add nanoparticle route

5 files changed, 120 insertions, 5 deletions

diff --git a/api/api.json b/api/api.json
index e253fe7..e30ff98 100644
--- a/api/api.json
+++ b/api/api.json
@@ -369,6 +369,91 @@
                 }
             }
         },
+        "/nanoparticle": {
+            "get": {
+                "tags": [
+                    "nanoparticle"
+                ],
+                "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"
+                        ]
+                    }
+                ],
+                "produces": [
+                    "text/uri-list",
+                    "application/json"
+                ],
+                "responses": {
+                    "200": {
+                        "$ref": "#/responses/200"
+                    },
+                    "400": {
+                        "$ref": "#/responses/400"
+                    },
+                    "401": {
+                        "$ref": "#/responses/401"
+                    },
+                    "404": {
+                        "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
+                    }
+                }
+            }
+        },
+        "/nanoparticle/{id}": {
+            "get": {
+                "tags": [
+                    "nanoparticle"
+                ],
+                "description": "Get nanoparticle representation",
+                "parameters": [
+                    {
+                        "name": "Content-Type",
+                        "in": "header",
+                        "description": "body Content-Type",
+                        "required": true,
+                        "type": "string",
+                        "enum": [
+                            "application/json"
+                        ]
+                    },
+                    {
+                        "$ref": "#/parameters/id"
+                    }
+                ],
+                "produces": [
+                    "application/json"
+                ],
+                "responses": {
+                    "200": {
+                        "$ref": "#/responses/200"
+                    },
+                    "400": {
+                        "$ref": "#/responses/400"
+                    },
+                    "401": {
+                        "$ref": "#/responses/401"
+                    },
+                    "403": {
+                        "$ref": "#/responses/403"
+                    },
+                    "404": {
+                        "$ref": "#/responses/404"
+                    }
+                }
+            }
+        },
         "/feature": {
             "get": {
                 "tags": [
@@ -894,6 +979,10 @@
             "description": "Substance"
         },
         {
+            "name": "nanoparticle",
+            "description": "Nanoparticle"
+        },
+        {
             "name": "feature",
             "description": "Feature"
         }
diff --git a/lib/lazar-rest.rb b/lib/lazar-rest.rb
index c0ea639..1e173fc 100644
--- a/lib/lazar-rest.rb
+++ b/lib/lazar-rest.rb
@@ -28,6 +28,7 @@ end
   "dataset.rb",
   "feature.rb",
   "model.rb",
+  "nanoparticle.rb",
   "substance.rb",
   "validation.rb"
 ].each{ |f| require_relative f }
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
new file mode 100644
index 0000000..f32d834
--- /dev/null
+++ b/lib/nanoparticle.rb
@@ -0,0 +1,25 @@
+# Get all Nanoparticles
+get "/nanoparticle/?" do
+  nanoparticles = Nanoparticle.all
+  case @accept
+  when "text/uri-list"
+    uri_list = nanoparticles.collect{|nanoparticle| uri("/nanoparticle/#{nanoparticle.id}")}
+    return uri_list.join("\n") + "\n"
+  when "application/json"
+    nanoparticles = JSON.parse nanoparticles.to_json
+    nanoparticles.each_index do |idx|
+      nanoparticles[idx][:URI] = uri("/nanoparticle/#{nanoparticles[idx]["_id"]["$oid"]}")
+    end
+    return nanoparticles.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+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
diff --git a/test/descriptor.rb b/test/descriptor.rb
index 8438898..834d56b 100644
--- a/test/descriptor.rb
+++ b/test/descriptor.rb
@@ -6,27 +6,27 @@ $host = "#{$host}"
 class DescriptorTest < MiniTest::Test
 
   def test_00_get_descriptors
-    result = RestClientWrapper.get File.join($host, "algorithm/descriptor"), {}, {:accept => "text/plain"}
+    result = RestClientWrapper.get File.join($host, "compound/descriptor"), {}, {:accept => "text/plain"}
     assert_equal result.code, 200
     assert result.include?("Joelib.KierShape1: no description available\nJoelib.KierShape2: no description available"), "Descriptor list is not complete."
     assert_equal 110, result.lines.count
   end
 
   def test_01_get_descriptor
-    result = RestClientWrapper.get File.join($host, "algorithm/descriptor", "Openbabel.MW"), {}, {:accept => "text/plain"}
+    result = RestClientWrapper.get File.join($host, "compound/descriptor", "Openbabel.MW"), {}, {:accept => "text/plain"}
     assert_equal result.code, 200
     assert_equal result, "Molecular Weight filter"
   end
 
   def test_02_post_descriptor
-    result = RestClientWrapper.post File.join($host, "algorithm/descriptor"), {:identifier => "CC(=O)CC(C)C#N", :descriptor => "Joelib.LogP"}, {:accept => "application/csv"}
+    result = RestClientWrapper.post File.join($host, "compound/descriptor"), {:identifier => "CC(=O)CC(C)C#N", :descriptor => "Joelib.LogP"}, {:accept => "application/csv"}
     assert_equal result.code, 200
     assert_equal "SMILES,Joelib.LogP\nCC(=O)CC(C)C#N,2.65908\n", result
   end
 
   def test_03_post_descriptor_file
     file = File.join(DATA_DIR, "hamster_carcinogenicity.mini.csv")
-    result = RestClientWrapper.post File.join($host, "algorithm/descriptor"), {:file => File.open(file), :descriptor => "Openbabel.logP,Cdk.AtomCount,Cdk.CarbonTypes,Joelib.LogP"}, {:accept => "application/json"}
+    result = RestClientWrapper.post File.join($host, "compound/descriptor"), {:file => File.open(file), :descriptor => "Openbabel.logP,Cdk.AtomCount,Cdk.CarbonTypes,Joelib.LogP"}, {:accept => "application/json"}
     assert_equal result.code, 200
     proof_result = File.read(File.join(REST_DATA_DIR, "test_03_post_descriptor_file.result"))
     assert_equal result, proof_result.strip
diff --git a/test/setup.rb b/test/setup.rb
index b670fdd..1c47dff 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'
-$host = "https://mr-test.in-silico.ch"
+$host = "https://enm.in-silico.ch"
 include OpenTox
 REST_TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
 REST_DATA_DIR ||= File.join(REST_TEST_DIR,"data")