Bug: IndexOutOfBoundsException during import in Insight

[mtbcarroll]

On current gretzky, if I try to import data_repo/test_images_metadata/leica-lif/Rosier.lif or a MIAS plate or various other files, Insight gives me,

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
	at java.util.ArrayList.get(ArrayList.java:322)
	at org.openmicroscopy.shoola.agents.fsimporter.util.FileImportComponent.getFileSetID(FileImportComponent.java:840)
	at org.openmicroscopy.shoola.agents.fsimporter.util.FileImportComponent.setStatus(FileImportComponent.java:1124)
	at org.openmicroscopy.shoola.agents.fsimporter.view.ImporterUIElement.setImportedFile(ImporterUIElement.java:722)
	at org.openmicroscopy.shoola.agents.fsimporter.view.ImporterComponent.setImportedFile(ImporterComponent.java:316)
	at org.openmicroscopy.shoola.agents.fsimporter.ImagesImporter.update(ImagesImporter.java:121)
	at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:75)
	at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:708)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:669)
	at java.awt.EventQueue$2.run(EventQueue.java:667)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:678)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

[bpindelski]

If testing locally, this needs Colin's import log file branch merged in.

[pwalczysko]

@bpindelski : not sure - I think I do not have this branch ​https://github.com/openmicroscopy/openmicroscopy/pull/1062 in - I did not merge it knowingly, and also my subsequent check did not find the commits from this branch in my local branch => I did not have it merged in. All I have is josh's kryo-memoizer and josh's fs-file-caching. This is all I have merged in. But, I still get the bug on my local build.

[bpindelski]

This is indirectly caused by the setStatus() method in FileImportComponent in Insight. The method modifies the passed in list of images, and then when the getFileSetID() method gets executed, the list is empty, hence the exception. More investigation needed to find a fix.

[pwalczysko]

Hit this exception again importing zeiss-czi/raw.czi. During testing of ​https://github.com/openmicroscopy/bioformats/pull/491.

[bpindelski]

Fixed in ​https://github.com/openmicroscopy/openmicroscopy/pull/1116.

[Blazej Pindelski <bpindelski@…>]

(In [dcfdf34fe0b4a8253840d965a83960c5656c29fd/ome.git] on branch develop) Fix IOOB when importing MIFs (see #10772)

[Josh Moore <josh@…>]

(In [43b619ab2eda7230a9e67cef5c0dfb16b68d1c49/ome.git] on branch develop) Merge pull request #1116 from bpindelski/ioob-import

Fix IOOB when importing MIFs (see #10772)