fixed error messages

12 files changed, 90 insertions, 74 deletions

diff --git a/api/api.json b/api/api.json
index c226c90..af9dac3 100644
--- a/api/api.json
+++ b/api/api.json
@@ -32,7 +32,7 @@
                 "description": "Get a list of all prediction models",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -77,7 +77,7 @@
                 "description": "Get model representation",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -164,7 +164,7 @@
                 "description": "Get a list of QMRF reports",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -209,7 +209,7 @@
                 "description": "Get a QMRF report prototype",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -255,7 +255,7 @@
                 "description": "Get a list of all datasets",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -300,7 +300,7 @@
                 "description": "Get dataset representation",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -348,7 +348,7 @@
                 "description": "Get dataset representation",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -407,7 +407,7 @@
                 "description": "Get a list of all substances",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -452,7 +452,7 @@
                 "description": "Get substance representation",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -498,7 +498,7 @@
                 "description": "Get a list of all nanoparticles",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -543,7 +543,7 @@
                 "description": "Get nanoparticle representation",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -589,7 +589,7 @@
                 "description": "Get a list of all features",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -631,7 +631,7 @@
                 "description": "Get feature representation",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -674,7 +674,7 @@
                 "description": "Get a list of all validation types",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -716,7 +716,7 @@
                 "description": "Get all validations of a validation type",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -764,7 +764,7 @@
                 "description": "Get validation representation",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -814,7 +814,7 @@
                 "description": "Get a list of all descriptors",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -853,10 +853,10 @@
                     "descriptor"
                 ],
                 "summary": "Descriptor calculation",
-                "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>.",
+                "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://api.in-silico.ch/compound/descriptor </pre>.",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -920,7 +920,7 @@
                 "description": "Get a list of a descriptors",
                 "parameters": [
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-Type",
                         "required": true,
@@ -972,7 +972,7 @@
                         "$ref": "#/parameters/InChI"
                     },
                     {
-                        "name": "accept",
+                        "name": "Accept",
                         "in": "header",
                         "description": "requested Content-type",
                         "required": true,
@@ -1144,6 +1144,7 @@
     },
     "responses": {
         "200": {
+            "schema": {"type":"string"},
             "description": "OK"
         },
         "400": {
diff --git a/lib/dataset.rb b/lib/dataset.rb
index a48b23f..7c74f39 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -7,10 +7,9 @@ get "/dataset/?" do
     return uri_list.join("\n") + "\n"
   when "application/json"
     datasets = JSON.parse datasets.to_json
-    datasets.each_index do |idx|
-      datasets[idx][:URI] = uri("/dataset/#{datasets[idx]["_id"]["$oid"]}")
-    end
-    return datasets.to_json
+    list = []
+    datasets.each{|d| list << uri("/dataset/#{d["_id"]["$oid"]}")}
+    return list.to_json
   else
     bad_request_error "Mime type #{@accept} is not supported."
   end
@@ -19,7 +18,7 @@ end
 # Get a dataset
 get "/dataset/:id/?" do
   dataset = Dataset.find :id => params[:id]
-  resource_not_found_error "Dataset with id: #{params[:id]} not found." unless dataset
+  not_found_error "Dataset with id: #{params[:id]} not found." unless dataset
   case @accept
   when "application/json"
     dataset.data_entries.each do |k, v|
@@ -39,9 +38,9 @@ end
 # Get a dataset attribute. One of compounds, nanoparticles, substances, features 
 get "/dataset/:id/:attribute/?" do
   dataset = Dataset.find :id => params[:id]
-  resource_not_found_error "Dataset with id: #{params[:id]} not found." unless dataset
+  not_found_error "Dataset with id: #{params[:id]} not found." unless dataset
   attribs = ["compounds", "nanoparticles", "substances", "features"]
   return "Attribute '#{params[:attribute]}' is not available. Choose one of #{attribs.join(', ')}." unless attribs.include? params[:attribute]
-  out = dataset.send(params[:attribute])
+  out = dataset.send("#{params[:attribute]}")
   return out.to_json
 end
diff --git a/lib/feature.rb b/lib/feature.rb
index 75e3f1f..140cc25 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -18,8 +18,13 @@ end
 
 # Get a feature
 get "/feature/:id/?" do
-  feature = Feature.find :id => params[:id]
-  resource_not_found_error "Feature with id: #{params[:id]} not found." unless feature
-  feature[:URI] = uri("/feature/#{feature.id}")
-  return feature.to_json
-end
\ No newline at end of file
+  case @accept
+  when "application/json"
+    feature = Feature.find :id => params[:id]
+    not_found_error "Feature with id: #{params[:id]} not found." unless feature
+    feature[:URI] = uri("/feature/#{feature.id}")
+    return feature.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
diff --git a/lib/lazar-rest.rb b/lib/lazar-rest.rb
index 41010e1..4fd806c 100644
--- a/lib/lazar-rest.rb
+++ b/lib/lazar-rest.rb
@@ -3,15 +3,19 @@ require "sinatra/reloader"
 require 'sinatra/cross_origin'
 
 configure do
-  enable :reloader if development?
+  enable :reloader #if development?
   enable :cross_origin
+  disable :show_exceptions
+  disable :raise_errors
 end
 
 #set :protection, :except => :frame_options
 
 # Environment setup from unicorn -E param
 ENV["LAZAR_ENV"] = ENV["RACK_ENV"]
-
+require "../lazar/lib/lazar.rb"
+require "../qsar-report/lib/qsar-report.rb"
+=begin
 if ENV["LAZAR_ENV"] == "development"
   require "../lazar/lib/lazar.rb"
   require "../qsar-report/lib/qsar-report.rb"
@@ -19,28 +23,28 @@ else
   require "lazar"
   require "qsar-report"
 end
+=end
 
 include OpenTox
-#require 'rack/cors'
-
 
-set :show_exceptions => false
-=begin
-# add CORS support for swagger
-  config.allow do |allow|
-    allow.origins '*'
-    allow.resource "/#{SERVICE}/*",
-      :methods => [:head, :get, :post, :put, :delete, :options],
-      :headers => :any,
-      :max_age => 0
-  end
-end
-=end
 before do
-  @accept = request.env['HTTP_ACCEPT'].split.last
+  @accept = request.env['HTTP_ACCEPT']
   response['Content-Type'] = @accept
 end
 
+not_found do
+  400
+  "Path '#{request.env["REQUEST_PATH"]}' not found.\n"
+end
+
+error do
+  response['Content-Type'] = "text/plain"
+  error = request.env['sinatra.error']
+  body = error.message+"\n"
+  error.respond_to?(:http_code) ? code = error.http_code : code = 500
+  halt code, body
+end
+
 # https://github.com/britg/sinatra-cross_origin#responding-to-options
 options "*" do
   response.headers["Allow"] = "HEAD,GET,PUT,POST,DELETE,OPTIONS"
@@ -48,8 +52,6 @@ options "*" do
   200
 end
 
-
-
 [
   "aa.rb",
   "api.rb",
@@ -63,3 +65,4 @@ end
   "swagger.rb",
   "validation.rb"
 ].each{ |f| require_relative f }
+
diff --git a/lib/model.rb b/lib/model.rb
index 22094e9..7a2fb47 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -10,11 +10,9 @@ get "/model/?" do
     return uri_list.join("\n") + "\n"
   when "application/json"
     models = JSON.parse models.to_json
-    models.each_index do |idx|
-      models[idx][:URI] = uri("/model/#{models[idx]["model_id"]["$oid"]}")
-      models[idx][:crossvalidation_uri] = uri("/crossvalidation/#{models[idx]["crossvalidation_id"]["$oid"]}") if models[idx]["crossvalidation_id"]
-    end
-    return models.to_json
+    list = []
+    models.each{|m| list << uri("/model/#{m["model_id"]["$oid"]}")}
+    return list.to_json
   else
     bad_request_error "Mime type #{@accept} is not supported."
   end
@@ -22,7 +20,7 @@ end
 
 get "/model/:id/?" do
   model = Model::Lazar.find params[:id]
-  resource_not_found_error "Model with id: #{params[:id]} not found." unless model
+  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
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
index f32d834..332493d 100644
--- a/lib/nanoparticle.rb
+++ b/lib/nanoparticle.rb
@@ -18,8 +18,13 @@ end
 
 # Get a nanoparticle
 get "/nanoparticle/:id/?" do
-  nanoparticle = Nanoparticle.find :id => params[:id]
-  resource_not_found_error "Nanoparticle with id: #{params[:id]} not found." unless nanoparticle
-  nanoparticle[:URI] = uri("/nanoparticle/#{nanoparticle.id}")
-  return nanoparticle.to_json
-end
\ No newline at end of file
+  case @accept
+  when "application/json"
+    nanoparticle = Nanoparticle.find :id => params[:id]
+    not_found_error "Nanoparticle with id: #{params[:id]} not found." unless nanoparticle
+    nanoparticle[:URI] = uri("/nanoparticle/#{nanoparticle.id}")
+    return nanoparticle.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
diff --git a/lib/report.rb b/lib/report.rb
index 9dff2f2..ae2526c 100644
--- a/lib/report.rb
+++ b/lib/report.rb
@@ -25,7 +25,7 @@ end
 
 get "/report/:id/?" do
   model = Model::Lazar.find params[:id]
-  resource_not_found_error "Model with id: #{params[:id]} not found." unless model
+  not_found_error "Model with id: #{params[:id]} not found." unless model
   prediction_model = Model::Validation.find_by :model_id => params[:id]
   validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml")
 
diff --git a/lib/substance.rb b/lib/substance.rb
index 1116e65..fef1b7e 100644
--- a/lib/substance.rb
+++ b/lib/substance.rb
@@ -18,8 +18,13 @@ end
 
 # Get a substance
 get "/substance/:id/?" do
-  substance = Substance.find :id => params[:id]
-  resource_not_found_error "Substance with id: #{params[:id]} not found." unless substance
-  substance[:URI] = uri("/substance/#{substance.id}")
-  return substance.to_json
-end
\ No newline at end of file
+  case @accept
+  when "application/json"
+    substance = Substance.find :id => params[:id]
+    not_found_error "Substance with id: #{params[:id]} not found." unless substance
+    substance[:URI] = uri("/substance/#{substance.id}")
+    return substance.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
diff --git a/lib/swagger.rb b/lib/swagger.rb
index 916439e..f6b42b2 100644
--- a/lib/swagger.rb
+++ b/lib/swagger.rb
@@ -3,6 +3,6 @@ set :public_folder, File.join("/home/ist/swagger-ui/dist/")
 get "/" do
   response['Content-Type'] = "text/html"
   index_file = File.join("/home/ist/swagger-ui/dist/index.html")
-  #bad_request_error "API Documentation in Swagger JSON is not implemented.", uri("/#{SERVICE}/api") unless File.exists?(index_file)
+  bad_request_error "API Documentation in Swagger JSON is not implemented.", uri("/#{SERVICE}/api") unless File.exists?(index_file)
   File.read(index_file)
 end
diff --git a/lib/validation.rb b/lib/validation.rb
index ce31c34..fad8a44 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -62,10 +62,10 @@ get "/validation/:validationtype/:id/?" do
     validation = Validation::RegressionCrossValidation.find params[:id]
   end
 
-  resource_not_found_error "#{params[:validationtype]} with id: #{params[:id]} not found." unless validation
+  not_found_error "#{params[:validationtype]} with id: #{params[:id]} not found." unless validation
   #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 validation.to_json
-end
\ No newline at end of file
+end
diff --git a/test/descriptor.rb b/test/descriptor.rb
index db4b6c7..14c8602 100644
--- a/test/descriptor.rb
+++ b/test/descriptor.rb
@@ -9,7 +9,7 @@ class DescriptorTest < MiniTest::Test
     result = RestClientWrapper.get File.join($host, "compound/descriptor"), {}, {:accept => "text/plain"}
     assert_equal result.code, 200
     assert result.include?("Joelib.KierShape1: JOELIb does not provide meaningful descriptions, see java/JoelibDescriptors.java for details.\nJoelib.KierShape2: JOELIb does not provide meaningful descriptions, see java/JoelibDescriptors.java for details."), "Descriptor list is not complete."
-    assert_equal 355, result.lines.count
+    assert_equal 346, result.lines.count
   end
 
   def test_01_get_descriptor
diff --git a/test/setup.rb b/test/setup.rb
index 1c47dff..aa17e54 100644
--- a/test/setup.rb
+++ b/test/setup.rb
@@ -2,7 +2,7 @@ require 'minitest/autorun'
 
 require_relative '../../lazar/lib/lazar.rb'
 require_relative '../../lazar/test/setup.rb'
-$host = "https://enm.in-silico.ch"
+$host = "https://api.in-silico.ch"
 include OpenTox
 REST_TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
 REST_DATA_DIR ||= File.join(REST_TEST_DIR,"data")