From 752ab5cfb8c82570d87f44856850b8c7756f5764 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 25 Aug 2010 14:49:33 +0200
Subject: opentox-api-wrapper bumped to 1.6.6

---
 application.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index fe3d593..d51e0bd 100644
--- a/application.rb
+++ b/application.rb
@@ -1,5 +1,5 @@
 require 'rubygems'
-gem "opentox-ruby-api-wrapper", "= 1.6.5"
+gem "opentox-ruby-api-wrapper", "= 1.6.6"
 require 'opentox-ruby-api-wrapper'
 #require "dm-is-tree"
 
-- 
cgit v1.2.3


From 52c02d588147c16dd0b32a7669324519027dbca2 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 19 Nov 2010 14:42:29 +0100
Subject: lazar predictions and toxcreate are working

---
 application.rb | 90 ++++++++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 72 insertions(+), 18 deletions(-)

diff --git a/application.rb b/application.rb
index d51e0bd..b0f0910 100644
--- a/application.rb
+++ b/application.rb
@@ -1,7 +1,6 @@
 require 'rubygems'
 gem "opentox-ruby-api-wrapper", "= 1.6.6"
 require 'opentox-ruby-api-wrapper'
-#require "dm-is-tree"
 
 class Task
 	include DataMapper::Resource
@@ -19,35 +18,47 @@ class Task
   property :title, String, :length => 255
   property :creator, String, :length => 255
   property :description, Text
+
+  def metadata
+    {
+      DC.creator => @creator,
+      DC.title => @title,
+      DC.date => @created_at,
+      OT.hasStatus => @hasStatus,
+      OT.resultURI => @resultURI,
+      OT.percentageCompleted => @percentageCompleted,
+      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
 	response['Content-Type'] = 'text/uri-list'
 	Task.all(params).collect{|t| t.uri}.join("\n") + "\n"
 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.get(params[:id])
   halt 404, "Task '#{params[:id]}' not found." unless task
-  
-  task_content = {:creator => task.creator, :title => task.title, :date => task.created_at, :hasStatus => task.hasStatus,
-   :resultURI => task.resultURI, :percentageCompleted => task.percentageCompleted, :description => task.description,
-   :due_to_time => task.due_to_time }
-  
   code = task.hasStatus == "Running" ? 202 : 200
   
   case request.env['HTTP_ACCEPT']
-  when /application\/x-yaml|\*\/\*/ # matches 'application/x-yaml', '*/*'
+  when /yaml/ 
     response['Content-Type'] = 'application/x-yaml'
-    task_content[:uri] = task.uri
-    halt code, task_content.to_yaml
-  when /application\/rdf\+xml|\*\/\*/
+    halt code, task.metadata.to_yaml
+  when /application\/rdf\+xml|\*\/\*/ # matches 'application/x-yaml', '*/*'
     response['Content-Type'] = 'application/rdf+xml'
-    owl = OpenTox::Owl.create 'Task', task.uri
-    task_content.each{ |k,v| owl.set(k.to_s,v)}
-    halt code, owl.rdf
+    t = OpenTox::Task.new task.uri
+    t.add_metadata task.metadata
+    halt code, t.to_rdfxml
   when /text\/uri\-list/
     response['Content-Type'] = 'text/uri-list'
     halt code, task.resultURI
@@ -56,26 +67,65 @@ get '/:id/?' do
   end
 end
 
-# dynamic access to Task properties
+# 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.get(params[:id])
   halt 404,"Task #{params[:id]} not found." unless task
-	eval("task.#{params[:property]}").to_s
+  begin
+    eval("task.#{params[:property]}").to_s
+  rescue
+    halt 404,"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)
-  task = Task.new(params)
-  task.save # needed to create id
+  task = Task.create(params)
+  #task.save # needed to create id
+  #LOGGER.debug task.uri
   task.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" unless task.save
+  raise "Could not save task #{task.uri}" unless task.save
   response['Content-Type'] = 'text/uri-list'
   task.uri + "\n"
 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
+# @return [] nil
 put '/:id/:hasStatus/?' do
   
 	task = Task.get(params[:id])
@@ -103,6 +153,8 @@ put '/:id/:hasStatus/?' do
     
 end
 
+# Delete a task
+# @return [text/plain] Status message
 delete '/:id/?' do
 	task = Task.get(params[:id])
   halt 404, "Task #{params[:id]} not found." unless task
@@ -116,6 +168,8 @@ delete '/:id/?' do
 	"Task #{params[:id]} deleted."
 end
 
+# Delete all tasks
+# @return [text/plain] Status message
 delete '/?' do
 	Task.all.each do |task|
 		begin
-- 
cgit v1.2.3


From ca6611821f7fca8d2fee77c63320113589e77d91 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 24 Nov 2010 11:48:32 +0100
Subject: status 503 for rejected tasks

---
 application.rb | 2 --
 1 file changed, 2 deletions(-)

diff --git a/application.rb b/application.rb
index b0f0910..e7ec409 100644
--- a/application.rb
+++ b/application.rb
@@ -106,8 +106,6 @@ 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)
   task = Task.create(params)
-  #task.save # needed to create id
-  #LOGGER.debug task.uri
   task.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
-- 
cgit v1.2.3


From f522ed3edf73fdcdaccf75e6b6c21f3b2da9fe87 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 24 Nov 2010 13:10:52 +0100
Subject: opentox-ruby-api-wrapper renamed to opentox-ruby

---
 application.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/application.rb b/application.rb
index e7ec409..ffda10d 100644
--- a/application.rb
+++ b/application.rb
@@ -1,6 +1,6 @@
 require 'rubygems'
-gem "opentox-ruby-api-wrapper", "= 1.6.6"
-require 'opentox-ruby-api-wrapper'
+gem "opentox-ruby", "~> 0"
+require 'opentox-ruby'
 
 class Task
 	include DataMapper::Resource
-- 
cgit v1.2.3


From 2ce3efc21035e622c14688ec8bb4129982f4b0c0 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 24 Nov 2010 14:43:20 +0100
Subject: opentox-ruby gem in config.ru

---
 config.ru | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config.ru b/config.ru
index 489932f..8f73955 100644
--- a/config.ru
+++ b/config.ru
@@ -1,5 +1,5 @@
 require 'rubygems'
-require 'opentox-ruby-api-wrapper'
+require 'opentox-ruby'
 require 'config/config_ru'
 run Sinatra::Application
 
-- 
cgit v1.2.3


From c89ceb400345efbc4c47e722e7dfa0938f013aab Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Thu, 13 Jan 2011 14:17:25 +0100
Subject: fix description loading

---
 application.rb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/application.rb b/application.rb
index ffda10d..91590a3 100644
--- a/application.rb
+++ b/application.rb
@@ -27,7 +27,8 @@ class Task
       OT.hasStatus => @hasStatus,
       OT.resultURI => @resultURI,
       OT.percentageCompleted => @percentageCompleted,
-      DC.description => @description,
+      #text fields are lazy loaded, using member variable can cause description to be nil
+      DC.description => description   
       #:due_to_time => @due_to_timer
     }
   end
@@ -148,7 +149,7 @@ put '/:id/:hasStatus/?' do
   end
 	
   halt 500,"could not save task" unless task.save
-    
+
 end
 
 # Delete a task
-- 
cgit v1.2.3


From a5eb942ea6eb61052d1873668c78fe329b7117e0 Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Fri, 14 Jan 2011 15:00:55 +0100
Subject: set percentage completed

---
 application.rb | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/application.rb b/application.rb
index 91590a3..917a6f1 100644
--- a/application.rb
+++ b/application.rb
@@ -39,8 +39,9 @@ DataMapper.auto_upgrade!
 # Get a list of all tasks
 # @return [text/uri-list] List of all tasks
 get '/?' do
-	response['Content-Type'] = 'text/uri-list'
-	Task.all(params).collect{|t| t.uri}.join("\n") + "\n"
+	LOGGER.debug "list all tasks "+params.inspect
+  response['Content-Type'] = 'text/uri-list'
+  Task.all(params).collect{|t| t.uri}.join("\n") + "\n"
 end
 
 # Get task representation
@@ -124,6 +125,7 @@ end
 # @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
   
@@ -138,9 +140,14 @@ put '/:id/:hasStatus/?' do
     halt 402,"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"
+    halt 400,"Task cannot be set to running after not running anymore" if task.hasStatus!="Running"
+    task.percentageCompleted = params[:percentageCompleted].to_f
+    LOGGER.debug "Task " + params[:id].to_s + " set percentage completed to: "+params[:percentageCompleted].to_s
 	when /Cancelled|Error/
 		Process.kill(9,task.pid) unless task.pid.nil?
 		task.pid = nil
-- 
cgit v1.2.3


From b7a88400107c1985f60060499e0e28b156d91a33 Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Thu, 20 Jan 2011 11:30:25 +0100
Subject: disable sinatra built in error handling to allow new ot error
 handling

---
 config.ru | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/config.ru b/config.ru
index 8f73955..8603270 100644
--- a/config.ru
+++ b/config.ru
@@ -2,4 +2,6 @@ require 'rubygems'
 require 'opentox-ruby'
 require 'config/config_ru'
 run Sinatra::Application
+set :raise_errors, false
+set :show_exceptions, false
 
-- 
cgit v1.2.3


From 4ab0164d5295e5d9665e205a221edfa977997a58 Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Fri, 21 Jan 2011 12:11:01 +0100
Subject: html support for tasks

---
 application.rb | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/application.rb b/application.rb
index 917a6f1..1cd32e0 100644
--- a/application.rb
+++ b/application.rb
@@ -40,8 +40,13 @@ DataMapper.auto_upgrade!
 # @return [text/uri-list] List of all tasks
 get '/?' do
 	LOGGER.debug "list all tasks "+params.inspect
-  response['Content-Type'] = 'text/uri-list'
-  Task.all(params).collect{|t| t.uri}.join("\n") + "\n"
+  if request.env['HTTP_ACCEPT'] =~ /html/
+    response['Content-Type'] = 'text/html'
+    OpenTox.text_to_html Task.all(params).collect{|t| t.uri}.join("\n") + "\n"
+  else
+    response['Content-Type'] = 'text/uri-list'
+    Task.all(params).collect{|t| t.uri}.join("\n") + "\n"
+  end
 end
 
 # Get task representation
@@ -56,6 +61,9 @@ get '/:id/?' do
   when /yaml/ 
     response['Content-Type'] = 'application/x-yaml'
     halt code, task.metadata.to_yaml
+  when /html/
+    response['Content-Type'] = 'text/html'
+    halt code, OpenTox.text_to_html(task.metadata.to_yaml)    
   when /application\/rdf\+xml|\*\/\*/ # matches 'application/x-yaml', '*/*'
     response['Content-Type'] = 'application/rdf+xml'
     t = OpenTox::Task.new task.uri
-- 
cgit v1.2.3


From 4c845ae7305fd5c71f79747f5f7d963edd4f4d22 Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Mon, 24 Jan 2011 17:23:16 +0100
Subject: adding field errorReport to task

---
 application.rb | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/application.rb b/application.rb
index 1cd32e0..bb16e19 100644
--- a/application.rb
+++ b/application.rb
@@ -18,6 +18,8 @@ class Task
   property :title, String, :length => 255
   property :creator, String, :length => 255
   property :description, Text
+  
+  property :errorReport, Object
 
   def metadata
     {
@@ -60,14 +62,19 @@ get '/:id/?' do
   case request.env['HTTP_ACCEPT']
   when /yaml/ 
     response['Content-Type'] = 'application/x-yaml'
-    halt code, task.metadata.to_yaml
+    metadata = task.metadata
+    metadata[OT.errorReport] = task.errorReport if task.errorReport
+    halt code, metadata.to_yaml
   when /html/
     response['Content-Type'] = 'text/html'
-    halt code, OpenTox.text_to_html(task.metadata.to_yaml)    
+    metadata = task.metadata
+    metadata[OT.errorReport] = task.errorReport if task.errorReport
+    halt code, OpenTox.text_to_html(metadata.to_yaml)    
   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'
@@ -137,10 +144,12 @@ end
 # @return [] nil
 put '/:id/:hasStatus/?' do
   
+  LOGGER.debug "put to task "+params.inspect
 	task = Task.get(params[:id])
   halt 404,"Task #{params[:id]} not found." unless task
 	task.hasStatus = params[:hasStatus] unless /pid/ =~ params[:hasStatus]
   task.description = params[:description] if params[:description]
+  task.errorReport = YAML.load(params[:errorReport]) if params[:errorReport]
   
 	case params[:hasStatus]
 	when "Completed"
-- 
cgit v1.2.3


From 39c988fe6fc4798690c0d6a4e0fa52bb097f670b Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Mon, 24 Jan 2011 19:33:14 +0100
Subject: fix task-with-error-report to rdf

---
 application.rb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/application.rb b/application.rb
index bb16e19..8dbd9fb 100644
--- a/application.rb
+++ b/application.rb
@@ -74,8 +74,8 @@ get '/:id/?' do
     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
+    t.add_error_report task.errorReport
+    halt t.to_rdfxml
   when /text\/uri\-list/
     response['Content-Type'] = 'text/uri-list'
     halt code, task.resultURI
@@ -84,6 +84,7 @@ get '/:id/?' do
   end
 end
 
+
 # Get Task properties. Works for
 # - /task/id
 # - /task/uri
-- 
cgit v1.2.3


From dce8c014595c85e991b001718fd2d5e8df7c5562 Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Tue, 8 Feb 2011 16:57:19 +0100
Subject: add waiting_for field for tasks

---
 application.rb | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/application.rb b/application.rb
index 8dbd9fb..f8c0e1f 100644
--- a/application.rb
+++ b/application.rb
@@ -19,6 +19,8 @@ class Task
   property :creator, String, :length => 255
   property :description, Text
   
+  property :waiting_for, String, :length => 255
+  
   property :errorReport, Object
 
   def metadata
@@ -63,11 +65,13 @@ get '/:id/?' do
   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
   when /html/
     response['Content-Type'] = 'text/html'
     metadata = task.metadata
+    metadata[OT.waitingFor] = task.waiting_for
     metadata[OT.errorReport] = task.errorReport if task.errorReport
     halt code, OpenTox.text_to_html(metadata.to_yaml)    
   when /application\/rdf\+xml|\*\/\*/ # matches 'application/x-yaml', '*/*'
@@ -145,7 +149,6 @@ end
 # @return [] nil
 put '/:id/:hasStatus/?' do
   
-  LOGGER.debug "put to task "+params.inspect
 	task = Task.get(params[:id])
   halt 404,"Task #{params[:id]} not found." unless task
 	task.hasStatus = params[:hasStatus] unless /pid/ =~ params[:hasStatus]
@@ -164,9 +167,14 @@ put '/:id/:hasStatus/?' do
     task.pid = params[:pid]
   when "Running"
     halt 400,"Task cannot be set to running after not running anymore" if task.hasStatus!="Running"
-    task.percentageCompleted = params[:percentageCompleted].to_f
-    LOGGER.debug "Task " + params[:id].to_s + " set percentage completed to: "+params[:percentageCompleted].to_s
+    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/
+    OpenTox::Task.find(task.waiting_for).cancel if task.waiting_for
+    LOGGER.debug("Aborting task "+task.uri.to_s)
 		Process.kill(9,task.pid) unless task.pid.nil?
 		task.pid = nil
   else
-- 
cgit v1.2.3


From 532ebf4d2e88b6ad982d5e4830a129f374f26bc6 Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Wed, 9 Feb 2011 14:08:25 +0100
Subject: fix check for waiting_for

---
 application.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index f8c0e1f..47cafa5 100644
--- a/application.rb
+++ b/application.rb
@@ -173,7 +173,7 @@ put '/:id/:hasStatus/?' do
       #LOGGER.debug "Task " + params[:id].to_s + " set percentage completed to: "+params[:percentageCompleted].to_s
     end
 	when /Cancelled|Error/
-    OpenTox::Task.find(task.waiting_for).cancel if task.waiting_for
+    OpenTox::Task.find(task.waiting_for).cancel if task.waiting_for and task.waiting_for.uri?
     LOGGER.debug("Aborting task "+task.uri.to_s)
 		Process.kill(9,task.pid) unless task.pid.nil?
 		task.pid = nil
-- 
cgit v1.2.3


From 1ea65758e446503c6202696580579ed1f994ce4e Mon Sep 17 00:00:00 2001
From: mguetlein <martin.guetlein@gmail.com>
Date: Thu, 10 Feb 2011 16:42:05 +0100
Subject: cancel child task in begin rescue block

---
 application.rb | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index 47cafa5..289ce8d 100644
--- a/application.rb
+++ b/application.rb
@@ -173,7 +173,14 @@ put '/:id/:hasStatus/?' do
       #LOGGER.debug "Task " + params[:id].to_s + " set percentage completed to: "+params[:percentageCompleted].to_s
     end
 	when /Cancelled|Error/
-    OpenTox::Task.find(task.waiting_for).cancel if task.waiting_for and task.waiting_for.uri?
+    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
+      end
+    end
     LOGGER.debug("Aborting task "+task.uri.to_s)
 		Process.kill(9,task.pid) unless task.pid.nil?
 		task.pid = nil
-- 
cgit v1.2.3


From 2dbb5523ea01a2bdec49b5c4403e0f07fb687870 Mon Sep 17 00:00:00 2001
From: root <root@ot-dev.in-silico.ch>
Date: Thu, 24 Feb 2011 11:30:27 +0000
Subject: set :lock, true added

---
 application.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/application.rb b/application.rb
index 289ce8d..f52094c 100644
--- a/application.rb
+++ b/application.rb
@@ -2,6 +2,8 @@ require 'rubygems'
 gem "opentox-ruby", "~> 0"
 require 'opentox-ruby'
 
+set :lock, true
+
 class Task
 	include DataMapper::Resource
 	property :id, Serial
-- 
cgit v1.2.3


From fb36679903857a42b2eaa3efdf081fb7cfa74c32 Mon Sep 17 00:00:00 2001
From: root <root@ot-dev.in-silico.ch>
Date: Fri, 25 Feb 2011 17:52:36 +0000
Subject: ohm/redis backend

---
 application.rb | 95 +++++++++++++++++++++++++++++++++-------------------------
 1 file changed, 54 insertions(+), 41 deletions(-)

diff --git a/application.rb b/application.rb
index f52094c..446ac86 100644
--- a/application.rb
+++ b/application.rb
@@ -4,43 +4,53 @@ require 'opentox-ruby'
 
 set :lock, true
 
-class Task
-	include DataMapper::Resource
-	property :id, Serial
-	property :uri, String, :length => 255
-  property :created_at, DateTime
-  
-  property :finished_at, DateTime
-  property :due_to_time, DateTime
-  property :pid, Integer
-  
-  property :resultURI, String, :length => 255
-  property :percentageCompleted, Float, :default => 0
-  property :hasStatus, String, :default => "Running" #possible states are: "Cancelled", "Completed", "Running", "Error"
-  property :title, String, :length => 255
-  property :creator, String, :length => 255
-  property :description, Text
-  
-  property :waiting_for, String, :length => 255
-  
-  property :errorReport, Object
+class Task < Ohm::Model
+	#include DataMapper::Resource
+	#property :id, Serial
+	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 :errorReport
 
   def metadata
     {
-      DC.creator => @creator,
-      DC.title => @title,
-      DC.date => @created_at,
-      OT.hasStatus => @hasStatus,
-      OT.resultURI => @resultURI,
-      OT.percentageCompleted => @percentageCompleted,
+      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
+
+=begin
+  def id
+    self.id.to_i
+  end
+  def self.create(params)
+    params[:created_at] = Time.now
+    super(params)
+  end
+=end
 end
 
-DataMapper.auto_upgrade!
+#DataMapper.auto_upgrade!
 
 # Get a list of all tasks
 # @return [text/uri-list] List of all tasks
@@ -48,10 +58,10 @@ 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(params).collect{|t| t.uri}.join("\n") + "\n"
+    OpenTox.text_to_html Task.all.collect{|t| t.uri}.join("\n") + "\n"
   else
     response['Content-Type'] = 'text/uri-list'
-    Task.all(params).collect{|t| t.uri}.join("\n") + "\n"
+    Task.all.collect{|t| t.uri}.join("\n") + "\n"
   end
 end
 
@@ -59,7 +69,7 @@ end
 # @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.get(params[:id])
+  task = Task[params[:id]]
   halt 404, "Task '#{params[:id]}' not found." unless task
   code = task.hasStatus == "Running" ? 202 : 200
   
@@ -70,6 +80,7 @@ get '/:id/?' do
     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
@@ -107,7 +118,7 @@ end
 # @return [String] Task property
 get '/:id/:property/?' do
 	response['Content-Type'] = 'text/plain'
-  task = Task.get(params[:id])
+  task = Task[params[:id]]
   halt 404,"Task #{params[:id]} not found." unless task
   begin
     eval("task.#{params[:property]}").to_s
@@ -129,10 +140,11 @@ end
 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)
-  task = Task.create(params)
-  task.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
+  #LOGGER.debug "PARAMS: #{params.inspect}"
+  task = Task.create :created_at => Time.now, :hasStatus => "Running"
+  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
@@ -151,7 +163,7 @@ end
 # @return [] nil
 put '/:id/:hasStatus/?' do
   
-	task = Task.get(params[:id])
+	task = Task[params[:id]]
   halt 404,"Task #{params[:id]} not found." unless task
 	task.hasStatus = params[:hasStatus] unless /pid/ =~ params[:hasStatus]
   task.description = params[:description] if params[:description]
@@ -184,7 +196,7 @@ put '/:id/:hasStatus/?' do
       end
     end
     LOGGER.debug("Aborting task "+task.uri.to_s)
-		Process.kill(9,task.pid) unless task.pid.nil?
+		Process.kill(9,task.pid.to_i) unless task.pid.nil?
 		task.pid = nil
   else
      halt 402,"Invalid value for hasStatus: '"+params[:hasStatus].to_s+"'"
@@ -197,14 +209,14 @@ end
 # Delete a task
 # @return [text/plain] Status message
 delete '/:id/?' do
-	task = Task.get(params[:id])
+	task = Task[params[:id]]
   halt 404, "Task #{params[:id]} not found." unless task
 	begin
 		Process.kill(9,task.pid) unless task.pid.nil?
 	rescue
 		halt 500,"Cannot kill task with pid #{task.pid}"
 	end
-	task.destroy!
+	task.delete
 	response['Content-Type'] = 'text/plain'
 	"Task #{params[:id]} deleted."
 end
@@ -214,13 +226,14 @@ end
 delete '/?' do
 	Task.all.each do |task|
 		begin
-			Process.kill(9,task.pid) unless task.pid.nil?
+			Process.kill(9,task.pid.to_i) unless task.pid.nil?
+      task.delete
 		rescue
 			"Cannot kill task with pid #{task.pid}"
 		end
 		#task.destroy!
 	end
-  Task.auto_migrate!
+  #Task.auto_migrate!
 	response['Content-Type'] = 'text/plain'
 	"All tasks deleted."
 end
-- 
cgit v1.2.3


From 1cce5f19131e8b0b36a69ba96543e046d928d43b Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Sun, 27 Feb 2011 09:32:57 +0100
Subject: code cleanup

---
 application.rb | 29 +++++++++--------------------
 1 file changed, 9 insertions(+), 20 deletions(-)

diff --git a/application.rb b/application.rb
index 446ac86..5ad846d 100644
--- a/application.rb
+++ b/application.rb
@@ -5,8 +5,7 @@ require 'opentox-ruby'
 set :lock, true
 
 class Task < Ohm::Model
-	#include DataMapper::Resource
-	#property :id, Serial
+	
 	attribute :uri
   attribute :created_at
 
@@ -39,15 +38,6 @@ class Task < Ohm::Model
     }
   end
 
-=begin
-  def id
-    self.id.to_i
-  end
-  def self.create(params)
-    params[:created_at] = Time.now
-    super(params)
-  end
-=end
 end
 
 #DataMapper.auto_upgrade!
@@ -140,8 +130,9 @@ end
 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)
-  #LOGGER.debug "PARAMS: #{params.inspect}"
-  task = Task.create :created_at => Time.now, :hasStatus => "Running"
+  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
@@ -213,12 +204,12 @@ delete '/:id/?' do
   halt 404, "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
 		halt 500,"Cannot kill task with pid #{task.pid}"
 	end
-	task.delete
-	response['Content-Type'] = 'text/plain'
-	"Task #{params[:id]} deleted."
 end
 
 # Delete all tasks
@@ -228,12 +219,10 @@ delete '/?' do
 		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
-		#task.destroy!
 	end
-  #Task.auto_migrate!
-	response['Content-Type'] = 'text/plain'
-	"All tasks deleted."
 end
-- 
cgit v1.2.3


From 0917543b4fb73b4049338790561af7fdf050d50b Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 3 Mar 2011 12:39:23 +0100
Subject: serialized error report

---
 application.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index 5ad846d..7db4ce9 100644
--- a/application.rb
+++ b/application.rb
@@ -158,7 +158,8 @@ put '/:id/:hasStatus/?' do
   halt 404,"Task #{params[:id]} not found." unless task
 	task.hasStatus = params[:hasStatus] unless /pid/ =~ params[:hasStatus]
   task.description = params[:description] if params[:description]
-  task.errorReport = YAML.load(params[:errorReport]) if params[:errorReport]
+  #task.errorReport = YAML.load(params[:errorReport]) if params[:errorReport]
+  task.errorReport = params[:errorReport] if params[:errorReport]
   
 	case params[:hasStatus]
 	when "Completed"
-- 
cgit v1.2.3


From 8be3ffc4c58dfccf43d6b216fe23dabbf0bd1e2c Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 9 Mar 2011 12:00:09 +0100
Subject: version bumped to 1.0.0

---
 application.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/application.rb b/application.rb
index 7db4ce9..673cc4d 100644
--- a/application.rb
+++ b/application.rb
@@ -1,5 +1,5 @@
 require 'rubygems'
-gem "opentox-ruby", "~> 0"
+gem "opentox-ruby", "~> 1"
 require 'opentox-ruby'
 
 set :lock, true
-- 
cgit v1.2.3


From 97821ad3851177f54e1999159ebf0b9987d40a27 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 10 Mar 2011 11:58:12 +0100
Subject: README updated

---
 README | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/README b/README
index 9eb993f..7122ccf 100644
--- a/README
+++ b/README
@@ -4,7 +4,8 @@ OpenTox Task
 * An OpenTox REST Webservice (http://www.opentox.org)
 * Does _not_ comply to the (incomplete) OpenTox API
 
-REST operations:
+REST operations
+---------------
 
 Get a list of all tasks     GET     /                 -                       Task URIs                             200
 Get the status of a  task   GET     /{id}/status      -                       created|started|completed|cancelled   200,404
@@ -17,10 +18,12 @@ Cancel a  task              PUT     /{id}/cancelled   ""                      -
 Delete a  task              DELETE  /{id}             -                       -                                     200, 404
 Delete all  tasks           DELETE  /                 -                       -                                     200
 
-IMPORTANT NOTE: My framework 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.
+IMPORTANT NOTE: Our framework 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.
 
-More documentation: Source code (application.rb)
+API documentation
+-----------------
 
-Copyright (c) 2009 Christoph Helma. See LICENSE for details.
+http://rdoc.info/github/opentox/task
 
+Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.
 
-- 
cgit v1.2.3