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  1. IGB
  2. IGBF-2238

Update biojava 2bit reader example App

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1.5
        • Epic Link:
        • Sprint:
          Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10

          Description

          Update:

          https://bitbucket.org/lorainelab/2bit-reader/

          To update the App:

          • Add code to the POM to trigger building of an OBR index file "repository.xml"
          • Ensure that repository.xml will get included with the jar file so that we can release the App on App Store
          • Add a bitbucket pipelines YML file to trigger building and copying of the jar file and repository.xml file to Downloads
          • Create an "md" file for display in the App Store and in IGB App Manager (not the current README.md file, which is for bitbucket users and developers)
          • Create an image we can use as a logo (something with base letters or?)
          • Contact Deepti Joshi (the author) to get her preferred contact information

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2264 Improve BioJava App POM.xml to only include necessary jars/classes

              • Major - Major loss of function.
              • Closed

                Activity

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                5 older comments
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                ann.loraine Ann Loraine added a comment -

                Try unpacking the jar - looks like some things are being packaged with the jar that may should not be, including:

                • guava-19.0.jar
                • log4j-api-2.5.jar
                • log4j-core-2.5.jar
                • log4j-slf4j-impl-2.5.jar

                $ jar xvf biojava-igb-app-0.0.1.jar
                inflated: META-INF/MANIFEST.MF
                created: META-INF/
                created: META-INF/maven/
                created: META-INF/maven/igb-app-examples/
                created: META-INF/maven/igb-app-examples/biojava-igb-app/
                inflated: META-INF/maven/igb-app-examples/biojava-igb-app/pom.properties
                inflated: META-INF/maven/igb-app-examples/biojava-igb-app/pom.xml
                created: OSGI-INF/
                inflated: OSGI-INF/org.lorainelab.igb.sequencereader.TwoBitReaderApp.xml
                inflated: biojava-alignment-4.2.8.jar
                inflated: biojava-core-4.2.8.jar
                inflated: biojava-genome-4.2.8.jar
                inflated: biojava-phylo-4.2.8.jar
                inflated: forester-1.038.jar
                inflated: guava-19.0.jar
                inflated: log4j-api-2.5.jar
                inflated: log4j-core-2.5.jar
                inflated: log4j-slf4j-impl-2.5.jar
                inflated: logo.png
                created: org/
                created: org/biojava/
                created: org/biojava/nbio/
                created: org/biojava/nbio/genome/
                created: org/biojava/nbio/genome/parsers/
                created: org/biojava/nbio/genome/parsers/twobit/
                inflated: org/biojava/nbio/genome/parsers/twobit/TwoBitParser.class
                created: org/lorainelab/
                created: org/lorainelab/igb/
                created: org/lorainelab/igb/sequencereader/
                inflated: org/lorainelab/igb/sequencereader/TwoBitFileSummarizer.class
                inflated: org/lorainelab/igb/sequencereader/TwoBitReaderApp.class
                inflated: repository.xml
                inflated: slf4j-api-1.7.14.jar
                inflated: summarize.png

                There's a lot going on here – we might want to make an all-new ticket called "Re-factor biojava 2bit parser POM" to omit some of these things that are probably not needed.

                I have a PDF that talks about how to transform 3rd party jars into OSGi bundles – I will add a link to it here. (I have to find it.)

                Show
                ann.loraine Ann Loraine added a comment - Try unpacking the jar - looks like some things are being packaged with the jar that may should not be, including: guava-19.0.jar log4j-api-2.5.jar log4j-core-2.5.jar log4j-slf4j-impl-2.5.jar $ jar xvf biojava-igb-app-0.0.1.jar inflated: META-INF/MANIFEST.MF created: META-INF/ created: META-INF/maven/ created: META-INF/maven/igb-app-examples/ created: META-INF/maven/igb-app-examples/biojava-igb-app/ inflated: META-INF/maven/igb-app-examples/biojava-igb-app/pom.properties inflated: META-INF/maven/igb-app-examples/biojava-igb-app/pom.xml created: OSGI-INF/ inflated: OSGI-INF/org.lorainelab.igb.sequencereader.TwoBitReaderApp.xml inflated: biojava-alignment-4.2.8.jar inflated: biojava-core-4.2.8.jar inflated: biojava-genome-4.2.8.jar inflated: biojava-phylo-4.2.8.jar inflated: forester-1.038.jar inflated: guava-19.0.jar inflated: log4j-api-2.5.jar inflated: log4j-core-2.5.jar inflated: log4j-slf4j-impl-2.5.jar inflated: logo.png created: org/ created: org/biojava/ created: org/biojava/nbio/ created: org/biojava/nbio/genome/ created: org/biojava/nbio/genome/parsers/ created: org/biojava/nbio/genome/parsers/twobit/ inflated: org/biojava/nbio/genome/parsers/twobit/TwoBitParser.class created: org/lorainelab/ created: org/lorainelab/igb/ created: org/lorainelab/igb/sequencereader/ inflated: org/lorainelab/igb/sequencereader/TwoBitFileSummarizer.class inflated: org/lorainelab/igb/sequencereader/TwoBitReaderApp.class inflated: repository.xml inflated: slf4j-api-1.7.14.jar inflated: summarize.png There's a lot going on here – we might want to make an all-new ticket called "Re-factor biojava 2bit parser POM" to omit some of these things that are probably not needed. I have a PDF that talks about how to transform 3rd party jars into OSGi bundles – I will add a link to it here. (I have to find it.)
                Hide
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                ann.loraine Ann Loraine added a comment -

                Moving previous two comments to a new ticket and recommending PR.

                Show
                ann.loraine Ann Loraine added a comment - Moving previous two comments to a new ticket and recommending PR.
                Hide
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                shamika Shamika Gajanan Kulkarni (Inactive) added a comment -

                Yes I found that many jars are being packaged in the target jar. I like the idea of making a separate ticket for it. I haven't submitted a pull request yet for this one.

                Show
                shamika Shamika Gajanan Kulkarni (Inactive) added a comment - Yes I found that many jars are being packaged in the target jar. I like the idea of making a separate ticket for it. I haven't submitted a pull request yet for this one.
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                ann.loraine Ann Loraine added a comment -

                Shamika Gajanan Kulkarni

                Please resolve conflict with your branch and submit PR:
                https://bitbucket.org/skulka2710/shamika-2bit-reader/branch/IGBF-2238#diff

                Show
                ann.loraine Ann Loraine added a comment - Shamika Gajanan Kulkarni Please resolve conflict with your branch and submit PR: https://bitbucket.org/skulka2710/shamika-2bit-reader/branch/IGBF-2238#diff
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                shamika Shamika Gajanan Kulkarni (Inactive) added a comment -

                Resolved the conflicts and submitted a PR.
                https://bitbucket.org/lorainelab/2bit-reader/pull-requests/2/igbf-2238-update-pomxml/diff

                Show
                shamika Shamika Gajanan Kulkarni (Inactive) added a comment - Resolved the conflicts and submitted a PR. https://bitbucket.org/lorainelab/2bit-reader/pull-requests/2/igbf-2238-update-pomxml/diff

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: