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  1. IGB
  2. IGBF-3425

Investigate FileNotFoundException when loading data from BioViz Connect

        Details

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

          Description

          Situation: I am seeing the below error when loading data via BioViz Connect. To reproduce the issue, follow the instructions here.

          Task: Investigate the issue to determine the cause. If a fix is possible, modify this ticket and fix the issue.

          htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: /Users/lorainelab/.igb/fileCache/ZGF0YS5jeXZlcnNlLm9yZy9kYXYtYW5vbi9pcGxhbnQvaG9tZS9zaGFyZWQvQmlvVml6L3JuYXNlcS9BX3RoYWxpYW5hX0p1bl8y/MDA5L1NSUDIyMDE1Ny9yZWFkcy9TUlIxMDA2MDkwNS5iYW0uYmFp/cache/data.dat (No such file or directory)
	at htsjdk.samtools.FileInputResource$1.get(SamInputResource.java:247)
	at htsjdk.samtools.FileInputResource$1.get(SamInputResource.java:241)
	at htsjdk.samtools.util.Lazy.get(Lazy.java:25)
	at htsjdk.samtools.FileInputResource.asUnbufferedSeekableStream(SamInputResource.java:282)
	at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:341)
	at org.lorainelab.igb.bam.BAM.getSAMFileReader(BAM.java:114)
	at org.lorainelab.igb.bam.BAM.init(BAM.java:158)
	at org.lorainelab.igb.bam.XAM.getChromosomeList(XAM.java:100)
	at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1005)
	at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:995)
	at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
	at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at javax.swing.SwingWorker.run(SwingWorker.java:334)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)
Caused by: java.io.FileNotFoundException: /Users/lorainelab/.igb/fileCache/ZGF0YS5jeXZlcnNlLm9yZy9kYXYtYW5vbi9pcGxhbnQvaG9tZS9zaGFyZWQvQmlvVml6L3JuYXNlcS9BX3RoYWxpYW5hX0p1bl8y/MDA5L1NSUDIyMDE1Ny9yZWFkcy9TUlIxMDA2MDkwNS5iYW0uYmFp/cache/data.dat (No such file or directory)
	at java.io.RandomAccessFile.open0(Native Method)
	at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
	at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
	at htsjdk.samtools.seekablestream.SeekableFileStream.<init>(SeekableFileStream.java:47)
	at htsjdk.samtools.FileInputResource$1.get(SamInputResource.java:245)
	... 16 more

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              relates to

              Task - A task that needs to be done. IGBF-3379 Edit SCR annotations to use R6 instead of R5 syntax and observe the effects

              • Major - Major loss of function.
              • Closed

                Activity

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                kgopu Kaushik Gopu added a comment - - edited

                Tested on windows:

                • Followed the instructions provided in the documentation to recreate the issue. However, no
                  exceptions were popped up while loading the data and everything works usual. After loading
                  data, I can see the blue colored track appearing on IGB screen.
                • It could be an OS issue(may be MAC is not allowing to cache the files).
                • No runtime errors were found in logs.
                  Moving ticket to first level review.
                Show
                kgopu Kaushik Gopu added a comment - - edited Tested on windows: Followed the instructions provided in the documentation to recreate the issue. However, no exceptions were popped up while loading the data and everything works usual. After loading data, I can see the blue colored track appearing on IGB screen. It could be an OS issue(may be MAC is not allowing to cache the files). No runtime errors were found in logs. Moving ticket to first level review.
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                Ann notes: We had issues with file names in the past on Windows. May be related?
                NF notes: Recall that this issue appeared on a Mac system only.

                Show
                ann.loraine Ann Loraine added a comment - - edited Ann notes: We had issues with file names in the past on Windows. May be related? NF notes: Recall that this issue appeared on a Mac system only.
                Hide
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                nfreese Nowlan Freese added a comment -

                When View in IGB is clicked in BioViz Connect on SRR10060893.bam, two calls are made to getSAMFileReader() in BAM.java. In the first call to BAM.java there is a folder in .igb/fileCache with a data.dat file. After the following line of code, a second folder appears in .igb/fileCache that also contains a data.dat file:

                Optional<InputStream> indexStream = remoteFileCacheService.getFilebyUrl(baiUri.toURL(), false);

                On the second time through getSAMFileReader() after the above code, the second folder in .igb/fileCache contents are deleted. This seems to be the cause of the error as the data.dat file is missing from that .igb/fileCache folder. However, the other .igb/fileCache folder still contains a data.dat file. Data load fine and subsequent clicks of View in IGB do not generate additional errors.

                Since this issue is consistent, but does not create affect IGB usability, I am placing it in the backlog.

                Show
                nfreese Nowlan Freese added a comment - When View in IGB is clicked in BioViz Connect on SRR10060893.bam, two calls are made to getSAMFileReader() in BAM.java. In the first call to BAM.java there is a folder in .igb/fileCache with a data.dat file. After the following line of code, a second folder appears in .igb/fileCache that also contains a data.dat file: Optional<InputStream> indexStream = remoteFileCacheService.getFilebyUrl(baiUri.toURL(), false ); On the second time through getSAMFileReader() after the above code, the second folder in .igb/fileCache contents are deleted. This seems to be the cause of the error as the data.dat file is missing from that .igb/fileCache folder. However, the other .igb/fileCache folder still contains a data.dat file. Data load fine and subsequent clicks of View in IGB do not generate additional errors. Since this issue is consistent, but does not create affect IGB usability, I am placing it in the backlog.

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    nfreese Nowlan Freese
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                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: