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Task #2367 (closed)

Opened 14 years ago

Closed 14 years ago

BUG: svs

Reported by: jburel Owned by: cxallan
Priority: blocker Milestone: OMERO-Beta4.2
Component: General Version: n.a.
Keywords: n.a. Cc: cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2010-05-13 (9)

Description

file 5794_001.svs

serverExceptionClass = "ome.conditions.InternalException"
    message = " Wrapped Exception: (java.lang.NullPointerException):
               null"
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:1800)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:257)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:436)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
	at java.util.concurrent.FutureTask.run(FutureTask.java:123)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:172)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:651)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:676)
	at java.lang.Thread.run(Thread.java:613)
Caused by: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NullPointerException):
                        null
                        	at ome.formats.OMEROMetadataStore.handle(OMEROMetadataStore.java:582)

Change History (7)

comment:1 Changed 14 years ago by cxallan

  • Status changed from new to closed

comment:2 Changed 14 years ago by cxallan

  • Status changed from closed to reopened

Problem with test_images_good/svs/UMD001_ORO.svs:

java.lang.RuntimeException: File is neither valid JP2 file nor valid JPEG 2000 codestream
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:696)
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.<init>(J2KReadState.java:189)
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader.read(J2KImageReader.java:443)
	at javax.imageio.ImageReader.read(ImageReader.java:923)
	at loci.formats.services.JAIIIOServiceImpl.readImage(JAIIIOServiceImpl.java:121)
	at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:184)
	at loci.formats.codec.BaseCodec.decompress(BaseCodec.java:170)
	at loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:175)
	at loci.formats.tiff.TiffParser.getTile(TiffParser.java:560)
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:686)
	at loci.formats.in.SVSReader.openBytes(SVSReader.java:69)
	at loci.formats.ImageReader.openBytes(ImageReader.java:384)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:170)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:117)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:180)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:252)
	at ome.formats.importer.OMEROWrapper.openPlane2D(OMEROWrapper.java:160)
	at ome.formats.importer.OMEROWrapper.openPlane2D(OMEROWrapper.java:130)
	at ome.formats.importer.ImportLibrary.writeDataPlanarBased(ImportLibrary.java:759)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:641)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:474)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	at ome.formats.importer.gui.ImportHandler.access$1(ImportHandler.java:149)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:637)
Caused by: java.lang.Error: File is neither valid JP2 file nor valid JPEG 2000 codestream
	at jj2000.j2k.fileformat.reader.FileFormatReader.readFileFormat(FileFormatReader.java:182)
	at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:418)
	... 34 more

comment:3 Changed 14 years ago by cxallan

  • Owner changed from bwzloranger to mlinkert-x
  • Status changed from reopened to new

comment:4 Changed 14 years ago by mlinkert

Should be fixed in ​bio-formats:r6350. This exception occurred because some of the pixel data is actually missing, so expect to see a black band along the bottom of the image.

comment:5 Changed 14 years ago by cxallan

  • Status changed from new to assigned

comment:6 Changed 14 years ago by cxallan

  • Owner changed from mlinkert-x to cxallan

comment:7 Changed 14 years ago by cxallan

  • Remaining Time set to 0
  • Resolution set to fixed
  • Status changed from assigned to closed

(In [7066]) Updating to ​bio-formats:r6355. (Fixes #2358, #2367, #2368, #2406)

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