netica 0.0.21-java → 1.0.0.pre-java

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 231e9845a73e728268cbc2db7801e44cf3d46c68
+  data.tar.gz: 30512cdcf0a3573a8dfe1c7f5f7546442a87fc14
+SHA512:
+  metadata.gz: d834a08e817f3e579c14906fb70f08680c8f0ab52772757ace63be7293f507f37e863e1127b7b028653e495851c21c5ae24b8e525b2e78a76c6979076f0d56aa
+  data.tar.gz: 16ed7f4c125df781c6b206dd8207db5e8fc22892f6ddde12d37f344b8ec58be691ef6923b6948e894d361e7a9fc1646e44fd60e86ce84d69ef0ce24f72b80690

data/.ruby-version

@@ -1 +1 @@
-jruby-1.7.3
+jruby-1.7.9

data/README.md

@@ -67,9 +67,11 @@ Then, re-read the value of the Belief node.
 
 ## Release Notes
 
-### Version 0.0.21
+### Version 1.0.0.pre
 
-Search multiple locations for NeticaJ.jar. 
+* Split ActiveNetwork's out-of-process storage and retrieval methods into a new subclass, StorableNetwork.
+* Add filename parameter to StorableNetwork#find, allowing a stored network's .dne file to be updated.
+* Built and tested with JRuby 1.7.9
 
 ### Version 0.0.20
 

data/examples/ChestClinicv2.dne

@@ -0,0 +1,110 @@
+// ~->[DNET-1]->~
+
+// File created by an unlicensed user using Netica 5.04 on 10/01/12 at 20:20:06.
+
+bnet ChestClinic {
+autoupdate = FALSE;
+
+node VisitAntarctica {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (visit, no_visit);
+	statetitles = ("Visited Antarctica within the last 3 years", );
+	parents = ();
+	probs = 
+		// Visited Antarctica wit no visit 
+		  (0.01,        0.99);
+	title = "Visit to Antarctica";
+	};
+
+node Tuberculosis {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (present, absent);
+	parents = (VisitAntarctica);
+	probs = 
+		// present      absent        // VisitAntarctica        
+		  (0.05,        0.95,         // Visited Antarctica wit 
+		   0.01,        0.99);        // no visit         ;
+	};
+
+node Smoking {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (smoker, nonsmoker);
+	parents = ();
+	probs = 
+		// smoker       nonsmoker    
+		  (0.5,         0.5);
+	};
+
+node Cancer {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (present, absent);
+	parents = (Smoking);
+	probs = 
+		// present      absent        // Smoking   
+		  (0.1,         0.9,          // smoker    
+		   0.01,        0.99);        // nonsmoker ;
+	title = "Lung Cancer";
+	};
+
+node TbOrCa {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = DETERMIN;
+	states = (true, false);
+	parents = (Tuberculosis, Cancer);
+	functable = 
+		                    // Tuberculosis Cancer  
+		  (true,            // present      present 
+		   true,            // present      absent  
+		   true,            // absent       present 
+		   false);          // absent       absent  ;
+	equation = "TbOrCa (Tuberculosis, Cancer) = Tuberculosis || Cancer";
+	title = "Tuberculosis or Cancer";
+	};
+
+node XRay {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (abnormal, normal);
+	parents = (TbOrCa);
+	probs = 
+		// abnormal     normal        // TbOrCa 
+		  (0.98,        0.02,         // true   
+		   0.05,        0.95);        // false  ;
+	};
+
+node Bronchitis {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (present, absent);
+	parents = (Smoking);
+	probs = 
+		// present      absent        // Smoking   
+		  (0.6,         0.4,          // smoker    
+		   0.3,         0.7);         // nonsmoker ;
+	};
+
+node Dyspnea {
+	kind = NATURE;
+	discrete = TRUE;
+	chance = CHANCE;
+	states = (present, absent);
+	parents = (TbOrCa, Bronchitis);
+	probs = 
+		// present      absent        // TbOrCa Bronchitis 
+		  (0.9,         0.1,          // true   present    
+		   0.7,         0.3,          // true   absent     
+		   0.8,         0.2,          // false  present    
+		   0.1,         0.9);         // false  absent     ;
+	};
+};

data/lib/netica.rb

@@ -1,20 +1,5 @@
 require 'java'
-
-loaded_netica_j = false
-
-locations = ['/Library/Java/Extensions/NeticaJ.jar', '/System/Library/Java/Extensions/NeticaJ.jar', '/usr/lib/java/NeticaJ.jar', '/lib/NeticaJ.jar']
-locations.each do |fname| 
-  if !loaded_netica_j && File.exists?(fname)
-    begin
-      require fname
-      loaded_netica_j = true
-    rescue LoadError
-      puts "NeticaJ.jar not found at '#{fname}'"
-    end
-  end
-end
-  
-raise "NeticaJ library files not found in #{locations}. See https://github.com/disruptive/netica for installation instructions." unless loaded_netica_j
+require '/lib/NeticaJ.jar'
 
 require "netica/version"
 require "netica/environ"
@@ -24,6 +9,7 @@ require "netica/node"
 require "netica/node_list"
 require "netica/bayes_network"
 require "netica/active_network"
+require "netica/storable_network"
 require "netica/java_library_path"
 
 module Netica

data/lib/netica/active_network.rb

@@ -6,7 +6,7 @@ module Netica
     class ActiveNetwork::NodeNotFound < RuntimeError; end
     class ActiveNetwork::NetworkNotFound < RuntimeError; end
 
-    attr_accessor :network, :token, :created_at, :updated_at, :reloaded_at, :in_use
+    attr_accessor :network, :token, :created_at, :updated_at, :reloaded_at, :in_use, :filepath
 
     def initialize(token, filepath = nil)
       Netica::NeticaLogger.info "Initializing #{self.class} for #{token}."
@@ -16,7 +16,8 @@ module Netica
       self.in_use     = false
       
       if filepath
-        self.network = BayesNetwork.new(filepath)
+        self.filepath = filepath
+        self.network  = BayesNetwork.new(filepath)
       end
       processor = Netica::Environment.instance
       processor.active_networks << self
@@ -58,21 +59,11 @@ module Netica
       }
     end
 
-    # Save ActiveNetwork to an associated redis store, if one is defined.
-    #
-    # @return [true,false,nil] outcome of redis.set, or nil if redis is not found
-    def save
-      if Netica::Environment.instance.redis
-        return Netica::Environment.instance.redis.set(token, JSON.dump(state))
-      end
-    end
-
     # Retrieve ActiveNetwork from current Netica Environment instance
-    # or an associated redis store, if one is defined.
     #
     # @param token [String] identifying token for ActiveNetwork sought
     # @return [ActiveNetwork] ActiveNetwork object found
-    def self.find(token, load_from_storage = true)
+    def self.find(token)
       environment = Netica::Environment.instance
       Netica::NeticaLogger.info "Searching in #{environment.network_container.class} #{environment.network_container.object_id} (length: #{environment.network_container.length}) for #{token}."
       environment.network_container.each do |an|
@@ -85,62 +76,31 @@ module Netica
         end
       end
       Netica::NeticaLogger.info "Network #{token} not found in current instance #{environment.object_id}."
-      if Netica::Environment.instance.redis
-        stored_state = Netica::Environment.instance.redis.get(token)
-        if stored_state && load_from_storage
-          hash = JSON.parse(stored_state)
-          active_network = Object.const_get(hash['class']).new(token)
-          active_network.load_from_saved_state(hash)
-          Netica::NeticaLogger.info "Network #{token} reloaded from saved state: #{hash}"
-          return active_network
-        elsif stored_state
-          return stored_state
-        else
-          Netica::NeticaLogger.info "Network #{token} not found in redis."
-        end
-      end
       return nil
     end
     
     # Destroy the ActiveNetwork
     #
-    # @param memory [Boolean] destroy the in-memory object?, default is `true`
-    # @param storage [Boolean] destroy object in redis?, default is `true`
-    # @return [Hash] outcome of deletion attempts per storage location
-    def destroy(memory = true, storage = true)
-      outcome = { token: token, deletion: { memory: nil, redis: nil}}
+    # @return [Hash] outcome of deletion attempt
+    def destroy
+      outcome = { token: token, deletion: { memory: nil }}
       environment = Netica::Environment.instance
-
-      if memory
-        rejection = environment.network_container.reject!{|network| network.token == token}
-        outcome[:deletion][:memory] = rejection.is_a?(Array)
-      end
-        
-      if environment.redis && storage == true
-        outcome[:deletion][:redis] = (environment.redis.del(token) > 0)
-      end
+      rejection = environment.network_container.reject!{|network| network.token == token}
+      outcome[:deletion][:memory] = rejection.is_a?(Array)
       outcome
     end
     
-    # Destroy a saved network
-    #
-    # @return [Hash] outcome of deletion attempts per storage location
-    def self.destroy_by_token(token)
-      outcome = { token: token, deletion: { memory: nil, redis: nil}}
-      environment = Netica::Environment.instance
-
-      if environment.redis
-        outcome[:deletion][:redis] = (environment.redis.del(token) > 0)
-      end
-
-      outcome
-    end
     
-    # Load ActiveNetwork from a saved state
+    # Load ActiveNetwork from a Hash
     #
     # @param hash [Hash] network state to be restored
     def load_from_saved_state(hash)
-      self.network = BayesNetwork.new(hash["network"]["dne_file_path"])
+      if filepath
+        self.network = BayesNetwork.new(filepath)
+      else
+        self.filepath = hash["network"]["dne_file_path"]
+        self.network = BayesNetwork.new(hash["network"]["dne_file_path"])
+      end
       self.reloaded_at = Time.now
       self.network.load_from_state(hash["network"])
     end

data/lib/netica/bayes_network.rb

@@ -42,11 +42,16 @@ module Netica
     end
 
     def load_from_state(network_hash)
-      Netica::NeticaLogger.info "Loading state from network_hash => #{network_hash}"
       network_hash["decision_nodes"].each do |node_name, node_value|
         Netica::NeticaLogger.info "Setting #{node_name} => #{node_value}"
         node(node_name).value = node_value
       end
+      
+      network_hash["nature_nodes"].each do |node_name, node_value_hash|
+        next unless node_name == 'XRay'
+        Netica::NeticaLogger.info "Setting #{node_name} => #{node_value_hash}"
+        node(node_name).value = node_value_hash
+      end
     end
 
     def state

data/lib/netica/node.rb

@@ -65,7 +65,16 @@ class Java::NorsysNetica::Node
       finding().setReal(new_value)
     elsif nature_node?
       Netica::NeticaLogger.info "Nature Node: Setting #{kind} #{type} node #{self.name} to #{new_value}"
-      finding.enterState(new_value)
+      if new_value.is_a?(Hash)
+        value_array = []
+        states.each do |s|
+          value_array << new_value[s.name]
+        end
+        finding().enter_likelihood(value_array)
+      else
+        finding.enterState(new_value)
+      end
+      Netica::NeticaLogger.info beliefs
     else
       throw "Could not set value for #{kind} #{type} node #{self.name} to #{new_value}"
     end

data/lib/netica/storable_network.rb

@@ -0,0 +1,74 @@
+# provides a persistable object container for a Netica Bayes net.
+class StorableNetwork < Netica::ActiveNetwork
+
+  # Save StorableNetwork to an associated redis store, if one is defined.
+  #
+  # @return [true,false,nil] outcome of redis.set, or nil if redis is not found
+  def save
+    if Netica::Environment.instance.redis
+      return Netica::Environment.instance.redis.set(token, JSON.dump(state))
+    end
+  end
+
+  # Retrieve ActiveNetwork from current Netica Environment instance
+  # or an associated redis store, if one is defined.
+  #
+  # @param token [String] identifying token for ActiveNetwork sought
+  # @return [ActiveNetwork] ActiveNetwork object found
+  def self.find(token, load_from_storage = true, filepath = nil)
+    environment = Netica::Environment.instance
+    redis = environment.redis
+    found_network = super(token)
+    if found_network.nil? && redis
+      stored_state = redis.get(token)
+      if stored_state && load_from_storage
+        hash = JSON.parse(stored_state)
+        found_network = Object::const_get(hash['class']).new(token)
+        found_network.filepath = filepath
+        found_network.load_from_saved_state(hash)
+        Netica::NeticaLogger.info "Network #{token} reloaded from saved state: #{hash}"
+        Netica::NeticaLogger.info "#{token} reloaded state: #{found_network.state}"
+        return found_network
+      elsif stored_state
+        return stored_state
+      else
+        Netica::NeticaLogger.info "Network #{token} not found in redis."
+      end
+    end
+    return nil
+  end
+  
+  # Destroy the ActiveNetwork
+  #
+  # @param memory [Boolean] destroy the in-memory object?, default is `true`
+  # @param storage [Boolean] destroy object in redis?, default is `true`
+  # @return [Hash] outcome of deletion attempts per storage location
+  def destroy(memory = true, storage = true)
+    outcome = { token: token, deletion: { memory: nil, redis: nil}}
+    environment = Netica::Environment.instance
+
+    if memory
+      rejection = environment.network_container.reject!{|network| network.token == token}
+      outcome[:deletion][:memory] = rejection.is_a?(Array)
+    end
+      
+    if environment.redis && storage == true
+      outcome[:deletion][:redis] = (environment.redis.del(token) > 0)
+    end
+    outcome
+  end
+  
+  # Destroy a saved network
+  #
+  # @return [Hash] outcome of deletion attempts per storage location
+  def self.destroy_by_token(token)
+    outcome = { token: token, deletion: { memory: nil, redis: nil}}
+    environment = Netica::Environment.instance
+
+    if environment.redis
+      outcome[:deletion][:redis] = (environment.redis.del(token) > 0)
+    end
+
+    outcome
+  end
+end

data/lib/netica/version.rb

@@ -1,3 +1,3 @@
 module Netica
-  VERSION = "0.0.21"
+  VERSION = "1.0.0.pre"
 end

data/spec/netica/active_network_spec.rb

@@ -31,7 +31,7 @@ describe Netica::ActiveNetwork do
       end
       
       it "should be returned when searched for" do
-        Netica::ActiveNetwork.find("fake_token_identifier", false).should === @active_network
+        Netica::ActiveNetwork.find("fake_token_identifier").should === @active_network
       end
 
       context "the tuberculosis node" do
@@ -49,67 +49,8 @@ describe Netica::ActiveNetwork do
         Netica::Environment.instance.active_networks.length.should eq(1)
         outcome = @active_network.destroy
         outcome[:deletion][:memory].should be_true
-        outcome[:deletion][:redis].should be_nil
         Netica::Environment.instance.active_networks.length.should eq(0)
       end
     end
   end
-  
-  context "with redis" do
-    before(:all) do
-      Java::NorsysNetica::Environ.__persistent__ = true
-      redis_settings = { :redis => { :host => "127.0.0.1", :port => 6379 }}
-      Netica::Environment.engage(redis_settings)
-      @redis = Redis.new(redis_settings)
-    end
-    
-    after(:all) do
-      Netica::Environment.instance.processor.finalize
-    end
-    
-    context "with ChestClinic.dne" do
-      before(:all) do
-        @active_network = Netica::ActiveNetwork.new("fake_token_identifier", "#{File.dirname(__FILE__)}/../../examples/ChestClinic.dne")
-        @active_network_token = @active_network.token
-      end
-
-      describe "#save" do
-        it "should be savable" do
-          @redis.get(@active_network_token).should be_nil
-          @active_network.save
-          @redis.get(@active_network_token).should_not be_nil
-        end
-      end
-    
-      describe "#destroy" do
-        it "should be deletable" do
-          Netica::Environment.instance.active_networks.length.should eq(1)
-          @redis.get(@active_network_token).should_not be_nil
-          outcome = @active_network.destroy
-          outcome[:deletion][:memory].should be_true
-          outcome[:deletion][:redis].should be_true
-          @redis.get(@active_network_token).should be_nil
-          Netica::Environment.instance.active_networks.length.should eq(0)
-        end
-      end
-      
-      describe "#destroy_by_token" do
-        context "A stored active network" do
-          it "should be deletable" do
-            @active_network.save
-            @active_network.destroy(true, false)
-            @redis.get(@active_network_token).should be_true
-            
-            outcome = Netica::ActiveNetwork.destroy_by_token(@active_network_token)
-            outcome[:deletion][:memory].should be_nil
-            outcome[:deletion][:redis].should be_true
-            
-            @redis.get(@active_network_token).should be_nil
-            Netica::Environment.instance.active_networks.length.should eq(0)
-          end
-        end
-      end
-    end
-  end
 end
-

