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# 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 'rubygems'
require 'rjb'
gem "opentox-ruby-api-wrapper", "= 1.6.1"
require 'opentox-ruby-api-wrapper'
#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
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"
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|
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
end
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.new(:inchi => inchi).smiles
when "chemical/x-daylight-smiles"
response['Content-Type'] = "chemical/x-daylight-smiles"
OpenTox::Compound.new(:inchi => inchi).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.new(:inchi => inchi).sdf
when "image/gif"
response['Content-Type'] = "image/gif"
OpenTox::Compound.new(:inchi => inchi).gif
when "image/png"
response['Content-Type'] = "image/png"
OpenTox::Compound.new(:inchi => inchi).png
when "text/plain"
response['Content-Type'] = "text/plain"
uri = File.join @@cactus_uri,inchi,"names"
RestClient.get(uri).body
else
halt 400, "Unsupported MIME type '#{request.env['HTTP_ACCEPT']}'"
end
end
post '/?' do
input = request.env["rack.input"].read
response['Content-Type'] = 'text/uri-list'
begin
case request.content_type
when /chemical\/x-daylight-smiles/
OpenTox::Compound.new(:smiles => input).uri + "\n"
when /chemical\/x-inchi/
OpenTox::Compound.new(:inchi => input).uri + "\n"
when /chemical\/x-mdl-sdfile|chemical\/x-mdl-molfile/
OpenTox::Compound.new(:sdf => input).uri + "\n"
when /text\/plain/
OpenTox::Compound.new(:name => input).uri + "\n"
else
status 400
"Unsupported MIME type '#{request.content_type}'"
end
rescue
status 400
"Cannot process request '#{input}' for content type '#{request.content_type}'"
end
end
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