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  1. IGB
  2. IGBF-3807

Create link outs for UCSC REST data sets / files

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: 10.1.0
    • Labels:
      None

      Description

      There is a way to link to UCSC track descriptions using this link pattern:

      Where "g" is a string identifying a track.

      You can also add a "db" parameter to specify the genome version of interest. With this new parameter, the URL pattern is:

      For example:

      opens a page at the UCSC genome browser with a page describing track "dbSnp155Composite" in the context of the hg18 genome version.

      This page is even an entry-point for the UCSC genome browser interface. The page has a "submit" button. When you click this "submit" button, a new page opens showing a genomic scene for the requested genome version, with the track shown, as well. It's hard to interpret this page if you are not already familiar with the browser, but it provides an entrée for a user to start comparing how the track data look in its native UCSC Genome Browser context with how it looks in IGB.

      It would be fantastic if we could provide link-outs going from the IGB UCSC REST data sets shown in IGB's Data Access panel.

      Doing this shouldn't be too difficult, and the goal of this task is to determine if it is feasible. If yes, we can include implementation in this ticket as well, as the developer sees fit.

      The code would construct the "link out" URLs using this pattern:

      or, even better:

      Let's call this "option 1" also known as (aka) "direct link into UCSC Web site."

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            jsirigin Jaya Sravani Sirigineedi added a comment -

            Fixed the exception issue and pushed the updated code to the above-mentioned branch. And for the test case log, I have mentioned a Slf4j error in the comment previously which is the cause for the log to not appear, currently, I am investigating this issue and another error as part of this ticket - https://jira.bioviz.org/browse/IGBF-3813

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - Fixed the exception issue and pushed the updated code to the above-mentioned branch. And for the test case log, I have mentioned a Slf4j error in the comment previously which is the cause for the log to not appear, currently, I am investigating this issue and another error as part of this ticket - https://jira.bioviz.org/browse/IGBF-3813
            Hide
            ann.loraine Ann Loraine added a comment -

            Just a quick FYI for Jaya Sravani Sirigineedi and Nowlan Freese:

            There's no rush from my side. Mentioning this because Nowlan Freese is at a meeting and might not be able to take a look as quickly as usual.

            Show
            ann.loraine Ann Loraine added a comment - Just a quick FYI for Jaya Sravani Sirigineedi and Nowlan Freese : There's no rush from my side. Mentioning this because Nowlan Freese is at a meeting and might not be able to take a look as quickly as usual.
            Hide
            jsirigin Jaya Sravani Sirigineedi added a comment -

            FYI, this feature can be tested along with this https://jira.bioviz.org/browse/IGBF-3813 ticket as that branch includes these changes.

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - FYI, this feature can be tested along with this https://jira.bioviz.org/browse/IGBF-3813 ticket as that branch includes these changes.
            Hide
            ann.loraine Ann Loraine added a comment -

            The PR containing the change is merged as part of another ticket. The new code is now available in the "early access" installers available from the BioViz.org Web site.
            Ready for testing.

            Show
            ann.loraine Ann Loraine added a comment - The PR containing the change is merged as part of another ticket. The new code is now available in the "early access" installers available from the BioViz.org Web site. Ready for testing.
            Hide
            nfreese Nowlan Freese added a comment -

            Tested main branch installer on Mac.

            Link outs worked correctly for several tested genomes (human, mouse, elephant). No errors in the log.

            Closing ticket.

            Show
            nfreese Nowlan Freese added a comment - Tested main branch installer on Mac. Link outs worked correctly for several tested genomes (human, mouse, elephant). No errors in the log. Closing ticket.

              People

              • Assignee:
                jsirigin Jaya Sravani Sirigineedi
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
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                Dates

                • Created:
                  Updated:
                  Resolved: