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XSD Fu

XSD Fu is a Python application designed to digest OME XML schema and produce an object oriented Java infrastructure to ease work with an XML DOM tree.

Requirements:

Python 2.4+
Genshi 0.5
Full checkout of the OME repository ( http://git.openmicroscopy.org/src/master/components/xsd-fu/)
Full checkout of the LOCI repository ( https://skyking.microscopy.wisc.edu/svn/java/trunk)

NOTE: Genshi 0.5 was released on June 9th 2008. You can either install from source or download a compatible .egg for your system on the Genshi download page.

Checking out the source

This will get the entire source tree. xsd-fu is in components/xsd-fu

git clone git://git.openmicroscopy.org/ome.git

Running the code generator

If you do have Genshi already installed you can run xsd-fu script with no arguments to examine the syntax:

$ ./xsd-fu 
Missing subcommand!
Usage: ./xsd-fu <subcommand> ...
Executes an OME-XML Schema definition parsing and code generation subcommand.

Available subcommands:
  java_classes
  omexml_metadata
  omero_metadata
  metadata_store
  metadata_retrieve
  metadata_aggregate
  enum_types
  enum_handlers
  doc_gen
  tab_gen
  debug

Report bugs to OME Devel <ome-devel@lists.openmicroscopy.org.uk>

If you do not have Genshi installed you can use a downloaded Python .egg for your platform as follows:

$ export PYTHONPATH=Genshi-0.5-py2.4-linux-i686.egg
$ ./xsd-fu 
Missing subcommand!
Usage: ./xsd-fu <subcommand> ...
Executes an OME-XML Schema definition parsing and code generation subcommand.

Available subcommands:
  java_classes
  omexml_metadata
  omero_metadata
  metadata_store
  metadata_retrieve
  metadata_aggregate
  enum_types
  enum_handlers
  doc_gen
  tab_gen
  debug

Report bugs to OME Devel <ome-devel@lists.openmicroscopy.org.uk>

NOTE: XsdFu is now used for many different types of code generation tasks (mostly targeted at the OMERO and Bio-Formats 4.2.0 releases) as outlined by the subcommand structure above.

Generating the OME-XML Java toolchain

We'll now outline how to generate parts of the OME-XML Java toolchain which are composed of:

OME model objects
Enumerations for OME model properties
Enumeration handlers for regular expression matching of enumeration strings
Metadata store and Metadata retrieve interfaces for all OME model properties
Various implementations of Metadata store and/or Metadata retrieve interfaces

NOTE: All the below examples assume a full OME-XML specification Subversion checkout.

Java classes for OME model objects

$ ./xsd-fu java_classes -p 'ome.xml.model' -o $LOCI_HOME/components/ome-xml/src/ome/xml/model/ \
	../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd ../specification/Released-Schema/2011-06/V1/ROI.xsd \
	../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd

Enumeration classes for OME model properties

$ ./xsd-fu enum_types -p 'ome.xml.model.enums' -o $LOCI_HOME/components/ome-xml/src/ome/xml/model/enums/ \
	../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd ../specification/Released-Schema/2011-06/V1/ROI.xsd \
	../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd

Enumeration handlers for OME model properties

$ ./xsd-fu enum_handlers -p 'ome.xml.model.enums.handlers' -o $LOCI_HOME/components/ome-xml/src/ome/xml/model/enums/handlers/ \
	../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd ../specification/Released-Schema/2011-06/V1/ROI.xsd \
	../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd

Metadata store and Metadata retrieve interfaces

$ ./xsd-fu metadata_store ../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd \
	../specification/Released-Schema/2011-06/V1/ROI.xsd ../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd
$ ./xsd-fu metadata_retrieve ../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd \
	../specification/Released-Schema/2011-06/V1/ROI.xsd ../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd
$ cp MetadataStore.java MetadataRetrieve.java $LOCI_HOME/components/bio-formats/src/loci/formats/meta/

OMEXMLMetadataImpl Metadata store and Metadata retrieve implementation

$ ./xsd-fu omexml_metadata ../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd \
	../specification/Released-Schema/2011-06/V1/ROI.xsd ../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd
$ ./xsd-fu metadata_aggregate ../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd \
	../specification/Released-Schema/2011-06/V1/ROI.xsd ../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd
$ ./xsd-fu dummy_metadata ../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd \
	../specification/Released-Schema/2011-06/V1/ROI.xsd ../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd
$ ./xsd-fu filter_metadata ../specification/Released-Schema/2011-06/V1/ome.xsd ../specification/Released-Schema/2011-06/V1/BinaryFile.xsd \
	../specification/Released-Schema/2011-06/V1/ROI.xsd ../specification/Released-Schema/2011-06/V1/SA.xsd ../specification/Released-Schema/2011-06/V1/SPW.xsd
$ cp AggregateMetadata.java DummyMetadata.java FilterMetadata.java $LOCI_HOME/components/bio-formats/src/loci/formats/meta/
$ cp OMEXMLMetadataImpl.java $LOCI_HOME/components/bio-formats/src/loci/formats/ome/

Working with Enumerations and Enumeration Handlers

XsdFu contains a flexible, configuration driven structure to code generate enumeration regular expressions. The configuration file is located off of the xsd-fu/trunk root, in the cfg folder:

http://git.openmicroscopy.org/src/master/components/xsd-fu/cfg/enum_handler.cfg

Each enumeration has a key-value listing of regular expression to exact enumeration value matches. For example:

...
[Correction]
".*Pl.*Apo.*" = "PlanApo"
".*Pl.*Flu.*" = "PlanFluor"
"^\\s*Vio.*Corr.*" = "VioletCorrected"
".*S.*Flu.*" = "SuperFluor"
".*Neo.*flu.*" = "Neofluar"
".*Flu.*tar.*" = "Fluotar"
".*Fluo.*" = "Fluor"
".*Flua.*" = "Fluar"
"^\\s*Apo.*" = "Apo"
...

Special Thanks

A special thanks goes out to Dave Kuhlman for his fabulous work on generateDS which XSD Fu makes heavy use of internally.

See also: EnumTool, http://www.openmicroscopy.org/site/support/file-formats/working-with-ome-xml/developer-information, http://genshi.edgewall.org/, http://www.rexx.com/~dkuhlman/generateDS.html

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