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  1. IGB
  2. IGBF-2869

Investigate adding UCSC JSON API as a new data provider

        Details

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

          Description

          Situation: The UCSC DAS data provider has access to a large number of genomes and datasets that are very useful for IGB users. However, the UCSC DAS endpoint can be slow and it is unclear how much longer UCSC will support it as they have created a new JSON API with the same functionality.

          Task: Investigate the feasibility of altering the IGB UCSC DAS logic to add a new JSON API endpoint.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2793 Restore DASv1 support

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2855 Investigate activating UCSC DAS source from External View tab

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2863 Use UCSC JSON endpoint to get list of genomes for External View tab

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese added a comment -

                Current UCSC DAS genomes: https://genome.ucsc.edu/cgi-bin/das/dsn
                Current UCSC API genomes: https://api.genome.ucsc.edu/list/ucscGenomes

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                nfreese Nowlan Freese added a comment - Current UCSC DAS genomes: https://genome.ucsc.edu/cgi-bin/das/dsn Current UCSC API genomes: https://api.genome.ucsc.edu/list/ucscGenomes
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                nfreese Nowlan Freese added a comment -

                Some documentation:

                DAS: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download23
                API: https://genome.ucsc.edu/goldenPath/help/api.html

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                nfreese Nowlan Freese added a comment - Some documentation: DAS: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download23 API: https://genome.ucsc.edu/goldenPath/help/api.html
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                nfreese Nowlan Freese added a comment -

                What would the same query to DAS look like for the API?

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                nfreese Nowlan Freese added a comment - What would the same query to DAS look like for the API?
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                ann.loraine Ann Loraine added a comment -

                Suggestion: Investigate adding a new data provider that consumes data from the JSON API (without changing the current DAS data provider infrastructure).

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                ann.loraine Ann Loraine added a comment - Suggestion: Investigate adding a new data provider that consumes data from the JSON API (without changing the current DAS data provider infrastructure).
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                ann.loraine Ann Loraine added a comment -

                Nowlan Freese: suggests this could be a good project for a student engineer (1 to 2 months, 15 hours/week, including training?)

                Show
                ann.loraine Ann Loraine added a comment - Nowlan Freese : suggests this could be a good project for a student engineer (1 to 2 months, 15 hours/week, including training?)

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: