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  1. IGB
  2. IGBF-2864

Improve External View error message displayed when no genome is selected

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      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.

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            omarne Omkar Marne (Inactive) 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 (Inactive) 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 (Inactive) added a comment - Pull request submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/882/igbf-2864-improve-external-view-error
            Hide
            ann.loraine Ann Loraine added a comment - - edited

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

            Show
            ann.loraine 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 (Inactive) 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 (Inactive) 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 (Inactive)
                Reporter:
                ann.loraine Ann Loraine
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                3 Start watching this issue

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                • Created:
                  Updated:
                  Resolved: