Merge branch 'development' of github.com:opentox/opentox-client into development

9 files changed, 158 insertions, 146 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 530296a..8576681 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,11 +1,11 @@
 module OpenTox
 
   # Wrapper for OpenTox Algorithms
-  class Algorithm 
+  class Algorithm
 
     # Execute algorithm with parameters, please consult the OpenTox API and the webservice documentation for acceptable parameters
     # @param [optional,Hash] params Algorithm parameters
-    # @param [optional,Boolean] set to true if method should wait for task result
+    # @param [optional,Boolean] wait set to true if method should wait for task result
     # @return [String] URI of new resource (dataset, model, ...)
     def run params=nil, wait=true
       uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid}
diff --git a/lib/authorization.rb b/lib/authorization.rb
index 469c16c..7f0e840 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -6,6 +6,7 @@ module OpenTox
   #  require "opentox-client"
   #  OpenTox::Authorization::AA = "https://opensso.in-silico.ch" #if not set in .opentox/conf/[SERVICE].rb
   #  subjectid = OpenTox::Authorization.authenticate("username", "password")
+  #  puts OpenTox::Authorization.authorize("http://example.uri/testpath/", "GET", subjectid)
   #@see http://www.opentox.org/dev/apis/api-1.2/AA OpenTox A&A API 1.2 specification
 
   module Authorization
@@ -29,7 +30,7 @@ module OpenTox
 
       #Cleans AA Policies and loads default xml file into policy attribute
       #set uri and user, returns Policyfile(XML) for open-sso
-      # @param [String] URI to create a policy for
+      # @param uri [String] URI to create a policy for
       def get_xml(uri)
         @policy.drop_policies
         @policy.load_default_policy(@user, uri)
@@ -37,7 +38,7 @@ module OpenTox
       end
 
       #Loads and sends Policyfile(XML) to open-sso server
-      # @param [String] URI to create a policy for
+      # @param uri [String] URI to create a policy for
       def send(uri)
         xml = get_xml(uri)
         ret = false
@@ -57,7 +58,8 @@ module OpenTox
     end
 
     #Authentication against OpenSSO. Returns token. Requires Username and Password.
-    # @param [String, String]Username,Password
+    # @param user [String] Username
+    # @param pw [String] Password
     # @return [String, nil] gives subjectid or nil
     def self.authenticate(user, pw)
       return nil if !AA
@@ -71,7 +73,7 @@ module OpenTox
     end
 
     #Logout on opensso. Make token invalid. Requires token
-    # @param [String]subjectid the subjectid
+    # @param [String] subjectid the subjectid
     # @return [Boolean] true if logout is OK
     def self.logout(subjectid)
       begin
@@ -84,7 +86,9 @@ module OpenTox
     end
 
     #Authorization against OpenSSO for a URI with request-method (action) [GET/POST/PUT/DELETE]
-    # @param [String,String,String]uri,action,subjectid
+    # @param [String] uri URI to request
+    # @param [String] action request method
+    # @param [String] subjectid
     # @return [Boolean, nil]  returns true, false or nil (if authorization-request fails).
     def self.authorize(uri, action, subjectid)
       return true if !AA
@@ -118,7 +122,8 @@ module OpenTox
     end
 
     #Returns a policy in xml-format
-    # @param [String, String]policy,subjectid
+    # @param policy [String] policyname
+    # @param subjectid [String]
     # @return [String] XML of the policy
     def self.list_policy(policy, subjectid)
       begin
@@ -150,7 +155,8 @@ module OpenTox
     end
 
     #Returns the owner (who created the first policy) of an URI
-    # @param [String, String]uri,subjectid
+    # @param uri [String] URI
+    # @param subjectid [String] subjectid
     # return [String, nil]owner,nil returns owner of the URI
     def self.get_uri_owner(uri, subjectid)
       begin
@@ -161,14 +167,16 @@ module OpenTox
     end
 
     #Returns true or false if owner (who created the first policy) of an URI
-    # @param [String, String]uri,subjectid
+    # @param uri [String] URI
+    # @param subjectid [String]
     # return [Boolean]true,false status of ownership of the URI
     def self.uri_owner?(uri, subjectid)
       get_uri_owner(uri, subjectid) == get_user(subjectid)
     end
 
     #Checks if a policy exists to a URI. Requires URI and token.
-    # @param [String, String]uri,subjectid
+    # @param uri [String] URI
+    # @param subjectid [String]
     # return [Boolean]
     def self.uri_has_policy(uri, subjectid)
       owner = get_uri_owner(uri, subjectid)
@@ -177,7 +185,8 @@ module OpenTox
     end
 
     #List all policynames for a URI. Requires URI and token.
-    # @param [String, String]uri,subjectid
+    # @param uri [String] URI
+    # @param subjectid [String]
     # return [Array, nil] returns an Array of policy names or nil if request fails
     def self.list_uri_policies(uri, subjectid)
       begin
@@ -194,7 +203,8 @@ module OpenTox
     end
 
     #Sends a policy in xml-format to opensso server. Requires policy-xml and token.
-    # @param [String, String]policyxml,subjectid
+    # @param policy [String] XML string of a policy
+    # @param subjectid [String]
     # return [Boolean] returns true if policy is created
     def self.create_policy(policy, subjectid)
       begin
@@ -206,7 +216,8 @@ module OpenTox
     end
 
     #Deletes a policy
-    # @param [String, String]policyname,subjectid
+    # @param policy [String] policyname
+    # @param subjectid [String]
     # @return [Boolean,nil]
     def self.delete_policy(policy, subjectid)
       begin
@@ -254,7 +265,8 @@ module OpenTox
     end
 
     #Send default policy with Authorization::Helper class
-    # @param [String, String]URI,subjectid
+    # @param uri [String] URI
+    # @param subjectid [String]
     def self.send_policy(uri, subjectid)
       return true if !AA
       aa  = Authorization::Helper.new(subjectid)
@@ -264,7 +276,8 @@ module OpenTox
     end
 
     #Deletes all policies of an URI
-    # @param [String, String]URI,subjectid
+    # @param uri [String] URI
+    # @param subjectid [String]
     # @return [Boolean]
     def self.delete_policies_from_uri(uri, subjectid)
       policies = list_uri_policies(uri, subjectid)
@@ -308,9 +321,9 @@ module OpenTox
     end
 
     # Check Authorization for a resource (identified via URI) with method and subjectid.
-    # @param [String] uri
-    # @param [String] request_method, should be GET, POST, PUT, DELETE
-    # @param [String] subjectid
+    # @param uri [String] URI
+    # @param request_method [String] GET, POST, PUT, DELETE
+    # @param subjectid [String]
     # @return [Boolean] true if access granted, else otherwise
     def self.authorized?(uri, request_method, subjectid)
       request_method = request_method.to_sym if request_method
@@ -345,7 +358,7 @@ module OpenTox
         define_method "#{method}?".to_sym do |uri, request_method|
           if $aa["#{method}s".to_sym]
             $aa["#{method}s".to_sym].each do |request_methods, uris|
-              if request_methods and uris and request_methods.include?(request_method.to_sym) 
+              if request_methods and uris and request_methods.include?(request_method.to_sym)
                 uris.each do |u|
                   return true if u.match uri
                 end
diff --git a/lib/compound.rb b/lib/compound.rb
index 2eccdcd..a278244 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -16,14 +16,14 @@ module OpenTox
     end
 
     # Create a compound from inchi string
-    # @param [String] smiles InChI string
+    # @param inchi [String] smiles InChI string
     # @return [OpenTox::Compound] Compound
     def self.from_inchi inchi, subjectid=nil
       Compound.new RestClientWrapper.post(service_uri, inchi, {:content_type => 'chemical/x-inchi', :subjectid => subjectid})
     end
 
     # Create a compound from sdf string
-    # @param [String] smiles SDF string
+    # @param sdf [String] smiles SDF string
     # @return [OpenTox::Compound] Compound
     def self.from_sdf sdf, subjectid=nil
       Compound.new RestClientWrapper.post(service_uri, sdf, {:content_type => 'chemical/x-mdl-sdfile', :subjectid => subjectid})
@@ -32,9 +32,8 @@ module OpenTox
     # Create a compound from name. Relies on an external service for name lookups.
     # @example
     #   compound = OpenTox::Compound.from_name("Benzene")
-    # @param [String] name name can be also an InChI/InChiKey, CAS number, etc
+    # @param name [String] can be also an InChI/InChiKey, CAS number, etc
     # @return [OpenTox::Compound] Compound
-    #
     def self.from_name name, subjectid=nil
       @inchi = RestClientWrapper.get File.join(CACTUS_URI,URI.escape(name),"stdinchi")
       Compound.new RestClientWrapper.post(service_uri, @inchi, {:content_type => 'chemical/x-inchi', :subjectid => subjectid})
@@ -191,7 +190,7 @@ module OpenTox
     # Match an array of smarts strings, returns hash
     # Keys: matching smarts, values: number of non-unique hits, or 1
     # @param [Array] smarts_array Array with Smarts strings
-    # @param [Boolean] Whether non-unique hits or 1 should be produced
+    # @param use_hits [Boolean] Whether non-unique hits or 1 should be produced
     # @return [Array] Array with matching Smarts strings
     # @example {
     #   compound = Compound.from_name("Benzene")
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 8d5f5d1..19d05c9 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -3,7 +3,7 @@ require 'csv'
 module OpenTox
 
   # Ruby wrapper for OpenTox Dataset Webservices (http://opentox.org/dev/apis/api-1.2/dataset).
-  class Dataset 
+  class Dataset
 
     attr_writer :features, :compounds, :data_entries
 
@@ -46,7 +46,7 @@ module OpenTox
       end
       @compounds
     end
-    
+
     def data_entries force_update=false
       if @data_entries.empty? or force_update
         sparql = "SELECT ?cidx ?fidx ?value FROM <#{uri}> WHERE {
@@ -55,7 +55,7 @@ module OpenTox
           ?v          <#{RDF::OT.feature}> ?f;
                       <#{RDF::OT.value}> ?value .
           ?f          <#{RDF::OLO.index}> ?fidx.
-          } ORDER BY ?fidx ?cidx" 
+          } ORDER BY ?fidx ?cidx"
           RestClientWrapper.get(service_uri,{:query => sparql},{:accept => "text/uri-list", :subjectid => @subjectid}).split("\n").each do |row|
             r,c,v = row.split("\t")
             @data_entries[r.to_i] ||= []
@@ -79,9 +79,9 @@ module OpenTox
       @data_entries
     end
 
-    # Find data entry values for a given compound and feature 
-    # @param [OpenTox::Compound] Compound 
-    # @param [OpenTox::Feature] Feature 
+    # Find data entry values for a given compound and feature
+    # @param compound [OpenTox::Compound] OpenTox Compound object
+    # @param feature [OpenTox::Feature] OpenTox Feature object
     # @return [Array] Data entry values
     def values(compound, feature)
       rows = (0 ... compounds.length).select { |r| compounds[r].uri == compound.uri }
@@ -92,14 +92,14 @@ module OpenTox
     # Convenience methods to search by compound/feature URIs
 
     # Search a dataset for a feature given its URI
-    # @param [String] Feature URI
+    # @param uri [String] Feature URI
     # @return [OpenTox::Feature] Feature object, or nil if not present
     def find_feature_uri(uri)
       features.select{|f| f.uri == uri}.first
     end
 
     # Search a dataset for a compound given its URI
-    # @param [String] Compound URI
+    # @param uri [String] Compound URI
     # @return [OpenTox::Compound] Compound object, or nil if not present
     def find_compound_uri(uri)
       compounds.select{|f| f.uri == uri}.first
@@ -133,7 +133,7 @@ module OpenTox
     def upload filename, wait=true
       uri = RestClientWrapper.put(@uri, {:file => File.new(filename)}, {:subjectid => @subjectid})
       wait_for_task uri if URI.task?(uri) and wait
-      metadata true 
+      metadata true
       @uri
     end
 
@@ -173,7 +173,7 @@ module OpenTox
     end
 
     RDF_FORMATS.each do |format|
-      
+
       # redefine rdf parse methods for all formats e.g. parse_rdfxml
       send :define_method, "parse_#{format}".to_sym do |rdf|
         # TODO: parse ordered dataset
@@ -194,13 +194,13 @@ module OpenTox
       end
 
 
-      # redefine rdf serialization methods 
+      # redefine rdf serialization methods
       send :define_method, "to_#{format}".to_sym do
-        @metadata[RDF.type] = RDF::OT.OrderedDataset 
+        @metadata[RDF.type] = RDF::OT.OrderedDataset
         create_rdf
         @features.each_with_index do |feature,i|
-          @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Feature)] 
-          @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)] 
+          @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Feature)]
+          @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)]
         end
         @compounds.each_with_index do |compound,i|
           @rdf << [RDF::URI.new(compound.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Compound)]
@@ -246,8 +246,8 @@ module OpenTox
         parameter.each { |k,v| ntriples <<  "#{p_node} <#{k}> '#{v}' .\n" }
       end
       @features.each_with_index do |feature,i|
-        ntriples <<  "<#{feature.uri}> <#{RDF.type}> <#{RDF::OT.Feature}> .\n" 
-        ntriples <<  "<#{feature.uri}> <#{RDF::OLO.index}> '#{i}' .\n" 
+        ntriples <<  "<#{feature.uri}> <#{RDF.type}> <#{RDF::OT.Feature}> .\n"
+        ntriples <<  "<#{feature.uri}> <#{RDF::OLO.index}> '#{i}' .\n"
       end
       @compounds.each_with_index do |compound,i|
         ntriples <<  "<#{compound.uri}> <#{RDF.type}> <#{RDF::OT.Compound}> .\n"
@@ -276,21 +276,21 @@ module OpenTox
 =end
 
     # Methods for for validation service
-    
+
     def split( compound_indices, feats, metadata, subjectid=nil)
-      
+
       bad_request_error "Dataset.split : Please give compounds as indices" if compound_indices.size==0 or !compound_indices[0].is_a?(Fixnum)
       bad_request_error "Dataset.split : Please give features as feature objects (given: #{feats})" if feats!=nil and feats.size>0 and !feats[0].is_a?(OpenTox::Feature)
       dataset = OpenTox::Dataset.new(nil, subjectid)
       dataset.metadata = metadata
       dataset.features = (feats ? feats : self.features)
       compound_indices.each do |c_idx|
-        dataset << [ self.compounds[c_idx] ] + dataset.features.each_with_index.collect{|f,f_idx| self.data_entries[c_idx][f_idx]} 
+        dataset << [ self.compounds[c_idx] ] + dataset.features.each_with_index.collect{|f,f_idx| self.data_entries[c_idx][f_idx]}
       end
       dataset.put
-      dataset    
+      dataset
     end
-    
+
 
     # maps a compound-index from another dataset to a compound-index from this dataset
     # mapping works as follows:
@@ -299,8 +299,8 @@ module OpenTox
     # * c occurs >1 in this dataset?
     # ** number of occurences is equal in both datasets? assume order is preserved(!) and map accordingly
     # ** number of occurences is not equal in both datasets? cannot map, raise error
-    # @param [OpenTox::Dataset] dataset that should be mapped to this dataset (fully loaded)
-    # @param [Fixnum] compound_index, corresponding to dataset
+    # @param dataset [OpenTox::Dataset] dataset that should be mapped to this dataset (fully loaded)
+    # @param compound_index [Fixnum], corresponding to dataset
     def compound_index( dataset, compound_index )
       unless defined?(@index_map) and @index_map[dataset.uri]
         map = {}
@@ -308,7 +308,7 @@ module OpenTox
           self_indices = compound_indices(compound)
           next unless self_indices
           dataset_indices = dataset.compound_indices(compound)
-          if self_indices.size==1  
+          if self_indices.size==1
             dataset_indices.size.times do |i|
               map[dataset_indices[i]] = self_indices[0]
             end
@@ -321,13 +321,13 @@ module OpenTox
             raise "cannot map compound #{compound} from dataset #{dataset.uri} to dataset #{uri}, "+
               "compound occurs #{dataset_indices.size} times and #{self_indices.size} times"
           end
-        end  
+        end
         @index_map = {} unless defined?(@index_map)
         @index_map[dataset.uri] = map
       end
       @index_map[dataset.uri][compound_index]
-    end    
-    
+    end
+
     def compound_indices( compound )
       unless defined?(@cmp_indices) and @cmp_indices.has_key?(compound)
         @cmp_indices = {}
@@ -337,12 +337,12 @@ module OpenTox
             @cmp_indices[c] = [i]
           else
             @cmp_indices[c] = @cmp_indices[c]+[i]
-          end   
+          end
         end
       end
       @cmp_indices[compound]
     end
-    
+
     def data_entry_value(compound_index, feature_uri)
       data_entries(true) if @data_entries.empty?
       col = @features.collect{|f| f.uri}.index feature_uri
diff --git a/lib/model.rb b/lib/model.rb
index a354cfa..e49eff3 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -3,8 +3,8 @@ module OpenTox
   class Model
 
     # Run a model with parameters
-    # @param [Hash] params Parameters for OpenTox model
-    # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @param params [Hash] Parameters for OpenTox model
+    # @param wait [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [text/uri-list] Task or resource URI
     def run params=nil, wait=true
       uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid}
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 305b5d9..adf0030 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -11,8 +11,8 @@ module OpenTox
   # Ruby interface
 
   # Create a new OpenTox object 
-  # @param [optional,String] URI
-  # @param [optional,String] subjectid
+  # @param uri [optional,String] URI
+  # @param subjectid [optional,String] 
   # @return [OpenTox] OpenTox object
   def initialize uri=nil, subjectid=nil
     @rdf = RDF::Graph.new
@@ -34,7 +34,7 @@ module OpenTox
   end
 
   # Metadata values 
-  # @param [String] Predicate URI
+  # @param predicate [String] Predicate URI
   # @return [Array, String] Predicate value(s)
   def [](predicate)
     return nil if metadata[predicate].nil?
@@ -42,8 +42,8 @@ module OpenTox
   end
 
   # Set a metadata entry
-  # @param [String] Predicate URI
-  # @param [Array, String] Predicate value(s)
+  # @param predicate [String] Predicate URI
+  # @param values [Array, String] Predicate value(s)
   def []=(predicate,values)
     @metadata[predicate] = [values].flatten
   end
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index 1579469..fbe8f7d 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -38,19 +38,18 @@ class String
   # format of text (=string params) is preserved (e.g. line breaks)
   # urls are marked as links
   #
-  # @param [String] text this is the actual content, 
-  # @param [optional,String] related_links info on related resources
-  # @param [optional,String] description general info
-  # @param [optional,Array] post_command, infos for the post operation, object defined below
+  # @param related_links [optional,String] uri on related resources
+  # @param description [optional,String] general info
+  # @param png_image [optional,String] imagename
   # @return [String] html page
   def to_html(related_links=nil, description=nil, png_image=nil  )
-    
+
     # TODO add title as parameter
     title = nil #$sinatra.to($sinatra.request.env['PATH_INFO'], :full) if $sinatra
     html = "<html>"
     html << "<title>"+title+"</title>" if title
     #html += "<img src=\""+OT_LOGO+"\"><\/img><body>"
-      
+
     html << "<h3>Description</h3><pre><p>"+description.link_urls+"</p></pre>" if description
     html << "<h3>Related links</h3><pre><p>"+related_links.link_urls+"</p></pre>" if related_links
     html << "<h3>Content</h3>" if description || related_links
@@ -60,7 +59,7 @@ class String
     html << "</p></pre></body></html>"
     html
   end
-  
+
   def uri?
     URI.valid?(self)
   end
@@ -76,7 +75,7 @@ module URI
   def self.task? uri
     uri =~ /task/ and URI.valid? uri
   end
-  
+
   def self.dataset? uri, subjectid=nil
     uri =~ /dataset/ and URI.accessible? uri, subjectid=nil
   end
@@ -119,7 +118,7 @@ end
 
 class File
   # @return [String] mime_type including charset using linux cmd command
-  def mime_type 
+  def mime_type
     `file -ib #{self.path}`.chomp
   end
 end
@@ -138,12 +137,12 @@ module Kernel
     internal_server_error "`" + cmd + "` failed.\n" + stdout + stderr unless status.success?
     return stdout
   rescue
-    internal_server_error $!.message 
+    internal_server_error $!.message
   end
 
   # @return [String] uri of task result, if task fails, an error according to task is raised
   def wait_for_task uri
-    if URI.task?(uri) 
+    if URI.task?(uri)
       t = OpenTox::Task.new uri
       t.wait
       unless t.completed?
diff --git a/lib/policy.rb b/lib/policy.rb
index 3e7c143..e5676ba 100644
--- a/lib/policy.rb
+++ b/lib/policy.rb
@@ -3,7 +3,7 @@ module OpenTox
 
   #Module for policy-processing
   # @see also http://www.opentox.org/dev/apis/api-1.2/AA for opentox API specs
-  # Class Policies corresponds to <policies> container of an xml-policy-fle
+  # Class Policies corresponds to <policies> container of an xml-policy-file
   class Policies
 
     #Hash for policy objects see {Policy Policy}
@@ -205,12 +205,13 @@ module OpenTox
     end
 
     # Subject type LDAPUsers or LDAPGroups
+    # @return [String]
     def type
       @subject.type
     end
 
     # Set subject type <LDAPUsers, LDAPGroups>
-    # @param [String],type
+    # @param type [String] the subjecttype
     def type=(type)
       @subject.type = type
     end
@@ -221,19 +222,19 @@ module OpenTox
     end
 
     # sets LDAP Distinguished Name (DN) for policy e.g.
-    # @param [String],LDAPString
+    # @param value [String] LDAPString
     def value=(value)
       @subject.value = value
     end
 
     # uri affected by policy
-    # @return uri affected by policy
+    # @return [String] uri affected by policy
     def uri
       @rule.uri
     end
 
     # sets uri affected by policy
-    # @param [String] set URI
+    # @param uri [String] set URI
     def uri=(uri)
       @rule.uri = uri
     end
@@ -251,14 +252,14 @@ module OpenTox
     end
 
     # helper method sets value and type to opentox LDAP Distinguished Name (DN) of a user
-    # @param [String]Username set a username into LDAP DN
+    # @param username [String] set a username into LDAP DN
     def set_ot_user(username)
       self.value = "uid=#{username},ou=people,dc=opentox,dc=org"
       self.type = "LDAPUsers"
       true
     end
 
-    # @param [String]Username set a groupname into LDAP DN
+    # @param groupname [String] Username set a groupname into LDAP DN
     def set_ot_group(groupname)
       self.value = "cn=#{groupname},ou=groups,dc=opentox,dc=org"
       self.type = "LDAPGroups"
@@ -277,7 +278,7 @@ module OpenTox
       end
 
       #Set Rule attribute for request-method GET
-      # @param [String]value (allow,deny,nil)
+      # @param value [String] (allow,deny,nil)
       def get=(value)
         @get = check_value(value, @get)
       end
diff --git a/lib/validation.rb b/lib/validation.rb
index c4f6868..cb73ce6 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -2,7 +2,7 @@ require "yaml"
 
 module OldOpenTox
   attr_accessor :metadata, :uri
-  
+
   def initialize(uri=nil)
     @metadata = {}
     self.uri = uri if uri
@@ -13,17 +13,17 @@ module OldOpenTox
     yaml = OpenTox::RestClientWrapper.get(uri,nil,{:subjectid => subjectid, :accept => "application/x-yaml"})
     @metadata = YAML.load(yaml)
   end
-  
+
   def delete (subjectid=nil)
     OpenTox::RestClientWrapper.delete(@uri.to_s,nil,{:subjectid => subjectid})
   end
 end
 
 module OpenTox
-  
+
   class Validation
     include OldOpenTox
-    
+
     # find validation, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -33,10 +33,10 @@ module OpenTox
       val.load_metadata( subjectid )
       val
     end
-    
+
     # returns a filtered list of validation uris
-    # @param [Hash,optional] params, validation-params to filter the uris (could be model, training_dataset, ..)  
-    # @return [Array]    
+    # @param params [Hash,optional] validation-params to filter the uris (could be model, training_dataset, ..)
+    # @return [Array]
     def self.list( params={} )
       filter_string = ""
       params.each do |k,v|
@@ -46,7 +46,7 @@ module OpenTox
       end
       (OpenTox::RestClientWrapper.get($validation[:uri]+filter_string).split("\n"))
     end
-    
+
     # creates a training test split validation, waits until it finishes, may take some time
     # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,split_ratio(0.67),random_seed(1))
     # @param [String,optional] subjectid
@@ -58,7 +58,7 @@ module OpenTox
         params,{:content_type => "text/uri-list"},waiting_task )
       Validation.new(wait_for_task(uri))
     end
-    
+
     # creates a training test validation, waits until it finishes, may take some time
     # @param [Hash] params (required:algorithm_uri,training_dataset_uri,prediction_feature,test_dataset_uri,optional:algorithm_params)
     # @param [String,optional] subjectid
@@ -70,7 +70,7 @@ module OpenTox
         params,{:content_type => "text/uri-list"},waiting_task )
       Validation.new(wait_for_task(uri))
     end
-    
+
     # creates a bootstrapping validation, waits until it finishes, may take some time
     # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,random_seed(1))
     # @param [String,optional] subjectid
@@ -82,7 +82,7 @@ module OpenTox
         params,{:content_type => "text/uri-list"},waiting_task )
       Validation.new(wait_for_task(uri))
     end
-    
+
     # looks for report for this validation, creates a report if no report is found
     # @param [String,optional] subjectid
     # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
@@ -92,20 +92,20 @@ module OpenTox
       @report = ValidationReport.create(@uri, {}, subjectid, waiting_task) unless @report
       @report.uri
     end
-    
+
     # creates a validation object from crossvaldiation statistics, raise error if not found
     # (as crossvaldiation statistics are returned as an average valdidation over all folds)
-    # @param [String] crossvalidation uri
+    # @param crossvalidation_uri [String] crossvalidation uri
     # @param [String,optional] subjectid
     # @return [OpenTox::Validation]
     def self.from_cv_statistics( crossvalidation_uri, subjectid=nil )
       find( File.join(crossvalidation_uri, 'statistics'),subjectid )
     end
-    
+
     # returns confusion matrix as array, predicted values are in rows
     # example:
     # [[nil,"active","moderate","inactive"],["active",1,3,99],["moderate",4,2,8],["inactive",3,8,6]]
-    # -> 99 inactive compounds have been predicted as active 
+    # -> 99 inactive compounds have been predicted as active
     def confusion_matrix
       raise "no classification statistics, probably a regression valdiation" unless @metadata[RDF::OT.classificationStatistics]
       matrix =  @metadata[RDF::OT.classificationStatistics][RDF::OT.confusionMatrix][RDF::OT.confusionMatrixCell]
@@ -124,38 +124,38 @@ module OpenTox
       end
       table
     end
-    
+
     # returns probability-distribution for a given prediction
     # it takes all predictions into account that have a confidence value that is >= confidence and that have the same predicted value
     # (minimum 12 predictions with the hightest confidence are selected (even if the confidence is lower than the given param)
-    # 
-    # @param [Float] confidence value (between 0 and 1)
-    # @param [String] predicted value
-    # @param [String,optional] subjectid
+    #
+    # @param confidence [Float] confidence value (between 0 and 1)
+    # @param prediction [String] predicted value
+    # @param subjectid [String,optional]
     # @return [Hash] see example
     #
     # Example 1:
-    # validation.probabilities(0.3,"active")
-    # -> {:min_confidence=>0.32, :num_predictions=>20, :probs=>{"active"=>0.7, "moderate"=>0.25 "inactive"=>0.05}}
+    #   validation.probabilities(0.3,"active")
+    #   -> { :min_confidence=>0.32, :num_predictions=>20, :probs=>{"active"=>0.7, "moderate"=>0.25 "inactive"=>0.05 } }
     # there have been 20 "active" predictions with confidence >= 0.3, 70 percent of them beeing correct
     #
     # Example 2:
-    # validation.probabilities(0.8,"active")
-    # -> {:min_confidence=>0.45, :num_predictions=>12, :probs=>{"active"=>0.9, "moderate"=>0.1 "inactive"=>0}}
+    #  validation.probabilities(0.8,"active")
+    #  -> { :min_confidence=>0.45, :num_predictions=>12, :probs=>{"active"=>0.9, "moderate"=>0.1 "inactive"=>0 } }
     # the given confidence value was to high (i.e. <12 predictions with confidence value >= 0.8)
     # the top 12 "active" predictions have a min_confidence of 0.45, 90 percent of them beeing correct
-    # 
+    #
     def probabilities( confidence, prediction, subjectid=nil )
       YAML.load(OpenTox::RestClientWrapper.get(@uri+"/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil,
         {:subjectid => subjectid, :accept => "application/x-yaml"}))
     end
   end
-  
+
   class Crossvalidation
     include OldOpenTox
 
     attr_reader :report
-    
+
     # find crossvalidation, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -165,10 +165,10 @@ module OpenTox
       cv.load_metadata( subjectid )
       cv
     end
-    
+
     # returns a filtered list of crossvalidation uris
-    # @param [Hash,optional] params, crossvalidation-params to filter the uris (could be algorithm, dataset, ..)  
-    # @return [Array]    
+    # @param params [Hash,optional] crossvalidation-params to filter the uris (could be algorithm, dataset, ..)
+    # @return [Array]
     def self.list( params={} )
       filter_string = ""
       params.each do |k,v|
@@ -201,29 +201,29 @@ module OpenTox
       @report = CrossvalidationReport.create(@uri, subjectid, waiting_task) unless @report
       @report.uri
     end
-    
+
     # loads metadata via yaml from crossvalidation object
     # fields (like for example the validations) can be acces via validation.metadata[RDF::OT.validation]
     def load_metadata( subjectid=nil )
       @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,nil,{:subjectid => subjectid, :accept => "application/x-yaml"}))
     end
-    
+
     # returns a Validation object containing the statistics of the crossavlidation
     def statistics( subjectid=nil )
       Validation.from_cv_statistics( @uri, subjectid )
     end
-    
+
     # documentation see OpenTox::Validation.probabilities
     def probabilities( confidence, prediction, subjectid=nil )
       YAML.load(OpenTox::RestClientWrapper.get(@uri+"/statistics/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil,
         {:subjectid => subjectid, :accept => "application/x-yaml"}))
     end
-    
+
   end
-  
+
   class ValidationReport
     include OldOpenTox
-    
+
     # finds ValidationReport via uri, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -234,23 +234,23 @@ module OpenTox
       rep.load_metadata( subjectid )
       rep
     end
-    
+
     # finds ValidationReport for a particular validation
-    # @param [String] crossvalidation uri 
-    # @param [String,optional] subjectid
+    # @param validation_uri [String] crossvalidation uri
+    # @param subjectid [String,optional]
     # @return [OpenTox::ValidationReport] nil if no report found
     def self.find_for_validation( validation_uri, subjectid=nil )
       uris = RestClientWrapper.get(File.join($validation[:uri],
         "/report/validation?validation="+validation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
       uris.size==0 ? nil : ValidationReport.new(uris[-1])
     end
-    
+
     # creates a validation report via validation
-    # @param [String] validation uri 
-    # @param [Hash] params addiditonal possible 
+    # @param validation_uri [String] validation uri
+    # @param params [Hash] params addiditonal possible
     #               (min_confidence, params={}, min_num_predictions, max_num_predictions)
-    # @param [String,optional] subjectid
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @param subjectid [String,optional]
+    # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [OpenTox::ValidationReport]
     def self.create( validation_uri, params={}, subjectid=nil, waiting_task=nil )
       params = {} if params==nil
@@ -262,12 +262,12 @@ module OpenTox
       uri = wait_for_task(uri)
       ValidationReport.new(uri)
     end
-    
+
   end
 
   class CrossvalidationReport
     include OldOpenTox
-    
+
     # finds CrossvalidationReport via uri, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -278,21 +278,21 @@ module OpenTox
       rep.load_metadata( subjectid )
       rep
     end
-    
+
     # finds CrossvalidationReport for a particular crossvalidation
-    # @param [String] crossvalidation uri 
-    # @param [String,optional] subjectid
+    # @param crossvalidation_uri [String] crossvalidation uri
+    # @param subjectid [String,optional]
     # @return [OpenTox::CrossvalidationReport] nil if no report found
     def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil )
       uris = RestClientWrapper.get(File.join($validation[:uri],
         "/report/crossvalidation?crossvalidation="+crossvalidation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
       uris.size==0 ? nil : CrossvalidationReport.new(uris[-1])
     end
-    
+
     # creates a crossvalidation report via crossvalidation
-    # @param [String] crossvalidation uri 
-    # @param [String,optional] subjectid
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @param crossvalidation_uri [String] crossvalidation uri
+    # @param subjectid [String,optional]
+    # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [OpenTox::CrossvalidationReport]
     def self.create( crossvalidation_uri, subjectid=nil, waiting_task=nil )
       uri = RestClientWrapper.post(File.join($validation[:uri],"/report/crossvalidation"),
@@ -301,11 +301,11 @@ module OpenTox
       CrossvalidationReport.new(uri)
     end
   end
-  
-  
+
+
   class AlgorithmComparisonReport
     include OldOpenTox
-    
+
     # finds AlgorithmComparisonReport via uri, raises error if not found
     # @param [String] uri
     # @param [String,optional] subjectid
@@ -316,23 +316,23 @@ module OpenTox
       rep.load_metadata( subjectid )
       rep
     end
-    
+
     # finds AlgorithmComparisonReport for a particular crossvalidation
-    # @param [String] crossvalidation uri 
-    # @param [String,optional] subjectid
+    # @param crossvalidation_uri [String] crossvalidation uri
+    # @param subjectid [String,optional]
     # @return [OpenTox::AlgorithmComparisonReport] nil if no report found
     def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil )
       uris = RestClientWrapper.get(File.join($validation[:uri],
         "/report/algorithm_comparison?crossvalidation="+crossvalidation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
       uris.size==0 ? nil : AlgorithmComparisonReport.new(uris[-1])
     end
-    
+
     # creates a algorithm comparison report via crossvalidation uris
-    # @param [Hash] crossvalidation uri_hash, see example 
-    # @param [Hash] params addiditonal possible 
+    # @param crossvalidation_uri_hash [Hash] crossvalidation uri_hash, see example
+    # @param params [Hash] params addiditonal possible
     #               (ttest_significance, ttest_attributes, min_confidence, min_num_predictions, max_num_predictions)
-    # @param [String,optional] subjectid
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @param subjectid [String,optional]
+    # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [OpenTox::AlgorithmComparisonReport]
     # example for hash:
     # { :lazar-bbrc => [ http://host/validation/crossvalidation/x1, http://host/validation/crossvalidation/x2 ],
@@ -355,7 +355,7 @@ module OpenTox
       uri = wait_for_task(uri)
       AlgorithmComparisonReport.new(uri)
     end
-  end  
-  
+  end
+
 end