BUG:APNGReader, ArrayIndexOutOfBounds

[omero-qa]

​https://www.openmicroscopy.org/qa2/qa2/qa/feedback/11038/

java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {message=5580, stacktrace=java.lang.ArrayIndexOutOfBoundsException: 5580
	at loci.formats.in.APNGReader.decode(APNGReader.java:482)
	at loci.formats.in.APNGReader.openBytes(APNGReader.java:150)
	at loci.formats.ImageReader.openBytes(ImageReader.java:453)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:196)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
	at ome.services.blitz.repo.ManagedImportRequestI.parseDataByPlane(ManagedImportRequestI.java:747)
	at ome.services.blitz.repo.ManagedImportRequestI.parseData(ManagedImportRequestI.java:678)
	at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:557)
	at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:408)
	at omero.cmd.HandleI.steps(HandleI.java:437)
	at omero.cmd.HandleI$1.doWork(HandleI.java:365)
	at omero.cmd.HandleI$1.doWork(HandleI.java:361)
	at sun.reflect.GeneratedMethodAccessor296.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:566)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at com.sun.proxy.$Proxy72.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:447)
	at omero.cmd.HandleI.run(HandleI.java:359)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
	at ome.services.util.Executor$Impl$1.call(Executor.java:488)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)
}

	at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:656)
	at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:301)
	at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
	at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
	at IceInternal.Incoming.invoke(Incoming.java:222)
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
	at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
	at Ice.ConnectionI.message(ConnectionI.java:1213)
	at IceInternal.ThreadPool.run(ThreadPool.java:321)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Unknown Source)

[dlindner]

Tried to fix it, but couldn't figure out, what's happening in this APNGReader.decode() method. Have to pass it on to you Melissa.

[mlinkert]

Fixed with : ​https://github.com/openmicroscopy/bioformats/pull/1855

[Melissa Linkert <melissa@…>]

(In [a700cf7e4a8eb5c9da269c90b6686ac7499e8330/bioformats.git] on branch develop) PNG: fix interlaced images that have a width or height that is not a multiple of 8

Fixes #12850.

See
​http://www.libpng.org/pub/png/spec/1.2/PNG-DataRep.html#DR.Interlaced-data-order