/ 
InterMine-Model-0.9904
River stage one • 1 direct dependent • 1 total dependent
/ InterMine::Model

NAME

InterMine::Model - the representation of an InterMine model

SYNOPSIS

use InterMine::Model;

my $model_file = 'flymine/dbmodel/build/model/genomic_model.xml';
my $model = InterMine::Model->new(file => $model_file);
my $gene = $model->make_new(
  Gene => {
      primaryIdentifier => "FBgn0004053",
      secondaryIdentifier => "CG1046",
      symbol              => "zen",
      name                => "zerknullt",
      length              => "3474",
      organism            => {
          shortName => "D. melanogaster",
      }
      ncbiGeneNumber      => 40828,
  });

$gene->getName(); # "zerknullt"

...

DESCRIPTION

The class is the Perl representation of an InterMine data model. The new() method can parse the model file. The get_classdescriptor_by_name() method will return an InterMine::Model::ClassDescriptor object for the class with the given name, and the make_new() method will return an instantiated object of the given class.

For an example model see: http://trac.flymine.org/browser/trunk/intermine/objectstore/model/testmodel/testmodel_model.xml

CLASS METHODS

new( %options )

Standard constructor - accepts key/value pairs. Possible options are:

  • source: the source of the xml

    can be a ScalarRef, filehandle, filename, or string (or anything that overloads "") (tested in that order)

  • file: The file to load the model from

    [deprecated - use source instead]

  • string: A string containing the xml to load the model from

    [deprecated - use source instead]

  • origin: Where this model comes from

    usually a mine name - optional

get_classdescriptor_by_name

Get the InterMine::Model::ClassDescriptor (meta-class) with the given name.

my $cd = $model->get_classdescriptor_by_name("Gene");

make_new($class_name, [%attributes|$attributes])

Return an object of the desired class, with the attributes given

my $gene = $model->make_new(Gene => {symbol => "zen", organism => {name => 'D. melanogaster}});

say $gene->getSymbol             # "zen"
say $gene->getOrganism->getName # "D. melanogaster"

get_all_classdescriptors

Return all the InterMine::Model::ClassDescriptors for this model

my @cds = $model->get_all_classdescriptors();

get_referenced_classdescriptor

Get the class descriptor at the other end of a reference. The main use for this method is internal, during the construction of a model

my $cd = $model->get_referenced_classdescriptor($ref);

find_classes_declaring_field( $name )

Get the class descriptors that declare fields of a certain name

my @classes = $model->find_classes_declaring_field($str);

package_name

Return the package name derived from the original java name space, eg. org.intermine.model

my $java_package = $model->package_name;

model_name

Return the name of this model. Conceptually, this maps to the enclosing package for the generated classes.

my $model_name = $model->model_name();

to_xml

Returns a string containing an XML representation of the model.

lazy_fetch

Always returns undef. This can be overriden by subclasses to provide lazy fetching capabilities for items, from a web-service or directly from a database.

AUTHOR

FlyMine <support@flymine.org>

BUGS

Please report any bugs or feature requests to support@flymine.org.

SUPPORT

You can find documentation for this module with the perldoc command.

perldoc InterMine::Model

You can also look for information at:

COPYRIGHT & LICENSE

Copyright 2006,2007,2008,2009, 2010, 2011 FlyMine, all rights reserved.

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.