[IGBF-2864] Improve External View error message displayed when no genome is selected - JIRA UNCC

Details

Type: Improvement
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.1.8 Major Release
Labels:
None

Story Points:
1.5
Epic Link:
Improve IGB for users
Sprint:
Spring 5 2021 May 17 - May 28

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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If genome is not selected..png
64 kB
26/May/21 12:39 PM
If plant genome is selected..png
123 kB
26/May/21 12:39 PM

Issue Links

is blocked by

IGBF-2855 Investigate activating UCSC DAS source from External View tab

Closed

relates to

IGBF-2860 Disable Ensembl external view

Closed

IGBF-2863 Use UCSC JSON endpoint to get list of genomes for External View tab

Closed

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Omkar Marne (Inactive) added a comment - 26/May/21 12:31 PM - 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.

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Omkar Marne (Inactive) added a comment - 26/May/21 12:31 PM - 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.

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Nowlan Freese added a comment - 26/May/21 2:31 PM

Tested installer on Mac.

Working correctly.

Recommend pull request.

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Nowlan Freese added a comment - 26/May/21 2:31 PM Tested installer on Mac. Working correctly. Recommend pull request.

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Omkar Marne (Inactive) added a comment - 26/May/21 3:04 PM

Pull request submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/882/igbf-2864-improve-external-view-error

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Omkar Marne (Inactive) added a comment - 26/May/21 3:04 PM Pull request submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/882/igbf-2864-improve-external-view-error

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Ann Loraine added a comment - 26/May/21 4:10 PM - edited

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

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Ann Loraine added a comment - 26/May/21 4:10 PM - edited Merged. Master branch installers are built and ready for final testing.

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Nowlan Freese added a comment - 27/May/21 9:52 AM

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.

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Nowlan Freese added a comment - 27/May/21 9:52 AM 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.

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Omkar Marne (Inactive) added a comment - 27/May/21 2:21 PM

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.

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Omkar Marne (Inactive) added a comment - 27/May/21 2:21 PM 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.

Improve External View error message displayed when no genome is selected

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