VERSION
This document describes UR version 0.44SYNOPSIS
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 interfaceUR::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::ObjectUR::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::SimpleAUTHORS
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 [email protected] 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 [email protected] David Dooling
LICENCE AND COPYRIGHT
Copyright (C) 2002-2015 Washington University in St. Louis, MO.This software is licensed under the same terms as Perl itself. See the LICENSE file in this distribution.