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require 'json'
require 'yaml'
#require_relative "../lazar/lib/lazar.rb"
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
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
nm.tox.uniq! if nm.tox
nm.p_chem.uniq! if nm.p_chem
nanomaterials << nm
end
end
puts "Total imported: #{nanomaterials.size}"
puts "With nanoparticle characterisation: #{nanomaterials.select{|n| n.p_chem}.size}"
modelling_data = nanomaterials.select{|n| n.tox and n.p_chem}
puts "With TOX data: #{nanomaterials.select{|n| n.tox}.size}"
puts "With TOX data and particle characterisation: #{modelling_data.size}"
endpoints = modelling_data.collect{|n| n.tox.collect{|t| t.keys}}.flatten.compact.uniq
puts "Endpoints: #{endpoints.size}"
single_value_endpoints = []
endpoint_values = {}
endpoints.each do |e|
#json = `curl -H "Accept:application/json" "#{e}" 2>/dev/null`
#f = JSON.parse(json)["feature"]
#p k unless f.keys.size == 1
#k = f.keys.first
#p e
#p modelling_data.select{|n| n.tox.select{|t| t[e]}}.size
i = 0
values = []
modelling_data.each do |n|
n.tox.each do |t|
if t[e]
i += 1
values << t[e]
end
end
end
single_value_endpoints << e if values.uniq.size == 1
endpoint_values[e] = values.size unless values.uniq.size == 1
#puts "#{f[k]['title']} [#{f[k]['units']}]: #{i} #{values}"
end
endpoints -= single_value_endpoints
puts "Endpoints with more than one measurement value: #{endpoints.size}"
#endpoint_values.sort{|a,b| b[1] <=> a[1]}
endpoint_values.select!{|k,v| v > 10}
puts "Endpoints with more than 10 measurements: #{endpoint_values.size}"
endpoints = endpoint_values.keys
#puts endpoints.to_yaml
endpoint_values.sort{|a,b| b[1] <=> a[1]}.each do |e,v|
json = `curl -H "Accept:application/json" "#{e}" 2>/dev/null`
f = JSON.parse(json)["feature"]
p k unless f.keys.size == 1
k = f.keys.first
p e
puts "#{f[k]['title']} [#{f[k]['units']}]: #{v} "
end
#puts "Endpoints with more than one value single_value_endpoints.size
#puts names.sort.uniq.to_yaml
#p nanomaterials.collect{|n| n.uri}.uniq.size
|
