From 063acd4dc63e9287287cc1ff78fff2064ff74e4f Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Thu, 7 Apr 2016 17:39:14 +0200
Subject: initial ambit import

---
 data/enm-dump.rb   | 16 ++++++++++++++++
 data/enm-import.rb | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100644 data/enm-dump.rb
 create mode 100644 data/enm-import.rb

(limited to 'data')

diff --git a/data/enm-dump.rb b/data/enm-dump.rb
new file mode 100644
index 0000000..c1c25e7
--- /dev/null
+++ b/data/enm-dump.rb
@@ -0,0 +1,16 @@
+require 'json'
+
+#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
diff --git a/data/enm-import.rb b/data/enm-import.rb
new file mode 100644
index 0000000..65fd3c7
--- /dev/null
+++ b/data/enm-import.rb
@@ -0,0 +1,50 @@
+require_relative '../lib/lazar.rb'
+include OpenTox
+
+
+#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"],
+      )
+      np["composition"].each do |comp|
+        case comp["relation"]
+        when "HAS_CORE"
+          nanoparticle[:core] = comp["component"]["compound"]["URI"]
+        when "HAS_COATING"
+          nanoparticle[:coating] ||= []
+          nanoparticle[:coating] << comp["component"]["compound"]["URI"]
+        end
+      end if np["composition"]
+      np["values"].each do |u,v|
+        if u.match(/property/)
+          name, unit = nil
+          features.each do |uri,feat|
+            if u.match(/#{uri}/)
+              name = feat["title"]
+              unit = feat["units"]
+            end
+          end
+          feature = Feature.find_or_create_by(
+            :name => name,
+            :unit => unit,
+            #:source => uri
+          )
+          nanoparticle[:features] ||= {}
+          if v.size == 1 and v.first.keys == ["loValue"]
+            nanoparticle[:features][feature.id] = v.first["loValue"]
+          else
+            #TODO
+          end
+        end
+      end
+      p nanoparticle
+      nanoparticle.save
+  end
+end
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