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require 'rubygems'
gem "opentox-ruby-api-wrapper", "= 1.6.6"
require 'opentox-ruby-api-wrapper'
require 'parser'
class Dataset
include DataMapper::Resource
property :id, Serial
property :uri, String, :length => 255
property :yaml, Text, :length => 2**32-1
property :created_at, DateTime
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
get '/:id' do
accept = request.env['HTTP_ACCEPT']
accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
begin
dataset = OpenTox::Dataset.from_yaml(Dataset.get(params[:id]).yaml)
halt 404, "Dataset #{params[:id]} not found." if dataset.nil? # not sure how an empty dataset can be returned, but if this happens stale processes keep runing at 100% cpu
rescue => e
LOGGER.error e.message
LOGGER.info e.backtrace
halt 404, "Dataset #{params[:id]} not found."
end
case accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
file = "public/#{params[:id]}.rdfxml"
if File.exists? file
response['Content-Type'] = 'application/rdf+xml'
#redirect url_for("/#{params[:id]}",:full)+ ".rdfxml" # confuses curl (needs -L flag)
File.read(file)
else
task_uri = OpenTox::Task.as_task("Converting dataset to OWL-DL (RDF/XML)", url_for(params[:id],:full)) do
File.open(file,"w+") { |f| f.puts dataset.rdfxml }
url_for("/#{params[:id]}",:full)+ ".rdfxml"
end
response['Content-Type'] = 'text/uri-list'
halt 202,task_uri.to_s+"\n"
end
when /yaml/
response['Content-Type'] = 'application/x-yaml'
dataset.yaml
when "text/csv"
response['Content-Type'] = 'text/csv'
dataset.csv
when /ms-excel/
file = "public/#{params[:id]}.xls"
if File.exists? file
response['Content-Type'] = 'application/ms-excel'
File.read(file)
else
task_uri = OpenTox::Task.as_task("Converting dataset to Excel", url_for(params[:id],:full)) do
dataset.excel.write(file)
url_for("/#{params[:id]}",:full)+ ".xls"
end
response['Content-Type'] = 'text/uri-list'
halt 202,task_uri.to_s+"\n"
end
else
halt 404, "Content-type #{accept} not supported."
end
end
get '/:id/metadata/?' do
metadata = YAML.load(Dataset.get(params[:id]).yaml).metadata
accept = request.env['HTTP_ACCEPT']
accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
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), "Dataset", metadata
serializer.rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
metadata.to_yaml
end
end
get %r{/(\d+)/feature/(.*)$} do |id,feature|
feature_uri = url_for("/#{id}/feature/#{feature}",:full)
dataset = OpenTox::Dataset.from_yaml(Dataset.get(id).yaml)
metadata = dataset.features[feature_uri]
accept = request.env['HTTP_ACCEPT']
accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
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.rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
metadata.to_yaml
end
end
get '/:id/features/?' do
response['Content-Type'] = 'text/uri-list'
YAML.load(Dataset.get(params[:id]).yaml).features.keys.join("\n") + "\n"
end
get '/:id/compounds/?' do
response['Content-Type'] = 'text/uri-list'
YAML.load(Dataset.get(params[:id]).yaml).compounds.join("\n") + "\n"
end
post '/?' do # create an empty dataset
response['Content-Type'] = 'text/uri-list'
dataset = Dataset.create
dataset.update(:uri => url_for("/#{dataset.id}", :full))
dataset.update(:yaml => OpenTox::Dataset.new(url_for("/#{dataset.id}", :full)).to_yaml)
"#{dataset.uri}\n"
end
post '/:id/?' do # insert data into a dataset
begin
dataset = Dataset.get(params[:id])
halt 404, "Dataset #{params[:id]} not found." unless dataset
data = request.env["rack.input"].read
content_type = request.content_type
content_type = "application/rdf+xml" if content_type.nil?
case content_type
when /yaml/
dataset.update(:yaml => data)
when "application/rdf+xml"
dataset.update(:yaml => OpenTox::Dataset.from_rdfxml(data).yaml)
when /multipart\/form-data/ # for file uploads
case params[:file][:type]
when /yaml/
dataset.update(:yaml => params[:file][:tempfile].read)
when "application/rdf+xml"
dataset.update(:yaml => OpenTox::Dataset.from_rdfxml(params[:file][:tempfile]).yaml)
when "text/csv"
metadata = {DC.title => File.basename(params[:file][:filename],".csv"), OT.hasSource => File.basename(params[:file][:filename])}
d = OpenTox::Dataset.from_csv(File.open(params[:file][:tempfile]).read)
d.add_metadata metadata
dataset.update(:yaml => d.yaml, :uri => d.uri)
when /ms-excel/
extension = File.extname(params[:file][:filename])
metadata = {DC.title => File.basename(params[:file][:filename],extension), OT.hasSource => File.basename(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
halt 404, "#{params[:file][:filename]} is not a valid Excel input file."
end
d = OpenTox::Dataset.from_spreadsheet(book)
d.add_metadata metadata
dataset.update(:yaml => d.yaml, :uri => d.uri)
else
halt 404, "MIME type \"#{params[:file][:type]}\" not supported."
end
else
halt 404, "MIME type \"#{content_type}\" not supported."
end
FileUtils.rm Dir["public/#{params[:id]}.*"] # delete all serialization files, will be recreated at next reques
response['Content-Type'] = 'text/uri-list'
"#{dataset.uri}\n"
rescue => e
LOGGER.error e.message
LOGGER.info e.backtrace
halt 500, "Could not save dataset #{dataset.uri}."
end
end
delete '/:id/?' do
begin
dataset = Dataset.get(params[:id])
FileUtils.rm Dir["public/#{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.all {|d| FileUtils.rm Dir["public/#{d.id}.*"] }
Dataset.auto_migrate!
response['Content-Type'] = 'text/plain'
"All datasets deleted."
end
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