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Task #11252 (closed)

Opened 6 years ago

Closed 4 years ago

Bug: OMEROMetadataStoreClient.postProcess fails to import ListAnnotations

Reported by: rleigh Owned by: sbesson
Priority: critical Milestone: OMERO-5.1.4
Component: Import Version: 4.4.8
Keywords: n.a. Cc: jburel, mlinkert, mtbcarroll, sbesson
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Affects both dev_4_4 and develop. File attached which triggers the problem made by Andrew.

Error processing references.
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:159)
	at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:2075)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:362)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:550)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6357)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1336)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.RuntimeException: Unable to synchronize reference Annotation:1 --> omero.model.Annotation:0
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:130)
	... 15 more

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6411)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1336)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: Error processing references.
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:159)
	at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:2075)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:362)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:550)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6357)
	... 11 more
Caused by: java.lang.RuntimeException: Unable to synchronize reference Annotation:1 --> omero.model.Annotation:0
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:130)
	... 15 more

Attachments (1)

fail-test-5.ome​ (7.2 KB) - added by rleigh 6 years ago.
Triggers import failure

Download all attachments as: .zip

Change History (8)

Changed 6 years ago by rleigh

Triggers import failure

comment:1 Changed 6 years ago by rleigh

  • Cc omero-team added
  • Owner jburel deleted

comment:2 Changed 4 years ago by jamoore

  • Cc jburel mlinkert mtbcarroll sbesson added; omero-team removed

Does anyone know the state of this?

comment:3 Changed 4 years ago by jburel

Probably to be covered as part of ​https://trello.com/c/22XfjucX/159-export-re-import
i.e. 5.1.3

comment:4 Changed 4 years ago by jamoore

  • Milestone changed from Unscheduled to 5.1.3

Moving it there, then. If anyone knows this to be more pressing, bump the milestone.

comment:5 Changed 4 years ago by jamoore

  • Milestone changed from 5.1.4 to OMERO-5.1.4

Splitting 5.1.4 due to milestone decoupling

comment:6 Changed 4 years ago by sbesson

  • Owner set to sbesson

comment:7 Changed 4 years ago by sbesson

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

See ​https://github.com/openmicroscopy/openmicroscopy/pull/4174

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