clean code , add minimal authorization and authentication

8 files changed, 189 insertions, 36 deletions

diff --git a/VERSION b/VERSION
index 8a9ecc2..4e379d2 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.0.1
\ No newline at end of file
+0.0.2
diff --git a/api/api.json b/api/api.json
index e30ff98..4cd07c7 100644
--- a/api/api.json
+++ b/api/api.json
@@ -14,7 +14,7 @@
             "url": "https://github.com/opentox/lazar-rest/blob/master/LICENSE"
         }
     },
-    "host": "mr-test.in-silico.ch",
+    "host": "enm.in-silico.ch",
     "basePath": "/",
     "schemes": [
         "https"
@@ -720,7 +720,7 @@
                     "descriptor"
                 ],
                 "summary": "Descriptor calculation",
-                "description": "Calculate descriptors for a single compound as SMILES string or a CSV compound file <br> <strong>curl example:</strong> <pre>curl -Lk -X POST -i  -H \"accept:application/json\" -F \"file=@../lazar/test/data/batch_prediction.csv;type=application/csv\" -F \"descriptor=Openbabel.HBA1,Openbabel.HBA2,JoeLib.LogP\" https://mr-test.in-silico.ch/algorithm/descriptor curl -Lk -X POST -i  -H \"accept:application/json\" -F \"identifier=O=C1NC(=O)NC=C1\" -F \"descriptor=Openbabel.MW,JoeLib.LogP\" https://mr-test.in-silico.ch/algorithm/descriptor </pre> CSV compound file has to be comma separated with SMILES strings in the first column.",
+                "description": "Calculate descriptors for a single compound as SMILES string <br>  <strong>curl example:</strong> <pre>curl -Lk -X POST -i  -H \"accept:application/json\" -F \"identifier=O=C1NC(=O)NC=C1\" -F \"descriptor=Openbabel.MW,JoeLib.LogP\" https://enm.in-silico.ch/compound/descriptor </pre>.",
                 "parameters": [
                     {
                         "name": "accept",
@@ -734,17 +734,10 @@
                         ]
                     },
                     {
-                        "name": "file",
-                        "in": "formData",
-                        "description": "CSV file of compounds",
-                        "required": false,
-                        "type": "file"
-                    },
-                    {
                         "name": "identifier",
                         "in": "formData",
                         "description": "SMILES identifier",
-                        "required": false,
+                        "required": true,
                         "type": "string"
                     },
                     {
@@ -900,6 +893,84 @@
                     }
                 }
             }
+        },
+        "/aa/authenticate": {
+            "post": {
+                "tags": [
+                    "authentication"
+                ],
+                "description": "Authentication against OpenSSO. Returns token. Requires Username and Password.",
+                "operationId": "login",
+                "consumes": [
+                    "text/plain"
+                ],
+                "produces": [
+                    "text/plain"
+                ],
+                "parameters": [
+                    {
+                        "in": "formData",
+                        "name": "username",
+                        "description": "username",
+                        "required": true,
+                        "type": "string"
+                    },
+                    {
+                        "in": "formData",
+                        "name": "password",
+                        "description": "password",
+                        "required": true,
+                        "type": "string",
+                        "format": "password"
+                    }
+                ],
+                "responses": {
+                    "200": {
+                        "$ref": "#/responses/200"
+                    },
+                    "400": {
+                        "$ref": "#/responses/400"
+                    },
+                    "401": {
+                        "$ref": "#/responses/401"
+                    }
+                }
+            }
+        },
+        "/aa/logout": {
+            "post": {
+                "description": "Devalidates a token. Requires Subjectid.",
+                "operationId": "logout",
+                "tags": [
+                    "authentication"
+                ],
+                "consumes": [
+                    "text/plain"
+                ],
+                "produces": [
+                    "text/plain"
+                ],
+                "parameters": [
+                    {
+                        "in": "formData",
+                        "name": "subjectid",
+                        "description": "subjectid",
+                        "required": true,
+                        "type": "string"
+                    }
+                ],
+                "responses": {
+                    "200": {
+                        "$ref": "#/responses/200"
+                    },
+                    "400": {
+                        "$ref": "#/responses/400"
+                    },
+                    "401": {
+                        "$ref": "#/responses/401"
+                    }
+                }
+            }
         }
     },
     "parameters": {
@@ -955,6 +1026,10 @@
             "description": "Swagger API representation in JSON"
         },
         {
+            "name": "authentication",
+            "description": "minimal Authentication service"
+        },
+        {
             "name": "descriptor",
             "description": "Descriptor"
         },
diff --git a/lib/aa.rb b/lib/aa.rb
new file mode 100644
index 0000000..6dfec4b
--- /dev/null
+++ b/lib/aa.rb
@@ -0,0 +1,82 @@
+post "/aa/authenticate/?" do
+  mime_types = ["text/plain"]
+  bad_request_error "Mime type #{@accept} not supported here. Please request data as  #{mime_types.join(', ')}." unless mime_types.include? @accept
+  bad_request_error "Please send formdata username." unless params[:username]
+  bad_request_error "Please send formdata password." unless params[:password]
+  case @accept
+  when "text/plain"
+    if OpenTox::Authorization.authenticate(params[:username], params[:password])
+      return OpenTox::RestClientWrapper.subjectid
+    else
+      return nil
+    end
+  else
+    bad_request_error "'#{@accept}' is not a supported content type."
+   end
+end
+
+post "/aa/logout/?" do
+  mime_types = ["text/plain"]
+  bad_request_error "Mime type #{@accept} not supported here. Please request data as  #{mime_types.join(', ')}." unless mime_types.include? @accept
+  bad_request_error "Please send formdata subjectid." unless params[:subjectid]
+  case @accept
+  when "text/plain"
+    if OpenTox::Authorization.logout(params[:subjectid])
+      return "Successfully logged out. \n"
+    else
+      return "Logout failed.\n"
+    end
+  else
+    bad_request_error "'#{@accept}' is not a supported content type."
+   end
+end
+
+module OpenTox
+
+  AA = "https://opensso.in-silico.ch"
+  
+  module Authorization
+    #Authentication against OpenSSO. Returns token. Requires Username and Password.
+    # @param user [String] Username
+    # @param pw [String] Password
+    # @return [Boolean] true if successful
+    def self.authenticate(user, pw)
+      begin
+        res = RestClientWrapper.post("#{AA}/auth/authenticate",{:username=>user, :password => pw},{:subjectid => ""}).sub("token.id=","").sub("\n","")
+        if is_token_valid(res)
+          RestClientWrapper.subjectid = res
+          return true
+        else
+          bad_request_error "Authentication failed #{res.inspect}"
+        end
+      rescue
+        bad_request_error "Authentication failed #{res.inspect}"
+      end
+    end
+
+    #Logout on opensso. Make token invalid. Requires token
+    # @param [String] subjectid the subjectid
+    # @return [Boolean] true if logout is OK
+    def self.logout(subjectid=RestClientWrapper.subjectid)
+      begin
+        out = RestClientWrapper.post("#{AA}/auth/logout", :subjectid => subjectid)
+        return true unless is_token_valid(subjectid)
+      rescue
+        return false
+      end
+      return false
+    end
+
+    #Checks if a token is a valid token
+    # @param [String]subjectid subjectid from openSSO session
+    # @return [Boolean] subjectid is valid or not.
+    def self.is_token_valid(subjectid=RestClientWrapper.subjectid)
+      begin
+        return true if RestClientWrapper.post("#{AA}/auth/isTokenValid",:tokenid => subjectid) == "boolean=true\n"
+      rescue #do rescue because openSSO throws 401
+        return false
+      end
+      return false
+    end
+  end
+end
\ No newline at end of file
diff --git a/lib/compound.rb b/lib/compound.rb
index fc4ec55..c8dd98c 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -5,23 +5,19 @@
 get "/compound/descriptor/?:descriptor?" do
   case @accept
   when "application/json"
-    return "#{JSON.pretty_generate OpenTox::PhysChem::DESCRIPTORS} "  unless params[:descriptor]
-    return {params[:descriptor] => OpenTox::PhysChem::DESCRIPTORS[params[:descriptor]]}.to_json
+    return "#{JSON.pretty_generate PhysChem::DESCRIPTORS} "  unless params[:descriptor]
+    return {params[:descriptor] => PhysChem::DESCRIPTORS[params[:descriptor]]}.to_json
   else
-    return OpenTox::PhysChem::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor]
-    return OpenTox::PhysChem::DESCRIPTORS[params[:descriptor]]
+    return PhysChem::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor]
+    return PhysChem::DESCRIPTORS[params[:descriptor]]
   end
 end
 
