1 files changed, 72 insertions, 0 deletions
diff --git a/import.rb b/import.rb
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index 0000000..b086a8c
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+++ b/import.rb
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+require 'json'
+require 'yaml'
+require_relative "lib/nano-lazar.rb"
+include OpenTox
+
+nanomaterials = []
+names = []
+
+["nanowiki.json",  "protein-corona.json", "marina.json"].each do |f|
+  JSON.parse(File.read(File.join("data",f)))["dataEntry"].each do |substance|
+    nm = Nanomaterial.new
+    nm.uri = substance["compound"]["URI"]
+    if substance["composition"]
+      nr_cores = substance["composition"].select{|c| c["relation"] == "HAS_CORE"}.size
+      puts "#{substance["compound"]["URI"]} has #{nr_cores} cores" if nr_cores !=1
+      #component = substance["composition"]#["component"]
+      substance["composition"].each do |composition|
+        component = composition["component"]
+        if component
+          name = component["values"]["https://apps.ideaconsult.net/enanomapper/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
+          names << name
+          if composition["relation"] == "HAS_CORE"
+            nm.core = name
+          elsif composition["relation"] == "HAS_COATING"
+            nm.coating ||= []
+            nm.coating << name
+          end
+        else
+          #puts substance.to_yaml
+        end
+      end
+    else
+      #puts substance.to_yaml
+    end
+    substance["values"].each do |k,v|
+      property = nil
+      if k.match(/TOX/)
+        nm.tox ||= []
+        property = "tox"
+      elsif k.match(/P-CHEM/)
+        nm.p_chem ||= []
+        property = "p_chem"
+      end
+      if property
+        v.each do |val|
+          if val.keys == ["loValue"]
+            nm.tox << {k => val["loValue"]} if property == "tox"
+            nm.p_chem << {k => val["loValue"]} if property == "p_chem"
+          elsif val.keys == ["loQualifier", "loValue"] and val["loQualifier"] == "mean"
+            nm.tox << {k => val["loValue"]} if property == "tox"
+            nm.p_chem << {k => val["loValue"]} if property == "p_chem"
+          elsif val.keys == ["loQualifier", "loValue", "upQualifier", "upValue" ]
+            nm.tox << {k => (val["loValue"]+val["upValue"])/2} if property == "tox"
+            nm.p_chem << {k => (val["loValue"]+val["upValue"])/2} if property == "p_chem"
+          elsif val.keys == ["loQualifier", "loValue"] and val["loQualifier"] == ">="
+          else
+          p val
+          end
+        end
+      else
+        #p k,v
+      end
+    end
+    nanomaterials << nm
+  end
+end
+puts "Total imported: #{nanomaterials.size}"
+puts "With TOX data: #{nanomaterials.select{|n| n.tox}.size}"
+puts "With nanoparticle characterisation: #{nanomaterials.select{|n| n.p_chem}.size}"
+puts "With TOX data and particle characterisation: #{nanomaterials.select{|n| n.tox and n.p_chem}.size}"
+#puts names.sort.uniq.to_yaml
+#p nanomaterials.collect{|n| n.uri}.uniq.size