File: ChangeLog

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2007-05-14  Jason E. Stewart <jason_e_stewart@users.sf.net>

	* All classes regenerated using new Mason template engine
	* MAGE-Utils hand-written classes are split into their own module
	* new version (20030502.3)

2004-05-25  Eric W. Deutsch <edeutsch@systemsbiology.org>	

	All classes updated to MAGE-OM 1.1

2003-01-11  Jason E. Stewart  <jason@openinformatics.com>

	* MAGE.pm (Repository): 
	new version (20020902.3)

2003-03-07  Jason E. Stewart  <jason@openinformatics.com>

	* MAGE/XML/Writer.pm (Repository): 
	to decide whether to only write a _ref element, the code delays
	   writing the start tag until after:
	   1) it's seen attributes other than identifier
	   2) it's seen an association with an object
	needed to add check for writing end tag as well
	write_start_tag() now buffers itself. It is flushed in
	   obj2mageml() when an association is seen, or when an empty
	   element is written

2002-12-08  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Repository): 
	moved setAssociation() from start_element to end_element

2002-11-25  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm: 
	reomoved XMLReader packages() and package_stack(). Package objects
	   are now just pushed onto the object stack.
	Fixed silliness that objects w/o parents were pushed onto a queue
	   - this can't happen now that packages are put on the stack

2002-11-23  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Repository): 
	typo: get/set_attribute => get/set_slot
	removed many attributes of Bio::MAGE::Handler that were simply
	   copies of the Reader's attributes, instead it now can access
	   the Reader directly
	removed many uses of Handler hash keys directly, made them
	   attributes, two cases remain: 
	   __PRIVATE: won't change
	   classes: will change by adding factory interface
	all attribute hash keys begin with '__' except class names which
	   will go away soon

2002-11-20  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Repository): 
	added resolve_identifiers to XMLReader
	added reader to Bio::MAGE::Handler

2002-11-19  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Message): 
	added count attribute to XMLReader

2002-11-16  Jason E. Stewart  <jason@openinformatics.com>

	* Association/Association.pm (Repository): 
	added new package, Bio::MAGE::Association::End
	Bio::MAGE::Association now has two end's 'self' and 'other'

	* XMLUtils/XMLUtils.pm (Repository): 
	added better POD
	fixed attr_indent usage
	fixed default values for attributes
	added external_data_dir attribute
	added cube_holds_path attribute
	associations now have both ends as objects
	no longer writes out objects from bi-navigable associations in
	  which self is owned by aggregate from other end 

	* Makefile.PL (Repository): 
	new version and scheme (20020902.1)

	* XMLUtils/XMLUtils.pm (Repository): 
	added fix to prevent writing of empty elements that were intended
	   to only be written as <*_ref> elements

2002-10-08  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Repository): 
	Must check that a reference to an array has any elements before
	   attempting to access the last element with $ref->[-1] notation
	writer should export the VALUE of the datum not the stringified
	   object 
	Added dir() to Bio::MAGE::Handler
	set dir() in read() if called with path
	reader can now handle data cube in any order

2002-10-07  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Repository): 
	needed to init $HANDLER inside read()
	modification to POD Synopsis
	Added support for BioDataTuples
	fix identifier bug in write_bio_data_tuples
	fix typo in write_bio_data_tuples
	added container tags around objects
	Added BioDataTuples support to XMLReader

2002-09-10  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Repository): 
	Fixed bug in XMLWriter in which cube attribute got written out
	added more POD to XMLReader
	made XMLReader handle .gz files
	created an init() subroutine to localize parser creation

	* MAGE.pm (Repository): 
	added an error check to add_objects() to ensure that an array ref
	   was used

2002-08-25  Jason E. Stewart  <jason@openinformatics.com>

	* MAGE.pm (Repository): 
	using croak instead of die to get proper caller in error message

	* XMLUtils/XMLUtils.pm (Repository): 
	removed extra copy of indent_level() found with -w
	eliminated warning by checking definedness of $attribute_val
	ensured that tags were created properly by using ucfirst()

2002-08-24  Jason E. Stewart  <jason@openinformatics.com>

	* Makefile.PL (Repository): 
	New version (0.08)

	* XMLUtils/XMLUtils.pm: 
	moved the reader from a standalone app to Bio::MAGE::XMLReader

2002-08-19  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Repository): 
	Writer now creates empty tags when an object has no associations 
	Fixed bug in empty tag creation
	More fixes for new namespace
	fixed obj2mageml_ref() for new namespaces
	fixed error with empty tags
	fixed DataInternal and DataExternal for BioDataCube

	* Base/Base.pm (Repository): 
	modified set_slots() to find slot methods as well

2002-05-21  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm (Repository): 
	subclasses from Bio::MAGE::Base instead of Class::ObjectTemplate

2002-01-17  Jason E. Stewart  <jason@openinformatics.com>

	* MAGE.pm (Repository): 
	Added NodeValue to import_all

	* scripts/mageml_reader.pl (Repository): 
	* XMLUtils/XMLUtils.pm (Repository): 
	removed some bogus attributes
	fixed handling of <InternalData> and  <ExternalData>

	* MAGE.pm (Repository): 
	Fixed a bogus directory

2001-12-19  Jason E. Stewart  <jason@openinformatics.com>

	* scripts/mageml_reader-sax1.pl (Repository): 
	obsolete

	* scripts/mageml_reader.pl (Repository): 
	Now supports --sax1 options to use a SAX1 parser instead of the
	   default SAX2 parser.

	* scripts/test-bio-data-cube.pl (Repository): 
	Added support for storing cube as 3D matrix
	Added support for storing cube in external file

	* scripts/mageml_reader.pl (Repository): 
	removed bad command line options
	added --dir option
	converted back to SAX2
	Added methods for storing cube as 3D matrix
	Added support for storing cube in external file

	* XMLUtils/XMLUtils.pm (Repository): 
	Added external_data() method for storing whether the cube should
	   be internal or external
	Added external_file_id() method	for generating a unique file id
	Added flatten() method for coverting cube to list
	Added support for cube as 3D matrix
	Added support for external data

2001-12-11  Jason E. Stewart  <jason@openinformatics.com>

	* scripts/test-bio-data-cube.pl (Repository): 
	Example script for creating a BioDataCube

	* MAGE.pm (Repository): 
	identifier is required for <MAGE-ML>
	packages now printed in proper order

	* XMLUtils/XMLUtils.pm (Repository): 
	substitute quotation marks into &quot;

2001-12-10  Jason E. Stewart  <jason@openinformatics.com>

	* MAGE.pm (Repository): 
	Added error checking for import_all()

2001-12-09  Jason E. Stewart  <jason@openinformatics.com>

	* scripts/mageml_reader.pl (Repository): 
	removed all the 'use ...' statements and added the ':ALL' key to
	   the 'use Bio::MAGE'

2001-12-08  Jason E. Stewart  <jason@openinformatics.com>

	* scripts/mageml_reader.pl (Repository): 
	Fixed the handling of unresolved identifiers

2001-09-20  Jason E. Stewart  <jason@openinformatics.com>

	* t/*.t (Repository): 
	Added tests for class_name() and package() class methods

	* *.pm (Repository): 
	now have package() method

	* MAGE.pm (Repository): 
	now 'requires' all packages because of new()

	* Pkg/*/*.pm (Repository): 
	Added xml writer code
	can now create instances of packages
	added code for registration of identifiable objects

	* scripts/mageml2obj_v2.pl: 
	Added test of XMLWriter

	* t/MAGE_package.t: 
	Added tests for the packages method
	Added tests for the identifiers method	
	Added tests for the objects method		

	* t/*_package.t: 
	Added tests for the *_list methods
	Added tests for the mageml_list method
	Added tests for the class2list method
	Added tests for the tagname method
	test creation of an instance

	* t/Person.t: 
	* Person/Person.pm (Repository): 
	Fixed 'affiliation' associtation

	* MAGE.pm (Repository): 
	All Package modules now have $VERSION

	* XMLUtils/XMLUtils.pm (Repository): 
	needs to return a true value

2001-09-19  Jason E. Stewart  <jason@openinformatics.com>

	* Pkg (Repository): 
	All other package modules now have mageml_lists() method

	* MAGE.pm (Repository): 
	Now has mageml_packages() method.

2001-09-18  Jason E. Stewart  <jason@openinformatics.com>

	* XMLUtils/XMLUtils.pm: 
	XMLWriter has unified register() and obj2mageml()
	Wrote rudimentary identifier generator.

	* Association/Association.pm (Repository): 
	New Class for association meta-data

2001-09-11  Jason E. Stewart  <jason@openinformatics.com>

	* scripts/mageml2obj.pl (Repository): 
	now handles <Affiliation_refcon> and setting state
	creates an Bio::MAGE::XMLWriter to create the output

	* XMLUtils/XMLUtils.pm (Repository): 
	Now has Bio::MAGE::XMLWriter for handling MAGE-ML export
	first step in export is register(), then obj2mageml()

2001-09-07  Jason E. Stewart  <jasons@openinformatics.com>

	* Makefile.PL (Repository): 
	New version (0.03)

	* scripts/mageml2obj.pl (Repository): 
	Test script for reading MAGEML. Currently only handles <Person>,
	   <Organization>, and <Organization_ref> in a <Person> context. 

	* XMLUtils/XMLUtils.pm (Repository): 
	Module for obj2mageml() methods

2001-09-01  Jason E. Stewart  <jason@openinformatics.com>

	* classes/create-mage-classes.pl (Repository): 
	{association,attribute}_methods() needed the class name argument
	   in order to invoke another class method (superclasses).

	* classes/xmi2class.pl (Repository): 
	update USAGE
	fixed --onefile to work again

2001-08-31  Jason E. Stewart  <jason@openinformatics.com>

	* classes/create-mage-classes.pl (Repository): 
	fixed the nomenclature for $*_qw variables
	Added class methods: class_name(), subclasses(), superclasses(),
	  attribute_methods(), and association_methods().
	@subclasses now uses full class names

2001-08-30  Jason E. Stewart  <jasons@openinformatics.com>

	* classes/xmi2class.pl (Repository): 
	Now correctly creates XML files with the 'standalone' attribute
	   set in the XMLDecl when in package mode.

2001-08-29  Jason E. Stewart  <jasons@openinformatics.com>

	* classes/create-mage-classes.pl (Repository): 
	Supports creation of *only* package modules
	Supports creation of helper package modules together with
	   individual class modules
	Removed all globals, each print_* method is passed in params

	* classes/xmi2class.pl (Repository): 
	Added --cache option to control using cached data structure
	   instead of reparsing XMI file
	added --packages option to control outputin *only* package modules
	added --dump-only option to not create *.xml output
	data dump now has package list as well. It needed to second call
	   to Dump() or class methods came out empty???
	Can now output as: one file, individual class files, or package
	   files
	Type nodes now handle new <type_list> and <type> structure
	<method_list> and <method> supported

	* classes/XMI.pm (Repository): 
	Added $F_C as abbreviation for 'Foundation.Core'
	new() now accepts 'TOP-LEVEL'=>'class_name' as arg
	fixed debug output to be hierarchical
	now handles parsing of *_package.xml files into packages
	All files not included in a package wind up in the TOP-LEVEL
	   package unless new() was instructed otherwise
	Each class records: all super classes, methods, abstract attr
	new method, get_type() returns a type structure
	

	* classes/QuantitationType_package.xml (Repository): 
	* classes/Protocol_package.xml (Repository): 
	* classes/Measurement_package.xml (Repository): 
	* classes/MAGE_package.xml (Repository): 
	* classes/HigherLevelAnalysis_package.xml (Repository): 
	* classes/Experiment_package.xml (Repository): 
	* classes/DesignElement_package.xml (Repository): 
	* classes/Description_package.xml (Repository): 
	* classes/BioSequence_package.xml (Repository): 
	* classes/BioMaterial_package.xml (Repository): 
	* classes/BioEvent_package.xml (Repository): 
	* classes/BioAssay_package.xml (Repository): 
	* classes/BioAssayData_package.xml (Repository): 
	* classes/BQS_package.xml (Repository): 
	* classes/AuditAndSecurity_package.xml (Repository): 
	* classes/Array_package.xml (Repository): 
	* classes/ArrayDesign_package.xml (Repository): 
	wrapper files with external entities to the classes contained
	   within the package

	* MAGE.pm (Repository): 
	Supports the export tag :ALL, that triggers loading every
	   Bio::MAGE::* module, e.g 'use Bio::MAGE qw(:ALL);'

	* Makefile.PL (Repository): 
	Contains $VERSION, since MAGE.pm is auto-generated

	* Pkg (Repository): 
	New modules that encapsulate use'ing all the classes of a given
	   package. e.g. 'use Bio::MAGE::Pkg::BioAssay;' is the same as
	   listing 'use *' for each class in the package

	* */*.pm (Repository): All modules now include:
	'use *;' pragma for each superclass (so @ISA can work)
	@ISA now includes superclasses (duh)
	class DESCRIPTION now has MAGE-OM documentation
	INHERITANCE section showing all super-/sub-classes
	CLASS METHODS now documents parameters to new()
	abstract base classes are marked as such
	ATTRIBUTES and ASSOCIATIONS have cardinality indicated (either
	   scalar return type or array return type
	METHODS section, that also has stub code for methods

	* classes/classes.dtd: 
	added %boolean
	<class> now has optional <method_list> and <type_list>, as well as
	   new attributes: package, abstract, and subclasses
	removed type info from <attribute> and added IDREF to <type> 
	added <method_list>, <parameter_list>, and <type_list> with
	   <method>, <parameter>, and <type>	

	* t: 
	All tests now test: subclasses, superclass, attributes, associations

2001-08-25  Jason E. Stewart  <jasons@openinformatics.com>

	* classes/xmi2class.pl (Repository): 
	script for creating XML class files from XMI

	* classes/XMI.pm (Repository): 
	Module for manipulating UniSys XMI files

	* classes/classes.xml (Repository): 
	* classes/classes.dtd: 
	* classes/VolumeUnit.xml: 
	* classes/TimeUnit.xml: 
	* classes/TemperatureUnit.xml: 
	* classes/SeqFeature.xml: 
	* classes/QuantityUnit.xml: 
	* classes/Measurement.xml: 
	* classes/MassUnit.xml: 
	* classes/DistanceUnit.xml: 
	* classes/ConcentrationUnit.xml: 
	* classes/BioDataCube.xml: 
	* classes/Audit.xml: 
	* classes/ArrayPackage.xml: 
	Changed any[][][] to plain 'any' so that type could be NMTOKEN
	Changed enum attribute back to enumeration

2001-08-23  Jason E. Stewart  <jasons@openinformatics.com>

	* Makefile.PL (Repository): 
	Added version attribute on Class::ObjectTemplate