diff options
Diffstat (limited to 'application.rb')
| -rw-r--r-- | application.rb | 77 |
1 files changed, 69 insertions, 8 deletions
diff --git a/application.rb b/application.rb index e0e469d..09e447a 100644 --- a/application.rb +++ b/application.rb @@ -1,6 +1,6 @@ # 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__)),"public/java" +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}" @@ -10,19 +10,78 @@ require 'rjb' gem "opentox-ruby-api-wrapper", "= 1.6.0" require 'opentox-ruby-api-wrapper' -post "/display" do +#set :lock, true # avoid JVM memory allocation problems +# -Xmx64m + +get "/display/activating/(.+)$" do content_type "image/png" attachment "#{params["smiles"]}.png" - s = Rjb::import('Structure').new(params["smiles"],200) + Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems + s = Rjb::import('Structure').new(params["smiles"],150) s.match_activating(params["smarts"]) - s.match_deactivating(["CC"]) s.show end -get %r{/smiles/(.+)/smarts/(.*)} do |smiles,smarts| +post "/display/deactivating" do + content_type "image/png" + attachment "#{params["smiles"]}.png" + Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems + s = Rjb::import('Structure').new(params["smiles"],150) + s.match_deactivating(params["smarts"]) + s.show +end + +get %r{/smiles/(.+)/smarts/activating/(.*)/deactivating/(.*)/highlight/(.*)$} 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 +end + +get %r{/smiles/(.+)/smarts/activating/(.*)/deactivating/(.*)$} do |smiles,activating,deactivating| + activating = activating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')} + deactivating = deactivating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')} + content_type "image/png" + attachment "#{smiles}.png" + Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems + s = Rjb::import('Structure').new(smiles,150) + s.match_deactivating(deactivating) + s.match_activating(activating) + s.show + #s = nil +end + +get %r{/smiles/(.+)/smarts/(.*)/(.*activating)$} 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) + end + s.show +end + +get %r{/smiles/(.+)/smarts/(.*)$} do |smiles,smarts| content_type "image/png" attachment "#{smiles}.png" - s = Rjb::import('Structure').new(smiles,200) + Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems + s = Rjb::import('Structure').new(smiles,150) s.match(smarts) s.show end @@ -30,14 +89,16 @@ end get %r{/smiles/(.+)} do |smiles| content_type "image/png" attachment "#{smiles}.png" - Rjb::import('Structure').new(smiles,200).show + 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::import('Structure').new(smiles,200).show + Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems + Rjb::import('Structure').new(smiles,150).show end get %r{/(.+)} do |inchi| # catches all remaining get requests |