From 710031f953429c6e1a76aff4984ee76f7a1ee485 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Fri, 9 Jun 2017 11:08:45 +0000
Subject: added addressable gem to avoid URI::InvalidURIError

---
 lazar.gemspec              | 1 +
 lib/lazar.rb               | 1 +
 lib/overwrite.rb           | 2 +-
 lib/rest-client-wrapper.rb | 1 +
 test/compound.rb           | 4 +++-
 5 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/lazar.gemspec b/lazar.gemspec
index 90f1cf2..3c704c8 100644
--- a/lazar.gemspec
+++ b/lazar.gemspec
@@ -20,6 +20,7 @@ Gem::Specification.new do |s|
   # specify any dependencies here; for example:
   s.add_runtime_dependency 'bundler'
   s.add_runtime_dependency 'rest-client'
+  s.add_runtime_dependency 'addressable'
   s.add_runtime_dependency 'nokogiri'
   s.add_runtime_dependency 'rserve-client'
   s.add_runtime_dependency 'mongoid'
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/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
diff --git a/test/compound.rb b/test/compound.rb
index bdfb749..c4e6161 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -61,7 +61,9 @@ print c.sdf
 
   def test_chemblid
     c = OpenTox::Compound.from_inchi "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
-    assert_equal "CHEMBL277500", c.chemblid
+    assert_equal "CHEMBL1531487", c.chemblid
+    c = OpenTox::Compound.from_smiles "OC[C@](c1onc(n1)c1ncn2c1CN(C)C(=O)c1c2cccc1Cl)(O)C"
+    assert_equal "CHEMBL145418", c.chemblid
   end
 
   def test_sdf_storage
-- 
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