consistent use of object class and update of description

3 files changed, 75 insertions, 253 deletions

diff --git a/api/api.json b/api/api.json
index df69149..7777f1e 100644
--- a/api/api.json
+++ b/api/api.json
@@ -32,17 +32,6 @@
                 "description": "Get a list of all prediction models",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/uri-list",
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/subjectid"
                     }
                 ],
@@ -75,27 +64,17 @@
                     "model"
                 ],
                 "description": "Get model representation",
+                "produces": [
+                    "application/json"
+                ],
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/id"
                     },
                     {
                         "$ref": "#/parameters/subjectid"
                     }
                 ],
-                "produces": [
-                    "application/json"
-                ],
                 "responses": {
                     "200": {
                         "$ref": "#/responses/200"
@@ -167,17 +146,6 @@
                 "description": "Get a list of QMRF reports",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/uri-list",
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/subjectid"
                     }
                 ],
@@ -209,19 +177,9 @@
                 "tags": [
                     "report"
                 ],
-                "description": "Get a QMRF report prototype",
+                "description": "Get QMRF for prediction model",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/xml"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/id"
                     },
                     {
@@ -258,17 +216,6 @@
                 "description": "Get a list of all datasets",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/uri-list",
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/subjectid"
                     }
                 ],
@@ -303,17 +250,6 @@
                 "description": "Get dataset representation",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/json",
-                            "text/csv"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/id"
                     },
                     {
@@ -339,6 +275,9 @@
                     },
                     "404": {
                         "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -351,16 +290,6 @@
                 "description": "Get dataset representation",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/json"
-                        ]
-                    },
-                    {
                         "name": "attribute",
                         "in": "path",
                         "description": "requested attribute",
@@ -398,6 +327,9 @@
                     },
                     "404": {
                         "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -410,17 +342,6 @@
                 "description": "Get a list of all substances",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/uri-list",
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/subjectid"
                     }
                 ],
@@ -455,16 +376,6 @@
                 "description": "Get substance representation",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/id"
                     },
                     {
@@ -489,6 +400,9 @@
                     },
                     "404": {
                         "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -501,17 +415,6 @@
                 "description": "Get a list of all nanoparticles",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/uri-list",
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/subjectid"
                     }
                 ],
@@ -546,16 +449,6 @@
                 "description": "Get nanoparticle representation",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/id"
                     },
                     {
@@ -580,6 +473,9 @@
                     },
                     "404": {
                         "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -589,18 +485,10 @@
                 "tags": [
                     "feature"
                 ],
-                "description": "Get a list of all features",
+                "description": "Get a list of ids for all features",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/uri-list",
-                            "application/json"
-                        ]
+                        "$ref": "#/parameters/subjectid"
                     }
                 ],
                 "produces": [
@@ -634,17 +522,10 @@
                 "description": "Get feature representation",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/json"
-                        ]
+                        "$ref": "#/parameters/id"
                     },
                     {
-                        "$ref": "#/parameters/id"
+                        "$ref": "#/parameters/subjectid"
                     }
                 ],
                 "produces": [
@@ -665,6 +546,9 @@
                     },
                     "404": {
                         "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -677,15 +561,7 @@
                 "description": "Get a list of all validation types",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/uri-list",
-                            "application/json"
-                        ]
+                        "$ref": "#/parameters/subjectid"
                     }
                 ],
                 "produces": [
@@ -719,17 +595,6 @@
                 "description": "Get all validations of a validation type",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/uri-list",
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/valtype"
                     },
                     {
@@ -755,6 +620,9 @@
                     },
                     "404": {
                         "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -767,16 +635,6 @@
                 "description": "Get validation representation",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/json"
-                        ]
-                    },
-                    {
                         "$ref": "#/parameters/valtype"
                     },
                     {
@@ -804,6 +662,9 @@
                     },
                     "404": {
                         "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -817,19 +678,11 @@
                 "description": "Get a list of all descriptors",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/plain",
-                            "application/json"
-                        ]
+                        "$ref": "#/parameters/subjectid"
                     }
                 ],
                 "produces": [
-                    "text/plain",
+                    "text/plain; charset=utf-8",
                     "application/json"
                 ],
                 "responses": {
@@ -862,18 +715,6 @@
                 ],
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/csv",
-                            "application/json"
-                        ],
-                        "default": "text/csv"
-                    },
-                    {
                         "name": "identifier",
                         "in": "formData",
                         "description": "SMILES identifier",
@@ -926,26 +767,18 @@
                 "description": "Get a list of a descriptors",
                 "parameters": [
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-Type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "text/plain",
-                            "application/json"
-                        ]
-                    },
-                    {
                         "name": "descriptor",
                         "in": "path",
                         "description": "descriptor name or ID",
                         "required": true,
                         "type": "string"
+                    },
+                    {
+                        "$ref": "#/parameters/subjectid"
                     }
                 ],
                 "produces": [
-                    "text/plain",
+                    "text/plain; charset=utf-8",
                     "application/json"
                 ],
                 "responses": {
@@ -978,21 +811,7 @@
                         "$ref": "#/parameters/InChI"
                     },
                     {
-                        "name": "Accept",
-                        "in": "header",
-                        "description": "requested Content-type",
-                        "required": true,
-                        "type": "string",
-                        "enum": [
-                            "application/json",
-                            "chemical/x-daylight-smiles",
-                            "chemical/x-inchi",
-                            "chemical/x-mdl-sdfile",
-                            "chemical/x-mdl-molfile",
-                            "image/png",
-                            "image/svg+xml",
-                            "text/plain"
-                        ]
+                        "$ref": "#/parameters/subjectid"
                     }
                 ],
                 "produces": [
@@ -1046,11 +865,11 @@
                 "description": "Authentication against OpenSSO. Returns authentication token. Requires Username and Password.",
                 "operationId": "login",
                 "consumes": [
-                    "text/plain",
+                    "text/plain; charset=utf-8",
                     "multipart/form-data"
                 ],
                 "produces": [
-                    "text/plain"
+                    "text/plain; charset=utf-8"
                 ],
                 "parameters": [
                     {
@@ -1078,6 +897,9 @@
                     },
                     "401": {
                         "$ref": "#/responses/401"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -1091,11 +913,11 @@
                     "authentication"
                 ],
                 "consumes": [
-                    "text/plain",
+                    "text/plain; charset=utf-8",
                     "multipart/form-data"
                 ],
                 "produces": [
-                    "text/plain"
+                    "text/plain; charset=utf-8"
                 ],
                 "parameters": [
                     {
@@ -1115,6 +937,9 @@
                     },
                     "401": {
                         "$ref": "#/responses/401"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
                     }
                 }
             }
@@ -1148,11 +973,17 @@
             "description": "authorization token",
             "required": false,
             "type": "string"
+        },
+        "subjectidRequired": {
+            "in": "header",
+            "name": "subjectid",
+            "description": "authorization token",
+            "required": true,
+            "type": "string"
         }
     },
     "responses": {
         "200": {
-            "schema": {"type":"string"},
             "description": "OK"
         },
         "400": {
@@ -1173,18 +1004,26 @@
     },
     "tags": [
         {
-            "name": "algorithm",
-            "description": "Algorithm"
-        },
-        {
             "name": "api",
             "description": "Swagger API representation in JSON"
         },
         {
+            "name": "algorithm",
+            "description": "Algorithm"
+        },
+        {
             "name": "authentication",
             "description": "minimal Authentication service"
         },
         {
+            "name": "compound",
+            "description": "Compound"
+        },
+        {
+            "name": "dataset",
+            "description": "Dataset"
+        },
+        {
             "name": "descriptor",
             "description": "Descriptor"
         },
@@ -1197,28 +1036,20 @@
             "description": "Lazar Model Service"
         },
         {
-            "name": "dataset",
-            "description": "Dataset"
-        },
-        {
-            "name": "validation",
-            "description": "Validation"
+            "name": "nanoparticle",
+            "description": "Nanoparticle"
         },
         {
             "name": "report",
             "description": "QMRF Reporting"
         },
         {
-            "name": "compound",
-            "description": "Compound"
-        },
-        {
             "name": "substance",
             "description": "Substance"
         },
         {
-            "name": "nanoparticle",
-            "description": "Nanoparticle"
+            "name": "validation",
+            "description": "Validation"
         }
     ]
 }
diff --git a/lib/lazar-rest.rb b/lib/lazar-rest.rb
index 4fd806c..255c52f 100644
--- a/lib/lazar-rest.rb
+++ b/lib/lazar-rest.rb
@@ -3,6 +3,7 @@ require "sinatra/reloader"
 require 'sinatra/cross_origin'
 
