From 1c74a684b8b2992d7e6fce5f1a4677d397ec4dd6 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Sat, 18 Jul 2015 08:52:39 +0200
Subject: dataset tests pass

---
 lib/opentox.rb | 179 ++++++++-------------------------------------------------
 1 file changed, 24 insertions(+), 155 deletions(-)

(limited to 'lib/opentox.rb')

diff --git a/lib/opentox.rb b/lib/opentox.rb
index 9be6078..96cefe0 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,172 +1,41 @@
-# defaults to stderr, may be changed to file output (e.g in opentox-service)
-$logger = OTLogger.new(STDERR) 
-$logger.level = Logger::DEBUG
-Mongo::Logger.logger = $logger
-Mongo::Logger.logger.level = Logger::WARN 
-$mongo = Mongo::Client.new($mongodb[:uri])
-
 module OpenTox
 
   # Ruby interface
-  attr_accessor :data
-
-  # Create a new OpenTox object 
-  # @param id [optional,String] ID
-  # @return [OpenTox] OpenTox object
-  def initialize 
-    @data = {}
-    @data["type"] = type
-  end
-
-  def created_at
-    @data["_id"].generation_time
-  end
-
-  # Object metadata (lazy loading)
-  # @return [Hash] Object metadata
-  def metadata 
-    get if exists?
-    @data
-  end
-
-  # Metadata values 
-  # @param predicate [String] Predicate URI
-  # @return [Array, String] Predicate value(s)
-  def [](predicate)
-    predicate = predicate.to_s
-    return nil if @data[predicate].nil?
-    @data[predicate].size == 1 ? @data[predicate].first : @data[predicate]
-  end
-
-  # Set a metadata entry
-  # @param predicate [String] Predicate URI
-  # @param values [Array, String] Predicate value(s)
-  def []=(predicate,values)
-    predicate = predicate.to_s
-    values.is_a?(Array) ? @data[predicate] = [values].flatten : @data[predicate] = values
-  end
-
-  def id
-    @data["_id"]
-  end
-
-  def exists? 
-    nr_items = $mongo[collection].find(:_id => @data["_id"]).count
-    nr_items > 0 ? true : false
-  end
-
-  # Get object from webservice
-  # @param [String,optional] mime_type
-  def get 
-    resource_not_found_error("#{@data[:type]} with ID #{@data["_id"]} not found.") unless exists?
-    @data = $mongo[collection].find(:_id => @data["_id"]).first
-  end
-
-  def save
-    @data["_id"] = $mongo[collection].insert_one(@data).inserted_id
-  end
-
-  # partial update 
-  def update metadata
-    $mongo[collection].find(:_id => @data["_id"]).find_one_and_replace('$set' => metadata)
-  end
-
-  # Save object at webservice (replace or create object)
-  def put 
-    #@data.delete("_id") # to enable updates
-    $mongo[collection].find(:_id => @data["_id"]).find_one_and_replace(@data, :upsert => true)
-  end
-
-  # Delete object at webservice
-  def delete 
-    $mongo[collection].find(:_id => @data["_id"]).find_one_and_delete
-  end
-
-  # @return [String] converts OpenTox object into html document (by first converting it to a string)
-  def to_html
-    @data.to_json.to_html
-  end
-
-  def type
-    self.class.to_s.split('::').last
-  end
-
-  def collection
-    type.downcase
-  end
-
-  # short access for metadata keys title, description and type
-  [ :title , :description ].each do |method|
-    send :define_method, method do 
-      self[method]
-    end
-    send :define_method, "#{method}=" do |value|
-      self[method] = value
-    end
-  end
-
-  # define class methods within module
-  def self.included(base)
-    base.extend(ClassMethods)
-  end
-
-  module ClassMethods
-    def subjectid
-      RestClientWrapper.subjectid
-    end
-    def subjectid=(subjectid)
-      RestClientWrapper.subjectid = subjectid
-    end
-  end
 
-  # create default OpenTox classes with class methods
-  # (defined in opentox-client.rb)
+  # create default OpenTox classes (defined in opentox-client.rb)
+  # provides Mongoid's query and persistence methods
+  # http://mongoid.org/en/mongoid/docs/persistence.html
+  # http://mongoid.org/en/mongoid/docs/querying.html
   CLASSES.each do |klass|
     c = Class.new do
       include OpenTox
+      include Mongoid::Document
+      include Mongoid::Timestamps
+      store_in collection: klass.downcase.pluralize
 
-      def self.all 
-        $mongo[collection].find.collect do |data|
-          f = self.new
-          f.data = data
-          f
-        end
-      end
+      field :title, type: String
+      field :description, type: String
 
-      def self.find_id id
-        self.find(:_id => id)
+      # TODO check if needed
+      def self.subjectid
+        RestClientWrapper.subjectid
       end
-
-      #@example fetching a model
-      #  OpenTox::Model.find(<model-id>) -> model-object
-      def self.find metadata
-        f = self.new
-        items = $mongo[collection].find metadata
-        items.count > 0 ? f.data = items.first : f = nil
-        f
+      def self.subjectid=(subjectid)
+        RestClientWrapper.subjectid = subjectid
       end
+    end
+    OpenTox.const_set klass,c
+  end
 
-      def self.create metadata
-        object = self.new 
-        object.data = metadata
-        object.save
-        object.get
-        object
-      end
+  def type
+    self.class.to_s.split('::').last
+  end
 
-      def self.find_or_create metadata
-        search = metadata
-        search.delete("_id")
-        ids = $mongo[collection].find(search).distinct(:_id)
-        ids.empty? ? self.create(metadata) : self.find_id(ids.first)
-      end
+  # Serialisation
 
-      private 
-      def self.collection
-        self.to_s.split('::').last.downcase
-      end
-    end
-    OpenTox.const_set klass,c
+  # @return [String] converts OpenTox object into html document (by first converting it to a string)
+  def to_html
+    self.to_json.to_html
   end
 
 end
-- 
cgit v1.2.3