Bio-MAGE - Changes

2007-05-14 Jason E. Stewart <jasonestewart@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 an association with an object needed to add check for writing end tag as well writestart_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 "

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 magemllist 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: classname(), 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, gettype() 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