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  1. IGB
  2. IGBF-1767

Fix bundle resolution error involving htsjdk-igb

    Details

    • Story Points:
      2
    • Sprint:
      Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10, Summer 2019 Sprint 11

      Description

      For details see:

      Investigate bundle resolution error involving htsjdk-igb
      https://jira.transvar.org/browse/IGBF-1627

      This requires understanding OSGi and how bundle dependencies get resolved during bundle installation and activation.

      Also, review how we made htsjdk-igb bundle in the first place by looking at linked Jira issues.

      Probably we have to make some changes to how we generate that bundle?

      Potentially useful resources:

      Please add more as you work on this.

      When done, please write up a short, plain English description of what you did to fix the problem. (This can be a useful case study to introduce devs to OSGi in IGB.)
      *

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            ann.loraine Ann Loraine added a comment -

            Our build.gradle file is using plugin osgi.

            According to:
            https://github.com/bndtools/bnd/blob/master/biz.aQute.bnd.gradle/README.md#gradle-plugin-for-workspace-builds

            we should biz.aQute.bnd.builder plugin instead.

            The above link contains example syntax for adding stuff to the MANIFEST.

            For example:

            jar {
            manifest

            { attributes('Export-Package': 'com.acme.api.*', '-sources': 'true', '-include': 'other.bnd') }

            }

            Show
            ann.loraine Ann Loraine added a comment - Our build.gradle file is using plugin osgi. According to: https://github.com/bndtools/bnd/blob/master/biz.aQute.bnd.gradle/README.md#gradle-plugin-for-workspace-builds we should biz.aQute.bnd.builder plugin instead. The above link contains example syntax for adding stuff to the MANIFEST. For example: jar { manifest { attributes('Export-Package': 'com.acme.api.*', '-sources': 'true', '-include': 'other.bnd') } }
            Hide
            svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - - edited

            [~aloraine]
            According to my understanding jexl2 is used by htsjdk-igb (htsjdk.variant.variantcontext). Does it mean we cannot keep jexl2 as optional or am I wrong?

            htsjdk.variant.variantcontext is extensively using jexl.
            jexl is used in below java files.
            1. src\main\java\htsjadk\variant\varaintcontext\JEXLMap.java
            2. src\main\java\htsjadk\variant\varaintcontext\JexlMissingValueTreatment.java
            3. src\main\java\htsjadk\variant\varaintcontext\VariantContextUtils.java
            4. src\main\java\htsjadk\variant\varaintcontext\VaraintJEXLContext.java
            5. src\main\java\htsjadk\variant\varaintcontext\VaraintJEXLContextUnitTest.java
            6. src\main\java\htsjadk\variant\varaintcontext\GenotypeJEXLContext.java

            Now the issue is htsjdk is exporting (2.16.2) and importing(2.16.3) the same library. I will look into it.

            Show
            svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - - edited [~aloraine] According to my understanding jexl2 is used by htsjdk-igb (htsjdk.variant.variantcontext). Does it mean we cannot keep jexl2 as optional or am I wrong? htsjdk.variant.variantcontext is extensively using jexl. jexl is used in below java files. 1. src\main\java\htsjadk\variant\varaintcontext\JEXLMap.java 2. src\main\java\htsjadk\variant\varaintcontext\JexlMissingValueTreatment.java 3. src\main\java\htsjadk\variant\varaintcontext\VariantContextUtils.java 4. src\main\java\htsjadk\variant\varaintcontext\VaraintJEXLContext.java 5. src\main\java\htsjadk\variant\varaintcontext\VaraintJEXLContextUnitTest.java 6. src\main\java\htsjadk\variant\varaintcontext\GenotypeJEXLContext.java Now the issue is htsjdk is exporting (2.16.2) and importing(2.16.3) the same library. I will look into it.
            Show
            svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - Branch: https://bitbucket.org/svallapu/charan_igb/branch/IGBF-1767#diff
            Hide
            svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment -

            Pull request submitted.

            Show
            svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - Pull request submitted.
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment -

            Works as expected.

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - Works as expected.

              People

              • Assignee:
                svallapu Sai Charan Reddy Vallapureddy (Inactive)
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
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                Watchers:
                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: