https://github.com/alexkalderimis/intermine-ws-ruby

Ruby InterMine client
https://github.com/alexkalderimis/intermine-ws-ruby

Last synced: 11 days ago
JSON representation

Ruby InterMine client

• Host: GitHub
• URL: https://github.com/alexkalderimis/intermine-ws-ruby
• Owner: alexkalderimis
• License: lgpl-3.0
• Created: 2011-07-02T16:56:36.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2013-07-04T14:23:13.000Z (over 11 years ago)
• Last Synced: 2024-04-09T22:22:37.712Z (10 months ago)
• Language: Ruby
• Homepage: www.intermine.org
• Size: 379 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rdoc

Awesome Lists containing this project

README

        
= Webservice Client Library for InterMine Data-Warehouses

This library provides an interface to the InterMine webservices

API. It makes construction and execution of queries more 

straightforward, safe and convenient, and allows for results

to be used directly in Ruby code. As well as traditional row based

access, the library provides an object-orientated record result

format (similar to ActiveRecords), and allows for fast, memory 

efficient iteration of result sets.

== Example

Get all protein domains associated with a set of genes and print their names:

    require "intermine/service"

    Service.new("www.flymine.org/query").

        new_query("Pathway")

        select(:name).

        where("genes.symbol" => ["zen", "hox", "h", "bib"]).

        each_row { |row| puts row[:name]}

== Who is this for?

InterMine data warehouses are typically constructed to hold

Biological data, and as this library facilitates programmatic

access to these data, this install is primarily aimed at 

bioinformaticians. In particular, users of the following services

may find it especially useful:

 * FlyMine (http://www.flymine.org/query)

 * YeastMine (http://yeastmine.yeastgenome.org/yeastmine)

 * RatMine (http://ratmine.mcw.edu/ratmine)

 * modMine (http://intermine.modencode.org/release-23)

 * metabolicMine (http://www.metabolicmine.org/beta)

== How to use this library:

We have tried to construct an interface to this library that

does not require you to learn an entirely new set of concepts. 

As such, as well as the underlying methods that are common

to all libraries, there is an additional set of aliases and sugar

methods that emulate the DSL style of SQL:

=== SQL style

  service = Service.new("www.flymine.org/query")

  service.model.

     table("Gene").

     select("*", "pathways.*").

     where(:symbol => "zen").

     order_by(:symbol).

     outerjoin(:pathways).

     each_row do |r|

       puts r

     end

=== Common InterMine interface

  service = Service.new("www.flymine.org/query")

  query = service.new_query("Gene")

  query.add_views("*", "pathways.*")

  query.add_constraint("symbol", "=", "zen")

  query.add_sort_order(:symbol)

  query.add_join(:pathways)

  query.each_row do |r|

    puts r

  end

For more details, see the accompanying documentation and the unit tests

for interface examples. Further documentation is available at www.intermine.org.

== Support

Support is available on our development mailing list: [email protected]

== License

This code is Open Source under the LGPL. Source code for all InterMine code

can be checked out from svn://subversion.flymine.org/flymine