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require 'rubygems'
gem "opentox-ruby", "~> 0"
require 'opentox-ruby'
class Dataset
include DataMapper::Resource
property :id, Serial
property :uri, String, :length => 255
property :yaml, Text, :length => 2**32-1
property :token_id, String, :length => 255
property :created_at, DateTime
after :save, :check_policy
def load(params,request)
data = request.env["rack.input"].read
content_type = request.content_type
content_type = "application/rdf+xml" if content_type.nil?
dataset = OpenTox::Dataset.new
case content_type
when /yaml/
dataset.load_yaml(data)
when "application/rdf+xml"
dataset.load_rdfxml(data)
when /multipart\/form-data/ # file uploads
case params[:file][:type]
when /yaml/
dataset.load_yaml(params[:file][:tempfile].read)
when "application/rdf+xml"
dataset.load_rdfxml_file(params[:file][:tempfile])
when "text/csv"
dataset = OpenTox::Dataset.new @uri
dataset.load_csv(params[:file][:tempfile].read)
dataset.add_metadata({
DC.title => File.basename(params[:file][:filename],".csv"),
OT.hasSource => File.basename(params[:file][:filename])
})
when /ms-excel/
extension = File.extname(params[:file][:filename])
case extension
when ".xls"
xls = params[:file][:tempfile].path + ".xls"
File.rename params[:file][:tempfile].path, xls # roo needs these endings
book = Excel.new xls
when ".xlsx"
xlsx = params[:file][:tempfile].path + ".xlsx"
File.rename params[:file][:tempfile].path, xlsx # roo needs these endings
book = Excel.new xlsx
else
raise "#{params[:file][:filename]} is not a valid Excel input file."
end
dataset.load_spreadsheet(book)
dataset.add_metadata({
DC.title => File.basename(params[:file][:filename],extension),
OT.hasSource => File.basename(params[:file][:filename])
})
else
raise "MIME type \"#{params[:file][:type]}\" not supported."
end
else
raise "MIME type \"#{@content_type}\" not supported."
end
dataset.uri = @uri # update uri (also in metdata)
dataset.features.keys.each { |f| dataset.features[f][OT.hasSource] = dataset.metadata[OT.hasSource] unless dataset.features[f][OT.hasSource]}
update(:yaml => dataset.to_yaml)
end
=begin
def create_representations
dataset = YAML.load yaml
["rdfxml","xls"].each do |extension|
file = "public/#{@id}.#{extension}"
FileUtils.rm Dir["public/#{file}"] if File.exists? file
File.open(file,"w+") { |f| f.puts eval("dataset.to_#{extension}") }
end
end
=end
private
def check_policy
OpenTox::Authorization.check_policy(uri, token_id)
end
end
DataMapper.auto_upgrade!
before do
@accept = request.env['HTTP_ACCEPT']
@accept = 'application/rdf+xml' if @accept == '*/*' or @accept == '' or @accept.nil?
end
## REST API
# Get a list of available datasets
# @return [text/uri-list] List of available datasets
get '/?' do
response['Content-Type'] = 'text/uri-list'
Dataset.all(params).collect{|d| d.uri}.join("\n") + "\n"
end
# Get a dataset representation
# @param [Header] Accept one of `application/rdf+xml, application-x-yaml, text/csv, application/ms-excel` (default application/rdf+xml)
# @return [application/rdf+xml, application-x-yaml, text/csv, application/ms-excel] Dataset representation
get '/:id' do
extension = File.extname(params[:id]).sub(/\./,'')
unless extension.empty?
params[:id].sub!(/\.#{extension}$/,'')
case extension
when "yaml"
@accept = 'application/x-yaml'
when "csv"
@accept = 'text/csv'
when "rdfxml"
@accept = 'application/rdf+xml'
when "xls"
@accept = 'application/ms-excel'
else
halt 404, "File format #{extension} not supported."
end
end
dataset = OpenTox::Dataset.new
dataset.load_yaml(Dataset.get(params[:id]).yaml)
halt 404, "Dataset #{params[:id]} empty." if dataset.nil? # not sure how an empty dataset can be returned, but if this happens stale processes keep runing at 100% cpu
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
file = "public/#{params[:id]}.rdfxml"
File.open(file,"w+") { |f| f.puts dataset.to_rdfxml } unless File.exists? file # lazy rdfxml generation
response['Content-Type'] = 'application/rdf+xml'
File.open(file).read
when /yaml/
response['Content-Type'] = 'application/x-yaml'
dataset.to_yaml
when "text/csv"
response['Content-Type'] = 'text/csv'
dataset.to_csv
when /ms-excel/
file = "public/#{params[:id]}.xls"
dataset.to_xls.write(file) unless File.exists? file # lazy xls generation
response['Content-Type'] = 'application/ms-excel'
File.open(file).read
else
halt 404, "Content-type #{@accept} not supported."
end
end
# Get metadata of the dataset
# @return [application/rdf+xml] Metadata OWL-DL
get '/:id/metadata' do
metadata = YAML.load(Dataset.get(params[:id]).yaml).metadata
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'application/rdf+xml'
serializer = OpenTox::Serializer::Owl.new
serializer.add_metadata url_for("/#{params[:id]}",:full), metadata
serializer.to_rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
metadata.to_yaml
end
end
# Get a dataset feature
# @param [Header] Accept one of `application/rdf+xml or application-x-yaml` (default application/rdf+xml)
# @return [application/rdf+xml,application/x-yaml] Feature metadata
get %r{/(\d+)/feature/(.*)$} do |id,feature|
#get '/:id/feature/:feature_name/?' do
#feature_uri = url_for("/#{params[:id]}/feature/#{URI.encode(params[:feature_name])}",:full) # work around racks internal uri decoding
#dataset = YAML.load(Dataset.get(params[:id]).yaml)
feature_uri = url_for("/#{id}/feature/#{URI.encode(feature)}",:full) # work around racks internal uri decoding
dataset = YAML.load(Dataset.get(id).yaml)
metadata = dataset.features[feature_uri]
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'application/rdf+xml'
serializer = OpenTox::Serializer::Owl.new
serializer.add_feature feature_uri, metadata
serializer.to_rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
metadata.to_yaml
end
end
# Get a list of all features
# @param [Header] Accept one of `application/rdf+xml, application-x-yaml, text/uri-list` (default application/rdf+xml)
# @return [application/rdf+xml, application-x-yaml, text/uri-list] Feature list
get '/:id/features' do
features = YAML.load(Dataset.get(params[:id]).yaml).features
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'application/rdf+xml'
serializer = OpenTox::Serializer::Owl.new
features.each { |feature,metadata| serializer.add_feature feature, metadata }
serializer.to_rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
features.to_yaml
when "text/uri-list"
response['Content-Type'] = 'text/uri-list'
YAML.load(Dataset.get(params[:id]).yaml).features.keys.join("\n") + "\n"
end
end
# Get a list of all compounds
# @return [text/uri-list] Feature list
get '/:id/compounds' do
response['Content-Type'] = 'text/uri-list'
YAML.load(Dataset.get(params[:id]).yaml).compounds.join("\n") + "\n"
end
# Create a new dataset.
#
# Posting without parameters creates and saves an empty dataset (with assigned URI).
# Posting with parameters creates and saves a new dataset.
# Data can be submitted either
# - in the message body with the appropriate Content-type header or
# - as file uploads with Content-type:multipart/form-data and a specified file type
# @example
# curl -X POST -F "file=@training.csv;type=text/csv" http://webservices.in-silico.ch/dataset
# @param [Header] Content-type one of `application/x-yaml, application/rdf+xml, multipart/form-data/`
# @param [BODY] - string with data in selected Content-type
# @param [optional] file, for file uploads, Content-type should be multipart/form-data, please specify the file type `application/rdf+xml, application-x-yaml, text/csv, application/ms-excel`
# @return [text/uri-list] Task URI or Dataset URI (empty datasets)
post '/?' do
@dataset = Dataset.create
@dataset.token_id = params[:token_id] if params[:token_id]
@dataset.token_id = request.env['HTTP_TOKEN_ID'] if !dataset.token_id and request.env['HTTP_TOKEN_ID']
response['Content-Type'] = 'text/uri-list'
@dataset.update(:uri => url_for("/#{@dataset.id}", :full))
if params.empty? and request.env["rack.input"].read.empty?
@dataset.update(:yaml => OpenTox::Dataset.new(@dataset.uri).to_yaml)
@dataset.uri
else
task = OpenTox::Task.create("Converting and saving dataset ", @dataset.uri) do
@dataset.load params, request
@dataset.uri
end
halt 503,task.uri+"\n" if task.status == "Cancelled"
halt 202,task.uri+"\n"
end
end
# Save a dataset, will overwrite all existing data
#
# Data can be submitted either
# - in the message body with the appropriate Content-type header or
# - as file uploads with Content-type:multipart/form-data and a specified file type
# @example
# curl -X POST -F "file=@training.csv;type=text/csv" http://webservices.in-silico.ch/dataset/1
# @param [Header] Content-type one of `application/x-yaml, application/rdf+xml, multipart/form-data/`
# @param [BODY] - string with data in selected Content-type
# @param [optional] file, for file uploads, Content-type should be multipart/form-data, please specify the file type `application/rdf+xml, application-x-yaml, text/csv, application/ms-excel`
# @return [text/uri-list] Task ID
post '/:id' do
@dataset = Dataset.get(params[:id])
halt 404, "Dataset #{params[:id]} not found." unless @dataset
response['Content-Type'] = 'text/uri-list'
task = OpenTox::Task.create("Converting and saving dataset ", @dataset.uri) do
@dataset.load params, request
FileUtils.rm Dir["public/#{params[:id]}.*"]
@dataset.uri
end
halt 503,task.uri+"\n" if task.status == "Cancelled"
halt 202,task.uri.to_s+"\n"
end
# Delete a dataset
# @return [text/plain] Status message
delete '/:id' do
begin
dataset = Dataset.get(params[:id])
FileUtils.rm Dir["public/#{params[:id]}.*"]
dataset.destroy!
if params[:token_id] and !Dataset.get(params[:id]) and uri
begin
aa = OpenTox::Authorization.delete_policies_from_uri(uri, params[:token_id])
LOGGER.debug "Policy deleted for Dataset URI: #{uri} with result: #{aa}"
rescue
LOGGER.warn "Policy delete error for Dataset URI: #{uri}"
end
end
response['Content-Type'] = 'text/plain'
"Dataset #{params[:id]} deleted."
rescue
halt 404, "Dataset #{params[:id]} does not exist."
end
end
# Delete all datasets
# @return [text/plain] Status message
delete '/?' do
FileUtils.rm Dir["public/*.rdfxml"]
FileUtils.rm Dir["public/*.xls"]
Dataset.auto_migrate!
response['Content-Type'] = 'text/plain'
"All datasets deleted."
end
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