From 43792e2322ded616c7eefb4b52083ba64e48e63c Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Wed, 16 Nov 2016 13:43:59 +0100
Subject: adapt code to lazar 1.0.0

---
 lib/compound.rb    | 8 ++++----
 lib/model.rb       | 2 +-
 test/aa.rb         | 4 ++++
 test/descriptor.rb | 4 ++--
 4 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/lib/compound.rb b/lib/compound.rb
index 9390a96..01ba036 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -23,14 +23,14 @@ post "/compound/descriptor/?" do
   descriptors.each do |descriptor|
     physchem_descriptors << PhysChem.find_by(:name => descriptor)
   end
-  result = compound.physchem physchem_descriptors
-  csv = result.collect{|k,v| "\"#{PhysChem.find(k).name}\",#{v}" }.join("\n")
-  csv = "SMILES,#{params[:identifier]}\n#{csv}" if params[:identifier]
+  result = compound.calculate_properties physchem_descriptors
+  csv = (0..result.size-1).collect{|i| "\"#{physchem_descriptors[i].name}\",#{result[i]}"}.join("\n")
+  csv = "SMILES,\"#{params[:identifier]}\"\n#{csv}" if params[:identifier]
   case @accept
   when "text/csv","application/csv"
     return csv
   when "application/json"
-    result_hash = result.collect{|k,v|  {"#{PhysChem.find(k).name}" => "#{v}"}}  # result.collect{|k,v| "\"#{PhysChem.find(k).name}\"" => "#{v}"}.join(",")
+    result_hash = (0..result.size-1).collect{|i| {"#{physchem_descriptors[i].name}" => "#{result[i]}"}}
     data = {"compound" => {"SMILES" => "#{params[:identifier]}"}}
     data["compound"]["InChI"] = "#{compound.inchi}" if compound.inchi
     data["compound"]["results"] = result_hash
diff --git a/lib/model.rb b/lib/model.rb
index db0c190..a20850b 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -24,7 +24,7 @@ get "/model/:id/?" do
   model = Model::Lazar.find params[:id]
   resource_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[: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 model.to_json
diff --git a/test/aa.rb b/test/aa.rb
index 927bc35..f785900 100644
--- a/test/aa.rb
+++ b/test/aa.rb
@@ -2,6 +2,10 @@ require_relative "setup.rb"
 
 class AATest < MiniTest::Test
 
+  def self.test_order
+    :alpha
+  end
+
   def test_0_login
     res = RestClientWrapper.post(File.join($host,"aa/authenticate"),{:username=>"guest", :password => "guest"},{:Accept => "text/plain"})
     assert_equal res.code, 200
diff --git a/test/descriptor.rb b/test/descriptor.rb
index eae3ebf..db4b6c7 100644
--- a/test/descriptor.rb
+++ b/test/descriptor.rb
@@ -27,13 +27,13 @@ class DescriptorTest < MiniTest::Test
     result = RestClientWrapper.get File.join($host, "compound/descriptor", bsonid), {}, {:accept => "application/json"}
     json = JSON.parse(result)
     assert_equal json["name"], "Openbabel.HBA1"
-    assert_equal json["numeric"], true
+    assert_equal json["calculated"], true
   end
 
   def test_04_post_descriptor
     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,CC(=O)CC(C)C#N\n\"Joelib.LogP\",2.65908", result
+    assert_equal "SMILES,\"CC(=O)CC(C)C#N\"\n\"Joelib.LogP\",2.65908", result
   end
 
   # currently not applicable
-- 
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