From b7e1a4bb8b8e47326928171044c0d7b54d62e278 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 6 Nov 2017 11:21:18 +0000
Subject: added prediction objects;re-ordered code and cleanup

---
 task.rb | 188 +++++++++++-----------------------------------------------------
 1 file changed, 32 insertions(+), 156 deletions(-)

(limited to 'task.rb')

diff --git a/task.rb b/task.rb
index 295e580..9b9ca26 100644
--- a/task.rb
+++ b/task.rb
@@ -1,177 +1,53 @@
 DEFAULT_TASK_MAX_DURATION = 36000
+
 module OpenTox
 
-  # Class for handling asynchronous tasks
   class Task
 
-    attr_accessor :pid, :observer_pid
+    include OpenTox
+    include Mongoid::Document
+    include Mongoid::Timestamps
+    store_in collection: "tasks"
+    field :pid, type: Integer
+    field :percent, type: Float, default: 0
+    field :predictions, type: Hash, default:{}
+    field :csv, type: String
 
-    def metadata
-      super true # always update metadata
-    end
+    attr_accessor :pid, :percent, :predictions, :csv
 
-    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)
+    def pid
+      self[:pid]
     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
+    def percent
+      self[:percent]
     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
+    
+    def predictions
+      self[:predictions]
     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
+    def csv
+      self[:csv]
     end
-    report
-  end
-
-  #TODO: subtasks (only for progress in validation)
-  class SubTask
     
-    def initialize(task, min, max)
-      #TODO add subtask code
+    def update_percent(percent)
+      self[:percent] = percent
+      save
     end
 
-    def self.create(task, min, max)
-      if task
-        SubTask.new(task, min, max)
-      else
-        nil
+    def self.run
+      task = Task.new #uri
+      pid = fork do
+        yield
       end
+      Process.detach(pid)
+      task[:pid] = pid
+      task.save
+      task
     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
+
-- 
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