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|
require 'rubygems'
gem "opentox-ruby", "~> 3"
require 'opentox-ruby'
require 'profiler'
require 'rjb'
require 'open3'
set :lock, true
@@datadir = "data"
@@idfile_path = @@datadir+"/id"
unless File.exist?(@@idfile_path)
id = Dir["./#{@@datadir}/*json"].collect{|f| File.basename(f.sub(/.json/,'')).to_i}.sort.last
id = 0 if id.nil?
open(@@idfile_path,"w") do |f|
f.puts(id)
end
end
helpers do
def next_id
open(@@idfile_path, "r+") do |f|
f.flock(File::LOCK_EX)
@id = f.gets.to_i + 1
f.rewind
f.print @id
end
return @id
end
def uri(id)
url_for "/#{id}", :full
end
# subjectid ist stored as memeber variable, not in params
def load_dataset(id, params,content_type,input_data)
@uri = uri id
raise "store subject-id in dataset-object, not in params" if params.has_key?(:subjectid) and @subjectid==nil
content_type = "application/rdf+xml" if content_type.nil?
dataset = OpenTox::Dataset.new(@uri, @subjectid)
case content_type
when /yaml/
dataset.load_yaml(input_data)
when /json/
dataset.load_json(input_data)
when "text/csv"
dataset.load_csv(input_data, @subjectid)
when /application\/rdf\+xml/
dataset.load_rdfxml(input_data, @subjectid)
when "chemical/x-mdl-sdfile"
dataset.load_sdf(input_data, @subjectid)
when /multipart\/form-data/ , "application/x-www-form-urlencoded" # file uploads
case params[:file][:type]
when "chemical/x-mdl-sdfile"
dataset.load_sdf(input_data, @subjectid)
when /json/
dataset.load_json(params[:file][:tempfile].read)
when /yaml/
dataset.load_yaml(params[:file][:tempfile].read)
when "application/rdf+xml"
dataset.load_rdfxml_file(params[:file][:tempfile], @subjectid)
when "text/csv"
dataset.load_csv(params[:file][:tempfile].read, @subjectid)
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, @subjectid)
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]}
zip_dataset( dataset )
end
def zip_dataset( dataset )
raise unless @id
LOGGER.debug "zipping #{@@datadir}/#{@id}.json.zip"
File.open("#{@@datadir}/#{@id}.json","w+"){|f| f.puts dataset.to_json}
stdin, stdout, stderr = Open3.popen3("/usr/bin/zip -D #{@@datadir}/#{@id}.json.zip #{@@datadir}/#{@id}.json")
LOGGER.debug stdout.readlines.collect{|l| l.chomp}.join(";")
LOGGER.debug stderr.readlines.collect{|l| l.chomp}.join(";")
stdout.close
stderr.close
stdin.close
#File.delete("#{@@datadir}/#{@id}.json")
end
def unzip_dataset()
if !File.exist?("#{@@datadir}/#{@id}.json")
LOGGER.debug "unzipping #{@@datadir}/#{@id}.json.zip"
output = IO.popen("/usr/bin/unzip -nj #{@json_zip_file} -d #{@@datadir}")
LOGGER.debug output.readlines.collect{|l| l.chomp}.join(";")
output.close
raise "could not unzip file" unless File.exist?("#{@@datadir}/#{@id}.json")
end
dataset = OpenTox::Dataset.from_json File.read("#{@@datadir}/#{@id}.json")
#File.delete("#{@@datadir}/#{@id}.json")
dataset
end
def unzip_json()
if !File.exist?("#{@@datadir}/#{@id}.json")
LOGGER.debug "unzipping #{@@datadir}/#{@id}.json.zip"
output = IO.popen("/usr/bin/unzip -nj #{@json_zip_file} -d #{@@datadir}")
LOGGER.debug output.readlines.collect{|l| l.chomp}.join(";")
output.close
raise "could not unzip file #{@json_zip_file} to #{@@datadir}/#{@id}.json" unless File.exist?("#{@@datadir}/#{@id}.json")
end
content = File.read("#{@@datadir}/#{@id}.json")
#File.delete("#{@@datadir}/#{@id}.json")
content
end
def zip_arff( arff )
LOGGER.debug "zipping #{@@datadir}/#{@id}.arff.zip"
file = "#{@@datadir}/#{@id}.arff"
File.open(file,"w+") { |f| f.puts arff }
output = IO.popen("/usr/bin/zip -D #{@@datadir}/#{@id}.arff.zip #{@@datadir}/#{@id}.arff")
LOGGER.debug output.readlines.collect{|l| l.chomp}.join(";")
output.close
#File.delete("#{@@datadir}/#{@id}.arff")
end
def unzip_arff()
if !File.exist?("#{@@datadir}/#{@id}.arff")
LOGGER.debug "unzipping #{@@datadir}/#{@id}.arff.zip"
output = IO.popen("/usr/bin/unzip -nj #{@@datadir}/#{@id}.arff.zip -d #{@@datadir}")
LOGGER.debug output.readlines.collect{|l| l.chomp}.join(";")
output.close
raise "could not unzip file" unless File.exist?("#{@@datadir}/#{@id}.arff")
end
content = File.read("#{@@datadir}/#{@id}.arff")
#File.delete("#{@@datadir}/#{@id}.arff")
content
end
def to_arff(dataset, subjectid=nil, features=nil )
LOGGER.debug "convert dataset to arff #{dataset.uri}"
# count duplicates
num_compounds = {}
dataset.features.keys.each do |f|
dataset.compounds.each do |c|
if dataset.data_entries[c]
val = dataset.data_entries[c][f]
size = val==nil ? 1 : val.size
num_compounds[c] = num_compounds[c]==nil ? size : [num_compounds[c],size].max
else
num_compounds[c] = 1
end
end
end
#puts "found duplicates"
# use either all, or the provided features, sorting is important as col-index := features
if features
features.sort!
else
features = dataset.features.keys.sort
end
compounds = []
compound_names = []
dataset.compounds.each do |c|
count = 0
num_compounds[c].times do |i|
compounds << c
compound_names << "#{c}$#{count}"
count+=1
end
end
missing = {}
arff = "@RELATION #{dataset.uri}\n\n"
features.each do |f|
numeric = dataset.features[f][RDF.type].to_a.flatten.include?(OT.NumericFeature)
#feat = OpenTox::Feature.find(f,subjectid)
#numeric = feat.metadata[RDF.type].to_a.flatten.include?(OT.NumericFeature)
if numeric
arff << "@ATTRIBUTE '#{f}' NUMERIC\n"
else
# HACK for binary 0,1 features without accept values (as returned by fminer):
# set missing value to 0 instead ?
# set accept value to [0,1]
accept_values = dataset.accept_values(f)
missing[f] = "0" if accept_values==nil
arff << "@ATTRIBUTE '#{f}' {#{(accept_values==nil ? [0,1] : accept_values).join(",")}}\n"
end
end
#puts "found feature types"
arff << "\n@DATA\n"
dataset.compounds.each do |c|
num_compounds[c].times do |i|
c_values = []
features.each do |f|
accept_values =
if dataset.data_entries[c]
val = dataset.data_entries[c][f]
v = val==nil ? "" : val[i].to_s
else
raise "wtf" if i>0
v = ""
end
v = (missing[f]==nil ? "?" : missing[f]) if v.size()==0
c_values << v
end
arff << "#{c_values.join(",")}\n"
end
end
arff
end
end
before do
@accept = request.env['HTTP_ACCEPT']
@accept = 'application/rdf+xml' if @accept == '*/*' or @accept == '' or @accept.nil?
@id = request.path_info.match(/^\/\d+/)
unless @id.nil?
@id = @id.to_s.sub(/\//,'').to_i
@uri = uri @id
@json_zip_file = "#{@@datadir}/#{@id}.json.zip"
raise OpenTox::NotFoundError.new "Dataset #{@id} not found." unless File.exists? @json_zip_file
extension = File.extname(request.path_info)
unless extension.empty?
case extension
when ".html"
@accept = 'text/html'
when ".json"
@accept = 'application/json'
when ".yaml"
@accept = 'application/x-yaml'
when ".csv"
@accept = 'text/csv'
when ".rdfxml"
@accept = 'application/rdf+xml'
when ".xls"
@accept = 'application/ms-excel'
when ".sdf"
@accept = 'chemical/x-mdl-sdfile'
else
raise OpenTox::NotFoundError.new "File format #{extension} not supported."
