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  1. IGB
  2. IGBF-2860

Disable Ensembl external view

        Details

          Description

          Currently the ensembl external view does not work, regardless of the genome shown.

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              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2776 Fix External View tab

              • Major - Major loss of function.
              • Closed

              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

              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

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                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 relates to IGBF-2855 [ IGBF-2855 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2776 [ IGBF-2776 ]
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                ann.loraine Ann Loraine added a comment -

                Can't fix at this time because I can't figure out how to construct the URL needed to retrieve the image to be shown in the tabbed panel interface.

                Show
                ann.loraine Ann Loraine added a comment - Can't fix at this time because I can't figure out how to construct the URL needed to retrieve the image to be shown in the tabbed panel interface.
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                ann.loraine Ann Loraine added a comment -

                Removed Ensembl option from the External View interface, added new testing code, updated comments, and reduced complexity a bit.
                See branch IGBF-2860 on fork https://bitbucket.org/aloraine/integrated-genome-browser.

                Nowlan Freese - could you review?

                Show
                ann.loraine Ann Loraine added a comment - Removed Ensembl option from the External View interface, added new testing code, updated comments, and reduced complexity a bit. See branch IGBF-2860 on fork https://bitbucket.org/aloraine/integrated-genome-browser . Nowlan Freese - could you review?
                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 -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2864 [ IGBF-2864 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                nfreese Nowlan Freese added a comment - - edited

                Tested on Mac using branch installer.

                The ensembl external view option does not appear. UCSC external view continues to work correctly.

                Recommend pull request.

                Sidenote: I was able to debut the test file. It seems the @Ignore causes the Netbeans debugger to skip over any breakpoints in the tagged method. Need to remove the @Ignore and do a mvn clean install -DskipTests and then debug the test file.

                I also could not get the ensembl image to work. A quick search of the ensembl API was not able to find any obvious solution.

                Show
                nfreese Nowlan Freese added a comment - - edited Tested on Mac using branch installer. The ensembl external view option does not appear. UCSC external view continues to work correctly. Recommend pull request. Sidenote: I was able to debut the test file. It seems the @Ignore causes the Netbeans debugger to skip over any breakpoints in the tagged method. Need to remove the @Ignore and do a mvn clean install -DskipTests and then debug the test file. I also could not get the ensembl image to work. A quick search of the ensembl API was not able to find any obvious solution.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Summary Fix Ensembl external view Disable Ensembl external view
                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 ]
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                ann.loraine Ann Loraine added a comment -

                PR is submitted and merged. Master branch installers are built and ready for final testing.

                Show
                ann.loraine Ann Loraine added a comment - PR is submitted and merged. Master branch installers are built and ready for final testing.
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                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 ]
                Hide
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                nfreese Nowlan Freese added a comment -

                Tested on Mac using master installer.

                The Ensembl External View tab dropdown option does not appear. UCSC External View continues to work correctly.

                Closing issue.

                Show
                nfreese Nowlan Freese added a comment - Tested on Mac using master installer. The Ensembl External View tab dropdown option does not appear. UCSC External View continues to work correctly. Closing issue.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ] Omkar Marne [ omarne ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 9.1.8 Major Release [ 10605 ]
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                omarne Omkar Marne (Inactive) added a comment -

                Tested on lnux using master.sh file. The ensemble option is not visible now in the dropdown box.

                Closing the issue

                Show
                omarne Omkar Marne (Inactive) added a comment - Tested on lnux using master.sh file. The ensemble option is not visible now in the dropdown box. 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 ]

                  People

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

                    Dates

                    • Created:
                      Updated:
                      Resolved: