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  1. IGB
  2. IGBF-1850

htsjdk-igb is importing packages from the same library

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      1.5
    • Sprint:
      Summer 2019 Sprint 9

      Description

      Tasks:

      1. Remove 'osgi' plugin and use 'biz.aQute.bnd.builder'.
      2. Don't import htsjdk-igb packages

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          Issue Links

            Activity

            svallapu Sai Charan Reddy Vallapureddy created issue -
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Field Original Value New Value
            Link This issue relates to IGBF-1767 [ IGBF-1767 ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Attachment build.gradle [ 14351 ]
            Hide
            svallapu Sai Charan Reddy Vallapureddy added a comment -

            Ann Loraine

            1. Changed osgi plugin to biz.aQute.bnd.builder.
            2. Made the necessary changes to build.gradle file to stop importing htsjdk packages from the same library.

            build.gradle file is attached to this ticket.

            I have tested with my IGB with the jar with current changes, it is working fine in IGB.

            (Note: IGBF-1767 (bundle resolution error) is also done. After this ticket, kindly review IGBF-1767 so that I can submit a pull request.

            Show
            svallapu Sai Charan Reddy Vallapureddy added a comment - Ann Loraine 1. Changed osgi plugin to biz.aQute.bnd.builder. 2. Made the necessary changes to build.gradle file to stop importing htsjdk packages from the same library. build.gradle file is attached to this ticket. I have tested with my IGB with the jar with current changes, it is working fine in IGB. (Note: IGBF-1767 (bundle resolution error) is also done. After this ticket, kindly review IGBF-1767 so that I can submit a pull request.
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Assignee Sai Charan Reddy Vallapureddy [ svallapu ] Ann Loraine [ aloraine ]
            Hide
            aloraine Ann Loraine added a comment -

            Review completed. Please proceed with pull request on github.

            Show
            aloraine Ann Loraine added a comment - Review completed. Please proceed with pull request on github.
            Show
            svallapu Sai Charan Reddy Vallapureddy added a comment - Ann Loraine Branch: https://github.com/VallapuCharan/htsjdk/commit/506df2c2ad245aa779fd25462da80c2e76222bcb Pull request submitted.
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Status Needs 1st Level Review [ 10005 ] Pull Request Submitted [ 10101 ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Assignee Ann Loraine [ aloraine ] Sai Charan Reddy Vallapureddy [ svallapu ]
            svallapu Sai Charan Reddy Vallapureddy made changes -
            Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
            aloraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Needs Testing [ 10002 ]
            Hide
            aloraine Ann Loraine added a comment -

            Merged pull request.

            Show
            aloraine Ann Loraine added a comment - Merged pull request.
            Hide
            aloraine Ann Loraine added a comment -

            Uploaded newly built jar to nexus.

            Show
            aloraine Ann Loraine added a comment - Uploaded newly built jar to nexus.
            Hide
            aloraine Ann Loraine added a comment - - edited

            To test:

            1. Download jar from nexus: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.2/htsjdk-igb-2.16.2.jar
            2. Use bnd (see comment from linked issue) to inspect MANIFEST of jar.
            3. Check that htsjdk does not import its own packages.
            4. Check that the newly deployed artifact can support building IGB installer via bitbucket pipeline. For this, you can trigger a build on the master branch of your fork.
            Show
            aloraine Ann Loraine added a comment - - edited To test: Download jar from nexus: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.2/htsjdk-igb-2.16.2.jar Use bnd (see comment from linked issue) to inspect MANIFEST of jar. Check that htsjdk does not import its own packages. Check that the newly deployed artifact can support building IGB installer via bitbucket pipeline. For this, you can trigger a build on the master branch of your fork.
            aloraine Ann Loraine made changes -
            Status Needs Testing [ 10002 ] Needs Testing [ 10002 ]
            Hide
            aloraine Ann Loraine added a comment -

            Confirmed items 2 and 3 above. Running:

            • bnd print htsjdk-igb-2.16.2.jar

            shows that the only packages being imported are:

            [IMPEXP]
            Import-Package
            org.apache.commons.compress.compressors.bzip2

            {version=[1.4,2)}
            org.apache.commons.compress.compressors.xz {version=[1.4,2)}

            org.apache.commons.compress.utils

            {version=[1.4,2)}

            org.apache.commons.jexl2

            {version=[2.1,3)}
            Show
            aloraine Ann Loraine added a comment - Confirmed items 2 and 3 above. Running: bnd print htsjdk-igb-2.16.2.jar shows that the only packages being imported are: [IMPEXP] Import-Package org.apache.commons.compress.compressors.bzip2 {version=[1.4,2)} org.apache.commons.compress.compressors.xz {version=[1.4,2)} org.apache.commons.compress.utils {version=[1.4,2)} org.apache.commons.jexl2 {version=[2.1,3)}
            Hide
            aloraine Ann Loraine added a comment - - edited

            Checking item 4 above:

            • Triggered re-run of master branch pipeline on team repository. The newly deployed htsjdk-igb artifact should be used to build.
              Build is successful.

            Based on above testing I am moving this to Closed.

            Show
            aloraine Ann Loraine added a comment - - edited Checking item 4 above: Triggered re-run of master branch pipeline on team repository. The newly deployed htsjdk-igb artifact should be used to build. Build is successful. Based on above testing I am moving this to Closed.
            Hide
            svallapu Sai Charan Reddy Vallapureddy added a comment -

            To test:

            1. Download biz.aQute.bnd-4.2.0.jar

            2. execute this command
            java -jar biz.aQute.bnd-4.2.0.jar print htsjdk-igb-2.16.2.jar

            3. Check Import-Packages, it should not contain htsjdk packages. It should only contain below-mentioned packages.

            Import-Package
            org.apache.commons.compress.compressors.bzip2

            {version=[1.4,2)}
            org.apache.commons.compress.compressors.xz {version=[1.4,2)}

            org.apache.commons.compress.utils

            {version=[1.4,2)}

            org.apache.commons.jexl2

            {version=[2.1,3)}
            Show
            svallapu Sai Charan Reddy Vallapureddy added a comment - To test: 1. Download biz.aQute.bnd-4.2.0.jar 2. execute this command java -jar biz.aQute.bnd-4.2.0.jar print htsjdk-igb-2.16.2.jar 3. Check Import-Packages, it should not contain htsjdk packages. It should only contain below-mentioned packages. Import-Package org.apache.commons.compress.compressors.bzip2 {version=[1.4,2)} org.apache.commons.compress.compressors.xz {version=[1.4,2)} org.apache.commons.compress.utils {version=[1.4,2)} org.apache.commons.jexl2 {version=[2.1,3)}
            aloraine Ann Loraine made changes -
            Resolution Done [ 10000 ]
            Status Needs Testing [ 10002 ] Closed [ 6 ]
            aloraine Ann Loraine made changes -
            Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
            aloraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 18572 ] Fall 2019 Workflow Update [ 20255 ]
            aloraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 20255 ] Revised Fall 2019 Workflow Update [ 22396 ]

              People

              • Assignee:
                svallapu Sai Charan Reddy Vallapureddy
                Reporter:
                svallapu Sai Charan Reddy Vallapureddy
              • Votes:
                0 Vote for this issue
                Watchers:
                2 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: