opentox-ruby-api-wrapper 1.6.0 → 1.6.1

data/lib/task.rb

@@ -23,9 +23,9 @@ module OpenTox
 		end
 
     public
-		def self.find(uri)
+    def self.find( uri, accept_header='application/rdf+xml' )
       task = Task.new(uri)
-      task.reload
+      task.reload( accept_header )
       return task
     end
     
@@ -36,8 +36,8 @@ module OpenTox
       return task
     end
     
-    def reload
-      result = RestClientWrapper.get(uri, {:accept => 'application/rdf+xml'}, false)#'application/x-yaml'})
+    def reload( accept_header='application/rdf+xml' )
+      result = RestClientWrapper.get(uri, {:accept => accept_header}, false)#'application/x-yaml'})
       @http_code = result.code
       reload_from_data(result, result.content_type, uri)
     end
@@ -95,8 +95,8 @@ module OpenTox
 		def wait_for_completion(dur=0.3)
       
       if (@uri.match(@@config[:services]["opentox-task"]))
-        due_to_time = Time.parse(@due_to_time)
-        running_time = due_to_time - Time.parse(@date)
+        due_to_time = (@due_to_time.is_a?(Time) ? @due_to_time : Time.parse(@due_to_time))
+        running_time = due_to_time - (@date.is_a?(Time) ? @date : Time.parse(@date))
       else
         # the date of the external task cannot be trusted, offest to local time might be to big
         due_to_time = Time.new + EXTERNAL_TASK_MAX_DURATION

data/lib/templates/config.yaml

@@ -4,12 +4,12 @@
 #
 # Example MySql:
 #
- :database: 
-   :adapter:  mysql
-   :database: production
-   :username: root
-   :password: opentox
-   :host:     localhost
+:database: 
+  :adapter:  mysql
+  :database: production
+  :username: root
+  :password: opentox
+  :host:     localhost
 #
 # Example 1: Using external test services
 #
@@ -22,42 +22,44 @@
 #  opentox-validation:    "http://opentox.informatik.uni-freiburg.de/validation/"
 #
 # Example 2: Using local services
- :base_dir: /home/ist/webservices
- :webserver: passenger
- :services:
-   opentox-compound:      "http://localhost/compound/"
-   opentox-dataset:       "http://localhost/dataset/"
-   opentox-algorithm:     "http://localhost/algorithm/"
-   opentox-model:         "http://localhost/model/"
-   opentox-task:          "http://localhost/task/"
-   opentox-validation:    "http://localhost/validation/"
+:base_dir: /home/ist/webservices
+:webserver: passenger
+:services:
+  opentox-compound:      "http://localhost/compound/"
+  opentox-dataset:       "http://localhost/dataset/"
+  opentox-algorithm:     "http://localhost/algorithm/"
+  opentox-model:         "http://localhost/model/"
+  opentox-task:          "http://localhost/task/"
+  opentox-validation:    "http://localhost/validation/"
 #
 # Accept headers:
 #
- :accept_headers:
-   opentox-compound:      
-     - "chemical/x-daylight-smiles"
-     - "chemical/x-inchi"
-     - "chemical/x-mdl-sdfile"
-     - "image/gif"
-     - "text/plain"
-   opentox-dataset:       
-     - "application/x-yaml"
-     - "application/rdf+xml"
-   opentox-algorithm:     
-     - "application/x-yaml"
-     - "application/rdf+xml"
-   opentox-model:         
-     - "application/x-yaml"
-     - "application/rdf+xml"
-   opentox-task:          
-     - "application/x-yaml"
-     - "application/rdf+xml"
-   opentox-validation:    
-     - "application/x-yaml"
-     - "application/rdf+xml"
+:accept_headers:
+  opentox-compound:      
+    - "chemical/x-daylight-smiles"
+    - "chemical/x-inchi"
+    - "chemical/x-mdl-sdfile"
+    - "image/gif"
+    - "text/plain"
+  opentox-dataset:       
+    - "application/x-yaml"
+    - "application/rdf+xml"
+  opentox-algorithm:     
+    - "application/x-yaml"
+    - "application/rdf+xml"
+  opentox-model:         
+    - "application/x-yaml"
+    - "application/rdf+xml"
+  opentox-task:          
+    - "application/x-yaml"
+    - "application/rdf+xml"
+  opentox-validation:    
+    - "application/x-yaml"
+    - "application/rdf+xml"
 
 # Timeouts:
-# 
- :default_task_max_duration: 3600
- :external_task_max_duration: 3600
+:default_task_max_duration: 3600
+:external_task_max_duration: 3600
+
+# Uncomment for verbose logging
+# :logger: debug

data/lib/utils.rb

@@ -28,6 +28,13 @@ module OpenTox
         return false
       end
     end
+    
+    def self.median(array)
+      return nil if array.empty?
+      array.sort!
+      m_pos = array.size / 2
+      return array.size % 2 == 1 ? array[m_pos] : (array[m_pos-1] + array[m_pos])/2
+    end
   
   end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  hash: 15
+  hash: 13
   prerelease: false
   segments: 
   - 1
   - 6
-  - 0
-  version: 1.6.0
+  - 1
+  version: 1.6.1
 platform: ruby
 authors: 
 - Christoph Helma, Martin Guetlein
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-07-19 00:00:00 +02:00
+date: 2010-08-09 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -243,21 +243,21 @@ dependencies:
   type: :runtime
   version_requirements: *id016
 - !ruby/object:Gem::Dependency 
-  name: dm-core
+  name: rjb
   prerelease: false
   requirement: &id017 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 1
+        hash: 3
         segments: 
-        - 1
-        version: "1"
+        - 0
+        version: "0"
   type: :runtime
   version_requirements: *id017
 - !ruby/object:Gem::Dependency 
-  name: dm-serializer
+  name: dm-core
   prerelease: false
   requirement: &id018 !ruby/object:Gem::Requirement 
     none: false
@@ -271,7 +271,7 @@ dependencies:
   type: :runtime
   version_requirements: *id018
 - !ruby/object:Gem::Dependency 
-  name: dm-timestamps
+  name: dm-serializer
   prerelease: false
   requirement: &id019 !ruby/object:Gem::Requirement 
     none: false
@@ -285,7 +285,7 @@ dependencies:
   type: :runtime
   version_requirements: *id019
 - !ruby/object:Gem::Dependency 
-  name: dm-types
+  name: dm-timestamps
   prerelease: false
   requirement: &id020 !ruby/object:Gem::Requirement 
     none: false
@@ -299,7 +299,7 @@ dependencies:
   type: :runtime
   version_requirements: *id020
 - !ruby/object:Gem::Dependency 
-  name: dm-migrations
+  name: dm-types
   prerelease: false
   requirement: &id021 !ruby/object:Gem::Requirement 
     none: false
@@ -313,7 +313,7 @@ dependencies:
   type: :runtime
   version_requirements: *id021
 - !ruby/object:Gem::Dependency 
-  name: dm-mysql-adapter
+  name: dm-migrations
   prerelease: false
   requirement: &id022 !ruby/object:Gem::Requirement 
     none: false
@@ -327,9 +327,23 @@ dependencies:
   type: :runtime
   version_requirements: *id022
 - !ruby/object:Gem::Dependency 
-  name: haml
+  name: dm-mysql-adapter
   prerelease: false
   requirement: &id023 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 1
+        segments: 
+        - 1
+        version: "1"
+  type: :runtime
+  version_requirements: *id023
+- !ruby/object:Gem::Dependency 
+  name: haml
+  prerelease: false
+  requirement: &id024 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -339,11 +353,11 @@ dependencies:
         - 3
         version: "3"
   type: :runtime
-  version_requirements: *id023
+  version_requirements: *id024
 - !ruby/object:Gem::Dependency 
   name: cucumber
   prerelease: false
-  requirement: &id024 !ruby/object:Gem::Requirement 
+  requirement: &id025 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -353,11 +367,11 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id024
+  version_requirements: *id025
 - !ruby/object:Gem::Dependency 
   name: jeweler
   prerelease: false
-  requirement: &id025 !ruby/object:Gem::Requirement 
+  requirement: &id026 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -367,7 +381,7 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id025
+  version_requirements: *id026
 description: Ruby wrapper for the OpenTox REST API (http://www.opentox.org)
 email: helma@in-silico.ch
 executables: 
@@ -398,11 +412,12 @@ files:
 - lib/model.rb
 - lib/opentox-ruby-api-wrapper.rb
 - lib/opentox.owl
+- lib/ot-logger.rb
+- lib/overwrite.rb
 - lib/owl.rb
 - lib/rest_client_wrapper.rb
 - lib/spork.rb
 - lib/task.rb
-- lib/tasks/opentox.rb
 - lib/templates/config.yaml
 - lib/templates/users.yaml
 - lib/utils.rb

data/lib/tasks/opentox.rb

@@ -1,107 +0,0 @@
-require File.join(File.dirname(__FILE__), '..', 'opentox-ruby-api-wrapper.rb')
-
-namespace :opentox do
-
-	namespace :services do
-
-		desc "Run opentox services"
-		task :start do
-			@@config[:services].each do |service,uri|
-				dir = File.join(@@config[:base_dir], service)
-				server = @@config[:webserver]
-				case server
-				when /thin|mongrel|webrick/
-					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
-					Dir.chdir dir
-					pid_file = File.join(TMP_DIR,"#{service}.pid") 
-					begin
-						`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
-						puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
-					rescue
-						puts "Cannot start #{service} on port #{port}."
-					end
-				when 'passenger'
-					FileUtils.mkdir_p File.join(dir, 'tmp')
-					FileUtils.touch File.join(dir, 'tmp/restart.txt')
-					puts "#{service} restarted."
-				else
-					puts "not yet implemented"
-				end
-			end
-		end
-
-		desc "Stop opentox services"
-		task :stop do
-			server = @@config[:webserver]
-			if server =~ /thin|mongrel|webrick/
-				@@config[:services].each do |service,uri|
-					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
-					pid_file = File.join(TMP_DIR,"#{service}.pid") 
-					begin
-						puts `#{server} stop -P #{pid_file}` 
-						puts "#{service} stopped on localhost:#{port}"
-					rescue
-						puts "Cannot stop #{service} on port #{port}."
-					end
-				end
-			end
-		end
-
-		desc "Restart opentox services"
-		task :restart => [:stop, :start]
-
-	end
-
-	desc "Run all OpenTox tests"
-	task :test do
-		@@config[:services].each do |service,uri|
-			dir = File.join(@@config[:base_dir], service)
-			Dir.chdir dir
-			puts "Running tests in #{dir}"
-			`rake test -t 1>&2`
-		end
-	end
-
-end
-
-desc "Start service in current directory"
-task :start do
-	service = File.basename(Dir.pwd).intern
-	server = @@config[:webserver]
-	case server 
-		when /thin|mongrel|webrick/
-			port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
-			pid_file = File.join(TMP_DIR,"#{service}.pid") 
-			begin
-				`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
-				puts "#{service} started on localhost:#{port} in #{ENV['RACK_ENV']} environment with PID file #{pid_file}."
-			rescue
-				puts "Cannot start #{service} on port #{port}."
-			end
-		when 'passenger'
-			FileUtils.mkdir_p File.join(dir, 'tmp')
-			FileUtils.touch File.join(dir, 'tmp/restart.txt')
-			puts "#{service} restarted."
-		else
-			puts "not yet implemented"
-		end
-end
-
-desc "Stop service in current directory"
-task :stop do
-	service = File.basename(Dir.pwd).intern
-	server = @@config[:webserver]
-	if server =~ /thin|mongrel|webrick/
-		port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
-		pid_file = File.join(TMP_DIR,"#{service}.pid") 
-		begin
-			puts `thin stop -P #{pid_file}` 
-			puts "#{service} stopped on localhost:#{port}"
-		rescue
-			puts "Cannot stop #{service} on port #{port}."
-		end
-	end
-end
-
-desc "Restart service in current directory"
-task :restart  => [:stop, :start]