Merge branch 'feature/opentox-client' into development

7 files changed, 101 insertions, 124 deletions

diff --git a/.gitignore b/.gitignore
index 8300cb2..4040c6c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,4 @@
-tmp/*
-log/*
+*.gem
+.bundle
+Gemfile.lock
+pkg/*
diff --git a/Gemfile b/Gemfile
new file mode 100644
index 0000000..2142a18
--- /dev/null
+++ b/Gemfile
@@ -0,0 +1,4 @@
+source :gemcutter
+gemspec
+gem "opentox-server", :path => "../opentox-server"
+gem "opentox-client", :path => "../opentox-client"
diff --git a/VERSION b/VERSION
new file mode 100644
index 0000000..8c5ba87
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+5.0.0pre1
diff --git a/application.rb b/application.rb
index d9e5df5..b59f484 100644
--- a/application.rb
+++ b/application.rb
@@ -1,124 +1,72 @@
-# Java environment
-ENV["JAVA_HOME"] = "/usr/lib/jvm/java-6-sun" unless ENV["JAVA_HOME"]
-java_dir = File.join File.expand_path(File.dirname(__FILE__)),"java"
-cdk = File.join java_dir, "cdk-1.3.5.jar"
-jchempaint = File.join java_dir, "cdk-jchempaint-15.jar"
-ENV["CLASSPATH"] = "#{ENV["CLASSPATH"]}:#{java_dir}:#{cdk}:#{jchempaint}"
+require 'openbabel'
+module OpenTox
+  class Application < Service
 
-require 'rubygems'
-require 'rjb'
-gem "opentox-ruby", "~> 4"
-require 'opentox-ruby'
+    FORMATS = {
+      "chemical/x-daylight-smiles" => "smi",
+      "chemical/x-inchi" => "inchi",
+      #"chemical/x-inchikey" => "inchikey",
+      # OpenBabel segfaults randomly durng inchikey calculation
+      "chemical/x-mdl-sdfile" => "sdf",
+      "chemical/x-mdl-molfile" => "sdf",
+      "image/png" => 'png',
+    }
 
-before do
-  @inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'').sub(/\/smarts.*$/,'').sub(/\/image/,'').sub(/\?.*$/,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
-  puts @inchi
-end
-
-# 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"
-  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
-end
+    helpers do
+      # Convert identifier from OpenBabel input_format to OpenBabel output_format
+      def obconversion(identifier,input_format,output_format)
+        obconversion = OpenBabel::OBConversion.new
+        obmol = OpenBabel::OBMol.new
+        obconversion.set_in_and_out_formats input_format, output_format
+        obconversion.read_string obmol, identifier
+        case output_format
+        when /smi|can|inchi/
+          obconversion.write_string(obmol).gsub(/\s/,'').chomp
+        else
+          obconversion.write_string(obmol)
+        end
+      end
+    end
 
-def png_from_smiles(smiles)
-  begin
-    Rjb.load(nil,["-Xmx64m","-Djava.awt.headless=true"])# avoid JVM memory allocation problems
-    Rjb::import('Structure').new(smiles,150).show
-  rescue
-    LOGGER.warn e.message
-  end
-end
+    before do
+      @inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'').sub(/\/smarts.*$/,'').sub(/\/image/,'').sub(/\?.*$/,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
+    end
 
