chemcaster 0.4.1

data/README.rdoc

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+= Chemcaster[http://chemcaster.com] Ruby API
+
+This is the Ruby interface for the Chemcaster[http://chemcaster.com] RESTful Web
+API. It consists of basic functionality needed to create
+applications using chemical structure registration, storage, imaging, and
+search.
+
+== Installation
+
+Installation through the Ruby Gem hosted on GitHub is recommended:
+
+  # add GitHub to your local list of gem sources:
+  gem sources -a http://gems.github.com/
+  
+  # install the gem:
+  gem install metamolecular-chemcaster
+
+== Example Use
+
+=== Connecting to the Service
+
+   require 'rubygems'
+   require 'chemcaster'
+
+   service = Chemcaster::Service.connect 'username', 'password'
+
+Because Chemcaster[http://chemcaster.com] authenticates using SSL, you'll need to make sure the
+Ruby HTTP library can find the root SSL certificates on your system. On
+Debian Linux systems, these files are found in /etc/ssl/certs. This is
+also the default location used by the Chemcaster Ruby Client.
+
+To override the default SSL certificates path, pass the +root_ca+ option to the
++connect+ method:
+
+   service = Chemcaster::Service.connect 'username', 'password',
+     :root_ca => 'path/to/root_ssl_certs'
+
+More information can be found here:
+
+* {Making an HTTPS Web Request}[http://codeidol.com/other/rubyckbk/Internet-Services/Making-an-HTTPS-Web-Request]
+* {SSL Certificates and Net::HTTPS}[http://redcorundum.blogspot.com/2008/03/ssl-certificates-and-nethttps.html]
+* {Verified HTTPS in Ruby}[http://notetoself.vrensk.com/2008/09/verified-https-in-ruby]
+
+=== Loading a Registry from a Listing
+
+   require 'rubygems'
+   require 'chemcaster'
+
+   service = Chemcaster::Service.connect 'username', 'password'
+   registries = service.registries
+   registries.size # => 3
+   registry = registries[0]
+
+=== Loading a Registry from a URI
+
+   require 'rubygems'
+   require 'chemcaster'
+
+   Chemcaster::Service.connect 'username', 'password'
+
+   link = Chemcaster::Link.new 'name'=> 'foo',
+     'uri' => 'https://chemcaster.com/registries/123456',
+     'media_type' => 'application/vnd.com.chemcaster.Registry+json'
+   registry = link.get
+
+Note: No assumptions should be made about Chemcaster[http://chemcaster.com] URI layout. Once
+you receive a resource URI, you can expect it to work at any point
+in the future for random-access. But URI templates are unnecessary
+when accessing resources.
+
+=== Creating a Registry
+
+   require 'rubygems'
+   require 'chemcaster'
+
+   service = Chemcaster::Service.connect 'username', 'password'
+   registries = service.registries
+
+   registries.create :name => 'CarboBlocks, Inc.'
+
+=== Changing a Registry Name
+
+   require 'rubygems'
+   require 'chemcaster'
+
+   service = Chemcaster::Service.connect 'username', 'password'
+   registry = service.registries[0]
+   registry.update :name => 'CarboBlocks International, Inc.'
+
+
+== API Documentation
+
+RDoc documentation is available at
+{rdoc.info}[http://rdoc.info/projects/metamolecular/chemcaster-ruby].

data/Rakefile

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+require 'rubygems'
+require 'rake'
+require 'spec/rake/spectask'
+require 'rake/rdoctask'
+  
+Spec::Rake::SpecTask.new(:spec) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.spec_files = FileList['spec/**/*_spec.rb']
+end
+
+desc 'Generate RDoc documentation for Chemcaster client.'
+Rake::RDocTask.new(:rdoc) do |rdoc|
+  rdoc.rdoc_files.include('README.rdoc', 'LICENSE').include('lib/**/*.rb')
+  
+  rdoc.main = "README.rdoc" # page to start on
+  rdoc.title = "Chemcaster Client Documentation"
+  
+  rdoc.rdoc_dir = 'doc' # rdoc output folder
+  rdoc.options << '--inline-source' << '--charset=UTF-8'
+  rdoc.options << '--webcvs=http://github.com/mislav/will_paginate/tree/master/'
+end

data/lib/chemcaster/archive.rb

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+module Chemcaster
+  class Archive < Item
+    attributes :created_at, :done
+    resources :zipfile, :registry
+  end
+end

data/lib/chemcaster/component.rb

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+module Chemcaster
+  class Component < Item
+    attributes :multiplier
+    resources :structure, :substance
+  end
+end

data/lib/chemcaster/error.rb

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+module Chemcaster
+  class Error < RuntimeError; end
+  class LinkNotDefined < Error; end
+  class HTTPError < Error
+    attr_accessor :response
+    def initialize response
+      @response = response
+    end
+    
+    def to_s
+      "received response code #{@response.code} with message:\n\n#{parse_errors}"
+    end
+    
+    protected
+    
+    def parse_errors
+      errors = nil
+      message = ""
+      begin
+        errors = JSON.parse response.body
+      rescue
+        return response.body
+      end
+      
+      errors.each do |error|
+        if error['field']
+          message << "- field '#{error['field']}' #{error['text']}\n"
+        else
+          message << "- #{error['text']}\n"
+        end
+      end
+      
+      message
+    end
+  end
+end

data/lib/chemcaster/execution.rb

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+module Chemcaster
+  class Execution < Item
+    attributes :cursor, :reverse, :next_cursor, :previous_cursor
+    resources :executable
+    attr_accessor :results
+    
+    protected
+    
+    def load_hash hash
+      super
+      
+      hash['results'] ||= []
+      
+      @results = hash['results'].inject([]) do |result, atts|
+        result << Link.new(atts)
+      end
+    end
+  end
+end

data/lib/chemcaster/image.rb

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+module Chemcaster
+  class Image < Item
+    attributes :width, :height, :data, :format
+    resources :imageable
+  end
+end

data/lib/chemcaster/index.rb

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+require File.dirname(__FILE__) + '/../chemcaster/representation'
+
+module Chemcaster
+  class Index < Representation
+    attr_accessor :item_links#, :items
+    resources :parent
+    
+    def create representation_attributes={}
+      @create_link.post representation_attributes
+    end
+    
+    def size
+      @item_links.size
+    end
+    
+    def [](index)
+      @item_links[index].get
+    end
+    
+    protected
+    
+    def load_hash atts
+      super
+
+      @create_link = Link.new atts['create']
+      @item_links = atts['items'].inject([]) do |result, atts|
+        result << Link.new(atts)
+      end
+    end
+  end
+end

data/lib/chemcaster/item.rb

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+require File.dirname(__FILE__) + '/../chemcaster/representation'
+
+module Chemcaster
+  class Item < Representation
+    resources :index
+    
+    def update representation_attributes
+      @update_link.put representation_attributes
+    end
+    
+    def destroy
+      @destroy_link.delete
+    end
+    
+    protected
+    
+    def load_hash atts
+      super
+      
+      @update_link = Link.new atts['update']
+      @destroy_link = Link.new atts['destroy']
+    end
+  end
+end

data/lib/chemcaster/link.rb

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+require 'net/http'
+require 'net/https'
+
+module Chemcaster  
+  class Link
+    def initialize atts=nil
+      if atts
+        @uri = URI.parse(atts['uri']) if atts['uri']
+        @media_type = atts['media_type']
+        @media_class = MediaType.representation(@media_type) if @media_type
+      end
+    end
+    
+    def get
+      do_http 'get'
+    end
+    
+    def put attributes
+      do_http 'put', attributes
+    end
+
+    def post attributes
+      do_http 'post', attributes
+    end
+    
+    def delete
+      do_http 'delete'
+    end
+    
+    private
+    
+    def do_http method, representation=nil
+      validate
+      request = request_for_method method, representation
+      response = send_request request
+
+      raise(HTTPError, response) unless response.code.to_i < 300
+      @media_class.new self, decode(response)
+    end
+    
+    def send_request request
+      http = Net::HTTP.new(@uri.host, @uri.port)
+      http.use_ssl = (@uri.scheme == 'https')
+      
+      if File.exists? Service.root_ca
+        http.verify_mode = OpenSSL::SSL::VERIFY_PEER
+        http.ca_path = Service.root_ca
+      else
+        message =
+          "net/http couldn't locate this system's root SSL certificate files."+
+          "On Debian Linux systems, these files are located at /etc/ssl/certs "+
+          "(this library's default). For more information, see:\n\n"+
+          "http://codeidol.com/other/rubyckbk/Internet-Services/Making-an-HTTPS-Web-Request\n"+
+          "http://redcorundum.blogspot.com/2008/03/ssl-certificates-and-nethttps.html\n"+
+          "http://notetoself.vrensk.com/2008/09/verified-https-in-ruby\n"
+        raise(message)
+      end
+      
+      http.request(request)
+    end
+    
+    def request_for_method method, attributes=nil
+      request = case method
+      when "get" then Net::HTTP::Get.new(@uri.path)
+      when "put" then Net::HTTP::Put.new(@uri.path)
+      when "post" then Net::HTTP::Post.new(@uri.path)
+      when "delete" then Net::HTTP::Delete.new(@uri.path)
+      end
+      
+      request['accept'] = @media_type
+      request.basic_auth Service.username, Service.password
+      
+      if attributes
+        request.body = {MediaType.hash_key(@media_type) => attributes}.to_json
+        request.content_type = @media_type
+      end
+      
+      request
+    end
+    
+    def validate
+      raise LinkNotDefined unless @uri && @media_class
+    end
+    
+    def decode response
+      if response.content_type.match(/application\/vnd\.com\.chemcaster\.(.*)\+json/)
+        JSON.parse response.body 
+      else
+        response.body
+      end
+    end
+  end
+end