end
end
end
# make sure subjectid is not included in params, subjectid is set as member variable
params.delete(:subjectid)
end
## REST API
# Get a list of available datasets
# @return [text/uri-list] List of available datasets
get '/?' do
uri_list = Dir["./#{@@datadir}/*json.zip"].collect{|f| File.basename(f.sub(/.json.zip/,'')).to_i}.sort.collect{|n| uri n}.join("\n") + "\n"
case @accept
when /html/
response['Content-Type'] = 'text/html'
OpenTox.text_to_html uri_list
else
response['Content-Type'] = 'text/uri-list'
uri_list
end
end
#post '/:id/rdf' do
# response['Content-Type'] = 'text/uri-list'
# task = OpenTox::Task.create("Converting dataset to rdf ", @uri) do
# file = "#{@@datadir}/#{params[:id]}.rdfxml"
# unless File.exists? file # lazy rdfxml generation
# dataset = OpenTox::Dataset.from_json File.read(@json_file)
# File.open(file,"w+") { |f| f.puts dataset.to_rdfxml }
# end
# @uri
# end
# return_task task
#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
case @accept
when /rdf/ # redland sends text/rdf instead of application/rdf+xml
file = "#{@@datadir}/#{params[:id]}.rdfxml"
unless File.exists? file # lazy rdfxml generation
#dataset = OpenTox::Dataset.from_json File.read(@json_file)
dataset = unzip_dataset()
File.open(file,"w+") { |f| f.puts dataset.to_rdfxml }
end
send_file file, :type => 'application/rdf+xml'
when /json/
#send_file @json_file, :type => 'application/x-yaml'
response['Content-Type'] = 'application/x-json'
unzip_json()
when /arff/
response['Content-Type'] = 'application/x-arff'
unless File.exists? "#{@@datadir}/#{params[:id]}.arff.zip"
arff_content = to_arff(unzip_dataset())
zip_arff(arff_content)
arff_content
else
unzip_arff()
end
when /yaml/
file = "#{@@datadir}/#{params[:id]}.yaml"
unless File.exists? file # lazy yaml generation
#dataset = OpenTox::Dataset.from_json File.read(@json_file)
dataset = unzip_dataset()
File.open(file,"w+") { |f| f.puts dataset.to_yaml }
end
send_file file, :type => 'application/x-yaml'
when /html/
response['Content-Type'] = 'text/html'
OpenTox.text_to_html JSON.pretty_generate(JSON.parse(unzip_json()))
when "text/csv"
response['Content-Type'] = 'text/csv'
#OpenTox::Dataset.from_json(File.read(@json_file)).to_csv
unzip_dataset().to_csv
when /ms-excel/
file = "#{@@datadir}/#{params[:id]}.xls"
#OpenTox::Dataset.from_json(File.read(@json_file)).to_xls.write(file) unless File.exists? file # lazy xls generation
unzip_dataset().to_xls.write(file) unless File.exists? file # lazy xls generation
send_file file, :type => 'application/ms-excel'
when /sdfile/
response['Content-Type'] = 'chemical/x-mdl-sdfile'
#OpenTox::Dataset.from_json(File.read(@json_file)).to_sdf
unzip_dataset().to_sdf
# when /uri-list/
# response['Content-Type'] = 'text/uri-list'
# Yajl::Parser.parse(File.read(@json_file)).to_urilist
else
raise OpenTox::NotFoundError.new "Content-type #{@accept} not supported."
end
end
# Get metadata of the dataset
# @return [application/rdf+xml] Metadata OWL-DL
get '/:id/metadata' do
metadata = unzip_dataset().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 '/:id/info' do
dataset = unzip_dataset()
array = []
array << @uri
array << "#{dataset.compounds.size} compounds"
array << "#{dataset.features.size} features"
array << ["metadata", dataset.metadata]
array << ["compounds", dataset.compounds]
array << ["features", dataset.features]
case @accept
when /html/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'text/html'
OpenTox.text_to_html array.to_yaml
else
response['Content-Type'] = 'application/x-yaml'
metadata.to_yaml
end
end
get '/:id/info_values' do
dataset = unzip_dataset()
array = []
array << @uri
array << "#{dataset.compounds.size} compounds"
array << "#{dataset.features.size} features"
array << ["metadata", dataset.metadata]
array << ["compounds", dataset.compounds]
array << ["features", dataset.features]
array << ["values", dataset.data_entries]
case @accept
when /html/ # redland sends text/rdf instead of application/rdf+xml
response['Content-Type'] = 'text/html'
OpenTox.text_to_html array.to_yaml
else
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|
@id = id
@uri = uri @id
#@json_file = "#{@@datadir}/#{@id}.json"
@json_zip_file = "#{@@datadir}/#{@id}.json.zip"
feature_uri = url_for("/#{@id}/feature/#{URI.encode(feature)}",:full) # work around racks internal uri decoding
metadata = unzip_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
when /json/
response['Content-Type'] = 'application/json'
Yajl::Encoder.encode(metadata)
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 = unzip_dataset().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 /json/
response['Content-Type'] = 'application/json'
Yajl::Encoder.encode(features)
when "text/uri-list"
response['Content-Type'] = 'text/uri-list'
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'
unzip_dataset().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
response['Content-Type'] = 'text/uri-list'
# it could be that the read function works only once!, store in varible
input_data = request.env["rack.input"].read
@id = next_id
@uri = uri @id
#@json_file = "#{@@datadir}/#{@id}.json"
@json_zip_file = "#{@@datadir}/#{@id}.json.zip"
if params.size == 0 and input_data.size==0
#File.open(@json_file,"w+"){|f| f.puts OpenTox::Dataset.new(@uri).to_json}
zip_dataset(OpenTox::Dataset.new(@uri))
#OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @json_file
OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @json_zip_file
@uri
else
task = OpenTox::Task.create("Converting and saving dataset ", @uri) do
load_dataset @id, params, request.content_type, input_data
#OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @json_file
OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @json_zip_file
@uri
end
raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
halt 202,task.uri+"\n"
end
end
post '/merge' do
LOGGER.info "merging datasets #{params.inspect}"
raise "dataset1 or dataset2 is missing" unless params["dataset1"] and params["dataset2"]
task = OpenTox::Task.create("Merging datasets", @uri) do
dataset1 = OpenTox::Dataset.find(params["dataset1"])
dataset2 = OpenTox::Dataset.find(params["dataset2"])
features1 = params.has_key?("features1") ? params["features1"].split(",") : nil
features2 = params.has_key?("features2") ? params["features2"].split(",") : nil
compounds1 = params.has_key?("compounds1") ? params["compounds1"].split(",") : nil
compounds2 = params.has_key?("compounds2") ? params["compounds2"].split(",") : nil
OpenTox::Dataset.merge(dataset1,dataset2,{},@subjectid,features1,features2,compounds1,compounds2).uri
end
return_task task
end
post '/filter' do
LOGGER.info "filtering dataset #{params.inspect}"
raise "dataset_uri is missing" unless params["dataset_uri"]
task = OpenTox::Task.create("Filtering dataset", @uri) do
dataset = OpenTox::Dataset.find(params["dataset_uri"])
dataset.filter( params.has_key?("features") ? params["features"].split(",") : nil ).uri
end
return_task task
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
response['Content-Type'] = 'text/uri-list'
task = OpenTox::Task.create("Converting and saving dataset ", @uri) do
FileUtils.rm Dir["#{@@datadir}/#{@id}.*"]
load_dataset @id, params, request.content_type, request.env["rack.input"].read
@uri
end
raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
halt 202,task.uri.to_s+"\n"
end
# Deletes datasets that have been created by a crossvalidatoin that does not exist anymore
# (This can happen if a crossvalidation fails unexpectedly)
delete '/cleanup' do
Dir["./#{@@datadir}/*json"].each do |file|
dataset = OpenTox::Dataset.from_json File.read(file)
if dataset.metadata[DC.creator] && dataset.metadata[DC.creator] =~ /crossvalidation\/[0-9]/
begin
cv = OpenTox::Crossvalidation.find(dataset.metadata[DC.creator],@subjectid)
raise unless cv
rescue
LOGGER.debug "deleting #{dataset.uri}, crossvalidation missing: #{dataset.metadata[DC.creator]}"
begin
dataset.delete @subjectid
rescue
end
end
end
end
"cleanup done"
end
# Delete a dataset
# @return [text/plain] Status message
delete '/:id' do
LOGGER.debug "deleting dataset with id #{@id}"
begin
FileUtils.rm Dir["#{@@datadir}/#{@id}.*"]
#if @subjectid and !File.exists? @json_file and @uri
if @subjectid and !File.exists? @json_zip_file and @uri
begin
res = OpenTox::Authorization.delete_policies_from_uri(@uri, @subjectid)
LOGGER.debug "Policy deleted for Dataset URI: #{@uri} with result: #{res}"
rescue
LOGGER.warn "Policy delete error for Dataset URI: #{@uri}"
end
end
response['Content-Type'] = 'text/plain'
"Dataset #{@id} deleted."
rescue
raise OpenTox::NotFoundError.new "Dataset #{@id} does not exist."
end
end
# Delete all datasets
# @return [text/plain] Status message
delete '/?' do
FileUtils.rm Dir["#{@@datadir}/*.rdfxml"]
FileUtils.rm Dir["#{@@datadir}/*.xls"]
FileUtils.rm Dir["#{@@datadir}/*.yaml"]
FileUtils.rm Dir["#{@@datadir}/*.json"]
response['Content-Type'] = 'text/plain'
"All datasets deleted."
end
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