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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"]
# Regular expressions for parsing classification data
TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
# defaults to stderr, may be changed to file output (e.g in opentox-service)
$logger = OTLogger.new(STDERR)
$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
def metadata reload=true
if reload or @metadata.empty?
@metadata = {}
kind_of?(OpenTox::Dataset) ? uri = File.join(@uri,"metadata") : uri = @uri
RDF::Reader.for(:rdfxml).new( RestClientWrapper.get(uri) ) do |reader|
reader.each_statement do |statement|
@metadata[statement.predicate] = statement.object if statement.subject == @uri
end
end
end
@metadata
end
def save
post self.to_rdfxml, { :content_type => 'application/rdf+xml'}
end
def to_rdfxml
rdf = RDF::Writer.for(:rdfxml).buffer do |writer|
@metadata.each { |p,o| writer << RDF::Statement.new(RDF::URI.new(@uri), p, o) }
end
rdf
end
# REST API
def get headers={}
headers[:subjectid] ||= @subjectid
headers[:accept] ||= 'application/rdf+xml'
@response = RestClientWrapper.get @uri, {}, headers
end
def post payload={}, headers={}
headers[:subjectid] ||= @subjectid
headers[:accept] ||= 'application/rdf+xml'
@response = RestClientWrapper.post(@uri.to_s, payload, headers)
end
def put payload={}, headers={}
headers[:subjectid] ||= @subjectid
headers[:accept] ||= 'application/rdf+xml'
@response = RestClientWrapper.put(@uri.to_s, payload, headers)
end
def delete headers={}
headers[:subjectid] ||= @subjectid
headers[:accept] ||= 'application/rdf+xml'
@response = RestClientWrapper.delete(@uri.to_s,:subjectid => @subjectid)
end
# class methods
module ClassMethods
def create service_uri, subjectid=nil
uri = RestClientWrapper.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
RestClientWrapper.post(service_uri, :file => File.new(file), :subjectid => subjectid).chomp.to_object
end
def all service_uri, subjectid=nil
uris = RestClientWrapper.get(service_uri, nil, {: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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