[IGBF-2632] Error while app repository is trying to load plugins - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
- Intermediate

Story Points:
1
Epic Link:
Test and release IGB 9.1.6
Sprint:
Fall 5 Nov 9 - Nov 20

Description

Getting a null pointer exception error while trying to refresh or add app repository. The app manager window is blank. Issue not present in the last IGB version(9.1.4)
To reproduce the error install the latest master branch installer and follow the steps.
1) Click on file and then click on preferences.
2) Go to App Repositories Tab.
3) Either load the present repositories by clicking on the refresh icon or add a new repositories.
4) Check the log window of IGB for the error.
5) Even the launch app manager window is blank.

Error:
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
at org.lorainelab.igb.plugin.manager.BundleInfoManager.lambda$isVersionOfBundleInstalled$9(BundleInfoManager.java:149)
at java.util.stream.MatchOps$1MatchSink.accept(Unknown Source)
at java.util.Spliterators$ArraySpliterator.tryAdvance(Unknown Source)
at java.util.stream.ReferencePipeline.forEachWithCancel(Unknown Source)
at java.util.stream.AbstractPipeline.copyIntoWithCancel(Unknown Source)
at java.util.stream.AbstractPipeline.copyInto(Unknown Source)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
at java.util.stream.MatchOps$MatchOp.evaluateSequential(Unknown Source)
at java.util.stream.MatchOps$MatchOp.evaluateSequential(Unknown Source)
at java.util.stream.AbstractPipeline.evaluate(Unknown Source)
at java.util.stream.ReferencePipeline.anyMatch(Unknown Source)
at org.lorainelab.igb.plugin.manager.BundleInfoManager.isVersionOfBundleInstalled(BundleInfoManager.java:149)
at org.lorainelab.igb.plugin.manager.AppManagerFxPanel.lambda$null$25(AppManagerFxPanel.java:150)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(Unknown Source)
at java.util.stream.ReferencePipeline$Head.forEach(Unknown Source)
at org.lorainelab.igb.plugin.manager.AppManagerFxPanel.lambda$udpateDataEventNotification$26(AppManagerFxPanel.java:149)
at com.sun.javafx.application.PlatformImpl.lambda$null$5(PlatformImpl.java:295)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.application.PlatformImpl.lambda$runLater$6(PlatformImpl.java:294)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)
at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at com.sun.glass.ui.win.WinApplication.lambda$null$4(WinApplication.java:186)
at java.lang.Thread.run(Unknown Source)

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IGB-app-manager-blank-error.png
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17/Nov/20 5:13 PM

Issue Links

relates to

IGBF-2598 Test App Manager - MacOS

Closed

IGBF-2594 Test App Manager - Windows

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Ann Loraine added a comment - 17/Nov/20 6:30 PM - edited

Also happens on startup. I built IGB on my local and ran it with run_igb.sh. Got the same exception.
Checked out and tested a previous commit: "8ce5517d1 ~~IGBF-2589~~: Fixing ftp quickload"

git checkout 8ce5517d1

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Ann Loraine added a comment - 17/Nov/20 6:30 PM - edited Also happens on startup. I built IGB on my local and ran it with run_igb.sh. Got the same exception. Checked out and tested a previous commit: "8ce5517d1 IGBF-2589 : Fixing ftp quickload" git checkout 8ce5517d1

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Ann Loraine added a comment - 17/Nov/20 7:16 PM - edited

During compilation there were a number of warnings related to packages being present in multiple jidesoft jars.
I tried reverting 470ed1b17, which is our recent commit changing how we import jidesoft code.
I re-built and tested the new build. The error appears to be gone.
Chirag Chandrahas Shetty - could you please try out this new installer?
Please see: https://bitbucket.org/aloraine/integrated-genome-browser/downloads/

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Ann Loraine added a comment - 17/Nov/20 7:16 PM - edited During compilation there were a number of warnings related to packages being present in multiple jidesoft jars. I tried reverting 470ed1b17, which is our recent commit changing how we import jidesoft code. I re-built and tested the new build. The error appears to be gone. Chirag Chandrahas Shetty - could you please try out this new installer? Please see: https://bitbucket.org/aloraine/integrated-genome-browser/downloads/

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Ann Loraine added a comment - 18/Nov/20 8:27 AM

Jidesoft imports:

