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module OpenTox
module Backend
class FourStore
@@accept_formats = [ "application/rdf+xml", "text/turtle", "text/plain", "text/uri-list", "text/html", 'application/sparql-results+xml' ]
@@content_type_formats = [ "application/rdf+xml", "text/turtle", "text/plain", "application/x-turtle" ]
def self.list mime_type
bad_request_error "'#{mime_type}' is not a supported mime type. Please specify one of #{@@accept_formats.join(", ")} in the Accept Header." unless @@accept_formats.include? mime_type
if mime_type =~ /(uri-list|html|sparql-results)/
sparql = "SELECT DISTINCT ?uri WHERE {GRAPH ?uri {?uri <#{RDF.type}> <#{klass}>.} }"
else
sparql = "CONSTRUCT {?uri <#{RDF.type}> <#{klass}>.} WHERE { GRAPH ?uri {?uri <#{RDF.type}> <#{klass}>.} }"
end
query sparql, mime_type
end
def self.head uri
sparql = "SELECT DISTINCT ?g WHERE {GRAPH ?g {<#{uri}> ?p ?o.} }"
rdf = query sparql, 'application/sparql-results+xml'
#resource_not_found_error "#{uri} not found." unless rdf.match("#{uri}")
return nil unless rdf.match("#{uri}")
rdf
end
def self.get uri, mime_type
bad_request_error "'#{mime_type}' is not a supported mime type. Please specify one of #{@@accept_formats.join(", ")} in the Accept Header." unless @@accept_formats.include? mime_type
sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{uri}> WHERE { ?s ?p ?o. }"
rdf = query sparql, mime_type
resource_not_found_error "#{uri} not found." if rdf.empty?
rdf
end
def self.post uri, rdf, mime_type
bad_request_error "'#{mime_type}' is not a supported content type. Please use one of #{@@content_type_formats.join(", ")}." unless @@content_type_formats.include? mime_type or mime_type == "multipart/form-data"
bad_request_error "Request body empty." unless rdf
mime_type = "application/x-turtle" if mime_type == "text/plain" # ntriples is turtle in 4store
RestClient::Resource.new(File.join(four_store_uri,"data")+"/", :verify_ssl => 0).post :data => rdf.gsub(/\\C/,'C'), :graph => uri, "mime-type" => mime_type # remove backslashes in SMILES (4store interprets them as UTF-8 \C even within single quotes)
update "INSERT DATA { GRAPH <#{uri}> { <#{uri}> <#{RDF::DC.modified}> \"#{DateTime.now}\" } }"
end
def self.put uri, rdf, mime_type
bad_request_error "'#{mime_type}' is not a supported content type. Please use one of #{@@content_type_formats.join(", ")}." unless @@content_type_formats.include? mime_type
bad_request_error "Reqest body empty." unless rdf
mime_type = "application/x-turtle" if mime_type == "text/plain"
RestClient::Resource.new(File.join(four_store_uri,"data",uri), :verify_ssl => 0).put rdf, :content_type => mime_type
update "INSERT DATA { GRAPH <#{uri}> { <#{uri}> <#{RDF::DC.modified}> \"#{DateTime.now}\" } }"
end
def self.delete uri
RestClientWrapper.delete data_uri(uri)
end
def self.update sparql
attempts = 0
begin
attempts += 1
RestClient::Resource.new(update_uri, :verify_ssl => 0).post(:update => sparql )
rescue
if attempts < 4 # 4store may return errors under heavy load
sleep 1
retry
else
bad_request_error $!.message, update_uri, $!.backtrace
end
end
end
def self.query sparql, mime_type
if sparql =~ /SELECT/i
# return list unless mime_type
case mime_type
when 'application/sparql-results+xml'
RestClient::Resource.new(sparql_uri, :verify_ssl => 0).get(:params => { :query => sparql }, :accept => mime_type)
when 'application/json'
RestClient::Resource.new(sparql_uri, :verify_ssl => 0).get(:params => { :query => sparql }, :accept => mime_type)
when /(uri-list|html)/
uri_list = RestClient::Resource.new(sparql_uri, :verify_ssl => 0).get(:params => { :query => sparql }, :accept => "text/plain").gsub(/"|<|>/,'').split("\n").drop(1).join("\n")
uri_list = uri_list.to_html if mime_type=~/html/
return uri_list
else
bad_request_error "#{mime_type} is not a supported mime type for SELECT statements."
end
elsif sparql =~ /CONSTRUCT/i
case mime_type
when "text/plain", "application/rdf+xml"
RestClient::Resource.new(sparql_uri, :verify_ssl => 0).get(:params => { :query => sparql }, :accept => mime_type)
when /turtle/
nt = RestClient::Resource.new(sparql_uri, :verify_ssl => 0).get(:params => { :query => sparql }, :accept => "text/tab-separated-values") # 4store returns ntriples for turtle
if !nt.empty?
rdf = RDF::Graph.new
RDF::Reader.for(:ntriples).new(nt) do |reader|
reader.each_statement { |statement| rdf << statement }
end
prefixes = {:rdf => "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"}
['OT', 'DC', 'XSD', 'OLO'].each{|p| prefixes[p.downcase.to_sym] = eval("RDF::#{p}.to_s") }
# TODO: fails for large datasets?? multi_cell_call
turtle = RDF::Turtle::Writer.for(:turtle).buffer(:prefixes => prefixes) do |writer|
writer << rdf
end
else
nt
end
when /html/
# modified ntriples output, delivers large datasets
#TODO optimize representation
nt = RestClient::Resource.new(sparql_uri, :verify_ssl => 0).get(:params => { :query => sparql }, :accept => "text/plain")
if !nt.empty?
regex = Regexp.new '(https?:\/\/[\S]+)([>"])'
bnode = Regexp.new '_:[a-z0-9]*'
html = "<html><body>" + nt.gsub(regex, '<a href="\1">\1</a>\2').gsub(/\n/,'<br/>').gsub(bnode, '<>') + "</body></html>"
html
else
nt
end
end
else
# TODO: check if this prevents SPARQL injections
bad_request_error "Only SELECT and CONSTRUCT are accepted SPARQL statements."
end
rescue
bad_request_error $!.message, sparql_uri, $!.backtrace
end
def self.klass
RDF::OT[SERVICE.capitalize]
end
def self.four_store_uri
# credentials are removed from uri in error.rb
$four_store[:uri].sub(%r{//},"//#{$four_store[:user]}:#{$four_store[:password]}@")
end
def self.sparql_uri
File.join(four_store_uri, "sparql") + '/'
end
def self.update_uri
File.join(four_store_uri, "update") + '/'
end
def self.data_uri uri
File.join(four_store_uri, "data","?graph=#{uri}")
end
end
end
end
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