Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2863

Use UCSC JSON endpoint to get list of genomes for External View tab

        Details

          Description

          As revealed in IGBF-2855 by Omkar Marne's investigations, the External View functionality for the UCSC Genome Browser fails when the UCSC Distributed Annotation Data source is not active.

          This is because the code is using the internal data source object to retrieve a listing of UCSC genome names.

          However, there is a much better way to get these information. Instead, the External View code can query the UCSC JSON API to get this same information, in JSON format.

          This ticket provides a record of how we are doing this.

            Attachments

              Issue Links

              is blocked by

              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
              relates to

              Task - A task that needs to be done. IGBF-2867 Disable UCSC DAS in igbdefaultprefs.json

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2869 Investigate adding UCSC JSON API as a new data provider

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3655 Replace DAS requirements in IGB and disable DAS by default

              • Major - Major loss of function.
              • To-Do

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-2864 Improve External View error message displayed when no genome is selected

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-2855 [ IGBF-2855 ]
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.8 Major Release [ 10605 ]
                Sprint Spring 5 2021 May 17 - May 28 [ 121 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                See: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2863?dest=master

                This new branch uses the UCSC JSON list genomes endpoint to get a list of all supported genome names from UCSC.
                It also includes test cases that fail if the endpoint stops working as expected.

                This fixes "Situation Three" mentioned in IGBF-2855 in which External View tab fails when the UCSC DAS data source has been de-activated within IGB.

                Show
                ann.loraine Ann Loraine added a comment - - edited See: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2863?dest=master This new branch uses the UCSC JSON list genomes endpoint to get a list of all supported genome names from UCSC. It also includes test cases that fail if the endpoint stops working as expected. This fixes "Situation Three" mentioned in IGBF-2855 in which External View tab fails when the UCSC DAS data source has been de-activated within IGB.
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2864 [ IGBF-2864 ]
                ann.loraine Ann Loraine made changes -
                Assignee Omkar Marne [ omarne ]
                Hide
                Permalink
                omarne Omkar Marne (Inactive) added a comment - - edited

                Tested the External View tab functionality. Went through the commits for IGBF-2855. The genome data is getting pulled from JSON end point instead of UCSC DAS data source. The External view tab functionality is working even if the UCSC DAS data source is disabled.

                Show
                omarne Omkar Marne (Inactive) added a comment - - edited Tested the External View tab functionality. Went through the commits for IGBF-2855 . The genome data is getting pulled from JSON end point instead of UCSC DAS data source. The External view tab functionality is working even if the UCSC DAS data source is disabled.
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Assignee Omkar Marne [ omarne ] Ann Loraine [ aloraine ]
                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 -
                Assignee Ann Loraine [ aloraine ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Merged. Built master branch installers. Ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - Merged. Built master branch installers. Ready for testing.
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Post-merge Testing In Progress [ 10003 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                omarne Omkar Marne (Inactive) made changes -
                Assignee Omkar Marne [ omarne ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Tested on Mac with master installer.

                Able to load UCSC External View image when the UCSC DAS data source is disabled.

                Working correctly.

                Show
                nfreese Nowlan Freese added a comment - Tested on Mac with master installer. Able to load UCSC External View image when the UCSC DAS data source is disabled. Working correctly.
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2867 [ IGBF-2867 ]
                Hide
                Permalink
                omarne Omkar Marne (Inactive) added a comment -

                Tested on Windows and Linux with master installer.

                Able to load UCSC External View image when the UCSC DAS data source is disabled.

                Working correctly.

                Closing the issue.

                Show
                omarne Omkar Marne (Inactive) added a comment - Tested on Windows and Linux with master installer. Able to load UCSC External View image when the UCSC DAS data source is disabled. Working correctly. Closing the issue.
                omarne Omkar Marne (Inactive) made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                omarne Omkar Marne (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Assignee Omkar Marne [ omarne ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2869 [ IGBF-2869 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3655 [ IGBF-3655 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: