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Task #2380 (closed)

Opened 14 years ago

Closed 14 years ago

BUG: importing Liff

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 (last modified by jburel)

Using latest revision
file DLD1...

    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:753)

Change History (10)

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

comment:3 Changed 14 years ago by cxallan

  • Status changed from reopened to closed

comment:4 Changed 14 years ago by jburel 

2010-05-17 14:44:57,294 61247      [2-thread-1] ERROR    ome.formats.importer.gui.ImportHandler  - Generic error while importing image.
java.lang.IllegalArgumentException: 0 must not be null and positive.
	at ome.xml.r201004.primitives.PositiveInteger.<init>(PositiveInteger.java:41)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:113)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:80)
	at loci.formats.in.PictReader.initFile(PictReader.java:314)
	at loci.formats.FormatReader.setId(FormatReader.java:1011)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
	at loci.formats.in.OpenlabReader.openBytes(OpenlabReader.java:207)
	at loci.formats.ImageReader.openBytes(ImageReader.java:384)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:170)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:209)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:246)
	at ome.formats.importer.OMEROWrapper.openPlane2D(OMEROWrapper.java:164)
	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$100(ImportHandler.java:59)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)

comment:5 Changed 14 years ago by jburel

  • Description modified (diff)
  • Status changed from closed to reopened

comment:6 Changed 14 years ago by cxallan

As of r7034 the failures:

2010-05-18 13:45:02,047 691023     [2-thread-1] ERROR  importer.gui.ErrorHandler$MyErrorHandler  - INTERNAL_EXCEPTION: /Volumes/ome/data_repo/test_images_good/liff/DLD1-MT-04_R3D_D3D.liff
java.lang.IllegalArgumentException: 0 must not be null and positive.
        at ome.xml.r201004.primitives.PositiveInteger.<init>(PositiveInteger.java:41)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:113)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:80)
        at loci.formats.in.PictReader.initFile(PictReader.java:314)
        at loci.formats.FormatReader.setId(FormatReader.java:1011)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
        at loci.formats.in.OpenlabReader.openBytes(OpenlabReader.java:207)
        at loci.formats.ImageReader.openBytes(ImageReader.java:384)
        at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:170)
        at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:209)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
        at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:246)
        at ome.formats.importer.OMEROWrapper.openPlane2D(OMEROWrapper.java:164)
        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)

2010-05-18 13:46:09,830 758806     [2-thread-1] ERROR  importer.gui.ErrorHandler$MyErrorHandler  - FILE_EXCEPTION: /Volumes/ome/data_repo/test_images_good/liff/e
mbryo2.liff
loci.formats.FormatException: Buffer too small (got 688128, expected 2064384).
        at loci.formats.FormatTools.checkBufferSize(FormatTools.java:721)
        at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:677)
        at loci.formats.in.OpenlabReader.openBytes(OpenlabReader.java:142)
        at loci.formats.ImageReader.openBytes(ImageReader.java:384)
        at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:170)
        at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:209)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
        at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:246)
        at ome.formats.importer.OMEROWrapper.openPlane2D(OMEROWrapper.java:164)
        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)

comment:7 Changed 14 years ago by cxallan

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

comment:8 Changed 14 years ago by mlinkert

Should be fixed in ​bio-formats:r6334.

comment:9 Changed 14 years ago by cxallan

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

comment:10 Changed 14 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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