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Task #10170 (closed)

Opened 7 years ago

Closed 6 years ago

Last modified 6 years ago

Bug: FS mias import

Reported by: wmoore Owned by: mlinkert
Priority: major Milestone: 5.0.0-beta1
Component: Import Version: n.a.
Keywords: FS Cc: fs@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: FS Demo 2

Description

Importing mias / frans / siRNA_PRIM1_03102008 / 001-365700055641

java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {message=ImageReader.getSeriesCount: Current file should not be null; call setId(String) first, stacktrace=java.lang.IllegalStateException: ImageReader.getSeriesCount: Current file should not be null; call setId(String) first
    at loci.formats.FormatTools.assertId(FormatTools.java:713)
    at loci.formats.ImageReader.getReader(ImageReader.java:202)
    at loci.formats.ImageReader.getSeriesCount(ImageReader.java:433)
    at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
    at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
    at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
    at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:374)
    at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:265)
    at omero.cmd.HandleI.steps(HandleI.java:435)
    at omero.cmd.HandleI$1.doWork(HandleI.java:365)
    at omero.cmd.HandleI$1.doWork(HandleI.java:363)

Change History (9)

comment:1 Changed 7 years ago by wmoore

Josh:

Well, that would explain it:

                MIASReader miasReader = (MIASReader) baseReader;
                String currentFile = miasReader.getCurrentFile();
                reader.close();
                ....

I.e. special handling of mias.

comment:2 Changed 7 years ago by pwalczysko

Originally reported by ajpatterson, see Ticket #10121.

Import of file failed after about 13 mins.

mias/frans/MIAS 3 D set 2 july 13 2009/

It did create an empty screen in insight.

java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {message=ImageReader.getSeriesCount: Current file should not be null; call setId(String) first, stacktrace=java.lang.IllegalStateException: ImageReader.getSeriesCount: Current file should not be null; call setId(String) first
	at loci.formats.FormatTools.assertId(FormatTools.java:713)
	at loci.formats.ImageReader.getReader(ImageReader.java:202)
	at loci.formats.ImageReader.getSeriesCount(ImageReader.java:433)
	at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
	at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
	at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
	at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:374)
	at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:265)
	at omero.cmd.HandleI.steps(HandleI.java:435)
	at omero.cmd.HandleI$1.doWork(HandleI.java:365)
	at omero.cmd.HandleI$1.doWork(HandleI.java:363)
	at sun.reflect.GeneratedMethodAccessor245.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
	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 $Proxy65.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:416)
	at omero.cmd.HandleI.run(HandleI.java:359)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
	at ome.services.util.Executor$Impl$1.call(Executor.java:447)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
	at java.util.concurrent.FutureTask.run(FutureTask.java:123)
	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:595)
}

	at ome.formats.importer.ImportLibrary.getImportResponse(ImportLibrary.java:437)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:397)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageNew(OMEROGateway.java:6537)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6520)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:201)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1327)
	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.importImageNew(OMEROGateway.java:6584)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6520)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:201)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1327)
	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.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {message=ImageReader.getSeriesCount: Current file should not be null; call setId(String) first, stacktrace=java.lang.IllegalStateException: ImageReader.getSeriesCount: Current file should not be null; call setId(String) first
	at loci.formats.FormatTools.assertId(FormatTools.java:713)
	at loci.formats.ImageReader.getReader(ImageReader.java:202)
	at loci.formats.ImageReader.getSeriesCount(ImageReader.java:433)
	at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
	at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
	at loci.formats.ReaderWrapper.getSeriesCount(ReaderWrapper.java:338)
	at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:374)
	at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:265)
	at omero.cmd.HandleI.steps(HandleI.java:435)
	at omero.cmd.HandleI$1.doWork(HandleI.java:365)
	at omero.cmd.HandleI$1.doWork(HandleI.java:363)
	at sun.reflect.GeneratedMethodAccessor245.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
	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 $Proxy65.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:416)
	at omero.cmd.HandleI.run(HandleI.java:359)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
	at ome.services.util.Executor$Impl$1.call(Executor.java:447)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
	at java.util.concurrent.FutureTask.run(FutureTask.java:123)
	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:595)
}

	at ome.formats.importer.ImportLibrary.getImportResponse(ImportLibrary.java:437)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:397)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageNew(OMEROGateway.java:6537)
	... 13 more

comment:3 Changed 6 years ago by jmoore

  • Milestone changed from OMERO-4.5 to OMERO-5
  • Sprint set to FS Demo 2

Melissa, is there any way to make these changes without closing the reader? Or will just calling setId in the finally suffice? Any faster way to do it?

    /**
     * If available, populates overlays for a given set of pixels objects.
     * @param pixelsList Pixels objects to populate overlays for.
     * @param plateIds Plate object IDs to populate overlays for.
     */
    private void importOverlays(
            List<Pixels> pixelsList, List<Long> plateIds)
        throws FormatException, IOException
    {
        IFormatReader baseReader = reader.getImageReader().getReader();
        if (baseReader instanceof MIASReader)
        {
            try
            {
                MIASReader miasReader = (MIASReader) baseReader;
                String currentFile = miasReader.getCurrentFile();
                reader.close();
                miasReader.setAutomaticallyParseMasks(true);
                ServiceFactoryPrx sf = store.getServiceFactory();
                OverlayMetadataStore s = new OverlayMetadataStore();
                s.initialize(sf, pixelsList, plateIds);
                reader.setMetadataStore(s);
                miasReader.close();
                miasReader.setAutomaticallyParseMasks(true);
                miasReader.setId(currentFile);
                s.complete();
            }
            catch (ServerError e)
            {
                log.warn("Error while populating MIAS overlays.", e);
            }
            finally
            {
                reader.close();
                reader.setMetadataStore(store);
            }
        }
    }

comment:4 Changed 6 years ago by mlinkert

Should be possible to split the mask parsing out into a single method that you can call post-setId. You would then end up with something like:

        IFormatReader baseReader = reader.getImageReader().getReader();
        if (baseReader instanceof MIASReader)
        {
            try
            {
                MIASReader miasReader = (MIASReader) baseReader;
               
                ServiceFactoryPrx sf = store.getServiceFactory();
                OverlayMetadataStore s = new OverlayMetadataStore();
                s.initialize(sf, pixelsList, plateIds);
                miasReader.parseMasks(s);
                s.complete();
            }
            catch (ServerError e)
            {
                log.warn("Error while populating MIAS overlays.", e);
            }
        }

comment:5 Changed 6 years ago by jmoore

  • Owner changed from jmoore to mlinkert

Melissa, that would be great. The only question is if this should be a part of an interface somewhere so that we don't have to cast to MIASReader, but I'll leave that to you.

comment:7 Changed 6 years ago by jmoore

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

OMERO PR opened: ​https://github.com/openmicroscopy/openmicroscopy/pull/726

Should be available in tomorrow's build. Closing.

comment:8 Changed 6 years ago by jmoore <josh@…>

  • Remaining Time set to 0

(In [9a08cc38819e88a873b25d8d728cdc32cebe1952/ome.git] on branch develop) Use MIASReader.parseMasks (Fix #10170)

Make use of the newly added parseMasks method which doesn't
require closing and re-opening the reader. This commit needs:

openmicroscopy/bioformats@20308cee521787e9ecab341953f84c7e0d08a9b7

comment:9 Changed 6 years ago by Josh Moore <josh@…>

(In [70a839eb6992dae75eb3fdd9795b689ca7bcf7ab/ome.git] on branch develop) Merge pull request #726 from joshmoore/10170-fs-mias

Use MIASReader.parseMasks (Fix #10170)

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