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# dataset.rb
# Loads libraries and webapps
# Author: Christoph Helma, Andreas Maunz
require 'roo'
require 'opentox-server'
require_relative 'helper.rb'
require_relative 'compound.rb'
# TODO: remove and find a better way to test task errors
require_relative 'test.rb'
# Library code
$logger.debug "Dataset booting: #{$dataset.collect{|k,v| "#{k}: '#{v}'"} }"
require 'profiler'
# Entry point
module OpenTox
class Application < Service
before do
#Profiler__::start_profile
end
after do
#Profiler__::stop_profile
#Profiler__::print_profile($stdout)
end
before "/#{SERVICE}/:id/:property" do
@uri = uri("/#{SERVICE}/#{params[:id]}")
end
# Create a new resource
post "/dataset/?" do
@uri = uri("/#{SERVICE}/#{SecureRandom.uuid}")
parse_put
end
head "/#{SERVICE}/:id/?" do
resource_not_found_error "#{uri} not found." unless FourStore.head(@uri.split('?').first)
end
get "/dataset/:id/?" do
case @accept
when "application/rdf+xml", "text/turtle", "text/plain", /html/
r = FourStore.get(@uri.split('?').first, @accept)
else
case @accept
when "text/csv"
r = to_csv
#when "application/vnd.ms-excel"
#to_spreadsheet Excel
#when "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
#to_xlsx
#when "application/vnd.oasis.opendocument.spreadsheet"
#to_spreadsheet Openoffice
#when "chemical/x-mdl-sdfile"
else
bad_request_error "'#{@accept}' is not a supported content type."
end
end
r
end
# Create or update a resource
put "/dataset/:id/?" do
parse_put
end
# Get metadata of the dataset
# @return [application/rdf+xml] Metadata OWL-DL
get '/dataset/:id/metadata' do
case @accept
when "application/rdf+xml", "text/turtle", "text/plain"
sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{@uri}> WHERE {
{ ?s ?p ?o. <#{@uri}> ?p ?o. } UNION
{ ?s ?p ?o. ?s <#{RDF.type}> <#{RDF::OT.Parameter}> . }
FILTER (?p != <#{RDF::OT.dataEntry}>)
} "
FourStore.query sparql, @accept
else
bad_request_error "'#{@accept}' is not a supported content type."
end
end
# Get a list of all features
# @param [Header] Accept one of `application/rdf+xml, text/turtle, text/plain, text/uri-list` (default application/rdf+xml)
# @return [application/rdf+xml, text/turtle, text/plain, text/uri-list] Feature data
get '/dataset/:id/features' do
case @accept
when "application/rdf+xml", "text/turtle", "text/plain"
sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Feature}>; ?p ?o. }"
when "text/uri-list"
sparql = "SELECT DISTINCT ?s FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Feature}>. ?s <#{RDF::OLO.index}> ?idx } ORDER BY ?idx"
else
bad_request_error "'#{@accept}' is not a supported content type."
end
FourStore.query sparql, @accept
end
# Get a list of all compounds
# @param [Header] Accept one of `application/rdf+xml, text/turtle, text/plain, text/uri-list` (default application/rdf+xml)
# @return [application/rdf+xml, text/turtle, text/plain, text/uri-list] Compound data
get '/dataset/:id/compounds' do
case @accept
when "application/rdf+xml", "text/turtle", "text/plain"
sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Compound}>; ?p ?o. }"
when "text/uri-list"
sparql = "SELECT DISTINCT ?s FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Compound}>. ?s <#{RDF::OLO.index}> ?idx } ORDER BY ?idx"
else
bad_request_error "'#{@accept}' is not a supported content type."
end
FourStore.query sparql, @accept
end
end
end
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