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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
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