Bug: View during Big image import removes lock file.

[wmoore]

Importing this file from_skyking\leica-lif\chris\free edge 6.lif (16 images) with the Importer, tried browsing the dataset and thumbnails in web after the first image had 'stored pixels'.

This is caused by the lock file being deleted when another thread checks whether or not the file is checked in isLockedByOthers (found by Chris).

[cxallan]

Importer error (moved out of description)

2011-05-30 09:37:52,695 838209     [2-thread-1] DEBUG        ome.formats.importer.ImportLibrary  - Plane:3 X:512 Y:1024 TileWidth:256 TileHeight:16 arrayBuf.length:4096
2011-05-30 09:37:52,755 838269     [2-thread-1] DEBUG        ome.formats.importer.ImportLibrary  - Plane:3 X:768 Y:1024 TileWidth:256 TileHeight:16 arrayBuf.length:4096
2011-05-30 09:37:52,830 838344     [2-thread-1] DEBUG        ome.formats.importer.ImportLibrary  - Plane:3 X:1024 Y:1024 TileWidth:256 TileHeight:16 arrayBuf.length:4096
2011-05-30 09:37:52,890 838404     [2-thread-1] DEBUG        ome.formats.importer.ImportLibrary  - Plane:3 X:1280 Y:1024 TileWidth:112 TileHeight:16 arrayBuf.length:1792
2011-05-30 09:37:52,982 838496     [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - IMPORT_STEP Image: 4 Series: 3 Total Series: 16
2011-05-30 09:37:52,984 838498     [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - DATA_STORED
2011-05-30 09:37:52,987 838501     [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - DATASET_STORED
2011-05-30 09:37:54,043 839557     [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - INTERNAL_EXCEPTION: /Users/will/Documents/biology-data/Test-Import-Images/Leica  LIF/chris/free edge 6.lif
omero.ResourceError
    serverStackTrace = "ome.conditions.ResourceError: FormatException: c:\OMERO\Pixels\795_pyramid
                        Invalid TIFF file
                        	at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:72)
                        	at ome.io.bioformats.BfPixelBuffer.getTileSize(BfPixelBuffer.java:483)
                        	at ome.io.bioformats.BfPyramidPixelBuffer.getTileSize(BfPyramidPixelBuffer.java:1156)
                        	at ome.services.RawPixelsBean.getTileSize(RawPixelsBean.java:698)
                        	at sun.reflect.GeneratedMethodAccessor1253.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
                        	at java.lang.reflect.Method.invoke(Unknown Source)
                        	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.security.basic.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
                        	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:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy85.getTileSize(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor1253.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
                        	at java.lang.reflect.Method.invoke(Unknown Source)
                        	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.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy85.getTileSize(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor1297.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
                        	at java.lang.reflect.Method.invoke(Unknown Source)
                        	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
                        	at ome.services.throttling.Callback.run(Callback.java:56)
                        	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
                        	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:136)
                        	at ome.services.blitz.impl.AbstractPyramidServant.getTileSize_async(AbstractPyramidServant.java:53)
                        	at omero.api._RawPixelsStoreTie.getTileSize_async(_RawPixelsStoreTie.java:78)
                        	at omero.api._PyramidServiceDisp.___getTileSize(_PyramidServiceDisp.java:216)
                        	at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1237)
                        	at IceInternal.Incoming.invoke(Incoming.java:159)
                        	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                        	at Ice.ConnectionI.message(ConnectionI.java:972)
                        	at IceInternal.ThreadPool.run(ThreadPool.java:577)
                        	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                        	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                        "
    serverExceptionClass = "ome.conditions.ResourceError"
    message = "FormatException: c:\OMERO\Pixels\795_pyramid
               Invalid TIFF file"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._RawPixelsStoreDelM.getTileSize(_RawPixelsStoreDelM.java:119)
	at omero.api.RawPixelsStorePrxHelper.getTileSize(RawPixelsStorePrxHelper.java:184)
	at omero.api.RawPixelsStorePrxHelper.getTileSize(RawPixelsStorePrxHelper.java:156)
	at ome.formats.OMEROMetadataStoreClient.getTileSize(OMEROMetadataStoreClient.java:2465)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:700)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:216)
	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: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)

2011-05-30 09:37:54,051 839565     [2-thread-1] ERROR      ome.formats.importer.gui.GuiImporter  - EXCEPTION_EVENT

[jmoore <josh@…>]

(In [bfe035dd210cc46a7e6aa06fcedf349659ec28a9/ome.git] on branch develop) Prevent deletion of lockFile (Fix #5655)

[cxallan]

Reopening for the race condition of reading before writing. This happens when there is a creation of a thumbnail store or rendering engine before writing has happened or archiving/params has been populated.

[Chris Allan <callan@…>]

(In [d7a15b8f443d94d41bf6ff64ce60b0c4a4edc37d/ome.git] on branch develop) Merge branch 'bug/5655' into develop

Fixes #5655.