Task #2380 (closed)
Opened 9 years ago
Closed 9 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 9 years ago by cxallan
- Status changed from new to closed
comment:2 Changed 9 years ago by cxallan
- Status changed from closed to reopened
comment:3 Changed 9 years ago by cxallan
- Status changed from reopened to closed
comment:4 Changed 9 years ago by jburel
comment:5 Changed 9 years ago by jburel
- Description modified (diff)
- Status changed from closed to reopened
comment:6 Changed 9 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 9 years ago by cxallan
- Owner changed from bwzloranger to mlinkert-x
- Status changed from reopened to new
comment:8 Changed 9 years ago by mlinkert
Should be fixed in bio-formats:r6334.
comment:9 Changed 9 years ago by cxallan
- Owner changed from mlinkert-x to cxallan
- Status changed from new to assigned
comment:10 Changed 9 years ago by cxallan
- Remaining Time set to 0
- Resolution set to fixed
- Status changed from assigned to closed
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