A&A implementation

5 files changed, 118 insertions, 8 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index c5704ae..bbd8b8b 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -6,6 +6,7 @@ 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
@@ -14,8 +15,9 @@ 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)
+    def initialize(uri=nil,token_id=nil)
       super uri
+      @token_id = token_id
       @features = {}
       @compounds = []
       @data_entries = {}
@@ -26,8 +28,9 @@ module OpenTox
     #   dataset = OpenTox::Dataset.create
     # @param [optional, String] uri Dataset URI
     # @return [OpenTox::Dataset] Dataset object
-    def self.create(uri=CONFIG[:services]["opentox-dataset"])
+    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
     end
@@ -252,7 +255,7 @@ module OpenTox
       @compounds.uniq!
       if @uri
         if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host))
-          RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml"},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
@@ -262,7 +265,7 @@ module OpenTox
         end
       else
         # create dataset if uri is empty
-        self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{}).to_s.chomp
+        self.uri = RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:token_id => @token_id}).to_s.chomp
       end
       @uri
     end
@@ -279,6 +282,7 @@ 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 b69f9b4..11f790b 100644
--- a/lib/helper.rb
+++ b/lib/helper.rb
@@ -17,7 +17,7 @@ helpers do
       ret = OpenTox::Authorization.authorize(request.env['SCRIPT_URI'], request.env['REQUEST_METHOD'], token_id)
       LOGGER.debug "OpenTox helpers OpenTox::Authorization authorized? method: #{request.env['REQUEST_METHOD']} , URI: #{request.env['SCRIPT_URI']}, token_id: #{token_id} with return #{ret}." 
       return ret
-    when "POST"
+    when "POST", "HEAD"
       if OpenTox::Authorization.is_token_valid(token_id)
         LOGGER.debug "OpenTox helpers OpenTox::Authorization.is_token_valid: true"  
         return true
@@ -25,7 +25,6 @@ helpers do
       LOGGER.warn "OpenTox helpers POST on #{request.env['SCRIPT_URI']} with token_id: #{token_id} false."  
     end 
     LOGGER.debug "Not authorized for: 1. #{request['SCRIPT_URI']} 2. #{request.env['SCRIPT_URI']}  with Method: #{request.env['REQUEST_METHOD']} with Token #{token_id}"
-    LOGGER.debug "Request infos: #{request.inspect}"
     return false
   end
 
@@ -55,6 +54,7 @@ before do
       token_id = params[:token_id]  if params[:token_id]  and !check_token_id(token_id)
       token_id = request.env['HTTP_TOKEN_ID'] if request.env['HTTP_TOKEN_ID'] and !check_token_id(token_id)
       # see http://rack.rubyforge.org/doc/SPEC.html
+      token_id = CGI.unescape(token_id) if token_id.include?("%23") 
     rescue
       LOGGER.debug "OpenTox api wrapper: helper before filter: NO token_id." 
       token_id = ""
diff --git a/lib/model.rb b/lib/model.rb
index 5654bcc..5dc4d4a 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -32,7 +32,7 @@ module OpenTox
       include Model
       include Algorithm
 
-      attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim
+      attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :min_sim, :token_id
 
       def initialize(uri=nil)
 
@@ -258,7 +258,7 @@ module OpenTox
 
       # Save model at model service
       def save
-        self.uri = RestClientWrapper.post(@uri,{:content_type =>  "application/x-yaml"},self.to_yaml)
+        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/templates/default_guest_policy.xml b/lib/templates/default_guest_policy.xml
new file mode 100644
index 0000000..a778070
--- /dev/null
+++ b/lib/templates/default_guest_policy.xml
@@ -0,0 +1,53 @@
+<!DOCTYPE Policies PUBLIC "-//Sun Java System Access Manager7.1 2006Q3
+   Admin CLI DTD//EN" "jar://com/sun/identity/policy/policyAdmin.dtd">
+
+<Policies>
+<Policy name="policy_user" referralPolicy="false" active="true">
+   <Rule name="rule_user">
+      <ServiceName name="iPlanetAMWebAgentService" />
+      <ResourceName name="uri"/>
+      <AttributeValuePair>
+         <Attribute name="GET" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+      <AttributeValuePair>
+         <Attribute name="POST" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+      <AttributeValuePair>
+         <Attribute name="PUT" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+      <AttributeValuePair>
+         <Attribute name="DELETE" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+   </Rule>
+   <Subjects name="subjects_user" description="">
+        <Subject name="subject_user" type="LDAPUsers" includeType="inclusive">
+            <AttributeValuePair>
+                <Attribute name="Values"/>
+                <Value>uid=guest,ou=people,dc=opentox,dc=org</Value>
+            </AttributeValuePair>
+        </Subject>
+   </Subjects>
+</Policy>
+<Policy name="policy_group" referralPolicy="false" active="true">
+   <Rule name="rule_group">
+      <ServiceName name="iPlanetAMWebAgentService" />
+      <ResourceName name="uri"/>
+      <AttributeValuePair>
+         <Attribute name="GET" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+   </Rule>
+   <Subjects name="subjects_group" description="">
+        <Subject name="subject_group" type="LDAPGroups" includeType="inclusive">
+            <AttributeValuePair>
+                <Attribute name="Values"/>
+                <Value>cn=member,ou=groups,dc=opentox,dc=org</Value>
+            </AttributeValuePair>
+        </Subject>
+   </Subjects>
+</Policy>
+</Policies>
diff --git a/lib/templates/default_policy.xml b/lib/templates/default_policy.xml
new file mode 100644
index 0000000..a778070
--- /dev/null
+++ b/lib/templates/default_policy.xml
@@ -0,0 +1,53 @@
+<!DOCTYPE Policies PUBLIC "-//Sun Java System Access Manager7.1 2006Q3
+   Admin CLI DTD//EN" "jar://com/sun/identity/policy/policyAdmin.dtd">
+
+<Policies>
+<Policy name="policy_user" referralPolicy="false" active="true">
+   <Rule name="rule_user">
+      <ServiceName name="iPlanetAMWebAgentService" />
+      <ResourceName name="uri"/>
+      <AttributeValuePair>
+         <Attribute name="GET" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+      <AttributeValuePair>
+         <Attribute name="POST" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+      <AttributeValuePair>
+         <Attribute name="PUT" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+      <AttributeValuePair>
+         <Attribute name="DELETE" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+   </Rule>
+   <Subjects name="subjects_user" description="">
+        <Subject name="subject_user" type="LDAPUsers" includeType="inclusive">
+            <AttributeValuePair>
+                <Attribute name="Values"/>
+                <Value>uid=guest,ou=people,dc=opentox,dc=org</Value>
+            </AttributeValuePair>
+        </Subject>
+   </Subjects>
+</Policy>
+<Policy name="policy_group" referralPolicy="false" active="true">
+   <Rule name="rule_group">
+      <ServiceName name="iPlanetAMWebAgentService" />
+      <ResourceName name="uri"/>
+      <AttributeValuePair>
+         <Attribute name="GET" />
+         <Value>allow</Value>
+      </AttributeValuePair>
+   </Rule>
+   <Subjects name="subjects_group" description="">
+        <Subject name="subject_group" type="LDAPGroups" includeType="inclusive">
+            <AttributeValuePair>
+                <Attribute name="Values"/>
+                <Value>cn=member,ou=groups,dc=opentox,dc=org</Value>
+            </AttributeValuePair>
+        </Subject>
+   </Subjects>
+</Policy>
+</Policies>