https://github.com/intermine/intermine-ws-perl-model

InterMine::Model for the InterMine Perl client
https://github.com/intermine/intermine-ws-perl-model

Last synced: 10 months ago
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InterMine::Model for the InterMine Perl client

• Host: GitHub
• URL: https://github.com/intermine/intermine-ws-perl-model
• Owner: intermine
• Created: 2019-04-11T14:50:56.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2019-04-11T16:45:18.000Z (over 6 years ago)
• Last Synced: 2025-01-19T18:52:36.400Z (12 months ago)
• Language: Perl
• Size: 64.5 KB
• Stars: 0
• Watchers: 9
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: Changes

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README

          
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.

    For an example model see:

    http://trac.flymine.org/browser/trunk/intermine/objectstore/model/testmo

    del/testmodel_model.xml

AUTHOR

    FlyMine ""

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:

    *   FlyMine

        

COPYRIGHT & LICENSE

    Copyright 2019 InterMine, all rights reserved.

    This program is free software; you can redistribute it and/or modify it

    under the same terms as Perl itself.

FUNCTIONS

  new

     Title   : new

     Usage   : $model = new InterMine::Model(file => $model_file);

                 or

               $model = new InterMine::Model(string => $model_string);

     Function: return a Model object for the given file

     Args    : file - the InterMine model XML file

  get_classdescriptor_by_name

     Title   : get_classdescriptor_by_name

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

     Function: return the InterMine::Model::ClassDescriptor for the given class or

               undef if the class isn't in the model

     Args    : the classname

  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->get_symbol             # "zen"

     say $gene->get_organism->get_name # "D. melanogaster"

  get_all_classdescriptors

     Title   : get_all_classdescriptors

     Usage   : @cds = $model->get_all_classdescriptors();

     Function: return all the InterMine::Model::ClassDescriptor objects for this

               model

     Args    : none

  get_referenced_classdescriptor

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

     Function : get the class descriptor at the other end of a reference

     Args     : The reference

  find_classes_declaring_field

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

     Function : get the class descriptors that declare fields of a certain name  

     Args     : The field's name

  package_name

     Title   : package_name

     Usage   : $package_name = $model->package_name();

     Function: return the package name derived from the name space

               eg. "org.intermine.model"

     Args    : none

  model_name

     Title   : model_name

     Usage   : $model_name = $model->model_name();

     Function: return the model name from the model file eg. "testmodel"

     Args    : none