BUG: Import OME-TIFF failures

[ajpatterson]

Multiple file failures:

Any ome-tiff or ome-xml file that uses namespaces seams to be failing with a lot of message like:

[ ome.xml.model.Pixels] () Expecting node name of Pixels  got OME:Pixels
[ome.xml.model.Channel] () Expecting node name of Channel got OME:Channel
[ome.xml.model.BinData] () Expecting node name of BinData got Bin:BinData

List of files:

ome/components/specification/Samples/OmeFiles/2011-06/
 LAMBDA-modulo-sample.ome.tiff
 SPIM-modulo-sample.ome.tiff
 6x4y1z1t3c8b-swatch-upgrade.ome

ome/components/specification/Samples/OmeFiles/2012-06/
 6x4y1z1t1c8b-swatch-downgrade.ome

[mlinkert]

2012-06/6x4y1z1t1c8b-swatch-downgrade.ome fails because the Screen is missing a Name (which is now required, if I am not mistaken). Manually added a Name to the Screen allows the file to import. Andrew, can you please verify that that's the case, and if so update the sample accordingly?

2011-06/LAMBDA-modulo-sample.ome.tiff and 2011-06/SPIM-modulo-sample.ome.tiff fail with this stack trace:

serverExceptionClass = "ome.conditions.ApiUsageException"
    message = "Missing reference handler for Annotation:3(ome.model.annotations.XmlAnnotation:Hash_1682867698) --> Pixels:0(ome.model.core.Pixels:Hash_1597769296) reference."
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._MetadataStoreDelM.updateReferences(_MetadataStoreDelM.java:315)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:460)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:432)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2143)
	... 14 more

2011-06/6x4y1z1t3c8b-swatch-upgrade.ome fails with this stack trace:

serverExceptionClass = "ome.conditions.ApiUsageException"
    message = "Missing reference handler for Annotation:1(ome.model.annotations.XmlAnnotation:Hash_515305035) --> Screen:1(ome.model.screen.Screen:Hash_2077658541) reference."
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._MetadataStoreDelM.updateReferences(_MetadataStoreDelM.java:315)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:460)
	at omero.api.MetadataStorePrxHelper.updateReferences(MetadataStorePrxHelper.java:432)
	at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2143)
	... 14 more

I'm not seeing anything obviously wrong in Bio-Formats at the moment, but I'll look more carefully in the (later) morning. Any bright ideas in the meantime would be most welcome. The "Expecting node name" messages are not really relevant (they are debugging messages, not errors).

[mlinkert]

Just double-checking, Screen.Name is not required in the OME-XML schema, but I guess is required in OMERO? In that case, updating MetadataConverter? to populate a blank Name is probably the easiest way to go, which I'll do a bit later here.

[mlinkert]

PRs opened:

​https://github.com/openmicroscopy/bioformats/pull/96
​https://github.com/openmicroscopy/openmicroscopy/pull/238

...which should allow all four files to import correctly.

[jmoore <josh@…>]

(In [313136fb2ee99acfc53a37362db613da0515e91b/ome.git] on branch develop) Add missing Annotation reference handlers

See #9318.