metamolecular-chemcaster 0.1.6 → 0.3.1

data/README.rdoc

@@ -1,4 +1,4 @@
-= Chemcaster Ruby API
+= 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
@@ -24,7 +24,24 @@ Installation through the Ruby Gem hosted on GitHub is recommended:
 
    service = Chemcaster::Service.connect 'username', 'password'
 
-=== Loading a Registry
+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'
@@ -34,6 +51,23 @@ Installation through the Ruby Gem hosted on GitHub is recommended:
    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'
@@ -51,4 +85,10 @@ Installation through the Ruby Gem hosted on GitHub is recommended:
 
    service = Chemcaster::Service.connect 'username', 'password'
    registry = service.registries[0]
-   registry.update :name => 'CarboBlocks International, Inc.'
+   registry.update :name => 'CarboBlocks International, Inc.'
+
+
+== API Documentation
+
+RDoc documentation is available at
+{rdoc.info}[http://rdoc.info/projects/metamolecular/chemcaster-ruby].

data/lib/chemcaster/component.rb

@@ -0,0 +1,6 @@
+module Chemcaster
+  class Component < Item
+    attributes :multiplier
+    resources :structure, :substance
+  end
+end

data/lib/chemcaster/image.rb

@@ -1,6 +1,6 @@
 module Chemcaster
   class Image < Item
-    attributes :width, :height, :data
+    attributes :width, :height, :data, :format
     resources :imageable
   end
 end

data/lib/chemcaster/index.rb

@@ -5,7 +5,7 @@ module Chemcaster
     attr_accessor :item_links#, :items
     resources :parent
     
-    def create representation_attributes
+    def create representation_attributes={}
       @create_link.post representation_attributes
     end
     

data/lib/chemcaster/query.rb

@@ -1,6 +1,6 @@
 module Chemcaster
   class Query < Item
-    attributes :molfile
-    resources :images, :registry
+    attributes :serialization
+    resources :images, :registry, :executions
   end
 end

data/lib/chemcaster/registration.rb

@@ -0,0 +1,8 @@
+require File.dirname(__FILE__) + '/../chemcaster/item'
+
+module Chemcaster
+  class Registration < Item
+    attributes :templates
+    resources :substance, :registry
+  end
+end

data/lib/chemcaster/registry.rb

@@ -3,6 +3,7 @@ require File.dirname(__FILE__) + '/../chemcaster/item'
 module Chemcaster
   class Registry < Item
     attributes :name, :deletable
-    resources :queries, :structures
+    resources :service, :queries, :structures, :substances,
+      :archives, :registrations
   end
 end

data/lib/chemcaster/service.rb

@@ -2,7 +2,8 @@ require File.dirname(__FILE__) + '/../chemcaster/representation'
 
 module Chemcaster
   class Service < Representation
-    attr_accessor :registries_link
+    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,
@@ -26,16 +27,5 @@ module Chemcaster
         'media_type' => 'application/vnd.com.chemcaster.Service+json', 'name' => 'root'
       service_link.get
     end
-    
-    def registries
-      @registries_link.get
-    end
-    
-    protected
-    
-    def load_hash hash
-      super
-      @registries_link = Link.new hash['registries']
-    end
   end
 end

data/lib/chemcaster/structure.rb

@@ -1,6 +1,6 @@
 module Chemcaster
   class Structure < Item
-    attributes :name, :molfile
-    resources :images, :registry
+    attributes :serialization, :inchi
+    resources :images, :registry, :components
   end
 end

data/lib/chemcaster.rb

@@ -1,9 +1,14 @@
 require File.dirname(__FILE__) + "/chemcaster/service"
 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'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: metamolecular-chemcaster
 version: !ruby/object:Gem::Version 
-  version: 0.1.6
+  version: 0.3.1
 platform: ruby
 authors: 
 - Richard Apodaca
@@ -45,8 +45,11 @@ files:
 - lib/chemcaster/representation.rb
 - lib/chemcaster/service.rb
 - lib/chemcaster/structure.rb
+- lib/chemcaster/registration.rb
+- lib/chemcaster/component.rb
 has_rdoc: false
 homepage: http://chemcaster.com
+licenses: 
 post_install_message: 
 rdoc_options: []
 
@@ -67,7 +70,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.2.0
+rubygems_version: 1.3.5
 signing_key: 
 specification_version: 2
 summary: A hypertext-driven Ruby client for the Chemcaster cheminformatics Web services platform. End.