Task #2388 (closed)
Opened 9 years ago
Closed 9 years ago
BUG: importing fv1000
| 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
2010-05-17 11:15:50,165 852758 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - Generic error while importing image. java.lang.NullPointerException at ome.formats.OMEROMetadataStoreClient.handleAbstractLightSource(OMEROMetadataStoreClient.java:1079) at ome.formats.OMEROMetadataStoreClient.getIObjectContainer(OMEROMetadataStoreClient.java:2322) at ome.formats.OMEROMetadataStoreClient.setLaserID(OMEROMetadataStoreClient.java:4401) at loci.formats.meta.FilterMetadata.setLaserID(FilterMetadata.java:973) at loci.formats.in.FV1000Reader.populateMetadataStore(FV1000Reader.java:941) at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:817)
Change History (17)
comment:1 Changed 9 years ago by cxallan
- Status changed from new to assigned
comment:2 Changed 9 years ago by cxallan
comment:3 Changed 9 years ago by cxallan
See #2381 for latest status. Test file: /ome/data_repo/test_images_good/fv1000/PIP2 ESCV Z 1 after.oib
comment:4 Changed 9 years ago by cxallan
comment:5 Changed 9 years ago by jmoore
comment:6 Changed 9 years ago by cxallan
As of r7033 PIP2 ESCV Z 1 after.oib imports but another file from the same directory (PIP2 ESCV control Z 1.oib does not:
2010-05-18 13:35:59,806 148782 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - Format exception while importing image.
loci.formats.FormatException: File PIP2 ESCV Z 1 after.oif.files/PIP2 ESCV Z 1 after_C001Z041.pty not found.
at loci.formats.in.FV1000Reader.getFile(FV1000Reader.java:1320)
at loci.formats.in.FV1000Reader.getIniFile(FV1000Reader.java:1403)
at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:589)
at loci.formats.FormatReader.setId(FormatReader.java:1011)
at loci.formats.ImageReader.setId(ImageReader.java:644)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:213)
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399)
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
With bio-formats:r6301 these are now failing with:
2010-05-18 15:43:24,846 1239255 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - INTERNAL_EXCEPTION: /Volumes/ome/data_repo/test_images_good/fv1000/PIP2 ESCV Z 1 after.oib Error processing references. at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:150) at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1659) at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:251) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:437) 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) Caused by: java.lang.RuntimeException: Unable to synchronize reference Filter:0:1 --> omero.model.LightPath:0:1:0 at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:121) ... 15 more
comment:8 Changed 9 years ago by cxallan
(In [7038]) Correct LightPath? support. (See #2388, #2358)
comment:9 Changed 9 years ago by cxallan
With r7038 the files fail with:
2010-05-18 16:55:22,037 1838363 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - Generic error while importing image.
java.lang.RuntimeException: omero.ApiUsageException
serverStackTrace = "ome.conditions.ApiUsageException: Unable to handle LightPath --> Filter reference: Filter:0:0
at ome.formats.OMEROMetadataStore.handleReference(OMEROMetadataStore.java:1046)
at ome.formats.OMEROMetadataStore.updateReferences(OMEROMetadataStore.java:360)
at ome.services.blitz.impl.MetadataStoreI$5.doWork(MetadataStoreI.java:214)
at sun.reflect.GeneratedMethodAccessor199.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:409)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:144)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175)
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 $Proxy54.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:339)
at ome.services.throttling.Adapter.run(Adapter.java:51)
at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:146)
at ome.services.blitz.impl.MetadataStoreI.updateReferences_async(MetadataStoreI.java:209)
at omero.api._MetadataStoreTie.updateReferences_async(_MetadataStoreTie.java:99)
at omero.api._MetadataStoreDisp.___updateReferences(_MetadataStoreDisp.java:194)
at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:341)
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) "
comment:10 Changed 9 years ago by cxallan
(In [7039]) Further LightPath? emission and excitation filter reference fixes. (See #2388, #2358)
comment:11 follow-up: ↓ 13 Changed 9 years ago by cxallan
With r7039 we're back to the single file failing to import. loci.formats.FormatException: File PIP2 ESCV Z 1 after.oif.files/PIP2 ESCV Z 1 after_C001Z041.pty not found., etc.
comment:12 Changed 9 years ago by cxallan
- Owner changed from bwzloranger to mlinkert-x
- Status changed from assigned to new
comment:13 in reply to: ↑ 11 ; follow-up: ↓ 14 Changed 9 years ago by mlinkert
Replying to cxallan:
With r7039 we're back to the single file failing to import. loci.formats.FormatException: File PIP2 ESCV Z 1 after.oif.files/PIP2 ESCV Z 1 after_C001Z041.pty not found., etc.
setId on 'test_images_good/fv1000/PIP2 ESCV Z 1 after.oib' works for me with bio-formats:r6339. Can you either post the full stack trace or confirm that updating Bio-Formats solves the problem?
comment:14 in reply to: ↑ 13 Changed 9 years ago by cxallan
Replying to mlinkert-x:
Replying to cxallan:
With r7039 we're back to the single file failing to import. loci.formats.FormatException: File PIP2 ESCV Z 1 after.oif.files/PIP2 ESCV Z 1 after_C001Z041.pty not found., etc.
setId on 'test_images_good/fv1000/PIP2 ESCV Z 1 after.oib' works for me with bio-formats:r6339. Can you either post the full stack trace or confirm that updating Bio-Formats solves the problem?
It's hiding in the other ticket, pasted here for brevity:
2010-05-18 21:59:42,396 51778 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: /Users/callan/testimages/fv1000/PIP2 ESCV control Z 1.oib
loci.formats.FormatException: File PIP2 ESCV Z 1 after.oif.files/PIP2 ESCV Z 1 after_C001Z041.pty not found.
at loci.formats.in.FV1000Reader.getFile(FV1000Reader.java:1317)
at loci.formats.in.FV1000Reader.getIniFile(FV1000Reader.java:1400)
at loci.formats.in.FV1000Reader.initFile(FV1000Reader.java:591)
at loci.formats.FormatReader.setId(FormatReader.java:1012)
at loci.formats.ImageReader.setId(ImageReader.java:644)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:213)
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399)
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)
The above fv1000 folder is identical to that within /ome/data_repo/test_images_good.
comment:15 Changed 9 years ago by cxallan
- Status changed from new to assigned
comment:16 Changed 9 years ago by cxallan
- Owner changed from mlinkert-x to cxallan
comment:17 Changed 9 years ago by cxallan
- Remaining Time set to 0
- Resolution set to fixed
- Status changed from assigned to closed
(In [7117]) Updating to bio-formats:r6399. (Fixes #2388)
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As of r7024 fails with:
java.lang.RuntimeException: omero.ApiUsageException serverStackTrace = "ome.conditions.ApiUsageException: Missing object handler for object type: class ome.model.acquisition.TransmittanceRange at ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:267) at ome.services.blitz.impl.MetadataStoreI$4.doWork(MetadataStoreI.java:198) at sun.reflect.GeneratedMethodAccessor288.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:409) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.security.basic.EventHandler.invoke(EventHandler.java:144) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175) 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 $Proxy54.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:339) at ome.services.throttling.Adapter.run(Adapter.java:51) at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89) at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:146) at ome.services.blitz.impl.MetadataStoreI.updateObjects_async(MetadataStoreI.java:183) at omero.api._MetadataStoreTie.updateObjects_async(_MetadataStoreTie.java:92) at omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:173) at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:337) 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) "