1 files changed, 69 insertions, 0 deletions
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
new file mode 100644
index 0000000..b934bb3
--- /dev/null
+++ b/lib/nanoparticle.rb
@@ -0,0 +1,69 @@
+module OpenTox
+
+  class Nanoparticle < Substance
+    include OpenTox
+
+    field :core, type: String
+    field :coating, type: Array, default: []
+    field :bundles, type: Array, default: []
+
+    def nanoparticle_neighbors params
+      Dataset.find(params[:training_dataset_id]).nanoparticles
+    end
+
+    def add_feature feature, value
+      case feature.category
+      when "P-CHEM"
+        physchem_descriptors[feature.id.to_s] ||= []
+        physchem_descriptors[feature.id.to_s] << value
+      when "TOX"
+        toxicities[feature.id.to_s] ||= []
+        toxicities[feature.id.to_s] << value
+      else
+        warn "Unknown feature type '#{feature.category}'. Value '#{value}' not inserted."
+      end
+      save
+    end
+
+    def parse_ambit_value feature, v
+      v.delete "unit"
+      # TODO: mmol/log10 conversion
+      if v.keys == ["textValue"]
+        add_feature feature, v["textValue"]
+      elsif v.keys == ["loValue"]
+        add_feature feature, v["loValue"]
+      elsif v.keys.size == 2 and v["errorValue"]
+        add_feature feature, v["loValue"]
+        warn "Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'."
+      elsif v.keys.size == 2 and v["loQualifier"] == "mean"
+        add_feature feature, v["loValue"]
+        warn "'#{feature.name}' is a mean value. Original data is not available."
+      elsif v.keys.size == 2 and v["loQualifier"] #== ">="
+        warn "Only min value available for '#{feature.name}', entry ignored"
+      elsif v.keys.size == 2 and v["upQualifier"] #== ">="
+        warn "Only max value available for '#{feature.name}', entry ignored"
+      elsif v.keys.size == 3 and v["loValue"] and v["loQualifier"].nil? and v["upQualifier"].nil?
+        add_feature feature, v["loValue"]
+        warn "loQualifier and upQualifier are empty."
+      elsif v.keys.size == 3 and v["loValue"] and v["loQualifier"] == "" and v["upQualifier"] == ""
+        add_feature feature, v["loValue"]
+        warn "loQualifier and upQualifier are empty."
+      elsif v.keys.size == 4 and v["loValue"] and v["loQualifier"].nil? and v["upQualifier"].nil?
+        add_feature feature, v["loValue"]
+        warn "loQualifier and upQualifier are empty."
+      elsif v.size == 4 and v["loQualifier"] and v["upQualifier"] and v["loValue"] and v["upValue"]
+        add_feature feature, [v["loValue"],v["upValue"]].mean
+        warn "Using mean value of range #{v["loValue"]} - #{v["upValue"]} for '#{feature.name}'. Original data is not available."
+      elsif v.size == 4 and v["loQualifier"] == "mean" and v["errorValue"]
+        warn "'#{feature.name}' is a mean value. Original data is not available. Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'."
+        add_feature feature, v["loValue"]
+      elsif v == {} # do nothing
+      else
+        warn "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'."
+      end
+    end
+
+  end
+end
+
+