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Task #2390 (closed)

Opened 9 years ago

Closed 9 years ago

BUG: importing bigtiff

Reported by: jburel Owned by: cxallan
Priority: blocker Milestone: OMERO-Beta4.2
Component: Import 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 

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)
                        	at ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:182)

Change History (7)

comment:1 Changed 9 years ago by cxallan

  • Status changed from new to closed

comment:2 Changed 9 years ago by jburel

  • Status changed from closed to reopened 
2010-05-17 14:52:14,915 498868     [2-thread-1] ERROR    ome.formats.importer.gui.ImportHandler  - Generic error while importing image.
loci.common.enumeration.EnumException: Unable to find IFDType with code: 32768
	at loci.formats.tiff.IFDType.get(IFDType.java:84)
	at loci.formats.tiff.TiffParser.readTiffIFDEntry(TiffParser.java:910)
	at loci.formats.tiff.TiffParser.getIFD(TiffParser.java:329)
	at loci.formats.tiff.TiffParser.getIFDs(TiffParser.java:161)
	at loci.formats.tiff.TiffParser.getNonThumbnailIFDs(TiffParser.java:199)
	at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:293)
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:494)
	at loci.formats.FormatReader.setId(FormatReader.java:1011)

comment:3 Changed 9 years ago by cxallan

As of r7040 and ​bio-formats:r6301 still fails with:

2010-05-18 17:59:53,108 159627     [2-thread-1] DEBUG      ome.formats.importer.gui.GuiImporter  - loci.common.enumeration.EnumException: Unable to find IFDType with code: 52678
        at loci.formats.tiff.IFDType.get(IFDType.java:84)
        at loci.formats.tiff.TiffParser.readTiffIFDEntry(TiffParser.java:910)
        at loci.formats.tiff.TiffParser.getIFD(TiffParser.java:329)
        at loci.formats.tiff.TiffParser.getIFDs(TiffParser.java:161)
        at loci.formats.tiff.TiffParser.getNonThumbnailIFDs(TiffParser.java:199)
        at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:293)
        at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:494)
        at loci.formats.FormatReader.setId(FormatReader.java:1012)
        at loci.formats.DelegateReader.setId(DelegateReader.java:216)
        at loci.formats.ImageReader.setId(ImageReader.java:644)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:213)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399)
        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)

comment:4 Changed 9 years ago by cxallan

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

comment:5 Changed 9 years ago by mlinkert

Fixed in ​bio-formats:r6339.

comment:6 Changed 9 years ago by cxallan

  • Owner changed from mlinkert-x to cxallan
  • Status changed from new to assigned

comment:7 Changed 9 years ago by cxallan

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

(In [7043]) Upgrading to ​bio-formats:r6340. (Fixes #2358, #2377, #2380, #2381, #2390)

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