compound added

6 files changed, 126 insertions, 58 deletions

diff --git a/lib/compound.rb b/lib/compound.rb
index 189db7b..974e46e 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -6,44 +6,27 @@ module OpenTox
   # Ruby wrapper for OpenTox Compound Webservices (http://opentox.org/dev/apis/api-1.2/structure).
 	class Compound 
 
-		attr_accessor :inchi, :uri
-
-		# Create compound with optional uri
-    # @example
-    #   compound = OpenTox::Compound.new("http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"")
-    # @param [optional, String] uri Compound URI
-    # @return [OpenTox::Compound] Compound
-		def initialize(uri=nil)
-      @uri = uri
-      case @uri
-      when /InChI/ # shortcut for IST services
-        @inchi = @uri.sub(/^.*InChI/, 'InChI')
-      else
-        @inchi = RestClientWrapper.get(@uri, :accept => 'chemical/x-inchi').to_s.chomp if @uri
-      end
-    end
-
     # Create a compound from smiles string
     # @example
     #   compound = OpenTox::Compound.from_smiles("c1ccccc1")
     # @param [String] smiles Smiles string
     # @return [OpenTox::Compound] Compound
-    def self.from_smiles(smiles)
-      Compound.new  RestClientWrapper.post(CONFIG[:services]["opentox-compound"], smiles, :content_type => 'chemical/x-daylight-smiles').to_s.chomp 
+    def self.from_smiles service_uri, smiles, subjectid=nil
+      Compound.new  RestClientWrapper.post(service_uri, smiles, :content_type => 'chemical/x-daylight-smiles').to_s.chomp 
     end
 
     # Create a compound from inchi string
     # @param [String] smiles InChI string
     # @return [OpenTox::Compound] Compound
-    def self.from_inchi(inchi)
-      Compound.new  RestClientWrapper.post(CONFIG[:services]["opentox-compound"], inchi, :content_type => 'chemical/x-inchi').to_s.chomp 
+    def self.from_inchi(service_uri, inchi)
+      Compound.new  RestClientWrapper.post(service_uri, inchi, :content_type => 'chemical/x-inchi').to_s.chomp 
     end
 
     # Create a compound from sdf string
     # @param [String] smiles SDF string
     # @return [OpenTox::Compound] Compound
-    def self.from_sdf(sdf)
-      Compound.new  RestClientWrapper.post(CONFIG[:services]["opentox-compound"], sdf, :content_type => 'chemical/x-mdl-sdfile').to_s.chomp 
+    def self.from_sdf(service_uri, sdf)
+      Compound.new  RestClientWrapper.post(service_uri, sdf, :content_type => 'chemical/x-mdl-sdfile').to_s.chomp 
     end
 
     # Create a compound from name. Relies on an external service for name lookups.
@@ -51,18 +34,16 @@ module OpenTox
     #   compound = OpenTox::Compound.from_name("Benzene")
     # @param [String] name name can be also an InChI/InChiKey, CAS number, etc
     # @return [OpenTox::Compound] Compound
-    def self.from_name(name)
-      c = Compound.new
+    def self.from_name(service_uri, name)
       # paranoid URI encoding to keep SMILES charges and brackets
-      c.inchi = RestClientWrapper.get("#{@@cactus_uri}#{URI.encode(name, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").to_s.chomp
-      c.uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(c.inchi))
-      c
+      inchi = RestClientWrapper.get("#{@@cactus_uri}#{URI.encode(name, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").to_s.chomp
+      Compound.new File.join(service_uri,URI.escape(inchi))
     end
 
 		# Get InChI
     # @return [String] InChI string
 		def to_inchi
-      @inchi
+      RestClientWrapper.get(@uri, :accept => 'chemical/x-inchi').to_s.chomp if @uri
 		end
 
 		# Get (canonical) smiles
diff --git a/lib/opentox-ruby-minimal.rb b/lib/opentox-ruby-minimal.rb
new file mode 100644
index 0000000..e0d5489
--- /dev/null
+++ b/lib/opentox-ruby-minimal.rb
@@ -0,0 +1,2 @@
+require "opentox"
+require "compound"
diff --git a/lib/opentox.rb b/lib/opentox.rb
index b0ffcb1..a6ac1d4 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -11,8 +11,8 @@ SERVICES = ["Compound", "Feature", "Dataset", "Algorithm", "Model", "Validation"
 
 module OpenTox
 
-  attr_accessor :subjectid, :uri #, :service_uri
-  #attr_writer :metadata
+  attr_accessor :subjectid, :uri 
+  attr_writer :metadata
 
   # Initialize OpenTox object with optional subjectid
   # @param [optional, String] subjectid
@@ -21,14 +21,26 @@ module OpenTox
     @subjectid = subjectid
   end
 
-  def metadata
-    metadata = {}
-    RDF::Reader.open(@uri) do |reader|
-      reader.each_statement do |statement|
-        metadata[statement.predicate] = statement.object if statement.subject == @uri
+  # Ruby interface
+
+  def metadata reload=true
+    if reload
+      @metadata = {}
+      RDF::Reader.open(@uri) do |reader|
+        reader.each_statement do |statement|
+          @metadata[statement.predicate] = statement.object if statement.subject == @uri
+        end
       end
     end
-    metadata
+    @metadata
+  end
+
+  def save
+    rdf = RDF::Writer.buffer do |writer|
+      @metadata.each { |p,o| writer << RDF::Statement.new(RDF::URI.new(@uri), p, o) }
+    end
+    puts rdf
+    #post(@uri, rdf, { :content_type => 'application/rdf+xml', :subjectid => subjectid}).to_s.chomp, @subjectid 
   end
 
   # REST API
@@ -74,17 +86,31 @@ module OpenTox
     RestClientWrapper.delete(@uri.to_s,:subjectid => @subjectid)
   end
 
+
+  module Service
+    def create service_uri, subjectid=nil
+      service = eval("#{self}.new(\"#{service_uri}\", #{subjectid})")
+      uri = service.post({}, {}, subjectid).to_s
+      eval "#{self}.new(\"#{uri}\", #{subjectid})"
+    end
+  end
+
   # create default classes
-  SERVICES.each { |s| eval "class #{s}; include OpenTox; end" }
+  SERVICES.each do |s|
+    eval "class #{s}
+      include OpenTox
+      extend OpenTox::Service
+    end"
+  end
 
 =begin
-  # Tools
+  private
 
   def uri_available?
     url = URI.parse(@uri)
-    req = Net::HTTP.new(url.host,url.port)
-    req['subjectid'] = @subjectid if @subjectid
-    req.start(url.host, url.port) do |http|
+    #req = Net::HTTP.new(url.host,url.port)
+    #req['subjectid'] = @subjectid if @subjectid
+    Net::HTTP.start(url.host, url.port) do |http|
       return http.head("#{url.request_uri}#{subjectidstr}").code == "200"
     end
   end
@@ -93,10 +119,6 @@ module OpenTox
 
     include OpenTox
 
-    def find 
-      uri_available? ? object_class.new(@uri, @subjectid) : nil
-    end
-
     def create metadata
       object_class.new post(service_uri, metadata.to_rdfxml, { :content_type => 'application/rdf+xml', :subjectid => subjectid}).to_s.chomp, @subject_id 
     end
@@ -107,14 +129,6 @@ module OpenTox
       get(:accept => "text/uri-list").to_s.split(/\n/).collect{|uri| object_class.new uri,@subjectid}
     end
 
-    def save object
-      object_class.new post(object.to_rdfxml, :content_type => 'application/rdf+xml').to_s, @subjectid
-    end
-
-    def object_class
-      eval self.class.to_s.sub(/::Collection/,'')
-    end
-
     # create collection classes
     SERVICES.each { |s| eval "class #{s}; include Collection; end" }
 
diff --git a/test/all.rb b/test/all.rb
index 6666e84..91a994c 100644
--- a/test/all.rb
+++ b/test/all.rb
@@ -1,10 +1,11 @@
-require 'rubygems'
-require 'test/unit'
-require 'opentox-ruby-minimal'
+#require 'rubygems'
+#require 'test/unit'
+#require 'opentox-ruby-minimal'
 require './rest.rb'
+require './ruby-api.rb'
 require './feature.rb'
+require './compound.rb'
 #require './authorization.rb'
-#require './compound.rb'
 #require './dataset.rb'
 #require './parser.rb'
 #require './task.rb'
diff --git a/test/compound.rb b/test/compound.rb
new file mode 100644
index 0000000..35fc514
--- /dev/null
+++ b/test/compound.rb
@@ -0,0 +1,53 @@
+$LOAD_PATH << File.expand_path( File.dirname(__FILE__) + '/../lib' )
+require 'rubygems'
+require 'opentox-ruby-minimal.rb'
+require 'test/unit'
+
+class CompoundTest < Test::Unit::TestCase
+
+  def setup
+    @service_uri = "http://ot-dev.in-silico.ch/compound"
+  end
+
+  def test_compound_from_smiles_0
+    c = OpenTox::Compound.from_smiles @service_uri, "F[B-](F)(F)F.[Na+]"
+    assert_equal "InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1", c.to_inchi
+    assert_equal "[Na+].F[B-](F)(F)F", c.to_smiles # still does not work on 64bit machines
+  end
+
+  def test_compound_from_smiles_1
+    c = OpenTox::Compound.from_smiles @service_uri, "CC(=O)CC(C)C#N"
+    assert_equal "InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3", c.to_inchi
+    assert_equal "CC(CC(=O)C)C#N", c.to_smiles
+  end
+
+  def test_compound_from_name
+    c = OpenTox::Compound.from_name @service_uri, "Benzene"
+    assert_equal "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H", c.to_inchi
+    assert_equal "c1ccccc1", c.to_smiles
+  end
+
+  def test_compound_from_smiles_2  
+    c = OpenTox::Compound.from_smiles @service_uri, "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
+    assert_equal "InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1", c.to_inchi
+    assert_equal "N#[N+]c1ccccc1.F[B-](F)(F)F", c.to_smiles
+  end
+
+  def test_compound_from_inchi
+    c = OpenTox::Compound.from_inchi @service_uri, "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
+    assert_equal "c1ccccc1", c.to_smiles
+  end
+
+  def test_compound_ambit
+    c = OpenTox::Compound.new "http://apps.ideaconsult.net:8080/ambit2/compound/144036"
+    assert_equal "InChI=1S/C6H11NO2/c1-3-5-6(4-2)7(8)9/h5H,3-4H2,1-2H3", c.to_inchi
+    assert_equal "CCC=C(CC)[N+](=O)[O-]", c.to_smiles
+  end
+
+=begin
+  def test_match_hits
+    c = OpenTox::Compound.from_smiles @service_uri, "N=C=C1CCC(=F=FO)C1"
+    assert_equal ({"FF"=>2, "CC"=>10, "C"=>6, "C1CCCC1"=>10, "C=C"=>2}), c.match_hits(['CC','F=F','C','C=C','FF','C1CCCC1','OO'])
+  end
+=end
+end
diff --git a/test/ruby-api.rb b/test/ruby-api.rb
new file mode 100644
index 0000000..be828fb
--- /dev/null
+++ b/test/ruby-api.rb
@@ -0,0 +1,17 @@
+$LOAD_PATH << File.expand_path( File.dirname(__FILE__) + '/../lib' )
+require 'rubygems'
+require 'opentox-ruby-minimal.rb'
+require 'test/unit'
+
+class RubyAPITest < Test::Unit::TestCase
+
+  def test_create
+    d = OpenTox::Dataset.create "http://ot-dev.in-silico.ch/dataset"#, {RDF::DC.title => "test dataset"}
+    assert_equal OpenTox::Dataset, d.class
+    assert_equal RDF::OT.Dataset, d.metadata[RDF.type]
+  end
+
+  def test_save
+  end
+
+end