Problem with Amazon IGV backend setup

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Arnau Bria

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Feb 27, 2020, 6:36:09 AM2/27/20

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Hi all,

I'll trying to configure IGV so it can read files from a S3 bucket and I'm following the guide in https://umccr.org/blog/igv-amazon-backend-setup/.

I managed to configure cognito and I could login, but, when I try to load a file from the bucket I get some errors that I don't fully understand (I believ the problem is located in the fetch token process, but I'm not sure.

Here's the igv.log:

INFO [2020-02-27T12:25:47,378] [Main.java:159]  Startup  IGV Version 2.8.0 01/06/2020 08:43 PM
INFO [2020-02-27T12:25:47,388] [Main.java:160]  Java 11.0.5 (build 11.0.5+10) 2019-10-15
INFO [2020-02-27T12:25:47,389] [Main.java:163]  Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/
INFO [2020-02-27T12:25:47,390] [Main.java:165]  JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK   
INFO [2020-02-27T12:25:47,390] [Main.java:168]  Default User Directory: \\XYZ\bria\Documents
INFO [2020-02-27T12:25:47,391] [Main.java:169]  OS: Windows 10 10.0 amd64
INFO [2020-02-27T12:25:47,807] [AmazonUtils.java:68]  AWS configuration found. AWS support enabled under 'Amazon' menu
INFO [2020-02-27T12:25:47,971] [GenomeManager.java:192]  Loading genome: C:\Users\bria\igv\genomes\hg19.genome
INFO [2020-02-27T12:25:54,628] [GenomeComboBox.java:90]  Enter genome combo box
INFO [2020-02-27T12:25:54,646] [GenomeManager.java:284]  Genome loaded.  id= hg19
INFO [2020-02-27T12:25:54,659] [CommandListener.java:120]  Listening on port 60151
INFO [2020-02-27T12:26:26,414] [CommandListener.java:186]  GET /oauthCallback?code=136fbf97-3a40-4d67-93b3-565546c0507a&state=abadf119-1dec-48f1-90a5-35bd185320c1 HTTP/1.1
ERROR [2020-02-27T12:26:27,390] [OAuthProvider.java:240]  java.lang.NullPointerException
INFO [2020-02-27T12:26:27,454] [CommandListener.java:186]  GET /favicon.ico HTTP/1.1
ERROR [2020-02-27T12:26:55,282] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException: null
	at org.broad.igv.util.AmazonUtils.GetCognitoAWSCredentials(AmazonUtils.java:100) ~[igv.jar:?]
	at org.broad.igv.util.AmazonUtils.ListBucketsForUser(AmazonUtils.java:191) ~[igv.jar:?]
	at org.broad.igv.ui.IGVMenuBar.lambda$createAWSMenu$6(IGVMenuBar.java:972) ~[igv.jar:?]
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) ~[?:?]
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) ~[?:?]
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) ~[?:?]
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source) ~[?:?]
	at javax.swing.AbstractButton.doClick(Unknown Source) ~[?:?]
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI.doClick(VsnetMenuItemUI.java:1395) ~[jide-common-3.7.3.jar:?]
	at com.jidesoft.plaf.vsnet.VsnetMenuItemUI$MouseInputHandler.mouseReleased(VsnetMenuItemUI.java:1190) ~[jide-common-3.7.3.jar:?]
	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.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$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.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:?]
	at java.awt.EventQueue$5.run(Unknown Source) ~[?:?]
	at java.awt.EventQueue$5.run(Unknown Source) ~[?:?]
	at java.security.AccessController.doPrivileged(Native Method) ~[?:?]
	at java.security.ProtectionDomain$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) [?:?]
INFO [2020-02-27T12:27:55,742] [IGV.java:1338]  Loading 1 resources.
INFO [2020-02-27T12:27:55,746] [TrackLoader.java:126]  Loading resource, path s3://bucket/de7e8cc8-7485-40c1-9ec4-961cbd206c8e_star_genome.mark_dups.bam
ERROR [2020-02-27T12:27:55,746] [TrackLoader.java:253]  null
java.lang.NullPointerException: null
	at org.broad.igv.util.AmazonUtils.GetCognitoAWSCredentials(AmazonUtils.java:100) ~[igv.jar:?]
	at org.broad.igv.util.AmazonUtils.createPresignedURL(AmazonUtils.java:309) ~[igv.jar:?]
	at org.broad.igv.util.AmazonUtils.translateAmazonCloudURL(AmazonUtils.java:340) ~[igv.jar:?]
	at org.broad.igv.util.HttpUtils.mapURL(HttpUtils.java:133) ~[igv.jar:?]
	at org.broad.igv.util.HttpUtils.createURL(HttpUtils.java:122) ~[igv.jar:?]
	at org.broad.igv.util.ResourceLocator.getTypeString(ResourceLocator.java:192) ~[igv.jar:?]
	at org.broad.igv.util.ResourceLocator.getTypeString(ResourceLocator.java:173) ~[igv.jar:?]
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:128) [igv.jar:?]
	at org.broad.igv.ui.IGV.load(IGV.java:1421) [igv.jar:?]
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1353) [igv.jar:?]
	at org.broad.igv.ui.IGV$4.run(IGV.java:474) [igv.jar:?]
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) [igv.jar:?]
	at java.util.concurrent.FutureTask.run(Unknown Source) [?:?]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:?]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:?]
	at java.lang.Thread.run(Unknown Source) [?:?]
ERROR [2020-02-27T12:27:55,747] [IGV.java:1356]  Error loading track
java.lang.NullPointerException: null
	at org.broad.igv.exceptions.DataLoadException.<init>(DataLoadException.java:38) ~[igv.jar:?]
	at org.broad.igv.track.TrackLoader.load(TrackLoader.java:255) ~[igv.jar:?]
	at org.broad.igv.ui.IGV.load(IGV.java:1421) ~[igv.jar:?]
	at org.broad.igv.ui.IGV.loadResources(IGV.java:1353) [igv.jar:?]
	at org.broad.igv.ui.IGV$4.run(IGV.java:474) [igv.jar:?]
	at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) [igv.jar:?]
	at java.util.concurrent.FutureTask.run(Unknown Source) [?:?]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:?]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:?]
	at java.lang.Thread.run(Unknown Source) [?:?]
INFO [2020-02-27T12:27:55,750] [MessageUtils.java:76]  Error loading s3://bucket/de7e8cc8-7485-40c1-9ec4-961cbd206c8e_star_genome.mark_dups.bam: null

I see a first error after the login:

ERROR [2020-02-27T12:26:27,390] [OAuthProvider.java:240] java.lang.NullPointerException

how can I debug it?

The second is when I try to browse the buscket:

ERROR [2020-02-27T12:26:55,282] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException: null

and the last one when I specify the url:

ERROR [2020-02-27T12:26:55,282] [DefaultExceptionHandler.java:49]  Unhandled exception
java.lang.NullPointerException: null

Anyone with more experience could help me?

TIA,

Arnau

James Robinson

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Feb 28, 2020, 1:32:44 AM2/28/20

to igv-help

Hi Arnau,

Could you open an issue at github.com/igvteam/igv/issues? The contributor of the AWS functionality can respond there, he doesn't monitor this group. Thanks.

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Arnau Bria

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Feb 28, 2020, 1:56:35 AM2/28/20

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Will do, thanks a lot James.

Best,

Arnau

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpupRv-LeApG9YeUfr4qxPk9a6y36fUkhUs2-xa3xznVjA%40mail.gmail.com.