data/lib/chemcaster/media_type.rb

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+module Chemcaster
+  class MediaType  
+    def self.representation name
+      name.match(/application\/vnd\.com\.chemcaster\.(.*)\+json/)
+      
+      unless klass = $1
+        klass = "Zip" if name == 'application/zip'
+      end
+        
+      raise "No such media type: #{name}" unless klass
+      
+      begin
+        Chemcaster.const_get("#{klass}")
+      rescue
+        raise "Unable to create class from media type: #{name}"
+      end
+    end
+    
+    def self.hash_key full_mime_type_name
+      full_mime_type_name.match(/application\/vnd\.com\.chemcaster\.(.*)\+json/)
+      raise "No such media type: #{full_mime_type_name}" unless key = $1
+      
+      begin
+        Chemcaster.const_get(key)
+      rescue
+        raise "No such class: #{key}"
+      end
+      
+      key.downcase
+    end
+  end
+end

data/lib/chemcaster/query.rb

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+module Chemcaster
+  class Query < Item
+    attributes :serialization
+    resources :images, :registry, :executions
+  end
+end

data/lib/chemcaster/registration.rb

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+require File.dirname(__FILE__) + '/../chemcaster/item'
+
+module Chemcaster
+  class Registration < Item
+    attributes :templates
+    resources :substance, :registry
+  end
+end

data/lib/chemcaster/registry.rb

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+require File.dirname(__FILE__) + '/../chemcaster/item'
+
+module Chemcaster
+  class Registry < Item
+    attributes :name, :deletable
+    resources :service, :queries, :structures, :substances,
+      :archives, :registrations
+  end
+end

data/lib/chemcaster/representation.rb

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+module Chemcaster
+  class Representation
+    # class instance variables - see: http://martinfowler.com/bliki/ClassInstanceVariable.html
+    class << self; attr_accessor :resource_ids; end
+    class << self; attr_accessor :attribute_ids; end
+
+    attr_accessor :attributes
+    attr_accessor :link
+    
+    def initialize link, raw
+      @link = link
+      @attributes = {}
+      load_hash raw
+    end
+    
+    def self.attributes *atts
+      self.attribute_ids ||= []
+      atts.each do |m|
+        self.attribute_ids << m.to_s
+        define_method(m) do
+          attributes[m.to_s]
+        end        
+
+        define_method("#{m}=") do |val|
+          attributes.merge!({m.to_s => val})
+        end
+      end
+    end
+    
+    def self.resources *res
+      self.resource_ids ||= self.superclass.resource_ids || []
+      res.each do |id|
+        self.resource_ids << id
+        define_method(id) do  
+          instance_variable_get("@#{id}_link").send('get')
+        end
+      end
+    end
+    
+    def to_json
+      JSON({attributes_name => @attributes})
+    end
+    
+    def attributes_name
+      self.class.to_s.gsub(/Chemcaster::/, '').downcase
+    end
+    
+    protected
+    
+    def load_hash hash
+      self.class.attribute_ids ||= []
+      if hash[name = attributes_name]
+        hash[name].each do |attribute|
+          if self.class.attribute_ids.member? attribute[0]
+            attributes[attribute[0]] = attribute[1]
+          end
+        end
+      end
+
+      self.class.resource_ids ||= []
+      self.class.resource_ids.each do |resource_id|
+        instance_variable_set("@#{resource_id}_link".to_sym, Link.new(hash[resource_id.to_s]))
+      end
+    end
+  end
+end

data/lib/chemcaster/service.rb

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+require File.dirname(__FILE__) + '/../chemcaster/representation'
+
+module Chemcaster
+  class Service < Representation
+    attributes :version
+    resources :registries
+    
+    # Ruby SSL needs to be told the location of the system's SSL CA files.
+    # On Debian Linux systems, these files are located at /etc/ssl/certs,
+    # which is this library's default. For more information, see:
+    # 
+    # http://codeidol.com/other/rubyckbk/Internet-Services/Making-an-HTTPS-Web-Request
+    # http://redcorundum.blogspot.com/2008/03/ssl-certificates-and-nethttps.html
+    # http://notetoself.vrensk.com/2008/09/verified-https-in-ruby
+    
+    @@root_ca = nil; def self.root_ca; @@root_ca; end
+    @@username = nil; def self.username; @@username; end
+    @@password = nil; def self.password; @@password; end
+    
+    def self.connect username, password, options = {}
+      @@username = username; @@password = password
+      
+      @@root_ca = options[:root_ca] || '/etc/ssl/certs'
+      uri = options[:uri] || 'https://chemcaster.com/rest'
+      
+      service_link = Link.new 'uri' => uri,
+        'media_type' => 'application/vnd.com.chemcaster.Service+json', 'name' => 'root'
+      service_link.get
+    end
+  end
+end

data/lib/chemcaster/structure.rb

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+module Chemcaster
+  class Structure < Item
+    attributes :serialization, :inchi
+    resources :images, :registry, :components
+  end
+end

data/lib/chemcaster/substance.rb

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+module Chemcaster
+  class Substance < Item
+    attributes :serialization, :inchi
+    resources :components, :registry, :images, :registration
+  end
+end

data/lib/chemcaster.rb

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+require File.dirname(__FILE__) + "/chemcaster/service"
+require File.dirname(__FILE__) + '/chemcaster/registry'
+require File.dirname(__FILE__) + '/chemcaster/registration'
+require File.dirname(__FILE__) + '/chemcaster/structure'
+require File.dirname(__FILE__) + '/chemcaster/substance'
+require File.dirname(__FILE__) + '/chemcaster/component'
+require File.dirname(__FILE__) + '/chemcaster/query'
+require File.dirname(__FILE__) + '/chemcaster/image'
+require File.dirname(__FILE__) + '/chemcaster/execution'
+require File.dirname(__FILE__) + '/chemcaster/archive'
+require File.dirname(__FILE__) + '/chemcaster/link'
+require File.dirname(__FILE__) + '/chemcaster/index'
+require File.dirname(__FILE__) + '/chemcaster/item'
+require File.dirname(__FILE__) + '/chemcaster/representation'
+require File.dirname(__FILE__) + '/chemcaster/media_type'
+require File.dirname(__FILE__) + '/chemcaster/error'
+require File.dirname(__FILE__) + '/chemcaster/zip'
+
+require 'rubygems'
+require 'json'

metadata

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+--- !ruby/object:Gem::Specification 
+name: chemcaster
+version: !ruby/object:Gem::Version 
+  version: 0.4.1
+platform: ruby
+authors: 
+- Richard Apodaca
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-08-17 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: json
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.1.4
+    version: 
+description: A hypertext-driven Ruby client for the Chemcaster cheminformatics Web services platform.
+email: info@metamolecular.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- README.rdoc
+- Rakefile
+- lib/chemcaster.rb
+- lib/chemcaster/error.rb
+- lib/chemcaster/index.rb
+- lib/chemcaster/item.rb
+- lib/chemcaster/link.rb
+- lib/chemcaster/media_type.rb
+- lib/chemcaster/representation.rb
+- lib/chemcaster/service.rb
+- lib/chemcaster/registry.rb
+- lib/chemcaster/registration.rb
+- lib/chemcaster/substance.rb
+- lib/chemcaster/structure.rb
+- lib/chemcaster/component.rb
+- lib/chemcaster/query.rb
+- lib/chemcaster/execution.rb
+- lib/chemcaster/archive.rb
+- lib/chemcaster/image.rb
+has_rdoc: true
+homepage: http://chemcaster.com
+licenses: []
+
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 3
+summary: A hypertext-driven Ruby client for the Chemcaster cheminformatics Web services platform. End.
+test_files: []
+