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require 'rubygems'
gem "opentox-ruby-api-wrapper", "= 1.6.6"
require 'opentox-ruby-api-wrapper'
class Dataset
include DataMapper::Resource
property :id, Serial
property :uri, String, :length => 255
property :yaml, Text, :length => 2**32-1
property :owl, Text, :length => 2**32-1
property :created_at, DateTime
def to_owl
data = YAML.load(yaml)
beginning = Time.now
owl = OpenTox::OwlSerializer.create 'Dataset', uri
owl.annotate "title", data.title
owl.annotate "creator", data.creator if data.creator
# if data.compounds
# data.compounds.each do |compound|
# owl.add_data_entries compound,data.data[compound]
# end
# end
nt = owl.rdf
LOGGER.debug "OWL creation took #{Time.now - beginning} seconds"
nt
end
end
DataMapper.auto_upgrade!
## REST API
get '/?' do
response['Content-Type'] = 'text/uri-list'
Dataset.all(params).collect{|d| d.uri}.join("\n") + "\n"
end
# provides dataset in various formats
#
# only_metadata=true => compounds and features are removed
#
def get_dataset( params, request, response, only_metadata=false )
accept = request.env['HTTP_ACCEPT']
accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
# workaround for browser links
case params[:id]
when /.yaml$/
params[:id].sub!(/.yaml$/,'')
accept = 'application/x-yaml'
when /.rdf$/
params[:id].sub!(/.rdf$/,'')
accept = 'application/rdf+xml'
when /.xls$/
params[:id].sub!(/.xls$/,'')
accept = 'application/vnd.ms-excel'
end
begin
dataset = Dataset.get(params[:id])
halt 404, "Dataset #{params[:id]} not found." unless dataset
rescue => e
raise e.message + e.backtrace
halt 404, "Dataset #{params[:id]} not found."
end
halt 404, "Dataset #{params[:id]} not found." if dataset.nil? # not sure how an empty cataset can be returned, but if this happens stale processes keep runing at 100% cpo
if only_metadata # remove compounds and feature data from yaml
d = YAML.load(dataset.yaml)
def d.to_yaml_properties
super - [ "@compounds", "@features", "@data"]
end
dataset.yaml = d.to_yaml
end
case accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'application/rdf+xml'
if only_metadata
dataset.to_owl
else
#unless dataset.owl # lazy owl creation
#dataset.owl = dataset.to_owl
#dataset.save
#end
#dataset.owl
dataset.to_owl
end
when /yaml/
response['Content-Type'] = 'application/x-yaml'
dataset.yaml
when /ms-excel/
require 'spreadsheet'
response['Content-Type'] = 'application/vnd.ms-excel'
Spreadsheet.client_encoding = 'UTF-8'
book = Spreadsheet::Workbook.new
tmp = Tempfile.new('opentox-feature-xls')
sheet = book.create_worksheet :name => 'Training Data'
sheet.column(0).width = 100
i = 0
YAML.load(dataset.yaml).data.each do |line|
begin
smilestring = RestClient.get(line[0], :accept => 'chemical/x-daylight-smiles').to_s
if line[1]
val = line[1][0].first[1]
LOGGER.debug val
#line[1][0] ? val = line[1][0].first[1] #? "1" : "0" : val = ""
sheet.update_row(i, smilestring , val)
end
i+=1
rescue
end
end
begin
book.write tmp.path
return tmp
rescue
end
tmp.close!
else
halt 400, "Unsupported MIME type '#{accept}'"
end
end
get '/:id' do
get_dataset(params, request, response)
end
get '/:id/metadata/?' do
get_dataset(params, request, response, true)
end
get '/:id/features/:feature_id/?' do
OpenTox::Dataset.find(url_for("/#{params[:id]}", :full)).feature(params[:feature_id])
end
get '/:id/features/?' do
YAML.load(Dataset.get(params[:id]).yaml).features.join("\n") + "\n"
end
get '/:id/compounds/?' do
YAML.load(Dataset.get(params[:id]).yaml).compounds.join("\n") + "\n"
end
post '/?' do
dataset = Dataset.new
dataset.save
dataset.uri = url_for("/#{dataset.id}", :full)
content_type = request.content_type
content_type = "application/rdf+xml" if content_type.nil?
case request.content_type
when /yaml/
dataset.yaml = request.env["rack.input"].read
when "application/rdf+xml"
dataset.yaml = OpenTox::Dataset.owl_to_yaml(request.env["rack.input"].read,dataset.uri)
else
halt 404, "MIME type \"#{request.content_type}\" not supported."
end
begin
raise "saving failed: "+dataset.errors.inspect unless dataset.save
rescue => e
LOGGER.error e.message
LOGGER.info e.backtrace
halt 500, "Could not save dataset #{dataset.uri}."
end
LOGGER.debug "#{dataset.uri} saved."
response['Content-Type'] = 'text/uri-list'
dataset.uri + "\n"
end
delete '/:id/?' do
begin
dataset = Dataset.get(params[:id])
dataset.destroy!
response['Content-Type'] = 'text/plain'
"Dataset #{params[:id]} deleted."
rescue
halt 404, "Dataset #{params[:id]} does not exist."
end
end
delete '/?' do
Dataset.auto_migrate!
response['Content-Type'] = 'text/plain'
"All datasets deleted."
end
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