opentox-ruby 0.0.2 → 1.0.0

data/lib/templates/config.yaml

@@ -39,3 +39,48 @@
 
 # Uncomment for verbose logging
 # :logger: debug
+# :backtrace: 1
+  
+  
+# OpenSSO Authorization
+# set ":server: " to disable A&A
+:authorization:
+  :server: "https://opensso.in-silico.ch"
+  :free_request: #request-method not controlled by A&A
+    - "GET"
+  :authenticate_request: #only for authenticated user
+    - "POST"
+  :authorize_request:  #only for authenticated and authorizeduser
+    - "DELETE"
+    - "PUT"
+  # Exceptions:
+  :free_uris: #request-method for uri not controlled by A&A
+    ? - :GET
+    : - !ruby/regexp /localhost\/algorithm/
+      - "http://localhost/dataset"
+      - "http://localhost/model"
+      - "http://localhost/validation"
+      - "http://localhost/validation/crossvalidation"
+      - "http://localhost/validation/reach_report"      
+      - "http://localhost/validation/reach_report/crossvalidation"
+      - "http://localhost/validation/report"   
+      - "http://localhost/validation/report/crossvalidation"
+      - "http://localhost/validation/reach_report/qmrf"
+    ? - :GET
+      - :POST
+    : - !ruby/regexp /localhost\/toxcreate/
+      - !ruby/regexp /localhost\/task/
+      - !ruby/regexp /localhost\/compound/
+    ? - :PUT
+    : - !ruby/regexp /localhost\/task/
+
+  :authorize_exceptions: #request-method for uri only authenticated, no authorization
+    ? - :POST
+    : - !ruby/regexp /localhost\/algorithm/
+      - "http://localhost/dataset"
+      - "http://localhost/model"
+      - "http://localhost/validation"
+      - !ruby/regexp /localhost\/validation\/[a-z,A-Z,\/,_\-]*$/
+
+  
+  

data/lib/templates/default_guest_policy.xml

@@ -0,0 +1,53 @@
+<!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>

data/lib/templates/default_policy.xml

@@ -0,0 +1,53 @@
+<!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>

data/lib/to-html.rb

@@ -0,0 +1,112 @@
+
+OT_LOGO = "http://opentox.informatik.uni-freiburg.de/ot-logo.png"
+
+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
+end
+
+module OpenTox
+  
+  # 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
+  # @example post params:
+  # [ [ [:mandatory_param_1], [:mandatory_param_2], [:optional_param,"default_value"] ],
+  #   [ [:alteranative_mandatory_param_1], [:alteranative_mandatory_param_2] ]
+  # ] 
+  # @param [String] text this is the actual content, 
+  # @param [optional,String] related_links info on related resources
+  # @param [optional,String] description general info
+  # @param [optional,Array] post_params, array of arrays containing info on POST operation, see example
+  # @return [String] html page
+  def self.text_to_html( text, subjectid=nil, related_links=nil, description=nil, post_params=nil  )
+    
+    # TODO add title as parameter
+    title = nil #$sinatra.url_for($sinatra.request.env['PATH_INFO'], :full) if $sinatra
+    html = "<html>"
+    html += "<title>"+title+"</title>" if title
+    html += "<img src="+OT_LOGO+"><body>"
+      
+    if AA_SERVER
+      user = OpenTox::Authorization.get_user(subjectid) if subjectid
+      html +=  "<pre><p align=\"right\">"
+      unless user
+        html += "You are currently not logged in to "+$url_provider.url_for("",:full)+
+          ", <a href="+$url_provider.url_for("/login",:full)+">login</a>"
+      else
+        html += "You are logged in as '#{user}' to "+$url_provider.url_for("",:full)+
+          ", <a href="+$url_provider.url_for("/logout",:full)+">logout</a>"
+      end
+      html += "  </p></pre>"
+    end 
+   
+    html += "<h3>Description</h3><pre><p>"+description.link_urls+"</p></pre>" if description
+    html += "<h3>Related links</h3><pre><p>"+related_links.link_urls+"</p></pre>" if related_links
+    if post_params
+      html += "<h3>POST parameters</h3>"
+      count = 0
+      post_params.each do |p|
+        html += "<pre><p>alternatively:</p></pre>" if count > 0
+        html += "<pre><p><table><thead><tr><th>param</th><th>default_value</th></tr></thead>"
+        p.each do |k,v|
+          html += "<tr><th>"+k.to_s+"</th><th>"+(v!=nil ? v.to_s : "<i>mandatory</i>")+"</th></tr>"
+        end
+        html += "</table></p></pre>"
+        count += 1
+      end
+    end
+    html += "<h3>Content</h3>" if description || related_links
+    html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
+    html += text.link_urls
+    html += "</p></pre></body><html>"
+    html
+  end
+  
+  def self.login( msg=nil )
+    html = "<html><title>Login</title><img src="+OT_LOGO+"><body>"
+    html += "<form method='POST' action='"+$url_provider.url_for("/login",:full)+"'>"
+    html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
+    html += msg+"\n\n" if msg
+    html += "Please login to "+$url_provider.url_for("",:full)+"\n\n"
+    html += "<table border=0>"
+    html += "<tr><td>user:</td><td><input type='text' name='user' size='15' /></td></tr>"+
+          "<tr><td>password:</td><td><input type='password' name='password' size='15' /></td></tr>"+
+          #"<input type=hidden name=back_to value="+back_to.to_s+">"+
+          "<tr><td><input type='submit' value='Login' /></td></tr>"
+    html += "</table></p></pre></form></body><html>"
+    html
+  end
+end
+
+=begin
+get '/logout/?' do
+  response.set_cookie("subjectid",{:value=>nil})
+  content_type "text/html"
+  content = "Sucessfully logged out from "+$url_provider.url_for("",:full)
+  OpenTox.text_to_html(content)
+end
+
+get '/login/?' do
+  content_type "text/html"
+  OpenTox.login
+end
+
+post '/login/?' do
+  subjectid = OpenTox::Authorization.authenticate(params[:user], params[:password])
+  if (subjectid)
+    response.set_cookie("subjectid",{:value=>subjectid})
+    content_type "text/html"
+    content = "Sucessfully logged in as '"+params[:user]+"' to "+$url_provider.url_for("",:full)
+    OpenTox.text_to_html(content,subjectid)    
+  else
+    content_type "text/html"
+    OpenTox.login("Login failed, please try again")
+  end
+end
+=end
+

data/lib/validation.rb

@@ -1,70 +1,196 @@
 module OpenTox
-	class Validation
+  class Validation
     include OpenTox
-
-		attr_accessor :report_uri, :qmrf_report_uri
-		
-		def self.create_crossvalidation(params)
-			params[:uri] = File.join(CONFIG[:services]['opentox-validation'], "crossvalidation")
-      params[:num_folds] = 10 unless params[:num_folds]
-		 	params[:random_seed] = 2 unless params[:random_seed]
-		 	params[:stratified] = false unless params[:stratified]
-      uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/crossvalidation"),params,nil,false)
-			OpenTox::Validation.new(uri)
-		end
-
-    def create_report
-			@report_uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"), :validation_uris => @uri).to_s
-      @report_uri
+    
+    # find validation, raises error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::Validation]
+    def self.find( uri, subjectid=nil )
+      val = Validation.new(uri)
+      val.load_metadata( subjectid )
+      val
     end
-
-    def create_qmrf_report
-      @qmrf_report_uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), :model_uri => @uri).to_s
-      @qmrf_report_uri
+    
+    # creates a validation object from crossvaldiation statistics, raise error if not found
+    # (as crossvaldiation statistics are returned as an average valdidation over all folds)
+    # @param [String] crossvalidation uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::Validation]
+    def self.from_cv_statistics( crossvalidation_uri, subjectid=nil )
+      find( File.join(crossvalidation_uri, 'statistics'),subjectid )
     end
-
-    def summary(type)
-      v = YAML.load RestClientWrappper.get(File.join(@uri, 'statistics'),:accept => "application/x-yaml").to_s
-
-      case type
-      when "classification"
-        tp=0; tn=0; fp=0; fn=0; n=0
-        v[:classification_statistics][:confusion_matrix][:confusion_matrix_cell].each do |cell|
-          if cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "true"
-            tp = cell[:confusion_matrix_value]
-            n += tp
-          elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "false"
-            tn = cell[:confusion_matrix_value]
-            n += tn
-          elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "true"
-            fn = cell[:confusion_matrix_value]
-            n += fn
-          elsif cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "false"
-            fp = cell[:confusion_matrix_value]
-            n += fp
+    
+    # loads metadata via yaml from validation object
+    # fields (like for example the validated model) can be acces via validation.metadata[OT.model]
+    def load_metadata( subjectid=nil )
+      @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"}))
+    end
+    
+    # PENDING: creates summary as used for ToxCreate
+    def summary
+      if @metadata[OT.classificationStatistics]
+        res = {
+          :nr_predictions => @metadata[OT.numInstances] - @metadata[OT.numUnpredicted],
+          :correct_predictions => @metadata[OT.classificationStatistics][OT.percentCorrect],
+          :weighted_area_under_roc => @metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc],
+        }
+        @metadata[OT.classificationStatistics][OT.classValueStatistics].each do |s|
+          if s[OT.classValue].to_s=="true"
+            res[:true_positives] = s[OT.numTruePositives]
+            res[:false_positives] = s[OT.numFalsePositives]
+            res[:true_negatives] = s[OT.numTrueNegatives]
+            res[:false_negatives] = s[OT.numFalseNegatives]
+            res[:sensitivity] = s[OT.truePositiveRate]
+            res[:specificity] = s[OT.falsePositiveRate]
+            break
           end
         end
+        res
+      elsif @metadata[OT.regressionStatistics]
         {
-          :nr_predictions => n,
-          :true_positives => tp,
-          :false_positives => fp,
-          :true_negatives => tn,
-          :false_negatives => fn,
-          :correct_predictions => 100*(tp+tn).to_f/n,
-          :weighted_area_under_roc => v[:classification_statistics][:weighted_area_under_roc].to_f,
-          :sensitivity => tp.to_f/(tp+fn),
-          :specificity => tn.to_f/(tn+fp),
-        }
-      when "regression"
-        {
-          :nr_predictions => v[:num_instances] - v[:num_unpredicted],
-          :r_square => v[:regression_statistics][:r_square],
-          :root_mean_squared_error => v[:regression_statistics][:root_mean_squared_error],
-          :mean_absolute_error => v[:regression_statistics][:mean_absolute_error],
+          :nr_predictions => @metadata[OT.numInstances] - @metadata[OT.numUnpredicted],
+          :r_square => @metadata[OT.regressionStatistics][OT.rSquare],
+          :root_mean_squared_error => @metadata[OT.regressionStatistics][OT.rootMeanSquaredError],
+          :mean_absolute_error => @metadata[OT.regressionStatistics][OT.meanAbsoluteError],
         }
       end
     end
+  end
+  
+  class Crossvalidation
+    include OpenTox
+
+    attr_reader :report
+    
+    # find crossvalidation, raises error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::Crossvalidation]
+    def self.find( uri, subjectid=nil )
+      cv = Crossvalidation.new(uri)
+      cv.load_metadata( subjectid )
+      cv
+    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 [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::Crossvalidation]
+    def self.create( params, subjectid=nil, waiting_task=nil )
+      params[:subjectid] = subjectid if subjectid
+      uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"crossvalidation"),
+        params,{:content_type => "text/uri-list"},waiting_task )
+      Crossvalidation.new(uri)
+    end
 
-	end
+    # looks for report for this crossvalidation, creates a report if no report is found
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [String] report uri
+    def find_or_create_report( subjectid=nil, waiting_task=nil )
+      @report = CrossvalidationReport.find_for_crossvalidation(@uri, subjectid) unless @report
+      @report = CrossvalidationReport.create(@uri, subjectid, waiting_task) unless @report
+      @report.uri
+    end
+    
+    # loads metadata via yaml from crossvalidation object
+    # fields (like for example the validations) can be acces via validation.metadata[OT.validation]
+    def load_metadata( subjectid=nil )
+      @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"}))
+    end
+    
+    # PENDING: creates summary as used for ToxCreate
+    def summary( subjectid=nil )
+      Validation.from_cv_statistics( @uri, subjectid ).summary
+    end
+  end
+  
+  class ValidationReport
+    include OpenTox
+    
+    # finds ValidationReport for a particular validation
+    # @param [String] crossvalidation uri 
+    # @param [String,optional] subjectid
+    # @return [OpenTox::ValidationReport] nil if no report found
+    def self.find_for_validation( validation_uri, subjectid=nil )
+      uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
+        "/report/validation?validation="+validation_uri), {:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : ValidationReport.new(uris[-1])
+    end
+    
+  end
+
+  class CrossvalidationReport
+    include OpenTox
+    
+    # finds CrossvalidationReport via uri, raises error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::CrossvalidationReport]
+    def self.find( uri, subjectid=nil )
+      # PENDING load report data?
+      OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
+      CrossvalidationReport.new(uri)
+    end
+    
+    # finds CrossvalidationReport for a particular crossvalidation
+    # @param [String] crossvalidation uri 
+    # @param [String,optional] subjectid
+    # @return [OpenTox::CrossvalidationReport] nil if no report found
+    def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil )
+      uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
+        "/report/crossvalidation?crossvalidation="+crossvalidation_uri), {:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : CrossvalidationReport.new(uris[-1])
+    end
+    
+    # creates a crossvalidation report via crossvalidation
+    # @param [String] crossvalidation uri 
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::CrossvalidationReport]
+    def self.create( crossvalidation_uri, subjectid=nil, waiting_task=nil )
+      uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"),
+        { :validation_uris => crossvalidation_uri, :subjectid => subjectid }, {}, waiting_task )
+      CrossvalidationReport.new(uri)
+    end
+  end
+  
+  class QMRFReport
+    include OpenTox
+    
+    # finds QMRFReport, raises Error if not found
+    # @param [String] uri
+    # @param [String,optional] subjectid
+    # @return [OpenTox::QMRFReport]
+    def self.find( uri, subjectid=nil )
+      # PENDING load crossvalidation data?
+      OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
+      QMRFReport.new(uri)
+    end
+    
+    # finds QMRF report for a particular model
+    # @param [String] model_uri 
+    # @param [String,optional] subjectid
+    # @return [OpenTox::QMRFReport] nil if no report found
+    def self.find_for_model( model_uri, subjectid=nil )
+      uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],
+        "/reach_report/qmrf?model="+model_uri), {:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : QMRFReport.new(uris[-1])
+    end
+    
+    # creates a qmrf report via model
+    # @param [String] model_uri 
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::QMRFReport]
+    def self.create( model_uri, subjectid=nil, waiting_task=nil )
+      uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), 
+        { :model_uri => model_uri, :subjectid => subjectid }, {}, waiting_task )
+      QMRFReport.new(uri)
+    end
+  end
+  
 end