 configure do
+  $logger = Logger.new(STDOUT)
   enable :reloader #if development?
   enable :cross_origin
   disable :show_exceptions
diff --git a/lib/model.rb b/lib/model.rb
index 7a2fb47..52553fa 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -6,7 +6,7 @@ get "/model/?" do
   models = Model::Validation.all
   case @accept
   when "text/uri-list"
-    uri_list = models.collect{|model| uri("/model/#{model.model_id}")}
+    uri_list = models.collect{|model| uri("/model/#{model.id}")}
     return uri_list.join("\n") + "\n"
   when "application/json"
     models = JSON.parse models.to_json
@@ -19,26 +19,16 @@ get "/model/?" do
 end
 
 get "/model/:id/?" do
-  model = Model::Lazar.find params[:id]
+  model = Model::Validation.find params[:id]
   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]
-  model[:training_dataset_uri] = uri("/dataset/#{model.training_dataset_id}") if model.training_dataset_id
-  model[:prediction_feature_uri] = uri("/dataset/#{model.prediction_feature_id}") if model.prediction_feature_id
   return model.to_json
 end
 
 
 post "/model/:id/?" do
   identifier = params[:identifier].split(",")
-  begin
-    # get compound from SMILES
-    compounds = identifier.collect{ |i| Compound.from_smiles i.strip }
-  rescue
-    @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string."
-    return @error_report
-  end
-  model = Model::Lazar.find params[:id]
+  compounds = identifier.collect{ |i| Compound.from_smiles i.strip }
+  model = Model::Validation.find params[:id]
   batch = {}
   compounds.each do |compound|
     prediction = model.predict(compound)