[IGBF-3381] Investigate: ProtAnnot can no longer query InterProScan - JIRA UNCC

Details

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

Story Points:
2
Epic Link:
Build & maintain IGB Apps
Sprint:
Summer 5 2023 July 10

Description

I attempted to run a search of InterPro using ProtAnnot but the search did not execute properly. (See attached image for a view of ProtAnnot.)

It looks like maybe the InterProScan Web service API has changed and ProtAnnot needs to be updated.

Note:
To understand how to run a search of InterPro using ProtAnnot, watch the video linked from the top page of https://apps.bioviz.org. The first part of the video explains how to install an IGB App using the App Store. You can skip the first part, since you probably should work with the development (current master branch) version of ProtAnnot available from the Downloads section of a ProtAnnot bitbucket repository. To just see how to run a search with ProtAnnot, you can skip ahead to 1:43 minutes into the video.

The error, copied from IGB "log" tab:

01:20:10.863 INFO com.affymetrix.igb.IGB - Completed loading sequence for Chr1 : 7,284,963 - 7,290,069 from IGB Quickload http://lorainelab-quickload.scidas.org/quickload/
01:21:04.688 INFO o.l.i.p.i.InterProscanServiceRest - iprscan5-R20230710-072102-0693-74435734-p1m
01:21:05.129 ERROR o.l.i.p.i.InterProscanServiceRest - No enum constant org.lorainelab.igb.protannot.interproscan.api.InterProscanService.Status.QUEUED
java.lang.IllegalArgumentException: No enum constant org.lorainelab.igb.protannot.interproscan.api.InterProscanService.Status.QUEUED
at java.lang.Enum.valueOf(Enum.java:238) ~[na:1.8.0_332]
at org.lorainelab.igb.protannot.interproscan.api.InterProscanService$Status.valueOf(InterProscanService.java:29) ~[-1688969961404:na]
at org.lorainelab.igb.protannot.interproscan.InterProscanServiceRest.status(InterProscanServiceRest.java:106) ~[-1688969961404:na]
at org.lorainelab.igb.protannot.ProtAnnotService$5.run(ProtAnnotService.java:692) [-1688969961404:na]
at java.util.TimerThread.mainLoop(Timer.java:555) [na:1.8.0_332]
at java.util.TimerThread.run(Timer.java:505) [na:1.8.0_332]
01:21:05.130 INFO o.l.igb.protannot.ProtAnnotService - iprscan5-R20230710-072102-0693-74435734-p1m Error

For this task, determine if this error re-occurs in other searches.

For your reference, one gene model searched. The gene model was "AT1G20920.7" from the "Araport" track of Arabidopsis genome version A_thaliana_Jun_2009.

I discovered the error during final testing of ~~IGBF-3202~~.

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Dscam1.png
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14/Jul/23 2:49 PM

Issue Links

blocks

IGBF-3380 Deploy ProtAnnot 9.1.4 to App Store.

Closed

relates to

IGBF-3349 Remove guava (google) upper bound version requirement for ProtAnnot

Closed

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Nowlan Freese added a comment - 10/Jul/23 10:39 AM - edited

Tested on IGB 9.1.10 release on Mac

Ran ProtAnnot and saw the error mentioned in the description as well as the following error.
Note: I ran ProtAnnot on two gene models, one Finished and one had a status of Error.

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at org.lorainelab.igb.protannot.model.InterProScanTableModel$InterProScanTableData.access$100(InterProScanTableModel.java:113)
	at org.lorainelab.igb.protannot.model.InterProScanTableModel.getValueAt(InterProScanTableModel.java:90)
	at javax.swing.JTable.getValueAt(JTable.java:2720)
	at com.jidesoft.grid.JideTable.getValueAt(Unknown Source)
	at com.jidesoft.grid.JideTable.prepareRenderer(Unknown Source)
	at com.affymetrix.igb.swing.jide.StyledJTable.prepareRenderer(StyledJTable.java:137)
	at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paintCell(Unknown Source)
	at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.a(Unknown Source)
	at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paint(Unknown Source)
	at com.jidesoft.plaf.aqua.AquaJideTableUI.paint(Unknown Source)
	at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
	at javax.swing.JComponent.paintComponent(JComponent.java:780)
	at javax.swing.JComponent.paint(JComponent.java:1056)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
	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.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	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)

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Nowlan Freese added a comment - 10/Jul/23 10:39 AM - edited Tested on IGB 9.1.10 release on Mac Ran ProtAnnot and saw the error mentioned in the description as well as the following error. Note: I ran ProtAnnot on two gene models, one Finished and one had a status of Error. Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at org.lorainelab.igb.protannot.model.InterProScanTableModel$InterProScanTableData.access$100(InterProScanTableModel.java:113) at org.lorainelab.igb.protannot.model.InterProScanTableModel.getValueAt(InterProScanTableModel.java:90) at javax.swing.JTable.getValueAt(JTable.java:2720) at com.jidesoft.grid.JideTable.getValueAt(Unknown Source) at com.jidesoft.grid.JideTable.prepareRenderer(Unknown Source) at com.affymetrix.igb.swing.jide.StyledJTable.prepareRenderer(StyledJTable.java:137) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paintCell(Unknown Source) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.a(Unknown Source) at com.jidesoft.plaf.basic.BasicJideTableUIDelegate.paint(Unknown Source) at com.jidesoft.plaf.aqua.AquaJideTableUI.paint(Unknown Source) at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161) at javax.swing.JComponent.paintComponent(JComponent.java:780) at javax.swing.JComponent.paint(JComponent.java:1056) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) at javax.swing.RepaintManager$4.run(RepaintManager.java:831) at javax.swing.RepaintManager$4.run(RepaintManager.java:814) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738) at javax.swing.RepaintManager.access$1200(RepaintManager.java:64) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) 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.awt.EventQueue.dispatchEvent(EventQueue.java:728) 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)

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Kaushik Gopu added a comment - 18/Jul/23 3:37 PM

The error does not persist in 9.1.10 since it has older guava version. The 9.1.12 has new guava version which is causing this error. currently, I'm working on this issue on branch 3349.

