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  1. IGB
  2. IGBF-3514

Investigate errors in IGB when View in IGB is invoked

        Details

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

          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)

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              Task - A task that needs to be done. IGBF-3510 Smoke Test JDK 21 in Windows

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment - - 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 Ann Loraine added a comment - - 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
                Hide
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                ann.loraine Ann Loraine added a comment -

                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.

                Show
                ann.loraine Ann Loraine added a comment - 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.
                Hide
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                ann.loraine Ann Loraine added a comment - - 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 Ann Loraine added a comment - - 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.)
                Hide
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                karthik Karthik Raveendran added a comment - - 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
                Show
                karthik Karthik Raveendran added a comment - - 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
                Hide
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                ann.loraine Ann Loraine added a comment - - 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 Ann Loraine added a comment - - 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
                Hide
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                nfreese Nowlan Freese added a comment -

                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
                nfreese Nowlan Freese added a comment - 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.

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    karthik Karthik Raveendran
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                    Dates

                    • Created:
                      Updated:
                      Resolved: