[ome-users] Custom annotations absent in exported metadata

[Graham Klyne]

Ilya,

After a long break and many distractions, I'm back to figuring out how
to export new Semantic Type annotations on the OME/XML file...

Ilya Goldberg wrote:
> The best place to start is definitely the current XML Export module: 
> src/perl2/OME/Web/XMLFileExport.pm
> The entire web UI is done using sub-classes of OME::Web (in 
> src/perl2/OME/Web.pm and the src/perl2/OME/Web/ directory tree)
> I would follow the same inheritance pattern and simply make a new class 
> similar to XMLFileExport - there's really no point to subclassing this 
> since its just an HTML interface for 
> src/perl2/OME/Tasks/OMEXMLImportExport.pm.  This 
> OME::Tasks::OMEXMLImportExport class performs the logic of gathering the 
> objects to export.  The export itself is performed by 
> OME::Tasks::OMEExport, which is the generalized exporter.
> 
> Since OMEXMLImportExport.pm just gathers objects and calls 
> OME::Tasks::OMEExport, the thing to do is copy the 
> OMEXMLImportExport->exportToXMLFile() method to your new class and 
> modify it to look for additional objects using a OME::Factory call 
> documented here:
> http://openmicroscopy.org/APIdocs/OME/Factory.html

Thanks.

I've made a start on this, but I'm familiar with neither Perl coding nor
the internal architecture details of OME.  Here's my first attempt at an
extended export function:  does it look reasonable as far as it goes?
Am I overlooking any key logic?

(The next here has got some rather ugly line-wrapping;  I also attach a
copy of the source file I'm tinkering with.)

[[
sub exportToXMLFile {

	my ($self, $images, $file) = @_ ;
	my $session = OME::Session->instance();
	my $factory = $session->Factory() ;

	# To-do check if can write in file
	my $exporter = OME::Tasks::OMEExport->new( session => $session ) ;
	my @exportObjects = () ;
	my $image_import_module = $session->Configuration()->image_import_module();
	my $annotation_module   =
$session->Configuration()->annotation_module();	###new
	my @outputs = $image_import_module->outputs();
	foreach my $image (@$images) {
		push(@exportObjects,$image) ; # Add the image

		# Get the import mex for this image
		my  $import_MEX = $factory->findObject ("OME::ModuleExecution",
			image_id => $image->id(),
			module   => $image_import_module,
		);

		### New code ###

		# Get the DTGED annotation mex for this image
		my  $dtged_MEX = $factory->findObject ("OME::ModuleExecution",
			image_id => $image->id(),
			module   => $annotation_module
		);
		### I guess this selects all annotations for the image;
		### how do I restrict additional results to those with Untyped Oputput
		### of the form/semantic type defined as "DTGEDImageAnnotation" ?

		###

		# Collect all the attributes produced by the import MEX
		my @untyped_outputs = $import_MEX->untypedOutputs();
		my @dtged_outputs   = $dtged_MEX->untypedOutputs();			### New
		foreach my $output (@outputs, at untyped_outputs, at dtged_outputs) {		###
Changed
			my $ST = $output->semantic_type();
			next unless $ST; # Skip the untyped output itself

			# Get the output's attributes, and push them on the list
			my $attributes = OME::Tasks::ModuleExecutionManager->
				getAttributesForMEX($import_MEX,$ST);
			push(@exportObjects,@$attributes);
		}

	}
	$exporter->buildDOM(\@exportObjects, ResolveAllRefs => 1, ExportSTDs =>
0) ;
	$exporter->exportFile($file);
	return ;
}
]]

As coded, I'm thinking this will add the untyped outputs of all
annotation module executions to the XML output.  Is this close?  If so,
how can I refine it to select just the "DTGEDImageAnnotation" values?
(This a detail I can't discern from
http://openmicroscopy.org/APIdocs/OME/Factory.html.)

Am I correct that the expression
(@outputs, at untyped_outputs, at dtged_outputs) "flattens" the content of
three lists into a single list?

If the new export function is about right, I guess I also need to modify 
the new module's getPageBody function to reference 
OME::Web::XMLFileExportDTGED->new($session) instead of 
OME::Tasks::OMEXMLImportExport->new($session).

What does the "1;" at the end of the Perl module file do?

#g

-- 
Graham Klyne
Image Bioinformatics Research Group (http://www.bioimage.org/)
Department of Zoology, University of Oxford
South Parks Road, Oxford OX1 3PS, UK
E-mail: <Graham.Klyne at zoo.ox.ac.uk>
Direct phone: +44-(0)1865-281991
Departmental fax: +44-(0)1865-310447

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