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module OpenTox
module Import
class Enanomapper
include OpenTox
def self.import
#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"]
dataset = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"])
nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"]+"?media=application%2Fjson"))["dataEntry"]
features = JSON.parse(RestClientWrapper.get(bundle["property"]+"?media=application%2Fjson"))["feature"]
nanoparticles.each do |np|
nanoparticle = Nanoparticle.find_or_create_by(
:name => np["values"]["https://data.enanomapper.net/identifier/name"],
:source => np["compound"]["URI"],
)
dataset.data_entries[nanoparticle.id.to_s] ||= {}
nanoparticle.bundles << uri
nanoparticle.dataset_ids << dataset.id
np["composition"].each do |comp|
case comp["relation"]
when "HAS_CORE"
nanoparticle.core = comp["component"]["compound"]["URI"]
when "HAS_COATING"
nanoparticle.coating << comp["component"]["compound"]["URI"]
end
end if np["composition"]
np["values"].each do |u,v|
if u.match(/property/)
name, unit, source = nil
features.each do |uri,feat|
if u.match(/#{uri}/)
name = feat["title"]
unit = feat["units"]
source = uri
end
end
feature = Feature.find_or_create_by(
:name => name,
:unit => unit,
:source => source
)
end
v.each{|value| nanoparticle.parse_ambit_value feature, value} if v.is_a? Array
end
nanoparticle.bundles.uniq!
nanoparticle.physchem_descriptors.each{|f,v| v.uniq!}
#nanoparticle.toxicities.each{|f,v| v.uniq!}
nanoparticle.toxicities.each do |f,v|
dataset.data_entries[nanoparticle.id.to_s][f.to_s] ||= []
dataset.data_entries[nanoparticle.id.to_s][f.to_s] += v
end
nanoparticle.save
end
dataset.save
datasets << dataset
end
datasets.collect{|d| d.id}
end
def self.dump
#get list of bundle URIs
`wget 'https://data.enanomapper.net/bundle?media=application%2Fjson' -O bundles.json`
json = JSON.parse File.read('./bundles.json')
json["dataset"].each do |dataset|
uri = dataset["URI"]
id = uri.split("/").last
`wget --header='accept:application/json' '#{uri}' -O 'bundle#{id}'`
`wget --header='accept:application/json' '#{dataset["summary"]}' -O 'summary#{id}.json'`
`wget --header='accept:application/json' '#{dataset["compound"]}' -O 'compound#{id}.json'`
`wget --header='accept:application/json' '#{dataset["substance"]}' -O 'substance#{id}.json'`
`wget --header='accept:application/json' '#{dataset["property"]}' -O 'property#{id}.json'`
`wget --header='accept:application/json' '#{dataset["dataset"]}' -O 'dataset#{id}.json'`
`wget --header='accept:application/json' '#{dataset["matrix"]}' -O 'matrix#{id}.json'`
end
end
end
end
end
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