transfer to new git project started

65 files changed, 50043 insertions, 2411 deletions

diff --git a/VERSION b/VERSION
index 274edc4..9ae0833 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.0.0pre1
+1.0.0beta1
diff --git a/bin/opentox-client-install b/bin/opentox-client-install
deleted file mode 100755
index 125db43..0000000
--- a/bin/opentox-client-install
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/bin/sh
-
-# Installs Opentox Webservice.
-# Author: Christoph Helma, Andreas Maunz.
-
-SELF=$(basename $0 -install)
-[ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1
-
-SILENT=false
-if [ -n "$1" ]
-then
-    if [ "$1" = "silent" ]
-    then
-        SILENT=true
-    fi
-fi
-
-if [ $SILENT = false ]; then
-  echo
-  echo "Welcome to service installation (<Return> to continue)."
-  read delete_me
-fi
-
-# check wd is root of service
-DIR=`pwd`
-if echo $DIR | grep "$SELF/bin" >/dev/null 2>&1 ; then cd ..; fi
-
-# # # Boot the script
-
-# load base config, helper funs, environment
-OT_CONFIG_DIR="$HOME/.opentox"
-! [ -f "$OT_CONFIG_DIR/config/install/config.sh" ] && echo "config.sh not found." 1>&2 && exit 1 || . $OT_CONFIG_DIR/config/install/config.sh
-! [ -f "$OT_PREFIX/install/utils.sh" ] && echo "utils.sh not found." 1>&2 && exit 1 || . $OT_PREFIX/install/utils.sh
-[ -f $OT_CONFIG_DIR/opentox-ui.sh ] && . $OT_CONFIG_DIR/opentox-ui.sh # should have been done by user already
-RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER"
-
-
-# config
-[ -f $OT_CONFIG_DIR/config/$SELF.rb ] || touch $OT_CONFIG_DIR/config/$SELF.rb
-if ! cat "$OT_CONFIG_DIR/config/$SELF.rb" | grep "default.rb">/dev/null 2>&1; then echo 'require_relative "default.rb"' >> $OT_CONFIG_DIR/config/$SELF.rb; fi
-
-
-# # # Install
-
-check_utils "rbenv find"
-check_log $SELF
-
-# Adjust ruby version here!
-RUBY_NUM_VER="2.0.0-p481"
-
-# ruby
-install_ruby
-
-# self
-echo
-install_with_bundler
-
-if [ $SILENT = false ]; then
-  notify
-fi
-
-# return to wd
-cd "$DIR"
diff --git a/doc/dsspeed.md b/doc/dsspeed.md
deleted file mode 100644
index 9f04efd..0000000
--- a/doc/dsspeed.md
+++ /dev/null
@@ -1,181 +0,0 @@
-Filename: `dsspeed.pdf`  
-Description: A benchmark comparison of different dataset implementations.  
-Author: Andreas Maunz `<andreas@maunz.de>`  
-Date: 10/2012
-
-Some experiments made on branch `development`, using a VirtualBox VM (2 CPU, 2G of RAM), Debian 6.0.5, 64bit.
-
-# Dataset Creation 
-
-Storing a dataset at the 4store backend.
-
-## Generating and Storing Triples.
-
-Implementation with querying the `/compound` service for compound URIs.
-
-    date
-    task=`curl -X POST \
-      -F "file=@/home/am/opentox-ruby/opentox-test/test/data/kazius.csv;type=text/csv"  
-      http://localhost:8083/dataset 2>/dev/null`
-    get_result $task
-    date
-
-Timings for uploading the Kazius dataset (>4000 compounds. Repeated three times, median reported):
-
-    Sat Nov  3 11:10:04 CET 2012
-    http://localhost:8083/dataset/6a92fbf1-9c46-4c72-a487-365589c1210d
-    Sat Nov  3 11:10:41 CET 2012
-
-Uploading takes 37s. This time is consumed by the workflow as follows:
-
-- Compound Triples: 33.236s (89.8 %)
-- Value Triples: 1.052s (0.03 %)
-- Other Triples: <1s (<0.03 %)
-- 4store upload: <3s (<0.1 %)
-
-Based on these results I suggest to avoid querying the compound service.
-  
-
-
-# Dataset Read-In
-
-Populating an `OpenTox::Dataset` object in memory, by reading from the 4store backend.
-
-## Request per row
-
-Implementation with one query for data entries **per compound**.
-
-    @compounds.each_with_index do |compound,i|
-      query = RDF::Query.new do
-        pattern [:data_entry, RDF::OLO.index, i]
-        pattern [:data_entry, RDF::OT.values, :values]
-        pattern [:values, RDF::OT.feature, :feature]
-        pattern [:feature, RDF::OLO.index, :feature_idx]
-        pattern [:values, RDF::OT.value, :value]
-      end
-      values = query.execute(@rdf).sort_by{|s| s.feature_idx}.collect do |s|
-        (numeric_features[s.feature_idx] and s.value.to_s != "") ? \
-         s.value.to_s.to_f : s.value.to_s
-      end
-      @data_entries << values.collect{|v| v == "" ? nil : v}
-    end
-
-Timings for reading a BBRC feature dataset (85 compounds, 53 features. Repeated three times, median reported):
-
-                     user     system      total        real
-    ds reading   6.640000   0.090000   6.730000 (  7.429505)
-
-
-## Single Table
-
-Now some optimized versions that retrieve entries all at once. A few variables have been renamed for clarity in the query:
-
-    query = RDF::Query.new do
-      # compound index: now a free variable
-      pattern [:data_entry, RDF::OLO.index, :cidx] 
-      pattern [:data_entry, RDF::OT.values, :vals]
-      pattern [:vals, RDF::OT.feature, :f]
-      pattern [:f, RDF::OLO.index, :fidx]
-      pattern [:vals, RDF::OT.value, :val]
-    end
-
-Also `RDF::Query::Solutions#order_by` is used instead of the generic `Enumerable#sort_by`, which may have advantages (not tested seperately).
-
-### 'Row Slicing' Version
-
-Results are sorted by compound, then by feature. The long array is sliced into rows.
-
-    @data_entries = query.execute(@rdf).order_by(:cidx, :fidx).collect { |entry| 
-      entry.val.to_s.blank? ? nil : \
-      (numeric_features[entry.fidx] ? entry.val.to_s.to_f : entry.val.to_s)
-    }.each_slice(@features.size).to_a
-
-Timings:
-
-                     user     system      total        real
-    ds reading   3.850000   0.090000   3.940000 (  4.643435)
-
-### 'Fill Table' Version
-
-Modification of 'Row Slicing' that avoids lookup operations where possible. Also pre-allocates `@data_entries`.
-
-    clim=(@compounds.size-1)
-    cidx=0
-    fidx=0
-    num=numeric_features[fidx]
-    @data_entries = \
-    (Array.new(@compounds.size*@features.size)).each_slice(@features.size).to_a
-    # order by feature index as to compute numeric status less frequently
-    query.execute(@rdf).order_by(:fidx, :cidx).each { |entry| 
-      val = entry.val.to_s
-      unless val.blank?
-        @data_entries[cidx][fidx] = (num ? val.to_f : val)
-      end
-      if (cidx < clim)
-        cidx+=1
-      else
-        cidx=0
-        fidx+=1
-        num=numeric_features[fidx]
-      end
-    }
-
-Timings:
-
-                     user     system      total        real
-    ds reading   3.820000   0.040000   3.860000 (  4.540800)
-
-### 'SPARQL' Version
-
-Modification of 'Fill Table' that loads data entries via SPARQL, not RDF query.
-
-    sparql = "SELECT ?value FROM <#{uri}> WHERE {
-      ?data_entry <#{RDF::OLO.index}> ?cidx ;
-                  <#{RDF::OT.values}> ?v .
-      ?v          <#{RDF::OT.feature}> ?f;
-                  <#{RDF::OT.value}> ?value .
-      ?f          <#{RDF::OLO.index}> ?fidx.
-      } ORDER BY ?fidx ?cidx" 
-
-Timings:
-
-                 user     system      total        real
-ds reading   1.690000   0.050000   1.740000 (  2.362236)
-
-
-## Dataset Tests
-
-Test runtimes changed as follows:
-
-Test             old     'Row Slicing' 'SPARQL'
----------------- ------- ------------- -------- 
-dataset.rb       6.998s  7.406s        6.341s
-dataset_large.rb 64.230s 25.231s       25.071
-
-Table: Runtimes
-
-
-### Conclusions
-
-In view of the results I implemented the 'SPARQL' version.
-
-
-### Note
-
-A further modification that avoids querying compounds separately made runtimes much worse again.
-The idea was to get the compound together with each data entry:
-
-    #<RDF::Query::Solution:0x24f41cc(
-      {
-        :compound=>#<RDF::URI:0x2638c68(http://loca [...]
-        :cidx=>#<RDF::Literal::Integer:0x2639190("3 [...]
-        :data_entry=>#<RDF::Node:0x2639618(_:b1324f [...]
-        :vals=>#<RDF::Node:0x17699d0(_:b32bf4000000 [...]
-        :f=>#<RDF::URI:0x1638ed0(http://localhost:8 [...]
-        :fidx=>#<RDF::Literal::Integer:0x271c170("0 [...]
-        :val=>#<RDF::Literal::Integer:0x176879c("0" [...]
-      }
-    )>
-
-One would add compounds to `@compounds` only for the first run through column no '1'.
-
diff --git a/lib/authorization.rb b/lib/authorization.rb
deleted file mode 100644
index b530815..0000000
--- a/lib/authorization.rb
+++ /dev/null
@@ -1,378 +0,0 @@
-module OpenTox
-
-  if defined?($aa) and $aa.has_key?(:uri) and !$aa[:uri].nil?
-    AA = $aa[:uri] 
-  else
-    AA = "https://opensso.in-silico.ch" #if not set in .opentox/conf/[SERVICE].rb
-  end
-
-  #Module for Authorization and Authentication
-  #@example Authentication
-  #  require "opentox-client"
-  #  OpenTox::Authorization::AA = "https://opensso.in-silico.ch" #if not set in .opentox/conf/[SERVICE].rb
-  #  OpenTox::Authorization.authenticate("username", "password")
-  #  puts OpenTox::Authorization.authorize("http://example.uri/testpath/", "GET")
-  #@see http://www.opentox.org/dev/apis/api-1.2/AA OpenTox A&A API 1.2 specification
-
-  module Authorization
-
-    #Helper Class to create and send default policies out of xml templates
-    #@example Creating a default policy to a URI
-    #  aa=OpenTox::Authorization::Helper.new
-    #  xml=aa.get_xml('http://uri....')
-    #  OpenTox::Authorization.create_policy(xml)
-
-    class Helper
-      attr_accessor :user, :policy
-
-      #Generates an AuthorizationHelper object - requires subjectid
-      # @param [String] subjectid
-      def initialize
-        @user = Authorization.get_user
-        @policy = Policies.new()
-      end
-
-      #Cleans Policies of AuthorizationHelper object and loads default xml file into policy attribute
-      #set uri and user, returns Policyfile(XML) for open-sso
-      # @param uri [String] URI to create a policy for
-      def get_xml(uri)
-        @policy.drop_policies
-        @policy.load_default_policy(@user, uri)
-        return @policy.to_xml
-      end
-
-      #Loads and sends Policyfile(XML) to open-sso server
-      # @param uri [String] URI to create a policy for
-      def send(uri)
-        xml = get_xml(uri)
-        ret = false
-        ret = Authorization.create_policy(xml)
-        $logger.warn "Create policy on openSSO failed for URI: #{uri} subjectid: #{RestClientWrapper.subjectid}. Will try again." if !ret
-        ret = Authorization.create_policy(xml) if !ret
-        $logger.debug "Policy send with subjectid: #{RestClientWrapper.subjectid}"
-        $logger.error "Not created Policy is: #{xml}" if !ret
-        ret
-      end
-    end
-
-    #Returns the open-sso server set in the config file .opentox/config/[environment].yaml
-    # @return [String, nil] the openSSO server URI or nil
-    def self.server
-      return AA
-    end
-
-    #Authentication against OpenSSO. Returns token. Requires Username and Password.
-    # @param user [String] Username
-    # @param pw [String] Password
-    # @return [Boolean] true if successful
-    def self.authenticate(user, pw)
-      begin
-        res = RestClientWrapper.post("#{AA}/auth/authenticate",{:username=>user, :password => pw},{:subjectid => ""}).sub("token.id=","").sub("\n","")
-        if is_token_valid(res)
-          RestClientWrapper.subjectid = res
-          return true
-        else
-          bad_request_error "Authentication failed #{res.inspect}"
-        end
-      rescue
-        bad_request_error "Authentication failed #{res.inspect}"
-      end
-    end
-
-    #Logout on opensso. Make token invalid. Requires token
-    # @param [String] subjectid the subjectid
-    # @return [Boolean] true if logout is OK
-    def self.logout(subjectid=RestClientWrapper.subjectid)
-      begin
-        out = RestClientWrapper.post("#{AA}/auth/logout", :subjectid => subjectid)
-        return true unless is_token_valid(subjectid)
-      rescue
-        return false
-      end
-      return false
-    end
-
-    #Authorization against OpenSSO for a URI with request-method (action) [GET/POST/PUT/DELETE]
-    # @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=RestClientWrapper.subjectid)
-      return true if RestClientWrapper.post("#{AA}/auth/authorize",{:subjectid => subjectid, :uri => uri, :action => action})== "boolean=true\n"
-      return false
-    end
-
-    #Checks if a token is a valid token
-    # @param [String]subjectid subjectid from openSSO session
-    # @return [Boolean] subjectid is valid or not.
-    def self.is_token_valid(subjectid=RestClientWrapper.subjectid)
-      begin
-        return true if RestClientWrapper.post("#{AA}/auth/isTokenValid",:tokenid => subjectid) == "boolean=true\n"
-      rescue #do rescue because openSSO throws 401
-        return false
-      end
-      return false
-    end
-
-    #Returns array with all policies of the token owner
-    # @param [String]subjectid requires subjectid
-    # @return [Array, nil] returns an Array of policy names or nil if request fails
-    def self.list_policies
-      begin
-        out = RestClientWrapper.get("#{AA}/pol",nil)
-        return out.split("\n")
-      rescue
-        return nil
-      end
-    end
-
-    #Returns a policy in xml-format
-    # @param policy [String] policyname
-    # @param subjectid [String]
-    # @return [String] XML of the policy
-    def self.list_policy(policy)
-      begin
-        return RestClientWrapper.get("#{AA}/pol",nil,{:id => policy})
-      rescue
-        return nil
-      end
-    end
-
-    # Lists policies alongside with affected uris
-    # @param [String] subjectid
-    # @return [Hash] keys: all policies of the subjectid owner, values: uris affected by those policies
-    def self.list_policies_uris
-      names = list_policies
-      policies = {}
-      names.each do |n|
-        policies[n] = list_policy_uris n 
-      end
-      policies
-    end
-
-    # Lists policies alongside with affected uris
-    # @param [String] subjectid
-    # @return [Hash] keys: all policies of the subjectid owner, values: uris affected by those policies
-    def self.list_policy_uris( policy )
-      p = OpenTox::Policies.new
-      p.load_xml( list_policy(policy) )
-      p.uris
-    end
-
-    #Returns the owner (who created the first policy) of an URI
-    # @param uri [String] URI
-    # @param subjectid [String] subjectid
-    # return [String, nil]owner,nil returns owner of the URI
-    def self.get_uri_owner(uri)
-      begin
-        return RestClientWrapper.get("#{AA}/pol",nil,{:uri => uri}).sub("\n","")
-      rescue
-        return nil
-      end
-    end
-
-    #Returns true or false if owner (who created the first policy) of an URI
-    # @param uri [String] URI
-    # @param subjectid [String]
-    # return [Boolean]true,false status of ownership of the URI
-    def self.uri_owner?(uri)
-      get_uri_owner(uri) == get_user
-    end
-
-    #Checks if a policy exists to a URI. Requires URI and token.
-    # @param uri [String] URI
-    # @param subjectid [String]
-    # return [Boolean]
-    def self.uri_has_policy(uri)
-      owner = get_uri_owner(uri)
-      return true if owner and owner != "null"
-      false
-    end
-
-    #List all policynames for a URI. Requires URI and token.
-    # @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)
-      begin
-        out = RestClientWrapper.get("#{AA}/pol",nil,{:uri => uri, :polnames => true})
-        policies = []; notfirstline = false
-        out.split("\n").each do |line|
-          policies << line if notfirstline
-          notfirstline = true
-        end
-        return policies
-      rescue
-        return nil
-      end
-    end
-
-    #Sends a policy in xml-format to opensso server. Requires policy-xml and token.
-    # @param policy [String] XML string of a policy
-    # @param subjectid [String]
-    # return [Boolean] returns true if policy is created
-    def self.create_policy(policy)
-      begin
-        $logger.debug "OpenTox::Authorization.create_policy policy: #{policy[168,43]} with token: #{RestClientWrapper.subjectid} ."
-        return true if RestClientWrapper.post("#{AA}/Pol/opensso-pol",policy, {:content_type =>  "application/xml"})
-      rescue
-        return false
-      end
-    end
-
-    #Deletes a policy
-    # @param policy [String] policyname
-    # @param subjectid [String]
-    # @return [Boolean,nil]
-    def self.delete_policy(policy)
-      begin
-        $logger.debug "OpenTox::Authorization.delete_policy policy: #{policy} with token: #{RestClientWrapper.subjectid}"
-        return true if RestClientWrapper.delete("#{AA}/pol",nil, {:id => policy})
-      rescue
-        return nil
-      end
-    end
-
-    #Returns array of the LDAP-Groups of an user
-    # @param [String]subjectid
-    # @return [Array] gives array of LDAP groups of a user
-    def self.list_user_groups(user)
-      begin
-        out = RestClientWrapper.post("#{AA}/opensso/identity/read", {:name => user, :admin => RestClientWrapper.subjectid, :attributes_names => "group"})
-        grps = []
-        out.split("\n").each do |line|
-          grps << line.sub("identitydetails.group=","") if line.include?("identitydetails.group=")
-        end
-        return grps
-      rescue
-        []
-      end
-    end
-
-    #Returns the owner (user id) of a token
-    # @param [String]subjectid optional (normally only used for testing)
-    # @return [String]user
-    def self.get_user subjectid=RestClientWrapper.subjectid
-      begin
-        out = RestClientWrapper.post("#{AA}/opensso/identity/attributes", {:subjectid => subjectid, :attributes_names => "uid"})
-        user = ""; check = false
-        out.split("\n").each do |line|
-          if check
-            user = line.sub("userdetails.attribute.value=","") if line.include?("userdetails.attribute.value=")
-            check = false
-          end
-          check = true if line.include?("userdetails.attribute.name=uid")
-        end
-        return user
-      rescue
-        nil
-      end
-    end
-
-    #Send default policy with Authorization::Helper class
-    # @param uri [String] URI
-    # @param subjectid [String]
-    def self.send_policy(uri)
-      aa  = Authorization::Helper.new
-      ret = aa.send(uri)
-      $logger.debug "OpenTox::Authorization send policy for URI: #{uri} | subjectid: #{RestClientWrapper.subjectid} - policy created: #{ret}"
-      ret
-    end
-
-    #Deletes all policies of an URI
-    # @param uri [String] URI
-    # @param subjectid [String]
-    # @return [Boolean]
-    def self.delete_policies_from_uri(uri)
-      policies = list_uri_policies(uri)
-      if policies
-        policies.each do |policy|
-          ret = delete_policy(policy)
-          $logger.debug "OpenTox::Authorization delete policy: #{policy} - with result: #{ret}"
-        end
-      end
-      return true
-    end
-
-    # Checks (if subjectid is valid) if a policy exist and create default policy if not
-    # @param [String] uri
-    # @param [String] subjectid
-    # @return [Boolean] true if policy checked/created successfully (or no uri/subjectid given), false else
-    def self.check_policy(uri)
-      return true unless uri and RestClientWrapper.subjectid
-      unless OpenTox::Authorization.is_token_valid(RestClientWrapper.subjectid)
-        $logger.error "OpenTox::Authorization.check_policy, subjectid NOT valid: #{RestClientWrapper.subjectid}"
-        return false
-      end
-
-      if !uri_has_policy(uri)
-        # if no policy exists, create a policy, return result of send policy
-        send_policy(uri)
-      else
-        # if policy exists check for POST rights
-        if authorize(uri, "POST")
-          true
-       else
-          $logger.error "OpenTox::Authorization.check_policy, already exists, but no POST-authorization with subjectid: #{RestClientWrapper.subjectid}"
-          false
-        end
-      end
-      true
-    end
-
-    class << self
-      alias :token_valid? :is_token_valid
-    end
-
-    # Check Authorization for a resource (identified via URI) with method and 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)
-      return true unless $aa[:uri]
-      request_method = request_method.to_sym if request_method
-      if $aa[:free_request].include?(request_method)
-        true
-      elsif OpenTox::Authorization.free_uri?(uri, request_method)
-        true
-      elsif $aa[:authenticate_request].include?(request_method)
-        ret = OpenTox::Authorization.is_token_valid(RestClientWrapper.subjectid)
-        $logger.debug "authorized? >>#{ret}<< (token is in/valid), method: #{request_method}, URI: #{uri}, subjectid: #{RestClientWrapper.subjectid}" unless ret
-        ret
-      elsif OpenTox::Authorization.authorize_exception?(uri, request_method)
-        ret = OpenTox::Authorization.is_token_valid(RestClientWrapper.subjectid)
-        $logger.debug "authorized? >>#{ret}<< (uris is authorize exception, token is in/valid), method: #{request_method}, URI: #{uri}, subjectid: #{RestClientWrapper.subjectid}" unless ret
-        ret
-      elsif $aa[:authorize_request].include?(request_method)
-        ret = OpenTox::Authorization.authorize(uri, request_method)
-        $logger.debug "authorized? >>#{ret}<< (uri (not) authorized), method: #{request_method}, URI: #{uri}, subjectid: #{RestClientWrapper.subjectid}" unless ret
-        ret
-      else
-        $logger.error "invalid request/uri method: #{request_method}, URI: #{uri}, subjectid: #{RestClientWrapper.subjectid}"
-        false
-      end
-    end
-
-    private
-    # extend class methods
-    class << self
-      # methods: free_uri and authorize_exception
-      # @return [Boolean] checks if uri-method pair is included in $aa[:free_uri] or $aa[:authorize_exception]
-      [:free_uri, :authorize_exception].each do |method|
-        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)
-                uris.each do |u|
-                  return true if u.match uri
-                end
-              end
-            end
-          end
-          return false
-        end
-      end
-    end
-  end
-end
diff --git a/lib/compound.rb b/lib/compound.rb
index 4e29938..3ba1670 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -11,32 +11,6 @@ module OpenTox
   class Compound
     include OpenTox
 
-    # OpenBabel FP4 fingerprints
-    # OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html
-    fp4 = FingerprintSmarts.all
-    unless fp4
-      fp4 = []
-      File.open(File.join(File.dirname(__FILE__),"SMARTS_InteLigand.txt")).each do |l| 
-        l.strip!
-        unless l.empty? or l.match /^#/
-          name,smarts = l.split(': ')
-          fp4 << OpenTox::FingerprintSmarts.find_or_create_by(:name => name, :smarts => smarts) unless smarts.nil?
-        end
-      end
-    end
-    FP4 = fp4
-
-    # TODO investigate other types of fingerprints (MACCS)
-    # OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html
-    # http://www.dalkescientific.com/writings/diary/archive/2008/06/26/fingerprint_background.html
-    # OpenBabel MNA http://openbabel.org/docs/dev/FileFormats/Multilevel_Neighborhoods_of_Atoms_(MNA).html#multilevel-neighborhoods-of-atoms-mna
-    # Morgan ECFP, FCFP
-    # http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/fingerprint/CircularFingerprinter.html
-    # http://www.rdkit.org/docs/GettingStartedInPython.html
-    # Chemfp
-    # https://chemfp.readthedocs.org/en/latest/using-tools.html
-    # CACTVS/PubChem
-
     field :inchi, type: String
     attr_readonly :inchi
     field :smiles, type: String
@@ -48,21 +22,17 @@ module OpenTox
     field :sdf_id, type: BSON::ObjectId
     field :fp4, type: Array
     field :fp4_size, type: Integer
-    #belongs_to :dataset
-    #belongs_to :data_entry
-
-    #def  == compound
-      #self.inchi == compound.inchi
-    #end
 
+    # Overwrites standard Mongoid method to create fingerprints before database insertion
     def self.find_or_create_by params
       compound = self.find_or_initialize_by params
-      unless compound.fp4
+      unless compound.fp4 and !compound.fp4.empty?
         compound.fp4_size = 0
         compound.fp4 = []
-        Algorithm::Descriptor.smarts_match(compound, FP4.collect{|f| f.smarts}).each_with_index do |m,i|
+        fingerprint = FingerprintSmarts.fingerprint
+        Algorithm::Descriptor.smarts_match(compound, fingerprint).each_with_index do |m,i|
           if m > 0
-            compound.fp4 << FP4[i].id
+            compound.fp4 << fingerprint[i].id
             compound.fp4_size += 1
           end
         end
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 509e897..0237adf 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -3,39 +3,19 @@ require 'tempfile'
 
 module OpenTox
 
-  class LazarPrediction < Dataset
-    field :creator, type: String
-    field :prediction_feature_id, type: String
-
-    def prediction_feature
-      Feature.find prediction_feature_id
-    end
-
-  end
-
-  class DescriptorDataset < Dataset
-    field :feature_calculation_algorithm, type: String
-  end
-
-  class FminerDataset < DescriptorDataset
-    field :training_algorithm, type: String
-    field :training_dataset_id, type: BSON::ObjectId
-    field :training_feature_id, type: BSON::ObjectId
-    field :training_parameters, type: Hash
-  end
-
   class Dataset
-    include Mongoid::Document
 
     attr_writer :data_entries
 
     # associations like has_many, belongs_to deteriorate performance
     field :feature_ids, type: Array, default: []
     field :compound_ids, type: Array, default: []
-    field :data_entries_id, type: BSON::ObjectId
+    field :data_entries_id, type: BSON::ObjectId, default: []
     field :source, type: String
     field :warnings, type: Array, default: []
 
+    # Save all data including data_entries
+    # Should be used instead of save
     def save_all
       dump = Marshal.dump(@data_entries)
       file = Mongo::Grid::File.new(dump, :filename => "#{self.id.to_s}.data_entries")
@@ -46,74 +26,32 @@ module OpenTox
 
     # Readers
 
+    # Get all compounds
     def compounds
       @compounds ||= self.compound_ids.collect{|id| OpenTox::Compound.find id}
       @compounds
     end
 
+    # Get all features
     def features
       @features ||= self.feature_ids.collect{|id| OpenTox::Feature.find(id)}
       @features
     end
 
-    def fill_nil_with n
-      (0 .. compound_ids.size-1).each do |i|
-        @data_entries[i] ||= []
-        (0 .. feature_ids.size-1).each do |j|
-          @data_entries[i][j] ||= n
-        end
-      end
-    end
-
-    def [](row,col)
-      @data_entries[row,col]
-    end
-
-    def []=(row,col,v)
-      @data_entries ||= []
-      @data_entries[row] ||= []
-      @data_entries[row][col] = v
-    end
-
-    def correlation_plot training_dataset
-      R.assign "features", data_entries
-      R.assign "activities", training_dataset.data_entries.collect{|de| de.first}
-      R.eval "featurePlot(features,activities)"
-    end
-
-    def density_plot
-      R.assign "acts", data_entries.collect{|r| r.first }#.compact
-      R.eval "plot(density(log(acts),na.rm= TRUE), main='log(#{features.first.name})')"
-      # TODO kill Rserve plots
-    end
-
-    # merge dataset (i.e. append features)
-    def +(dataset)
-      bad_request_error "Dataset merge failed because the argument is not a OpenTox::Dataset but a #{dataset.class}" unless dataset.is_a? Dataset
-      bad_request_error "Dataset merge failed because compounds are unequal in datasets #{self.id} and #{dataset.id}" unless compound_ids == dataset.compound_ids
-      self.feature_ids ||= []
-      self.feature_ids = self.feature_ids + dataset.feature_ids
-      @data_entries ||= Array.new(compound_ids.size){[]}
-      @data_entries.each_with_index do |row,i|
-        @data_entries[i] = row + dataset.fingerprint(compounds[i])
-      end
-      self
-
-    end
-
-    def fingerprint(compound)
-      i = compound_ids.index(compound.id)
-      i.nil? ? nil : data_entries[i] 
-    end
-
+    # Get all data_entries
     def data_entries
       unless @data_entries
         t = Time.now
-        @data_entries = Marshal.load($gridfs.find_one(_id: data_entries_id).data)
-        bad_request_error "Data entries (#{data_entries_id}) are not a 2D-Array" unless @data_entries.is_a? Array and @data_entries.first.is_a? Array
-        bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries.size} rows, but dataset (#{id}) has #{compound_ids.size} compounds" unless @data_entries.size == compound_ids.size
-        bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries..first.size} columns, but dataset (#{id}) has #{feature_ids.size} features" unless @data_entries.first.size == feature_ids.size
-        $logger.debug "Retrieving data: #{Time.now-t}"
+        data_entry_file = $gridfs.find_one(_id: data_entries_id)
+        if data_entry_file.nil?
+          @data_entries = []
+        else
+          @data_entries = Marshal.load(data_entry_file.data)
+          bad_request_error "Data entries (#{data_entries_id}) are not a 2D-Array" unless @data_entries.is_a? Array and @data_entries.first.is_a? Array
+          bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries.size} rows, but dataset (#{id}) has #{compound_ids.size} compounds" unless @data_entries.size == compound_ids.size
+          bad_request_error "Data entries (#{data_entries_id}) have #{@data_entries..first.size} columns, but dataset (#{id}) has #{feature_ids.size} features" unless @data_entries.first.size == feature_ids.size
+          $logger.debug "Retrieving data: #{Time.now-t}"
+        end
       end
       @data_entries
     end
@@ -130,50 +68,21 @@ module OpenTox
 
     # Writers
 
+    # Set compounds
     def compounds=(compounds)
       self.compound_ids = compounds.collect{|c| c.id}
     end
 
-    def add_compound compound
-        self.compound_ids << compound.id
-    end
-
+    # Set features
     def features=(features)
       self.feature_ids = features.collect{|f| f.id}
     end
 
-    def add_feature feature
-      self.feature_ids << feature.id
-    end
-
-    def self.create compounds, features, warnings=[], source=nil
-      dataset = Dataset.new(:warnings => warnings)
-      dataset.compounds = compounds
-      dataset.features = features
-      dataset
-    end
-
-    # for prediction result datasets
-    # assumes that there are feature_ids with title prediction and confidence
-    # @return [Array] of Hashes with keys { :compound, :value ,:confidence } (compound value is object not uri)
-    # TODO
-    #def predictions
-    #end
-
-    # Serialisation
-    
-    # converts dataset to csv format including compound smiles as first column, other column headers are feature titles
-    # @return [String]
-    def to_csv(inchi=false)
-      CSV.generate() do |csv| #{:force_quotes=>true}
-        csv << [inchi ? "InChI" : "SMILES"] + features.collect{|f| f.title}
-        compounds.each_with_index do |c,i|
-          csv << [inchi ? c.inchi : c.smiles] + data_entries[i]
-        end
-      end
-    end
+    # Dataset operations
 
-    # split dataset into n folds
+    # Split a dataset into n folds
+    # @param [Integer] number of folds
+    # @return [Array] Array with folds [training_dataset,test_dataset]
     def folds n
       len = self.compound_ids.size
       indices = (0..len-1).to_a.shuffle
@@ -199,9 +108,36 @@ module OpenTox
       chunks
     end
 
+    # Diagnostics
+
+    def correlation_plot training_dataset
+      # TODO: create/store svg
+      R.assign "features", data_entries
+      R.assign "activities", training_dataset.data_entries.collect{|de| de.first}
+      R.eval "featurePlot(features,activities)"
+    end
+
+    def density_plot
+      # TODO: create/store svg
+      R.assign "acts", data_entries.collect{|r| r.first }#.compact
+      R.eval "plot(density(log(acts),na.rm= TRUE), main='log(#{features.first.name})')"
+    end
+
+    # Serialisation
+    
+    # converts dataset to csv format including compound smiles as first column, other column headers are feature titles
+    # @return [String]
+    def to_csv(inchi=false)
+      CSV.generate() do |csv| #{:force_quotes=>true}
+        csv << [inchi ? "InChI" : "SMILES"] + features.collect{|f| f.title}
+        compounds.each_with_index do |c,i|
+          csv << [inchi ? c.inchi : c.smiles] + data_entries[i]
+        end
+      end
+    end
+
 
-    # Adding data methods
-    # (Alternatively, you can directly change @data["feature_ids"] and @data["compounds"])
+    # Parsers
 
     # Create a dataset from file (csv,sdf,...)
     # @param filename [String]
@@ -210,6 +146,8 @@ module OpenTox
     #def self.from_sdf_file
     #end
 
+    # Create a dataset from CSV file
+    # TODO: document structure
     def self.from_csv_file file, source=nil, bioassay=true
       source ||= file
       table = CSV.read file, :skip_blanks => true
@@ -222,8 +160,6 @@ module OpenTox
     # does a lot of guesswork in order to determine feature types
     def parse_table table, bioassay=true
 
-      # TODO: remove empty entries + write tests
-
       time = Time.now
 
       # features
@@ -277,24 +213,21 @@ module OpenTox
       table.each_with_index do |vals,i|
         ct = Time.now
         identifier = vals.shift
-        #if vals.compact.empty?
-          #warnings << "No values for compound at position #{i+2}, all entries are ignored."
-          #@data_entries.pop
-          #next
-        #end
+        warnings << "No feature values for compound at position #{i+2}." if vals.compact.empty?
         begin
+          # TODO parse inchi and catch openbabel errors (and segfaults) in compound.rb
           case compound_format
           when /SMILES/i
             compound = OpenTox::Compound.from_smiles(identifier)
             if compound.inchi.empty?
-              warnings << "Cannot parse #{compound_format} compound '#{compound.strip}' at position #{i+2}, all entries are ignored."
+              warnings << "Cannot parse #{compound_format} compound '#{identifier}' at position #{i+2}, all entries are ignored."
               next
             end
           when /InChI/i
             compound = OpenTox::Compound.from_inchi(identifier)
           end
         rescue
-          warnings << "Cannot parse #{compound_format} compound '#{compound}' at position #{i+2}, all entries are ignored."
+          warnings << "Cannot parse #{compound_format} compound '#{identifier}' at position #{i+2}, all entries are ignored."
           next
         end
         compound_time += Time.now-ct
@@ -330,5 +263,71 @@ module OpenTox
       $logger.debug "Saving: #{Time.now-time}"
 
     end
+
+=begin
+    # TODO remove
+
+    # Create a dataset with compounds and features
+    def self.create compounds, features, warnings=[], source=nil
+      dataset = Dataset.new(:warnings => warnings)
+      dataset.compounds = compounds
+      dataset.features = features
+      dataset
+    end
+    # merge dataset (i.e. append features)
+    def +(dataset)
+      bad_request_error "Dataset merge failed because the argument is not a OpenTox::Dataset but a #{dataset.class}" unless dataset.is_a? Dataset
+      bad_request_error "Dataset merge failed because compounds are unequal in datasets #{self.id} and #{dataset.id}" unless compound_ids == dataset.compound_ids
+      self.feature_ids ||= []
+      self.feature_ids = self.feature_ids + dataset.feature_ids
+      @data_entries ||= Array.new(compound_ids.size){[]}
+      @data_entries.each_with_index do |row,i|
+        @data_entries[i] = row + dataset.fingerprint(compounds[i])
+      end
+      self
+
+    end
+
+    def fingerprint(compound)
+      i = compound_ids.index(compound.id)
+      i.nil? ? nil : data_entries[i] 
+    end
+=end
+
+    private
+
+    def fill_nil_with n
+      (0 .. compound_ids.size-1).each do |i|
+        @data_entries[i] ||= []
+        (0 .. feature_ids.size-1).each do |j|
+          @data_entries[i][j] ||= n
+        end
+      end
+    end
+  end
+
+  # Dataset for lazar predictions
+  class LazarPrediction < Dataset
+    field :creator, type: String
+    field :prediction_feature_id, type: String
+
+    def prediction_feature
+      Feature.find prediction_feature_id
+    end
+
+  end
+
+  # Dataset for descriptors (physchem)
+  class DescriptorDataset < Dataset
+    field :feature_calculation_algorithm, type: String
   end
+
+  # Dataset for fminer descriptors
+  class FminerDataset < DescriptorDataset
+    field :training_algorithm, type: String
+    field :training_dataset_id, type: BSON::ObjectId
+    field :training_feature_id, type: BSON::ObjectId
+    field :training_parameters, type: Hash
+  end
+
 end
diff --git a/lib/descriptor.rb b/lib/descriptor.rb
new file mode 100644
index 0000000..68bc7a2
--- /dev/null
+++ b/lib/descriptor.rb
@@ -0,0 +1,253 @@
+require 'digest/md5'
+ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk" 
+BABEL_3D_CACHE_DIR = File.join(File.dirname(__FILE__),"..",'/babel_3d_cache')
+# TODO store descriptors in mongodb
+
+module OpenTox
+
+  module Algorithm 
+    class Descriptor 
+      include OpenTox
+
+      JAVA_DIR = File.join(File.dirname(__FILE__),"..","java")
+      CDK_JAR = Dir[File.join(JAVA_DIR,"cdk-*jar")].last
+      JOELIB_JAR = File.join(JAVA_DIR,"joelib2.jar")
+      LOG4J_JAR = File.join(JAVA_DIR,"log4j.jar")
+      JMOL_JAR = File.join(JAVA_DIR,"Jmol.jar")
+
+      obexclude = ["cansmi","cansmiNS","formula","InChI","InChIKey","s","smarts","title"]
+      OBDESCRIPTORS = Hash[OpenBabel::OBDescriptor.list_as_string("descriptors").split("\n").collect do |d|
+        name,description = d.split(/\s+/,2)
+        ["Openbabel."+name,description] unless obexclude.include? name
+      end.compact.sort{|a,b| a[0] <=> b[0]}]
+
+      cdk_desc = YAML.load(`java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptorInfo`)
+      CDKDESCRIPTORS = Hash[cdk_desc.collect { |d| ["Cdk."+d[:java_class].split('.').last.sub(/Descriptor/,''), d[:description]] }.sort{|a,b| a[0] <=> b[0]}]
+      CDKDESCRIPTOR_VALUES = cdk_desc.collect { |d| prefix="Cdk."+d[:java_class].split('.').last.sub(/Descriptor/,''); d[:names].collect{ |name| prefix+"."+name } }.flatten
+
+      # exclude Hashcode (not a physchem property) and GlobalTopologicalChargeIndex (Joelib bug)
+      joelibexclude = ["MoleculeHashcode","GlobalTopologicalChargeIndex"]
+      # strip Joelib messages from stdout
+      JOELIBDESCRIPTORS = Hash[YAML.load(`java -classpath #{JOELIB_JAR}:#{LOG4J_JAR}:#{JAVA_DIR}  JoelibDescriptorInfo | sed '0,/---/d'`).collect do |d|
+        name = d[:java_class].sub(/^joelib2.feature.types./,'')
+        # impossible to obtain meaningful descriptions from JOELIb, see java/JoelibDescriptors.java
+        ["Joelib."+name, "no description available"] unless joelibexclude.include? name
+      end.compact.sort{|a,b| a[0] <=> b[0]}] 
+
+      DESCRIPTORS = OBDESCRIPTORS.merge(CDKDESCRIPTORS.merge(JOELIBDESCRIPTORS))
+      DESCRIPTOR_VALUES = OBDESCRIPTORS.keys + CDKDESCRIPTOR_VALUES + JOELIBDESCRIPTORS.keys
+
+      require_relative "unique_descriptors.rb"
+
+      def self.description descriptor
+        lib = descriptor.split('.').first
+        case lib
+        when "Openbabel"
+          OBDESCRIPTORS[descriptor]
+        when "Cdk"
+          name = descriptor.split('.')[0..-2].join('.')
+          CDKDESCRIPTORS[name]
+        when "Joelib"
+          JOELIBDESCRIPTORS[descriptor]
+        when "lookup"
+          "Read feature values from a dataset"
+        end
+      end
+
+      def self.smarts_match compounds, smarts_features, count=false
+        bad_request_error "Compounds for smarts_match are empty" unless compounds
+        bad_request_error "Smarts features for smarts_match are empty" unless smarts_features
+        parse compounds
+        @count = count
+        obconversion = OpenBabel::OBConversion.new
+        obmol = OpenBabel::OBMol.new
+        obconversion.set_in_format('inchi')
+        smarts_pattern = OpenBabel::OBSmartsPattern.new
+        smarts_features = [smarts_features] if smarts_features.is_a?(Feature)
+        @smarts = smarts_features.collect{|f| f.smarts}
+        @physchem_descriptors = nil
+        @data_entries = Array.new(@compounds.size){Array.new(@smarts.size,false)}
+        @compounds.each_with_index do |compound,c|
+          # TODO OpenBabel may segfault here
+          # catch inchi errors in compound.rb
+          # eg. at line 249 of rat_feature_dataset
+          # which worked with opentox-client
+          # (but no smarts_match)
+          p "'#{compound.inchi}'"
+          obconversion.read_string(obmol,compound.inchi)
+          @smarts.each_with_index do |smart,s|
+            smarts_pattern.init(smart)
+            if smarts_pattern.match(obmol)
+              count ? value = smarts_pattern.get_map_list.to_a.size : value = 1
+            else
+              value = 0 
+            end
+            @data_entries[c][s] = value
+          end
+        end
+        serialize 
+      end
+
+      def self.smarts_count compounds, smarts
+        smarts_match compounds,smarts,true
+      end
+
+      def self.serialize
+        case @input_class
+        when "OpenTox::Compound"
+          if @with_names and @physchem_descriptors
+            [@physchem_descriptors,@data_entries.first]
+          else
+            @data_entries.first
+          end
+        when "Array"
+          if @with_names and @physchem_descriptors
+            [@physchem_descriptors,@data_entries.first]
+          else
+            @data_entries
+          end
+        when "OpenTox::Dataset"
+          dataset = OpenTox::DescriptorDataset.new(:compound_ids => @compounds.collect{|c| c.id})
+          if @smarts
+            dataset.feature_ids = @smarts.collect{|smart| Smarts.find_or_create_by(:smarts => smart).id}
+            @count ? algo = "count" : algo = "match"
+            dataset.feature_calculation_algorithm = "#{self}.smarts_#{algo}"
+            
+          elsif @physchem_descriptors
+            dataset.feature_ids = @physchem_descriptors.collect{|d| PhysChemDescriptor.find_or_create_by(:name => d, :creator => __FILE__).id}
+            dataset.data_entries = @data_entries
+            dataset.feature_calculation_algorithm = "#{self}.physchem"
+            #TODO params?
+          end
+          dataset.save_all
+          dataset
+        end
+      end
+
+      def self.physchem compounds, descriptors=UNIQUEDESCRIPTORS, with_names=false
+        parse compounds
+        @data_entries = Array.new(@compounds.size){[]}
+        @descriptors = descriptors
+        @smarts = nil
+        @physchem_descriptors = [] # CDK may return more than one result per descriptor, they are stored as separate features
+        @with_names = with_names
+        des = {}
+        @descriptors.each do |d|
+          lib, descriptor = d.split(".",2)
+          lib = lib.downcase.to_sym
+          des[lib] ||= []
+          des[lib] << descriptor
+        end
+        des.each do |lib,descriptors|
+          send(lib, descriptors)
+        end
+        serialize
+      end
+
+      def self.openbabel descriptors
+        $logger.debug "compute #{descriptors.size} openbabel descriptors for #{@compounds.size} compounds"
+        obdescriptors = descriptors.collect{|d| OpenBabel::OBDescriptor.find_type d}
+        obmol = OpenBabel::OBMol.new
+        obconversion = OpenBabel::OBConversion.new
+        obconversion.set_in_format 'inchi'
+        last_feature_idx = @physchem_descriptors.size
+        @compounds.each_with_index do |compound,c|
+          obconversion.read_string obmol, compound.inchi
+          obdescriptors.each_with_index do |descriptor,d|
+            @data_entries[c][d+last_feature_idx] = fix_value(descriptor.predict(obmol))
+          end
+        end
+        @physchem_descriptors += descriptors.collect{|d| "Openbabel.#{d}"}
+      end
+
+      def self.java_descriptors descriptors, lib
+        $logger.debug "compute #{descriptors.size} cdk descriptors for #{@compounds.size} compounds"
+        sdf = sdf_3d 
+        # use java system call (rjb blocks within tasks)
+        # use Tempfiles to avoid "Argument list too long" error 
+        case lib
+        when "cdk"
+          run_cmd "java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptors #{sdf} #{descriptors.join(" ")}"
+        when "joelib"
+          run_cmd "java -classpath #{JOELIB_JAR}:#{JMOL_JAR}:#{LOG4J_JAR}:#{JAVA_DIR}  JoelibDescriptors  #{sdf} #{descriptors.join(' ')}"
+        end
+        last_feature_idx = @physchem_descriptors.size
+        YAML.load_file("#{sdf}#{lib}.yaml").each_with_index do |calculation,i|
+          $logger.error "Descriptor calculation failed for compound #{compounds[i].inchi}." if calculation.empty?
+          # CDK Descriptors may calculate multiple values, they are stored in separate features
+          @physchem_descriptors += calculation.keys if i == 0
+          calculation.keys.each_with_index do |name,j|
+            @data_entries[i][j+last_feature_idx] = fix_value(calculation[name])
+          end
+        end
+        FileUtils.rm "#{sdf}#{lib}.yaml"
+      end
+
+      def self.cdk descriptors
+        java_descriptors descriptors, "cdk"
+      end
+
+      def self.joelib descriptors
+        java_descriptors descriptors, "joelib"
+      end
+
+      def self.lookup compounds, features, dataset
+        parse compounds
+        fingerprint = []
+        compounds.each do |compound|
+          fingerprint << []
+          features.each do |feature|
+          end
+        end
+      end
+
+      def self.run_cmd cmd
+        cmd = "#{cmd} 2>&1"
+        $logger.debug "running external cmd: '#{cmd}'"
+        p = IO.popen(cmd) do |io|
+          while line = io.gets
+            $logger.debug "> #{line.chomp}"
+          end
+          io.close
+          raise "external cmd failed '#{cmd}' (see log file for error msg)" unless $?.to_i == 0
+        end
+      end
+
+      def self.sdf_3d 
+        # TODO check if 3d sdfs are stored in GridFS
+        sdf = ""
+        @compounds.each do |compound|
+          sdf << compound.sdf
+        end
+        sdf_file = "/tmp/#{SecureRandom.uuid}.sdf"
+        File.open(sdf_file,"w+"){|f| f.print sdf}
+        sdf_file
+      end
+
+      def self.parse compounds
+        @input_class = compounds.class.to_s
+        case @input_class
+        when "OpenTox::Compound"
+          @compounds = [compounds]
+        when "Array"
+          @compounds = compounds
+        when "OpenTox::Dataset"
+          @compounds = compounds.compounds
+        else
+          bad_request_error "Cannot calculate descriptors for #{compounds.class} objects."
+        end
+      end
+
+      def self.fix_value val
+        val = val.first if val.is_a? Array and val.size == 1
+        val = nil if val == "NaN"
+        if val.numeric?
+          val = Float(val)
+          val = nil if val.nan? or val.infinite?
+        end
+        val
+      end
+      private_class_method :sdf_3d, :fix_value, :parse, :run_cmd, :serialize
+    end
+  end
+end
diff --git a/lib/error.rb b/lib/error.rb
index 12e22ff..8fe8a1e 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -1,36 +1,19 @@
-require 'open4'
-
-# add additional fields to Exception class to format errors according to OT-API
 module OpenToxError
-  attr_accessor :http_code, :uri, :error_cause, :metadata
-  def initialize(message=nil, uri=nil, cause=nil)
+  attr_accessor :http_code, :message, :cause
+  def initialize message=nil
     message = message.to_s.gsub(/\A"|"\Z/, '') if message # remove quotes
-    @error_cause = cause ? OpenToxError::cut_backtrace(cause) : short_backtrace
-    
     super message
-      @uri = uri.to_s.sub(%r{//.*:.*@},'//') # remove credentials from uri
-      @http_code ||= 500
-      @metadata = {
-        :type => "ErrorReport",
-        :actor => @uri,
-        :message => message.to_s,
-        :statusCode => @http_code,
-        :errorCode => self.class.to_s,
-        :errorCause => @error_cause,
-      }
-      $logger.error("\n"+JSON.pretty_generate(@metadata)) 
-  end
-
-=begin
-  # this method defines what is used for to_yaml (override to skip large @rdf graph)
-  def encode_with coder
-    @rdf.each do |statement|
-      coder[statement.predicate.fragment.to_s] = statement.object.to_s
-    end
+    @http_code ||= 500
+    @message = message.to_s
+    @cause = cut_backtrace(caller)
+    $logger.error("\n"+JSON.pretty_generate({
+      :http_code => @http_code,
+      :message => @message,
+      :cause => @cause
+    })) 
   end
-=end
   
-  def self.cut_backtrace(trace)
+  def cut_backtrace(trace)
     if trace.is_a?(Array)
       cut_index = trace.find_index{|line| line.match(/sinatra|minitest/)}
       cut_index ||= trace.size
@@ -41,34 +24,6 @@ module OpenToxError
       trace
     end
   end
-  
-  def short_backtrace
-    backtrace = caller.collect{|line| line unless line =~ /#{File.dirname(__FILE__)}/}.compact
-    OpenToxError::cut_backtrace(backtrace)
-  end
-
-=begin
-  RDF_FORMATS.each do |format|
-    # rdf serialization methods for all formats e.g. to_rdfxml
-    send :define_method, "to_#{format}".to_sym do
-      RDF::Writer.for(format).buffer do |writer|
-        @rdf.each{|statement| writer << statement} if @rdf
-      end
-    end
-  end
-
-  def to_turtle # redefine to use prefixes (not supported by RDF::Writer)
-    prefixes = {:rdf => "http://www.w3.org/1999/02/22-rdf-syntax-ns#"}
-    ['OT', 'DC', 'XSD', 'OLO'].each{|p| prefixes[p.downcase.to_sym] = eval("RDF::#{p}.to_s") }
-    RDF::Turtle::Writer.for(:turtle).buffer(:prefixes => prefixes)  do |writer|
-      @rdf.each{|statement| writer << statement} if @rdf
-    end
-  end
-=end
-  
-  def to_json
-    @metadata.to_json
-  end
 
 end
 
@@ -76,7 +31,7 @@ class RuntimeError
   include OpenToxError
 end
 
-# clutters log file with library errors
+# clutters log file with library errors 
 #class NoMethodError
   #include OpenToxError
 #end
@@ -86,9 +41,9 @@ module OpenTox
   class Error < RuntimeError
     include OpenToxError
     
-    def initialize(code, message=nil, uri=nil, cause=nil)
+    def initialize(code, message=nil)
       @http_code = code
-      super message, uri, cause
+      super message
     end
   end
 
@@ -96,15 +51,15 @@ module OpenTox
   RestClientWrapper.known_errors.each do |error|
     # create error classes 
     c = Class.new Error do
-      define_method :initialize do |message=nil, uri=nil, cause=nil|
-        super error[:code], message, uri, cause
+      define_method :initialize do |message=nil|
+        super error[:code], message
       end
     end
     OpenTox.const_set error[:class],c
     
     # define global methods for raising errors, eg. bad_request_error
     Object.send(:define_method, error[:method]) do |message,uri=nil,cause=nil|
-      raise c.new(message, uri, cause)
+      raise c.new(message)
     end
   end
   
diff --git a/lib/feature.rb b/lib/feature.rb
index 005d78f..9deb199 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -1,17 +1,16 @@
 module OpenTox
 
+  # Basic feature class
   class Feature
     field :name, as: :title, type: String
     field :nominal, type: Boolean
     field :numeric, type: Boolean
     field :measured, type: Boolean
-    field :calculated, type: Boolean
-    field :supervised, type: Boolean
-    field :source, as: :title, type: String
-    #belongs_to :dataset
   end
 
+  # Feature for categorical variables
   class NominalFeature < Feature
+    # TODO check if accept_values are still needed 
     field :accept_values, type: Array
     def initialize params
       super params
@@ -19,6 +18,7 @@ module OpenTox
     end
   end
 
+  # Feature for quantitative variables
   class NumericFeature < Feature
     def initialize params
       super params
@@ -26,43 +26,69 @@ module OpenTox
     end
   end
 
+  # Feature for SMARTS fragments
   class Smarts < NominalFeature
     field :smarts, type: String 
-    #field :name, as: :smarts, type: String # causes warnings
-    field :algorithm, type: String, default: "OpenTox::Algorithm::Descriptors.smarts_match"
-    field :parameters, type: Hash, default: {:count => false}
-    def initialize params
-      super params
-      nominal = true
-    end
   end
 
+  # Feature for supervised fragments from Fminer algorithm
   class FminerSmarts < Smarts
-    field :pValue, type: Float
+    field :p_value, type: Float
+    # TODO check if effect is used
     field :effect, type: String
     field :dataset_id 
-    def initialize params
-      super params
-      supervised = true
-    end
   end
 
+  # Feature for database fingerprints
+  # needs count for efficient retrieval (see compound.rb)
   class FingerprintSmarts < Smarts
     field :count, type: Integer
+    def self.fingerprint
+      @@fp4 ||= OpenTox::FingerprintSmarts.all
+      unless @@fp4.size == 306
+        @@fp4 = []
+        # OpenBabel FP4 fingerprints
+        # OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html
+        # TODO investigate other types of fingerprints (MACCS)
+        # OpenBabel http://open-babel.readthedocs.org/en/latest/Fingerprints/intro.html
+        # http://www.dalkescientific.com/writings/diary/archive/2008/06/26/fingerprint_background.html
+        # OpenBabel MNA http://openbabel.org/docs/dev/FileFormats/Multilevel_Neighborhoods_of_Atoms_(MNA).html#multilevel-neighborhoods-of-atoms-mna
+        # Morgan ECFP, FCFP
+        # http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/fingerprint/CircularFingerprinter.html
+        # http://www.rdkit.org/docs/GettingStartedInPython.html
+        # Chemfp
+        # https://chemfp.readthedocs.org/en/latest/using-tools.html
+        # CACTVS/PubChem
+
+        File.open(File.join(File.dirname(__FILE__),"SMARTS_InteLigand.txt")).each do |l| 
+          l.strip!
+          unless l.empty? or l.match /^#/
+            name,smarts = l.split(': ')
+            @@fp4 << OpenTox::FingerprintSmarts.find_or_create_by(:name => name, :smarts => smarts) unless smarts.nil?
+          end
+        end
+      end
+      @@fp4
+    end
   end
 
+  # Feature for physico-chemical descriptors
+  class PhysChemDescriptor < NumericFeature
+    field :algorithm, type: String, default: "OpenTox::Algorithm::Descriptor.physchem"
+    field :parameters, type: Hash
+    field :creator, type: String
+  end
+
+  # Feature for categorical bioassay results
   class NominalBioAssay < NominalFeature
+    # TODO: needed? move to dataset?
     field :description, type: String
   end
 
+  # Feature for quantitative bioassay results
   class NumericBioAssay < NumericFeature
+    # TODO: needed? move to dataset?
     field :description, type: String
   end
 
-  class PhysChemDescriptor < NumericFeature
-    field :algorithm, type: String, default: "OpenTox::Algorithm::Descriptor.physchem"
-    field :parameters, type: Hash
-    field :creator, type: String
-  end
-
 end
diff --git a/lib/format-conversion.rb b/lib/format-conversion.rb
deleted file mode 100644
index 7563b94..0000000
--- a/lib/format-conversion.rb
+++ /dev/null
@@ -1,406 +0,0 @@
-# defaults to stderr, may be changed to file output (e.g in opentox-service)
-$logger = OTLogger.new(STDERR) 
-$logger.level = Logger::DEBUG
-
-module OpenTox
-
-  # Ruby interface
-
-  attr_accessor :data
-
-  # Create a new OpenTox object 
-  # @param uri [optional,String] URI
-  # @return [OpenTox] OpenTox object
-  def initialize uri=nil
-    @data = {}
-    if uri
-      @data[:uri] = uri.to_s.chomp
-      get
-    else
-      @data[:uuid] = SecureRandom.uuid
-      @data[:uri] = File.join(service_uri, @data[:uuid])
-    end
-  end
-
-  # Object metadata (lazy loading)
-  # @return [Hash] Object metadata
-  def metadata force_update=false
-    get #if (@metadata.nil? or @metadata.empty? or force_update) and URI.accessible? @uri
-    @data
-  end
-
-  # Metadata values 
-  # @param predicate [String] Predicate URI
-  # @return [Array, String] Predicate value(s)
-  def [](predicate)
-    predicate = predicate.to_s
-    return nil if metadata[predicate].nil?
-    metadata[predicate].size == 1 ? metadata[predicate].first : metadata[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
-    @data[predicate] = [values].flatten
-  end
-
-=begin
-  # Object parameters (lazy loading)
-  # {http://opentox.org/dev/apis/api-1.2/interfaces OpenTox API}
-  # @return [Hash] Object parameters
-  def parameters force_update=false
-    if (@parameters.empty? or force_update) and URI.accessible? @uri
-      get #if @rdf.empty? or force_update
-      params = {}
-      query = RDF::Query.new({
-        :parameter => {
-          RDF.type  => RDF::OT.Parameter,
-          :property => :value,
-        }
-      })
-      query.execute(@rdf).each do |solution|
-        params[solution.parameter] = {} unless params[solution.parameter] 
-        params[solution.parameter][solution.property] = solution.value
-      end
-      @parameters = params.values
-    end
-    @parameters
-  end
-  
-  # Parameter value 
-  # @param [String] title 
-  # @return [String] value
-  def parameter_value title
-    @parameters.collect{|p| p[RDF::OT.paramValue] if p[RDF::DC.title] == title}.compact.first
-  end
-=end
-
-  # Get object from webservice
-  # @param [String,optional] mime_type
-  def get mime_type="application/json"
-    bad_request_error "Mime type #{mime_type} is not supported. Please use 'application/json' (default), 'text/plain' (ntriples) or mime_type == 'application/rdf+xml'."  unless mime_type == "application/json" or mime_type == "text/plain" or mime_type == "application/rdf+xml"
-    p @data[:uri]
-    response = RestClientWrapper.get(@data[:uri],{},{:accept => mime_type})
-    if URI.task?(response)
-      uri = wait_for_task response
-      response = RestClientWrapper.get(uri,{},{:accept => mime_type})
-      p uri
-    end
-    case mime_type
-    when 'application/json'
-      p response
-      @data = JSON.parse(response) if response
-    when "text/plain"
-      parse_ntriples response 
-    when "application/rdf+xml"
-      parse_rdfxml response
-    end
-  end
-
-=begin
-  # Post object to webservice (append to object), rarely useful and deprecated 
-  # @deprecated
-  def post wait=true, mime_type="text/plain"
-    bad_request_error "Mime type #{mime_type} is not supported. Please use 'text/plain' (default) or 'application/rdf+xml'." unless mime_type == "text/plain" or mime_type == "application/rdf+xml"
-    case mime_type
-    when 'text/plain'
-      body = self.to_ntriples
-    when 'application/rdf+xml'
-      body = self.to_rdfxml
-    end
-    #Authorization.check_policy(@uri) if $aa[:uri]
-    uri = RestClientWrapper.post @uri.to_s, body, { :content_type => mime_type}
-    wait ? wait_for_task(uri) : uri
-  end
-=end
-
-  # Save object at webservice (replace or create object)
-  def put wait=true, mime_type="application/json"
-    bad_request_error "Mime type #{mime_type} is not supported. Please use 'application/json' (default)."  unless mime_type == "application/json" or mime_type == "text/plain" or mime_type == "application/rdf+xml"
-    @data[:created_at] = DateTime.now unless URI.accessible? @data[:uri]
-    #@metadata[RDF::DC.modified] = DateTime.now
-    @data[:uri] ? @data[:uri] = uri.to_s.chomp : @data[:uri] = File.join(service_uri, SecureRandom.uuid)
-    case mime_type
-    when 'text/plain'
-      body = self.to_ntriples
-    when 'application/rdf+xml'
-      body = self.to_rdfxml
-    when 'application/json'
-      body = self.to_json
-    end
-    uri = RestClientWrapper.put @data[:uri], body, { :content_type => mime_type}
-    wait ? wait_for_task(uri) : uri
-  end
-
-  # Delete object at webservice
-  def delete 
-    RestClientWrapper.delete(@data[:uri])
-    #Authorization.delete_policies_from_uri(@data[:uri]) if $aa[:uri]
-  end
-
-  def service_uri
-    self.class.service_uri
-  end
-  
-  def create_rdf
-    #$logger.debug "#{eval("RDF::OT."+self.class.to_s.split('::').last)}\n"
-    @rdf = RDF::Graph.new
-    # DG: since model is no self.class anymore 
-    @metadata[RDF.type] ||= (eval("RDF::OT."+self.class.to_s.split('::').last) =~ /Lazar|Generic/) ? RDF::URI.new(RDF::OT.Model) : RDF::URI.new(eval("RDF::OT."+self.class.to_s.split('::').last))
-    #@metadata[RDF.type] ||= RDF::URI.new(eval("RDF::OT."+self.class.to_s.split('::').last))
-    @metadata[RDF::DC.date] ||= DateTime.now
-    # DG: uri in object should be in brackets, otherwise query for uri-list ignores the object.
-    # see: http://www.w3.org/TR/rdf-testcases/#sec-uri-encoding
-    @metadata.each do |predicate,values|
-      [values].flatten.each{ |value| @rdf << [RDF::URI.new(@data[:uri]), predicate, (URI.valid?(value) ? RDF::URI.new(value) : value)] unless value.nil? }
-    end
-    @parameters.each do |parameter|
-      p_node = RDF::Node.new
-      @rdf << [RDF::URI.new(@data[:uri]), RDF::OT.parameters, p_node]
-      @rdf << [p_node, RDF.type, RDF::OT.Parameter]
-      parameter.each { |k,v| @rdf << [p_node, k, v] unless v.nil?}
-    end
-  end
-  
-  # as defined in opentox-client.rb
-  RDF_FORMATS.each do |format|
-
-    # rdf parse methods for all formats e.g. parse_rdfxml
-    send :define_method, "parse_#{format}".to_sym do |rdf|
-      @rdf = RDF::Graph.new
-      RDF::Reader.for(format).new(rdf) do |reader|
-        reader.each_statement{ |statement| @rdf << statement }
-      end
-      # return values as plain strings instead of RDF objects
-      @metadata = @rdf.to_hash[RDF::URI.new(@data[:uri])].inject({}) { |h, (predicate, values)| h[predicate] = values.collect{|v| v.to_s}; h }
-    end
-
-=begin
-    # rdf serialization methods for all formats e.g. to_rdfxml
-    send :define_method, "to_#{format}".to_sym do
-      create_rdf
-      # if encoding is used iteration is necessary
-      # see: http://rubydoc.info/github/ruby-rdf/rdf/RDF/NTriples/Writer
-      RDF::Writer.for(format).buffer(:encoding => Encoding::ASCII) do |writer|
-        @rdf.each_statement do |statement|
-          writer << statement
-        end
-      end
-    end
-=end
-  end
-  
-  # @return [String] converts object to turtle-string
-  def to_turtle # redefined to use prefixes (not supported by RDF::Writer)
-    prefixes = {:rdf => "http://www.w3.org/1999/02/22-rdf-syntax-ns#"}
-    ['OT', 'DC', 'XSD', 'OLO'].each{|p| prefixes[p.downcase.to_sym] = eval("RDF::#{p}.to_s") }
-    create_rdf
-    RDF::Turtle::Writer.for(:turtle).buffer(:prefixes => prefixes)  do |writer|
-      writer << @rdf
-    end
-  end
-
-  def to_json
-    @data.to_json
-  end
-
-  # @return [String] converts OpenTox object into html document (by first converting it to a string)
-  def to_html
-    to_turtle.to_html
-  end
-
-  # short access for metadata keys title, description and type
-  [ :title , :description , :type , :uri, :uuid ].each do |method|
-    send :define_method, method do 
-      self.data[method]
-    end
-    send :define_method, "#{method}=" do |value|
-      self.data[method] = value
-    end
-  end
-
-  # define class methods within module
-  def self.included(base)
-    base.extend(ClassMethods)
-  end
-
-  module ClassMethods
-    def service_uri
-      service = self.to_s.split('::')[1].downcase
-      eval("$#{service}[:uri]")
-    rescue
-      bad_request_error "$#{service}[:uri] variable not set. Please set $#{service}[:uri] or use an explicit uri as first constructor argument "
-    end
-    def subjectid
-      RestClientWrapper.subjectid
-    end
-    def subjectid=(subjectid)
-      RestClientWrapper.subjectid = subjectid
-    end
-  end
-
-  # create default OpenTox classes with class methods
-  # (defined in opentox-client.rb)
-  CLASSES.each do |klass|
-    c = Class.new do
-      include OpenTox
-
-      def self.all 
-        uris = RestClientWrapper.get(service_uri, {},{:accept => 'text/uri-list'}).split("\n").compact
-        uris.collect{|uri| self.new(uri)}
-      end
-
-      #@example fetching a model
-      #  OpenTox::Model.find(<model-uri>) -> model-object
-      def self.find uri
-        URI.accessible?(uri) ? self.new(uri) : nil
-      end
-
-      def self.create metadata
-        object = self.new 
-        object.data = metadata
-        object.put
-        object
-      end
-
-      def self.find_or_create metadata
-        uris = RestClientWrapper.get(service_uri,{:query => @data},{:accept => "text/uri-list"}).split("\n")
-        uris.empty? ? self.create(@data) : self.new(uris.first)
-      end
-    end
-    OpenTox.const_set klass,c
-  end
-
-end
-
-# from overwrite.rb
-class String
-
-  # encloses URI in text with with link tag
-  # @return [String] new text with marked links
-  def link_urls
-    self.gsub(/(?i)http(s?):\/\/[^\r\n\s']*/, '<a href="\0">\0</a>')
-  end
-
-  # produces a html page for making web services browser friendly
-  # format of text (=string params) is preserved (e.g. line breaks)
-  # urls are marked as links
-  #
-  # @param related_links [optional,String] uri on related resources
-  # @param description [optional,String] general info
-  # @param png_image [optional,String] imagename
-  # @return [String] html page
-  def to_html(related_links=nil, description=nil, png_image=nil  )
-
-    # TODO add title as parameter
-    title = nil #$sinatra.to($sinatra.request.env['PATH_INFO'], :full) if $sinatra
-    html = "<html><body>"
-    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
-    html << "<pre><p style=\"padding:15px; border:10px solid \#C5C1E4\">"
-    html << "<img src=\"data:image/png;base64,#{Base64.encode64(png_image)}\">\n" if png_image
-    html << self.link_urls
-    html << "</p></pre></body></html>"
-    html
-  end
-
-  def uri?
-    URI.valid?(self)
-  end
-end
-
-module Kernel
-
-=begin
-  # overwrite backtick operator to catch system errors
-  # Override raises an error if _cmd_ returns a non-zero exit status. CH: I do not understand this comment
-  # Returns stdout if _cmd_ succeeds.  Note that these are simply concatenated; STDERR is not inline. CH: I do not understand this comment
-  def ` cmd
-    stdout, stderr = ''
-    status = Open4::popen4(cmd) do |pid, stdin_stream, stdout_stream, stderr_stream|
-      stdout = stdout_stream.read
-      stderr = stderr_stream.read
-    end
-    internal_server_error "`" + cmd + "` failed.\n" + stdout + stderr unless status.success?
-    return stdout
-  rescue
-    internal_server_error $!.message
-  end
-=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)
-      t = OpenTox::Task.new uri
-      t.wait
-      unless t.completed?
-        error = OpenTox::RestClientWrapper.known_errors.select{|error| error[:code] == t.code}.first
-        error_method = error ? error[:method] : :internal_server_error
-        report = t.error_report
-        error_message = report ? report[:message] : $!.message
-        error_cause = report ? report[:errorCause] : nil 
-        Object.send(error_method,error_message,t.uri,error_cause)
-      end
-      uri = t.resultURI
-    end
-    uri
-  end
-
-
-end
-module URI
-
-  def self.compound? uri
-    uri =~ /compound/ and URI.valid? uri
-  end
-
-  def self.task? uri
-    uri =~ /task/ and URI.valid? uri
-  end
-
-  def self.dataset? uri
-    uri =~ /dataset/ and URI.accessible? uri
-  end
-
-  def self.model? uri
-    uri =~ /model/ and URI.accessible? uri
-  end
-
-  def self.ssl? uri
-    URI.parse(uri).instance_of? URI::HTTPS
-  end
-
-  # @return [Boolean] checks if resource exists by making a HEAD-request
-  def self.accessible?(uri)
-    parsed_uri = URI.parse(uri + (OpenTox::RestClientWrapper.subjectid ? "?subjectid=#{CGI.escape OpenTox::RestClientWrapper.subjectid}" : ""))
-    http_code = URI.task?(uri) ? 600 : 400
-    http = Net::HTTP.new(parsed_uri.host, parsed_uri.port)
-    unless (URI.ssl? uri) == true
-      http = Net::HTTP.new(parsed_uri.host, parsed_uri.port)
-      request = Net::HTTP::Head.new(parsed_uri.request_uri)
-      http.request(request).code.to_i < http_code
-    else
-      http = Net::HTTP.new(parsed_uri.host, parsed_uri.port)
-      http.use_ssl = true
-      http.verify_mode = OpenSSL::SSL::VERIFY_NONE
-      request = Net::HTTP::Head.new(parsed_uri.request_uri)
-      http.request(request).code.to_i < http_code
-    end
-  rescue
-    false
-  end
-
-  def self.valid? uri
-    u = URI.parse(uri)
-    u.scheme!=nil and u.host!=nil
-  rescue URI::InvalidURIError
-    false
-  end
-
-end
diff --git a/lib/lazar.rb b/lib/lazar.rb
new file mode 100644
index 0000000..8831ba2
--- /dev/null
+++ b/lib/lazar.rb
@@ -0,0 +1,46 @@
+require 'rubygems'
+require "bundler/setup"
+require "rest-client"
+require 'yaml'
+require 'json'
+require 'logger'
+require 'mongoid'
+require 'rserve'
+
+# Mongo setup
+# TODO retrieve correct environment from Rack/Sinatra
+ENV["MONGOID_ENV"] ||= "development"
+# TODO remove config files, change default via ENV or directly in Mongoid class
+Mongoid.load!("#{ENV['HOME']}/.opentox/config/mongoid.yml")
+# TODO get Mongo::Client from Mongoid
+$mongo = Mongo::Client.new('mongodb://127.0.0.1:27017/opentox')
+# TODO same for GridFS
+$gridfs = $mongo.database.fs
+
+# R setup
+R = Rserve::Connection.new
+
+# Logger setup
+$logger = Logger.new STDOUT # STDERR did not work on my development machine (CH)
+$logger.level = Logger::DEBUG
+Mongo::Logger.logger = $logger
+Mongo::Logger.level = Logger::WARN 
+#Mongoid.logger = $logger
+
+# OpenTox classes and includes
+CLASSES = ["Feature","Compound",  "Dataset", "Validation", "CrossValidation"]# Algorithm and Models are modules
+
+[ # be aware of the require sequence as it affects class/method overwrites
+  "overwrite.rb",
+  "rest-client-wrapper.rb", 
+  "error.rb",
+  "opentox.rb",
+  "feature.rb",
+  "compound.rb",
+  "dataset.rb",
+  "descriptor.rb",
+  #"algorithm.rb",
+  #"model.rb",
+  #"validation.rb"
+].each{ |f| require_relative f }
+
diff --git a/lib/model.rb b/lib/model.rb
deleted file mode 100644
index 2b90a46..0000000
--- a/lib/model.rb
+++ /dev/null
@@ -1,56 +0,0 @@
-module OpenTox
-
-  module Model
-
-    def feature_type
-      unless @feature_type
-        bad_request_error "Cannot determine feature type, dependent variable missing in model #{@uri}" unless metadata[RDF::OT.dependentVariables]
-        @feature_type = OpenTox::Feature.new( metadata[RDF::OT.dependentVariables][0]).feature_type
-      end
-      @feature_type
-    end
-    
-    def predicted_variable
-      load_predicted_variables unless defined? @predicted_variable
-      @predicted_variable
-    end
-    
-    def predicted_confidence
-      load_predicted_variables unless defined? @predicted_confidence
-      @predicted_confidence
-    end
-    
-    private
-    def load_predicted_variables
-      metadata[RDF::OT.predictedVariables].each do |f|
-        feat = OpenTox::Feature.new( f)
-        if feat.title =~ /confidence/
-          @predicted_confidence = f
-        else
-          @predicted_variable = f unless @predicted_variable
-        end 
-      end
-    end
-
-    class Generic
-      include OpenTox
-      include OpenTox::Algorithm
-      include Model
-      
-      def self.find uri
-          URI.accessible?(uri) ? self.new(uri) : nil
-      end
-
-      def predict params
-        run params
-      end
-    end
-
-    class Lazar < Generic
-
-      def self.create params
-        Lazar.new(File.join($algorithm[:uri], "lazar")).run params
-      end
-    end
-  end
-end
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb
deleted file mode 100644
index e1e27c9..0000000
--- a/lib/opentox-client.rb
+++ /dev/null
@@ -1,52 +0,0 @@
-require 'rubygems'
-require "bundler/setup"
-require "rest-client"
-require 'yaml'
-require 'json'
-require 'logger'
-require 'mongoid'
-require 'rserve'
-
-# TODO store development/test, validation, production in separate databases
-ENV["MONGOID_ENV"] ||= "development"
-Mongoid.load!("#{ENV['HOME']}/.opentox/config/mongoid.yml")
-R = Rserve::Connection.new
-
-CLASSES = ["Feature","Compound",  "Dataset", "Validation", "CrossValidation"]#, "Task", "Investigation"]
-#CLASSES = ["Feature", "Dataset", "Validation", "Task", "Investigation"]
-
-# Regular expressions for parsing classification data
-#TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
-#FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
-
-[
-  "overwrite.rb",
-  "rest-client-wrapper.rb", 
-  "error.rb",
-  #"authorization.rb", 
-  #"policy.rb", 
-  #"otlogger.rb", 
-  "opentox.rb",
-  #"task.rb",
-  "feature.rb",
-  "compound.rb",
-  #"data_entry.rb",
-  "dataset.rb",
-  #"algorithm.rb",
-  #"model.rb",
-  #"validation.rb"
-].each{ |f| require_relative f }
-
-#if defined?($aa) and $aa[:uri] 
-#  OpenTox::Authorization.authenticate($aa[:user],$aa[:password])
-#  unauthorized_error "Failed to authenticate user \"#{$aa[:user]}\"." unless OpenTox::Authorization.is_token_valid(OpenTox::RestClientWrapper.subjectid)
-#end
-
-# defaults to stderr, may be changed to file output (e.g in opentox-service)
-$logger = Logger.new STDOUT #OTLogger.new(STDOUT) # STDERR did not work on my development machine (CH)
-$logger.level = Logger::DEBUG
-#Mongo::Logger.logger = $logger
-Mongo::Logger.level = Logger::WARN 
-$mongo = Mongo::Client.new('mongodb://127.0.0.1:27017/opentox')
-$gridfs = $mongo.database.fs
-#Mongoid.logger = $logger
diff --git a/lib/otlogger.rb b/lib/otlogger.rb
deleted file mode 100644
index 0f0caa4..0000000
--- a/lib/otlogger.rb
+++ /dev/null
@@ -1,47 +0,0 @@
-
-# extend logger to add current source file, line-number and source location where the log command is called
-class OTLogger < Logger
-  
-  def pwd
-    path = Dir.pwd.to_s
-    index = path.rindex(/\//)
-    return path if index==nil
-    path[(index+1)..-1]
-  end
-  
-  def trace()
-    lines = caller(0)
-    n = 2
-    line = lines[n]
-    
-    while (line =~ /error.rb/ or line =~ /create/ or line =~ /#{File.basename(__FILE__)}/)
-      n += 1
-      line = lines[n]
-    end
-  
-    index = line.rindex(/\/.*\.rb/)
-    return line if index==nil
-    line[index..-1]
-  end
-  
-  def format(msg)
-    pwd.ljust(18)+" :: "+msg.to_s+"           :: "+trace
-  end
-  
-  def debug(msg)
-    super format(msg)
-  end
-  
-  def info(msg)
-    super format(msg)
-  end
-  
-  def warn(msg)
-    super format(msg)
-  end
-
-  def error(msg)
-    super format(msg)
-  end
-
-end
diff --git a/lib/policy.rb b/lib/policy.rb
deleted file mode 100644
index e5676ba..0000000
--- a/lib/policy.rb
+++ /dev/null
@@ -1,354 +0,0 @@
-module OpenTox
-  require "rexml/document"
-
-  #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-file
-  class Policies
-
-    #Hash for policy objects see {Policy Policy}
-    attr_accessor :policies, :name
-
-    def initialize()
-      @policies = {}
-    end
-
-    #create new policy instance with name
-    # @param [String]name of the policy
-    def new_policy(name)
-      @policies[name] = Policy.new(name)
-    end
-
-    #drop a specific policy in a policies instance
-    # @param [String]name of the policy
-    # @return [Boolean]
-    def drop_policy(name)
-      return true if @policies.delete(name)
-    end
-
-    #drop all policies in a policies instance
-    def drop_policies
-      @policies.each do |name, policy|
-        drop_policy(name)
-      end
-      return true
-    end
-
-    # @return [Array] set of arrays affected by policies
-    def uris
-      @policies.collect{ |k,v| v.uri }.flatten.uniq
-    end
-
-    #list all policy names in a policies instance
-    # @return [Array]
-    def names
-      out = []
-      @policies.each do |name, policy|
-        out << name
-      end
-      return out
-    end
-
-    # Loads a default policy template in a policies instance
-    # @param [String]user username in LDAP string of user policy: 'uid=<user>,ou=people,dc=opentox,dc=org'
-    # @param [String]uri URI
-    # @param [String]group groupname in LDAP string of group policy: 'cn=<group>,ou=groups,dc=opentox,dc=org'
-    def load_default_policy(user, uri, group="member")
-      template = case user
-        when "guest", "anonymous" then "default_guest_policy"
-        else "default_policy"
-      end
-      xml = get_xml_template(template)
-      self.load_xml(xml)
-      datestring = Time.now.strftime("%Y-%m-%d-%H-%M-%S-x") + rand(1000).to_s
-
-      @policies["policy_user"].name = "policy_user_#{user}_#{datestring}"
-      @policies["policy_user"].rule.uri = uri
-      @policies["policy_user"].rule.name = "rule_user_#{user}_#{datestring}"
-      @policies["policy_user"].subject.name = "subject_user_#{user}_#{datestring}"
-      @policies["policy_user"].subject.value = "uid=#{user},ou=people,dc=opentox,dc=org"
-      @policies["policy_user"].subject_group = "subjects_user_#{user}_#{datestring}"
-
-      @policies["policy_group"].name = "policy_group_#{group}_#{datestring}"
-      @policies["policy_group"].rule.uri = uri
-      @policies["policy_group"].rule.name = "rule_group_#{group}_#{datestring}"
-      @policies["policy_group"].subject.name = "subject_group_#{group}_#{datestring}"
-      @policies["policy_group"].subject.value = "cn=#{group},ou=groups,dc=opentox,dc=org"
-      @policies["policy_group"].subject_group = "subjects_#{group}_#{datestring}"
-      return true
-    end
-
-    def get_xml_template(template)
-      File.read(File.join(File.dirname(__FILE__), "templates/#{template}.xml"))
-    end
-
-    #loads a xml template
-    def load_xml(xml)
-      rexml = REXML::Document.new(xml)
-      rexml.elements.each("Policies/Policy") do |pol|    #Policies
-        policy_name = pol.attributes["name"]
-        new_policy(policy_name)
-        #@policies[policy_name] = Policy.new(policy_name)
-        rexml.elements.each("Policies/Policy[@name='#{policy_name}']/Rule") do |r|    #Rules
-          rule_name = r.attributes["name"]
-          uri = rexml.elements["Policies/Policy[@name='#{policy_name}']/Rule[@name='#{rule_name}']/ResourceName"].attributes["name"]
-          @policies[policy_name].rule.name = rule_name
-          @policies[policy_name].uri = uri
-          rexml.elements.each("Policies/Policy[@name='#{policy_name}']/Rule[@name='#{rule_name}']/AttributeValuePair") do |attribute_pairs|
-            action=nil; value=nil;
-            attribute_pairs.each_element do |elem|
-              action = elem.attributes["name"] if elem.attributes["name"]
-              value = elem.text if elem.text
-            end
-            if action and value
-              case action
-              when "GET"
-                @policies[policy_name].rule.get    = value
-              when "POST"
-                @policies[policy_name].rule.post   = value
-              when "PUT"
-                @policies[policy_name].rule.put    = value
-              when "DELETE"
-                @policies[policy_name].rule.delete = value
-              end
-            end
-          end
-        end
-        rexml.elements.each("Policies/Policy[@name='#{policy_name}']/Subjects") do |subjects|    #Subjects
-          @policies[policy_name].subject_group = subjects.attributes["name"]
-          rexml.elements.each("Policies/Policy[@name='#{policy_name}']/Subjects[@name='#{@policies[policy_name].subject_group}']/Subject") do |s|    #Subject
-            subject_name  = s.attributes["name"]
-            subject_type  = s.attributes["type"]
-            subject_value = rexml.elements["Policies/Policy[@name='#{policy_name}']/Subjects[@name='#{@policies[policy_name].subject_group}']/Subject[@name='#{subject_name}']/AttributeValuePair/Value"].text
-            if subject_name and subject_type and subject_value
-              @policies[policy_name].subject.name = subject_name
-              @policies[policy_name].type = subject_type
-              @policies[policy_name].value = subject_value
-            end
-          end
-        end
-      end
-    end
-
-    #generates xml from policies instance
-    def to_xml
-      doc = REXML::Document.new()
-      doc <<  REXML::DocType.new("Policies", "PUBLIC  \"-//Sun Java System Access Manager7.1 2006Q3\n Admin CLI DTD//EN\" \"jar://com/sun/identity/policy/policyAdmin.dtd\"")
-      doc.add_element(REXML::Element.new("Policies"))
-
-      @policies.each do |name, pol|
-        policy = REXML::Element.new("Policy")
-        policy.attributes["name"] = pol.name
-        policy.attributes["referralPolicy"] = false
-        policy.attributes["active"] = true
-        rule = @policies[name].rule
-        out_rule = REXML::Element.new("Rule")
-        out_rule.attributes["name"] = rule.name
-        servicename = REXML::Element.new("ServiceName")
-        servicename.attributes["name"]="iPlanetAMWebAgentService"
-        out_rule.add_element(servicename)
-        rescourcename = REXML::Element.new("ResourceName")
-        rescourcename.attributes["name"] = rule.uri
-        out_rule.add_element(rescourcename)
-
-        ["get","post","delete","put"].each do |act|
-          if rule.method(act).call
-            attribute = REXML::Element.new("Attribute")
-            attribute.attributes["name"] = act.upcase
-            attributevaluepair = REXML::Element.new("AttributeValuePair")
-            attributevaluepair.add_element(attribute)
-            attributevalue = REXML::Element.new("Value")
-            attributevaluepair.add_element(attributevalue)
-            attributevalue.add_text REXML::Text.new(rule.method(act).call)
-            out_rule.add_element(attributevaluepair)
-          end
-        end
-        policy.add_element(out_rule)
-
-        subjects = REXML::Element.new("Subjects")
-        subjects.attributes["name"] = pol.subject_group
-        subjects.attributes["description"] = ""
-        subj = @policies[name].subject.name
-        subject = REXML::Element.new("Subject")
-        subject.attributes["name"] = pol.subject.name
-        subject.attributes["type"] = pol.subject.type
-        subject.attributes["includeType"] = "inclusive"
-        attributevaluepair = REXML::Element.new("AttributeValuePair")
-        attribute = REXML::Element.new("Attribute")
-        attribute.attributes["name"] = "Values"
-        attributevaluepair.add_element(attribute)
-        attributevalue = REXML::Element.new("Value")
-        attributevalue.add_text REXML::Text.new(pol.subject.value)
-        attributevaluepair.add_element(attributevalue)
-        subject.add_element(attributevaluepair)
-        subjects.add_element(subject)
-        policy.add_element(subjects)
-        doc.root.add_element(policy)
-      end
-      out = ""
-      doc.write(out, 2)
-      return out
-    end
-
-  end
-
-  #single policy in a {Policies Policies} instance
-  class Policy
-
-    attr_accessor :name, :rule, :subject_group, :subject, :value, :type, :uri, :group, :user
-
-    def initialize(name)
-      @name = name
-      @rule = Rule.new("#{name}_rule", nil)
-      @subject_group = "#{name}_subjects"
-      @subject = Subject.new("#{name}_subject", nil, nil)
-    end
-
-    # Subject type LDAPUsers or LDAPGroups
-    # @return [String]
-    def type
-      @subject.type
-    end
-
-    # Set subject type <LDAPUsers, LDAPGroups>
-    # @param type [String] the subjecttype
-    def type=(type)
-      @subject.type = type
-    end
-
-    # returns LDAP Distinguished Name (DN) e.g. uid=username,ou=people,dc=opentox,dc=org or cn=membergroup,ou=groups,dc=opentox,dc=org
-    def value
-      @subject.value
-    end
-
-    # sets LDAP Distinguished Name (DN) for policy e.g.
-    # @param value [String] LDAPString
-    def value=(value)
-      @subject.value = value
-    end
-
-    # uri affected by policy
-    # @return [String] uri affected by policy
-    def uri
-      @rule.uri
-    end
-
-    # sets uri affected by policy
-    # @param uri [String] set URI
-    def uri=(uri)
-      @rule.uri = uri
-    end
-
-    # Get the groupname from within the LDAP Distinguished Name (DN)
-    def group
-      return false if !value && type != "LDAPGroups"
-      value.split(",").each{|part| return part.gsub("cn=","") if part.match("cn=")}
-    end
-
-    # Get the username from within the LDAP Distinguished Name (DN)
-    def user
-      return false if !value && type != "LDAPUsers"
-      value.split(",").each{|part| return part.gsub("uid=","") if part.match("uid=")}
-    end
-
-    # helper method sets value and type to opentox LDAP Distinguished Name (DN) of a user
-    # @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 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"
-      true
-    end
-
-    # policyrule
-    # sets the permission for REST actions (GET, POST, PUT, DELETE) of a specific URI to allow/deny/nil
-    class Rule
-
-      attr_accessor :name, :uri, :get, :post, :put, :delete, :read, :readwrite
-
-      def initialize(name, uri)
-        @name = name
-        @uri = uri
-      end
-
-      #Set Rule attribute for request-method GET
-      # @param value [String] (allow,deny,nil)
-      def get=(value)
-        @get = check_value(value, @get)
-      end
-
-      #Set Rule attribute for request-method POST
-      # @param [String]value (allow,deny,nil)
-      def post=(value)
-        @post = check_value(value, @post)
-      end
-
-      #Set Rule attribute for request-method DELETE
-      # @param [String]value (allow,deny,nil)
-      def delete=(value)
-        @delete = check_value(value, @delete)
-      end
-
-      #Set Rule attribute for request-method PUT
-      # @param [String]value (allow,deny,nil)
-      def put=(value)
-        @put = check_value(value, @put)
-      end
-
-      # read getter method
-      def read
-        return true if @get == "allow" && (@put == "deny" || !@put) && (@post == "deny" || !@post)
-      end
-
-      # readwrite getter method
-      def readwrite
-        return true if @get == "allow" && @put == "allow" && @post == "allow"
-      end
-
-      # Set(true case) or remove read(GET=allow) permissions.
-      # @param [Boolean]value (true,false)
-      def read=(value)
-        if value
-          @get = "allow"; @put = nil; @post = nil
-        else
-          @get = nil; @put = nil; @post = nil
-        end
-      end
-
-      # Set(true case) or remove readwrite(GET=allow,POST=allow,PUT=allow) permissions.
-      # @param [Boolean]value (true,false)
-      def readwrite=(value)
-        if value
-          @get = "allow"; @put = "allow"; @post = "allow"
-        else
-          @get = nil; @put = nil; @post = nil
-        end
-      end
-
-      private
-      #checks if value is allow, deny or nil. returns old value if not valid.
-      def check_value(new_value, old_value)
-        return (new_value=="allow" || new_value=="deny" || new_value==nil) ? new_value : old_value
-      end
-    end
-
-    # Subject of a policy
-    # name(subjectname), type('LDAPUsers' or 'LDAPGroups'), value(LDAP DN e.G.:'uid=guest,ou=people,dc=opentox,dc=org')
-    class Subject
-
-      attr_accessor :name, :type, :value
-
-      def initialize(name, type, value)
-        @name  = name
-        @type  = type
-        @value = value
-      end
-    end
-  end
-end
diff --git a/lib/task.rb b/lib/task.rb
deleted file mode 100644
index cd2dd92..0000000
--- a/lib/task.rb
+++ /dev/null
@@ -1,142 +0,0 @@
-# TODO: task seems to run twice, see fminser tests
-# TODO: do we need tasks for internal use
-DEFAULT_TASK_MAX_DURATION = 36000
-module OpenTox
-  # TODO: fix error reports
-  # TODO: fix field names and overwrite accessors
-
-  # Class for handling asynchronous tasks
-  class Task 
-    include Mongoid::Document
-    include Mongoid::Timestamps
-
-    field :creator, type: String
-    field :percentageCompleted, type: Float
-    field :error_code, type: Integer # workaround name, cannot overwrite accessors in current mongoid version
-    field :finished, type: Time # workaround name, cannot overwrite accessors in current mongoid version
-    # TODO
-    field :result_type, type: String
-    field :result_id, type: BSON::ObjectId
-    field :report, type: String
-    field :pid, type: Integer
-    field :observer_pid, type: Integer
-
-    def self.run(description, creator=nil)
-
-      task = Task.new
-      task[:description] = description.to_s
-      task[:creator] = creator.to_s
-      task[:percentageCompleted] = 0
-      task[:error_code] = 202 
-      task.save
-
-      pid = fork do
-        begin
-          task.completed yield
-        rescue => e
-          # wrap non-opentox-errors first
-          e = OpenTox::Error.new(500,e.message,nil,e.backtrace) unless e.is_a?(OpenTox::Error)
-          $logger.error "error in task #{task.id} created by #{creator}" # creator is not logged because error is logged when thrown
-          task.update(:report => e.metadata, :error_code => e.http_code, :finished => Time.now)
-          task.kill
-        end
-      end
-      Process.detach(pid)
-      task[:pid] = pid
-
-      # watch if task has been cancelled 
-      observer_pid = fork do
-        task.wait
-        begin
-          Process.kill(9,task[:pid]) if task.cancelled?
-        rescue
-          $logger.warn "Could not kill process of task #{task.id}, pid: #{task[:pid]}"
-        end
-      end
-      Process.detach(observer_pid)
-      task[:observer_pid] = observer_pid
-      task
-
-    end
-
-    def kill
-      Process.kill(9,task[:pid])
-      Process.kill(9,task[:observer_pid])
-    rescue # no need to raise an exception if processes are not running
-    end
-
-    def cancel
-      kill
-      update_attributes(:error_code => 503, :finished => Time.now)
-    end
-
-    def completed(result)
-      update_attributes(:error_code => 200, :finished => Time.now, :percentageCompleted => 100, :result_type => result.type, :result_id => result.id)
-    end
-
-    # waits for a task, unless time exceeds or state is no longer running
-    def wait
-      start_time = Time.new
-      due_to_time = start_time + DEFAULT_TASK_MAX_DURATION
-      dur = 0.2
-      while running? 
-        sleep dur
-        dur = [[(Time.new - start_time)/20.0,0.3].max,300.0].min
-        request_timeout_error "max wait time exceeded ("+DEFAULT_TASK_MAX_DURATION.to_s+"sec), task: '"+id.to_s+"'" if (Time.new > due_to_time)
-      end
-    end
-
-  end
-
-  def error_report
-    OpenTox::Task.find(id).report
-  end
-
-  def code
-    OpenTox::Task.find(id).error_code
-  end
-
-  def result
-    c = OpenTox::Task.find(id).result_type.downcase.to_sym
-    rid = OpenTox::Task.find(id).result_id
-    p c, rid
-    p $mongo[collection].all
-    $mongo[collection].find(rid).first
-  end
-
-  def finished_at
-    OpenTox::Task.find(id).finished
-  end
-
-  def running?
-    code == 202 
-  end
-
-  def cancelled?
-    code == 503
-  end
-
-  def completed?
-    code == 200
-  end
-
-  def error?
-    code >= 400 and code != 503
-  end
-
-  # Check status of a task
-  # @return [String] Status
-  def status
-    case code
-    when 202
-      "Running"
-    when 200
-      "Completed"
-    when 503
-      "Cancelled"
-    else
-      "Error"
-    end
-  end
-
-end
diff --git a/lib/templates/default_guest_policy.xml b/lib/templates/default_guest_policy.xml
deleted file mode 100644
index a778070..0000000
--- a/lib/templates/default_guest_policy.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<!DOCTYPE Policies PUBLIC "-//Sun Java System Access Manager7.1 2006Q3
-   Admin CLI DTD//EN" "jar://com/sun/identity/policy/policyAdmin.dtd">
-
-<Policies>
-<Policy name="policy_user" referralPolicy="false" active="true">
-   <Rule name="rule_user">
-      <ServiceName name="iPlanetAMWebAgentService" />
-      <ResourceName name="uri"/>
-      <AttributeValuePair>
-         <Attribute name="GET" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-      <AttributeValuePair>
-         <Attribute name="POST" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-      <AttributeValuePair>
-         <Attribute name="PUT" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-      <AttributeValuePair>
-         <Attribute name="DELETE" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-   </Rule>
-   <Subjects name="subjects_user" description="">
-        <Subject name="subject_user" type="LDAPUsers" includeType="inclusive">
-            <AttributeValuePair>
-                <Attribute name="Values"/>
-                <Value>uid=guest,ou=people,dc=opentox,dc=org</Value>
-            </AttributeValuePair>
-        </Subject>
-   </Subjects>
-</Policy>
-<Policy name="policy_group" referralPolicy="false" active="true">
-   <Rule name="rule_group">
-      <ServiceName name="iPlanetAMWebAgentService" />
-      <ResourceName name="uri"/>
-      <AttributeValuePair>
-         <Attribute name="GET" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-   </Rule>
-   <Subjects name="subjects_group" description="">
-        <Subject name="subject_group" type="LDAPGroups" includeType="inclusive">
-            <AttributeValuePair>
-                <Attribute name="Values"/>
-                <Value>cn=member,ou=groups,dc=opentox,dc=org</Value>
-            </AttributeValuePair>
-        </Subject>
-   </Subjects>
-</Policy>
-</Policies>
diff --git a/lib/templates/default_policy.xml b/lib/templates/default_policy.xml
deleted file mode 100644
index a778070..0000000
--- a/lib/templates/default_policy.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<!DOCTYPE Policies PUBLIC "-//Sun Java System Access Manager7.1 2006Q3
-   Admin CLI DTD//EN" "jar://com/sun/identity/policy/policyAdmin.dtd">
-
-<Policies>
-<Policy name="policy_user" referralPolicy="false" active="true">
-   <Rule name="rule_user">
-      <ServiceName name="iPlanetAMWebAgentService" />
-      <ResourceName name="uri"/>
-      <AttributeValuePair>
-         <Attribute name="GET" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-      <AttributeValuePair>
-         <Attribute name="POST" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-      <AttributeValuePair>
-         <Attribute name="PUT" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-      <AttributeValuePair>
-         <Attribute name="DELETE" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-   </Rule>
-   <Subjects name="subjects_user" description="">
-        <Subject name="subject_user" type="LDAPUsers" includeType="inclusive">
-            <AttributeValuePair>
-                <Attribute name="Values"/>
-                <Value>uid=guest,ou=people,dc=opentox,dc=org</Value>
-            </AttributeValuePair>
-        </Subject>
-   </Subjects>
-</Policy>
-<Policy name="policy_group" referralPolicy="false" active="true">
-   <Rule name="rule_group">
-      <ServiceName name="iPlanetAMWebAgentService" />
-      <ResourceName name="uri"/>
-      <AttributeValuePair>
-         <Attribute name="GET" />
-         <Value>allow</Value>
-      </AttributeValuePair>
-   </Rule>
-   <Subjects name="subjects_group" description="">
-        <Subject name="subject_group" type="LDAPGroups" includeType="inclusive">
-            <AttributeValuePair>
-                <Attribute name="Values"/>
-                <Value>cn=member,ou=groups,dc=opentox,dc=org</Value>
-            </AttributeValuePair>
-        </Subject>
-   </Subjects>
-</Policy>
-</Policies>
diff --git a/lib/unique_descriptors.rb b/lib/unique_descriptors.rb
new file mode 100644
index 0000000..676f34a
--- /dev/null
+++ b/lib/unique_descriptors.rb
@@ -0,0 +1,120 @@
+# set of non redundant descriptors, faster algorithms are preferred
+# TODO:
+# select logP algorithm
+# select l5 algorithm
+# use smarts matcher for atom counts
+# check correlations
+UNIQUEDESCRIPTORS = [
+  "Openbabel.abonds", #Number of aromatic bonds
+  "Openbabel.atoms", #Number of atoms
+  "Openbabel.bonds", #Number of bonds
+  "Openbabel.dbonds", #Number of double bonds
+  "Openbabel.HBA1", #Number of Hydrogen Bond Acceptors 1 (JoelLib)
+  "Openbabel.HBA2", #Number of Hydrogen Bond Acceptors 2 (JoelLib)
+  "Openbabel.HBD", #Number of Hydrogen Bond Donors (JoelLib)
+  "Openbabel.L5", #Lipinski Rule of Five
+  "Openbabel.logP", #octanol/water partition coefficient
+  "Openbabel.MP", #Melting point
+  "Openbabel.MR", #molar refractivity
+  "Openbabel.MW", #Molecular Weight filter
+  "Openbabel.nF", #Number of Fluorine Atoms
+  "Openbabel.sbonds", #Number of single bonds
+  "Openbabel.tbonds", #Number of triple bonds
+  "Openbabel.TPSA", #topological polar surface area
+  "Cdk.ALOGP", #Calculates atom additive logP and molar refractivity values as described by Ghose and Crippen and
+  "Cdk.APol", #Descriptor that calculates the sum of the atomic polarizabilities (including implicit hydrogens).
+  "Cdk.AcidicGroupCount", #Returns the number of acidic groups.
+  "Cdk.AminoAcidCount", #Returns the number of amino acids found in the system
+  #"Cdk.AromaticAtomsCount", #Descriptor based on the number of aromatic atoms of a molecule.
+  #"Cdk.AromaticBondsCount", #Descriptor based on the number of aromatic bonds of a molecule.
+  #"Cdk.AtomCount", #Descriptor based on the number of atoms of a certain element type.
+  "Cdk.AutocorrelationCharge", #The Moreau-Broto autocorrelation descriptors using partial charges
+  "Cdk.AutocorrelationMass", #The Moreau-Broto autocorrelation descriptors using atomic weight
+  "Cdk.AutocorrelationPolarizability", #The Moreau-Broto autocorrelation descriptors using polarizability
+  "Cdk.BCUT", #Eigenvalue based descriptor noted for its utility in chemical diversity described by Pearlman et al. .
+  "Cdk.BPol", #Descriptor that calculates the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens).
+  "Cdk.BasicGroupCount", #Returns the number of basic groups.
+  #"Cdk.BondCount", #Descriptor based on the number of bonds of a certain bond order.
+  "Cdk.CPSA", #A variety of descriptors combining surface area and partial charge information
+  "Cdk.CarbonTypes", #Characterizes the carbon connectivity in terms of hybridization
+  "Cdk.ChiChain", #Evaluates the Kier & Hall Chi chain indices of orders 3,4,5 and 6
+  "Cdk.ChiCluster", #Evaluates the Kier & Hall Chi cluster indices of orders 3,4,5,6 and 7
+  "Cdk.ChiPathCluster", #Evaluates the Kier & Hall Chi path cluster indices of orders 4,5 and 6
+  "Cdk.ChiPath", #Evaluates the Kier & Hall Chi path indices of orders 0,1,2,3,4,5,6 and 7
+  "Cdk.EccentricConnectivityIndex", #A topological descriptor combining distance and adjacency information.
+  "Cdk.FMF", #Descriptor characterizing molecular complexity in terms of its Murcko framework
+  "Cdk.FragmentComplexity", #Class that returns the complexity of a system. The complexity is defined as @cdk.cite{Nilakantan06}
+  "Cdk.GravitationalIndex", #Descriptor characterizing the mass distribution of the molecule.
+  #"Cdk.HBondAcceptorCount", #Descriptor that calculates the number of hydrogen bond acceptors.
+  #"Cdk.HBondDonorCount", #Descriptor that calculates the number of hydrogen bond donors.
+  "Cdk.HybridizationRatio", #Characterizes molecular complexity in terms of carbon hybridization states.
+  "Cdk.IPMolecularLearning", #Descriptor that evaluates the ionization potential.
+  "Cdk.KappaShapeIndices", #Descriptor that calculates Kier and Hall kappa molecular shape indices.
+  "Cdk.KierHallSmarts", #Counts the number of occurrences of the E-state fragments
+  "Cdk.LargestChain", #Returns the number of atoms in the largest chain
+  "Cdk.LargestPiSystem", #Returns the number of atoms in the largest pi chain
+  "Cdk.LengthOverBreadth", #Calculates the ratio of length to breadth.
+  "Cdk.LongestAliphaticChain", #Returns the number of atoms in the longest aliphatic chain
+  "Cdk.MDE", #Evaluate molecular distance edge descriptors for C, N and O
+  "Cdk.MannholdLogP", #Descriptor that calculates the LogP based on a simple equation using the number of carbons and hetero atoms .
+  "Cdk.MomentOfInertia", #Descriptor that calculates the principal moments of inertia and ratios of the principal moments. Als calculates the radius of gyration.
+  "Cdk.PetitjeanNumber", #Descriptor that calculates the Petitjean Number of a molecule.
+  "Cdk.PetitjeanShapeIndex", #The topological and geometric shape indices described Petitjean and Bath et al. respectively. Both measure the anisotropy in a molecule.
+  "Cdk.RotatableBondsCount", #Descriptor that calculates the number of nonrotatable bonds on a molecule.
+  #"Cdk.RuleOfFive", #This Class contains a method that returns the number failures of the Lipinski's Rule Of Five.
+  #"Cdk.TPSA", #Calculation of topological polar surface area based on fragment contributions .
+  "Cdk.VABC", #Describes the volume of a molecule.
+  "Cdk.VAdjMa", #Descriptor that calculates the vertex adjacency information of a molecule.
+  "Cdk.WHIM", #Holistic descriptors described by Todeschini et al .
+  #"Cdk.Weight", #Descriptor based on the weight of atoms of a certain element type. If no element is specified, the returned value is the Molecular Weight
+  "Cdk.WeightedPath", #The weighted path (molecular ID) descriptors described by Randic. They characterize molecular branching.
+  "Cdk.WienerNumbers", #This class calculates Wiener path number and Wiener polarity number.
+  "Cdk.XLogP", #Prediction of logP based on the atom-type method called XLogP.
+  "Cdk.ZagrebIndex", #The sum of the squared atom degrees of all heavy atoms.
+  "Joelib.count.NumberOfS", #no description available
+  "Joelib.count.NumberOfP", #no description available
+  "Joelib.count.NumberOfO", #no description available
+  "Joelib.count.NumberOfN", #no description available
+  #"Joelib.count.AromaticBonds", #no description available
+  "Joelib.count.NumberOfI", #no description available
+  "Joelib.count.NumberOfF", #no description available
+  "Joelib.count.NumberOfC", #no description available
+  "Joelib.count.NumberOfB", #no description available
+  "Joelib.count.HydrophobicGroups", #no description available
+  #"Joelib.KierShape3", #no description available
+  #"Joelib.KierShape2", #no description available
+  #"Joelib.KierShape1", #no description available
+  #"Joelib.count.AcidicGroups", #no description available
+  "Joelib.count.AliphaticOHGroups", #no description available
+  #"Joelib.count.NumberOfAtoms", #no description available
+  "Joelib.TopologicalRadius", #no description available
+  "Joelib.GeometricalShapeCoefficient", #no description available
+  #"Joelib.MolecularWeight", #no description available
+  "Joelib.FractionRotatableBonds", #no description available
+  #"Joelib.count.HBD2", #no description available
+  #"Joelib.count.HBD1", #no description available
+  "Joelib.LogP", #no description available
+  "Joelib.GraphShapeCoefficient", #no description available
+  "Joelib.count.BasicGroups", #no description available
+  #"Joelib.count.RotatableBonds", #no description available
+  "Joelib.count.HeavyBonds", #no description available
+  "Joelib.PolarSurfaceArea", #no description available
+  #"Joelib.ZagrebIndex1", #no description available
+  "Joelib.GeometricalRadius", #no description available
+  "Joelib.count.SO2Groups", #no description available
+  "Joelib.count.AromaticOHGroups", #no description available
+  "Joelib.GeometricalDiameter", #no description available
+  #"Joelib.MolarRefractivity", #no description available
+  "Joelib.count.NumberOfCl", #no description available
+  "Joelib.count.OSOGroups", #no description available
+  "Joelib.count.NumberOfBr", #no description available
+  "Joelib.count.NO2Groups", #no description available
+  "Joelib.count.HeteroCycles", #no description available
+  #"Joelib.count.HBA2", #no description available
+  #"Joelib.count.HBA1", #no description available
+  #"Joelib.count.NumberOfBonds", #no description available
+  "Joelib.count.SOGroups", #no description available
+  "Joelib.TopologicalDiameter", #no description available
+  "Joelib.count.NumberOfHal", #no description available
+
+].sort
diff --git a/lib/validation.rb b/lib/validation.rb
deleted file mode 100644
index deba1e3..0000000
--- a/lib/validation.rb
+++ /dev/null
@@ -1,348 +0,0 @@
-require "yaml"
-
-module OldOpenTox
-  attr_accessor :metadata, :uri
-
-  def initialize(uri=nil)
-    @metadata = {}
-    self.uri = uri if uri
-  end
-
-  # loads metadata via yaml
-  def load_metadata
-    yaml = OpenTox::RestClientWrapper.get(uri,nil,{:accept => "application/x-yaml"})
-    @metadata = YAML.load(yaml)
-  end
-
-  def delete 
-    OpenTox::RestClientWrapper.delete @uri.to_s
-  end
-end
-
-module OpenTox
-
-  class Validation
-    include OldOpenTox
-
-    # find validation, raises error if not found
-    # @param [String] uri
-    # @return [OpenTox::Validation]
-    def self.find( uri )
-      val = Validation.new(uri)
-      val.load_metadata
-      val
-    end
-
-    # returns a filtered list of validation uris
-    # @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|
-        filter_string += (filter_string.length==0 ? "?" : "&")
-        v = v.to_s.gsub(/;/, "%3b") if v.to_s =~ /;/
-        filter_string += k.to_s+"="+v.to_s
-      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 [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
-    # @return [OpenTox::Validation]
-    def self.create_training_test_split( params, waiting_task=nil )
-      uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"training_test_split"),
-        params,{:content_type => "text/uri-list"},waiting_task )
-      Validation.new(wait_for_task(uri))
-    end
-
-    # creates a training test validation, waits until it finishes, may take some time
-    # @param [Hash] params (required:algorithm_uri,training_dataset_uri,prediction_feature,test_dataset_uri,optional:algorithm_params)
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
-    # @return [OpenTox::Validation]
-    def self.create_training_test_validation( params, waiting_task=nil )
-      uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"training_test_validation"),
-        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 [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
-    # @return [OpenTox::Validation]
-    def self.create_bootstrapping_validation( params, waiting_task=nil )
-      uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"bootstrapping"),
-        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 [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
-    # @return [String] report uri
-    def find_or_create_report( waiting_task=nil )
-      @report = ValidationReport.find_for_validation(@uri) unless @report
-      @report = ValidationReport.create(@uri, 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 crossvalidation_uri [String] crossvalidation uri
-    # @return [OpenTox::Validation]
-    def self.from_cv_statistics( crossvalidation_uri )
-      find( File.join(crossvalidation_uri, 'statistics') )
-    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
-    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]
-      values = matrix.collect{|cell| cell[RDF::OT.confusionMatrixPredicted]}.uniq
-      table = [[nil]+values]
-      values.each do |c|
-        table << [c]
-        values.each do |r|
-          matrix.each do |cell|
-            if cell[RDF::OT.confusionMatrixPredicted]==c and cell[RDF::OT.confusionMatrixActual]==r
-              table[-1] << cell[RDF::OT.confusionMatrixValue].to_f
-              break
-            end
-          end
-        end
-      end
-      table
-    end
-
-    # filters the validation-predictions and returns validation-metadata with filtered statistics
-    # @param min_confidence [Float] predictions with confidence < min_confidence are filtered out
-    # @param min_num_predictions [Integer] optional, additional param to min_confidence, the top min_num_predictions are selected, even if confidence to low
-    # @param max_num_predictions [Integer] returns the top max_num_predictions (with the highest confidence), not compatible to min_confidence
-    # return [Hash] metadata
-    def filter_metadata( min_confidence, min_num_predictions=nil, max_num_predictions=nil )
-      conf = min_confidence ? "min_confidence=#{min_confidence}" : nil
-      min = min_num_predictions ? "min_num_predictions=#{min_num_predictions}" : nil
-      max = max_num_predictions ? "max_num_predictions=#{max_num_predictions}" : nil
-      YAML.load(OpenTox::RestClientWrapper.get("#{@uri}?#{[conf,min,max].compact.join("&")}",nil,{:accept => "application/x-yaml"}))
-    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 confidence [Float] confidence value (between 0 and 1)
-    # @param prediction [String] predicted value
-    # @return [Hash] see example
-    # @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 } }
-    #  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 } }
-    #  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 )
-      YAML.load(OpenTox::RestClientWrapper.get(@uri+"/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil,
-        {:accept => "application/x-yaml"}))
-    end
-  end
-
-  class Crossvalidation
-    include OldOpenTox
-
-    attr_reader :report
-
-    # find crossvalidation, raises error if not found
-    # @param [String] uri
-    # @return [OpenTox::Crossvalidation]
-    def self.find( uri )
-      cv = Crossvalidation.new(uri)
-      cv.load_metadata
-      cv
-    end
-
-    # returns a filtered list of crossvalidation uris
-    # @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|
-        filter_string += (filter_string.length==0 ? "?" : "&")
-        v = v.to_s.gsub(/;/, "%3b") if v.to_s =~ /;/
-        filter_string += k.to_s+"="+v.to_s
-      end
-      (OpenTox::RestClientWrapper.get(File.join($validation[:uri],"crossvalidation")+filter_string).split("\n"))
-    end
-		
-    # creates a crossvalidations, waits until it finishes, may take some time
-    # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,num_folds(10),random_seed(1),stratified(false))
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
-    # @return [OpenTox::Crossvalidation]
-    def self.create( params, waiting_task=nil )
-      uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"crossvalidation"),
-        params,{:content_type => "text/uri-list"},waiting_task )
-      uri = wait_for_task(uri)
-      Crossvalidation.new(uri)
-    end
-
-    # looks for report for this crossvalidation, creates a report if no report is found
-    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
-    # @return [String] report uri
-    def find_or_create_report( waiting_task=nil )
-      @report = CrossvalidationReport.find_for_crossvalidation(@uri) unless @report
-      @report = CrossvalidationReport.create(@uri, 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
-      @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,nil,{:accept => "application/x-yaml"}))
-    end
-
-    # returns a Validation object containing the statistics of the crossavlidation
-    def statistics
-      Validation.from_cv_statistics( @uri )
-    end
-
-    # documentation see OpenTox::Validation.probabilities
-    def probabilities( confidence, prediction )
-      YAML.load(OpenTox::RestClientWrapper.get(@uri+"/statistics/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil,
-        {:accept => "application/x-yaml"}))
-    end
-
-  end
-
-  class ValidationReport
-    include OldOpenTox
-
-    # finds ValidationReport via uri, raises error if not found
-    # @param [String] uri
-    # @return [OpenTox::ValidationReport]
-    def self.find( uri )
-      OpenTox::RestClientWrapper.get(uri)
-      rep = ValidationReport.new(uri)
-      rep.load_metadata
-      rep
-    end
-
-    # finds ValidationReport for a particular validation
-    # @param validation_uri [String] crossvalidation uri
-    # @return [OpenTox::ValidationReport] nil if no report found
-    def self.find_for_validation( validation_uri )
-      uris = RestClientWrapper.get(File.join($validation[:uri],
-        "/report/validation?validation="+validation_uri)).chomp.split("\n")
-      uris.size==0 ? nil : ValidationReport.new(uris[-1])
-    end
-
-    # creates a validation report via validation
-    # @param validation_uri [String] validation uri
-    # @param params [Hash] params addiditonal possible
-    #               (min_confidence, params={}, min_num_predictions, max_num_predictions)
-    # @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={}, waiting_task=nil )
-      params = {} if params==nil
-      bad_request_error "params is no hash" unless params.is_a?(Hash)
-      params[:validation_uris] = validation_uri
-      uri = RestClientWrapper.post(File.join($validation[:uri],"/report/validation"),
-        params, {}, waiting_task )
-      uri = wait_for_task(uri)
-      ValidationReport.new(uri)
-    end
-
-  end
-
-  class CrossvalidationReport
-    include OldOpenTox
-
-    # finds CrossvalidationReport via uri, raises error if not found
-    # @param [String] uri
-    # @return [OpenTox::CrossvalidationReport]
-    def self.find( uri )
-      OpenTox::RestClientWrapper.get(uri)
-      rep = CrossvalidationReport.new(uri)
-      rep.load_metadata
-      rep
-    end
-
-    # finds CrossvalidationReport for a particular crossvalidation
-    # @param crossvalidation_uri [String] crossvalidation uri
-    # @return [OpenTox::CrossvalidationReport] nil if no report found
-    def self.find_for_crossvalidation( crossvalidation_uri )
-      uris = RestClientWrapper.get(File.join($validation[:uri],
-        "/report/crossvalidation?crossvalidation="+crossvalidation_uri)).chomp.split("\n")
-      uris.size==0 ? nil : CrossvalidationReport.new(uris[-1])
-    end
-
-    # creates a crossvalidation report via crossvalidation
-    # @param crossvalidation_uri [String] crossvalidation uri
-    # @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, waiting_task=nil )
-      uri = RestClientWrapper.post(File.join($validation[:uri],"/report/crossvalidation"),
-        { :validation_uris => crossvalidation_uri }, {}, waiting_task )
-      uri = wait_for_task(uri)
-      CrossvalidationReport.new(uri)
-    end
-  end
-
-
-  class AlgorithmComparisonReport
-    include OldOpenTox
-
-    # finds AlgorithmComparisonReport via uri, raises error if not found
-    # @param [String] uri
-    # @return [OpenTox::CrossvalidationReport]
-    def self.find( uri )
-      OpenTox::RestClientWrapper.get(uri)
-      rep = AlgorithmComparisonReport.new(uri)
-      rep.load_metadata
-      rep
-    end
-
-    # finds AlgorithmComparisonReport for a particular crossvalidation
-    # @param crossvalidation_uri [String] crossvalidation uri
-    # @return [OpenTox::AlgorithmComparisonReport] nil if no report found
-    def self.find_for_crossvalidation( crossvalidation_uri )
-      uris = RestClientWrapper.get(File.join($validation[:uri],
-        "/report/algorithm_comparison?crossvalidation="+crossvalidation_uri)).chomp.split("\n")
-      uris.size==0 ? nil : AlgorithmComparisonReport.new(uris[-1])
-    end
-
-    # creates a algorithm comparison report via crossvalidation uris
-    # @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 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 ],
-    #   :lazar-last => [ http://host/validation/crossvalidation/xy, http://host/validation/crossvalidation/xy ] }
-    def self.create( crossvalidation_uri_hash, params={}, waiting_task=nil )
-      identifier = []
-      validation_uris = []
-      crossvalidation_uri_hash.each do |id, uris|
-        uris.each do |uri|
-          identifier << id
-          validation_uris << uri
-        end
-      end
-      params = {} if params==nil
-      raise OpenTox::BadRequestError.new "params is no hash" unless params.is_a?(Hash)
-      params[:validation_uris] = validation_uris.join(",")
-      params[:identifier] = identifier.join(",")
-      uri = RestClientWrapper.post(File.join($validation[:uri],"/report/algorithm_comparison"), params, {}, waiting_task )
-      uri = wait_for_task(uri)
-      AlgorithmComparisonReport.new(uri)
-    end
-  end
-
-end
-
diff --git a/opentox-client.gemspec b/opentox-client.gemspec
deleted file mode 100644
index 3bba11c..0000000
--- a/opentox-client.gemspec
+++ /dev/null
@@ -1,34 +0,0 @@
-# -*- encoding: utf-8 -*-
-$:.push File.expand_path("../lib", __FILE__)
-
-Gem::Specification.new do |s|
-  s.name        = "opentox-client"
-  s.version     = File.read("./VERSION").strip
-  s.authors     = ["Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler"]
-  s.email       = ["helma@in-silico.ch"]
-  s.homepage    = "http://github.com/opentox/opentox-client"
-  s.summary     = %q{Ruby wrapper for the OpenTox REST API}
-  s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
-  s.license     = 'GPL-3'
-
-  s.rubyforge_project = "opentox-client"
-
-  s.files         = `git ls-files`.split("\n")
-  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
-  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
-  s.require_paths = ["lib"]
-
-  # specify any dependencies here; for example:
-  s.add_runtime_dependency "bundler"
-  s.add_runtime_dependency "rest-client"
-  #s.add_runtime_dependency "rdf"
-  #s.add_runtime_dependency "rdf-raptor"
-  #s.add_runtime_dependency 'rdf-turtle'
-  s.add_runtime_dependency "open4"
-  s.add_runtime_dependency "openbabel"
-  s.add_runtime_dependency "mongoid", '~> 5.0beta'  
-
-  # external requirements
-  #["libraptor-dev"].each{|r| s.requirements << r}
-  #s.post_install_message = "Please check the version of your libraptor library, if installation of rdf.rb fails"
-end
diff --git a/test/compound.rb b/test/compound.rb
new file mode 100644
index 0000000..7bbba58
--- /dev/null
+++ b/test/compound.rb
@@ -0,0 +1,93 @@
+require_relative "setup.rb"
+
+class CompoundTest < MiniTest::Test
+
+  def test_0_compound_from_smiles
+    c = OpenTox::Compound.from_smiles "F[B-](F)(F)F.[Na+]"
+    assert_equal "InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1", c.inchi
+    assert_equal "[B-](F)(F)(F)F.[Na+]", c.smiles, "A failure here might be caused by a compound webservice running on 64bit architectures using an outdated version of OpenBabel. Please install OpenBabel version 2.3.2 or higher." # seems to be fixed in 2.3.2
+  end
+
+  def test_1_compound_from_smiles
+    c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+    assert_equal "InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3", c.inchi
+    assert_equal "CC(CC(=O)C)C#N", c.smiles
+  end
+
+  def test_2_compound_from_smiles
+    c = OpenTox::Compound.from_smiles "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
+    assert_equal "InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1", c.inchi
+    assert_equal "c1ccc(cc1)[N+]#N.[B-](F)(F)(F)F", c.smiles
+  end
+
+  def test_compound_from_name
+    c = OpenTox::Compound.from_name "Benzene"
+    assert_equal "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H", c.inchi
+    assert_equal "c1ccccc1", c.smiles
+  end
+
+  def test_compound_from_inchi
+    c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+    assert_equal "c1ccccc1", c.smiles
+  end
+
+  def test_sdf_import
+    c = OpenTox::Compound.from_sdf File.read(File.join DATA_DIR, "acetaldehyde.sdf")
+    assert_equal "InChI=1S/C2H4O/c1-2-3/h2H,1H3", c.inchi
+    assert_equal "CC=O", c.smiles
+    assert c.names.include? "Acetylaldehyde"
+  end
+
+  def test_sdf_export
+    c = OpenTox::Compound.from_smiles "CC=O"
+    assert_match /7  6  0  0  0  0  0  0  0  0999 V2000/, c.sdf
+  end
+
+  def test_compound_image
+    c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+    testbild = "/tmp/testbild.png"
+    File.open(testbild, "w"){|f| f.puts c.png}
+    assert_match "image/png", `file -b --mime-type /tmp/testbild.png`
+    File.unlink(testbild)
+  end
+
+  # OpenBabel segfaults randomly during inchikey calculation
+  def test_inchikey
+    c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+    assert_equal "UHOVQNZJYSORNB-UHFFFAOYSA-N", c.inchikey
+  end
+
+  def test_cid
+    c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+    assert_equal "241", c.cid
+  end
+
+  def test_chemblid
+    c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+    #assert_equal "CHEMBL277500", c.chemblid
+    assert_equal "CHEMBL581676", c.chemblid
+  end
+
+  def test_sdf_storage
+    c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+    c.sdf
+    assert !c.sdf_id.nil?
+  end
+
+  def test_fingerprint
+    c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
+
+    assert c.fp4.collect{|fid| Feature.find(fid).name}.include? ("1,3-Tautomerizable")
+    assert_equal c.fp4.size, c.fp4_size
+  end
+
+  def test_neighbors
+    d = Dataset.from_csv_file "data/EPAFHM.csv"
+    d.compounds.each do |c|
+      refute_nil c.fp4
+    end
+    c = d.compounds[371]
+    assert_equal 19, c.neighbors.size
+  end
+
+end
diff --git a/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf b/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf
new file mode 100644
index 0000000..d7eb740
--- /dev/null
+++ b/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf
@@ -0,0 +1,13553 @@
+

+

+

+ 14 16  0  0  0  0  0  0  0  0  1 V2000

+    7.3615   -3.7543    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

+    6.2131   -3.0918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    6.2131   -1.7594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    5.0573   -1.0969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    3.9089   -1.7594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    3.9089   -3.0918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    5.0573   -3.7543    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

+    2.6428   -3.5041    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

+    1.8624   -2.4219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    0.5374   -2.2894    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    0.0000   -1.0748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    0.7803    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.1054   -0.1325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.6428   -1.3471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+  1  2  1  0  0  0  0

+  2  3  1  0  0  0  0

+  2  7  2  0  0  0  0

+  3  4  2  0  0  0  0

+  4  5  1  0  0  0  0

+  5  6  2  0  0  0  0

+  5 14  1  0  0  0  0

+  6  7  1  0  0  0  0

+  6  8  1  0  0  0  0

+  8  9  1  0  0  0  0

+  9 10  2  0  0  0  0

+  9 14  1  0  0  0  0

+ 10 11  1  0  0  0  0

+ 11 12  2  0  0  0  0

+ 12 13  1  0  0  0  0

+ 13 14  2  0  0  0  0

+M  END

+>  <DSSTox_RID>

+20001

+

+>  <DSSTox_CID>

+1

+

+>  <DSSTox_Generic_SID>

+20001

+

+>  <DSSTox_FileID>

+1_CPDBAS_v5c

+

+>  <STRUCTURE_Formula>

+C11H9N3

+

+>  <STRUCTURE_MolecularWeight>

+183.2122

+

+>  <STRUCTURE_ChemicalType>

+defined organic

+

+>  <STRUCTURE_TestedForm_DefinedOrganic>

+parent

+

+>  <STRUCTURE_Shown>

+tested chemical

+

+>  <TestSubstance_ChemicalName>

+A-alpha-C

+

+>  <TestSubstance_CASRN>

+26148-68-5

+

+>  <TestSubstance_Description>

+single chemical compound

+

+>  <ChemicalNote>

+blank

+

+>  <STRUCTURE_ChemicalName_IUPAC>

+9H-pyrido[2,3-b]indol-2-amine

+

+>  <STRUCTURE_SMILES>

+NC1C=CC2=C(N=1)NC3=CC=CC=C23

+

+>  <STRUCTURE_Parent_SMILES>

+NC1C=CC2=C(N=1)NC3=CC=CC=C23

+

+>  <STRUCTURE_InChI>

+InChI=1/C11H9N3/c12-10-6-5-8-7-3-1-2-4-9(7)13-11(8)14-10/h1-6H,(H3,12,13,14)/f/h13H,12H2

+

+>  <STRUCTURE_InChIKey>

+FJTNLJLPLJDTRM-DXMPFREMCP

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+mouse

+

+>  <ActivityOutcome_CPDBAS_Mutagenicity>

+active

+

+>  <TD50_Rat_mg>

+blank

+

+>  <TD50_Rat_mmol>

+blank

+

+>  <ActivityScore_CPDBAS_Rat>

+blank

+

+>  <TD50_Rat_Note>

+blank

+

+>  <TargetSites_Rat_Male>

+blank

+

+>  <TargetSites_Rat_Female>

+blank

+

+>  <TargetSites_Rat_BothSexes>

+blank

+

+>  <ActivityOutcome_CPDBAS_Rat>

+blank

+

+>  <TD50_Mouse_mg>

+49.8

+

+>  <TD50_Mouse_mmol>

+0.271815959854202

+

+>  <ActivityScore_CPDBAS_Mouse>

+35

+

+>  <TD50_Mouse_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Mouse_Male>

+liver; vascular system

+

+>  <TargetSites_Mouse_Female>

+liver; vascular system

+

+>  <TargetSites_Mouse_BothSexes>

+blank

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+active

+

+>  <TD50_Hamster_mg>

+blank

+

+>  <TD50_Hamster_mmol>

+blank

+

+>  <ActivityScore_CPDBAS_Hamster>

+blank

+

+>  <TD50_Hamster_Note>

+blank

+

+>  <TargetSites_Hamster_Male>

+blank

+

+>  <TargetSites_Hamster_Female>

+blank

+

+>  <TargetSites_Hamster_BothSexes>

+blank

+

+>  <ActivityOutcome_CPDBAS_Hamster>

+blank

+

+>  <TD50_Dog_mg>

+blank

+

+>  <TargetSites_Dog>

+blank

+

+>  <TD50_Rhesus_mg>

+blank

+

+>  <TargetSites_Rhesus>

+blank

+

+>  <TD50_Cynomolgus_mg>

+blank

+

+>  <TargetSites_Cynomolgus>

+blank

+

+>  <TD50_Dog_Primates_Note>

+blank

+

+>  <ActivityOutcome_CPDBAS_Dog_Primates>

+blank

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisite active; multisex active

+

+>  <Note_CPDBAS>

+blank

+

+>  <NTP_TechnicalReport>

+blank

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/A-alpha-C.html

+

+$$$$

+

+

+

+ 11 10  0  0  0  0  0  0  0  0  2 V2000

+    3.4800   -1.1526    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0

+    3.4800   -2.4613    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0

+    2.3349   -3.1008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.3349   -0.4610    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    1.1749   -2.4613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    1.1749   -1.1526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    4.1344    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    4.8110   -1.1526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    2.3349   -4.4392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    0.0000   -0.4610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    7.4359   -2.2159    0.0000 K   0  3  0  0  0  0  0  0  0  0  0  0

+  1  2  1  0  0  0  0

+  1  4  1  0  0  0  0

+  1  7  2  0  0  0  0

+  1  8  2  0  0  0  0

+  2  3  1  0  0  0  0

+  3  9  2  0  0  0  0

+  3  5  1  0  0  0  0

+  4  6  1  0  0  0  0

+  5  6  2  0  0  0  0

+  6 10  1  0  0  0  0

+M  CHG  2   2  -1  11   1

+M  END

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

+$$$$

+

+

+

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+M  END

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+

+>  <TD50_Hamster_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Hamster_Male>

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+>  <TargetSites_Hamster_Female>

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+

+$$$$

+

+

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+

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+

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+

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+

+>  <STRUCTURE_InChIKey>

+IMAGWKUTFZRWSB-HWKANZROBR

+

+>  <StudyType>

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+

+>  <Endpoint>

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+

+>  <Species>

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+

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+

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+

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+

+>  <ActivityScore_CPDBAS_Mouse>

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+

+>  <TD50_Mouse_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Mouse_Male>

+lung; preputial gland

+

+>  <TargetSites_Mouse_Female>

+clitoral gland; lung; stomach

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+active

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+active

+

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+active

+

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+multisite active; multisex active

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ACETALDEHYDE%20METHYLFORMYLHYDRAZONE.html

+

+$$$$

+

+

+

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+

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+

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+

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+parent 

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+

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+

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+>  <TestSubstance_Description>

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+(1E)-acetaldehyde oxime

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+

+>  <STRUCTURE_InChIKey>

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+>  <StudyType>

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+>  <Endpoint>

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+

+>  <TD50_Rat_Note>

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+

+>  <ActivityOutcome_CPDBAS_Rat>

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+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+inactive

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ACETALDOXIME.html

+

+$$$$

+

+

+

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+

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+

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+

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+

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+

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+

+>  <STRUCTURE_Shown>

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+

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+

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+

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+

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+

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+

+>  <STRUCTURE_InChIKey>

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+

+>  <StudyType>

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+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

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+

+>  <ActivityOutcome_CPDBAS_Mutagenicity>

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+

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+

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+

+>  <TD50_Rat_Note>

+TD50 is harmonic mean of more than one positive test

+

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+

+>  <TargetSites_Rat_Female>

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+

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+

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+

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+

+>  <ActivityScore_CPDBAS_Mouse>

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+

+>  <TargetSites_Mouse_Male>

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+

+>  <TargetSites_Mouse_Female>

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+

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+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisite active; multisex active; multispecies active

+

+>  <ChemicalPage_URL>

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+

+$$$$

+

+

+

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+

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+

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+

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+

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+

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+

+>  <STRUCTURE_TestedForm_DefinedOrganic>

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+

+>  <STRUCTURE_Shown>

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+

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+

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+

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+

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+

+>  <STRUCTURE_Parent_SMILES>

+C1(=CC=C(C=C1)O)NC(C)=O

+

+>  <STRUCTURE_InChI>

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+

+>  <STRUCTURE_InChIKey>

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+

+>  <StudyType>

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+

+>  <Endpoint>

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+

+>  <Species>

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+

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+

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+

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+

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+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Rat_Male>

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+

+>  <TargetSites_Rat_Female>

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+

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+

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+

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+

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+

+>  <TD50_Mouse_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Mouse_Male>

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+

+>  <TargetSites_Mouse_Female>

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+

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+

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+

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+multisite active; multisex active; multispecies active

+

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+TR 394; final call in CPDB differs due to additional data

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ACETAMINOPHEN.html

+

+$$$$

+

+

+

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+

+$$$$

+

+

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+

+$$$$

+

+

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+tautomers

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+

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+

+>  <Species>

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+

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+

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+

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+

+

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+

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+

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+

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+

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+

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+

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+

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+

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+

+>  <StudyType>

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+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

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+

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+

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+

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+

+>  <TD50_Mouse_Note>

+TD50 is harmonic mean of more than one positive test

+

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+

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+

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+

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+

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+

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+

+$$$$

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+

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+

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+

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+

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+

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+

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+

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+

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+parent 

+

+>  <STRUCTURE_Shown>

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+

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+

+>  <TestSubstance_CASRN>

+4075-79-0

+

+>  <TestSubstance_Description>

+single chemical compound

+

+>  <STRUCTURE_ChemicalName_IUPAC>

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+

+>  <STRUCTURE_SMILES>

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+

+>  <STRUCTURE_Parent_SMILES>

+CC(=O)NC1=CC=C(C=C1)C2=CC=CC=C2

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+

+>  <STRUCTURE_InChIKey>

+SVLDILRDQOVJED-YAQRNVERCM

+

+>  <StudyType>

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+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

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+

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+1.18

+

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+5.58546038393887E-03

+

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+

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+active

+

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+active

+

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+

+$$$$

+

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+

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+

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+

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+

+$$$$

+

+

+

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+

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+

+$$$$

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+

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+

+>  <STRUCTURE_InChIKey>

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+

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+

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+

+$$$$

+

+

+

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+

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+18699-02-0

+

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+single chemical compound

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+[4-(acetylamino)phenyl]acetic acid

+

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+

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+

+>  <STRUCTURE_InChIKey>

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+

+>  <StudyType>

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+

+>  <Endpoint>

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+

+>  <Species>

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+

+>  <ActivityScore_CPDBAS_Rat>

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+Rat added v2a; Mouse added v2a

+

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+

+$$$$

+

+

+

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+

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+

+

+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+M  END

+>  <DSSTox_RID>

+20030

+

+>  <DSSTox_CID>

+30

+

+>  <DSSTox_Generic_SID>

+20030

+

+>  <DSSTox_FileID>

+31_CPDBAS_v5c

+

+>  <STRUCTURE_Formula>

+C63H88N12O16

+

+>  <STRUCTURE_MolecularWeight>

+1269.4436

+

+>  <STRUCTURE_ChemicalType>

+defined organic

+

+>  <STRUCTURE_TestedForm_DefinedOrganic>

+parent 

+

+>  <STRUCTURE_Shown>

+representative component in mixture

+

+>  <TestSubstance_ChemicalName>

+Actinomycin C

+

+>  <TestSubstance_CASRN>

+8052-16-2

+

+>  <TestSubstance_Description>

+mixture or formulation

+

+>  <ChemicalNote>

+mixture of actinomycin C1 [50-76-0] (10%), actinomycin C2 [2612-14-8] (45%), and actinomycin C3 [6156-47-4] (45%), structure shown C2, stereochem

+

+>  <STRUCTURE_ChemicalName_IUPAC>

+2-amino-4,6-dimethyl-3-oxo-N~9~-[(6S,9R,10S,13R,18aS)-2,5,9-trimethyl-6,13-bis(1-methylethyl)-1,4,7,11,14-pentaoxohexadecahydro-1H-pyrrolo[2,1-i][1,4,7,10,13]oxatetraazacyclohexadecin-10-yl]-N~1~-{(6S,9R,10S,13R,18aS)-2,5,9-trimethyl-6-(1-methylethyl)

+

+>  <STRUCTURE_SMILES>

+O=C(N[C@@H]([C@H](OC([C@@H]5[C@@H](C)C)=O)C)C(N[C@H]([C@@H](C)CC)C(N4CCC[C@@](C(N(C)CC(N5C)=O)=O)4[H])=O)=O)C(C(C(OC2=C(C)C=C3)=C(C)C1=O)=NC2=C3C(N[C@@H]([C@H](OC([C@@H]7[C@H](C)C)=O)C)C(N[C@H](C(C)C)C(N6CCC[C@@](C(N(C)CC(N7C)=O)=O)6[H])=O)=O)=O)=C1N

+

+>  <STRUCTURE_Parent_SMILES>

+O=C(N[C@@H]([C@H](OC([C@@H]5[C@@H](C)C)=O)C)C(N[C@H]([C@@H](C)CC)C(N4CCC[C@@](C(N(C)CC(N5C)=O)=O)4[H])=O)=O)C(C(C(OC2=C(C)C=C3)=C(C)C1=O)=NC2=C3C(N[C@@H]([C@H](OC([C@@H]7[C@H](C)C)=O)C)C(N[C@H](C(C)C)C(N6CCC[C@@](C(N(C)CC(N7C)=O)=O)6[H])=O)=O)=O)=C1N

+

+>  <STRUCTURE_InChI>

+InChI=1/C63H88N12O16/c1-17-31(8)44-61(86)75-25-19-21-38(75)59(84)71(14)27-40(77)73(16)50(30(6)7)63(88)90-35(12)46(57(82)67-44)69-55(80)41-42(64)51(78)33(10)53-48(41)65-47-36(23-22-32(9)52(47)91-53)54(79)68-45-34(11)89-62(87)49(29(4)5)72(15)39(76)26-70(13)58(83)37-20-18-24-74(37)60(85)43(28(2)3)66-56(45)81/h22-23,28-31,34-35,37-38,43-46,49-50H,17-21,24-27,64H2,1-16H3,(H,66,81)(H,67,82)(H,68,79)(H,69,80)/t31-,34+,35+,37-,38-,43+,44+,45-,46-,49-,50-/m0/s1/f/h66-69H

+

+>  <STRUCTURE_InChIKey>

+QCXJFISCRQIYID-IFORFJDKDU

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat

+

+>  <ActivityScore_CPDBAS_Rat>

+0

+

+>  <TD50_Rat_Note>

+no positive results

+

+>  <TargetSites_Rat_Male>

+no positive results

+

+>  <ActivityOutcome_CPDBAS_Rat>

+inactive

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+inactive

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ACTINOMYCIN%20C.html

+

+$$$$

+

+

+

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+

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+

+

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+

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+

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+

+>  <ChemicalPage_URL>

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+

+$$$$

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+

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+

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+

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+

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+

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+

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+

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+

+$$$$

+

+

+

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+

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+

+$$$$

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+TR 21; final call in CPDB differs due to additional data 

+

+>  <ChemicalPage_URL>

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+

+$$$$

+

+

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+

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+

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+

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+

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+

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+mixture of C10-13 alkylbenzenesulfonates average 11.6; with phenyl attachment varying in apprpx equal amounts between C-2,3,4,5 or 6; structure shown C12 attached at C2

+

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+

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+

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+

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+

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+

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+

+$$$$

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+

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+

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+

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+$$$$

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+

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+

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+

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+

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+

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+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Mouse_Male>

+liver; lung; stomach

+

+>  <TargetSites_Mouse_Female>

+liver; lung; stomach

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisite active; multisex active; multispecies active

+

+>  <NTP_TechnicalReport>

+TR 383 

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/1-AMINO-2,4-DIBROMOANTHRAQUINONE.html

+

+$$$$

+

+

+

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+

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+

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+

+>  <TestSubstance_ChemicalName>

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+

+>  <TestSubstance_CASRN>

+17026-81-2

+

+>  <TestSubstance_Description>

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+

+>  <STRUCTURE_ChemicalName_IUPAC>

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+

+>  <STRUCTURE_SMILES>

+NC1=C(C=CC(=C1)NC(=O)C)OCC

+

+>  <STRUCTURE_Parent_SMILES>

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+

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+

+>  <STRUCTURE_InChIKey>

+XTXFAVHDQCHWCS-XWKXFZRBCV

+

+>  <StudyType>

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+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat; mouse

+

+>  <ActivityOutcome_CPDBAS_Mutagenicity>

+active

+

+>  <ActivityScore_CPDBAS_Rat>

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+

+>  <TD50_Rat_Note>

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+

+>  <TargetSites_Rat_Male>

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+

+>  <TargetSites_Rat_Female>

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+

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+

+>  <TD50_Mouse_mg>

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+

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+

+>  <ActivityScore_CPDBAS_Mouse>

+17

+

+>  <TargetSites_Mouse_Male>

+thyroid gland

+

+>  <TargetSites_Mouse_Female>

+no positive results

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <NTP_TechnicalReport>

+TR 112

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/3-AMINO-4-ETHOXYACETANILIDE.html

+

+$$$$

+

+

+

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+

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+

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+

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+

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+

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+

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+

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+6109-97-3

+

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+

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+

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+

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+

+>  <STRUCTURE_InChIKey>

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+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

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+active

+

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+

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+

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+32

+

+>  <TD50_Rat_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Rat_Male>

+ear Zymbals gland; liver; skin

+

+>  <TargetSites_Rat_Female>

+ear Zymbals gland; liver; uterus

+

+>  <ActivityOutcome_CPDBAS_Rat>

+active

+

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+38.6

+

+>  <TD50_Mouse_mmol>

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+

+>  <ActivityScore_CPDBAS_Mouse>

+37

+

+>  <TD50_Mouse_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Mouse_Male>

+liver

+

+>  <TargetSites_Mouse_Female>

+liver

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisite active; multisex active; multispecies active

+

+>  <NTP_TechnicalReport>

+TR 93

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/3-AMINO-9-ETHYLCARBAZOLE.HCl.html

+

+$$$$

+

+

+

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+

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+

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+

+>  <STRUCTURE_Shown>

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+

+>  <TestSubstance_ChemicalName>

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+

+>  <TestSubstance_CASRN>

+NOCAS

+

+>  <TestSubstance_Description>

+mixture or formulation

+

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+mixture, structure shown 3-Amino-9-ethylcarbazole [132-32-1]

+

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+9-ethyl-9H-carbazol-3-amine

+

+>  <STRUCTURE_SMILES>

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+

+>  <STRUCTURE_Parent_SMILES>

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+

+>  <STRUCTURE_InChI>

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+

+>  <STRUCTURE_InChIKey>

+OXEUETBFKVCRNP-UHFFFAOYAV

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat; mouse

+

+>  <ActivityOutcome_CPDBAS_Mutagenicity>

+active

+

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+

+>  <ActivityScore_CPDBAS_Rat>

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+

+>  <TD50_Rat_Note>

+TD50 is harmonic mean of more than one positive test; TD50_Rat_mmol was not calculated for this mixture, but Activiity Score is assigned value of "50" to indicate active

+

+>  <TargetSites_Rat_Male>

+ear Zymbals gland; liver; skin

+

+>  <TargetSites_Rat_Female>

+ear Zymbals gland

+

+>  <ActivityOutcome_CPDBAS_Rat>

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+

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+38

+

+>  <ActivityScore_CPDBAS_Mouse>

+50

+

+>  <TD50_Mouse_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Mouse_Male>

+liver

+

+>  <TargetSites_Mouse_Female>

+liver

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisite active; multisex active; multispecies active

+

+>  <Note_CPDBAS>

+TD50_Rat_mmol and TD50_Mouse_mmol conversions from mg values not provided due substance being a mixture

+

+>  <NTP_TechnicalReport>

+TR 93

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/3-AMINO-9-ETHYLCARBAZOLE%20MIXTURE.html

+

+$$$$

+

+

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+

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+

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+

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+

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+

+>  <TestSubstance_CASRN>

+78441-84-6

+

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+

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+

+$$$$

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+

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+

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+

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+

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+

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+$$$$

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+M  END

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+

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+

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+

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+

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+

+

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+

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+

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+active

+

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+multisex active

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/o-AMINOAZOTOLUENE.html

+

+$$$$

+

+

+

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+

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+

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+

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+parent 

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+

+>  <TestSubstance_ChemicalName>

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+

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+92-67-1

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+single chemical compound

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+

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+

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+TD50 is harmonic mean of more than one positive test

+

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+

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+

+$$$$

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+

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+>  <STRUCTURE_Shown>

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+

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+

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+

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+

+$$$$

+

+

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+

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+

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+

+$$$$

+

+

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+

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+

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+60142-96-3

+

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+

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+

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+

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+

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+

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+

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+

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+$$$$

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

+>  <Species>

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+

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+

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+

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+

+$$$$

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

+>  <STRUCTURE_InChIKey>

+VIROVYVQCGLCII-BAINRFMOCW

+

+>  <StudyType>

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+

+>  <Endpoint>

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+

+>  <Species>

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+

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+

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+

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+

+$$$$

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+

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+

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+

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+>  <STRUCTURE_Shown>

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+dl-Amphetamine sulfate

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+

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+

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+

+>  <STRUCTURE_InChIKey>

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+

+>  <StudyType>

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+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

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+

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+

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+

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+

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+

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+

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+

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+

+>  <ChemicalPage_URL>

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+

+$$$$

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+

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+

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+

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+

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+

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+

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+

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+

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+

+>  <STRUCTURE_Shown>

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+

+>  <TestSubstance_ChemicalName>

+Ampicillin trihydrate

+

+>  <TestSubstance_CASRN>

+7177-48-2

+

+>  <TestSubstance_Description>

+single chemical compound

+

+>  <ChemicalNote>

+stereochem; parent [69-53-4]

+

+>  <STRUCTURE_ChemicalName_IUPAC>

+(2S,5R,6R)-6-{[(2R)-2-amino-2-phenylacetyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid trihydrate

+

+>  <STRUCTURE_SMILES>

+[H][C@@]12[C@]([H])(NC([C@H](N)C3=CC=CC=C3)=O)C(N1[C@@H]([C@@](O)=O)C(C)(C)S2)=O.O.O.O

+

+>  <STRUCTURE_Parent_SMILES>

+[H][C@@]12[C@]([H])(NC([C@H](N)C3=CC=CC=C3)=O)C(N1[C@@H]([C@@](O)=O)C(C)(C)S2)=O

+

+>  <STRUCTURE_InChI>

+InChI=1/C16H19N3O4S.3H2O/c1-16(2)11(15(22)23)19-13(21)10(14(19)24-16)18-12(20)9(17)8-6-4-3-5-7-8;;;/h3-7,9-11,14H,17H2,1-2H3,(H,18,20)(H,22,23);3*1H2/t9-,10-,11+,14-;;;/m1.../s1/f/h18,22H;;;

+

+>  <STRUCTURE_InChIKey>

+RXDALBZNGVATNY-FQLIROBNDT

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat; mouse

+

+>  <ActivityOutcome_CPDBAS_Mutagenicity>

+inactive

+

+>  <ActivityScore_CPDBAS_Rat>

+0

+

+>  <TD50_Rat_Note>

+no positive results

+

+>  <TargetSites_Rat_Male>

+no positive results

+

+>  <TargetSites_Rat_Female>

+no positive results

+

+>  <ActivityOutcome_CPDBAS_Rat>

+inactive

+

+>  <ActivityScore_CPDBAS_Mouse>

+0

+

+>  <TD50_Mouse_Note>

+no positive results

+

+>  <TargetSites_Mouse_Male>

+no positive results

+

+>  <TargetSites_Mouse_Female>

+no positive results

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+inactive

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+inactive

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+inactive

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisex inactive; multispecies inactive

+

+>  <Note_CPDBAS>

+structure modified v5b

+

+>  <NTP_TechnicalReport>

+TR 318

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/AMPICILLIN%20TRIHYDRATE.html

+

+$$$$

+

+

+

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+>  <DSSTox_RID>

+20084

+

+>  <DSSTox_CID>

+84

+

+>  <DSSTox_Generic_SID>

+20084

+

+>  <DSSTox_FileID>

+85_CPDBAS_v5c

+

+>  <STRUCTURE_Formula>

+C6H13N3O2

+

+>  <STRUCTURE_MolecularWeight>

+159.1876

+

+>  <STRUCTURE_ChemicalType>

+defined organic

+

+>  <STRUCTURE_TestedForm_DefinedOrganic>

+parent 

+

+>  <STRUCTURE_Shown>

+tested chemical

+

+>  <TestSubstance_ChemicalName>

+1-Amyl-1-nitrosourea

+

+>  <TestSubstance_CASRN>

+10589-74-9

+

+>  <TestSubstance_Description>

+single chemical compound

+

+>  <STRUCTURE_ChemicalName_IUPAC>

+1-nitroso-1-pentylurea

+

+>  <STRUCTURE_SMILES>

+O=C(N(CCCCC)N=O)N

+

+>  <STRUCTURE_Parent_SMILES>

+O=C(N(CCCCC)N=O)N

+

+>  <STRUCTURE_InChI>

+InChI=1/C6H13N3O2/c1-2-3-4-5-9(8-11)6(7)10/h2-5H2,1H3,(H2,7,10)/f/h7H2

+

+>  <STRUCTURE_InChIKey>

+YYTNAQDGJQPZFU-IAUQMDSZCI

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat

+

+>  <TD50_Rat_mg>

+0.555

+

+>  <TD50_Rat_mmol>

+3.48645246237772E-03

+

+>  <ActivityScore_CPDBAS_Rat>

+51

+

+>  <TD50_Rat_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Rat_Male>

+hematopoietic system; lung; stomach

+

+>  <TargetSites_Rat_Female>

+hematopoietic system; lung; mammary gland; stomach; uterus

+

+>  <ActivityOutcome_CPDBAS_Rat>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisite active; multisex active

+

+>  <Note_CPDBAS>

+TD50_Rat modified v5a

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/1-AMYL-1-NITROSOUREA.html

+

+$$$$

+

+

+

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+M  END

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+20085

+

+>  <DSSTox_Generic_SID>

+20085

+

+>  <DSSTox_FileID>

+86_CPDBAS_v5c

+

+>  <STRUCTURE_ChemicalType>

+no structure

+

+>  <STRUCTURE_Shown>

+no structure

+

+>  <TestSubstance_ChemicalName>

+Amylopectin sulfate

+

+>  <TestSubstance_CASRN>

+9047-13-6

+

+>  <TestSubstance_Description>

+macromolecule

+

+>  <ChemicalNote>

+non-linear polymer of glucose (Merck - amylopectic)

+

+>  <STRUCTURE_InChI>

+InChI=1//

+

+>  <STRUCTURE_InChIKey>

+MOSFIJXAXDLOML-UHFFFAOYAM

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat

+

+>  <TD50_Rat_mg>

+283

+

+>  <ActivityScore_CPDBAS_Rat>

+50

+

+>  <TD50_Rat_Note>

+TD50 is harmonic mean of more than one positive test; TD50_Rat_mmol was not calculated for this mixture, but Activiity Score is assigned value of "50" to indicate active

+

+>  <TargetSites_Rat_Male>

+large intestine

+

+>  <ActivityOutcome_CPDBAS_Rat>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <Note_CPDBAS>

+TD50_Rat_mmol and TD50_Mouse_mmol conversions from mg values not provided due substance being a mixture

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/AMYLOPECTIN%20SULFATE.html

+

+$$$$

+

+

+

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+

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+

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+

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+

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+

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+

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+defined organic

+

+>  <STRUCTURE_TestedForm_DefinedOrganic>

+parent 

+

+>  <STRUCTURE_Shown>

+representative isomer in mixture

+

+>  <TestSubstance_ChemicalName>

+Anethole

+

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+

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+mixture or formulation

+

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+mixture of Z [25679-28-1], E [4180-23-8] isomers, structure shown Z, stereochem

+

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+1-(methyloxy)-4-[(1Z)-prop-1-en-1-yl]benzene

+

+>  <STRUCTURE_SMILES>

+CC=CC1=CC=C(C=C1)OC

+

+>  <STRUCTURE_Parent_SMILES>

+CC=CC1=CC=C(C=C1)OC

+

+>  <STRUCTURE_InChI>

+InChI=1/C10H12O/c1-3-4-9-5-7-10(11-2)8-6-9/h3-8H,1-2H3/b4-3-

+

+>  <STRUCTURE_InChIKey>

+RUVINXPYWBROJD-ARJAWSKDBC

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+mouse

+

+>  <ActivityOutcome_CPDBAS_Mutagenicity>

+inactive

+

+>  <ActivityScore_CPDBAS_Mouse>

+0

+

+>  <TD50_Mouse_Note>

+no positive results

+

+>  <TargetSites_Mouse_Female>

+no positive results

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+inactive

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+inactive

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ANETHOLE.html

+

+$$$$

+

+

+

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+

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+

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+

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+

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+

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+

+>  <STRUCTURE_ChemicalType>

+defined organic

+

+>  <STRUCTURE_TestedForm_DefinedOrganic>

+parent 

+

+>  <STRUCTURE_Shown>

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+

+>  <TestSubstance_ChemicalName>

+trans-Anethole

+

+>  <TestSubstance_CASRN>

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+

+>  <TestSubstance_Description>

+single chemical compound

+

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+stereochem

+

+>  <STRUCTURE_ChemicalName_IUPAC>

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+

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+

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+

+>  <STRUCTURE_InChI>

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+

+>  <STRUCTURE_InChIKey>

+RUVINXPYWBROJD-ONEGZZNKBR

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat

+

+>  <ActivityScore_CPDBAS_Rat>

+0

+

+>  <TD50_Rat_Note>

+no positive results

+

+>  <TargetSites_Rat_Male>

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+

+>  <TargetSites_Rat_Female>

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+

+>  <ActivityOutcome_CPDBAS_Rat>

+inactive

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+inactive

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+inactive

+

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+multisex inactive

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/trans-ANETHOLE.html

+

+$$$$

+

+

+

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+

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+

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+

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+

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+

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+

+>  <STRUCTURE_ChemicalType>

+defined organic

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+

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+

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+15879-93-3

+

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+

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+

+>  <STRUCTURE_SMILES>

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+

+>  <STRUCTURE_Parent_SMILES>

+O[C@H]1[C@@H]([C@H](O)CO)O[C@H]2[C@@H]1O[C@@H]([C@@](Cl)(Cl)Cl)O2

+

+>  <STRUCTURE_InChI>

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+

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+

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+

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+

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+

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+0

+

+>  <TD50_Mouse_Note>

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+

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+

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+

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+

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+

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+

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+multisex inactive

+

+>  <Note_CPDBAS>

+structure modified v5b

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ANHYDROGLUCOCHLORAL.html

+

+$$$$

+

+

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+

+$$$$

+

+

+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

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+

+>  <ChemicalPage_URL>

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+

+$$$$

+

+

+

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+

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+

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+

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+

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+

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+defined organic

+

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+parent 

+

+>  <STRUCTURE_Shown>

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+

+>  <TestSubstance_ChemicalName>

+9,10-Anthraquinone

+

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+84-65-1

+

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+single chemical compound

+

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+9,10-anthraquinone

+

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+

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+

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+

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+

+>  <Endpoint>

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+

+>  <Species>

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+

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+active

+

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+

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+

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+

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+

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+

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+

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+

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+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/9,10-ANTHRAQUINONE.html

+

+$$$$

+

+

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+M  END

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+

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+

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+

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+

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+667.8726

+

+>  <STRUCTURE_ChemicalType>

+organometallic

+

+>  <STRUCTURE_Shown>

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+

+>  <TestSubstance_ChemicalName>

+Antimony potassium tartrate

+

+>  <TestSubstance_CASRN>

+28300-74-5

+

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+single chemical compound

+

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+dipotassium 5,11-dioxo-2,6,8,12,13,14-hexaoxa-1,7-distibatricyclo[8.2.1.1~4,7~]tetradecane-3,9-dicarboxylate trihydrate

+

+>  <STRUCTURE_SMILES>

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+

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+

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+

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+$$$$

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+

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+M  END

+>  <DSSTox_RID>

+20097

+

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+

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+

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+

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+

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+

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+

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+Aramite

+

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+

+>  <TestSubstance_Description>

+single chemical compound

+

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+

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+

+>  <STRUCTURE_InChI>

+InChI=1/C15H23ClO4S/c1-12(20-21(17)19-10-9-16)11-18-14-7-5-13(6-8-14)15(2,3)4/h5-8,12H,9-11H2,1-4H3

+

+>  <STRUCTURE_InChIKey>

+YKFRAOGHWKADFJ-UHFFFAOYAL

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat; mouse

+

+>  <TD50_Rat_mg>

+96.7

+

+>  <TD50_Rat_mmol>

+0.288778520611828

+

+>  <ActivityScore_CPDBAS_Rat>

+31

+

+>  <TD50_Rat_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Rat_BothSexes>

+liver

+

+>  <ActivityOutcome_CPDBAS_Rat>

+active

+

+>  <TD50_Mouse_mg>

+158

+

+>  <TD50_Mouse_mmol>

+0.471840809272687

+

+>  <ActivityScore_CPDBAS_Mouse>

+32

+

+>  <TargetSites_Mouse_Male>

+liver

+

+>  <TargetSites_Mouse_Female>

+no positive results

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multispecies active

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ARAMITE.html

+

+$$$$

+

+

+

+ 13 12  0  0  0  0  0  0  0  0  1 V2000

+    4.6515   -2.3038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    5.3171   -1.1556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    6.6482   -1.1556    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

+    7.3137   -2.3038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    6.6482   -3.4594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    5.3171   -3.4594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    7.3137    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    3.3278   -2.3038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.6622   -3.4594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    3.3278   -4.6077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.6622   -1.1556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    0.0000   -2.3477    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

+    1.3311   -2.3477    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0

+  1  2  1  0  0  0  0

+  1  6  2  0  0  0  0

+  1  8  1  0  0  0  0

+  2  3  1  0  0  0  0

+  3  4  1  0  0  0  0

+  3  7  1  0  0  0  0

+  4  5  1  0  0  0  0

+  5  6  1  0  0  0  0

+  8  9  1  0  0  0  0

+  8 11  2  0  0  0  0

+  9 10  1  0  0  0  0

+ 12 13  1  0  0  0  0

+M  END

+>  <DSSTox_RID>

+20098

+

+>  <DSSTox_CID>

+98

+

+>  <DSSTox_Generic_SID>

+20098

+

+>  <DSSTox_FileID>

+99_CPDBAS_v5c

+

+>  <STRUCTURE_Formula>

+C8H14ClNO2

+

+>  <STRUCTURE_MolecularWeight>

+191.6571

+

+>  <STRUCTURE_ChemicalType>

+defined organic

+

+>  <STRUCTURE_TestedForm_DefinedOrganic>

+complex HCl

+

+>  <STRUCTURE_Shown>

+tested chemical

+

+>  <TestSubstance_ChemicalName>

+Arecoline.HCl

+

+>  <TestSubstance_CASRN>

+61-94-9

+

+>  <TestSubstance_Description>

+single chemical compound

+

+>  <ChemicalNote>

+parent [63-75-2]

+

+>  <STRUCTURE_ChemicalName_IUPAC>

+methyl 1-methyl-1,2,5,6-tetrahydropyridine-3-carboxylate hydrochloride

+

+>  <STRUCTURE_SMILES>

+O=C(OC)C1=CCCN(C)C1.[H]Cl

+

+>  <STRUCTURE_Parent_SMILES>

+O=C(OC)C1=CCCN(C)C1

+

+>  <STRUCTURE_InChI>

+InChI=1/C8H13NO2.ClH/c1-9-5-3-4-7(6-9)8(10)11-2;/h4H,3,5-6H2,1-2H3;1H

+

+>  <STRUCTURE_InChIKey>

+LQSWCSYIDIBGRR-UHFFFAOYAO

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+mouse

+

+>  <TD50_Mouse_mg>

+39.5

+

+>  <TD50_Mouse_mmol>

+0.206097243462413

+

+>  <ActivityScore_CPDBAS_Mouse>

+36

+

+>  <TD50_Mouse_Note>

+TD50 is harmonic mean of more than one positive test

+

+>  <TargetSites_Mouse_Male>

+lung; stomach; vascular system

+

+>  <TargetSites_Mouse_Female>

+lung; vascular system

+

+>  <ActivityOutcome_CPDBAS_Mouse>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisite active; multisex active

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ARECOLINE.HCl.html

+

+$$$$

+

+

+

+ 26 28  0  0  0  0  0  0  0  0  2 V2000

+    4.6012   -5.3648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    3.9551   -4.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    3.4264   -7.5675    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0

+    4.6012   -3.1229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.6530   -4.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    5.9032   -3.1229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    6.5493   -4.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    3.9551   -1.9971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    5.9032   -5.3648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.0069   -3.1229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.6530   -1.9971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    2.0069   -5.3648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    4.3564   -0.7636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    2.1244   -7.5675    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0

+    2.2516   -0.7636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    4.0725   -8.6933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    3.3089    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    7.8416   -4.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    0.7147   -5.3648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    2.5258   -6.2361    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0

+    6.5493   -1.9971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    8.4975   -5.3648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

+    7.8416   -1.9971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    8.4975   -3.1229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    9.7897   -5.3648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

+    0.0000   -3.4949    0.0000 Na  0  3  0  0  0  0  0  0  0  0  0  0

+  1  2  1  0  0  0  0

+  1  3  1  0  0  0  0

+  1  9  2  0  0  0  0

+  2  4  2  0  0  0  0

+  2  5  1  0  0  0  0

+  3 14  1  0  0  0  0

+  3 16  2  0  0  0  0

+  4  8  1  0  0  0  0

+  4  6  1  0  0  0  0

+  5 10  2  0  0  0  0

+  5 12  1  0  0  0  0

+  6  7  2  0  0  0  0

+  6 21  1  0  0  0  0

+  7  9  1  0  0  0  0

+  7 18  1  0  0  0  0

+  8 13  1  0  0  0  0

+  8 11  2  0  0  0  0

+ 10 11  1  0  0  0  0

+ 11 15  1  0  0  0  0

+ 12 19  2  0  0  0  0

+ 12 20  1  0  0  0  0

+ 13 17  1  0  0  0  0

+ 15 17  1  0  0  0  0

+ 18 22  1  0  0  0  0

+ 18 24  2  0  0  0  0

+ 21 23  2  0  0  0  0

+ 22 25  1  0  0  0  0

+ 23 24  1  0  0  0  0

+M  CHG  4   3   1  14  -1  20  -1  26   1

+M  END

+>  <DSSTox_RID>

+20099

+

+>  <DSSTox_CID>

+99

+

+>  <DSSTox_Generic_SID>

+20099

+

+>  <DSSTox_FileID>

+100_CPDBAS_v5c

+

+>  <STRUCTURE_Formula>

+C17H10NNaO7

+

+>  <STRUCTURE_MolecularWeight>

+363.2536

+

+>  <STRUCTURE_ChemicalType>

+defined organic

+

+>  <STRUCTURE_TestedForm_DefinedOrganic>

+salt Na

+

+>  <STRUCTURE_Shown>

+representative component in mixture

+

+>  <TestSubstance_ChemicalName>

+Aristolochic acid, sodium salt (77% AA I, 21% AA II)

+

+>  <TestSubstance_CASRN>

+10190-99-5

+

+>  <TestSubstance_Description>

+mixture or formulation

+

+>  <ChemicalNote>

+structure shown AA I,  parent [313-67-7]; AA II 6-Nitrophenanthro(3,4-d)-1,3-dioxole-5-carboxylic acid, sodium salt, AA II parent [475-80-9]

+

+>  <STRUCTURE_ChemicalName_IUPAC>

+sodium 8-(methyloxy)-6-nitrophenanthro[3,4-d][1,3]dioxole-5-carboxylate

+

+>  <STRUCTURE_SMILES>

+[O-][N+](C1=CC(C(OC)=CC=C4)=C4C2=C1C(C([O-])=O)=CC3=C2OCO3)=O.[Na+]

+

+>  <STRUCTURE_Parent_SMILES>

+[O-][N+](C1=CC(C(OC)=CC=C4)=C4C2=C1C(C(O)=O)=CC3=C2OCO3)=O

+

+>  <STRUCTURE_InChI>

+InChI=1/C17H11NO7.Na/c1-23-12-4-2-3-8-9(12)5-11(18(21)22)14-10(17(19)20)6-13-16(15(8)14)25-7-24-13;/h2-6H,7H2,1H3,(H,19,20);/q;+1/p-1/fC17H10NO7.Na/q-1;m

+

+>  <STRUCTURE_InChIKey>

+BQVOPWJSBBMGBR-KEMNOBITCY

+

+>  <StudyType>

+Carcinogenicity

+

+>  <Endpoint>

+TD50; Tumor Target Sites

+

+>  <Species>

+rat

+

+>  <ActivityOutcome_CPDBAS_Mutagenicity>

+active

+

+>  <TD50_Rat_mg>

+0.0141

+

+>  <ActivityScore_CPDBAS_Rat>

+50

+

+>  <TD50_Rat_Note>

+TD50 is harmonic mean of more than one positive test; TD50_Rat_mmol was not calculated for this mixture, but Activiity Score is assigned value of "50" to indicate active

+

+>  <TargetSites_Rat_Male>

+stomach 

+

+>  <TargetSites_Rat_Female>

+stomach

+

+>  <ActivityOutcome_CPDBAS_Rat>

+active

+

+>  <ActivityOutcome_CPDBAS_SingleCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall>

+active

+

+>  <ActivityOutcome_CPDBAS_MultiCellCall_Details>

+multisex active

+

+>  <Note_CPDBAS>

+kidney and urinary bladder were additional target sites but experiments too short to meet the inclusion rules of the CPDB; Rat added v2a; Mutagenicity_SAL_CPDB added v3a; TD50_Rat_mmol conversion from mg value not provided due to substance being a mixture

+

+>  <ChemicalPage_URL>

+http://potency.berkeley.edu/chempages/ARISTOLOCHIC%20ACID,%20SODIUM%20SALT%20(77%25%20AA%20I,%2021%25%20AA%20I.html

+

+$$$$

diff --git a/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv b/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv
new file mode 100644
index 0000000..a726ad8
--- /dev/null
+++ b/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv
@@ -0,0 +1,436 @@
+STRUCTURE_SMILES,TD50_Mouse_mmol
+ClC1=CC2=C(C=C1Cl)OC3=C(C=C(C(=C3)Cl)Cl)O2,0.000000485
+ClC1=C(Cl)C(Cl)=CC2=C1OC3=C(C=C(Cl)C(Cl)=C3Cl)O2,0.00000366
+CC(C)(O)CC[C@@H](O)[C@@H](C)[C@H]2CC[C@@]1(O)C/3=C/C(=O)[C@@H]4C[C@@H](O)[C@@H](O)C[C@]4(C)[C@H]\3CC[C@@]12C,0.000077
+OC2=CC=C(C=C2)/C(CC)=C(CC)/C1=CC=C(O)C=C1,0.000146
+N/C1=N/C(=O)N(/C=N1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O,0.000317
+CC1=C2C=CC=CC2=C(C3=CC=C4C(=C13)C=CC=C4)C,0.000328
+ClCCN(C1=CC=C(C=C1)CCCC(=O)O)CCCl,0.000437
+OC([C@H](CC1=CC=C(N(CCCl)CCCl)C=C1)N)=O,0.000491
+BrC2=C(C=C(Br)C(Br)=C2)C1=C(Br)C=C(Br)C(Br)=C1,0.000529
+N(NC)C.[H]Cl.[H]Cl,0.000857
+O=C(O[C@@H]5CC([C@@](CC5)(C)[C@]([H])3CC4)=CC[C@@]3([H])[C@@]2([H])[C@@]4(C)[C@]([C@H](C)CCCC(C)C)([H])CC2)CC1=CC=C(N(CCCl)CCCl)C=C1,0.000955
+[C@@H]1(NC(N(N=O)C)=O)[C@H]([C@H](O)[C@H](O[C@@H]1O)CO)O,0.00103
+S=P(N1CC1)(N1CC1)N1CC1,0.00118
+NC(=O)OC=C,0.00142
+ClCOCCl,0.00158
+ClCCN(CCCl)C1=CC=C(CC(OC3=CC=C(C4=C3)[C@]2([H])[C@](CC4)([H])[C@@](CC[C@@H]5OC(CC6=CC=C(N(CCCl)CCCl)C=C6)=O)([H])[C@]5(C)CC2)=O)C=C1,0.00184
+CC(C)CC(=O)O[C@H]1C[C@]2(COC(C)=O)[C@@]4(C)[C@H](OC(C)=O)[C@@H](O)[C@@H](O[C@@H]2/C=C1/C)[C@]34CO3,0.00189
+ClC54C(=O)C1(Cl)C2(Cl)C5(Cl)C3(Cl)C4(Cl)C1(Cl)C2(Cl)C3(Cl)Cl,0.002
+ClC(C1=CC=CC=C1)(Cl)Cl,0.00203
+CNNCC1(=CC=C(C=C1)C(=O)NC(C)C).[H]Cl,0.00216
+[S-]C(N(CC)CC)=S.[S-]C(N(CC)CC)=S.[S-]C(N(CC)CC)=S.[S-]C(N(CC)CC)=S.[Se+4],0.00222
+Cl[C@@]1(C(C)2C)C(Cl)(Cl)C(Cl)([C@](Cl)(C2=C)C1Cl)Cl,0.00234
+Cl\C2=C(/Cl)C3(Cl)C1C4CC(C1C2(Cl)C3(Cl)Cl)C5OC45,0.00239
+CN(N=O)C,0.00255
+ClC53C1(Cl)C4(Cl)C2(Cl)C1(Cl)C(Cl)(Cl)C5(Cl)C2(Cl)C3(Cl)C4(Cl)Cl,0.00266
+CC/C(=C/CC)[N+](=O)[O-],0.00268
+O.O.O.O.[Co+2].O.O.O.[O-]S([O-])(=O)=O,0.00269
+O=C1C2=C(C=C3C(=C2OC4=CC=CC(=C14)O)C5C(O3)OC=C5)OC,0.0028
+ClC1/C=C\C2C1C3(Cl)C(/Cl)=C(/Cl)C2(Cl)C3(Cl)Cl,0.00324
+ClC2(C(Cl)3Cl)C(Cl)=C(Cl)C3(Cl)C1CC(Cl)C(Cl)C12,0.00334
+ClC(C(Cl)(Cl)C43Cl)(C(Cl)=C4Cl)C1C3C2C=CC1C2,0.00348
+O=NN1CCCCCC1,0.00412
+Brc1c(c(Br)c(Br)c(Br)c1Br)c2c(Br)cc(Br)c(Br)c2Br,0.00418
+OCCNN,0.00522
+O=C(N)C1=C(N=CN1)/N=N/N(C)C,0.0053
+[H][C@]12C3=CCN1CC[C@H]2OC(/C(CC([C@@](CO)(O)C(OC3)=O)=C)=C\C)=O,0.00564
+C[Hg]Cl,0.00578
+O=C1C2=C(C(=CC=C2C(=O)C3=C1C=CC=C3)C)[N+](=O)[O-],0.00584
+ClCC(Cl)CCl,0.00593
+ClC#CCl,0.00605
+O[C@]1(C(C)2C)[C@]2([H])[C@@](C=C(CO)C4)([H])[C@]([C@@](C=C3C)([H])[C@@]4(O)C3=O)(O)[C@H](C)[C@H]1O,0.00606
+O=[N+](C([N+](=O)[O-])([N+](=O)[O-])[N+](=O)[O-])[O-],0.00607
+NC1=CC=C(C=C1)C2=CC=C(C=C2)F,0.00609
+O=C(N(CCO)N=O)N,0.00615
+O=NN1CCCC1,0.00678
+O=NN(CCCC)CCCC,0.00689
+CC/C(C2=CC=CC=C2)=C(C1=CC=CC=C1)/C(C=C3)=CC=C3OCCN(C)C.OC(C(CC(O)=O)(O)CC(O)=O)=O,0.00779
+O=C(C(C)(OC1=CC=C(C=C1)C2=CC=C(C=C2)Cl)C)OC,0.00824
+O=C(C4=CC(OC)=C(OC)C(OC)=C4)O[C@@H]1C[C@@]3([H])[C@@](C[C@](N5C3)([H])C2=C(CC5)C(C=C6)=C(C=C6OC)N2)([H])[C@H]([C@](OC)=O)[C@H]1OC,0.00825
+C1CN1,0.00875
+O=C(C[C@@H]([C@@](O)=O)CC(O)=O)O[C@H]([C@@H](C)CCCC)[C@@H](C[C@H](C)C[C@@H](O)CCCC[C@@H](O)C[C@H](O)[C@@H](N)C)OC(C[C@@H]([C@@](O)=O)CC(O)=O)=O,0.00941
+O=NN1CCCCC1,0.0114
+BrC(CCl)CBr,0.0115
+CN(C(=O)N)N=O,0.0119
+ClC/C=C/CCl,0.0122
+NC1=CC=C(C=C1)C2=CC=CC=C2,0.0124
+C1=CC(=CC=C1COCCl)COCCl,0.0132
+C1=CC2=CC=CC3=CC=C4C(=C23)C1=C5C(=C4)C=CC=C5,0.0138
+N=C(N(N=O)C)N[N+](=O)[O-],0.0138
+C(C(COCCl)OCCl)OCCl,0.0145
+CCCCC/C=N/N(C=O)C,0.0149
+CC(C/C=N/N(C=O)C)C,0.0157
+ClCCN(C(COC2=CC=CC=C2)C)CC1=CC=CC=C1.Cl,0.0158
+O=C(O[C@H](C)C2)C1=C2C(Cl)=CC(C(N[C@@H](CC3=CC=CC=C3)[C@@](O)=O)=O)=C1O,0.0159
+O=C1CCO1,0.0172
+N=C(N(CC)N=O)N[N+]([O-])=O,0.0176
+CN(N)C=O,0.0185
+N(C)[N+].S(=O)(=O)([O-])O,0.0189
+ClCCN[P]1(=O)OCCCN1CCCl,0.0194
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diff --git a/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv b/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv
new file mode 100644
index 0000000..7c8e38b
--- /dev/null
+++ b/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv
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diff --git a/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv b/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv
new file mode 100644
index 0000000..c0e8158
--- /dev/null
+++ b/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv
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diff --git a/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv b/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv
new file mode 100644
index 0000000..d1583c2
--- /dev/null
+++ b/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv
@@ -0,0 +1,978 @@
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diff --git a/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv b/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv
new file mode 100644
index 0000000..8f8bbf4
--- /dev/null
+++ b/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv
@@ -0,0 +1,1120 @@
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+O=P(OCCCl)(OCCCl)OCCCl,active
+O=S(=O)(C1=CC=C(C=C1)N)C2=CC=C(C=C2)N,active
+OC(C1=CC=C(C=C1)Cl)(C2=CC=C(C=C2)Cl)C(=O)OCC,active
+ClC(Cl)Cl,active
+O=P(OC(CCl)CCl)(OC(CCl)CCl)OC(CCl)CCl,active
+O=C2C1=C(OC)C=C(OC)C(Cl)=C1O[C@]32C(OC)=CC(C[C@@](C)3[H])=O,active
+O=NN1CCSCC1,active
+O=NN1CCN(N=O)CC1,active
+ClC(CCl)(Cl)Cl,active
+O=P(OC=C(Cl)Cl)(OC)OC,active
+O=P(H)(OC)OC,active
+O=C1OC2=C(C=CC=C2)CC1,active
+O=C1OC2=C(C=CC=C2)C=C1,active
+O=CC1=CC=CO1,active
+OC1=C(C=CC(=C1)/C=C/C(=O)O)O,active
+O=C3C[C@@H]4CC[C@@H]1[C@H](CC[C@]2(C)[C@@](C)(O)CC[C@@H]12)[C@@]4(C)C\C3=C\O,active
+O=C1N2CC3=CC=CC=C3C(=O)N2CC4C=CC=CC1=4,active
+O=C1N(C2=CC=CC=C2)N(C3=CC=CC=C3)C(=O)C1CCCC,active
+O[C@@H]3C\C4=C\C[C@@H]2[C@H](CC[C@]1(C)C(=O)CC[C@H]12)[C@@]4(C)CC3,active
+O=C1OC(O)C(C(Cl)Cl)=C1Cl,active
+[K+].[I-],active
+O=C1NC(=S)NC=C1,active
+NC2=CC=C(C=C2N)C1=CC=C(N)C(N)=C1.Cl.Cl.Cl.Cl,active
+O=NN(C)CCCCCCCCCCCC,active
+O=NN(C)C1=NC=NC2=C1N=CN2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O,active
+O=NN(CC(C)O)CC(C)O,active
+O=NN(CC(=O)C)CC(=O)C,active
+O=NN(C1=CC=CC=C1)C2=CC=CC=C2,active
+C=C(Cl)C=C,active
+O=CC1=CC=CC=C1,active
+C1=C(CO)OC=C1,active
+C1(N=C(SC=1)NN)C2=CC=C(C=C2)N,active
+O=N[O-].[Na+],active
+O=CNNC=O,active
+[O-][N+](C2=CC=C(O2)C1=CSC=N1)=O,active
+OCC(CO)(CBr)CBr,active
+CC=NN(C)C=O,active
+O=C(OCC)C=C,active
+OCCBr,active
+ClC1=C(C(=C(C(=C1C#N)Cl)Cl)Cl)C#N,active
+OC1=C(C=CC(=C1)C)O,active
+BrC2=C(C=C(Br)C(Br)=C2)C1=C(Br)C=C(Br)C(Br)=C1,active
+OC1=C(C=C(C=C1Cl)Cl)Cl,active
+OC2=CC=C(C=C2)/C(CC)=C(CC)/C1=CC=C(O)C=C1,active
+OC1=CC=C(C=C1C(C)(C)C)OC,active
+OC1=CC(=CC2=C1C(=O)O[C@H](CCCC(=O)CCC/C=C\2)C)O,active
+O=NN(CCN1)CC1,active
+O=C1C2=C(C(=CC=C2C(=O)C3=C1C=CC=C3)C)N,active
+O(CC1(C)C)C1=O,active
+S