opentox-ruby 0.0.2 → 1.0.0

data/README.markdown

@@ -0,0 +1,41 @@
+opentox-ruby
+============
+
+Ruby wrapper for the [OpenTox](http://www.opentox.org) REST API 
+
+Installation
+------------
+
+opentox-ruby depends on many third party programs and libraries, which makes the setup complicated and error prone. For this reason we recommend to use the installer from [opentox-install](http://github.com/opentox/opentox-install). If you want to install manually you can find the necessary steps in the installation scripts.
+
+Quickstart
+----------
+
+This example shows how to create a lazar model and predict a compound, it assumes that you have access to a working installation of OpenTox services with corresponding settings in $HOME/.opentox/config. Run the following code in irb or from a ruby script:
+
+    require 'rubygems'
+    require 'opentox-ruby'
+
+    # Authenticate
+    subjectid = OpenTox::Authorization.authenticate(USER,PASSWORD) 
+
+    # Upload a dataset
+    training_dataset = OpenTox::Dataset.create_from_csv_file(TRAINING_DATASET, subjectid)
+
+    # Create a prediction model
+    model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => training_dataset.uri, :subjectid => subjectid}).to_s
+    lazar = OpenTox::Model::Lazar.find model_uri, subjectid
+    
+    # Predict a compound
+    compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
+    prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => subjectid)
+    prediction = OpenTox::LazarPrediction.find(prediction_uri, subjectid)
+    puts prediction.to_yaml
+
+[API documentation](http://rdoc.info/gems/opentox-ruby/1.0.0/frames)
+-------------------------------------------------------------------
+
+Copyright
+---------
+
+Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.

data/Rakefile

@@ -27,8 +27,11 @@ begin
       "yajl-ruby",
       "tmail",
       "rinruby",
+      "ohm",
+      "SystemTimer",
       "rjb"
     ].each { |dep| gem.add_dependency dep }
+=begin
     [ "dm-core",
       'dm-serializer',
       'dm-timestamps',
@@ -37,6 +40,7 @@ begin
       "dm-mysql-adapter",
       "dm-validations",
     ].each {|dep| gem.add_dependency dep, ">= 1" }
+=end
     gem.add_dependency "haml", ">=3"
     ['jeweler'].each { |dep| gem.add_development_dependency dep }
     gem.files =  FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore']

data/VERSION

@@ -1 +1 @@
-0.0.2
+1.0.0

data/lib/algorithm.rb

@@ -13,9 +13,10 @@ module OpenTox
 
     # Execute algorithm with parameters, please consult the OpenTox API and the webservice documentation for acceptable parameters
     # @param [optional,Hash] params Algorithm parameters
+    # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [String] URI of new resource (dataset, model, ...)
-    def run(params=nil)
-      RestClientWrapper.post(@uri, {:accept => 'text/uri-list'}, params).to_s
+    def run(params=nil, waiting_task=nil)
+      RestClientWrapper.post(@uri, params, {:accept => 'text/uri-list'}, waiting_task).to_s
     end
     
     # Get OWL-DL representation in RDF/XML format
@@ -29,6 +30,18 @@ module OpenTox
     # Generic Algorithm class, should work with all OpenTox webservices
     class Generic 
       include Algorithm
+      
+      # Find Generic Opentox Algorithm via URI, and loads metadata, could raise NotFound/NotAuthorized error
+      # @param [String] uri Algorithm URI
+      # @return [OpenTox::Algorithm::Generic] Algorithm instance
+      def self.find(uri, subjectid=nil)
+        return nil unless uri
+        alg = Generic.new(uri)
+        alg.load_metadata( subjectid )
+        raise "cannot load algorithm metadata" if alg.metadata==nil or alg.metadata.size==0
+        alg
+      end
+      
     end
 
     # Fminer algorithms (https://github.com/amaunz/fminer2)

data/lib/authorization.rb

@@ -0,0 +1,381 @@
+module OpenTox
+
+  #Module for Authorization and Authentication
+  #@example Authentication
+  #  require "opentox-ruby-api-wrapper" 
+  #  OpenTox::Authorization::AA_SERVER = "https://opensso.in-silico.ch" #if not set in .opentox/conf/[environment].yaml 
+  #  token = OpenTox::Authorization.authenticate("benutzer", "passwort") 
+  #@see http://www.opentox.org/dev/apis/api-1.2/AA OpenTox A&A API 1.2 specification
+   
+  module Authorization
+
+    #Helper Class AA to create and send default policies out of xml templates
+    #@example Creating a default policy to a URI 
+    #  aa=OpenTox::Authorization::AA.new(tok)  
+    #  xml=aa.get_xml('http://uri....')
+    #  OpenTox::Authorization.create_policy(xml,tok)   
+    
+    class AA
+      attr_accessor :user, :subjectid, :policy  
+      
+      #Generates AA object - requires subjectid
+      # @param [String] subjectid  
+      def initialize(subjectid)
+        @user = Authorization.get_user(subjectid)
+        @subjectid = subjectid
+        @policy = Policies.new()
+      end
+      
+      #Cleans AA Policies and loads default xml file into policy attribute
+      #set uri and user, returns Policyfile(XML) for open-sso 
+      # @param [String] URI to create a policy for
+      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 [String] URI to create a policy for      
+      def send(uri)    
+        xml = get_xml(uri)
+        ret = false
+        ret = Authorization.create_policy(xml, @subjectid) 
+        LOGGER.debug "Policy send with subjectid: #{@subjectid}"
+        LOGGER.warn "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_SERVER
+    end
+
+    #Authentication against OpenSSO. Returns token. Requires Username and Password.
+    # @param [String, String]Username,Password 
+    # @return [String, nil] gives subjectid or nil
+    def self.authenticate(user, pw)
+      return nil if !AA_SERVER
+      begin 
+        resource = RestClient::Resource.new("#{AA_SERVER}/auth/authenticate")
+        out = resource.post(:username=>user, :password => pw).sub("token.id=","").sub("\n","")
+        return out
+      rescue
+        return nil
+      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)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/auth/logout")
+        resource.post(:subjectid => subjectid)
+        return true 
+      rescue
+        return false
+      end
+    end    
+    
+    #Authorization against OpenSSO for a URI with request-method (action) [GET/POST/PUT/DELETE]
+    # @param [String,String,String]uri,action,subjectid
+    # @return [Boolean, nil]  returns true, false or nil (if authorization-request fails).
+    def self.authorize(uri, action, subjectid)
+      return true if !AA_SERVER
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/auth/authorize")
+        return true if resource.post(:uri => uri, :action => action, :subjectid => subjectid) == "boolean=true\n"
+      rescue
+        return nil
+      end    
+    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)
+      return true if !AA_SERVER
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/auth/isTokenValid")
+        return true if resource.post(:tokenid => subjectid) == "boolean=true\n"
+      rescue
+        return false
+      end
+    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(subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/pol")
+        out = resource.get(:subjectid => subjectid)
+        return out.split("\n")
+      rescue RestClient::InternalServerError => e
+        raise e.response  
+      rescue
+        return nil
+      end
+    end
+
+    #Returns a policy in xml-format
+    # @param [String, String]policy,subjectid 
+    # @return [String] XML of the policy 
+    def self.list_policy(policy, subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/pol")
+        return resource.get(:subjectid => subjectid,: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_policy_uris( subjectid )
+      names = list_policies(subjectid)
+      policies = {}
+      names.each do |n|
+        p = OpenTox::Policies.new
+        p.load_xml( list_policy(n, subjectid) )
+        policies[n] = p.uris
+      end
+      policies
+    end
+    
+    #Returns the owner (who created the first policy) of an URI
+    # @param [String, String]uri,subjectid
+    # return [String, nil]owner,nil returns owner of the URI
+    def self.get_uri_owner(uri, subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/pol")
+        return resource.get(:uri => uri, :subjectid => subjectid).sub("\n","")
+      rescue
+        return nil
+      end      
+    end    
+    
+    #Checks if a policy exists to a URI. Requires URI and token.
+    # @param [String, String]uri,subjectid
+    # return [Boolean] 
+    def self.uri_has_policy(uri, subjectid)
+      owner = get_uri_owner(uri, subjectid)
+      return true if owner and owner != "null"
+      false
+    end
+    
+    #List all policynames for a URI. Requires URI and token.
+    # @param [String, String]uri,subjectid
+    # return [Array, nil] returns an Array of policy names or nil if request fails   
+    def self.list_uri_policies(uri, subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/pol")
+        out = resource.get(:uri => uri, :polnames => true, :subjectid => subjectid)        
+        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 [String, String]policyxml,subjectid
+    # return [Boolean] returns true if policy is created   
+    def self.create_policy(policy, subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/Pol/opensso-pol")
+        LOGGER.debug "OpenTox::Authorization.create_policy policy: #{policy[168,43]} with token:" + subjectid.to_s + " length: " + subjectid.length.to_s 
+        return true if resource.post(policy, :subjectid => subjectid, :content_type =>  "application/xml")
+      rescue
+        return false
+      end
+    end
+    
+    #Deletes a policy
+    # @param [String, String]policyname,subjectid
+    # @return [Boolean,nil]
+    def self.delete_policy(policy, subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/pol")
+        LOGGER.debug "OpenTox::Authorization.delete_policy policy: #{policy} with token: #{subjectid}"
+        return true if resource.delete(:subjectid => subjectid, :id => policy)        
+      rescue
+        return nil
+      end
+    end
+
+    #Returns array of all possible LDAP-Groups
+    # @param [String]subjectid
+    # @return [Array]    
+    def self.list_groups(subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/opensso/identity/search")
+        grps = resource.post(:admin => subjectid, :attributes_names => "objecttype", :attributes_values_objecttype => "group")
+        grps.split("\n").collect{|x|  x.sub("string=","")}
+      rescue
+        []
+      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, subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/opensso/identity/read")
+        out = resource.post(:name => user, :admin => 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
+    # @return [String]user 
+    def self.get_user(subjectid)
+      begin
+        resource = RestClient::Resource.new("#{AA_SERVER}/opensso/identity/attributes")
+        out = resource.post(: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::AA class
+    # @param [String, String]URI,subjectid
+    def self.send_policy(uri, subjectid)
+      return true if !AA_SERVER
+      aa  = Authorization::AA.new(subjectid)
+      ret = aa.send(uri)
+      LOGGER.debug "OpenTox::Authorization send policy for URI: #{uri} | subjectid: #{subjectid} - policy created: #{ret}"
+      ret
+    end
+    
+    #Deletes all policies of an URI
+    # @param [String, String]URI,subjectid
+    # @return [Boolean]
+    def self.delete_policies_from_uri(uri, subjectid)
+      policies = list_uri_policies(uri, subjectid)
+      policies.each do |policy|
+        ret = delete_policy(policy, subjectid)
+        LOGGER.debug "OpenTox::Authorization delete policy: #{policy} - with result: #{ret}"
+      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, subjectid)
+      return true unless uri and subjectid
+      token_valid = OpenTox::Authorization.is_token_valid(subjectid)      
+      LOGGER.debug "OpenTox::Authorization.check_policy with uri: #{uri}, subjectid: #{subjectid} is valid: #{token_valid}"
+      # check if subjectid is valid
+      unless token_valid
+        # abort if invalid
+        LOGGER.error "OpenTox::Authorization.check_policy, subjectid NOT valid: #{subjectid}" 
+        return false
+      end
+      
+      if !uri_has_policy(uri, subjectid)
+        # if no policy exists, create a policy, return result of send policy
+        send_policy(uri, subjectid)
+      else
+        # if policy exists check for POST rights 
+        if authorize(uri, "POST", subjectid)
+          true
+       else
+          LOGGER.error "OpenTox::Authorization.check_policy, already exists, but no POST-authorization with subjectid: #{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 [String] uri
+    # @param [String] request_method, should be GET, POST, PUT, DELETE
+    # @param [String] subjectid
+    # @return [Boolean] true if access granted, else otherwise
+    def self.authorized?(uri, request_method, subjectid)
+      if CONFIG[:authorization][:free_request].include?(request_method)  
+        #LOGGER.debug "authorized? >>true<< (request is free), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}"
+        true
+      elsif OpenTox::Authorization.free_uri?(uri, request_method)
+        #LOGGER.debug "authorized? >>true<< (uris is free_uri), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}"
+        true
+      elsif CONFIG[:authorization][:authenticate_request].include?(request_method)
+        ret = OpenTox::Authorization.is_token_valid(subjectid)
+        LOGGER.debug "authorized? >>#{ret}<< (token is in/valid), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}" unless ret
+        ret
+      elsif OpenTox::Authorization.authorize_exception?(uri, request_method)
+        ret = OpenTox::Authorization.is_token_valid(subjectid)
+        LOGGER.debug "authorized? >>#{ret}<< (uris is authorize exception, token is in/valid), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}" unless ret
+        ret
+      elsif CONFIG[:authorization][:authorize_request].include?(request_method)
+        ret = OpenTox::Authorization.authorize(uri, request_method, subjectid)
+        LOGGER.debug "authorized? >>#{ret}<< (uri (not) authorized), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}" unless ret
+        ret
+      else 
+        LOGGER.error "invalid request/uri method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}"
+        false
+      end
+    end
+    
+    private
+    def self.free_uri?(uri, request_method)
+      if CONFIG[:authorization][:free_uris]
+        CONFIG[:authorization][:free_uris].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
+    
+    def self.authorize_exception?(uri, request_method)
+      if CONFIG[:authorization][:authorize_exceptions]
+        CONFIG[:authorization][:authorize_exceptions].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