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Kaushik Gopu added a comment - 18/Jul/23 3:37 PM The error does not persist in 9.1.10 since it has older guava version. The 9.1.12 has new guava version which is causing this error. currently, I'm working on this issue on branch 3349.

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Nowlan Freese added a comment - 21/Jul/23 12:38 PM

Testing on Mac with IGB 9.1.10
Fetched Kaushik's ~~IGBF-3381~~ branch, built locally and added as a repo.
Tested multiple genes including Dscam1.
ProtAnnot worked correctly, no errors in log, all gene models finished except those that reported Invalid Protein Sequence (unrelated to this ticket).

I believe the EventBus error that Dr. Loraine was seeing was due to a change from ~~IGBF-3349~~ being accidentally merged/included in the downloads folder.
Kaushik Gopu - you will need to rebase ~~IGBF-3381~~ on top of master before submitting a pull request.

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Nowlan Freese added a comment - 21/Jul/23 12:38 PM Testing on Mac with IGB 9.1.10 Fetched Kaushik's IGBF-3381 branch, built locally and added as a repo. Tested multiple genes including Dscam1. ProtAnnot worked correctly, no errors in log, all gene models finished except those that reported Invalid Protein Sequence (unrelated to this ticket). I believe the EventBus error that Dr. Loraine was seeing was due to a change from IGBF-3349 being accidentally merged/included in the downloads folder. Kaushik Gopu - you will need to rebase IGBF-3381 on top of master before submitting a pull request.

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Kaushik Gopu added a comment - 21/Jul/23 3:19 PM

Pull request submitted: https://bitbucket.org/lorainelab/protannot/pull-requests/15.

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Kaushik Gopu added a comment - 21/Jul/23 3:19 PM Pull request submitted: https://bitbucket.org/lorainelab/protannot/pull-requests/15 .

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Ann Loraine added a comment - 23/Jul/23 11:54 AM - edited

Merged PR.

To test:

Download IGB 9.1.10 - the released version of IGB - and install it onto your computer
When IGB 9.1.10 starts, choose "File > Preferences > Other Options > Research Preferences to Defaults" to ensure you are working with a "fresh" installation of IGB, thus simulating what a naïve user would experience
Restart IGB 9.1.10
Choose Tools > Open App Manager
Observe that version 9.1.3 is the currently available version of ProtAnnot
Visit the IGB App Store (https://apps.bioviz.org) and open the page for ProtAnnot
Observe that the version available for installation is version 9.1.3 of ProtAnnot
Use either the App Manager interface or the App Store page to install version 9.1.3 of ProtAnnot
In IGB, choose Tools > Open App Manager > Manage Repositories
Add new repository "https://bitbucket.org/lorainelab/protannot/downloads/"
Quit IGB and then start IGB again.
Choose Tools > Open App Manager
Observe that the App Manager interface shows an option to update ProtAnnot to version 9.1.4
In IGB, visit the latest fruit fly genome and follow the instructions above to select Dscam1 gene models
Start ProtAnnot with Dscam1 gene models (as many as you can!)
Observe that ProtAnnots opens with Dscam1 gene models displayed in the IGB interface
Choose "run interproscan" button
Observe that every job runs and finishes, and ProtAnnot updates to show protein sequence motif "hits" (in green) beneath every gene model

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Ann Loraine added a comment - 23/Jul/23 11:54 AM - edited Merged PR. To test: Download IGB 9.1.10 - the released version of IGB - and install it onto your computer When IGB 9.1.10 starts, choose "File > Preferences > Other Options > Research Preferences to Defaults" to ensure you are working with a "fresh" installation of IGB, thus simulating what a naïve user would experience Restart IGB 9.1.10 Choose Tools > Open App Manager Observe that version 9.1.3 is the currently available version of ProtAnnot Visit the IGB App Store ( https://apps.bioviz.org ) and open the page for ProtAnnot Observe that the version available for installation is version 9.1.3 of ProtAnnot Use either the App Manager interface or the App Store page to install version 9.1.3 of ProtAnnot In IGB, choose Tools > Open App Manager > Manage Repositories Add new repository "https://bitbucket.org/lorainelab/protannot/downloads/" Quit IGB and then start IGB again. Choose Tools > Open App Manager Observe that the App Manager interface shows an option to update ProtAnnot to version 9.1.4 In IGB, visit the latest fruit fly genome and follow the instructions above to select Dscam1 gene models Start ProtAnnot with Dscam1 gene models (as many as you can!) Observe that ProtAnnots opens with Dscam1 gene models displayed in the IGB interface Choose "run interproscan" button Observe that every job runs and finishes, and ProtAnnot updates to show protein sequence motif "hits" (in green) beneath every gene model

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Nowlan Freese added a comment - 24/Jul/23 10:05 AM

Following the above testing gene models loaded in ProtAnnot and results were successful.

Closing ticket

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Nowlan Freese added a comment - 24/Jul/23 10:05 AM Following the above testing gene models loaded in ProtAnnot and results were successful. Closing ticket

Investigate: ProtAnnot can no longer query InterProScan

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