manifest giving an upper bound of version="[10.0,11)". It would be more "correct" to have the upper bound, as the assumption is that by changing to a new major version we are indicating that there are new changes that would break backwards compatibility. However, it would mean that anytime we changed the major version of IGB, we would need to re-release all apps, whether or not they were compatible.
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Jaya Sravani Sirigineedi [ jsirigin ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Sprint Winter 1 [ 209 ] Winter 1, Spring 1 [ 209, 210 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            Hide
            jsirigin Jaya Sravani Sirigineedi added a comment -

            I found what's the issue, it was a small change that wasn't pushed to my remote somehow, fixed that and it was working in the 10 version. I checked and fixed both the apps for the 11 version and now both of them are working for both the 10 and 11 versions of IGB. Here are the branches:
            https://bitbucket.org/jaya-sravani/hello-world-igb-app/branch/IGBF-4039
            https://bitbucket.org/jaya-sravani/ncbi-primer/branch/IGBF-4039

            Note when testing: Change the IGB version i.e., change the version in all the poms in igb project to 11.0.0 (you can do this simply by using the Replace in Files option in IntelliJ) and try to add the apps for that version too.

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - I found what's the issue, it was a small change that wasn't pushed to my remote somehow, fixed that and it was working in the 10 version. I checked and fixed both the apps for the 11 version and now both of them are working for both the 10 and 11 versions of IGB. Here are the branches: https://bitbucket.org/jaya-sravani/hello-world-igb-app/branch/IGBF-4039 https://bitbucket.org/jaya-sravani/ncbi-primer/branch/IGBF-4039 Note when testing: Change the IGB version i.e., change the version in all the poms in igb project to 11.0.0 (you can do this simply by using the Replace in Files option in IntelliJ) and try to add the apps for that version too.
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Assignee Jaya Sravani Sirigineedi [ jsirigin ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] saideepthi jagarapu [ sjagarap ]
            sjagarap saideepthi jagarapu made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            Hide
            sjagarap saideepthi jagarapu added a comment -

            checked main branch to reproduce the issue, observed that we are not able to add both the apps, then tested both the branches by changing igb project versions to 11.0.0, 10.0.0, 10.1.0, 10.2.0, now im able to see both the apps in the IGB App Manager as it should and the app is working as expected. Moving this to ready to PR state

            Show
            sjagarap saideepthi jagarapu added a comment - checked main branch to reproduce the issue, observed that we are not able to add both the apps, then tested both the branches by changing igb project versions to 11.0.0, 10.0.0, 10.1.0, 10.2.0, now im able to see both the apps in the IGB App Manager as it should and the app is working as expected. Moving this to ready to PR state
            sjagarap saideepthi jagarapu made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            nfreese Nowlan Freese made changes -
            Assignee saideepthi jagarapu [ sjagarap ] Jaya Sravani Sirigineedi [ jsirigin ]
            ann.loraine Ann Loraine made changes -
            Sprint Winter 1, Spring 1 [ 209, 210 ] Winter 1, Spring 1, Spring 2 [ 209, 210, 211 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - Raised pull requests for both the apps: https://bitbucket.org/lorainelab/hello-world-igb-app/pull-requests/1 https://bitbucket.org/lorainelab/ncbi-primer/pull-requests/6
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Assignee Jaya Sravani Sirigineedi [ jsirigin ]
            ann.loraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Hello world PR merged.
            NCBI Primer app PR merged.

            Show
            ann.loraine Ann Loraine added a comment - - edited Hello world PR merged. NCBI Primer app PR merged.
            ann.loraine Ann Loraine made changes -
            Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            New jar files are built and available for downloading from the two repositories: hello world app and ncbi primer app.

            Note for testers! Please check this:

            One thing I noticed is that the app micro versions have incremented in these new versions of the apps. I'm not sure, but it is possible that a non-10+ version of IGB might allow the new versions to be installed. Whoever tests this should launch the pre-JDK 21 version of IGB and check that the new versions of the apps are not available to install. If they can actually be installed, then go ahead and install them and see what happens.

            Show
            ann.loraine Ann Loraine added a comment - - edited New jar files are built and available for downloading from the two repositories: hello world app and ncbi primer app. Note for testers! Please check this: One thing I noticed is that the app micro versions have incremented in these new versions of the apps. I'm not sure, but it is possible that a non-10+ version of IGB might allow the new versions to be installed. Whoever tests this should launch the pre-JDK 21 version of IGB and check that the new versions of the apps are not available to install. If they can actually be installed, then go ahead and install them and see what happens.
            nfreese Nowlan Freese made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            Hide
            nfreese Nowlan Freese added a comment -

            Tested on main branch with Mac

            IGB 9.1.10
            Hello World: does not appear in App manager
            NCBI Primer App: does not appear in App manager

            IGB 10.1.0
            Hello World: appears in app manager, runs
            NCBI Primer App: appears in app manager, runs

            IGB 11.0.0
            Hello World: appears in app manager, runs
            NCBI Primer App: appears in app manager, runs

            This seems like the expected behavior. Closing ticket.

            Show
            nfreese Nowlan Freese added a comment - Tested on main branch with Mac IGB 9.1.10 Hello World: does not appear in App manager NCBI Primer App: does not appear in App manager IGB 10.1.0 Hello World: appears in app manager, runs NCBI Primer App: appears in app manager, runs IGB 11.0.0 Hello World: appears in app manager, runs NCBI Primer App: appears in app manager, runs This seems like the expected behavior. Closing ticket.
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Jaya Sravani Sirigineedi [ jsirigin ]
            nfreese Nowlan Freese made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

              People

              • Assignee:
                jsirigin Jaya Sravani Sirigineedi
                Reporter:
                jsirigin Jaya Sravani Sirigineedi
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                • Created:
                  Updated:
                  Resolved: