bio-band 0.1.0

data/lib/bio-band/weka/db/db.rb

@@ -0,0 +1,74 @@
+require 'java'
+
+module Weka
+	module Db
+		java_import 'weka.core.Instances'
+		java_import 'weka.core.converters.DatabaseLoader'
+		java_import 'weka.core.converters.DatabaseSaver'
+
+		# Query data from a MySQL database
+		# * *Args*    :
+      	#   - +db_url+ -> The database URL
+      	#   - +user+ -> User name
+      	#   - +psw+ -> Password
+      	#   - +quey+ -> A query to submit
+		def Db.query_mysql(db_url,user,psw,query)
+			open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
+				open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_mysql'),'r') do |f|
+					f.each_line do |line|
+						out.write line
+					end
+				end
+			end
+		    loader = DatabaseLoader.new
+			loader.setSource(db_url,user,psw)
+			loader.setQuery(query)
+			data = loader.getDataSet
+			return data
+		end
+
+		# Query data from a PostgreSQL database
+		# * *Args*    :
+      	#   - +db_url+ -> The database URL
+      	#   - +user+ -> User name
+      	#   - +psw+ -> Password
+      	#   - +quey+ -> A query to submit
+		def Db.query_postgresql(db_url,user,psw,query)
+			open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
+				open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_postgresql'),'r') do |f|
+					f.each_line do |line|
+						out.write line
+					end
+				end
+			end
+		    loader = DatabaseLoader.new
+			loader.setSource(db_url,user,psw)
+			loader.setQuery(query)
+			data = loader.getDataSet
+			return data
+		end
+
+		# Save an Instances class object to a Mysql database
+		# * *Args*    :
+      	#   - +db_url+ -> The database URL
+      	#   - +user+ -> User name
+      	#   - +psw+ -> Password
+      	#   - +data+ -> An Instances class object 
+      	#   - +table+ -> The destination table in the database     	
+		def Db.save_to_mysql(db_url,user,psw,data,table)
+			open([[Dir.home],["DatabaseUtils.props"]].join("/"),'w') do |out|
+				open(File.join(File.dirname(File.expand_path(__FILE__)), 'DatabaseUtils_mysql'),'r') do |f|
+					f.each_line do |line|
+						out.write line
+					end
+				end
+			end
+			saver = DatabaseSaver.new
+			saver.setDestination(db_url,user,psw)
+			saver.setTableName(table)
+			saver.setRelationForTableName(false)
+			saver.setInstances(data)
+			saver.writeBatch
+		end
+	end
+end

data/lib/bio-band/weka/filters/supervised/attribute/attribute.rb

@@ -0,0 +1,25 @@
+$:.unshift(File.expand_path(File.join(File.dirname(__FILE__),"../")))
+require 'java'
+require 'supervised_utils'
+
+module Weka
+  module Filter
+  	module Supervised
+  		module Attribute
+  			java_import "weka.core.Utils"
+  			java_import "weka.filters.Filter"
+   			java_import "weka.filters.supervised.attribute.AttributeSelection"
+        java_import "weka.filters.supervised.attribute.Discretize"
+
+   			class AttributeSelection
+          include Supervised_Util
+   			end
+
+        class Discretize  
+          include Supervised_Util
+        end
+  			
+  		end
+  	end
+  end
+end

data/lib/bio-band/weka/filters/supervised/instance/instance.rb

@@ -0,0 +1,17 @@
+$:.unshift(File.expand_path(File.join(File.dirname(__FILE__),"../")))
+require 'java'
+require 'supervised_utils'
+
+module Weka
+  module Filter
+  	module Supervised
+  		module Instance
+  			java_import "weka.filters.supervised.instance.Resample"
+
+        class Resample
+          include Supervised_Util
+        end
+  		end
+  	end
+  end
+end

data/lib/bio-band/weka/filters/supervised/supervised_utils.rb

@@ -0,0 +1,32 @@
+module Supervised_Util
+	java_import "weka.core.Utils"
+	java_import "weka.filters.Filter"
+
+	#Instance methods list
+	def filter_options
+		begin
+			listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
+		rescue
+			puts  "Sorry, list option is available for this filter"
+		end
+	end
+
+	def set_filter_options(options_string)
+		options = Utils.splitOptions(options_string)
+		setOptions(options)
+	end
+
+	def set_data(instances)
+		setInputFormat(instances)
+		@input = instances
+	end
+
+	def description
+    begin; puts globalInfo; rescue; NoMethodError; puts "Sorry, no description available for this filter"; end
+	end
+
+	def use
+		Filter.useFilter(@input,self)
+	end
+
+end

data/lib/bio-band/weka/filters/unsupervised/attribute/attribute.rb

@@ -0,0 +1,70 @@
+$:.unshift(File.expand_path(File.join(File.dirname(__FILE__),"../")))
+require 'java'
+require 'unsupervised_utils'
+
+module Weka
+  module Filter
+  	module Unsupervised
+  		module Attribute
+
+  			java_import "weka.filters.unsupervised.attribute.Add"
+  			java_import "weka.filters.unsupervised.attribute.Center"
+  			java_import "weka.filters.unsupervised.attribute.Discretize"
+  			java_import "weka.filters.unsupervised.attribute.NominalToString"
+  			java_import "weka.filters.unsupervised.attribute.Normalize"
+  			java_import "weka.filters.unsupervised.attribute.Remove"
+  			java_import "weka.filters.unsupervised.attribute.Standardize"
+  			java_import "weka.filters.unsupervised.attribute.PrincipalComponents"
+        java_import "weka.filters.unsupervised.attribute.StringToWordVector"
+  			java_import "weka.core.Utils"
+  			java_import "weka.filters.Filter"
+
+  			class Add
+          include Unsupervised_Util
+  			end
+
+  			class Center
+          include Unsupervised_Util
+  			end
+
+  			class Discretize
+          include Unsupervised_Util
+  			end
+
+  			class NominalToString
+          include Unsupervised_Util
+  			end
+
+  			class Normalize
+          include Unsupervised_Util
+  			end
+
+  			class PrincipalComponents
+          include Unsupervised_Util
+  			end
+
+  			class Remove
+          include Unsupervised_Util
+  			end
+
+  			class Standardize
+          include Unsupervised_Util
+  			end
+
+        class StringToWordVector
+          include Unsupervised_Util
+        end
+
+        Weka::Filter::Unsupervised::Attribute::PrincipalComponents.__persistent__ = true
+        Weka::Filter::Unsupervised::Attribute::Add.__persistent__ = true
+        Weka::Filter::Unsupervised::Attribute::Standardize.__persistent__ = true
+        Weka::Filter::Unsupervised::Attribute::Remove.__persistent__ = true
+        Weka::Filter::Unsupervised::Attribute::Normalize.__persistent__ = true
+        Weka::Filter::Unsupervised::Attribute::Discretize.__persistent__ = true
+        Weka::Filter::Unsupervised::Attribute::Center.__persistent__ = true
+        Weka::Filter::Unsupervised::Attribute::NominalToString.__persistent__ = true
+        Weka::Filter::Unsupervised::Attribute::StringToWordVector.__persistent__ = true
+  		end
+  	end
+  end
+end

