remove token_id from tables in database

5 files changed, 14 insertions, 17 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index bbd8b8b..b7feeec 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -6,7 +6,6 @@ module OpenTox
     include OpenTox
 
     attr_reader :features, :compounds, :data_entries, :metadata
-    attr_accessor :token_id
 
     # Create dataset with optional URI. Does not load data into the dataset - you will need to execute one of the load_* methods to pull data from a service or to insert it from other representations.
     # @example Create an empty dataset
@@ -15,9 +14,8 @@ module OpenTox
     #   dataset = OpenTox::Dataset.new("http:://webservices.in-silico/ch/dataset/1")
     # @param [optional, String] uri Dataset URI
     # @return [OpenTox::Dataset] Dataset object
-    def initialize(uri=nil,token_id=nil)
+    def initialize(uri=nil)
       super uri
-      @token_id = token_id
       @features = {}
       @compounds = []
       @data_entries = {}
@@ -30,8 +28,7 @@ module OpenTox
     # @return [OpenTox::Dataset] Dataset object
     def self.create(uri=CONFIG[:services]["opentox-dataset"], token_id=nil)
       dataset = Dataset.new
-      dataset.token_id = token_id if token_id
-      dataset.save
+      dataset.save(token_id)
       dataset
     end
 
@@ -250,22 +247,22 @@ module OpenTox
     # - creates a new dataset if uri is not set
     # - overwrites dataset if uri exists
     # @return [String] Dataset URI
-    def save
+    def save(token_id=nil)
       # TODO: rewrite feature URI's ??
       @compounds.uniq!
       if @uri
         if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-          RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml", :token_id => @token_id},self.to_yaml)
+          RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml", :token_id => token_id},self.to_yaml)
         else
           File.open("ot-post-file.rdf","w+") { |f| f.write(self.to_rdfxml); @path = f.path }
-          task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list"}).to_s.chomp
+          task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list" , :token_id => token_id}).to_s.chomp
           #task_uri = `curl -X POST -H "Accept:text/uri-list" -F "file=@#{@path};type=application/rdf+xml" http://apps.ideaconsult.net:8080/ambit2/dataset`
           Task.find(task_uri).wait_for_completion
           self.uri = RestClientWrapper.get(task_uri,:accept => 'text/uri-list')
         end
       else
         # create dataset if uri is empty
-        self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:token_id => @token_id}).to_s.chomp
+        self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:token_id => token_id}).to_s.chomp
       end
       @uri
     end
@@ -282,7 +279,6 @@ module OpenTox
       @data_entries = dataset.data_entries
       @compounds = dataset.compounds
       @features = dataset.features
-      @token_id = dataset.token_id
       if @uri
         self.uri = @uri 
       else
diff --git a/lib/helper.rb b/lib/helper.rb
index 6247460..42c35e8 100644
--- a/lib/helper.rb
+++ b/lib/helper.rb
@@ -32,7 +32,7 @@ helpers do
 
   def unprotected_requests
     case  env['REQUEST_URI']
-    when /\/login$|\/logout$|\/predict$|\/upload$/
+    when /\/login$|\/logout$|\/predict$|\/toxcreate\/models$/
       return true
     when /\/compound|\/feature|\/task|\/toxcreate/   #to fix: read from config | validation should be protected
       return true
diff --git a/lib/model.rb b/lib/model.rb
index 5dc4d4a..9c2fb97 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -111,7 +111,7 @@ module OpenTox
       # @param [String] compound_uri Compound URI
       # @param [optinal,Boolean] verbose Verbose prediction (output includes neighbors and features)
       # @return [OpenTox::Dataset] Dataset with prediction
-      def predict(compound_uri,verbose=false)
+      def predict(compound_uri,verbose=false,token_id=nil)
 
         @compound = Compound.new compound_uri
         features = {}
@@ -119,7 +119,7 @@ module OpenTox
         unless @prediction_dataset
           #@prediction_dataset = cached_prediction
           #return @prediction_dataset if cached_prediction
-          @prediction_dataset = Dataset.create
+          @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], token_id)
           @prediction_dataset.add_metadata( {
             OT.hasSource => @uri,
             DC.creator => @uri,
@@ -217,7 +217,7 @@ module OpenTox
           end
         end
 
-        @prediction_dataset.save
+        @prediction_dataset.save(token_id)
         @prediction_dataset
       end
 
@@ -257,8 +257,8 @@ module OpenTox
       end
 
       # Save model at model service
-      def save
-        self.uri = RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml", :token_id => @token_id},self.to_yaml)
+      def save(token_id)
+        self.uri = RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml", :token_id => token_id},self.to_yaml)
       end
 
       # Delete model at model service
diff --git a/lib/task.rb b/lib/task.rb
index 17f95e6..18fba6e 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -49,6 +49,7 @@ module OpenTox
 
       cpu_load = `cat /proc/loadavg`.split(/\s+/)[0..2].collect{|c| c.to_f}
       nr_cpu_cores = `cat /proc/cpuinfo |grep "cpu cores"|cut -d ":" -f2|tr -d " "`.split("\n").collect{|c| c.to_i}.inject{|sum,n| sum+n}
+      nr_cpu_cores = 1 if !nr_cpu_cores
       if cpu_load[0] > nr_cpu_cores and cpu_load[0] > cpu_load[1] and cpu_load[1] > cpu_load[2] # average CPU load of the last minute is high and CPU load is increasing
         LOGGER.warn "Cannot start task  - CPU load too high (#{cpu_load.join(", ")})"
         task.cancel
diff --git a/lib/templates/config.yaml b/lib/templates/config.yaml
index db11006..116f462 100644
--- a/lib/templates/config.yaml
+++ b/lib/templates/config.yaml
@@ -41,7 +41,7 @@
 # :logger: debug
 
 # OpenSSO Authorization
-# set ":server: nil" to disable A&A
+# set ":server: " to disable A&A
 :authorization:
   :server: "https://opensso.in-silico.ch"
   :free_request: #not controlled by A&A