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  1. IGB
  2. IGBF-2860

Disable Ensembl external view

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          Description

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

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              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 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 - 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?

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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?
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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.

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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.
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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.

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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.
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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.

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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.
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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

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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

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: