Merge branch 'feature/opentox-client' into development

7 files changed, 93 insertions, 281 deletions

diff --git a/Gemfile b/Gemfile
new file mode 100644
index 0000000..36f1a90
--- /dev/null
+++ b/Gemfile
@@ -0,0 +1,4 @@
+source :gemcutter
+gemspec
+gem "opentox-server", :path => "~/opentox-server"
+gem "opentox-client", :path => "~/opentox-client"
diff --git a/Rakefile b/Rakefile
new file mode 100644
index 0000000..2995527
--- /dev/null
+++ b/Rakefile
@@ -0,0 +1 @@
+require "bundler/gem_tasks"
diff --git a/VERSION b/VERSION
new file mode 100644
index 0000000..3eefcb9
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+1.0.0
diff --git a/application.rb b/application.rb
index 8c5b81a..e0a33ab 100644
--- a/application.rb
+++ b/application.rb
@@ -1,282 +1,65 @@
-require 'rubygems'
-gem "opentox-ruby", "~> 3"
-require 'opentox-ruby'
-
-set :lock, true
-
-class Task < Ohm::Model
-	
-	attribute :uri
-  attribute :created_at
-
-  attribute :finished_at
-  attribute :due_to_time
-  attribute :pid
-
-  attribute :resultURI
-  attribute :percentageCompleted
-  attribute :hasStatus
-  attribute :title
-  attribute :creator
-  attribute :description
-
-  attribute :waiting_for
-
-  attribute :error_report_yaml
-  
-  # convenience method to store object in redis
-  def errorReport
-    YAML.load(self.error_report_yaml) if self.error_report_yaml
-  end
-
-  # convenience method to store object in redis
-  def errorReport=(er)
-    self.error_report_yaml = er.to_yaml
-  end
-  
-
-  def metadata
-    {
-      DC.creator => creator,
-      DC.title => title,
-      DC.date => created_at,
-      OT.hasStatus => hasStatus,
-      OT.resultURI => resultURI,
-      OT.percentageCompleted => percentageCompleted.to_f,
-      #text fields are lazy loaded, using member variable can cause description to be nil
-      DC.description => description   
-      #:due_to_time => @due_to_timer
-    }
-  end
-
-end
-
-#DataMapper.auto_upgrade!
-
-# Get a list of all tasks
-# @return [text/uri-list] List of all tasks
-get '/?' do
-	LOGGER.debug "list all tasks "+params.inspect
-  if request.env['HTTP_ACCEPT'] =~ /html/
-    response['Content-Type'] = 'text/html'
-    OpenTox.text_to_html Task.all.sort.collect{|t| t.uri}.join("\n") + "\n"
-  else
-    response['Content-Type'] = 'text/uri-list'
-    Task.all.collect{|t| t.uri}.join("\n") + "\n"
-  end
-end
+module OpenTox
+  class Application < Service
+
+    helpers do
+      def status_code uri
+        sparql = "SELECT ?o WHERE { GRAPH <#{uri}> { <#{uri}> <#{RDF::OT.hasStatus}> ?o. } }"
+        status = Backend::FourStore.query(sparql,nil).last.gsub(/"|'/,'').gsub(/\^\^.*$/,'') 
+        case status
+        when "Completed"
+          200
+        when "Running"
+          202
+        when "Cancelled"
+          503
+        when "Error"
+          sparql = "SELECT ?code WHERE { GRAPH <#{uri}> { <#{uri}> <#{RDF::OT.error}> ?error. ?error <#{RDF::OT.statusCode}> ?code } }"
+          code = Backend::FourStore.query(sparql,nil).last.to_i
+          code ? code : 500
+        end
+      end
 
-# Get task representation
-# @param [Header] Accept Mime type of accepted representation, may be one of `application/rdf+xml,application/x-yaml,text/uri-list`
-# @return [application/rdf+xml,application/x-yaml,text/uri-list] Task representation in requested format, Accept:text/uri-list returns URI of the created resource if task status is "Completed"
-get '/:id/?' do
-  task = Task[params[:id]]
-  raise OpenTox::NotFoundError.new "Task '#{params[:id]}' not found." unless task
-  
-  # set task http code according to status
-  case task.hasStatus
-  when "Running"
-    code = 202
-  when "Cancelled"
-    code = 503
-  when "Error"
-    if task.errorReport
-       code = task.errorReport.http_code.to_i
-    else
-     code = 500
     end
-  else #Completed
-    code = 200
-  end
-  
-  case request.env['HTTP_ACCEPT']
-  when /yaml/ 
-    response['Content-Type'] = 'application/x-yaml'
-    metadata = task.metadata
-    metadata[OT.waitingFor] = task.waiting_for
-    metadata[OT.errorReport] = task.errorReport if task.errorReport
-    halt code, metadata.to_yaml
-    #halt code, task.created_at
-  when /html/
-    response['Content-Type'] = 'text/html'
-    metadata = task.metadata
-    description = task.title ? "This task computes '"+task.title+"'" : "This task performs a process that is running on the server."
-    if task.hasStatus=="Running"
-      description << "\nRefresh your browser (presss F5) to see if the task has finished."
-    elsif task.hasStatus=="Completed"
-      description << "\nThe task is completed, click on the link below to see your result."
-    elsif task.errorReport
-      description << "\nUnfortunately, the task has failed."
-    end
-    related_links = task.hasStatus=="Completed" ? "The task result: "+task.resultURI : nil
-    metadata[OT.waitingFor] = task.waiting_for
-    metadata[OT.errorReport] = task.errorReport if task.errorReport
-    halt code, OpenTox.text_to_html(metadata.to_yaml, @subjectid, related_links, description)    
-  when /application\/rdf\+xml|\*\/\*/ # matches 'application/x-yaml', '*/*'
-    response['Content-Type'] = 'application/rdf+xml'
-    t = OpenTox::Task.new task.uri
-    t.add_metadata task.metadata
-    t.add_error_report task.errorReport if task.errorReport
-    halt code, t.to_rdfxml
-  when /text\/uri\-list/
-    response['Content-Type'] = 'text/uri-list'
-    if task.hasStatus=="Completed"
-      halt code, task.resultURI
-    else
-      halt code, task.uri
-    end
-  else
-    raise OpenTox::BadRequestError.new "MIME type '"+request.env['HTTP_ACCEPT'].to_s+"' not supported, valid Accept-Headers are \"application/rdf+xml\" and \"application/x-yaml\"."
-  end
-end
-
-
-# Get Task properties. Works for
-# - /task/id
-# - /task/uri
-# - /task/created_at
-# - /task/finished_at
-# - /task/due_to_time
-# - /task/pid
-# - /task/resultURI
-# - /task/percentageCompleted
-# - /task/hasStatus
-# - /task/title
-# - /task/creator
-# - /task/description
-# @return [String] Task property
-get '/:id/:property/?' do
-	response['Content-Type'] = 'text/plain'
-  task = Task[params[:id]]
-  raise OpenTox::NotFoundError.new"Task #{params[:id]} not found." unless task
-  begin
-    eval("task.#{params[:property]}").to_s
-  rescue
-    raise OpenTox::NotFoundError.new"Unknown task property #{params[:property]}."
-  end
-end
-
-# Create a new task
-# @param [optional,String] max_duration
-# @param [optional,String] pid
-# @param [optional,String] resultURI
-# @param [optional,String] percentageCompleted
-# @param [optional,String] hasStatus
-# @param [optional,String] title
-# @param [optional,String] creator
-# @param [optional,String] description
-# @return [text/uri-list] URI for new task
-post '/?' do
-  LOGGER.debug "Creating new task with params "+params.inspect
-  max_duration = params.delete(:max_duration.to_s) if params.has_key?(:max_duration.to_s)
-  params[:created_at] = Time.now
-  params[:hasStatus] = "Running" unless params[:hasStatus]
-  task = Task.create params
-  task.update :uri => url_for("/#{task.id}", :full)
-  #task.due_to_time = DateTime.parse((Time.parse(task.created_at.to_s) + max_duration.to_f).to_s) if max_duration
-  #raise "Could not save task #{task.uri}" unless task.save
-  response['Content-Type'] = 'text/uri-list'
-  task.uri + "\n"
-end
 
-# Clean tasks. Delete every completed task older than 30 days
-delete '/cleanup' do
-  begin
-    tasklist = Task.all
-    tasklist.each do |task|
-      if task.metadata[OT.hasStatus] == 'Completed'
-        task.delete if Time.now - Time.parse(task.created_at) > 2592000
-      end
+    get '/task/:id/?' do
+      uri = uri("/task/#{params[:id]}")
+      rdf = FourStore.get(uri, request.env['HTTP_ACCEPT'])
+      halt status_code(uri), rdf
     end
-  rescue
-    return false
-  end
-  return true
-end
 
-# Change task status. Possible URIs are: `
-# - /task/Cancelled
-# - /task/Completed: requires taskURI argument
-# - /task/Running
-# - /task/Error
-# - /task/pid: requires pid argument
-# IMPORTANT NOTE: Rack does not accept empty PUT requests. Please send an empty parameter (e.g. with -d '' for curl) or you will receive a "411 Length Required" error.
-# @param [optional, String] resultURI URI of created resource, required for /task/Completed
-# @param [optional, String] pid Task PID, required for /task/pid
-# @param [optional, String] description Task description
-# @param [optional, String] percentageCompleted progress value, can only be set while running
-# @return [] nil
-put '/:id/:hasStatus/?' do
-  
-	task = Task[params[:id]]
-  raise OpenTox::NotFoundError.new"Task #{params[:id]} not found." unless task
-	task.hasStatus = params[:hasStatus] unless /pid/ =~ params[:hasStatus]
-  task.description = params[:description] if params[:description]
-  # error report comes as yaml string
-  task.error_report_yaml = params[:errorReport] if params[:errorReport]
-  
-	case params[:hasStatus]
-	when "Completed"
-		LOGGER.debug "Task " + params[:id].to_s + " completed"
-    raise OpenTox::BadRequestError.new"no param resultURI when completing task" unless params[:resultURI]
-    task.resultURI = params[:resultURI]
-		task.finished_at = DateTime.now
-    task.percentageCompleted = 100
-    task.pid = nil
-  when "pid"
-    task.pid = params[:pid]
-  when "Running"
-    raise OpenTox::BadRequestError.new"Task cannot be set to running after not running anymore" if task.hasStatus!="Running"
-    task.waiting_for = params[:waiting_for] if params.has_key?("waiting_for")
-    if params.has_key?("percentageCompleted")
-      task.percentageCompleted = params[:percentageCompleted].to_f
-      #LOGGER.debug "Task " + params[:id].to_s + " set percentage completed to: "+params[:percentageCompleted].to_s
-    end
-	when /Cancelled|Error/
-    if task.waiting_for and task.waiting_for.uri?
-      # try cancelling the child task
-      begin
-        w = OpenTox::Task.find(task.waiting_for)
-        w.cancel if w.running?
-      rescue
+    put '/task/:id/:status/?' do
+      uri = uri("/task/#{params[:id]}")
+      sparql = []
+      case params[:status]
+      when "Completed"
+        bad_request_error "No resultURI parameter recieved. Cannot complete task '#{uri}' without resultURI." unless params[:resultURI]
+        sparql << "DELETE DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.hasStatus}> \"Running\"}}"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.hasStatus}> \"Completed\"}}"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.resultURI}> <#{params[:resultURI]}>}}"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.percentageCompleted}> \"100.0\"}}"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.finished_at}> \"#{RDF::Literal.new(DateTime.now).to_s}\"}}"
+      when "Running"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.percentageCompleted}> \"#{params["percentageCompleted"].to_f}\"^^#{RDF::XSD.float}}" if params["percentageCompleted"]
+        #task.waiting_for = params[:waiting_for] if params.has_key?("waiting_for")
+      when "Cancelled"
+        sparql << "DELETE DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.hasStatus}> \"Running\"}}"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.hasStatus}> \"Cancelled\"}}"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.finished_at}> \"#{DateTime.now}\"}}"
+      when "Error"
+        sparql << "DELETE DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.hasStatus}> \"Running\"}}"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.hasStatus}> \"Error\"}}"
+        sparql << "INSERT DATA { GRAPH <#{uri}> {<#{uri}> <#{RDF::OT.finished_at}> \"#{DateTime.now}\"}}"
+        id = params[:errorReport].split("\n").first.sub(/^(_:\w+) .*/,'\1')
+        params[:errorReport] += "\n<#{uri}> <#{RDF::OT.error}> #{id} ."
+        Backend::FourStore.post uri, params[:errorReport], "text/plain" if params[:errorReport]
+        #if task.waiting_for and task.waiting_for.uri?
+          # try cancelling the child task
+      else
+         bad_request_error "Invalid status value: '"+params[:status].to_s+"'"
       end
+      sparql.each{|q| Backend::FourStore.update q}
     end
-    LOGGER.debug("Aborting task '"+task.uri.to_s+"' with pid: '"+task.pid.to_s+"'")
-		Process.kill(9,task.pid.to_i) unless task.pid.nil?
-		task.pid = nil
-  else
-     raise OpenTox::BadRequestError.new"Invalid value for hasStatus: '"+params[:hasStatus].to_s+"'"
-  end
-	
-  raise"could not save task" unless task.save
-end
 
-# Delete a task
-# @return [text/plain] Status message
-delete '/:id/?' do
-	task = Task[params[:id]]
-  raise OpenTox::NotFoundError.new "Task #{params[:id]} not found." unless task
-	begin
-		Process.kill(9,task.pid) unless task.pid.nil?
-    task.delete
-    response['Content-Type'] = 'text/plain'
-    "Task #{params[:id]} deleted."
-	rescue
-		raise"Cannot kill task with pid #{task.pid}"
-	end
+  end
 end
 
-# Delete all tasks
-# @return [text/plain] Status message
-delete '/?' do
-	Task.all.each do |task|
-		begin
-			Process.kill(9,task.pid.to_i) unless task.pid.nil?
-      task.delete
-      response['Content-Type'] = 'text/plain'
-      "All tasks deleted."
-		rescue
-			"Cannot kill task with pid #{task.pid}"
-		end
-	end
-end
diff --git a/config.ru b/config.ru
index 8603270..72224f6 100644
--- a/config.ru
+++ b/config.ru
@@ -1,7 +1,5 @@
-require 'rubygems'
-require 'opentox-ruby'
-require 'config/config_ru'
-run Sinatra::Application
-set :raise_errors, false
-set :show_exceptions, false
-
+SERVICE = "task"
+require 'bundler'
+Bundler.require
+require './application.rb'
+run OpenTox::Application
diff --git a/public/robots.txt b/public/robots.txt
deleted file mode 100644
index 1f53798..0000000
--- a/public/robots.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-User-agent: *
-Disallow: /
diff --git a/task.gemspec b/task.gemspec
new file mode 100644
index 0000000..d1ac00d
--- /dev/null
+++ b/task.gemspec
@@ -0,0 +1,27 @@
+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+
+Gem::Specification.new do |s|
+  s.name        = "task"
+  s.version     = File.read("./VERSION")
+  s.authors     = ["Christoph Helma","Denis Gebele","Micha Rautenberg"]
+  s.email       = ["helma@in-silico.ch","gebele@in-silico.ch","rautenenberg@in-silico.ch"]
+  s.homepage    = "http://github.com/OpenTox/task"
+  s.summary     = %q{Toxbank task service}
+  s.description = %q{Toxbank task service}
+  s.license     = 'GPL-3'
+  #s.platform    = Gem::Platform::CURRENT
+
+  s.rubyforge_project = "task"
+
+  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"]
+  s.required_ruby_version = '>= 1.9.2'
+
+  # specify any dependencies here; for example:
+  s.add_runtime_dependency "opentox-server"
+  s.post_install_message = "Please configure your service in ~/.opentox/config/task.rb"
+end
+