add initial reporting on QMRF

3 files changed, 161 insertions, 0 deletions

diff --git a/api/api.json b/api/api.json
index abc4a0b..550c547 100644
--- a/api/api.json
+++ b/api/api.json
@@ -143,6 +143,91 @@
                 }
             }
         },
+        "/model/report": {
+            "get": {
+                "tags": [
+                    "report"
+                ],
+                "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"
+                        ]
+                    }
+                ],
+                "produces": [
+                    "text/uri-list",
+                    "application/json"
+                ],
+                "responses": {
+                    "200": {
+                        "$ref": "#/responses/200"
+                    },
+                    "400": {
+                        "$ref": "#/responses/400"
+                    },
+                    "401": {
+                        "$ref": "#/responses/401"
+                    },
+                    "404": {
+                        "$ref": "#/responses/404"
+                    },
+                    "500": {
+                        "$ref": "#/responses/500"
+                    }
+                }
+            }
+        },
+        "/model/report/{id}": {
+            "get": {
+                "tags": [
+                    "report"
+                ],
+                "description": "Get a QMRF report",
+                "parameters": [
+                    {
+                        "name": "accept",
+                        "in": "header",
+                        "description": "requested Content-Type",
+                        "required": true,
+                        "type": "string",
+                        "enum": [
+                            "application/xml"
+                        ]
+                    },
+                    {
+                        "$ref": "#/parameters/id"
+                    }
+                ],
+                "produces": [
+                    "application/xml"
+                ],
+                "responses": {
+                    "200": {
+                        "$ref": "#/responses/200"
+                    },
+                    "400": {
+                        "$ref": "#/responses/400"
+                    },
+                    "401": {
+                        "$ref": "#/responses/401"
+                    },
+                    "403": {
+                        "$ref": "#/responses/403"
+                    },
+                    "404": {
+                        "$ref": "#/responses/404"
+                    }
+                }
+            }
+        },
         "/dataset": {
             "get": {
                 "tags": [
@@ -1062,6 +1147,10 @@
         {
             "name": "feature",
             "description": "Feature"
+        },
+        {
+            "name": "report",
+            "description": "QMRF Reporting"
         }
     ]
 }
\ No newline at end of file
diff --git a/lib/lazar-rest.rb b/lib/lazar-rest.rb
index 7514ba1..2de3998 100644
--- a/lib/lazar-rest.rb
+++ b/lib/lazar-rest.rb
@@ -1,5 +1,6 @@
 require "sinatra"
 require "../lazar/lib/lazar.rb"
+require "../qsar-report/lib/qsar-report.rb"
 include OpenTox
 
 require 'rack/cors'
@@ -30,6 +31,7 @@ end
   "feature.rb",
   "model.rb",
   "nanoparticle.rb",
+  "report.rb",
   "substance.rb",
   "validation.rb"
 ].each{ |f| require_relative f }
diff --git a/lib/report.rb b/lib/report.rb
new file mode 100644
index 0000000..c8b8165
--- /dev/null
+++ b/lib/report.rb
@@ -0,0 +1,70 @@
+# Get a list of all possible reports to prediction models
+# @param [Header] Accept one of text/uri-list,
+# @return [text/uri-list] list of all prediction models
+get "/model/report/?" do
+  models = Model::Prediction.all
+  case @accept
+  when "text/uri-list"
+    uri_list = models.collect{|model| uri("/model/report/#{model.model_id}")}
+    return uri_list.join("\n") + "\n"
+  when "application/json"
+    reports = [{}]
+    #models = JSON.parse models.to_json
+    models.each_index do |idx|
+      reports[idx] = {}
+      reports[idx][:URI] = uri("/model/report/#{models[idx]["model_id"]}")
+      reports[idx][:repeated_crossvalidation_uri] = uri("/validation/repeatedcrossvalidation/#{models[idx]["repeated_crossvalidation_id"]}") if models[idx]["repeated_crossvalidation_id"]
+      reports[idx][:leave_one_out_validation_uri] = uri("/validation/leaveoneoutvalidation/#{models[idx]["leave_one_out_validation_id"]}") if models[idx]["leave_one_out_validation_id"]
+      reports[idx][:training_dataset_URI] = uri("/dataset/#{models[idx].training_dataset.id}") if models[idx].training_dataset.id 
+    end
+    return reports.to_json
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+
+get "/model/report/:id/?" do
+  model = Model::Lazar.find params[:id]
+  resource_not_found_error "Model with id: #{params[:id]} not found." unless model
+  prediction_model = Model::Prediction.find_by :model_id => params[:id]
+
+  report = OpenTox::QMRFReport.new
+  
+  # QSAR Identifier Title 1.1
+  report.value "QSAR_title", "Lazar model for #{prediction_model.species} #{prediction_model.endpoint}"
+
+  # Software coding the model 1.3
+  report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :description => "lazar Lazy Structure- Activity Relationships", :number => "1", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"}
+  report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware
+  
+  # Date of QMRF 2.1
+  report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}"
+  
+  # QMRF author(s) and contact details 2.1
+  report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"}
+  report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor
+  
+  # Model developer(s) and contact details 2.5
+  report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"}
+  report.ref_catalog :model_authors, :authors_catalog, :modelauthor
+  
+  # Date of model development and/or publication 2.6
+  report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}"
+  
+  # Reference(s) to main scientific papers and/or software package 2.7
+  report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "lazar: a modular predictive toxicology framework", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"}
+  report.ref_catalog :references, :publications_catalog, :publications_catalog_1
+  
+  # Species 3.1
+  report.value "model_species", prediction_model.species 
+  
+  # Endpoint 3.2 
+  report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""}
+  report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1
+  
+  # Endpoint Units 3.4
+  report.value "endpoint_units", "#{prediction_model.unit}"
+  response['Content-Type'] = "application/xml"
+  return report.to_xml
+
+end