NAME

UR - rich declarative transactional objects

VERSION

This document describes UR version 0.44

SYNOPSIS

use UR;

## no database

class Foo { is => 'Bar', has => [qw/prop1 prop2 prop3/] };

$o1 = Foo->create(prop1 => 111, prop2 => 222, prop3 => 333);

@o = Foo->get(prop2 => 222, prop1 => [101,111,121], 'prop3 between' => [200, 400]);
# returns one object

$o1->delete;

@o = Foo->get(prop2 => 222, prop1 => [101,111,121], 'prop3 between' => [200, 400]);
# returns zero objects

@o = Foo->get(prop2 => 222, prop1 => [101,111,121], 'prop3 between' => [200, 400]);
# returns one object again

## database

class Animal {
    has => [
        favorite_food => { is => 'Text', doc => "what's yummy?" },
    ],
    data_source => 'MyDB1',
    table_name => 'Animal'
};

class Cat {
    is => 'Animal',
    has => [
        feet    => { is => 'Number', default_value => 4 },
        fur     => { is => 'Text', valid_values => [qw/fluffy scruffy/] },
    ],
    data_source => 'MyDB1',
    table_name => 'Cat'
};

Cat->create(feet => 4, fur => 'fluffy', favorite_food => 'taters');

@cats = Cat->get(favorite_food => ['taters','sea bass']);

$c = $cats[0];

print $c->feet,"\n";

$c->fur('scruffy');

UR::Context->commit();

DESCRIPTION

UR is a class framework and object/relational mapper for Perl. It starts with the familiar Perl meme of the blessed hash reference as the basis for object instances, and extends its capabilities with ORM (object-relational mapping) capabilities, object cache, in-memory transactions, more formal class definitions, metadata, documentation system, iterators, command line tools, etc.

UR can handle multiple column primary and foreign keys, SQL joins involving class inheritance and relationships, and does its best to avoid querying the database unless the requested data has not been loaded before. It has support for SQLite, Oracle, Mysql and Postgres databases, and the ability to use a text file as a table.

UR uses the same syntax to define non-persistent objects, and supports in-memory transactions for both.

DOCUMENTATION

Manuals

ur - command line interface

UR::Manual::Overview - UR from Ten Thousand Feet

UR::Manual::Tutorial - Getting started with UR

UR::Manual::Presentation - Slides for a presentation on UR

UR::Manual::Cookbook - Recepies for getting stuff working

UR::Manual::Metadata - UR's metadata system

UR::Object::Type::Initializer - Defining classes

Basic Entities

UR::Object - Pretty much everything is-a UR::Object

UR::Object::Type - Metadata class for Classes

UR::Object::Property - Metadata class for Properties

UR::Namespace - Manage packages and classes

UR::Context - Software transactions and More!

UR::DataSource - How and where to get data

QUICK TUTORIAL

First create a Namespace class for your application, Music.pm:

package Music;
use UR;

class Music {
    is => 'UR::Namespace'
};

1;

Next, define a data source representing your database, Music/DataSource/DB1.pm

package Music::DataSource::DB1;
use Music;

class Music::DataSource::DB1 {
    is => ['UR::DataSource::MySQL', 'UR::Singleton'],
    has_constant => [
        server  => { value => 'database=music' },
        owner   => { value => 'music' },
        login   => { value => 'mysqluser' },
        auth    => { value => 'mysqlpasswd' },
    ]
};

or to get something going quickly, SQLite has smart defaults...

class Music::DataSource::DB1 {
    is => ['UR::DataSource::SQLite', 'UR::Singleton'],
};

Create a class to represent artists, who have many CDs, in Music/Artist.pm

package Music::Artist;
use Music;

class Music::Artist {
    id_by => 'artist_id',
    has => [
        name => { is => 'Text' },
        cds  => { is => 'Music::Cd', is_many => 1, reverse_as => 'artist' }
    ],
    data_source => 'Music::DataSource::DB1',
    table_name => 'ARTIST',
};

