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Task #9396 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: NPE importing SVS Images

Reported by: rleigh Owned by: mlinkert
Priority: critical Milestone: OMERO-4.4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Files are on squig in "/ome/data_repo/Scotts User Images/Aperio? Scanned Images/Aperio? image 4" (78153.svs, 78192.svs, 78204.svs).

java.lang.NullPointerException
	at loci.formats.in.SVSReader.initStandardMetadata(SVSReader.java:199)
	at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:98)
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:519)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.formats.ImageReader.setId(ImageReader.java:695)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6335)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6384)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NullPointerException
	at loci.formats.in.SVSReader.initStandardMetadata(SVSReader.java:199)
	at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:98)
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:519)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.formats.ImageReader.setId(ImageReader.java:695)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6335)
	... 11 more

Change History (1)

comment:1 Changed 12 years ago by mlinkert

  • Resolution set to fixed
  • Status changed from new to closed

Fixed with this commit: ​https://github.com/melissalinkert/bioformats/commit/0706976736054730b91cf8d261a17111c03ef40f

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