 post "/compound/descriptor/?" do
-  bad_request_error "Missing Parameter " unless (params[:identifier] or params[:file]) and params[:descriptor]
+  bad_request_error "Missing Parameter " unless params[:identifier] && params[:descriptor]
   descriptor = params['descriptor'].split(',')
-  if params[:file]
-    data = OpenTox::Dataset.from_csv_file params[:file][:tempfile]
-  else
-    data = OpenTox::Compound.from_smiles params[:identifier]
-  end
-  d = Algorithm::Descriptor.physchem data, descriptor
+  compound = Compound.from_smiles params[:identifier]
+  d = compound.physchem descriptor
   csv = d.to_csv
   csv = "SMILES,#{params[:descriptor]}\n#{params[:identifier]},#{csv}" if params[:identifier]
   case @accept
@@ -37,7 +33,7 @@ end
 
 get %r{/compound/(.+)} do |inchi|
   bad_request_error "Input parameter #{inchi} is not an InChI" unless inchi.match(/^InChI=/)
-  compound = OpenTox::Compound.from_inchi URI.unescape(inchi)
+  compound = Compound.from_inchi URI.unescape(inchi)
   response['Content-Type'] = @accept
   case @accept
   when "application/json"
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 56f510f..ff16640 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -1,6 +1,6 @@
 # Get all datasets
 get "/dataset/?" do
-  datasets = OpenTox::Dataset.all
+  datasets = Dataset.all
   case @accept
   when "text/uri-list"
     uri_list = datasets.collect{|dataset| uri("/dataset/#{dataset.id}")}
diff --git a/lib/model.rb b/lib/model.rb
index 6188cce..db0c190 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -3,7 +3,7 @@
 # @param [Header] Accept one of text/uri-list,
 # @return [text/uri-list] list of all prediction models
 get "/model/?" do
-  models = OpenTox::Model::Prediction.all
+  models = Model::Prediction.all
   case @accept
   when "text/uri-list"
     uri_list = models.collect{|model| uri("/model/#{model.model_id}")}
@@ -21,7 +21,7 @@ get "/model/?" do
 end
 
 get "/model/:id/?" do
-  model = OpenTox::Model::Lazar.find params[:id]
+  model = Model::Lazar.find params[:id]
   resource_not_found_error "Model with id: #{params[:id]} not found." unless model
   model[:URI] = uri("/model/#{model.id}")
   model[:neighbor_algorithm_parameters][:feature_dataset_uri] = uri("/dataset/#{model[:neighbor_algorithm_parameters][:feature_dataset_id]}") if model[:neighbor_algorithm_parameters][:feature_dataset_id]
@@ -40,7 +40,7 @@ post "/model/:id/?" do
     @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string."
     return @error_report
   end
-  model = OpenTox::Model::Lazar.find params[:id]
+  model = Model::Lazar.find params[:id]
   batch = {}
   compounds.each do |compound|
     prediction = model.predict(compound)
diff --git a/lib/validation.rb b/lib/validation.rb
index 5963c63..ce31c34 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -24,13 +24,13 @@ get "/validation/:validationtype/?" do
   bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype]
   case params[:validationtype]
   when "repeatedcrossvalidation"
-    validations = OpenTox::Validation::RepeatedCrossValidation.all
+    validations = Validation::RepeatedCrossValidation.all
   when "leaveoneout"
-    validations = OpenTox::Validation::LeaveOneOut.all
+    validations = Validation::LeaveOneOut.all
   when "crossvalidation"
-    validations = OpenTox::Validation::CrossValidation.all
+    validations = Validation::CrossValidation.all
   when "regressioncrossvalidation"
-    validations = OpenTox::Validation::RegressionCrossValidation.all
+    validations = Validation::RegressionCrossValidation.all
   end
 
   case @accept
@@ -53,13 +53,13 @@ get "/validation/:validationtype/:id/?" do
   bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype]
   case params[:validationtype]
   when "repeatedcrossvalidation"
-    validation = OpenTox::Validation::RepeatedCrossValidation.find params[:id]
+    validation = Validation::RepeatedCrossValidation.find params[:id]
   when "leaveoneout"
-    validation = OpenTox::Validation::LeaveOneOut.find params[:id]
+    validation = Validation::LeaveOneOut.find params[:id]
   when "crossvalidation"
-    validation = OpenTox::Validation::CrossValidation.find params[:id]
+    validation = Validation::CrossValidation.find params[:id]
   when "regressioncrossvalidation"
-    validation = OpenTox::Validation::RegressionCrossValidation.find params[:id]
+    validation = Validation::RegressionCrossValidation.find params[:id]
   end
 
   resource_not_found_error "#{params[:validationtype]} with id: #{params[:id]} not found." unless validation
diff --git a/test/compound.rb b/test/compound.rb
index 5fac83d..cacd292 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -39,7 +39,7 @@ class CompoundTest < MiniTest::Test
     res = RestClientWrapper.get File.join($compound_uri, $compound[0]), {}, {:accept => "application/json"}
     assert_equal res.code, 200
     js = JSON.parse res
-    assert_equal js["chemblid"], "CHEMBL581676"
+    assert_equal js["chemblid"], "CHEMBL277500"
     assert_equal js["names"].first, "BENZENE"
     assert_equal js["names"][6], "71-43-2"
   end