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  1. IGB
  2. IGBF-3416

Implement r6 Annotations: Plugins

        Details

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

          Description

          Implementing r6 annotations for the following plugins:
          Plugin - Toolbar Preferences GUI
          Plugin - Data caching GUI
          Plugin - Data caching API
          Plugin - Feedback
          Plugin - Track Operations API, GUI
          Plugin - Sorting API and Impl
          Plugin - Narrowpeak data format handler
          Plugin - File Handler - Genotyping Results
          Plugin - BED file format handler
          Plugin - BAM data format handler
          Plugin - BAI index visualization handler
          Plugin - App Store REST API
          Plugin - Search Id or Props
          Plugin - App Manager GUI
          Plugin - Paired-end Read Preprocessor
          Plugin - Keyword Search
          Plugin - Script handler
          Plugin - Graph thresholding visual analytics

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              kgopu Kaushik Gopu created issue -
              kgopu Kaushik Gopu made changes -
              Field Original Value New Value
              Description Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI
              Plugin - Paired-end Read Preprocessor
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI
              Plugin - Paired-end Read Preprocessor               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              -Plugin - App Manager GUI-
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              -Plugin - App Manager GUI-
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              -Plugin - Track Operations API, GUI-
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              -Plugin - App Manager GUI-
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              -Plugin - Track Operations API, GUI-
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              -Plugin - App Manager GUI-
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              -Plugin - Track Operations API, GUI-
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              -Plugin - App Manager GUI-
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler
              -Plugin - Graph thresholding visual analytics-
              Hide
              Permalink
              kgopu Kaushik Gopu added a comment - - edited

              Done (Includes Dr.Freese's work as well):
              Plugin - Graph thresholding visual analytics
              Plugin - Track Operations API, GUI
              Plugin - App Manager GUI
              Plugin - Save Image GUI
              Plugin - Save Session Manager
              Plugin - Advanced Search Tab
              Plugin - Selection Info tab
              Plugin - Graph Tab
              Plugin - Selection Info tab
              Plugin - BAM data format handler
              Plugin - Restriction Sites tab
              Plugin - Bigbed data format handler
              Plugin - Bigwig data format handler
              Plugin - Annotation Tab
              Plugin - App Store REST API
              Plugin - BAI index visualization handler
              Plugin - Console Tab
              Plugin - Sorting API and Impl
              Plugin - BED file format handler
              Plugin - Feedback
              Plugin - Bookmarks and REST API
              Plugin - Data caching GUI
              Plugin - Toolbar Preferences GUI
              Plugin - Keyword Search
              Plugin - Data caching API
              Plugin - External View
              Plugin - Sequence Viewer GUI
              Plugin - File Handler - Genotyping Results
              Plugin - Script handler
              Plugin - Paired-end Read Preprocessor
              Plugin - Search Id or Props

              Show
              kgopu Kaushik Gopu added a comment - - edited Done (Includes Dr.Freese's work as well): Plugin - Graph thresholding visual analytics Plugin - Track Operations API, GUI Plugin - App Manager GUI Plugin - Save Image GUI Plugin - Save Session Manager Plugin - Advanced Search Tab Plugin - Selection Info tab Plugin - Graph Tab Plugin - Selection Info tab Plugin - BAM data format handler Plugin - Restriction Sites tab Plugin - Bigbed data format handler Plugin - Bigwig data format handler Plugin - Annotation Tab Plugin - App Store REST API Plugin - BAI index visualization handler Plugin - Console Tab Plugin - Sorting API and Impl Plugin - BED file format handler Plugin - Feedback Plugin - Bookmarks and REST API Plugin - Data caching GUI Plugin - Toolbar Preferences GUI Plugin - Keyword Search Plugin - Data caching API Plugin - External View Plugin - Sequence Viewer GUI Plugin - File Handler - Genotyping Results Plugin - Script handler Plugin - Paired-end Read Preprocessor Plugin - Search Id or Props
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              -Plugin - Track Operations API, GUI-
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              -Plugin - App Manager GUI-
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler
              -Plugin - Graph thresholding visual analytics-               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Track Operations API, GUI
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              -Plugin - App Manager GUI-
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler
              Plugin - Graph thresholding visual analytics
              kgopu Kaushik Gopu made changes -
              Description Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Track Operations API, GUI
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              -Plugin - App Manager GUI-
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler
              Plugin - Graph thresholding visual analytics               		Implementing r6 annotations for the following plugins:
              Plugin - Toolbar Preferences GUI
              Plugin - Data caching GUI
              Plugin - Data caching API
              Plugin - Feedback
              Plugin - Track Operations API, GUI
              Plugin - Sorting API and Impl
              Plugin - Narrowpeak data format handler
              Plugin - File Handler - Genotyping Results
              Plugin - BED file format handler
              Plugin - BAM data format handler
              Plugin - BAI index visualization handler
              Plugin - App Store REST API
              Plugin - Search Id or Props
              Plugin - App Manager GUI
              Plugin - Paired-end Read Preprocessor
              Plugin - Keyword Search
              Plugin - Script handler
              Plugin - Graph thresholding visual analytics
              nfreese Nowlan Freese made changes -
              Parent IGBF-3411 [ 22434 ]
              Issue Type Sub-task [ 5 ] Task [ 3 ]
              nfreese Nowlan Freese made changes -
              Epic Link IGBF-3411 [ 22434 ]
              nfreese Nowlan Freese made changes -
              Story Points 2
              Sprint Summer 8 2023 Aug 21 [ 177 ]
              Hide
              Permalink
              nfreese Nowlan Freese added a comment -

              Moving to first level review.
              pull this branch in order to test.

              Show
              nfreese Nowlan Freese added a comment - Moving to first level review. pull this branch in order to test.
              nfreese Nowlan Freese made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              nfreese Nowlan Freese made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              nfreese Nowlan Freese made changes -
              Assignee Kaushik Gopu [ kgopu ] Nowlan Freese [ nfreese ]
              nfreese Nowlan Freese made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              Hide
              Permalink
              nfreese Nowlan Freese added a comment -

              Tested on Mac.

              Everything is working as expected.

              Regarding the commits, please revert 0945a70 (This is a combination of 2 commits) and recommit the changes for the two plugins separately. Then create a pull request to main-JDK8-r6.

              Show
              nfreese Nowlan Freese added a comment - Tested on Mac. Everything is working as expected. Regarding the commits, please revert 0945a70 (This is a combination of 2 commits) and recommit the changes for the two plugins separately. Then create a pull request to main-JDK8-r6.
              nfreese Nowlan Freese made changes -
              Assignee Nowlan Freese [ nfreese ] Kaushik Gopu [ kgopu ]
              nfreese Nowlan Freese made changes -
              Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
              nfreese Nowlan Freese made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              nfreese Nowlan Freese made changes -
              Status In Progress [ 3 ] To-Do [ 10305 ]
              nfreese Nowlan Freese made changes -
              Status To-Do [ 10305 ] Pull Request Submitted [ 10101 ]
              nfreese Nowlan Freese made changes -
              Assignee Kaushik Gopu [ kgopu ]
              nfreese Nowlan Freese made changes -
              Assignee Kaushik Gopu [ kgopu ]
              nfreese Nowlan Freese made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              nfreese Nowlan Freese made changes -
              Status Reviewing Pull Request [ 10303 ] To-Do [ 10305 ]
              nfreese Nowlan Freese made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              nfreese Nowlan Freese made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              nfreese Nowlan Freese made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              nfreese Nowlan Freese made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              Hide
              Permalink
              nfreese Nowlan Freese added a comment -

              Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/941

              Show
              nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/941
              nfreese Nowlan Freese made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              nfreese Nowlan Freese made changes -
              Assignee Kaushik Gopu [ kgopu ] 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 ]
              Hide
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              ann.loraine Ann Loraine added a comment -

              Installers are built and ready for testing. See: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/

              Show
              ann.loraine Ann Loraine added a comment - Installers are built and ready for testing. See: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              Hide
              Permalink
              nfreese Nowlan Freese added a comment -

              Tested Mac Installer.

              IGB started with no errors in log. Behavior was normal, able to load all plugins (did not try MI bundle which has its own ticket).

              Closing ticket.

              Show
              nfreese Nowlan Freese added a comment - Tested Mac Installer. IGB started with no errors in log. Behavior was normal, able to load all plugins (did not try MI bundle which has its own ticket). Closing ticket.
              nfreese Nowlan Freese made changes -
              Assignee Kaushik Gopu [ kgopu ]
              nfreese Nowlan Freese made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              nfreese Nowlan Freese made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                People

                • Assignee:
                  kgopu Kaushik Gopu
                  Reporter:
                  kgopu Kaushik Gopu
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  3 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: