From 962773d59d94f8d16dae11b6290fdf30aaf09d7b Mon Sep 17 00:00:00 2001 From: rautenberg Date: Mon, 3 Jun 2013 15:25:33 +0200 Subject: make yard documentation full yard 0.8.6.1 compatible --- lib/algorithm.rb | 4 +- lib/authorization.rb | 49 ++++++++++++------- lib/compound.rb | 9 ++-- lib/dataset.rb | 58 +++++++++++----------- lib/model.rb | 4 +- lib/opentox.rb | 10 ++-- lib/overwrite.rb | 21 ++++---- lib/policy.rb | 17 +++---- lib/validation.rb | 132 +++++++++++++++++++++++++-------------------------- 9 files changed, 158 insertions(+), 146 deletions(-) diff --git a/lib/algorithm.rb b/lib/algorithm.rb index 530296a..8576681 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -1,11 +1,11 @@ module OpenTox # Wrapper for OpenTox Algorithms - class Algorithm + class Algorithm # Execute algorithm with parameters, please consult the OpenTox API and the webservice documentation for acceptable parameters # @param [optional,Hash] params Algorithm parameters - # @param [optional,Boolean] set to true if method should wait for task result + # @param [optional,Boolean] wait set to true if method should wait for task result # @return [String] URI of new resource (dataset, model, ...) def run params=nil, wait=true uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid} diff --git a/lib/authorization.rb b/lib/authorization.rb index 469c16c..7f0e840 100644 --- a/lib/authorization.rb +++ b/lib/authorization.rb @@ -6,6 +6,7 @@ module OpenTox # require "opentox-client" # OpenTox::Authorization::AA = "https://opensso.in-silico.ch" #if not set in .opentox/conf/[SERVICE].rb # subjectid = OpenTox::Authorization.authenticate("username", "password") + # puts OpenTox::Authorization.authorize("http://example.uri/testpath/", "GET", subjectid) #@see http://www.opentox.org/dev/apis/api-1.2/AA OpenTox A&A API 1.2 specification module Authorization @@ -29,7 +30,7 @@ module OpenTox #Cleans AA Policies and loads default xml file into policy attribute #set uri and user, returns Policyfile(XML) for open-sso - # @param [String] URI to create a policy for + # @param uri [String] URI to create a policy for def get_xml(uri) @policy.drop_policies @policy.load_default_policy(@user, uri) @@ -37,7 +38,7 @@ module OpenTox end #Loads and sends Policyfile(XML) to open-sso server - # @param [String] URI to create a policy for + # @param uri [String] URI to create a policy for def send(uri) xml = get_xml(uri) ret = false @@ -57,7 +58,8 @@ module OpenTox end #Authentication against OpenSSO. Returns token. Requires Username and Password. - # @param [String, String]Username,Password + # @param user [String] Username + # @param pw [String] Password # @return [String, nil] gives subjectid or nil def self.authenticate(user, pw) return nil if !AA @@ -71,7 +73,7 @@ module OpenTox end #Logout on opensso. Make token invalid. Requires token - # @param [String]subjectid the subjectid + # @param [String] subjectid the subjectid # @return [Boolean] true if logout is OK def self.logout(subjectid) begin @@ -84,7 +86,9 @@ module OpenTox end #Authorization against OpenSSO for a URI with request-method (action) [GET/POST/PUT/DELETE] - # @param [String,String,String]uri,action,subjectid + # @param [String] uri URI to request + # @param [String] action request method + # @param [String] subjectid # @return [Boolean, nil] returns true, false or nil (if authorization-request fails). def self.authorize(uri, action, subjectid) return true if !AA @@ -118,7 +122,8 @@ module OpenTox end #Returns a policy in xml-format - # @param [String, String]policy,subjectid + # @param policy [String] policyname + # @param subjectid [String] # @return [String] XML of the policy def self.list_policy(policy, subjectid) begin @@ -150,7 +155,8 @@ module OpenTox end #Returns the owner (who created the first policy) of an URI - # @param [String, String]uri,subjectid + # @param uri [String] URI + # @param subjectid [String] subjectid # return [String, nil]owner,nil returns owner of the URI def self.get_uri_owner(uri, subjectid) begin @@ -161,14 +167,16 @@ module OpenTox end #Returns true or false if owner (who created the first policy) of an URI - # @param [String, String]uri,subjectid + # @param uri [String] URI + # @param subjectid [String] # return [Boolean]true,false status of ownership of the URI def self.uri_owner?(uri, subjectid) get_uri_owner(uri, subjectid) == get_user(subjectid) end #Checks if a policy exists to a URI. Requires URI and token. - # @param [String, String]uri,subjectid + # @param uri [String] URI + # @param subjectid [String] # return [Boolean] def self.uri_has_policy(uri, subjectid) owner = get_uri_owner(uri, subjectid) @@ -177,7 +185,8 @@ module OpenTox end #List all policynames for a URI. Requires URI and token. - # @param [String, String]uri,subjectid + # @param uri [String] URI + # @param subjectid [String] # return [Array, nil] returns an Array of policy names or nil if request fails def self.list_uri_policies(uri, subjectid) begin @@ -194,7 +203,8 @@ module OpenTox end #Sends a policy in xml-format to opensso server. Requires policy-xml and token. - # @param [String, String]policyxml,subjectid + # @param policy [String] XML string of a policy + # @param subjectid [String] # return [Boolean] returns true if policy is created def self.create_policy(policy, subjectid) begin @@ -206,7 +216,8 @@ module OpenTox end #Deletes a policy - # @param [String, String]policyname,subjectid + # @param policy [String] policyname + # @param subjectid [String] # @return [Boolean,nil] def self.delete_policy(policy, subjectid) begin @@ -254,7 +265,8 @@ module OpenTox end #Send default policy with Authorization::Helper class - # @param [String, String]URI,subjectid + # @param uri [String] URI + # @param subjectid [String] def self.send_policy(uri, subjectid) return true if !AA aa = Authorization::Helper.new(subjectid) @@ -264,7 +276,8 @@ module OpenTox end #Deletes all policies of an URI - # @param [String, String]URI,subjectid + # @param uri [String] URI + # @param subjectid [String] # @return [Boolean] def self.delete_policies_from_uri(uri, subjectid) policies = list_uri_policies(uri, subjectid) @@ -308,9 +321,9 @@ module OpenTox end # Check Authorization for a resource (identified via URI) with method and subjectid. - # @param [String] uri - # @param [String] request_method, should be GET, POST, PUT, DELETE - # @param [String] subjectid + # @param uri [String] URI + # @param request_method [String] GET, POST, PUT, DELETE + # @param subjectid [String] # @return [Boolean] true if access granted, else otherwise def self.authorized?(uri, request_method, subjectid) request_method = request_method.to_sym if request_method @@ -345,7 +358,7 @@ module OpenTox define_method "#{method}?".to_sym do |uri, request_method| if $aa["#{method}s".to_sym] $aa["#{method}s".to_sym].each do |request_methods, uris| - if request_methods and uris and request_methods.include?(request_method.to_sym) + if request_methods and uris and request_methods.include?(request_method.to_sym) uris.each do |u| return true if u.match uri end diff --git a/lib/compound.rb b/lib/compound.rb index 2eccdcd..a278244 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -16,14 +16,14 @@ module OpenTox end # Create a compound from inchi string - # @param [String] smiles InChI string + # @param inchi [String] smiles InChI string # @return [OpenTox::Compound] Compound def self.from_inchi inchi, subjectid=nil Compound.new RestClientWrapper.post(service_uri, inchi, {:content_type => 'chemical/x-inchi', :subjectid => subjectid}) end # Create a compound from sdf string - # @param [String] smiles SDF string + # @param sdf [String] smiles SDF string # @return [OpenTox::Compound] Compound def self.from_sdf sdf, subjectid=nil Compound.new RestClientWrapper.post(service_uri, sdf, {:content_type => 'chemical/x-mdl-sdfile', :subjectid => subjectid}) @@ -32,9 +32,8 @@ module OpenTox # Create a compound from name. Relies on an external service for name lookups. # @example # compound = OpenTox::Compound.from_name("Benzene") - # @param [String] name name can be also an InChI/InChiKey, CAS number, etc + # @param name [String] can be also an InChI/InChiKey, CAS number, etc # @return [OpenTox::Compound] Compound - # def self.from_name name, subjectid=nil @inchi = RestClientWrapper.get File.join(CACTUS_URI,URI.escape(name),"stdinchi") Compound.new RestClientWrapper.post(service_uri, @inchi, {:content_type => 'chemical/x-inchi', :subjectid => subjectid}) @@ -191,7 +190,7 @@ module OpenTox # Match an array of smarts strings, returns hash # Keys: matching smarts, values: number of non-unique hits, or 1 # @param [Array] smarts_array Array with Smarts strings - # @param [Boolean] Whether non-unique hits or 1 should be produced + # @param use_hits [Boolean] Whether non-unique hits or 1 should be produced # @return [Array] Array with matching Smarts strings # @example { # compound = Compound.from_name("Benzene") diff --git a/lib/dataset.rb b/lib/dataset.rb index 8d5f5d1..19d05c9 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -3,7 +3,7 @@ require 'csv' module OpenTox # Ruby wrapper for OpenTox Dataset Webservices (http://opentox.org/dev/apis/api-1.2/dataset). - class Dataset + class Dataset attr_writer :features, :compounds, :data_entries @@ -46,7 +46,7 @@ module OpenTox end @compounds end - + def data_entries force_update=false if @data_entries.empty? or force_update sparql = "SELECT ?cidx ?fidx ?value FROM <#{uri}> WHERE { @@ -55,7 +55,7 @@ module OpenTox ?v <#{RDF::OT.feature}> ?f; <#{RDF::OT.value}> ?value . ?f <#{RDF::OLO.index}> ?fidx. - } ORDER BY ?fidx ?cidx" + } ORDER BY ?fidx ?cidx" RestClientWrapper.get(service_uri,{:query => sparql},{:accept => "text/uri-list", :subjectid => @subjectid}).split("\n").each do |row| r,c,v = row.split("\t") @data_entries[r.to_i] ||= [] @@ -79,9 +79,9 @@ module OpenTox @data_entries end - # Find data entry values for a given compound and feature - # @param [OpenTox::Compound] Compound - # @param [OpenTox::Feature] Feature + # Find data entry values for a given compound and feature + # @param compound [OpenTox::Compound] OpenTox Compound object + # @param feature [OpenTox::Feature] OpenTox Feature object # @return [Array] Data entry values def values(compound, feature) rows = (0 ... compounds.length).select { |r| compounds[r].uri == compound.uri } @@ -92,14 +92,14 @@ module OpenTox # Convenience methods to search by compound/feature URIs # Search a dataset for a feature given its URI - # @param [String] Feature URI + # @param uri [String] Feature URI # @return [OpenTox::Feature] Feature object, or nil if not present def find_feature_uri(uri) features.select{|f| f.uri == uri}.first end # Search a dataset for a compound given its URI - # @param [String] Compound URI + # @param uri [String] Compound URI # @return [OpenTox::Compound] Compound object, or nil if not present def find_compound_uri(uri) compounds.select{|f| f.uri == uri}.first @@ -133,7 +133,7 @@ module OpenTox def upload filename, wait=true uri = RestClientWrapper.put(@uri, {:file => File.new(filename)}, {:subjectid => @subjectid}) wait_for_task uri if URI.task?(uri) and wait - metadata true + metadata true @uri end @@ -173,7 +173,7 @@ module OpenTox end RDF_FORMATS.each do |format| - + # redefine rdf parse methods for all formats e.g. parse_rdfxml send :define_method, "parse_#{format}".to_sym do |rdf| # TODO: parse ordered dataset @@ -194,13 +194,13 @@ module OpenTox end - # redefine rdf serialization methods + # redefine rdf serialization methods send :define_method, "to_#{format}".to_sym do - @metadata[RDF.type] = RDF::OT.OrderedDataset + @metadata[RDF.type] = RDF::OT.OrderedDataset create_rdf @features.each_with_index do |feature,i| - @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Feature)] - @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)] + @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Feature)] + @rdf << [RDF::URI.new(feature.uri), RDF::URI.new(RDF::OLO.index), RDF::Literal.new(i)] end @compounds.each_with_index do |compound,i| @rdf << [RDF::URI.new(compound.uri), RDF::URI.new(RDF.type), RDF::URI.new(RDF::OT.Compound)] @@ -246,8 +246,8 @@ module OpenTox parameter.each { |k,v| ntriples << "#{p_node} <#{k}> '#{v}' .\n" } end @features.each_with_index do |feature,i| - ntriples << "<#{feature.uri}> <#{RDF.type}> <#{RDF::OT.Feature}> .\n" - ntriples << "<#{feature.uri}> <#{RDF::OLO.index}> '#{i}' .\n" + ntriples << "<#{feature.uri}> <#{RDF.type}> <#{RDF::OT.Feature}> .\n" + ntriples << "<#{feature.uri}> <#{RDF::OLO.index}> '#{i}' .\n" end @compounds.each_with_index do |compound,i| ntriples << "<#{compound.uri}> <#{RDF.type}> <#{RDF::OT.Compound}> .\n" @@ -276,21 +276,21 @@ module OpenTox =end # Methods for for validation service - + def split( compound_indices, feats, metadata, subjectid=nil) - + bad_request_error "Dataset.split : Please give compounds as indices" if compound_indices.size==0 or !compound_indices[0].is_a?(Fixnum) bad_request_error "Dataset.split : Please give features as feature objects (given: #{feats})" if feats!=nil and feats.size>0 and !feats[0].is_a?(OpenTox::Feature) dataset = OpenTox::Dataset.new(nil, subjectid) dataset.metadata = metadata dataset.features = (feats ? feats : self.features) compound_indices.each do |c_idx| - dataset << [ self.compounds[c_idx] ] + dataset.features.each_with_index.collect{|f,f_idx| self.data_entries[c_idx][f_idx]} + dataset << [ self.compounds[c_idx] ] + dataset.features.each_with_index.collect{|f,f_idx| self.data_entries[c_idx][f_idx]} end dataset.put - dataset + dataset end - + # maps a compound-index from another dataset to a compound-index from this dataset # mapping works as follows: @@ -299,8 +299,8 @@ module OpenTox # * c occurs >1 in this dataset? # ** number of occurences is equal in both datasets? assume order is preserved(!) and map accordingly # ** number of occurences is not equal in both datasets? cannot map, raise error - # @param [OpenTox::Dataset] dataset that should be mapped to this dataset (fully loaded) - # @param [Fixnum] compound_index, corresponding to dataset + # @param dataset [OpenTox::Dataset] dataset that should be mapped to this dataset (fully loaded) + # @param compound_index [Fixnum], corresponding to dataset def compound_index( dataset, compound_index ) unless defined?(@index_map) and @index_map[dataset.uri] map = {} @@ -308,7 +308,7 @@ module OpenTox self_indices = compound_indices(compound) next unless self_indices dataset_indices = dataset.compound_indices(compound) - if self_indices.size==1 + if self_indices.size==1 dataset_indices.size.times do |i| map[dataset_indices[i]] = self_indices[0] end @@ -321,13 +321,13 @@ module OpenTox raise "cannot map compound #{compound} from dataset #{dataset.uri} to dataset #{uri}, "+ "compound occurs #{dataset_indices.size} times and #{self_indices.size} times" end - end + end @index_map = {} unless defined?(@index_map) @index_map[dataset.uri] = map end @index_map[dataset.uri][compound_index] - end - + end + def compound_indices( compound ) unless defined?(@cmp_indices) and @cmp_indices.has_key?(compound) @cmp_indices = {} @@ -337,12 +337,12 @@ module OpenTox @cmp_indices[c] = [i] else @cmp_indices[c] = @cmp_indices[c]+[i] - end + end end end @cmp_indices[compound] end - + def data_entry_value(compound_index, feature_uri) data_entries(true) if @data_entries.empty? col = @features.collect{|f| f.uri}.index feature_uri diff --git a/lib/model.rb b/lib/model.rb index a354cfa..e49eff3 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -3,8 +3,8 @@ module OpenTox class Model # Run a model with parameters - # @param [Hash] params Parameters for OpenTox model - # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly + # @param params [Hash] Parameters for OpenTox model + # @param wait [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly # @return [text/uri-list] Task or resource URI def run params=nil, wait=true uri = RestClientWrapper.post @uri, params, { :content_type => "text/uri-list", :subjectid => @subjectid} diff --git a/lib/opentox.rb b/lib/opentox.rb index 211fc7b..171e397 100644 --- a/lib/opentox.rb +++ b/lib/opentox.rb @@ -11,8 +11,8 @@ module OpenTox # Ruby interface # Create a new OpenTox object - # @param [optional,String] URI - # @param [optional,String] subjectid + # @param uri [optional,String] URI + # @param subjectid [optional,String] # @return [OpenTox] OpenTox object def initialize uri=nil, subjectid=nil @rdf = RDF::Graph.new @@ -34,7 +34,7 @@ module OpenTox end # Metadata values - # @param [String] Predicate URI + # @param predicate [String] Predicate URI # @return [Array, String] Predicate value(s) def [](predicate) return nil if metadata[predicate].nil? @@ -42,8 +42,8 @@ module OpenTox end # Set a metadata entry - # @param [String] Predicate URI - # @param [Array, String] Predicate value(s) + # @param predicate [String] Predicate URI + # @param values [Array, String] Predicate value(s) def []=(predicate,values) @metadata[predicate] = [values].flatten end diff --git a/lib/overwrite.rb b/lib/overwrite.rb index 52b8a9f..6a71338 100644 --- a/lib/overwrite.rb +++ b/lib/overwrite.rb @@ -38,19 +38,18 @@ class String # format of text (=string params) is preserved (e.g. line breaks) # urls are marked as links # - # @param [String] text this is the actual content, - # @param [optional,String] related_links info on related resources - # @param [optional,String] description general info - # @param [optional,Array] post_command, infos for the post operation, object defined below + # @param related_links [optional,String] uri on related resources + # @param description [optional,String] general info + # @param png_image [optional,String] imagename # @return [String] html page def to_html(related_links=nil, description=nil, png_image=nil ) - + # TODO add title as parameter title = nil #$sinatra.to($sinatra.request.env['PATH_INFO'], :full) if $sinatra html = "" html << ""+title+"" if title #html += "<\/img>" - + html << "

Description

"+description.link_urls+"
" if description html << "

Related links

"+related_links.link_urls+"
" if related_links html << "

Content

" if description || related_links @@ -60,7 +59,7 @@ class String html << "

" html end - + def uri? URI.valid?(self) end @@ -76,7 +75,7 @@ module URI def self.task? uri uri =~ /task/ and URI.valid? uri end - + def self.dataset? uri, subjectid=nil uri =~ /dataset/ and URI.accessible? uri, subjectid=nil end @@ -119,7 +118,7 @@ end class File # @return [String] mime_type including charset using linux cmd command - def mime_type + def mime_type `file -ib #{self.path}`.chomp end end @@ -138,12 +137,12 @@ module Kernel internal_server_error "`" + cmd + "` failed.\n" + stdout + stderr unless status.success? return stdout rescue - internal_server_error $!.message + internal_server_error $!.message end # @return [String] uri of task result, if task fails, an error according to task is raised def wait_for_task uri - if URI.task?(uri) + if URI.task?(uri) t = OpenTox::Task.new uri t.wait unless t.completed? diff --git a/lib/policy.rb b/lib/policy.rb index 3e7c143..e5676ba 100644 --- a/lib/policy.rb +++ b/lib/policy.rb @@ -3,7 +3,7 @@ module OpenTox #Module for policy-processing # @see also http://www.opentox.org/dev/apis/api-1.2/AA for opentox API specs - # Class Policies corresponds to container of an xml-policy-fle + # Class Policies corresponds to container of an xml-policy-file class Policies #Hash for policy objects see {Policy Policy} @@ -205,12 +205,13 @@ module OpenTox end # Subject type LDAPUsers or LDAPGroups + # @return [String] def type @subject.type end # Set subject type - # @param [String],type + # @param type [String] the subjecttype def type=(type) @subject.type = type end @@ -221,19 +222,19 @@ module OpenTox end # sets LDAP Distinguished Name (DN) for policy e.g. - # @param [String],LDAPString + # @param value [String] LDAPString def value=(value) @subject.value = value end # uri affected by policy - # @return uri affected by policy + # @return [String] uri affected by policy def uri @rule.uri end # sets uri affected by policy - # @param [String] set URI + # @param uri [String] set URI def uri=(uri) @rule.uri = uri end @@ -251,14 +252,14 @@ module OpenTox end # helper method sets value and type to opentox LDAP Distinguished Name (DN) of a user - # @param [String]Username set a username into LDAP DN + # @param username [String] set a username into LDAP DN def set_ot_user(username) self.value = "uid=#{username},ou=people,dc=opentox,dc=org" self.type = "LDAPUsers" true end - # @param [String]Username set a groupname into LDAP DN + # @param groupname [String] Username set a groupname into LDAP DN def set_ot_group(groupname) self.value = "cn=#{groupname},ou=groups,dc=opentox,dc=org" self.type = "LDAPGroups" @@ -277,7 +278,7 @@ module OpenTox end #Set Rule attribute for request-method GET - # @param [String]value (allow,deny,nil) + # @param value [String] (allow,deny,nil) def get=(value) @get = check_value(value, @get) end diff --git a/lib/validation.rb b/lib/validation.rb index c4f6868..cb73ce6 100644 --- a/lib/validation.rb +++ b/lib/validation.rb @@ -2,7 +2,7 @@ require "yaml" module OldOpenTox attr_accessor :metadata, :uri - + def initialize(uri=nil) @metadata = {} self.uri = uri if uri @@ -13,17 +13,17 @@ module OldOpenTox yaml = OpenTox::RestClientWrapper.get(uri,nil,{:subjectid => subjectid, :accept => "application/x-yaml"}) @metadata = YAML.load(yaml) end - + def delete (subjectid=nil) OpenTox::RestClientWrapper.delete(@uri.to_s,nil,{:subjectid => subjectid}) end end module OpenTox - + class Validation include OldOpenTox - + # find validation, raises error if not found # @param [String] uri # @param [String,optional] subjectid @@ -33,10 +33,10 @@ module OpenTox val.load_metadata( subjectid ) val end - + # returns a filtered list of validation uris - # @param [Hash,optional] params, validation-params to filter the uris (could be model, training_dataset, ..) - # @return [Array] + # @param params [Hash,optional] validation-params to filter the uris (could be model, training_dataset, ..) + # @return [Array] def self.list( params={} ) filter_string = "" params.each do |k,v| @@ -46,7 +46,7 @@ module OpenTox end (OpenTox::RestClientWrapper.get($validation[:uri]+filter_string).split("\n")) end - + # creates a training test split validation, waits until it finishes, may take some time # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,split_ratio(0.67),random_seed(1)) # @param [String,optional] subjectid @@ -58,7 +58,7 @@ module OpenTox params,{:content_type => "text/uri-list"},waiting_task ) Validation.new(wait_for_task(uri)) end - + # creates a training test validation, waits until it finishes, may take some time # @param [Hash] params (required:algorithm_uri,training_dataset_uri,prediction_feature,test_dataset_uri,optional:algorithm_params) # @param [String,optional] subjectid @@ -70,7 +70,7 @@ module OpenTox params,{:content_type => "text/uri-list"},waiting_task ) Validation.new(wait_for_task(uri)) end - + # creates a bootstrapping validation, waits until it finishes, may take some time # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,random_seed(1)) # @param [String,optional] subjectid @@ -82,7 +82,7 @@ module OpenTox params,{:content_type => "text/uri-list"},waiting_task ) Validation.new(wait_for_task(uri)) end - + # looks for report for this validation, creates a report if no report is found # @param [String,optional] subjectid # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly @@ -92,20 +92,20 @@ module OpenTox @report = ValidationReport.create(@uri, {}, subjectid, waiting_task) unless @report @report.uri end - + # creates a validation object from crossvaldiation statistics, raise error if not found # (as crossvaldiation statistics are returned as an average valdidation over all folds) - # @param [String] crossvalidation uri + # @param crossvalidation_uri [String] crossvalidation uri # @param [String,optional] subjectid # @return [OpenTox::Validation] def self.from_cv_statistics( crossvalidation_uri, subjectid=nil ) find( File.join(crossvalidation_uri, 'statistics'),subjectid ) end - + # returns confusion matrix as array, predicted values are in rows # example: # [[nil,"active","moderate","inactive"],["active",1,3,99],["moderate",4,2,8],["inactive",3,8,6]] - # -> 99 inactive compounds have been predicted as active + # -> 99 inactive compounds have been predicted as active def confusion_matrix raise "no classification statistics, probably a regression valdiation" unless @metadata[RDF::OT.classificationStatistics] matrix = @metadata[RDF::OT.classificationStatistics][RDF::OT.confusionMatrix][RDF::OT.confusionMatrixCell] @@ -124,38 +124,38 @@ module OpenTox end table end - + # returns