diff options
| -rw-r--r-- | lib/authorization.rb | 13 | ||||
| -rw-r--r-- | lib/dataset.rb | 50 | ||||
| -rw-r--r-- | lib/environment.rb | 3 | ||||
| -rw-r--r-- | lib/feature.rb | 8 | ||||
| -rw-r--r-- | lib/helper.rb | 41 | ||||
| -rw-r--r-- | lib/model.rb | 12 | ||||
| -rw-r--r-- | lib/opentox.rb | 8 | ||||
| -rw-r--r-- | lib/parser.rb | 17 | ||||
| -rw-r--r-- | lib/policy.rb | 9 | ||||
| -rw-r--r-- | lib/task.rb | 12 |
10 files changed, 103 insertions, 70 deletions
diff --git a/lib/authorization.rb b/lib/authorization.rb index c33f712..5bc690a 100644 --- a/lib/authorization.rb +++ b/lib/authorization.rb @@ -114,7 +114,9 @@ module OpenTox begin resource = RestClient::Resource.new("#{AA_SERVER}/pol") out = resource.get(:subjectid => subjectid) - return out.split("\n") + return out.split("\n") + rescue RestClient::InternalServerError => e + raise e.response rescue return nil end @@ -313,9 +315,14 @@ module OpenTox false end end + true + end + + class << self + alias :token_valid? :is_token_valid end - - end + + end end diff --git a/lib/dataset.rb b/lib/dataset.rb index ae86f5f..640e3da 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -14,7 +14,7 @@ module OpenTox # dataset = OpenTox::Dataset.new("http:://webservices.in-silico/ch/dataset/1") # @param [optional, String] uri Dataset URI # @return [OpenTox::Dataset] Dataset object - def initialize(uri=nil) + def initialize(uri=nil,subjectid=nil) super uri @features = {} @compounds = [] @@ -27,7 +27,7 @@ module OpenTox # @param [optional, String] uri Dataset URI # @return [OpenTox::Dataset] Dataset object def self.create(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil) - dataset = Dataset.new + dataset = Dataset.new(nil,subjectid) dataset.save(subjectid) dataset end @@ -50,17 +50,17 @@ module OpenTox # Find a dataset and load all data. This can be time consuming, use Dataset.new together with one of the load_* methods for a fine grained control over data loading. # @param [String] uri Dataset URI # @return [OpenTox::Dataset] Dataset object with all data - def self.find(uri) - dataset = Dataset.new(uri) - dataset.load_all + def self.find(uri, subjectid=nil) + dataset = Dataset.new(uri, subjectid) + dataset.load_all(subjectid) dataset end # Get all datasets from a service # @param [optional,String] uri URI of the dataset service, defaults to service specified in configuration # @return [Array] Array of dataset object without data (use one of the load_* methods to pull data from the server) - def self.all(uri=CONFIG[:services]["opentox-dataset"]) - RestClientWrapper.get(uri,:accept => "text/uri-list").to_s.each_line.collect{|u| Dataset.new(u)} + def self.all(uri=CONFIG[:services]["opentox-dataset"], subjectid=nil) + RestClientWrapper.get(uri,{:accept => "text/uri-list",:subjectid => subjectid}).to_s.each_line.collect{|u| Dataset.new(u, subjectid)} end # Load YAML representation into the dataset @@ -77,10 +77,10 @@ module OpenTox # Load RDF/XML representation from a file # @param [String] file File with RDF/XML representation of the dataset # @return [OpenTox::Dataset] Dataset object with RDF/XML data - def load_rdfxml_file(file) - parser = Parser::Owl::Dataset.new @uri + def load_rdfxml_file(file, subjectid=nil) + parser = Parser::Owl::Dataset.new @uri, subjectid parser.uri = file.path - copy parser.load_uri + copy parser.load_uri(subjectid) end # Load CSV string (format specification: http://toxcreate.org/help) @@ -111,26 +111,26 @@ module OpenTox # Load and return only metadata of a Dataset object # @return [Hash] Metadata of the dataset - def load_metadata - add_metadata Parser::Owl::Dataset.new(@uri).load_metadata + def load_metadata(subjectid=nil) + add_metadata Parser::Owl::Dataset.new(@uri, subjectid).load_metadata(subjectid) self.uri = @uri if @uri # keep uri @metadata end # Load all data (metadata, data_entries, compounds and features) from URI - def load_all + def load_all(subjectid=nil) if (CONFIG[:yaml_hosts].include?