Merge branch 'release/v1.0.0'

3 files changed, 59 insertions, 95 deletions

diff --git a/Rakefile b/Rakefile
index fbfcd62..d43e8f3 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,7 +1,6 @@
 require 'rubygems'
 require 'rake'
-require 'opentox-ruby-api-wrapper'
-#require 'tasks/opentox'
+require 'opentox-ruby'
 
 @gems = "sinatra rest-client emk-sinatra-url-for sinatra-respond_to"
 
diff --git a/application.rb b/application.rb
index 58106d1..0a3794a 100644
--- a/application.rb
+++ b/application.rb
@@ -7,130 +7,93 @@ ENV["CLASSPATH"] = "#{ENV["CLASSPATH"]}:#{java_dir}:#{cdk}:#{jchempaint}"
 
 require 'rubygems'
 require 'rjb'
-gem "opentox-ruby-api-wrapper", "= 1.6.5"
-require 'opentox-ruby-api-wrapper'
+gem "opentox-ruby", "~> 1"
+require 'opentox-ruby'
 
-#set :lock, true # avoid JVM memory allocation problems
-# -Xmx64m
-
-get "/display/activating/(.+)$" do
-  content_type "image/png"
-  attachment "#{params["smiles"]}.png"
-  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
-  s = Rjb::import('Structure').new(params["smiles"],150)
-  s.match_activating(params["smarts"])
-  s.show
-end
-
-post "/display/deactivating" do
-  content_type "image/png"
-  attachment "#{params["smiles"]}.png"
-  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
-  s = Rjb::import('Structure').new(params["smiles"],150)
-  s.match_deactivating(params["smarts"])
-  s.show
-end
-
-get %r{/smiles/(.+)/smarts/activating/(.*)/deactivating/(.*)/highlight/(.*)$} do |smiles,activating,deactivating,smarts| 
-  activating = activating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')}
-  deactivating = deactivating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')}
-  content_type "image/png"
-  attachment "#{smiles}.png"
-  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
-  s = Rjb::import('Structure').new(smiles,150)
-  s.match_deactivating(deactivating) unless deactivating.empty?
-  s.match_activating(activating) unless activating.empty?
-  s.match(smarts)
-  s.show
-  #s = nil
+before do
+  @inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'').sub(/\/smarts.*$/,'').sub(/\/image/,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
 end
 
-get %r{/smiles/(.+)/smarts/activating/(.*)/deactivating/(.*)$} do |smiles,activating,deactivating| 
+# Display activating (red) and deactivating (green) substructures. Overlaps betwen activating and deactivating structures are marked in yellow.
+# @example
+#   curl http://webservices.in-silico.ch/compound/compound/InChI=1S/C6H5NO2/c8-7(9)6-4-2-1-3-5-6/h1-5H/smarts/activating/cN/ccN/deactivating/cc" > img.png
+# @return [image/png] Image with highlighted substructures
+get %r{/(.+)/smarts/activating/(.*)/deactivating/(.*)$} do |inchi,activating,deactivating| 
+  smiles = OpenTox::Compound.from_inchi(@inchi).to_smiles
   activating = activating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')}
   deactivating = deactivating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')}
   content_type "image/png"
   attachment "#{smiles}.png"
-  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
-  s = Rjb::import('Structure').new(smiles,150)
-  s.match_deactivating(deactivating)
-  s.match_activating(activating)
-  s.show
-  #s = nil
-end
-
-get %r{/smiles/(.+)/smarts/(.*)/(.*activating)$} do |smiles,allsmarts,effect| 
-  LOGGER.debug "String:"
-  LOGGER.debug allsmarts
-  smarts = allsmarts.to_s.split(/\//)
-  smarts.collect!{|s| s.gsub(/"/,'')}
-  LOGGER.debug "Smarts:"
-  LOGGER.debug smarts.to_yaml
-  content_type "image/png"
-  attachment "#{smiles}.png"
-  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
-  s = Rjb::import('Structure').new(smiles,150)
-  if effect == "activating"
-    s.match_activating(smarts)
-  elsif effect == "deactivating"
-    s.match_deactivating(smarts)
+  begin
+    Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+    s = Rjb::import('Structure').new(smiles,150)
+    s.match_deactivating(deactivating)
+    s.match_activating(activating)
+    s.show
+  rescue => e
+    LOGGER.warn e.message
   end
-  s.show
 end
 
-get %r{/smiles/(.+)/smarts/(.*)$} do |smiles,smarts| 
-  content_type "image/png"
-  attachment "#{smiles}.png"
-  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
-  s = Rjb::import('Structure').new(smiles,150)
-  s.match(smarts)
-  s.show
-end
-
-get %r{/smiles/(.+)} do |smiles| 
+# Get png image
+# @return [image/png] Image data
+get %r{/(.+)/image} do |inchi| # catches all remaining get requests
+  smiles = OpenTox::Compound.from_inchi(@inchi).to_smiles
   content_type "image/png"
   attachment "#{smiles}.png"
-  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
-  Rjb::import('Structure').new(smiles,150).show
-end
-
-get %r{/(.+)/image} do |inchi| # catches all remaining get requests
-   smiles = OpenTox::Compound.new(:inchi => inchi).smiles
-   content_type "image/png"
-   attachment "#{smiles}.png"
-   Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
-   Rjb::import('Structure').new(smiles,150).show
+  begin
+    Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+    Rjb::import('Structure').new(smiles,150).show
+  rescue
+    LOGGER.warn e.message
+  end
 end
 