data/lib/bio-band/weka/filters/unsupervised/instance/instance.rb

@@ -0,0 +1,48 @@
+$:.unshift(File.expand_path(File.join(File.dirname(__FILE__),"../")))
+require 'java'
+require 'unsupervised_utils'
+
+module Weka
+  module Filter
+  	module Unsupervised
+  		module Instance
+  			java_import "weka.core.Utils"
+  			java_import "weka.filters.Filter"
+  			java_import "weka.filters.unsupervised.instance.Normalize"
+  			java_import "weka.filters.unsupervised.instance.NonSparseToSparse"
+  			java_import "weka.filters.unsupervised.instance.SparseToNonSparse"
+  			java_import "weka.filters.unsupervised.instance.RemoveRange"
+  			java_import "weka.filters.unsupervised.instance.SubsetByExpression"
+        java_import "weka.filters.unsupervised.instance.RemoveWithValues"
+
+  			class Normalize
+          include Unsupervised_Util
+  			end
+
+  			class NonSparseToSparse
+          include Unsupervised_Util
+  			end
+
+  			class RemoveRange
+          include Unsupervised_Util
+  			end
+
+        class RemoveWithValues
+          include Unsupervised_Util
+        end
+
+  			class SparseToNonSparse
+          include Unsupervised_Util
+  			end
+
+  			class SubsetByExpression
+          include Unsupervised_Util
+  				def description
+            begin; puts globalInfo.split("\n").each {|line| puts line}; rescue; NoMethodError; puts "Sorry, no description available for this filter"; end
+  				end
+  			end
+
+  		end
+  	end
+  end
+end

data/lib/bio-band/weka/filters/unsupervised/unsupervised_utils.rb

@@ -0,0 +1,33 @@
+module Unsupervised_Util
+	java_import "weka.core.Utils"
+	java_import "weka.filters.Filter"
+
+	#Instance methods list
+	def filter_options
+		begin
+			listOptions.each {|key| puts "#{key.synopsis} #{key.description}"}
+		rescue
+			puts  "Sorry, list option is available for this filter"
+		end
+	end
+
+	def set_filter_options(options_string)
+		options = Utils.splitOptions(options_string)
+		setOptions(options)
+	end
+
+	def set_data(instances)
+		setInputFormat(instances)
+		@input = instances
+	end
+
+	def description
+    begin; puts globalInfo; rescue; NoMethodError; puts "Sorry, no description available for this filter"; end
+	end
+
+	def use
+		Filter.useFilter(@input,self)
+	end
+
+end
+

data/resources/weather.csv

@@ -0,0 +1,15 @@
+outlook,temperature,humidity,windy,play
+sunny,85,85,FALSE,no
+sunny,80,90,TRUE,no
+overcast,83,86,FALSE,yes
+rainy,70,96,FALSE,yes
+rainy,68,80,FALSE,yes
+rainy,65,70,TRUE,no
+overcast,64,65,TRUE,yes
+sunny,72,95,FALSE,no
+sunny,69,70,FALSE,yes
+rainy,75,80,FALSE,yes
+sunny,75,70,TRUE,yes
+overcast,72,90,TRUE,yes
+overcast,81,75,FALSE,yes
+rainy,71,91,TRUE,no

data/resources/weather.numeric.arff

@@ -0,0 +1,23 @@
+@relation weather
+
+@attribute outlook {sunny, overcast, rainy}
+@attribute temperature real
+@attribute humidity real
+@attribute windy {TRUE, FALSE}
+@attribute play {yes, no}
+
+@data
+sunny,85,85,FALSE,no
+sunny,80,90,TRUE,no
+overcast,83,86,FALSE,yes
+rainy,70,96,FALSE,yes
+rainy,68,80,FALSE,yes
+rainy,65,70,TRUE,no
+overcast,64,65,TRUE,yes
+sunny,72,95,FALSE,no
+sunny,69,70,FALSE,yes
+rainy,75,80,FALSE,yes
+sunny,75,70,TRUE,yes
+overcast,72,90,TRUE,yes
+overcast,81,75,FALSE,yes
+rainy,71,91,TRUE,no

data/spec/bio-band_spec.rb

@@ -0,0 +1,7 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioBand" do
+  it "fails" do
+    fail "hey buddy, you should probably rename this file and start specing for real"
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,12 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-band'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

@@ -0,0 +1,302 @@
+--- !ruby/object:Gem::Specification
+name: bio-band
+version: !ruby/object:Gem::Version
+  prerelease:
+  version: 0.1.0
+platform: ruby
+authors:
+- arrigonialberto86
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2013-07-25 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: bundler
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.3.5
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.3.5
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: jbundler
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: ruport
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: rspec
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: json
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MA==
+    none: false
+  prerelease: false
+  type: :development
+- !ruby/object:Gem::Dependency
+  name: bio
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+    none: false
+  prerelease: false
+  type: :development
+description: ! 'Data mining and machine learning algorithms for JRuby '
+email: arrigonialberto86@gmail.com
+executables:
+- bio-band
+extensions:
+- ext/mkrf_conf.rb
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- Gemfile
+- Gemfile.lock
+- Jarfile
+- Jarfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/bio-band
+- bio-band.gemspec
+- ext/mkrf_conf.rb
+- features/create_dataset.feature
+- features/step_definitions/create_dataset.rb
+- features/step_definitions/weka_classifiers.rb
+- features/step_definitions/weka_clustering.rb
+- features/step_definitions/weka_filters.rb
+- features/step_definitions/weka_parsers.rb
+- features/support/env.rb
+- features/weka_classifiers.feature
+- features/weka_clustering.feature
+- features/weka_filters.feature
+- features/weka_parsers.feature
+- features/weka_pipeline.feature
+- lib/bio-band.rb
+- lib/bio-band/apache.rb
+- lib/bio-band/apache/stat/inference.rb
+- lib/bio-band/core.rb
+- lib/bio-band/core/parser/parser.rb
+- lib/bio-band/core/type/apache_matrices.rb
+- lib/bio-band/core/type/attribute.rb
+- lib/bio-band/core/type/instance.rb
+- lib/bio-band/core/type/instances.rb
+- lib/bio-band/core/type/utils.rb
+- lib/bio-band/weka.rb
+- lib/bio-band/weka/classifiers/bayes/bayes.rb
+- lib/bio-band/weka/classifiers/bayes/bayes_utils.rb
+- lib/bio-band/weka/classifiers/evaluation.rb
+- lib/bio-band/weka/classifiers/functions/functions.rb
+- lib/bio-band/weka/classifiers/functions/functions_utils.rb
+- lib/bio-band/weka/classifiers/lazy/lazy.rb
+- lib/bio-band/weka/classifiers/lazy/lazy_utils.rb
+- lib/bio-band/weka/classifiers/trees/trees.rb
+- lib/bio-band/weka/classifiers/trees/trees_utils.rb
+- lib/bio-band/weka/clusterers/clusterers.rb
+- lib/bio-band/weka/clusterers/clusterers_utils.rb
+- lib/bio-band/weka/db/DatabaseUtils_mysql
+- lib/bio-band/weka/db/DatabaseUtils_postgresql
+- lib/bio-band/weka/db/db.rb
+- lib/bio-band/weka/filters/supervised/attribute/attribute.rb
+- lib/bio-band/weka/filters/supervised/instance/instance.rb
+- lib/bio-band/weka/filters/supervised/supervised_utils.rb
+- lib/bio-band/weka/filters/unsupervised/attribute/attribute.rb
+- lib/bio-band/weka/filters/unsupervised/instance/instance.rb
+- lib/bio-band/weka/filters/unsupervised/unsupervised_utils.rb
+- resources/weather.csv
+- resources/weather.numeric.arff
+- spec/bio-band_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/arrigonialberto86/bioruby-band
+licenses:
+- MIT
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: !binary |-
+        MA==
+      segments:
+      - 0
+      hash: 2
+  none: false
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: !binary |-
+        MA==
+  none: false
+requirements: []
+rubyforge_project:
+rubygems_version: 1.8.24
+signing_key:
+specification_version: 3
+summary: Data mining algorithms for JRuby
+test_files: []