fixed cramer

2 files changed, 236 insertions, 40 deletions

diff --git a/application.rb b/application.rb
index b46c5d2..e4b9e38 100644
--- a/application.rb
+++ b/application.rb
@@ -207,49 +207,61 @@ get '/task/?' do
     smiles = compound.smiles
     task = Task.find(params[:predictions].to_s)
     unless task.predictions[params[:model]].nil?
-      html = "<table class=\"table table-bordered single-batch\"><tr>"
-      html += "<td>#{image}</br>#{smiles}</br></td>"
-      string = "<td><table class=\"table\">"
-      prediction = task.predictions[params[:model]][pageNumber.to_i]
-      sorter = []
-      if prediction[:info]
-        sorter << {"Info" => prediction[:info]}
-        if prediction[:measurements_string].kind_of?(Array)
-          sorter << {"Measured activity" => "#{prediction[:measurements_string].join(";")}</br>#{prediction[:converted_measurements].join(";")}"}
-        else
-          sorter << {"Measured activity" => "#{prediction[:measurements_string]}</br>#{prediction[:converted_measurements]}"}
+      if params[:model] == "Cramer"
+        prediction = task.predictions[params[:model]]
+        html = "<table class=\"table table-bordered single-batch\"><tr>"
+        html += "<td>#{image}</br>#{smiles}</br></td>"
+        string = "<td><table class=\"table\">"
+        string += "<tr class=\"hide-top\"><td>Cramer rules:</td><td>#{prediction["Cramer rules"][pageNumber.to_i]}</td>"
+        string += "<tr><td>Cramer rules, with extensions:</td><td>#{prediction["Cramer rules, with extensions"][pageNumber.to_i]}</td>"
+        string += "</table></td>"
+        html += "#{string}</tr></table>"
+      else
+        html = "<table class=\"table table-bordered single-batch\"><tr>"
+        html += "<td>#{image}</br>#{smiles}</br></td>"
+        string = "<td><table class=\"table\">"
+        prediction = task.predictions[params[:model]][pageNumber.to_i]
+        sorter = []
+        $logger.debug prediction
+        if prediction[:info]
+          sorter << {"Info" => prediction[:info]}
+          if prediction[:measurements_string].kind_of?(Array)
+            sorter << {"Measured activity" => "#{prediction[:measurements_string].join(";")}</br>#{prediction[:converted_measurements].join(";")}"}
+          else
+            sorter << {"Measured activity" => "#{prediction[:measurements_string]}</br>#{prediction[:converted_measurements]}"}
+          end
         end
-      end
 
-      # regression
-      if prediction[:prediction_interval]
-        sorter << {"Prediction" => "#{prediction[:prediction_value]}</br>#{prediction[:converted_prediction_value]}"}
-        sorter << {"95% Prediction interval" => "#{prediction[:interval]}</br>#{prediction[:converted_interval]}"}
-        sorter << {"Warnings" => prediction[:warnings].join("</br>")}
-      # classification
-      elsif prediction[:probabilities]
-        sorter << {"Consensus prediction" => prediction["Consensus prediction"]}
-        sorter << {"Consensus confidence" => prediction["Consensus confidence"]}
-        sorter << {"Structural alerts for mutagenicity" => prediction["Structural alerts for mutagenicity"]}
-        sorter << {"Lazar mutagenicity (Salmonella typhimurium)" => ""}
-        sorter << {"Prediction" => prediction[:value]}
-        sorter << {"Probability" => prediction[:probabilities].collect{|k,v| "#{k}: #{v.signif(3)}"}.join("</br>")}
-      else
-        sorter << {"Warnings" => prediction[:warnings].join("</br>")}
-      end
-      sorter.each_with_index do |hash,idx|
-        k = hash.keys[0]
-        v = hash.values[0]
-        string += (idx == 0 ? "<tr class=\"hide-top\">" : "<tr>")+(k =~ /lazar/i ? "<td colspan=\"2\">" : "<td>")
-        # keyword
-        string += "#{k}:"
-        string += "</td><td>"
-        # values
-        string += "#{v}"
-        string += "</td></tr>"
+        # regression
+        if prediction[:prediction_interval]
+          sorter << {"Prediction" => "#{prediction[:prediction_value]}</br>#{prediction[:converted_prediction_value]}"}
+          sorter << {"95% Prediction interval" => "#{prediction[:interval]}</br>#{prediction[:converted_interval]}"}
+          sorter << {"Warnings" => prediction[:warnings].join("</br>")}
+        # classification
+        elsif prediction[:probabilities]
+          sorter << {"Consensus prediction" => prediction["Consensus prediction"]}
+          sorter << {"Consensus confidence" => prediction["Consensus confidence"]}
+          sorter << {"Structural alerts for mutagenicity" => prediction["Structural alerts for mutagenicity"]}
+          sorter << {"Lazar mutagenicity (Salmonella typhimurium)" => ""}
+          sorter << {"Prediction" => prediction[:value]}
+          sorter << {"Probability" => prediction[:probabilities].collect{|k,v| "#{k}: #{v.signif(3)}"}.join("</br>")}
+        else
+          sorter << {"Warnings" => prediction[:warnings].join("</br>")}
+        end
+        sorter.each_with_index do |hash,idx|
+          k = hash.keys[0]
+          v = hash.values[0]
+          string += (idx == 0 ? "<tr class=\"hide-top\">" : "<tr>")+(k =~ /lazar/i ? "<td colspan=\"2\">" : "<td>")
+          # keyword
+          string += "#{k}:"
+          string += "</td><td>"
+          # values
+          string += "#{v}"
+          string += "</td></tr>"
+        end
+        string += "</table></td>"
+        html += "#{string}</tr></table>"
       end
-      string += "</table></td>"
-      html += "#{string}</tr></table>"
     end
     return JSON.pretty_generate(:predictions => [html])
   end
@@ -409,6 +421,13 @@ post '/predict/?' do
               "#{output["cramer_rules"][idx] != "nil" ? output["cramer_rules"][idx] : "none" },"\
               "#{output["cramer_rules_extensions"][idx] != "nil" ? output["cramer_rules_extensions"][idx] : "none"}\n"
           end
+          #predictions = []
+          #predictions << {"Cramer rules" => output["cramer_rules"]}
+          #predictions << {"Cramer rules, with extensions" => output["cramer_rules_extensions"]}
+          predictions = {}
+          predictions["Cramer rules"] = output["cramer_rules"].collect{|rule| rule != "nil" ? rule : "none"}
+          predictions["Cramer rules, with extensions"] = output["cramer_rules_extensions"].collect{|rule| rule != "nil" ? rule : "none"}
+
           # write csv
           t[:csv] = csv
           # write predictions
diff --git a/task.rb b/task.rb
new file mode 100644
index 0000000..295e580
--- /dev/null
+++ b/task.rb
@@ -0,0 +1,177 @@
+DEFAULT_TASK_MAX_DURATION = 36000
+module OpenTox
+
+  # Class for handling asynchronous tasks
+  class Task
+
+    attr_accessor :pid, :observer_pid
+
+    def metadata
+      super true # always update metadata
+    end
+
+    def self.task_uri
+      Task.new.uri
+    end
+
+    def self.run(description, creator=nil, uri=nil)
+
+      task = Task.new uri
+      #task[RDF::OT.created_at] = DateTime.now
+      #task[RDF::OT.hasStatus] = "Running"
+      #task[RDF::DC.description] = description.to_s
+      #task[RDF::DC.creator] = creator.to_s
+      #task[RDF::OT.percentageCompleted] = "0"
+      #task.put
+      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.uri} created by #{creator}" # creator is not logged because error is logged when thrown
+          #RestClientWrapper.put(File.join(task.uri,'Error'),{:errorReport => e.to_ntriples},{:content_type => 'text/plain'})
+          #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.uri}, pid: #{task.pid}"
+      #  end
+      #end
+      #Process.detach(observer_pid)
+      #task.observer_pid = observer_pid
+      #task
+      pid
+
+    end
+
+    def kill
+      Process.kill(9,@pid)
+      Process.kill(9,@observer_pid)
+    rescue # no need to raise an exception if processes are not running
+    end
+
+    def description
+      self.[](RDF::DC.description)
+    end
+
+    def creator
+      self.[](RDF::DC.creator)
+    end
+    
+    def cancel
+      kill
+      self.[]=(RDF::OT.hasStatus, "Cancelled")
+      self.[]=(RDF::OT.finished_at, DateTime.now)
+      put
+    end
+
+    def completed(uri)
+      self.[]=(RDF::OT.resultURI, uri)
+      self.[]=(RDF::OT.hasStatus, "Completed")
+      self.[]=(RDF::OT.finished_at, DateTime.now)
+      self.[]=(RDF::OT.percentageCompleted, "100")
+      put
+    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: '"+@uri.to_s+"'" if (Time.new > due_to_time)
+      end
+    end
+
+  end
+
+  def code
+    RestClientWrapper.get(@uri).code.to_i
+  end
+
+  # get only header for status requests
+  def running?
+    code == 202 
+  end
+
+  def cancelled?
+    code == 503
+  end
+
+  def completed?
+    code == 200
+  end
+
+  def error?
+    code >= 400 and code != 503
+  end
+
+  [:hasStatus, :resultURI, :created_at, :finished_at, :percentageCompleted].each do |method|
+    define_method method do
+      response = self.[](RDF::OT[method])
+      response = self.[](RDF::OT1[method]) unless response  # API 1.1 compatibility
+      response
+    end
+  end
+
+  # Check status of a task
+  # @return [String] Status
+  def status
+    self[RDF::OT.hasStatus]
+  end
+
+  def error_report
+    get
+    report = {}
+    query = RDF::Query.new({
+      :report => {
+        RDF.type  => RDF::OT.ErrorReport,
+        :property => :value,
+      }
+    })
+    query.execute(@rdf).each do |solution|
+      report[solution.property] = solution.value.to_s
+    end
+    report
+  end
+
+  #TODO: subtasks (only for progress in validation)
+  class SubTask
+    
+    def initialize(task, min, max)
+      #TODO add subtask code
+    end
+
+    def self.create(task, min, max)
+      if task
+        SubTask.new(task, min, max)
+      else
+        nil
+      end
+    end
+    
+    def waiting_for(task_uri)
+      #TODO add subtask code
+    end
+    
+    def progress(pct)
+      #TODO add subtask code
+    end
+    
+    def running?()
+      #TODO add subtask code
+    end
+  end
+
+end