Create a class to represent CDs, in Music/Cd.pm

package Music::Cd;
use Music;

class Music::Cd {
    id_by => 'cd_id',
    has => [
        artist => { is => 'Music::Artist', id_by => 'artist_id' },
        title  => { is => 'Text' },
        year   => { is => 'Integer' },
        artist_name => { via => 'artist', to => 'name' },
    ],
    data_source => 'Music::DataSource::DB1',
    table_name => 'CD',
};

If the database does not exist, you can run this to generate the tables and columns from the classes you've written (very experimental):

$ cd Music
$ ur update schema

If the database existed already, you could have done this to get it to write the last 2 classes for you:

$ cd Music;
$ ur update classes

Regardless, if the classes and database tables are present, you can then use these classes in your application code:

# Using the namespace enables auto-loading of modules upon first attempt to call a method
use Music;

# This would get back all Artist objects:
my @all_artists = Music::Artist->get();

# After the above, further requests would be cached
# if that set were large though, you might want to iterate gradually:
my $artist_iter = Music::Artist->create_iterator();

# Get the first object off of the iterator
my $first_artist = $artist_iter->next();

# Get all the CDs published in 2007 for the first artist
my @cds_2007 = Music::Cd->get(year => 2007, artist => $first_artist);

# Use non-equality operators:
my @some_cds = Music::Cd->get(
    'year between' => ['2004','2009']
);

# This will use a JOIN with the ARTISTS table internally to filter
# the data in the database.  @some_cds will contain Music::Cd objects.
# As a side effect, related Artist objects will be loaded into the cache
@some_cds = Music::Cd->get(
    year => '2007',
    'artist_name like' => 'Bob%'
);

# These values would be cached...
my @artists_for_some_cds = map { $_->artist } @some_cds;

# This will use a join to prefetch Artist objects related to the
# objects that match the filter
my @other_cds = Music::Cd->get(
    'title like' => '%White%',
    -hints => ['artist']
);
my $other_artist_0 = $other_cds[0]->artist;  # already loaded so no query

# create() instantiates a new object in the current "context", but does not save
# it in the database.  It will autogenerate its own cd_id:
my $new_cd = Music::Cd->create(
    title => 'Cool Album',
    year  => 2009
);

# Assign it to an artist; fills in the artist_id field of $new_cd
$first_artist->add_cd($new_cd);

# Save all changes in the current transaction back to the database(s)
# which are behind the changed objects.
UR::Context->current->commit;

Environment Variables

UR uses several environment variables to do things like run with database commits disabled, watching SQL queries run, examine query plans, and control cache size, etc.

These make development and debugging fast and easy.

See UR::Env for details.

DEPENDENCIES

Class::Autouse Cwd Data::Dumper Date::Format DBI File::Basename FindBin FreezeThaw Path::Class Scalar::Util Sub::Installer Sub::Name Sys::Hostname Text::Diff Time::HiRes XML::Simple

AUTHORS

UR was built by the software development team at the McDonnell Genome Institute at Washington University School of Medicine (Richard K. Wilson, PI).

Incarnations of it run laboratory automation and analysis systems for high-throughput genomics.

Anthony Brummett   brummett@cpan.org
Nathan Nutter
Josh McMichael
Eric Clark
Ben Oberkfell
Eddie Belter
Feiyu Du
Adam Dukes
Brian Derickson
Craig Pohl
Gabe Sanderson
Todd Hepler
Jason Walker
James Weible
Indraniel Das
Shin Leong
Ken Swanson
Scott Abbott
Alice Diec
William Schroeder
Shawn Leonard
Lynn Carmichael
Amy Hawkins
Michael Kiwala
Kevin Crouse
Mark Johnson
Kyung Kim
Jon Schindler
Justin Lolofie
Jerome Peirick
Ryan Richt
John Osborne
Chris Harris
Philip Kimmey
Robert Long
Travis Abbott
Matthew Callaway
James Eldred
Scott Smith        sakoht@cpan.org
David Dooling

LICENCE AND COPYRIGHT

Copyright (C) 2002-2015 Washington University in St. Louis, MO.

This sofware is licensed under the same terms as Perl itself. See the LICENSE file in this distribution.