./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackDefaultViewGUI.java:    private com.jidesoft.combobox.ColorComboBox bgColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackDefaultViewGUI.java:    private com.jidesoft.combobox.ColorComboBox fgColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackDefaultViewGUI.java:    private com.jidesoft.combobox.ColorComboBox negativeColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackDefaultViewGUI.java:    private com.jidesoft.combobox.ColorComboBox possitiveColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox AColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox CColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox DynamicORFColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox GColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox OtherColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox StopCodonColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox TColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox bgComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java:    private com.jidesoft.combobox.ColorComboBox edgeMatchColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferences.java:import com.jidesoft.combobox.ColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferences.java:import com.jidesoft.combobox.ColorExComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java:    private com.jidesoft.combobox.ColorComboBox bgColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java:    private com.jidesoft.combobox.ColorComboBox fgColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java:    private com.jidesoft.combobox.ColorComboBox labelColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java:    private com.jidesoft.combobox.ColorComboBox negativeColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java:    private com.jidesoft.combobox.ColorComboBox positiveColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TierPrefsViewGUI.java:    private com.jidesoft.combobox.ColorComboBox bgColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TierPrefsViewGUI.java:    private com.jidesoft.combobox.ColorComboBox fgColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TierPrefsViewGUI.java:    private com.jidesoft.combobox.ColorComboBox negativeColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/prefs/TierPrefsViewGUI.java:    private com.jidesoft.combobox.ColorComboBox possitiveColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/util/ColorUtils.java:import com.jidesoft.combobox.ColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/IGB.java:import com.jidesoft.plaf.LookAndFeelFactory;
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanelImpl.java:import com.jidesoft.combobox.ColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/shared/ConfigureOptionsPanel.java:import com.jidesoft.combobox.ColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:        foregroundColorComboBox = new com.jidesoft.combobox.ColorComboBox();
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:        backgroundColorComboBox = new com.jidesoft.combobox.ColorComboBox();
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:        labelColorComboBox = new com.jidesoft.combobox.ColorComboBox();
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:    public com.jidesoft.combobox.ColorComboBox getBackgroundColorComboBox() {
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:    public com.jidesoft.combobox.ColorComboBox getForegroundColorComboBox() {
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:    public com.jidesoft.combobox.ColorComboBox getLabelColorComboBox() {
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:    private com.jidesoft.combobox.ColorComboBox backgroundColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:    private com.jidesoft.combobox.ColorComboBox foregroundColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java:    private com.jidesoft.combobox.ColorComboBox labelColorComboBox;
./core/igb/src/main/java/com/affymetrix/igb/Activator.java:        // Verify jidesoft license.
./core/igb/src/main/java/com/affymetrix/igb/Activator.java:        com.jidesoft.utils.Lm.verifyLicense("Dept. of Bioinformatics and Genomics, UNCC",
./core/igb/src/main/java/com/affymetrix/igb/view/MapRangeBox.java:import com.jidesoft.hints.ListDataIntelliHints;
./core/igb/src/main/java/com/affymetrix/igb/view/StatusBar.java:import com.jidesoft.status.MemoryStatusBarItem;
./core/igb/src/main/java/com/affymetrix/igb/view/load/DataManagementTable.java:import com.jidesoft.combobox.ColorExComboBox;
./core/igb-swing-ext/src/main/java/com/affymetrix/igb/swing/jide/StyledJTable.java:import com.jidesoft.grid.JideTable;
./core/weblinks/src/main/java/org/lorainelab/igb/preferences/weblink/view/WebLinksView.java:import com.jidesoft.grid.JideTable;
./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java:        strandsReverseColorComboBox = new com.jidesoft.combobox.ColorComboBox();
./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java:        strandsForwardColorComboBox = new com.jidesoft.combobox.ColorComboBox();
./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java:    public com.jidesoft.combobox.ColorComboBox getStrandsForwardColorComboBox() {
./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java:    public com.jidesoft.combobox.ColorComboBox getStrandsReverseColorComboBox() {
./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java:    private com.jidesoft.combobox.ColorComboBox strandsForwardColorComboBox;
./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java:    private com.jidesoft.combobox.ColorComboBox strandsReverseColorComboBox;
./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanelImpl.java:import com.jidesoft.combobox.ColorComboBox;
./plugins/SearchView/src/main/java/com/affymetrix/igb/search/SearchView.java:import com.jidesoft.hints.ListDataIntelliHints;

