[IGBF-3425] Investigate FileNotFoundException when loading data from BioViz Connect - JIRA UNCC

Details

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

Story Points:
1
Epic Link:
Maintain BioViz Connect

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

Attachments

Issue Links

relates to

IGBF-3379 Edit SCR annotations to use R6 instead of R5 syntax and observe the effects

Closed

Activity

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Nowlan Freese created issue - 30/Aug/23 2:24 PM

Nowlan Freese made changes - 30/Aug/23 2:24 PM

Field	Original Value	New Value
Epic Link		IGBF-2376 [ 18533 ]

Nowlan Freese made changes - 30/Aug/23 2:24 PM

Link

This issue relates to ~~IGBF-3379~~ [ ~~IGBF-3379~~ ]

Ann Loraine made changes - 04/Sep/23 9:25 PM

Sprint

Fall 1 2023 Sep 5 [ 178 ]

Fall 1 - Sep [ 82 ]

Ann Loraine made changes - 04/Sep/23 9:25 PM

Rank

Ranked higher

Nowlan Freese made changes - 05/Sep/23 10:29 AM

Assignee

Kaushik Gopu [ kgopu ]

Nowlan Freese made changes - 05/Sep/23 11:56 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Kaushik Gopu added a comment - 05/Sep/23 3:46 PM - 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

Kaushik Gopu added a comment - 05/Sep/23 3:46 PM - 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.

Kaushik Gopu made changes - 05/Sep/23 3:48 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 06/Sep/23 9:59 AM

Assignee

Kaushik Gopu [ kgopu ]

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Ann Loraine added a comment - 06/Sep/23 10:16 AM - 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.

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Ann Loraine added a comment - 06/Sep/23 10:16 AM - 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.

Nowlan Freese made changes - 06/Sep/23 1:55 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 06/Sep/23 1:55 PM

Assignee

Nowlan Freese [ nfreese ]

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Nowlan Freese added a comment - 06/Sep/23 3:28 PM

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

Nowlan Freese added a comment - 06/Sep/23 3:28 PM 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.

Nowlan Freese made changes - 06/Sep/23 3:28 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 06/Sep/23 3:28 PM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Nowlan Freese made changes - 06/Sep/23 3:28 PM

Sprint

Fall 1 - Sep 5 [ 82 ]