[IGBF-3514] Investigate errors in IGB when View in IGB is invoked - 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:
Maintain BioViz Connect
Sprint:
Fall 8, Spring 1

Description

When the View in IGB in Bioviz Connect is clicked on IGB loads the file the first time but when View in IGB in another file is clicked it throws the following error:

java.lang.NullPointerException: Cannot invoke "java.util.Optional.ifPresent(java.util.function.Consumer)" because the return value of "com.affymetrix.igb.view.load.GeneralLoadUtils.getDataSet(java.net.URI, java.util.Optional, String, String, com.affymetrix.genometry.GenomeVersion, boolean)" is null
	at com.affymetrix.igb.view.load.GeneralLoadUtils.openURI(GeneralLoadUtils.java:967)
	at com.affymetrix.igb.IgbServiceImpl.openURI(IgbServiceImpl.java:363)
	at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet.directlyLoadFile(BookmarkUnibrowControlServlet.java:589)
	at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet.lambda$directlyLoadUrls$8(BookmarkUnibrowControlServlet.java:578)
	at java.base/java.util.HashMap.forEach(HashMap.java:1429)
	at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet.directlyLoadUrls(BookmarkUnibrowControlServlet.java:577)
	at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet$1.runInBackground(BookmarkUnibrowControlServlet.java:247)
	at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
	at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)

Attachments

Issue Links

blocks

IGBF-3510 Smoke Test JDK 21 in Windows

Closed

Activity

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Karthik Raveendran created issue - 11/Dec/23 10:57 AM

Karthik Raveendran made changes - 11/Dec/23 10:57 AM

Field	Original Value	New Value
Epic Link		~~IGBF-3142~~ [ 21688 ]

Karthik Raveendran made changes - 11/Dec/23 10:57 AM

Link

This issue blocks ~~IGBF-3510~~ [ ~~IGBF-3510~~ ]

Karthik Raveendran made changes - 11/Dec/23 10:57 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Karthik Raveendran made changes - 11/Dec/23 11:11 AM

Description

When the View in IGB in Bioviz Connect is clicked on IGB loads the file the first time but when View in IGB in another file is clicked it throws the following error:

{code:java}
java.lang.NullPointerException: Cannot invoke "java.util.Optional.ifPresent(java.util.function.Consumer)" because the return value of "com.affymetrix.igb.view.load.GeneralLoadUtils.getDataSet(java.net.URI, java.util.Optional, String, String, com.affymetrix.genometry.GenomeVersion, boolean)" is null
at com.affymetrix.igb.view.load.GeneralLoadUtils.openURI(GeneralLoadUtils.java:967)
at com.affymetrix.igb.IgbServiceImpl.openURI(IgbServiceImpl.java:363)
at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet.directlyLoadFile(BookmarkUnibrowControlServlet.java:589)
at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet.lambda$directlyLoadUrls$8(BookmarkUnibrowControlServlet.java:578)
at java.base/java.util.HashMap.forEach(HashMap.java:1429)
at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet.directlyLoadUrls(BookmarkUnibrowControlServlet.java:577)
at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet$1.runInBackground(BookmarkUnibrowControlServlet.java:247)
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)

{code}

Karthik Raveendran made changes - 11/Dec/23 11:11 AM

Summary

Fix errors in IGB when View in IGB is invoked

errors in IGB when View in IGB is invoked

Karthik Raveendran made changes - 11/Dec/23 11:11 AM

Summary

errors in IGB when View in IGB is invoked

Investigate errors in IGB when View in IGB is invoked

Ann Loraine made changes - 12/Dec/23 10:41 AM

Epic Link

~~IGBF-3142~~ [ 21688 ]

IGBF-2376 [ 18533 ]

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Ann Loraine added a comment - 12/Dec/23 10:42 AM - edited

During scrum, Nowlan Freese noted:

The problem may be due to the tester account being over its storage limit.
The error happens on both the main-JDK8, main-JDK21 branches, and release-9.1.10

More details on error:

NF sees "500" error within IGB when clicking the "load in igb" button

Show

Ann Loraine added a comment - 12/Dec/23 10:42 AM - edited During scrum, Nowlan Freese noted: The problem may be due to the tester account being over its storage limit. The error happens on both the main-JDK8, main-JDK21 branches, and release-9.1.10 More details on error: NF sees "500" error within IGB when clicking the "load in igb" button

Karthik Raveendran made changes - 15/Dec/23 10:36 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

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Ann Loraine added a comment - 22/Dec/23 10:24 AM

We are going to try to fix this and if a change in IGB is required, we want to include it in our upcoming release.

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Ann Loraine added a comment - 22/Dec/23 10:24 AM We are going to try to fix this and if a change in IGB is required, we want to include it in our upcoming release.

