From 01141de159d7b39209b284df9230127aef09a793 Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Thu, 8 Sep 2016 11:49:50 +0200
Subject: add initial reporting on QMRF

---
 lib/lazar-rest.rb |  2 ++
 lib/report.rb     | 70 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+)
 create mode 100644 lib/report.rb

(limited to 'lib')

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
-- 
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