Investigate: Is it possible to implement IGBF-1443 as an App that can run in IGB 9.1.4

[~aloraine] - One doubt I had about IGB App - Does this mean the app needs to be installable? or it means just a plugin similar to Bookmark service?

I tried creating a repository for soft clip depth track operation and tried installing it as an app. Looks like it works .

Code diff https://bitbucket.org/noorzahara/softclip_track_operation/commits/25a02d17a93113bd8ab1427c89574137773ec234

Also a question about nexus - IGB 9.1.6 is not yet a part of nexus right? Because I was not able to add the genometry dependency.

Could you try it with IGB 9.1.4 as the platform version instead of IGB 9.1.6?

The function SeqSymSummarizer.getSymmetrySoftclipSummary(..) is currently present just in IGB 9.1.6. So, IGB 9.1.4 will also not work.

Can you put that function into the App?

The goal here is to find out if adding this new functionality requires modifying IGB itself. In other words, could an external developer implement this new functionality using 9.1.4 and the existing API?

I could put that into the App. getSymmetrySoftclipSummary(..) is internally dependent on getSpanSummary() which is currently a private function. Do you suggest to change that to public? Or include that function within the App?

Yes - please try to include that function within the App.

I have included the function within the App and have pushed the code

I am still seeing a dependency on 9.1.6 code. Can you take a look?

attn: Noor Zahara

I had changed the IGB version in a different commit - https://bitbucket.org/noorzahara/softclip_track_operation/commits/a03eb3bc1af071607671ed8db4d7428bd96cf65b

When you change the version, does it work?
(Asking because it seemed like more code needed to be migrated from 9.1.6.)

When I change the version it does work but the only issue is if genometry jar is not present in nexus then the build fails i.e if I change the version to 9.1.6, since genometry 9.1.6 is not present in nexus, it fails.

OK I understand!

Can you dig a little deeper into the genometry code base and copy the "soft clip" depth graph code from 9.1.6 genometry bundle into the App? The goal here is to get the App to run inside IGB 9.1.4.

This is so that we can demonstrate to new developers how to create the soft-clip depth graph visualization without making any changes to IGB itself.

I have got all the code that softclip feature is dependent to this App. I have placed it under utils folder.

Currently, the app gets installed in IGB 9.1.4.

Quick request:

• Please remove .gitproperties from src/main/resources

I am sorry about that. I have removed it.

For functional review:

• Confirm you can install the App in IGB 9.1.4 without error
• Confirm that when you install the App in IGB 9.1.4, the expected menu item appears when you right-click the track label for a BAM "reads" file track (see RNA-Seq folder under human genome)
• Confirm you can execute the functionality, e.g., a new graph is made when you select the menu item in previous step
• Examine the code and compare to other Apps
• Confirm that the App still works when run in IGB 9.1.6 - note there could potentially be a problem with name collision if the App is exported any packages

For code review:

• Note that the App should use declarative services. That is, the App is providing a service that is immediately available when the App gets installed into IGB's OSGi container. The business logic that creates the context menus upon right-clicking a track label consumes the service to display the provided menu item.
• Check for unneeded dependencies in the App POM.
• Check for copy-paste problems. Confirm that the "utils" code migrated from 9.1.6 is all necessary and being used.
• Inspect the built jar manifest. Ensure that no OSGi packages are exported.

When I tested this feature in 9.1.6, It worked fine but when I tested in 9.1.4 my right-click options are not popping out. Please find the attached error log
Exception in thread "AWT-EventQueue-0" java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key operator_alignment_softclip_depth
at java.util.ResourceBundle.getObject(ResourceBundle.java:450)
at java.util.ResourceBundle.getString(ResourceBundle.java:407)
at com.affymetrix.genometry.operator.AbstractAnnotationTransformer.getDisplay(AbstractAnnotationTransformer.java:20)
at com.affymetrix.genometry.util.IDComparator.compare(IDComparator.java:32)
at com.affymetrix.genometry.util.IDComparator.compare(IDComparator.java:11)
at java.util.TreeMap.put(TreeMap.java:552)
at java.util.TreeSet.add(TreeSet.java:255)
at java.util.AbstractCollection.addAll(AbstractCollection.java:344)
at java.util.TreeSet.addAll(TreeSet.java:312)
at org.lorainelab.igb.track.operations.api.OperationsPanel.loadOperators(OperationsPanel.java:155)
at org.lorainelab.igb.track.operations.api.OperationsPanel.resetAll(OperationsPanel.java:91)
at org.lorainelab.igb.track.operations.api.OperationsPanel.selectionRefreshed(OperationsPanel.java:85)
at com.affymetrix.igb.shared.Selections.notifyRefreshListener(Selections.java:346)
at com.affymetrix.igb.shared.Selections.refreshSelection(Selections.java:150)
at com.affymetrix.igb.shared.Selections.access$100(Selections.java:36)
at com.affymetrix.igb.shared.Selections$Listeners.symSelectionChanged(Selections.java:381)
at com.affymetrix.genometry.GenometryModel.fireSymSelectionEvent(GenometryModel.java:220)
at com.affymetrix.genometry.GenometryModel.setSelectedSymmetries(GenometryModel.java:235)
at com.affymetrix.igb.view.SeqMapView.postSelections(SeqMapView.java:1207)
at com.affymetrix.igb.view.SeqMapView.select(SeqMapView.java:1187)
at com.affymetrix.igb.view.SeqMapViewSymSelectionListenerImpl.symSelectionChanged(SeqMapViewSymSelectionListenerImpl.java:46)
at com.affymetrix.genometry.GenometryModel.fireSymSelectionEvent(GenometryModel.java:220)
at com.affymetrix.genometry.GenometryModel.setSelectedSymmetries(GenometryModel.java:235)
at com.affymetrix.igb.tiers.TierLabelManager.doGraphSelections(TierLabelManager.java:529)
at com.affymetrix.igb.tiers.TierLabelManager$2.mousePressed(TierLabelManager.java:262)
at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1330)
at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1589)
at com.affymetrix.genoviz.widget.NeoAbstractWidget.mousePressed(NeoAbstractWidget.java:811)
at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:969)
at com.affymetrix.genoviz.bioviews.View.mousePressed(View.java:869)
at java.awt.Component.processMouseEvent(Component.java:6536)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4532)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Sai Supreeth Segu - I have fixed the issue. Kindly try to install the app on 9.1.4 IGB.

I have tested this feature.

For functional review:

• I have successfully installed the App in IGB 9.1.4 without an error and was able to generate a graph on the test bam file.
• For the test bam file, the expected menu item appears when I right-clicked the track label it.
• I have installed the app in IGB 9.1.6 and was able to perform everything as expected.

For code review:

• There are no unneeded dependencies in the App POM.
• All the "utils" code migrated from 9.1.6 is all necessary and being used.

cc: [~aloraine] and Noor Zahara

Noor Zahara - please submit PR.

[~aloraine] - It is a new repository. It should be added to larainelab repositories. Mostly ownership transfer is needed right?

You can keep in your account and LoraineLab can fork it. Or, you can transfer it to LoraineLab. I prefer the first option, like we did with Genome Dashboard by Sameer Shanbhag.
Please indicate what you would like to do.

Forking is a good option. I am fine that. Thanks!

Forked: https://bitbucket.org/lorainelab/softclip_track_operation/