Details

    • Type: Sub-task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      0.5
    • Sprint:
      Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10, Summer 2019 Sprint 11

      Description

      • Create new repository for Geometric Mean Operator.
      • Configure to allow compilation on your local
      • Check that you are able to run it within the IGB platform

      Once it is finished (to your satisfaction), request to transfer repository ownership to Loraine Lab team for next steps.

      Note: Make sure that the build process generates a working bundle and also a working OBR index.

        Attachments

          Activity

          Hide
          prutha Prutha Kulkarni (Inactive) added a comment -

          Created a new repository for the geometric-mean app. After changing the pom.xml when(added version tag as 9.0.0 for igb-services and genometry dependencies because the online repository present at http://maven.bioviz.org/repo2 has only 9.0.0 version of the JAR files) I tried to build the app on the EC2 instance(because it does not have a local copy of the IGB) then it is giving following error:

          [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project geometric-mean: Compilation failure: Compilation failure:
          [ERROR] /Users/pruthakulkarni/IGB_AppStore/prutha_geometric-mean/src/main/java/com/gene/geometricmean/Activator.java:[12,34] type org.osgi.framework.ServiceRegistration does not take parameters
          [ERROR] /Users/pruthakulkarni/IGB_AppStore/prutha_geometric-mean/src/main/java/com/gene/geometricmean/Activator.java:[14,26] no suitable method found for registerService(java.lang.Class<com.affymetrix.genometry.operator.Operator>,com.gene.geometricmean.GeometricMeanOperator,<nulltype>)
          [ERROR] method org.osgi.framework.BundleContext.registerService(java.lang.String[],java.lang.Object,java.util.Dictionary) is not applicable
          [ERROR] (argument mismatch; java.lang.Class<com.affymetrix.genometry.operator.Operator> cannot be converted to java.lang.String[])
          [ERROR] method org.osgi.framework.BundleContext.registerService(java.lang.String,java.lang.Object,java.util.Dictionary) is not applicable
          [ERROR] (argument mismatch; java.lang.Class<com.affymetrix.genometry.operator.Operator> cannot be converted to java.lang.String)

          When I tried to build it on my local machine with 9.1.0 version of the dependencies, the build is successful as the machine has a copy of 9.1.0 versioned JAR files of the dependencies.
          Do we need to update the online repository or is there any other online repository which has the latest version of these JAR files and which can be referenced into the pom.xml in order to build the geometric-mean app?

          Show
          prutha Prutha Kulkarni (Inactive) added a comment - Created a new repository for the geometric-mean app. After changing the pom.xml when(added version tag as 9.0.0 for igb-services and genometry dependencies because the online repository present at http://maven.bioviz.org/repo2 has only 9.0.0 version of the JAR files) I tried to build the app on the EC2 instance(because it does not have a local copy of the IGB) then it is giving following error: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project geometric-mean: Compilation failure: Compilation failure: [ERROR] /Users/pruthakulkarni/IGB_AppStore/prutha_geometric-mean/src/main/java/com/gene/geometricmean/Activator.java: [12,34] type org.osgi.framework.ServiceRegistration does not take parameters [ERROR] /Users/pruthakulkarni/IGB_AppStore/prutha_geometric-mean/src/main/java/com/gene/geometricmean/Activator.java: [14,26] no suitable method found for registerService(java.lang.Class<com.affymetrix.genometry.operator.Operator>,com.gene.geometricmean.GeometricMeanOperator,<nulltype>) [ERROR] method org.osgi.framework.BundleContext.registerService(java.lang.String[],java.lang.Object,java.util.Dictionary) is not applicable [ERROR] (argument mismatch; java.lang.Class<com.affymetrix.genometry.operator.Operator> cannot be converted to java.lang.String[]) [ERROR] method org.osgi.framework.BundleContext.registerService(java.lang.String,java.lang.Object,java.util.Dictionary) is not applicable [ERROR] (argument mismatch; java.lang.Class<com.affymetrix.genometry.operator.Operator> cannot be converted to java.lang.String) When I tried to build it on my local machine with 9.1.0 version of the dependencies, the build is successful as the machine has a copy of 9.1.0 versioned JAR files of the dependencies. Do we need to update the online repository or is there any other online repository which has the latest version of these JAR files and which can be referenced into the pom.xml in order to build the geometric-mean app?
          Hide
          ann.loraine Ann Loraine added a comment - - edited

          Please add a link to the new git repository for geometric mean graph operator.