-# 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"
-  png_from_smiles(smiles)
-end
+    get "/compound/?" do
+      not_implemented_error "Object listing not implemented, because compounds are not stored at the server.", to("/compound")
+    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, ..."
-  case request.env['HTTP_ACCEPT']
-  when "*/*"
-    response['Content-Type'] = "chemical/x-daylight-smiles"
-    OpenTox::Compound.from_inchi(@inchi).to_smiles
-  when "chemical/x-daylight-smiles"
-    response['Content-Type'] = "chemical/x-daylight-smiles"
-    OpenTox::Compound.from_inchi(@inchi).to_smiles
-  when "chemical/x-inchi"
-    response['Content-Type'] = "chemical/x-inchi"
-    @inchi 
-  when "chemical/x-mdl-sdfile"
-    response['Content-Type'] = "chemical/x-mdl-sdfile"
-    OpenTox::Compound.from_inchi(@inchi).to_sdf
-  when "image/gif"
-    response['Content-Type'] = "image/gif"
-    OpenTox::Compound.from_inchi(@inchi).to_gif
-  when "image/png"
-    response['Content-Type'] = "image/png"
-    png_from_smiles(OpenTox::Compound.from_inchi(@inchi).to_smiles)
-  when "text/plain"
-    response['Content-Type'] = "text/plain"
-    uri = File.join @@cactus_uri,@inchi,"names"
-    RestClient.get(uri).body
-  else
-    raise OpenTox::BadRequestError.new "Unsupported MIME type '#{request.env['HTTP_ACCEPT']}'"
-  end
-end
+    get %r{/compound/(.+)/image} do |inchi| # catches all remaining get requests
+      obconversion @inchi, "inchi", "png"
+    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 
+    # 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{/compound/(.+)} do |inchi| # catches all remaining get requests
+      bad_request_error "Unsupported MIME type '#{@accept}.", uri unless FORMATS.keys.include? @accept
+      return @inchi if @accept == "chemical/x-inchi"
+      obconversion @inchi, "inchi", FORMATS[@accept]
+    end
 
-  input = request.env["rack.input"].read
-  response['Content-Type'] = 'text/uri-list'
-  begin
-    case request.content_type
-    when /chemical\/x-daylight-smiles/
-      OpenTox::Compound.from_smiles(input).uri + "\n"
-    when /chemical\/x-inchi/
-      OpenTox::Compound.from_inchi(input).uri + "\n"
-    when /chemical\/x-mdl-sdfile|chemical\/x-mdl-molfile/
-      OpenTox::Compound.from_sdf(input).uri + "\n"
-    when /text\/plain/
-      OpenTox::Compound.from_name(input).uri + "\n"
-    else
-      status 400
-      "Unsupported MIME type '#{request.content_type}'"
+    # 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 '/compound/?' do 
+      response['Content-Type'] = 'text/uri-list'
+      bad_request_error "Unsupported MIME type '#{@content_type}.", uri unless FORMATS.keys.include? @content_type
+      return to(File.join("/compound",@body)) if @content_type == "chemical/x-inchi"
+      to(File.join("compound",obconversion(@body, FORMATS[@content_type], "inchi")))
     end
-  rescue
-    status 400
-    "Cannot process request '#{input}' for content type '#{request.content_type}'"
+
   end
 end
diff --git a/compound.gemspec b/compound.gemspec
new file mode 100644
index 0000000..0d0e9d2
--- /dev/null
+++ b/compound.gemspec
@@ -0,0 +1,25 @@
+# -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+
+Gem::Specification.new do |s|
+  s.name        = "opentox-compound"
+  s.version     = File.read("./VERSION")
+  s.authors     = ["Christoph Helma"]
+  s.email       = ["helma@in-silico.ch"]
+  s.homepage    = "http://github.com/OpenTox/compound"
+  s.summary     = %q{Toxbank compound service}
+  s.description = %q{Toxbank compound service}
+  s.license     = 'GPL-3'
+
+  s.rubyforge_project = "task"
+
+  s.files         = `git ls-files`.split("\n")
+  s.required_ruby_version = '>= 1.9.2'
+
+  # specify any dependencies here; for example:
+  s.add_runtime_dependency "opentox-server", "#{VERSION}"
+  s.add_runtime_dependency "rjb"
+  s.add_runtime_dependency "openbabel"
+  s.post_install_message = "Please configure your service in ~/.opentox/config/compound.rb"
+end
+
diff --git a/config.ru b/config.ru
index a1aab0d..41e7811 100644
--- a/config.ru
+++ b/config.ru
@@ -1,6 +1,5 @@
-require 'rubygems'
-require 'opentox-ruby'
-require 'config/config_ru'
-run Sinatra::Application
-set :raise_errors, false
-set :show_exceptions, false
\ No newline at end of file
+SERVICE = "compound"
+require 'bundler'
+Bundler.require
+require './application.rb'
+run OpenTox::Application
diff --git a/public/robots.txt b/public/robots.txt
deleted file mode 100644
index 1f53798..0000000
--- a/public/robots.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-User-agent: *
-Disallow: /