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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
# id/summary
# id/compound
# id/substance
# id/property
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|
if bundle["id"] == 3
datasets[bundle["URI"]] = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"])
end
end
# TODO this is only for protein corona
Dir[File.join(dir,"study-F*.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_id = nil
coating_ids = []
np["composition"].each do |c|
uri = c["component"]["compound"]["URI"]
uri = CGI.escape File.join(uri,"&media=application/json")
data = JSON.parse(RestClientWrapper.get "https://data.enanomapper.net/query/compound/url/all?media=application/json&search=#{uri}")
smiles = data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23SMILESDefault"]
names = []
names << data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
names << data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23IUPACNameDefault"]
if smiles
compound = Compound.find_or_create_by(:smiles => smiles)
compound.names = names.compact
else
compound = Compound.find_or_create_by(:names => names)
end
compound.save
if c["relation"] == "HAS_CORE"
core_id = compound.id.to_s
elsif c["relation"] == "HAS_COATING"
coating_ids << compound.id.to_s
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_id => core_id,
:coating_ids => coating_ids
)
np["bundles"].keys.each do |bundle_uri|
nanoparticle.dataset_ids << datasets[bundle_uri].id
end
dataset = datasets[np["bundles"].keys.first]
proteomics_features = {}
category = study["protocol"]["topcategory"]
source = study["protocol"]["category"]["term"]
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
JSON.parse(effect["result"]["textValue"]).each do |identifier, value| # time critical step
proteomics_features[identifier] ||= NumericFeature.find_or_create_by(:name => identifier, :category => "Proteomics", :unit => "Spectral counts", :source => source,:measured => true)
nanoparticle.parse_ambit_value proteomics_features[identifier], value, dataset
end
else
name = effect["endpoint"]
unit = effect["result"]["unit"]
warnings = []
case name
when "Log2 transformed" # use a sensible name
name = "log2(Net cell association)"
warnings = ["Original name was 'Log2 transformed'"]
unit = "log2(mL/ug(Mg))"
when "Total protein (BCA assay)"
category = "P-CHEM"
warnings = ["Category changed from TOX to P-CHEM"]
end
feature = klass.find_or_create_by(
:name => name,
:unit => unit,
:category => category,
:conditions => effect["conditions"],
:source => study["protocol"]["category"]["term"],
:measured => true,
:warnings => warnings
)
nanoparticle.parse_ambit_value feature, effect["result"], dataset
end
end
p nanoparticle
nanoparticle.save
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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