          Show
          ann.loraine Ann Loraine added a comment - - edited Please add a link to the new git repository for geometric mean graph operator.
          Hide
          prutha Prutha Kulkarni (Inactive) added a comment -

          Here is the link of the new git repository:
          https://bitbucket.org/pkulka10/geometric-mean/src/master/

          Show
          prutha Prutha Kulkarni (Inactive) added a comment - Here is the link of the new git repository: https://bitbucket.org/pkulka10/geometric-mean/src/master/
          Hide
          ann.loraine Ann Loraine added a comment -

          IGB platform 9.1.0 bundles are available from maven repository 3 - see IGB project top-level pom.xml for the coordinates.
          However, I don't think this problem will be solved by increasing the version of the IGB bundles to 9.1.0 because I don't think that IGB APIs being used by the geometric mean graph operator App were changed between versions 9.0.0 and 9.1.0. The IGB code used by the App is the same. I think the problem is in the POM.

          Show
          ann.loraine Ann Loraine added a comment - IGB platform 9.1.0 bundles are available from maven repository 3 - see IGB project top-level pom.xml for the coordinates. However, I don't think this problem will be solved by increasing the version of the IGB bundles to 9.1.0 because I don't think that IGB APIs being used by the geometric mean graph operator App were changed between versions 9.0.0 and 9.1.0. The IGB code used by the App is the same. I think the problem is in the POM.
          Hide
          prutha Prutha Kulkarni (Inactive) added a comment -

          Thanks Prof. [~aloraine] for the help.
          Even I was thinking that the code for both the versions is same and that is why I was not able to figure out.
          I will try changing the pom again and will provide an update on this soon.

          Show
          prutha Prutha Kulkarni (Inactive) added a comment - Thanks Prof. [~aloraine] for the help. Even I was thinking that the code for both the versions is same and that is why I was not able to figure out. I will try changing the pom again and will provide an update on this soon.
          Hide
          prutha Prutha Kulkarni (Inactive) added a comment - - edited

          I was successfully able to build the JAR file and repository.xml file under the downloads section of the bitbucket. Also, tested the downloads path with IGB platform.
          I have transferred the ownership of the repository to 'lorainelab'.
          You can check the repository on the following path:
          https://bitbucket.org/pkulka10/geometric-mean/src/master/
          If you are accessing the repo after accepting the ownership for it then instead of 'pkulka10' you just need to add 'lorainelab'.

          Show
          prutha Prutha Kulkarni (Inactive) added a comment - - edited I was successfully able to build the JAR file and repository.xml file under the downloads section of the bitbucket. Also, tested the downloads path with IGB platform. I have transferred the ownership of the repository to 'lorainelab'. You can check the repository on the following path: https://bitbucket.org/pkulka10/geometric-mean/src/master/ If you are accessing the repo after accepting the ownership for it then instead of 'pkulka10' you just need to add 'lorainelab'.
          Hide
          ann.loraine Ann Loraine added a comment - - edited

          Excellent!

          For the next steps, I simplified the build process a great deal. This will be helpful (I hope!) to new App developers so that they can easily use the bitbucket pipelines infrastructure to build & test their Apps.

          Because this is working as expected, I am moving this ticket to "Closed" and re-assigne to the original dev.

          Show
          ann.loraine Ann Loraine added a comment - - edited Excellent! For the next steps, I simplified the build process a great deal. This will be helpful (I hope!) to new App developers so that they can easily use the bitbucket pipelines infrastructure to build & test their Apps. Because this is working as expected, I am moving this ticket to "Closed" and re-assigne to the original dev.

            People

            • Assignee:
              prutha Prutha Kulkarni (Inactive)
              Reporter:
              ann.loraine Ann Loraine
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                Updated:
                Resolved: