/ 
InterMine-Item-0.991
River stage zero No dependents
/ InterMine::Item::Document

NAME

InterMine::Item::Document - a module for writing InterMine-Items-XML files

SYNOPSIS

 use InterMine::Model;
 use InterMine::Item::Document;

 my ($model_file, $output_file) = @ARGV;

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

 my $doc   = InterMine::Item::Document->new(
   model      => $model,
   output     => $output_file, # defaults to STDOUT
   auto_write => 1, # automatically write each item as it is made
 );

 my $organism = $doc->add_item(
   "Organism",
   "taxonId" => 7227
 );

 my $pub1 = $doc->add_item(
   "Publication",
   "pubMedId" => 11700288,
 );
 my $pub2 = $doc->make_item(
   "Publication",
   "pubMedId" => 16496002,
 );

 $doc->add_item(
   'Gene',
   'identifier'   => "CG10811",
   'organism'     => $organism,
   'publications' => [$pub1, $pub2],
 );

 $doc->close; # writes the end tags - only needed when auto_write is on

DESCRIPTION

This module allows you to make and write out InterMine-Items-XML for integrating data into InterMine databases

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::ItemFactory

You can also look for information at:

COPYRIGHT & LICENSE

Copyright 2006,2007,2008 FlyMine, 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

return a factory that can be used to create Item objects.

$document = new InterMine::Item::Document(model => $model);

Args:

model - the InterMine::Model object to use to check field validity
output - [optional] The file to write to (defaults to standard out)
ignore_null - [optional] Whether or not to be tolerant of undefined field values (defaults to intolerant)

writer

Function : Return the writer for this document

add_default_fields(key => value, key => value)

Function : add the given key value pairs to the default fields list
           that will be appplied to every item made. If a default field
           is not valid for a particular item, it will not be set.

get_default_fields()

Function : get the current default fields
Returns  : a hash in list context, or a hash-reference in scalar context

write

Function : write all unwritten items to the xml output. This is 
           called automatically on item creation if auto_write is 
           set.

close

Function : close the document by writing any unwritten
           items and closing the items tag.

make_item

Title   : make_item
Usage   : $item = $doc->make_item("Gene", [%attributes]);
Function: return a new Item object of the given type
          while not storing it 
Args    : the classname of the new Item
          Any attributes for the item

add_item

Title   : add_item
Usage   : $item = $doc->add_item("Gene");
Function: return a new Item object of the given type,
          while storing it in an internal record for writing
          out later
Args    : the classname of the new Item
          Any attributes for the item