bumped version

5 files changed, 8 insertions, 6 deletions

diff --git a/lib/import.rb b/lib/import.rb
index 96e7ad1..0857717 100644
--- a/lib/import.rb
+++ b/lib/import.rb
@@ -10,18 +10,17 @@ module OpenTox
       def self.import
         # time critical step: JSON parsing (>99%), Oj brings only minor speed gains (~1%)
         datasets = {}
-        bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle?media=application%2Fjson'))["dataset"]
+        bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle', {}, {accept: :json}))["dataset"]
         bundles.each do |bundle|
           datasets[bundle["URI"]] = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"].strip)
           $logger.debug bundle["title"].strip
-          nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"]+"?media=application%2Fjson"))["dataEntry"]
+          nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"], {}, {accept: :json}))["dataEntry"]
           nanoparticles.each_with_index do |np,n|
             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}")
+              data = JSON.parse(RestClientWrapper.get("https://data.enanomapper.net/query/compound/url/all?search=#{uri}", {}, {accept: :json}))
               source = data["dataEntry"][0]["compound"]["URI"]
               smiles = data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23SMILESDefault"]
               names = []
@@ -52,7 +51,7 @@ module OpenTox
               nanoparticle.dataset_ids << datasets[bundle_uri].id
             end
 
-            studies = JSON.parse(RestClientWrapper.get(File.join(np["compound"]["URI"],"study")))["study"]
+            studies = JSON.parse(RestClientWrapper.get(File.join(np["compound"]["URI"],"study"), {}, {accept: :json}))["study"]
             studies.each do |study|
               dataset = datasets[np["bundles"].keys.first]
               proteomics_features = {}
diff --git a/lib/lazar.rb b/lib/lazar.rb
index a756742..fff5598 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -1,6 +1,7 @@
 require 'rubygems'
 require "bundler/setup"
 require "rest-client"
+require 'addressable'
 require 'yaml'
 require 'json'
 require 'logger'
diff --git a/lib/model.rb b/lib/model.rb
index 475a346..ba52c84 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -395,6 +395,7 @@ module OpenTox
       include Mongoid::Timestamps
 
       field :endpoint, type: String
+      field :qmrf, type: Hash
       field :species, type: String
       field :source, type: String
       field :unit, type: String
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index 91bc9e1..89e57a0 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -197,7 +197,7 @@ module URI
   # @param [String]
   # @return [TrueClass,FalseClass]
   def self.valid? uri
-    u = URI.parse(uri)
+    u = Addressable::URI.parse(uri)
     u.scheme!=nil and u.host!=nil
   rescue URI::InvalidURIError
     false
diff --git a/lib/rest-client-wrapper.rb b/lib/rest-client-wrapper.rb
index f76a296..c9fd40f 100644
--- a/lib/rest-client-wrapper.rb
+++ b/lib/rest-client-wrapper.rb
@@ -26,6 +26,7 @@ module OpenTox
 
       define_singleton_method method do |uri,payload={},headers={},waiting_task=nil|
 
+        uri = Addressable::URI.encode(uri)
         # check input
         bad_request_error "Headers are not a hash: #{headers.inspect} for #{uri}." unless headers==nil or headers.is_a?(Hash) 
         headers[:subjectid] ||= @@subjectid