enm import test

1 files changed, 77 insertions, 0 deletions

diff --git a/lib/import.rb b/lib/import.rb
new file mode 100644
index 0000000..86c633a
--- /dev/null
+++ b/lib/import.rb
@@ -0,0 +1,77 @@
+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"]
+        bundles.each do |bundle|
+          uri = bundle["URI"]
+          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"],
+              )
+              nanoparticle.bundles << uri
+              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.save!
+          end
+        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
+
+end
+