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  1. IGB
  2. IGBF-2863

Use UCSC JSON endpoint to get list of genomes for External View tab

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      Description

      As revealed in IGBF-2855 by Omkar Marne's investigations, the External View functionality for the UCSC Genome Browser fails when the UCSC Distributed Annotation Data source is not active.

      This is because the code is using the internal data source object to retrieve a listing of UCSC genome names.

      However, there is a much better way to get these information. Instead, the External View code can query the UCSC JSON API to get this same information, in JSON format.

      This ticket provides a record of how we are doing this.

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          aloraine Ann Loraine added a comment - - edited

          See: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2863?dest=master

          This new branch uses the UCSC JSON list genomes endpoint to get a list of all supported genome names from UCSC.
          It also includes test cases that fail if the endpoint stops working as expected.

          This fixes "Situation Three" mentioned in IGBF-2855 in which External View tab fails when the UCSC DAS data source has been de-activated within IGB.

          Show
          aloraine Ann Loraine added a comment - - edited See: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2863?dest=master This new branch uses the UCSC JSON list genomes endpoint to get a list of all supported genome names from UCSC. It also includes test cases that fail if the endpoint stops working as expected. This fixes "Situation Three" mentioned in IGBF-2855 in which External View tab fails when the UCSC DAS data source has been de-activated within IGB.
          Hide
          omarne Omkar Marne added a comment - - edited

          Tested the External View tab functionality. Went through the commits for IGBF-2855. The genome data is getting pulled from JSON end point instead of UCSC DAS data source. The External view tab functionality is working even if the UCSC DAS data source is disabled.

          Show
          omarne Omkar Marne added a comment - - edited Tested the External View tab functionality. Went through the commits for IGBF-2855 . The genome data is getting pulled from JSON end point instead of UCSC DAS data source. The External view tab functionality is working even if the UCSC DAS data source is disabled.
          Hide
          aloraine Ann Loraine added a comment -

          Merged. Built master branch installers. Ready for testing.

          Show
          aloraine Ann Loraine added a comment - Merged. Built master branch installers. Ready for testing.
          Hide
          nfreese Nowlan Freese added a comment -

          Tested on Mac with master installer.

          Able to load UCSC External View image when the UCSC DAS data source is disabled.

          Working correctly.

          Show
          nfreese Nowlan Freese added a comment - Tested on Mac with master installer. Able to load UCSC External View image when the UCSC DAS data source is disabled. Working correctly.
          Hide
          omarne Omkar Marne added a comment -

          Tested on Windows and Linux with master installer.

          Able to load UCSC External View image when the UCSC DAS data source is disabled.

          Working correctly.

          Closing the issue.

          Show
          omarne Omkar Marne added a comment - Tested on Windows and Linux with master installer. Able to load UCSC External View image when the UCSC DAS data source is disabled. Working correctly. Closing the issue.

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            • Assignee:
              aloraine Ann Loraine
              Reporter:
              aloraine Ann Loraine
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                Updated:
                Resolved:

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