Bug: OMEXMLMetadataImpl.dumpXML() can alter the model

[crueden-x]

In some cases, calling OMEXMLMetadataImpl.dumpXML() to dump an OME model object to OME-XML can result in the model itself being modified. Here is an example:

//
// OMEXMLBug.java
//

import loci.common.services.ServiceFactory;
import loci.common.xml.XMLTools;
import loci.formats.meta.IMetadata;
import loci.formats.services.OMEXMLService;

public class OMEXMLBug {

	public static void main(final String[] args) throws Exception {
		final ServiceFactory serviceFactory = new ServiceFactory();
		final OMEXMLService omexmlService =
			serviceFactory.getInstance(OMEXMLService.class);

		// construct OME metadata object hierarchy
		final IMetadata omeMeta = omexmlService.createOMEXMLMetadata();
		omeMeta.setInstrumentID("Instrument:0", 0);
		omeMeta.setFilterID("Filter:0", 0, 0);
		omeMeta.setImageID("Image:0", 0);
		omeMeta.setChannelID("Channel:0", 0, 0);
		omeMeta.setLightPathExcitationFilterRef("Filter:0", 0, 0, 0);

		// dump OME metadata to XML
		for (int i = 1; i <= 3; i++) {
			System.out.println("---------- " + i + " ------------");
			final String xml = omexmlService.getOMEXML(omeMeta);
			System.out.println(XMLTools.indentXML(xml, true));
		}
	}

}

The first time through the print loop, there is (correctly so) one instance of excitation filter ref. Each time through the loop, another instance of the ref appears.

I traced the problem to a call to OMEModelObject#link in OMEModelImpl#resolveReferences, but thought I would file a ticket for review before going further, since Chris is more familiar with this code.

[jmoore]

Changing to "Bug:" since we don't use the ticket type Bug.

[Melissa Linkert <melissa@…>]

(In [8ee54ead17d74d38f4168bf628e1167693fe6155/ome.git] on branch develop) Do not link objects that have already been linked

If an object can reference multiple objects of the same type, then
before adding a reference to an object we must check if that object is
already referenced. This prevents additional references to the same
object from being created on successive calls to link(...).

Closes #7017.

[Melissa Linkert <melissa@…>]

(In [f91d95188be8780d183c8f4966c55af013ef9474/bioformats.git] on branch develop) Results of running xsd-fu against latest templates

See #7017.

[Melissa Linkert <melissa@…>]

(In [17db504da0a667b48901f8efdb55055b4e73a67c/bioformats.git] on branch develop) Results of running xsd-fu against latest templates

See #7017.