+# Get compound representation
+# @param [optinal, HEADER] Accept one of `chemical/x-daylight-smiles, chemical/x-inchi, chemical/x-mdl-sdfile, chemical/x-mdl-molfile, text/plain, image/gif, image/png`, defaults to chemical/x-daylight-smiles
+# @example Get smiles
+#   curl http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
+# @example Get all known names 
+#   curl -H "Accept:text/plain" http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
+# @return [chemical/x-daylight-smiles, chemical/x-inchi, chemical/x-mdl-sdfile, chemical/x-mdl-molfile, text/plain, image/gif, image/png] Compound representation
 get %r{/(.+)} do |inchi| # catches all remaining get requests
-  inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
+  #inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
   case request.env['HTTP_ACCEPT']
   when "*/*"
     response['Content-Type'] = "chemical/x-daylight-smiles"
-    OpenTox::Compound.new(:inchi => inchi).smiles
+    OpenTox::Compound.from_inchi(@inchi).to_smiles
   when "chemical/x-daylight-smiles"
     response['Content-Type'] = "chemical/x-daylight-smiles"
-    OpenTox::Compound.new(:inchi => inchi).smiles
+    OpenTox::Compound.from_inchi(@inchi).to_smiles
   when "chemical/x-inchi"
     response['Content-Type'] = "chemical/x-inchi"
-    inchi 
+    @inchi 
   when "chemical/x-mdl-sdfile"
     response['Content-Type'] = "chemical/x-mdl-sdfile"
-    OpenTox::Compound.new(:inchi => inchi).sdf
+    OpenTox::Compound.from_inchi(@inchi).to_sdf
   when "image/gif"
     response['Content-Type'] = "image/gif"
-    OpenTox::Compound.new(:inchi => inchi).gif
+    OpenTox::Compound.from_inchi(@inchi).to_gif
   when "image/png"
     response['Content-Type'] = "image/png"
-    OpenTox::Compound.new(:inchi => inchi).png
+    OpenTox::Compound.from_inchi(@inchi).to_png
   when "text/plain"
     response['Content-Type'] = "text/plain"
-    uri = File.join @@cactus_uri,inchi,"names"
+    uri = File.join @@cactus_uri,@inchi,"names"
     RestClient.get(uri).body
   else
     halt 400, "Unsupported MIME type '#{request.env['HTTP_ACCEPT']}'"
   end
 end
 
+# Create a new compound URI (compounds are not saved at the compound service)
+# @param [HEADER] Content-type one of `chemical/x-daylight-smiles, chemical/x-inchi, chemical/x-mdl-sdfile, chemical/x-mdl-molfile, text/plain`
+# @example Create compound from Smiles string
+#   curl -X POST -H "Content-type:chemical/x-daylight-smiles" --data "c1ccccc1" http://webservices.in-silico.ch/compound
+# @example Create compound from name, uses an external lookup service and should work also with trade names, CAS numbers, ...
+#   curl -X POST -H "Content-type:text/plain" --data "Benzene" http://webservices.in-silico.ch/compound
+# @param [BODY] - string with identifier/data in selected Content-type
+# @return [text/uri-list] compound URI
 post '/?' do 
 
   input = request.env["rack.input"].read
@@ -138,13 +101,13 @@ post '/?' do
   begin
     case request.content_type
     when /chemical\/x-daylight-smiles/
-      OpenTox::Compound.new(:smiles => input).uri + "\n"
+      OpenTox::Compound.from_smiles(input).uri + "\n"
     when /chemical\/x-inchi/
-      OpenTox::Compound.new(:inchi => input).uri + "\n"
+      OpenTox::Compound.from_inchi(input).uri + "\n"
     when /chemical\/x-mdl-sdfile|chemical\/x-mdl-molfile/
-      OpenTox::Compound.new(:sdf => input).uri + "\n"
+      OpenTox::Compound.from_sdf(input).uri + "\n"
     when /text\/plain/
-      OpenTox::Compound.new(:name => input).uri + "\n"
+      OpenTox::Compound.from_name(input).uri + "\n"
     else
       status 400
       "Unsupported MIME type '#{request.content_type}'"
diff --git a/config.ru b/config.ru
index ec0402a..a1aab0d 100644
--- a/config.ru
+++ b/config.ru
@@ -1,4 +1,6 @@
 require 'rubygems'
-require 'opentox-ruby-api-wrapper'
+require 'opentox-ruby'
 require 'config/config_ru'
 run Sinatra::Application
+set :raise_errors, false
+set :show_exceptions, false
\ No newline at end of file