(URI.parse(@uri).host)) - copy YAML.load(RestClientWrapper.get(@uri, :accept => "application/x-yaml")) + copy YAML.load(RestClientWrapper.get(@uri, {:accept => "application/x-yaml", :subjectid => subjectid})) else - parser = Parser::Owl::Dataset.new(@uri) - copy parser.load_uri + parser = Parser::Owl::Dataset.new(@uri, subjectid) + copy parser.load_uri(subjectid) end end # Load and return only compound URIs from the dataset service # @return [Array] Compound URIs in the dataset - def load_compounds - RestClientWrapper.get(File.join(uri,"compounds"),:accept=> "text/uri-list").to_s.each_line do |compound_uri| + def load_compounds(subjectid=nil) + RestClientWrapper.get(File.join(uri,"compounds"),{:accept=> "text/uri-list", :subjectid => subjectid}).to_s.each_line do |compound_uri| @compounds << compound_uri.chomp end @compounds.uniq! @@ -138,9 +138,9 @@ module OpenTox # Load and return only features from the dataset service # @return [Hash] Features of the dataset - def load_features - parser = Parser::Owl::Dataset.new(@uri) - @features = parser.load_features + def load_features(subjectid=nil) + parser = Parser::Owl::Dataset.new(@uri, subjectid) + @features = parser.load_features(subjectid) @features end @@ -290,7 +290,7 @@ module OpenTox task_uri = RestClient.post(@uri, {:file => File.new(@path)},{:accept => "text/uri-list" , :subjectid => subjectid}).to_s.chomp #task_uri = `curl -X POST -H "Accept:text/uri-list" -F "file=@#{@path};type=application/rdf+xml" http://apps.ideaconsult.net:8080/ambit2/dataset` Task.find(task_uri).wait_for_completion - self.uri = RestClientWrapper.get(task_uri,:accept => 'text/uri-list') + self.uri = RestClientWrapper.get(task_uri,{:accept => 'text/uri-list', :subjectid => subjectid}) end else # create dataset if uri is empty @@ -325,9 +325,9 @@ module OpenTox # Find a prediction dataset and load all data. # @param [String] uri Prediction dataset URI # @return [OpenTox::Dataset] Prediction dataset object with all data - def self.find(uri) - prediction = LazarPrediction.new(uri) - prediction.load_all + def self.find(uri, subjectid=nil) + prediction = LazarPrediction.new(uri, subjectid) + prediction.load_all(subjectid) prediction end diff --git a/lib/environment.rb b/lib/environment.rb index 1761d92..203ebc6 100644 --- a/lib/environment.rb +++ b/lib/environment.rb @@ -84,6 +84,9 @@ class OwlNamespace end AA_SERVER = CONFIG[:authorization] ? (CONFIG[:authorization][:server] ? CONFIG[:authorization][:server] : nil) : nil +CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorization][:authenticate_request] +CONFIG[:authorization][:authorize_request] = [""] unless CONFIG[:authorization][:authorize_request] +CONFIG[:authorization][:free_request] = [""] unless CONFIG[:authorization][:free_request] RDF = OwlNamespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' OWL = OwlNamespace.new 'http://www.w3.org/2002/07/owl#' diff --git a/lib/feature.rb b/lib/feature.rb index de7c757..28ac0c5 100644 --- a/lib/feature.rb +++ b/lib/feature.rb @@ -1,11 +1,11 @@ module OpenTox class Feature include OpenTox - - def self.find(uri) - feature = Feature.new uri + + def self.find(uri, subjectid=nil) + feature = Feature.new uri if (CONFIG[:yaml_hosts].include?(URI.parse(uri).host)) - feature.add_metadata YAML.load(RestClientWrapper.get(uri,:accept => "application/x-yaml")) + feature.add_metadata YAML.load(RestClientWrapper.get(uri,{:accept => "application/x-yaml", :subjectid => subjectid})) else feature.add_metadata Parser::Owl::Dataset.new(uri).load_metadata end diff --git a/lib/helper.rb b/lib/helper.rb index ff5e908..e82c8fb 100644 --- a/lib/helper.rb +++ b/lib/helper.rb @@ -16,25 +16,39 @@ helpers do end end + + #Check Authorization for URI with method and subjectid. def authorized?(subjectid) - if CONFIG[:authorization][:authorize_request].include?(request.env['REQUEST_METHOD']) - ret = OpenTox::Authorization.authorize("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}", request.env['REQUEST_METHOD'], subjectid) - LOGGER.debug "OpenTox helpers OpenTox::Authorization authorized? method: #{request.env['REQUEST_METHOD']}, URI: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}, subjectid: #{subjectid} with return #{ret}." + request_method = request.env['REQUEST_METHOD'] + uri = clean_uri("#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}") + request_method = "GET" if request_method == "POST" && uri =~ /\/model\/\d+\/?$/ + if CONFIG[:authorization][:authorize_request].include?(request_method) + ret = OpenTox::Authorization.authorize(uri, request_method, subjectid) + LOGGER.debug "OpenTox helpers OpenTox::Authorization authorized? method: #{request_method} , URI: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}, subjectid: #{subjectid} with return >>#{ret}<<" return ret end - if CONFIG[:authorization][:authenticate_request].include?(env['REQUEST_METHOD']) - if OpenTox::Authorization.is_token_valid(subjectid) - return true - end + if CONFIG[:authorization][:authenticate_request].include?(request_method) + return true if OpenTox::Authorization.is_token_valid(subjectid) end - LOGGER.debug "Not authorized for: #{request.env['rack.url_scheme']}://#{request['REQUEST_URI']} with Method: #{request.env['REQUEST_METHOD']} with Token #{subjectid}" + LOGGER.debug "Not authorized for: #{uri} with Method: #{request.env['REQUEST_METHOD']}/#{request_method} with Token #{subjectid}" return false end + #cleans URI from querystring and file-extension. Sets port 80 to emptystring + # @param [String] uri + def clean_uri(uri) + out = URI.parse(uri) + out.path = out.path[0, out.path.rindex(/[0-9]/) + 1] if out.path.rindex(/[0-9]/) #cuts after id for a&a + "#{out.scheme}:" + (out.port != 80 ? out.port : "") + "//#{out.host}#{out.path}" + end + + #unprotected uris for login/logout, webapplication ... def unprotected_requests case env['REQUEST_URI'] when /\/login$|\/logout$|\/predict$|\/toxcreate\/models$/ return true + when /\/features/ + return false when /\/compound|\/feature|\/task|\/toxcreate/ #to fix: read from config | validation should be protected return true else @@ -42,21 +56,18 @@ helpers do end end - def check_subjectid(subjectid) - return false if !subjectid - return true if subjectid.size > 62 - false - end end before do unless !AA_SERVER or unprotected_requests or CONFIG[:authorization][:free_request].include?(env['REQUEST_METHOD']) begin + subjectid = nil subjectid = session[:subjectid] if session[:subjectid] - subjectid = params[:subjectid] if params[:subjectid] and !check_subjectid(subjectid) - subjectid = request.env['HTTP_SUBJECTID'] if request.env['HTTP_SUBJECTID'] and !check_subjectid(subjectid) + subjectid = params[:subjectid] if params[:subjectid] and !subjectid + subjectid = request.env['HTTP_SUBJECTID'] if request.env['HTTP_SUBJECTID'] and !subjectid # see http://rack.rubyforge.org/doc/SPEC.html subjectid = CGI.unescape(subjectid) if subjectid.include?("%23") + @subjectid = subjectid rescue LOGGER.debug "OpenTox ruby api wrapper: helper before filter: NO subjectid for URI: #{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}" subjectid = "" diff --git a/lib/model.rb b/lib/model.rb index efa273b..85be1b5 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -88,15 +88,15 @@ module OpenTox # Get URIs of all lazar models # @return [Array] List of lazar model URIs - def self.all - RestClientWrapper.get(CONFIG[:services]["opentox-model"]).to_s.split("\n") + def self.all(subjectid=nil) + RestClientWrapper.get(CONFIG[:services]["opentox-model"], :subjectid => subjectid).to_s.split("\n") end # Find a lazar model # @param [String] uri Model URI # @return [OpenTox::Model::Lazar] lazar model - def self.find(uri) - YAML.load RestClientWrapper.get(uri,:accept => 'application/x-yaml') + def self.find(uri, subjectid=nil) + YAML.load RestClientWrapper.get(uri,{:accept => 'application/x-yaml', :subjectid => subjectid}) end # Create a new lazar model @@ -105,7 +105,7 @@ module OpenTox def self.create(params) lazar_algorithm = OpenTox::Algorithm::Generic.new File.join( CONFIG[:services]["opentox-algorithm"],"lazar") model_uri = lazar_algorithm.run(params) - OpenTox::Model::Lazar.find(model_uri) + OpenTox::Model::Lazar.find(model_uri, params[:subjectid]) end # Get a parameter value @@ -128,7 +128,7 @@ module OpenTox DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )), OT.parameters => [{DC.title => "dataset_uri", OT.paramValue => dataset_uri}] }) - d = Dataset.new(dataset_uri) + d = Dataset.new(dataset_uri,subjectid) d.load_compounds count = 0 d.compounds.each do |compound_uri| diff --git a/lib/opentox.rb b/lib/opentox.rb index 90683e5..f1af5c3 100644 --- a/lib/opentox.rb +++ b/lib/opentox.rb @@ -19,14 +19,14 @@ module OpenTox # Get all objects from a service # @return [Array] List of available URIs - def self.all(uri) - RestClientWrapper.get(uri,:accept => "text/uri-list").to_s.split(/\n/) + def self.all(uri, subjectid=nil) + RestClientWrapper.get(uri,:accept => "text/uri-list", :subjectid => subjectid).to_s.split(/\n/) end # Load (and return) metadata from object URI # @return [Hash] Metadata - def load_metadata - @metadata = Parser::Owl::Generic.new(@uri).load_metadata + def load_metadata(subjectid=nil) + @metadata = Parser::Owl::Generic.new(@uri).load_metadata(subjectid) @metadata end diff --git a/lib/parser.rb b/lib/parser.rb index b727412..a913cf2 100644 --- a/lib/parser.rb +++ b/lib/parser.rb @@ -29,14 +29,14 @@ module OpenTox # Read metadata from opentox service # @return [Hash] Object metadata - def load_metadata + def load_metadata(subjectid=nil) if @dataset uri = File.join(@uri,"metadata") else uri = @uri end - + uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid statements = [] parameter_ids = [] `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line| @@ -71,9 +71,9 @@ module OpenTox # Create a new OWL-DL dataset parser # @param uri Dataset URI # @return [OpenTox::Parser::Owl::Dataset] OWL-DL parser - def initialize(uri) + def initialize(uri, subjectid=nil) super uri - @dataset = ::OpenTox::Dataset.new(@uri) + @dataset = ::OpenTox::Dataset.new(@uri, subjectid) end # Read data from dataset service. Files can be parsed by setting #uri to a filename (after initialization with a real URI) @@ -87,12 +87,14 @@ module OpenTox # dataset = parser.load_uri # dataset.save # @return [Hash] Internal dataset representation - def load_uri + def load_uri(subjectid=nil) + uri = @uri + uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid data = {} feature_values = {} feature = {} other_statements = {} - `rapper -i rdfxml -o ntriples #{@uri} 2>/dev/null`.each_line do |line| + `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line| triple = line.chomp.split(' ',3) triple = triple[0..2].collect{|i| i.sub(/\s+.$/,'').gsub(/[<>"]/,'')} case triple[1] @@ -122,8 +124,9 @@ module OpenTox # Read only features from a dataset service. # @return [Hash] Internal features representation - def load_features + def load_features(subjectid=nil) uri = File.join(@uri,"features") + uri += "?subjectid=#{CGI.escape(subjectid)}" if subjectid statements = [] features = Set.new `rapper -i rdfxml -o ntriples #{uri} 2>/dev/null`.each_line do |line| diff --git a/lib/policy.rb b/lib/policy.rb index 08bf6ed..8591d52 100644 --- a/lib/policy.rb +++ b/lib/policy.rb @@ -38,6 +38,15 @@ module OpenTox @policies.collect{ |k,v| v.uris }.flatten.uniq end + #drop all policies in a policies instance + def names + out = [] + @policies.each do |name, policy| + out << name + end + return out + end + #loads a default policy template in policies instance def load_default_policy(user, uri, group="member") template = case user diff --git a/lib/task.rb b/lib/task.rb index 4d1ee90..3c6aba5 100644 --- a/lib/task.rb +++ b/lib/task.rb @@ -49,12 +49,12 @@ module OpenTox cpu_load = `cat /proc/loadavg`.split(/\s+/)[0..2].collect{|c| c.to_f} nr_cpu_cores = `cat /proc/cpuinfo |grep "cpu cores"|cut -d ":" -f2|tr -d " "`.split("\n").collect{|c| c.to_i}.inject{|sum,n| sum+n} nr_cpu_cores = 1 if !nr_cpu_cores - if cpu_load[0] > nr_cpu_cores and cpu_load[0] > cpu_load[1] and cpu_load[1] > cpu_load[2] # average CPU load of the last minute is high and CPU load is increasing - LOGGER.warn "Cannot start task - CPU load too high (#{cpu_load.join(", ")})" - task.cancel - return task - #raise "Server too busy to start a new task" - end + #if cpu_load[0] > nr_cpu_cores and cpu_load[0] > cpu_load[1] and cpu_load[1] > cpu_load[2] # average CPU load of the last minute is high and CPU load is increasing + # LOGGER.warn "Cannot start task - CPU load too high (#{cpu_load.join(", ")})" + # task.cancel + # return task + # #raise "Server too busy to start a new task" + #end task_pid = Spork.spork(:logger => LOGGER) do LOGGER.debug "Task #{task.uri} started #{Time.now}" |