probability-distribution for a given prediction # it takes all predictions into account that have a confidence value that is >= confidence and that have the same predicted value # (minimum 12 predictions with the hightest confidence are selected (even if the confidence is lower than the given param) - # - # @param [Float] confidence value (between 0 and 1) - # @param [String] predicted value - # @param [String,optional] subjectid + # + # @param confidence [Float] confidence value (between 0 and 1) + # @param prediction [String] predicted value + # @param subjectid [String,optional] # @return [Hash] see example # # Example 1: - # validation.probabilities(0.3,"active") - # -> {:min_confidence=>0.32, :num_predictions=>20, :probs=>{"active"=>0.7, "moderate"=>0.25 "inactive"=>0.05}} + # validation.probabilities(0.3,"active") + # -> { :min_confidence=>0.32, :num_predictions=>20, :probs=>{"active"=>0.7, "moderate"=>0.25 "inactive"=>0.05 } } # there have been 20 "active" predictions with confidence >= 0.3, 70 percent of them beeing correct # # Example 2: - # validation.probabilities(0.8,"active") - # -> {:min_confidence=>0.45, :num_predictions=>12, :probs=>{"active"=>0.9, "moderate"=>0.1 "inactive"=>0}} + # validation.probabilities(0.8,"active") + # -> { :min_confidence=>0.45, :num_predictions=>12, :probs=>{"active"=>0.9, "moderate"=>0.1 "inactive"=>0 } } # the given confidence value was to high (i.e. <12 predictions with confidence value >= 0.8) # the top 12 "active" predictions have a min_confidence of 0.45, 90 percent of them beeing correct - # + # def probabilities( confidence, prediction, subjectid=nil ) YAML.load(OpenTox::RestClientWrapper.get(@uri+"/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil, {:subjectid => subjectid, :accept => "application/x-yaml"})) end end - + class Crossvalidation include OldOpenTox attr_reader :report - + # find crossvalidation, raises error if not found # @param [String] uri # @param [String,optional] subjectid @@ -165,10 +165,10 @@ module OpenTox cv.load_metadata( subjectid ) cv end - + # returns a filtered list of crossvalidation uris - # @param [Hash,optional] params, crossvalidation-params to filter the uris (could be algorithm, dataset, ..) - # @return [Array] + # @param params [Hash,optional] crossvalidation-params to filter the uris (could be algorithm, dataset, ..) + # @return [Array] def self.list( params={} ) filter_string = "" params.each do |k,v| @@ -201,29 +201,29 @@ module OpenTox @report = CrossvalidationReport.create(@uri, subjectid, waiting_task) unless @report @report.uri end - + # loads metadata via yaml from crossvalidation object # fields (like for example the validations) can be acces via validation.metadata[RDF::OT.validation] def load_metadata( subjectid=nil ) @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,nil,{:subjectid => subjectid, :accept => "application/x-yaml"})) end - + # returns a Validation object containing the statistics of the crossavlidation def statistics( subjectid=nil ) Validation.from_cv_statistics( @uri, subjectid ) end - + # documentation see OpenTox::Validation.probabilities def probabilities( confidence, prediction, subjectid=nil ) YAML.load(OpenTox::RestClientWrapper.get(@uri+"/statistics/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil, {:subjectid => subjectid, :accept => "application/x-yaml"})) end - + end - + class ValidationReport include OldOpenTox - + # finds ValidationReport via uri, raises error if not found # @param [String] uri # @param [String,optional] subjectid @@ -234,23 +234,23 @@ module OpenTox rep.load_metadata( subjectid ) rep end - + # finds ValidationReport for a particular validation - # @param [String] crossvalidation uri - # @param [String,optional] subjectid + # @param validation_uri [String] crossvalidation uri + # @param subjectid [String,optional] # @return [OpenTox::ValidationReport] nil if no report found def self.find_for_validation( validation_uri, subjectid=nil ) uris = RestClientWrapper.get(File.join($validation[:uri], "/report/validation?validation="+validation_uri),nil,{:subjectid => subjectid}).chomp.split("\n") uris.size==0 ? nil : ValidationReport.new(uris[-1]) end - + # creates a validation report via validation - # @param [String] validation uri - # @param [Hash] params addiditonal possible + # @param validation_uri [String] validation uri + # @param params [Hash] params addiditonal possible # (min_confidence, params={}, min_num_predictions, max_num_predictions) - # @param [String,optional] subjectid - # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly + # @param subjectid [String,optional] + # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly # @return [OpenTox::ValidationReport] def self.create( validation_uri, params={}, subjectid=nil, waiting_task=nil ) params = {} if params==nil @@ -262,12 +262,12 @@ module OpenTox uri = wait_for_task(uri) ValidationReport.new(uri) end - + end class CrossvalidationReport include OldOpenTox - + # finds CrossvalidationReport via uri, raises error if not found # @param [String] uri # @param [String,optional] subjectid @@ -278,21 +278,21 @@ module OpenTox rep.load_metadata( subjectid ) rep end - + # finds CrossvalidationReport for a particular crossvalidation - # @param [String] crossvalidation uri - # @param [String,optional] subjectid + # @param crossvalidation_uri [String] crossvalidation uri + # @param subjectid [String,optional] # @return [OpenTox::CrossvalidationReport] nil if no report found def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil ) uris = RestClientWrapper.get(File.join($validation[:uri], "/report/crossvalidation?crossvalidation="+crossvalidation_uri),nil,{:subjectid => subjectid}).chomp.split("\n") uris.size==0 ? nil : CrossvalidationReport.new(uris[-1]) end - + # creates a crossvalidation report via crossvalidation - # @param [String] crossvalidation uri - # @param [String,optional] subjectid - # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly + # @param crossvalidation_uri [String] crossvalidation uri + # @param subjectid [String,optional] + # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly # @return [OpenTox::CrossvalidationReport] def self.create( crossvalidation_uri, subjectid=nil, waiting_task=nil ) uri = RestClientWrapper.post(File.join($validation[:uri],"/report/crossvalidation"), @@ -301,11 +301,11 @@ module OpenTox CrossvalidationReport.new(uri) end end - - + + class AlgorithmComparisonReport include OldOpenTox - + # finds AlgorithmComparisonReport via uri, raises error if not found # @param [String] uri # @param [String,optional] subjectid @@ -316,23 +316,23 @@ module OpenTox rep.load_metadata( subjectid ) rep end - + # finds AlgorithmComparisonReport for a particular crossvalidation - # @param [String] crossvalidation uri - # @param [String,optional] subjectid + # @param crossvalidation_uri [String] crossvalidation uri + # @param subjectid [String,optional] # @return [OpenTox::AlgorithmComparisonReport] nil if no report found def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil ) uris = RestClientWrapper.get(File.join($validation[:uri], "/report/algorithm_comparison?crossvalidation="+crossvalidation_uri),nil,{:subjectid => subjectid}).chomp.split("\n") uris.size==0 ? nil : AlgorithmComparisonReport.new(uris[-1]) end - + # creates a algorithm comparison report via crossvalidation uris - # @param [Hash] crossvalidation uri_hash, see example - # @param [Hash] params addiditonal possible + # @param crossvalidation_uri_hash [Hash] crossvalidation uri_hash, see example + # @param params [Hash] params addiditonal possible # (ttest_significance, ttest_attributes, min_confidence, min_num_predictions, max_num_predictions) - # @param [String,optional] subjectid - # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly + # @param subjectid [String,optional] + # @param waiting_task [OpenTox::Task,optional] (can be a OpenTox::Subtask as well), progress is updated accordingly # @return [OpenTox::AlgorithmComparisonReport] # example for hash: # { :lazar-bbrc => [ http://host/validation/crossvalidation/x1, http://host/validation/crossvalidation/x2 ], @@ -355,7 +355,7 @@ module OpenTox uri = wait_for_task(uri) AlgorithmComparisonReport.new(uri) end - end - + end + end -- cgit v1.2.3