From 878f014ec6cc808af99af5045bcc1a1143cab8d9 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Thu, 5 Jul 2018 10:38:55 +0000
Subject: updated with endpoint list; refined error handling; refined
 prediction input

---
 api/api.json    | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 application.rb  | 16 ++++++++---
 lib/endpoint.rb | 23 ++++++++++++++++
 lib/model.rb    |  2 +-
 4 files changed, 119 insertions(+), 6 deletions(-)
 create mode 100644 lib/endpoint.rb

diff --git a/api/api.json b/api/api.json
index 6aa95ad..718421f 100644
--- a/api/api.json
+++ b/api/api.json
@@ -32,6 +32,75 @@
     "url": "https://github.com/opentox/lazar-rest"
   },
   "paths": {
+    "/endpoint": {
+      "get": {
+        "x-orn-@type": "x-orn:Endpoint",
+        "x-orn:path": "https://lazar.prod.openrisknet.org/endpoint",
+        "x-orn:method": "Get",
+        "tags": [
+          "endpoint"
+        ],
+        "description": "Get a list of all available endpoints",
+        "parameters": [
+          {
+            "$ref": "#/components/parameters/subjectid"
+          }
+        ],
+        "responses": {
+          "200": {
+            "$ref": "#/components/responses/200"
+          },
+          "400": {
+            "$ref": "#/components/responses/400"
+          },
+          "401": {
+            "$ref": "#/components/responses/401"
+          },
+          "404": {
+            "$ref": "#/components/responses/404"
+          },
+          "500": {
+            "$ref": "#/components/responses/500"
+          }
+        }
+      }
+    },
+    "/endpoint/{endpoint}": {
+      "get": {
+        "x-orn-@type": "x-orn:Endpoint",
+        "x-orn:path": "https://lazar.prod.openrisknet.org/endpoint",
+        "x-orn:method": "Get",
+        "tags": [
+          "endpoint"
+        ],
+        "description": "Get a list of all available models for an endpoint",
+        "parameters": [
+          {
+            "$ref": "#/components/parameters/endpoint"
+          },
+          {
+            "$ref": "#/components/parameters/subjectid"
+          }
+        ],
+        "responses": {
+          "200": {
+            "$ref": "#/components/responses/200"
+          },
+          "400": {
+            "$ref": "#/components/responses/400"
+          },
+          "401": {
+            "$ref": "#/components/responses/401"
+          },
+          "404": {
+            "$ref": "#/components/responses/404"
+          },
+          "500": {
+            "$ref": "#/components/responses/500"
+          }
+        }
+      }
+    },
     "/model": {
       "get": {
         "x-orn-@type": "x-orn:Model",
@@ -107,7 +176,7 @@
         "tags": [
           "model"
         ],
-        "description": "Predict a compound or a nanoparticle",
+        "description": "Predict a compound or a nanoparticle. Also a comma seperated list is allowed.",
         "parameters": [
           {
             "$ref": "#/components/parameters/id"
@@ -1030,6 +1099,10 @@
       "name": "descriptor",
       "description": "Descriptor"
     },
+    {
+      "name": "endpoint",
+      "description": "Endpoint"
+    },
     {
       "name": "feature",
       "description": "Feature"
@@ -1116,6 +1189,15 @@
           "type": "string"
         }
       },
+      "endpoint": {
+        "name": "endpoint",
+        "in": "path",
+        "description": "type",
+        "required": true,
+        "schema": {
+          "type": "string"
+        }
+      },
       "InChI": {
         "name": "InChI",
         "in": "path",
diff --git a/application.rb b/application.rb
index ebcb0af..a5f9ff2 100644
--- a/application.rb
+++ b/application.rb
@@ -7,6 +7,7 @@ include OpenTox
   "api.rb",
   "compound.rb",
   "dataset.rb",
+  "endpoint.rb",
   "feature.rb",
   "model.rb",
   "nanoparticle.rb",
@@ -28,12 +29,13 @@ configure :development do
 end
 
 before do
-  paths = [
+  $paths = [
   "/",
   "aa",
   "api",
   "compound",
   "dataset",
+  "endpoint",
   "feature",
   "model",
   "nanoparticle",
@@ -41,7 +43,7 @@ before do
   "substance",
   "swagger",
   "validation"]
-  if request.path == "/" || paths.include?(request.path.split("/")[1])
+  if request.path == "/" || $paths.include?(request.path.split("/")[1])
     @accept = request.env['HTTP_ACCEPT']
     response['Content-Type'] = @accept
   else
@@ -54,8 +56,14 @@ not_found do
 end
 
 error do
-  @error = request.env['sinatra.error']
-  haml :error
+  if request.path == "/" || $paths.include?(request.path.split("/")[1])
+    @accept = request.env['HTTP_ACCEPT']
+    response['Content-Type'] = @accept
+    @accept == "text/plain" ? request.env['sinatra.error'] : request.env['sinatra.error'].to_json
+  else
+    @error = request.env['sinatra.error']
+    haml :error
+  end
 end
 
 # https://github.com/britg/sinatra-cross_origin#responding-to-options
diff --git a/lib/endpoint.rb b/lib/endpoint.rb
new file mode 100644
index 0000000..ef39787
--- /dev/null
+++ b/lib/endpoint.rb
@@ -0,0 +1,23 @@
+# Get a list of all endpoints
+# @param [Header] Accept one of text/uri-list,
+# @return [text/uri-list] list of all prediction models
+get "/endpoint/?" do
+  models = Model::Validation.all
+  endpoints = models.collect{|m| m.endpoint}.uniq
+  case @accept
+  when "text/uri-list"
+    return endpoints.join("\n") + "\n"
+  when "application/json"
+    return endpoints.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+get "/endpoint/:endpoint/?" do
+  models = Model::Validation.where(endpoint: params[:endpoint])
+  list = []
+  models.each{|m| list << {m.species => uri("/model/#{m.id}")} }
+  not_found_error "Endpoint: #{params[:endpoint]} not found." if models.blank?
+  return list.to_json
+end
diff --git a/lib/model.rb b/lib/model.rb
index 9fbd90f..3764ee2 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -27,7 +27,7 @@ end
 
 post "/model/:id/?" do
   identifier = params[:identifier].split(",")
-  compounds = identifier.collect{ |i| Compound.from_smiles i.strip }
+  compounds = identifier.collect{ |i| Compound.from_smiles i.strip.gsub(/\A"|"\Z/,'') }
   model = Model::Validation.find params[:id]
   batch = {}
   compounds.each do |compound|
-- 
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