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Ann Loraine added a comment - 18/Nov/20 8:27 AM Jidesoft imports: ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackDefaultViewGUI.java: private com.jidesoft.combobox.ColorComboBox bgColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackDefaultViewGUI.java: private com.jidesoft.combobox.ColorComboBox fgColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackDefaultViewGUI.java: private com.jidesoft.combobox.ColorComboBox negativeColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackDefaultViewGUI.java: private com.jidesoft.combobox.ColorComboBox possitiveColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox AColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox CColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox DynamicORFColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox GColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox OtherColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox StopCodonColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox TColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox bgComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/OtherOptionsView.java: private com.jidesoft.combobox.ColorComboBox edgeMatchColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferences.java: import com.jidesoft.combobox.ColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferences.java: import com.jidesoft.combobox.ColorExComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java: private com.jidesoft.combobox.ColorComboBox bgColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java: private com.jidesoft.combobox.ColorComboBox fgColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java: private com.jidesoft.combobox.ColorComboBox labelColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java: private com.jidesoft.combobox.ColorComboBox negativeColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TrackPreferencesPanel.java: private com.jidesoft.combobox.ColorComboBox positiveColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TierPrefsViewGUI.java: private com.jidesoft.combobox.ColorComboBox bgColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TierPrefsViewGUI.java: private com.jidesoft.combobox.ColorComboBox fgColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TierPrefsViewGUI.java: private com.jidesoft.combobox.ColorComboBox negativeColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/prefs/TierPrefsViewGUI.java: private com.jidesoft.combobox.ColorComboBox possitiveColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/util/ColorUtils.java: import com.jidesoft.combobox.ColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/IGB.java: import com.jidesoft.plaf.LookAndFeelFactory; ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanelImpl.java: import com.jidesoft.combobox.ColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/shared/ConfigureOptionsPanel.java: import com.jidesoft.combobox.ColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: foregroundColorComboBox = new com.jidesoft.combobox.ColorComboBox(); ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: backgroundColorComboBox = new com.jidesoft.combobox.ColorComboBox(); ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: labelColorComboBox = new com.jidesoft.combobox.ColorComboBox(); ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: public com.jidesoft.combobox.ColorComboBox getBackgroundColorComboBox() { ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: public com.jidesoft.combobox.ColorComboBox getForegroundColorComboBox() { ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: public com.jidesoft.combobox.ColorComboBox getLabelColorComboBox() { ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: private com.jidesoft.combobox.ColorComboBox backgroundColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: private com.jidesoft.combobox.ColorComboBox foregroundColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/shared/StylePanel.java: private com.jidesoft.combobox.ColorComboBox labelColorComboBox; ./core/igb/src/main/java/com/affymetrix/igb/Activator.java: // Verify jidesoft license. ./core/igb/src/main/java/com/affymetrix/igb/Activator.java: com.jidesoft.utils.Lm.verifyLicense( "Dept. of Bioinformatics and Genomics, UNCC" , ./core/igb/src/main/java/com/affymetrix/igb/view/MapRangeBox.java: import com.jidesoft.hints.ListDataIntelliHints; ./core/igb/src/main/java/com/affymetrix/igb/view/StatusBar.java: import com.jidesoft.status.MemoryStatusBarItem; ./core/igb/src/main/java/com/affymetrix/igb/view/load/DataManagementTable.java: import com.jidesoft.combobox.ColorExComboBox; ./core/igb-swing-ext/src/main/java/com/affymetrix/igb/swing/jide/StyledJTable.java: import com.jidesoft.grid.JideTable; ./core/weblinks/src/main/java/org/lorainelab/igb/preferences/weblink/view/WebLinksView.java: import com.jidesoft.grid.JideTable; ./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java: strandsReverseColorComboBox = new com.jidesoft.combobox.ColorComboBox(); ./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java: strandsForwardColorComboBox = new com.jidesoft.combobox.ColorComboBox(); ./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java: public com.jidesoft.combobox.ColorComboBox getStrandsForwardColorComboBox() { ./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java: public com.jidesoft.combobox.ColorComboBox getStrandsReverseColorComboBox() { ./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java: private com.jidesoft.combobox.ColorComboBox strandsForwardColorComboBox; ./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanel.java: private com.jidesoft.combobox.ColorComboBox strandsReverseColorComboBox; ./plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanelImpl.java: import com.jidesoft.combobox.ColorComboBox; ./plugins/SearchView/src/main/java/com/affymetrix/igb/search/SearchView.java: import com.jidesoft.hints.ListDataIntelliHints;

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Ann Loraine added a comment - 18/Nov/20 8:32 AM - edited

Jidesoft classes used:

com.jidesoft.combobox.ColorComboBox
com.jidesoft.combobox.ColorExComboBox
com.jidesoft.grid.JideTable
com.jidesoft.hints.ListDataIntelliHints
com.jidesoft.plaf.LookAndFeelFactory
com.jidesoft.status.MemoryStatusBarItem
com.jidesoft.utils.Lm (license manager)

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Ann Loraine added a comment - 18/Nov/20 8:32 AM - edited Jidesoft classes used: com.jidesoft.combobox.ColorComboBox com.jidesoft.combobox.ColorExComboBox com.jidesoft.grid.JideTable com.jidesoft.hints.ListDataIntelliHints com.jidesoft.plaf.LookAndFeelFactory com.jidesoft.status.MemoryStatusBarItem com.jidesoft.utils.Lm (license manager)

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Chirag Chandrahas Shetty (Inactive) added a comment - 18/Nov/20 11:05 AM

Tested app manager subsystem using Dr. Loraine's repository installer. Everything works fine. I think we can merge it to master.

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Chirag Chandrahas Shetty (Inactive) added a comment - 18/Nov/20 11:05 AM Tested app manager subsystem using Dr. Loraine's repository installer. Everything works fine. I think we can merge it to master.

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Chirag Chandrahas Shetty (Inactive) added a comment - 18/Nov/20 3:34 PM

Everything looks good as per the app manager functional checklist

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Chirag Chandrahas Shetty (Inactive) added a comment - 18/Nov/20 3:34 PM Everything looks good as per the app manager functional checklist

Error while app repository is trying to load plugins

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