Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2864

Improve External View error message displayed when no genome is selected

    Details

      Description

      The External View tab is supposed to display an external genome browser image when the user clicks "update".

      However, if a user has not yet selected a genome and clicks "update", a misleading error message is shown. See IGBF-2855 for details.

      We should instead display a more helpful message that lets the user know that before they can use the External View tab, they first must select a genome version.

        Issue Links

          Activity

          Hide
          omarne Omkar Marne added a comment - - edited

          I did below code changes in the file external.properties and Browserview.java. The error messaged has been improved and we are getting more meaningful messages when user does not select the genome and when user selects the plant genome. I have uploaded the images of the messages. Please check.

          
          resolveError=An external viewer is not available for this genome. If you have questions, please contact the IGB team.
          
          NoGenomeSelectedError=Please select Species and Genome Version from the Current Genome tab.
          
          
          
          import com.affymetrix.genometry.GenomeVersion;
          import com.affymetrix.genometry.GenometryModel;
          
                                GenomeVersion genomeVersion = GenometryModel.getInstance().getSelectedGenomeVersion();
                                  String ucscQuery = ucscViewAction.getUCSCQuery();
                                  Loc loc = Loc.fromUCSCQuery(ucscQuery);
                              
                                  Logger.getLogger(BrowserView.class.getName()).log(Level.SEVERE, "HELOO");
                                  
                                  if (genomeVersion == null) {
                                      return BrowserLoader.createErrorImage(ExternalViewer.BUNDLE.getString("NoGenomeSelectedError"), pixWidth);
                                  }
                                  if (ucscQuery.length() == 0 || loc.db.length() == 0) {
                                      return BrowserLoader.createErrorImage(ExternalViewer.BUNDLE.getString("resolveError"), pixWidth);
                                  }
                                  return getImage(loc, pixWidth);
          
          
          
          

          I have pushed the changes in my local branch. Link - https://bitbucket.org/omarne/integrated-genome-browser/downloads/

          Dr. Nowlan Freese Please review my changes and submit a pull request.

          Show
          omarne Omkar Marne added a comment - - edited I did below code changes in the file external.properties and Browserview.java. The error messaged has been improved and we are getting more meaningful messages when user does not select the genome and when user selects the plant genome. I have uploaded the images of the messages. Please check. resolveError=An external viewer is not available for this genome. If you have questions, please contact the IGB team. NoGenomeSelectedError=Please select Species and Genome Version from the Current Genome tab. import com.affymetrix.genometry.GenomeVersion; import com.affymetrix.genometry.GenometryModel; GenomeVersion genomeVersion = GenometryModel.getInstance().getSelectedGenomeVersion(); String ucscQuery = ucscViewAction.getUCSCQuery(); Loc loc = Loc.fromUCSCQuery(ucscQuery); Logger.getLogger(BrowserView.class.getName()).log(Level.SEVERE, "HELOO" ); if (genomeVersion == null ) { return BrowserLoader.createErrorImage(ExternalViewer.BUNDLE.getString( "NoGenomeSelectedError" ), pixWidth); } if (ucscQuery.length() == 0 || loc.db.length() == 0) { return BrowserLoader.createErrorImage(ExternalViewer.BUNDLE.getString( "resolveError" ), pixWidth); } return getImage(loc, pixWidth); I have pushed the changes in my local branch. Link - https://bitbucket.org/omarne/integrated-genome-browser/downloads/ Dr. Nowlan Freese Please review my changes and submit a pull request.
          Hide
          nfreese Nowlan Freese added a comment -

          Tested installer on Mac.

          Working correctly.

          Recommend pull request.

          Show
          nfreese Nowlan Freese added a comment - Tested installer on Mac. Working correctly. Recommend pull request.
          Show
          omarne Omkar Marne added a comment - Pull request submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/882/igbf-2864-improve-external-view-error
          Hide
          aloraine Ann Loraine added a comment - - edited

          Merged. Master branch installers are built and ready for final testing.

          Show
          aloraine Ann Loraine added a comment - - edited Merged. Master branch installers are built and ready for final testing.
          Hide
          nfreese Nowlan Freese added a comment -

          Test on Mac using the master installer.

          If user has not selected a Species and Genome Version they are instructed to select those after clicking update in the External View tab.
          If the genome version is not supported by UCSC then they are told that genome is not supported.
          If the genome version is supported by UCSC the image is loaded.

          Closing issue.

          Show
          nfreese Nowlan Freese added a comment - Test on Mac using the master installer. If user has not selected a Species and Genome Version they are instructed to select those after clicking update in the External View tab. If the genome version is not supported by UCSC then they are told that genome is not supported. If the genome version is supported by UCSC the image is loaded. Closing issue.
          Hide
          omarne Omkar Marne added a comment -

          Tested on Linux and Windows. The results are as expected. Works perfectly fine.

          If user has not selected a Species and Genome Version they are instructed to select those after clicking update in the External View tab.
          If the genome version is not supported by UCSC then they are told that genome is not supported.
          If the genome version is supported by UCSC the image is loaded.

          Closing the issue.

          Show
          omarne Omkar Marne added a comment - Tested on Linux and Windows. The results are as expected. Works perfectly fine. If user has not selected a Species and Genome Version they are instructed to select those after clicking update in the External View tab. If the genome version is not supported by UCSC then they are told that genome is not supported. If the genome version is supported by UCSC the image is loaded. Closing the issue.

            People

            • Assignee:
              omarne Omkar Marne
              Reporter:
              aloraine Ann Loraine
            • Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved:

                Development

                  Agile