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  1. IGB
  2. IGBF-2858

Write R or python notebook to compare data retrieved from UCSC DAS and JSON APIs

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          We are updating and improving the External View module in IGB to use the new JSON API instead of the older DAS (xml-based) API.

          The two endpoints are:

          Answer these questions:

          • Which field does the "id" attribute from DAS XML correspond to within the JSON output? (on first glance, looks like JSON keys equate to "id" in the XML)
          • Are all the genomes available via DAS XML also available via the JSON API?

            Attachments

              Issue Links

              relates to

              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

                Activity

                Descending order - Click to sort in ascending order
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 120, 121 ] Spring 4 2021 May 3 - May 14 [ 120 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 4 2021 May 3 - May 14 [ 120 ] Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 120, 121 ]
                ann.loraine Ann Loraine made changes -
                Description We are updating and improving the External View module in IGB to use the new JSON API instead of the older DAS (xml-based) API.

                The two endpoints are:

                * DAS - https://genome.ucsc.edu/cgi-bin/das/dsn
                * JSON - https://api.genome.ucsc.edu/list/ucscGenomes

                Answer these questions:

                * Which field does the "id" attribute from DAS XML correspond to within the JSON output? (on first glance, it looks like "nibPath" is the closest to what we need)
                * Are all the genomes available via DAS XML also available via the JSON API?

                		We are updating and improving the External View module in IGB to use the new JSON API instead of the older DAS (xml-based) API.

                The two endpoints are:

                * DAS - https://genome.ucsc.edu/cgi-bin/das/dsn
                * JSON - https://api.genome.ucsc.edu/list/ucscGenomes

                Answer these questions:

                * Which field does the "id" attribute from DAS XML correspond to within the JSON output? (on first glance, looks like JSON keys equate to "id" in the XML)
                * Are all the genomes available via DAS XML also available via the JSON API?

                ann.loraine Ann Loraine made changes -
                Description We are updating and improving the External View module in IGB to use the new JSON API instead of the older DAS (xml-based) API.

                The two endpoints are:

                * DAS -
                * JSON -

                Answer these questions:

                * Which field does the "id" attribute from DAS XML correspond to within the JSON output? (on first glance, it looks like
                * Are all genomes available via DAS XML also available via the JSON API

                On first glance, it looks like the                 		We are updating and improving the External View module in IGB to use the new JSON API instead of the older DAS (xml-based) API.

                The two endpoints are:

                * DAS - https://genome.ucsc.edu/cgi-bin/das/dsn
                * JSON - https://api.genome.ucsc.edu/list/ucscGenomes

                Answer these questions:

                * Which field does the "id" attribute from DAS XML correspond to within the JSON output? (on first glance, it looks like "nibPath" is the closest to what we need)
                * Are all the genomes available via DAS XML also available via the JSON API?

                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2855 [ IGBF-2855 ]
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine created issue -

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated: