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  1. IGB
  2. IGBF-2228

Build javadocs for Genoviz SDK and copy compiled javadocs to Downloads

        Details

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

          Description

          GenoViz SDK is a library of visualization components for building genome-browser applications.

          Currently we do not distribute compiled javadocs for the library. We should start doing this.

          For this task:

          • add code to the GenoViz POM to build the javadocs.
          • add code to the bitbucket pipelines yml file to copy the javadocs to the Downloads section of the repository

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2243 Deploy Genoviz SDK Javadocs on Bioviz

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-1862 Fix or update Genoviz SDK tutorial

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1531 [ 17617 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1862 [ IGBF-1862 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Story Points 0.25 1
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
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                ann.loraine Ann Loraine added a comment -

                Was this moved to Needs Review by mistake?
                (There are no comments or notes explaining what was done.)

                Show
                ann.loraine Ann Loraine added a comment - Was this moved to Needs Review by mistake? (There are no comments or notes explaining what was done.)
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Changes Summary:
                1. Corrected parent pom parameter as it was no longer compiling.
                2. Fixed problems in Javadocs like missing tags, syntax error, malformed HTML etc.
                3. Added command to build javadoc in default pipeline - ( mvn clean install javadoc:jar -D skipTests=false) and commands to copy javadoc jars to downloads directory

                Files changed:
                bitbucket-pipelines.yml
                genoviz_sdk/src/main/java/com/affymetrix/genoviz/bioviews/MapGlyphFactory.java
                genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/AbstractResiduesGlyph.java
                genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/AlignmentGlyph.java
                genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/AxisGlyph.java
                genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/ColorSepGlyph.java
                genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/FlyPointLinkerGlyph.java
                genoviz_sdk/src/main/java/com/affymetrix/genoviz/parser/ContentParser.java
                genoviz_sdk/src/main/java/com/affymetrix/genoviz/widget/NeoAssembler.java
                pom.xml

                Please find the commit below for review:
                https://bitbucket.org/srishtitiwari/genoviz-sdk/commits/eb85e3467de50e2112cbd01323a60ab7f7da4e51

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Changes Summary: 1. Corrected parent pom parameter as it was no longer compiling. 2. Fixed problems in Javadocs like missing tags, syntax error, malformed HTML etc. 3. Added command to build javadoc in default pipeline - ( mvn clean install javadoc:jar -D skipTests=false) and commands to copy javadoc jars to downloads directory Files changed: bitbucket-pipelines.yml genoviz_sdk/src/main/java/com/affymetrix/genoviz/bioviews/MapGlyphFactory.java genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/AbstractResiduesGlyph.java genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/AlignmentGlyph.java genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/AxisGlyph.java genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/ColorSepGlyph.java genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/FlyPointLinkerGlyph.java genoviz_sdk/src/main/java/com/affymetrix/genoviz/parser/ContentParser.java genoviz_sdk/src/main/java/com/affymetrix/genoviz/widget/NeoAssembler.java pom.xml Please find the commit below for review: https://bitbucket.org/srishtitiwari/genoviz-sdk/commits/eb85e3467de50e2112cbd01323a60ab7f7da4e51
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                Change request:

                • Add javadoc plugin to the POM.xml so that it will build the javadoc jar file as part of the default lifecycle
                • Check that when you run "mvn install" the javadocs get created and added to your local .m2 (for extra awesomeness, check that you can now navigate to the javadocs for GenoViz methods and classes.)
                • Change the mvn commands in the bitbucket pipelines yml file to "mvn install" (I'm pretty sure we don't need "clean")

                If we ever start developing GenoViz SDK, then we will move the javadoc plugin jar task into a separate profile (out of the default profile) to allow for building code without building the javadoc jar. But for now, we should compile the library and the javadoc jar files during the default lifecycle. Also, if we do this, then I can run the "deploy to nexus" custom pipeline and the javadocs will get released along with the compiled code and source code.

                Show
                ann.loraine Ann Loraine added a comment - Change request: Add javadoc plugin to the POM.xml so that it will build the javadoc jar file as part of the default lifecycle Check that when you run "mvn install" the javadocs get created and added to your local .m2 (for extra awesomeness, check that you can now navigate to the javadocs for GenoViz methods and classes.) Change the mvn commands in the bitbucket pipelines yml file to "mvn install" (I'm pretty sure we don't need "clean") If we ever start developing GenoViz SDK, then we will move the javadoc plugin jar task into a separate profile (out of the default profile) to allow for building code without building the javadoc jar. But for now, we should compile the library and the javadoc jar files during the default lifecycle. Also, if we do this, then I can run the "deploy to nexus" custom pipeline and the javadocs will get released along with the compiled code and source code.
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Srishti Tiwari [ stiwari8 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Hide
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                ann.loraine Ann Loraine added a comment -

                Link showing how to configure javadoc plugin in a POM.xml:

                https://mkyong.com/maven/generate-javadoc-jar-for-maven-based-project/

                Show
                ann.loraine Ann Loraine added a comment - Link showing how to configure javadoc plugin in a POM.xml: https://mkyong.com/maven/generate-javadoc-jar-for-maven-based-project/
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Hi Professor, I have made changes accordingly. Please have a look.

                https://bitbucket.org/srishtitiwari/genoviz-sdk/branch/IGBF-2228#diff

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Hi Professor, I have made changes accordingly. Please have a look. https://bitbucket.org/srishtitiwari/genoviz-sdk/branch/IGBF-2228#diff
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
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                ann.loraine Ann Loraine added a comment -

                Please check: Is the maven javadoc plugin already included in the super POM? If yes, you do not need to declare it in the Plugins section.

                Show
                ann.loraine Ann Loraine added a comment - Please check: Is the maven javadoc plugin already included in the super POM? If yes, you do not need to declare it in the Plugins section.
                ann.loraine Ann Loraine made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
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                ann.loraine Ann Loraine added a comment -

                Please submit PR.

                Show
                ann.loraine Ann Loraine added a comment - Please submit PR.
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Pull Request Submitted:

                https://bitbucket.org/lorainelab/genoviz-sdk/pull-requests/18/igbf-2228/diff

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Pull Request Submitted: https://bitbucket.org/lorainelab/genoviz-sdk/pull-requests/18/igbf-2228/diff
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                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 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2243 [ IGBF-2243 ]
                pbole Pawan Bole (Inactive) made changes -
                Assignee Pawan Bole [ pbole ]
                pbole Pawan Bole (Inactive) made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 : 20 Jan to 31 Jan [ 85 ] Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb [ 85, 86 ]
                Hide
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                pbole Pawan Bole (Inactive) added a comment -

                I am able to open the javadocs..

                Show
                pbole Pawan Bole (Inactive) added a comment - I am able to open the javadocs..
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pbole Pawan Bole (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                pbole Pawan Bole (Inactive) made changes -
                Assignee Pawan Bole [ pbole ] Srishti Tiwari [ stiwari8 ]

                  People

                  • Assignee:
                    stiwari8 Srishti Tiwari (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: