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Cannot import images coming from 2 different groups during the same connection #24

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Rdornier opened this issue Sep 17, 2024 · 1 comment

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@Rdornier
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A user is part of 2 different groups A and B on OMERO.

  • If an image is imported from group A, the image is imported in QuPath without any issue.
  • Then, if we try to import a second image from the group B, it fails with the following error :

15:22:31.722	[project-import11]	ERROR	qupath.ext.omero.core.imageserver.OmeroImageServer	Couldn't create pixel API reader	java.io.IOException: Couldn't find requested image of ID 516335
	at qupath.ext.omero.core.pixelapis.ice.IceReader.<init>(IceReader.java:111)
	at qupath.ext.omero.core.pixelapis.ice.IceAPI.createReader(IceAPI.java:143)
	at qupath.ext.omero.core.imageserver.OmeroImageServer.create(OmeroImageServer.java:111)
	at qupath.ext.omero.core.imageserver.OmeroImageServerBuilder.lambda$buildServer$0(OmeroImageServerBuilder.java:30)
	at java.base/java.util.Optional.flatMap(Unknown Source)
	at qupath.ext.omero.core.imageserver.OmeroImageServerBuilder.buildServer(OmeroImageServerBuilder.java:30)
	at qupath.lib.images.servers.ImageServerBuilder$DefaultImageServerBuilder.buildOriginal(ImageServerBuilder.java:350)
	at qupath.lib.images.servers.ImageServerBuilder$AbstractServerBuilder.build(ImageServerBuilder.java:174)
	at qupath.lib.gui.commands.ProjectImportImagesCommand.initializeEntry(ProjectImportImagesCommand.java:727)
	at qupath.lib.gui.commands.ProjectImportImagesCommand$1.lambda$call$2(ProjectImportImagesCommand.java:468)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)

My guess is that the security context is not updated to access to the correct group (I already had this issue on my side, reported here BIOP/qupath-extension-biop-omero#7).
this.securityContext = new SecurityContext(groupId); to switch group.

@Rylern
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Rylern commented Feb 20, 2025

So I was able to partially fix this in v0.1.0-rc6. However, there are two limitations:

  • Two images of two different groups cannot be read at the same time (see this issue). If an image is open, all images of different groups are now automatically closed.
  • If you open an image belonging to group A, then open an image of group B, then open an image of group A, an exception is thrown (see this issue). I wasn't able to find a workaround for that.

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