From f3780d7507092b643216054fa3ca1e6146281e43 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 8 Apr 2016 13:04:56 +0200
Subject: enm import test

---
 lib/compound.rb     |  1 +
 lib/lazar.rb        |  1 +
 lib/nanoparticle.rb | 45 ++++++++++++++++++++++++++++++++++++++++-----
 3 files changed, 42 insertions(+), 5 deletions(-)

(limited to 'lib')

diff --git a/lib/compound.rb b/lib/compound.rb
index 2a79fd6..a7518ed 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -21,6 +21,7 @@ module OpenTox
     field :default_fingerprint_size, type: Integer
     field :physchem_descriptors, type: Hash, default: {}
     field :dataset_ids, type: Array, default: []
+    # TODO separate between physchem, bio and tox
     field :features, type: Hash, default: {}
 
     index({smiles: 1}, {unique: true})
diff --git a/lib/lazar.rb b/lib/lazar.rb
index 39dd8fa..0e2cec2 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -81,5 +81,6 @@ CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveO
   "crossvalidation.rb",
   "leave-one-out-validation.rb",
   "experiment.rb",
+  "import.rb",
 ].each{ |f| require_relative f }
 OpenTox::PhysChem.descriptors # load descriptor features
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
index 3783ece..cda431a 100644
--- a/lib/nanoparticle.rb
+++ b/lib/nanoparticle.rb
@@ -3,13 +3,48 @@ module OpenTox
   class Nanoparticle
     include OpenTox
 
-    field :particle_id, type: String
+    #field :particle_id, type: String
     field :core, type: String
-    field :coatings, type: Array
+    field :coating, type: Array, default: []
 
-    #field :physchem_descriptors, type: Hash, default: {}
-    #field :toxicities, type: Hash, default: {}
-    field :features, type: Hash, default: {}
+    field :physchem_descriptors, type: Hash, default: {}
+    field :toxicities, type: Hash, default: {}
+    #field :features, type: Hash, default: {}
+    field :bundles, type: Array, default: []
+
+    def predict
+    end
+
+    def add_feature feature, value
+      if feature.source.match /property\/P-CHEM/
+        physchem_descriptors[feature.id.to_s] ||= []
+        physchem_descriptors[feature.id.to_s] << value
+      elsif feature.source.match /property\/TOX/
+        toxicities[feature.id.to_s] ||= []
+        toxicities[feature.id.to_s] << value
+      else
+        $logger.warn "Unknown feature type '#{feature.source}'. Value '#{value}' not inserted."
+        warnings << "Unknown feature type '#{feature.source}'. Value '#{value}' not inserted."
+      end
+    end
+
+    def parse_ambit_value feature, v
+      if v.keys == ["loValue"]
+        add_feature feature, v["loValue"]
+      elsif v.keys.size == 2 and v["loQualifier"] == "mean"
+        add_feature feature, {:mean => v["loValue"]}
+      elsif v.keys.size == 2 and v["loQualifier"] #== ">="
+        add_feature feature, {:min => v["loValue"],:max => Float::INFINITY}
+      elsif v.keys.size == 2 and v["upQualifier"] #== ">="
+        add_feature feature, {:max => v["upValue"],:min => -Float::INFINITY}
+      elsif v.size == 4 and v["loQualifier"] and v["upQualifier"] 
+        add_feature feature, {:min => v["loValue"],:max => v["upValue"]}
+      elsif v == {} # do nothing
+      else
+        $logger.warn "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'."
+        warnings << "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'."
+      end
+    end
 
   end
 end
-- 
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