data/spec/netica/storable_network_spec.rb

@@ -0,0 +1,87 @@
+require 'spec_helper'
+
+describe StorableNetwork do
+  context "with redis" do
+    before(:all) do
+      Java::NorsysNetica::Environ.__persistent__ = true
+      redis_settings = { :redis => { :host => "127.0.0.1", :port => 6379 }}
+      Netica::Environment.engage(redis_settings)
+      @redis = Redis.new(redis_settings)
+    end
+    
+    after(:all) do
+      Netica::Environment.instance.processor.finalize
+    end
+    
+    context "with ChestClinic.dne" do
+      before(:all) do
+        @active_network = StorableNetwork.new("storable_fake_token_identifier", "#{File.dirname(__FILE__)}/../../examples/ChestClinic.dne")
+        @active_network_token = @active_network.token
+      end
+      
+      after(:all) do
+        @redis.del("storable_fake_token_identifier")
+      end
+
+      describe "#save" do
+        it "should be savable" do
+          @redis.get(@active_network_token).should be_nil
+          @active_network.save
+          @redis.get(@active_network_token).should_not be_nil
+        end
+      end
+    
+      describe "#destroy" do
+        it "should be deletable" do
+          Netica::Environment.instance.active_networks.length.should eq(1)
+          @redis.get(@active_network_token).should_not be_nil
+          outcome = @active_network.destroy
+          outcome[:deletion][:memory].should be_true
+          outcome[:deletion][:redis].should be_true
+          @redis.get(@active_network_token).should be_nil
+          Netica::Environment.instance.active_networks.length.should eq(0)
+        end
+      end
+      
+      describe "#destroy_by_token" do
+        context "A stored active network" do
+          it "should be deletable" do
+            @active_network.save
+            @active_network.destroy(true, false)
+            @redis.get(@active_network_token).should be_true
+            
+            outcome = StorableNetwork.destroy_by_token(@active_network_token)
+            outcome[:deletion][:memory].should be_nil
+            outcome[:deletion][:redis].should be_true
+            
+            @redis.get(@active_network_token).should be_nil
+            Netica::Environment.instance.active_networks.length.should eq(0)
+          end
+        end
+      end
+      
+      describe "#find" do
+        it "should be reloadable" do
+          @active_network.network.node("Tuberculosis").value("present").should be_less_than 0.011
+          @active_network.network.node("XRay").value = "abnormal"
+
+          @active_network.network.node("Tuberculosis").value("present").should be_greater_than 0.092
+          @active_network.save
+          
+          @active_network.destroy(true, false)
+          
+          Netica::Environment.instance.active_networks.length.should eq(0)
+          
+          @reloaded_network = StorableNetwork.find(@active_network_token, true)
+          Netica::Environment.instance.active_networks.length.should eq(1)
+          
+          @reloaded_network.network.node("Tuberculosis").value("present").should be_greater_than 0.092
+          
+          @reloaded_network.destroy
+          Netica::Environment.instance.active_networks.length.should eq(0)
+        end
+      end
+    end
+  end
+end
+

metadata

@@ -1,32 +1,27 @@
 --- !ruby/object:Gem::Specification
 name: netica
 version: !ruby/object:Gem::Version
-  prerelease:
-  version: 0.0.21
+  version: 1.0.0.pre
 platform: java
 authors:
 - Jerry Richardson
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2014-06-03 00:00:00.000000000 Z
+date: 2013-12-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: redis
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
-    none: false
+        version: '0'
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
-        version: !binary |-
-          MA==
-    none: false
+        version: '0'
   prerelease: false
   type: :development
 description: Netica Bayes Network Management
@@ -36,15 +31,16 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- ".gitignore"
-- ".rspec"
-- ".ruby-version"
+- .gitignore
+- .rspec
+- .ruby-version
 - CONTRIBUTING.md
 - Gemfile
 - LICENSE.txt
 - README.md
 - Rakefile
 - examples/ChestClinic.dne
+- examples/ChestClinicv2.dne
 - examples/chest_clinic.rb
 - lib/netica.rb
 - lib/netica/active_network.rb
@@ -57,43 +53,43 @@ files:
 - lib/netica/node_list.rb
 - lib/netica/railtie.rb
 - lib/netica/state.rb
+- lib/netica/storable_network.rb
 - lib/netica/version.rb
 - lib/tasks/netica.rake
 - log/.gitignore
 - netica.gemspec
 - spec/netica/active_network_spec.rb
 - spec/netica/environment_spec.rb
+- spec/netica/storable_network_spec.rb
 - spec/netica_spec.rb
 - spec/spec_helper.rb
 homepage: http://disruptive.github.io/netica/
 licenses:
 - MIT
+metadata: {}
 post_install_message:
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
-      version: !binary |-
-        MA==
-  none: false
+      version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>'
     - !ruby/object:Gem::Version
-      version: !binary |-
-        MA==
-  none: false
+      version: 1.3.1
 requirements: []
 rubyforge_project:
-rubygems_version: 1.8.24
+rubygems_version: 2.1.9
 signing_key:
-specification_version: 3
+specification_version: 4
 summary: Tools to manage Bayes Networks with the NeticaJ API
 test_files:
 - spec/netica/active_network_spec.rb
 - spec/netica/environment_spec.rb
+- spec/netica/storable_network_spec.rb
 - spec/netica_spec.rb
 - spec/spec_helper.rb