When users "install" an App, a new bundle corresponding to that App gets downloaded from the App repository and saved in the users' bundle cache directory.

When the user un-installs an App, that bundle is supposed to get deleted from the bundle cache directory. Also, each installed version of IGB gets its own bundle cache.

On Mac and Linux, the v9.0.1 bundles cache is .igb/bundles/v9.0.1-bundle-cache.

On Windows, IGB v9.0.1, the apps are in-consistent. Sometimes they do install in v9.0.1, and when they do, the main UI is corrupted.

Check version of java being packaged with the installer.

Use the jar files produced in the release branch to make a local repository of apps. See if these can install on 9.0.1.

Made a copy of repository.xml from release branch and copied in the local cloned repo of IGB 9.0.1. Changed paths to give the relative paths to all the app jars (downloaded from release branch).
But it still doesn't install apps from App manager!
There are no console logs in "Help" or Netbeans.

Analysis so far:

The issue is not related to user preferences nor to the IGB cache folder, the issue exists without the presence of 9.0.0 in the system.
The behaviour of App manager is not predictable, it lets the users install applications sometimes.
When it does not allow the users to install applications just closing and reopening the IGB resolves the issue.
But, When we install the 23andMe SNP Converter application there is a slight change in the UI (At least in windows system), after this if you hover the mouse pointer over the region in the attached image ( screenshot-1.png), IGB starts throwing exceptions and also the tabs in the Image stop working.

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at javax.swing.plaf.basic.BasicTabbedPaneUI.scrollableTabLayoutEnabled(Unknown Source)
at javax.swing.plaf.basic.BasicTabbedPaneUI.tabForCoordinate(Unknown Source)
at javax.swing.plaf.basic.BasicTabbedPaneUI.setRolloverTab(Unknown Source)
at javax.swing.plaf.basic.BasicTabbedPaneUI.access$2100(Unknown Source)
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mouseEntered(Unknown Source)
at com.affymetrix.igb.window.service.def.JTabbedTrayPane$2.mouseEntered(JTabbedTrayPane.java:158)
at java.awt.AWTEventMulticaster.mouseEntered(Unknown Source)
at java.awt.AWTEventMulticaster.mouseEntered(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEnterExit(Unknown Source)
at java.awt.LightweightDispatcher.trackMouseEnterExit(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

The same exception is raised in 9.0.0 as well, so this might be one of those issues related to High Resolution.
Need to check in other windows machine before concluding on this.

All issues closed since 9.0.0 release:
https://wiki.transvar.org/display/ITD/9.0.1

One touched App Manager code: https://jira.transvar.org/browse/IGBF-1157
Issue IGBF 1157 was closed by commit: 0109c9b
See:
https://bitbucket.org/lorainelab/integrated-genome-browser/commits/0109c9b8982258b75e5dbbfe6bd7574a43e0a58f

Used git revert to revert commit 0109c9b on a new branch:
https://bitbucket.org/aloraine/alorainefork/commits/branch/IGBF-1244-AppManagerBroke

Installers for the new branch are now available here:
https://bitbucket.org/aloraine/alorainefork/downloads/

Mason - can you test these installers?

ICB comment:

"Good find. I checked out the previous commit for each of those two files (leaving everything else on current commit).

Clear bundles, clean & build, run, open app manager ... IGB 9.0.1 is able to install the apps via the app manager."

Git commands:

get up to date commits
$ git pull upstream master

make a new branch
$ git checkout -b AppManagerRevertTest

Look at the history of the those files
$ git log plugins/plugin-manager/src/main/java/org/lorainelab/igb/plugin/manager/repos/view/AddBundleRepositoryFrame.java

See that this commit is the commit just before the change.
b845609bc1c09797a637a59e24896ed8c861171e

checkout that commit for both of the changed files
$ git checkout b845609bc1c09797a637a59e24896ed8c861171e plugins/plugin-manager/src/main/java/org/lorainelab/igb/plugin/manager/repos/view/AddBundleRepositoryFrame.java
$ git checkout b845609bc1c09797a637a59e24896ed8c861171e plugins/plugin-manager/pom.xml

push this branch
$ git push --set-upstream origin AppManagerRevertTest

Branch is on bitbucket at:
https://bitbucket.org/IvoryBlak/integrated-genome-browser/branch/IGBF-1244_AppManagerRevertTest
(I changed the branch name to include the issue id)

That ran into build issues...
Try again, but this time revert the java file all the way back to this commit:
0b1ac564f0a2f03c8dda5863e55fdf0857442b96

Build success!
But I ran the installer and the bug persists. Poop.

Kiran showed me that the app manager DOES work in 9.0.1 some portion of the time.
On my computer I cleared preferences and then opened 9.0.1, opened app manager and repeated this cycle many times.
The app manager did not work in the first 3 times, on the 4th time it worked fine. On the 5th time, it worked for about a minute, then stopped working. On the 6th time it did not work.

If 9.0.1 does work some random fraction of the time, then that might explain why it seemed to be working fine in my test on Friday even though the changes did not fix anything.

I saved the preferences file during the working/ not working and stopped-working moments to see if some state was preserved there, but the three copies are identical.

Ann thinks this issue may relate to an incompatibility between swing event loop and the javaFX event loop.
Or possibly a java version issue.

The fix for the issue is in the branch :
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1244-AppManager

A reference link which speaks about the problem and solution:
https://stackoverflow.com/questions/41903154/javafx-webview-callback-from-javascript-failing-after-garbage-collection

Need a review for the branch

https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1244-AppManager

Thanks