Ann Loraine made changes - 27/Dec/23 5:36 AM

Sprint

Fall 8 [ 184 ]

Fall 8, Spring 1 [ 184, 185 ]

Ann Loraine made changes - 27/Dec/23 5:36 AM

Rank

Ranked higher

Karthik Raveendran made changes - 29/Dec/23 2:14 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Ann Loraine added a comment - 11/Jan/24 10:25 AM - edited

Suggestion: Check if the host can still support http range requests.

Potentially useful reference: https://developer.mozilla.org/en-US/docs/Web/HTTP/Range_requests

NF suggestion: Send me the URL of the file and he will test if the samtools software and do a usual range request. (Command-line samtools does this also.)

Show

Ann Loraine added a comment - 11/Jan/24 10:25 AM - edited Suggestion: Check if the host can still support http range requests. Potentially useful reference: https://developer.mozilla.org/en-US/docs/Web/HTTP/Range_requests NF suggestion: Send me the URL of the file and he will test if the samtools software and do a usual range request. (Command-line samtools does this also.)

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Karthik Raveendran added a comment - 12/Jan/24 9:50 AM - edited

Dr. Nowlan Freese used the URL below to check with samtools software for a range request and it worked as expected. I used curl commands for http requests on the same URL and it required a redirect flag (-L) for it to work. The range requests did work as well with the redirect flag. I am trying to confirm if the error is caused because the redirect was not handled.

curl -L -X 0-500 GET https://data.cyverse.org/dav-anon/iplant/home/shared/BioViz/rnaseq/A_thaliana_Jun_2009/SRP220157/reads/SRR10060893.bam > outFile

This worked from Samtools:

samtools view https://data.cyverse.org/dav-anon/iplant/home/shared/BioViz/rnaseq/A_thaliana_Jun_2009/SRP220157/reads/SRR10060893.bam Chr1:3599079-3600963

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Karthik Raveendran added a comment - 12/Jan/24 9:50 AM - edited Dr. Nowlan Freese used the URL below to check with samtools software for a range request and it worked as expected. I used curl commands for http requests on the same URL and it required a redirect flag (-L) for it to work. The range requests did work as well with the redirect flag. I am trying to confirm if the error is caused because the redirect was not handled. curl -L -X 0-500 GET https: //data.cyverse.org/dav-anon/iplant/home/shared/BioViz/rnaseq/A_thaliana_Jun_2009/SRP220157/reads/SRR10060893.bam > outFile This worked from Samtools: samtools view https: //data.cyverse.org/dav-anon/iplant/home/shared/BioViz/rnaseq/A_thaliana_Jun_2009/SRP220157/reads/SRR10060893.bam Chr1:3599079-3600963

Ann Loraine made changes - 17/Jan/24 10:43 AM

Comment

[ Note from scrum:

* Be sure to check to see if this same problem is affecting the released version of IGB - version 9.1.10 ]

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Ann Loraine added a comment - 17/Jan/24 10:47 AM - edited

Suggestion:

Investigate if anyone has complained about "track hubs" no longer working for Cyverse hosted data files (see google group for the UCSC genome browser for mention of this)
Maybe create a very simple Java client program that will try to retrieve data from CyVerse similarly to how IGB is doing it
Check whether the redirection is somehow depending on the user agent
Ask CyVerse for help

Show

Ann Loraine added a comment - 17/Jan/24 10:47 AM - edited Suggestion: Investigate if anyone has complained about "track hubs" no longer working for Cyverse hosted data files (see google group for the UCSC genome browser for mention of this) Maybe create a very simple Java client program that will try to retrieve data from CyVerse similarly to how IGB is doing it Check whether the redirection is somehow depending on the user agent Ask CyVerse for help

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Nowlan Freese added a comment - 17/Jan/24 10:55 AM

On Mac

Testing on 9.1.10
Successful:

Loaded bigwig from nowlanf account from Community folder.
Loaded bigwig from nowlanf account from Home folder.
Loaded bam from nowlanf account from Home folder.

Tested on main-JDK21-with-javafx-no-theme
Successful:

Loaded bam from nowlanf account from Home folder.
Loaded bigwig from nowlanf account from Home folder.

Show

Nowlan Freese added a comment - 17/Jan/24 10:55 AM On Mac Testing on 9.1.10 Successful: Loaded bigwig from nowlanf account from Community folder. Loaded bigwig from nowlanf account from Home folder. Loaded bam from nowlanf account from Home folder. Tested on main-JDK21-with-javafx-no-theme Successful: Loaded bam from nowlanf account from Home folder. Loaded bigwig from nowlanf account from Home folder.

Karthik Raveendran made changes - 17/Jan/24 3:14 PM

Assignee

Karthik Raveendran [ karthik ]