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module OpenTox
module Import
class Enanomapper
include OpenTox
def self.mirror dir="."
#get list of bundle URIs
bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle?media=application%2Fjson'))["dataset"]
File.open(File.join(dir,"bundles.json"),"w+"){|f| f.puts JSON.pretty_generate(bundles)}
bundles.each do |bundle|
$logger.debug bundle["title"]
nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"]+"?media=application%2Fjson"))["dataEntry"]
$logger.debug nanoparticles.size
nanoparticles.each do |nanoparticle|
uuid = nanoparticle["values"]["https://data.enanomapper.net/identifier/uuid"]
$logger.debug uuid
File.open(File.join(dir,"nanoparticle-#{uuid}.json"),"w+"){|f| f.puts JSON.pretty_generate(nanoparticle)}
studies = JSON.parse(RestClientWrapper.get(File.join(nanoparticle["compound"]["URI"],"study")))["study"]
$logger.debug uuid if studies.size < 1
studies.each do |study|
File.open(File.join(dir,"study-#{study["uuid"]}.json"),"w+"){|f| f.puts JSON.pretty_generate(study)}
end
end
end
end
def self.import dir="."
start_time = Time.now
t1 = 0
t2 = 0
datasets = {}
JSON.parse(File.read(File.join(dir,"bundles.json"))).each do |bundle|
datasets[bundle["URI"]] = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"])
end
Dir[File.join(dir,"study*.json")].each do |s|
t = Time.now
study = JSON.parse(File.read(s))
np = JSON.parse(File.read(File.join(dir,"nanoparticle-#{study['owner']['substance']['uuid']}.json")))
core = {}
coating = []
np["composition"].each do |c|
if c["relation"] == "HAS_CORE"
core = {
:uri => c["component"]["compound"]["URI"],
:name => c["component"]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
}
elsif c["relation"] == "HAS_COATING"
coating << {
:uri => c["component"]["compound"]["URI"],
:name => c["component"]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
}
end
end if np["composition"]
nanoparticle = Nanoparticle.find_or_create_by(
:name => np["values"]["https://data.enanomapper.net/identifier/name"],
:source => np["compound"]["URI"],
:core => core,
:coating => coating
)
np["bundles"].keys.each do |bundle_uri|
nanoparticle.dataset_ids << datasets[bundle_uri].id
end
dataset = datasets[np["bundles"].keys.first]
proteomics_features = {}
study["effects"].each do |effect|
effect["result"]["textValue"] ? klass = NominalFeature : klass = NumericFeature
effect["conditions"].delete_if { |k, v| v.nil? }
if study["protocol"]["category"]["title"].match(/Proteomics/) and effect["result"]["textValue"] and effect["result"]["textValue"].length > 50 # parse proteomics data
=begin
JSON.parse(effect["result"]["textValue"]).each do |identifier, value|
# time critical step
t = Time.now
proteomics_features[identifier] ||= klass.find_or_create_by(:name => identifier, :category => "Proteomics")
t1 += Time.now - t
t = Time.now
nanoparticle.parse_ambit_value proteomics_features[identifier], value, dataset
t2 += Time.now - t
end
=end
else
feature = klass.find_or_create_by(
:name => effect["endpoint"],
:unit => effect["result"]["unit"],
:category => study["protocol"]["topcategory"],
:conditions => effect["conditions"]
)
nanoparticle.parse_ambit_value feature, effect["result"], dataset
end
end
nanoparticle.save
#p "Total time: #{Time.now - start_time}"
#p "Proteomics features: #{t1}"
#p "Proteomics values: #{t2}"
#p "Time2: #{t2}"
end
datasets.each { |u,d| d.save }
end
=begin
def self.import_ld # defunct, AMBIT JSON_LD does not have substance entries
#get list of bundle URIs
bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle?media=application%2Fjson'))["dataset"]
datasets = []
bundles.each do |bundle|
uri = bundle["URI"]
study = JSON.parse(`curl -H 'Accept:application/ld+json' '#{uri}/substance'`)
study["@graph"].each do |i|
puts i.to_yaml if i.keys.include? "sio:has-value"
end
end
datasets.collect{|d| d.id}
end
=end
end
end
end
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