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#TODO: switch services to 1.2
RDF::OT = RDF::Vocabulary.new 'http://www.opentox.org/api/1.2#'
RDF::OT1 = RDF::Vocabulary.new 'http://www.opentox.org/api/1.1#'
RDF::OTA = RDF::Vocabulary.new 'http://www.opentox.org/algorithmTypes.owl#'
SERVICES = ["Compound", "Feature", "Dataset", "Algorithm", "Model", "Validation", "Task", "Investigation"]
class String
def underscore
self.gsub(/::/, '/').
gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
gsub(/([a-z\d])([A-Z])/,'\1_\2').
tr("-", "_").
downcase
end
end
module URI
def self.task? uri
uri =~ /task/ and URI.valid? uri
end
def self.dataset? uri, subjectid=nil
uri =~ /dataset/ and URI.accessible? uri, subjectid=nil
end
def self.model? uri, subjectid=nil
uri =~ /model/ and URI.accessible? uri, subjectid=nil
end
def self.accessible? uri, subjectid=nil
Net::HTTP.get_response(URI.parse(uri))
true
rescue
false
end
def self.valid? uri
u = URI::parse(uri)
u.scheme!=nil and u.host!=nil
rescue URI::InvalidURIError
false
end
end
# defaults to stderr, may be changed to file output
$logger = OTLogger.new(STDERR) # no rotation
$logger.level = Logger::DEBUG
module OpenTox
attr_accessor :subjectid, :uri, :response
attr_writer :metadata
def initialize uri=nil, subjectid=nil
@uri = uri.chomp
@subjectid = subjectid
end
# Ruby interface
# override to read all error codes
def metadata reload=true
if reload
@metadata = {}
# ignore error codes from Task services (may contain eg 500 which causes exceptions in RestClient and RDF::Reader
RestClient.get(@uri) do |response, request, result, &block|
$logger.warn "#{@uri} returned #{result}" unless response.code == 200 or response.code == 202 or URI.task? @uri
RDF::Reader.for(:rdfxml).new(response) do |reader|
reader.each_statement do |statement|
@metadata[statement.predicate] = statement.object if statement.subject == @uri
end
end
end
end
@metadata
end
def save
rdf = RDF::Writer.for(:rdfxml).buffer do |writer|
@metadata.each { |p,o| writer << RDF::Statement.new(RDF::URI.new(@uri), p, o) }
end
post rdf, { :content_type => 'application/rdf+xml'}
end
# REST API
def get params={}
params[:subjectid] ||= @subjectid
params[:accept] ||= 'application/rdf+xml'
@response = RestClient.get @uri, params
end
def post payload={}, params={}
params[:subjectid] ||= @subjectid
params[:accept] ||= 'application/rdf+xml'
@response = RestClient.post(@uri.to_s, payload, params)
begin
@response.to_s.to_object
rescue
@response
end
end
def put payload={}, params={}
params[:subjectid] ||= @subjectid
params[:accept] ||= 'application/rdf+xml'
@response = RestClient.put(@uri.to_s, payload, params)
end
def delete params={}
params[:subjectid] ||= @subjectid
params[:accept] ||= 'application/rdf+xml'
@response = RestClient.delete(@uri.to_s,:subjectid => @subjectid)
end
# class methods
module ClassMethods
def create service_uri, subjectid=nil
uri = RestClient.post(service_uri, {}, :subjectid => subjectid).chomp
subjectid ? eval("#{self}.new(\"#{uri}\", #{subjectid})") : eval("#{self}.new(\"#{uri}\")")
end
def from_file service_uri, file, subjectid=nil
RestClient.post(service_uri, :file => File.new(file), :subjectid => subjectid).chomp.to_object
end
def all service_uri, subjectid=nil
uris = RestClient.get(service_uri, {:accept => 'text/uri-list'}).split("\n").compact
uris.collect{|uri| subjectid ? eval("#{self}.new(\"#{uri}\", #{subjectid})") : eval("#{self}.new(\"#{uri}\")")}
end
end
# create default classes
SERVICES.each do |s|
eval "class #{s}
include OpenTox
extend OpenTox::ClassMethods
end"
end
end
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