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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"]
# not working
RestClient.add_before_execution_proc do |req, params|
params[:subjectid] = @subjectid
end
class String
def to_object
# TODO: fix, this is unsafe
self =~ /dataset/ ? uri = File.join(self.chomp,"metadata") : uri = self.chomp
#raise "#{uri} is not a valid URI." unless RDF::URI.new(uri).uri?
raise "#{uri} is not a valid URI." unless uri.uri?
RDF::Reader.open(uri) do |reader|
reader.each_statement do |statement|
if statement.predicate == RDF.type and statement.subject == uri
klass = "OpenTox::#{statement.object.to_s.split("#").last}"
object = eval "#{klass}.new \"#{uri}\""
end
end
end
# fallback: guess class from uri
# TODO: fix services and remove
unless object
case uri
when /compound/
object = OpenTox::Compound.new uri
when /feature/
object = OpenTox::Feature.new uri
when /dataset/
object = OpenTox::Dataset.new uri.sub(/\/metadata/,'')
when /algorithm/
object = OpenTox::Algorithm.new uri
when /model/
object = OpenTox::Model.new uri
when /validation/
object = OpenTox::Validation.new uri
when /task/
object = OpenTox::Task.new uri
else
raise "Class for #{uri} not found."
end
end
if object.class == Task # wait for tasks
object.wait_for_completion
object = object.result_uri.to_s.to_object
end
object
end
def uri?
begin
Net::HTTP.get_response(URI.parse(self))
true
rescue
false
end
end
end
# defaults to stderr, may be changed to file output
$logger = OTLogger.new(STDERR) # no rotation
$logger.level = Logger::DEBUG
module OpenTox
attr_accessor :subjectid, :uri, :response
attr_writer :metadata
def initialize uri=nil, subjectid=nil
@uri = uri.chomp
@subjectid = subjectid
end
# Ruby interface
def metadata reload=true
if reload
@metadata = {}
begin
#puts self.class
#self.kind_of?(OpenTox::Dataset) ? uri = URI.join(@uri,"metadata") : uri = @uri
#$logger.debug uri
RDF::Reader.open(uri) do |reader|
reader.each_statement do |statement|
@metadata[statement.predicate] = statement.object if statement.subject == @uri
end
end
rescue
$logger.error "Cannot read RDF metadata from #{@uri}: #{$!}.\n#{$!.backtrace.join("\n")}"
raise
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
|
