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  1. IGB
  2. IGBF-2929

Fix hub URL validation

        Details

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

          Description

          Validating trackhub URLs is currently done in the browser and involves making requests for their content and ensuring that it conforms to the UCSC trackhub specification. The UCSC CORS policy does not allow websites to make these requests, however. Implement a work-around.

          Possibilities:

          • See if the UCSC API can be used to validate a trackhub.
          • Implement a validation endpoint on our hub facade API.
          • Use a public CORS proxy to forward browser requests.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2898 Add listing of UCSC hubs to the bioviz trackhubs page

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                pbadzuh Philip Badzuh (Inactive) created issue -
                pbadzuh Philip Badzuh (Inactive) made changes -
                Field Original Value New Value
                Epic Link IGBF-2831 [ 19524 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Link This issue relates to IGBF-2898 [ IGBF-2898 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 1 2021 Aug 16 - Aug 27 [ 127 ] Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Aug 10 [ 127, 128 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                pbadzuh Philip Badzuh (Inactive) added a comment -

                I was able to find a UCSC API endpoint that can be used to validate track hubs. Please see my changes here.

                I tested this with both track hubs in UCSC public list as well as others that I found online e.g.

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - I was able to find a UCSC API endpoint that can be used to validate track hubs. Please see my changes here . I tested this with both track hubs in UCSC public list as well as others that I found online e.g. https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://trackhub.genome.duke.edu/gordanlab/tf-dna-binding-predictions/hub.txt https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://nibiru.tbi.univie.ac.at/ViennaNGS/tutorial03/hg19_trackHub/trackHub/hub.txt https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://krishna.gs.washington.edu/content/members/ajh24/mouse_atlas_data_release/bigwigs/trackhub/hub.txt
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                Hide
                Permalink
                pbadzuh Philip Badzuh (Inactive) added a comment -

                Changes are now deployed and accessible at https://bioviztest.bioviz.org/trackhubs.html

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - Changes are now deployed and accessible at https://bioviztest.bioviz.org/trackhubs.html
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Changes look good. Comment is updated to reflect improved functionality. Please submit PR when ready.

                Show
                ann.loraine Ann Loraine added a comment - Changes look good. Comment is updated to reflect improved functionality. Please submit PR when ready.
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Philip Badzuh [ pbadzuh ]
                Hide
                Permalink
                pbadzuh Philip Badzuh (Inactive) added a comment -

                Please see PR here.

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - Please see PR here .
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Merged.

                Show
                ann.loraine Ann Loraine added a comment - Merged.
                Hide
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                ann.loraine Ann Loraine added a comment -

                Deployed to bioviztest.bioviz.org for testing.

                Show
                ann.loraine Ann Loraine added a comment - Deployed to bioviztest.bioviz.org for testing.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Confirmed that the example URL and others are functioning as expected. Moving to Closed.

                Show
                ann.loraine Ann Loraine added a comment - Confirmed that the example URL and others are functioning as expected. Moving to Closed.
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                I spoke too soon. The track hub site referenced is on localhost. Looking into it.

                Show
                ann.loraine Ann Loraine added a comment - I spoke too soon. The track hub site referenced is on localhost. Looking into it.
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                Hard reload in my browser fixed the problem. Playbooks working as designed. For future reference: a line in trackhubs.js containing:

                const BACKEND_DOMAIN

                gets changed.

                Show
                ann.loraine Ann Loraine added a comment - - edited Hard reload in my browser fixed the problem. Playbooks working as designed. For future reference: a line in trackhubs.js containing: const BACKEND_DOMAIN gets changed.
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Philip Badzuh [ pbadzuh ]

                  People

                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    pbadzuh Philip Badzuh (Inactive)
                  • Votes:
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: