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  1. IGB
  2. IGBF-4382

Investigate UCSC External View not working

        Details

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

          Description

          Situation: The External View tab does not appear to be working for UCSC. Based on the following URL, it looks like UCSC is blocking programmatic access to the site:
          https://genome.ucsc.edu/cgi-bin/hgTracks?pix=800&db=hg19&position=chr1:6203693-6206373

          There is a FAQ on the UCSC website that says programmatic access can be restored with an API key:
          https://genome.ucsc.edu/FAQ/FAQdownloads.html#CAPTCHA

          Task: Email the UCSC team to determine if we can get an API key for IGB or if they can whitelist us. In the meantime, disable the external view tab.

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              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-4355 Investigate com.affymetrix.igb.external.LoaderTest failing

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

                Activity

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                pkulzer Paige Kulzer added a comment -

                Looks good! Closing ticket.

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                pkulzer Paige Kulzer added a comment - Looks good! Closing ticket.
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                nfreese Nowlan Freese added a comment -

                Good catch!

                Documentation should be updated for user's guide and release documentation.

                Show
                nfreese Nowlan Freese added a comment - Good catch! Documentation should be updated for user's guide and release documentation.
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                pkulzer Paige Kulzer added a comment -

                At Step 4 in the User's Guide documentation, I had to click a hyperlink that read, "Show as updateable table." in order to see an hguid field to copy. You'll need to add this step to the Release testing documentation, as well.

                After step 6, I had to click "update" again in order to get rid of the error in the External View tab.

                All else looks good! It's easy to follow and no obvious grammatical/spelling issues.

                Show
                pkulzer Paige Kulzer added a comment - At Step 4 in the User's Guide documentation, I had to click a hyperlink that read, "Show as updateable table." in order to see an hguid field to copy. You'll need to add this step to the Release testing documentation, as well. After step 6, I had to click "update" again in order to get rid of the error in the External View tab. All else looks good! It's easy to follow and no obvious grammatical/spelling issues.
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                nfreese Nowlan Freese added a comment - - edited

                Updated documentation:
                User's guide: https://wiki.bioviz.org/confluence/display/igbman/External+View
                Release testing: https://wiki.bioviz.org/confluence/display/ITD/External+View

                To test, follow the instructions provided in the documentation above. Make sure that it works and the instructions are clear.

                Once testing is complete and successful, this ticket can be closed.

                Show
                nfreese Nowlan Freese added a comment - - edited Updated documentation: User's guide: https://wiki.bioviz.org/confluence/display/igbman/External+View Release testing: https://wiki.bioviz.org/confluence/display/ITD/External+View To test, follow the instructions provided in the documentation above. Make sure that it works and the instructions are clear. Once testing is complete and successful, this ticket can be closed.
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                nfreese Nowlan Freese added a comment -

                In the External View tab there is a settings button. Clicking on it and following the directions there to add a UCSC user id does work to enable the External View to work. My recommendation would be that we leave the External View tab enabled and add some additional documentation to the IGB users guide saying that it is now a requirement to add a UCSC user id.

                Show
                nfreese Nowlan Freese added a comment - In the External View tab there is a settings button. Clicking on it and following the directions there to add a UCSC user id does work to enable the External View to work. My recommendation would be that we leave the External View tab enabled and add some additional documentation to the IGB users guide saying that it is now a requirement to add a UCSC user id.
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                nfreese Nowlan Freese added a comment -

                I have emailed the UCSC team.

                Show
                nfreese Nowlan Freese added a comment - I have emailed the UCSC team.

                  People

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

                    • Created:
                      Updated:
                      Resolved: