From 8ada8380bc906c8ffbb16d4f9cc787eb800b7796 Mon Sep 17 00:00:00 2001 From: mguetlein Date: Thu, 19 Aug 2010 11:18:32 +0200 Subject: adding task title and creator --- lazar.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lazar.rb b/lazar.rb index f79b901..80015b4 100644 --- a/lazar.rb +++ b/lazar.rb @@ -337,7 +337,7 @@ post '/:id/?' do # create prediction elsif dataset_uri response['Content-Type'] = 'text/uri-list' - task_uri = OpenTox::Task.as_task do + task_uri = OpenTox::Task.as_task("Predict dataset",url_for("/#{lazar.id}", :full)) do input_dataset = OpenTox::Dataset.find(dataset_uri) input_dataset.compounds.each do |compound_uri| # AM: switch here between regression and classification -- cgit v1.2.3 From 7f99548d0044b57556a7ec8727c19d878bbe9cd7 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 20 Aug 2010 10:35:46 +0200 Subject: api wrapper bumped to 1.6.4 --- application.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/application.rb b/application.rb index 195dcaf..b892201 100644 --- a/application.rb +++ b/application.rb @@ -1,5 +1,5 @@ require 'rubygems' -gem "opentox-ruby-api-wrapper", "= 1.6.3" +gem "opentox-ruby-api-wrapper", "= 1.6.4" require 'opentox-ruby-api-wrapper' class Model -- cgit v1.2.3 From c499e94395f91aeb52ee36d755a4958a9b7942ae Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 25 Aug 2010 12:27:32 +0200 Subject: initial version for quantitative features --- application.rb | 1 + lazar.rb | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/application.rb b/application.rb index b892201..0cec82a 100644 --- a/application.rb +++ b/application.rb @@ -23,6 +23,7 @@ end DataMapper.auto_upgrade! require 'lazar.rb' +require 'property_lazar.rb' helpers do diff --git a/lazar.rb b/lazar.rb index 83f926d..7d2198a 100644 --- a/lazar.rb +++ b/lazar.rb @@ -54,7 +54,6 @@ class Lazar < Model sims << OpenTox::Utils.gauss(sim) #TODO check for 0 s acts << Math.log10(act.to_f) - #acts << act.to_f neighbor_matches[i] = matches i+=1 end -- cgit v1.2.3 From 48684b9438ff48772972375e9a97f981592da191 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 25 Aug 2010 12:29:42 +0200 Subject: property_lazar.rb added --- property_lazar.rb | 303 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 303 insertions(+) create mode 100644 property_lazar.rb diff --git a/property_lazar.rb b/property_lazar.rb new file mode 100644 index 0000000..6e68718 --- /dev/null +++ b/property_lazar.rb @@ -0,0 +1,303 @@ +# R integration +# workaround to initialize R non-interactively (former rinruby versions did this by default) +# avoids compiling R with X +R = nil +require "rinruby" +require "haml" + +class PropertyLazar < Model + + attr_accessor :prediction_dataset + +=begin + # AM begin + # regression function, created 06/10 + def regression(compound_uri,prediction,verbose=false) + + lazar = YAML.load self.yaml + compound = OpenTox::Compound.new(:uri => compound_uri) + + # obtain X values for query compound + compound_matches = compound.match lazar.features + + conf = 0.0 + features = { :activating => [], :deactivating => [] } + neighbors = {} + regression = nil + + regr_occurrences = [] # occurrence vector with {0,1} entries + sims = [] # similarity values between query and neighbors + acts = [] # activities of neighbors for supervised learning + neighbor_matches = [] # as in classification: URIs of matches + gram_matrix = [] # square matrix of similarities between neighbors; implements weighted tanimoto kernel + i = 0 + + # aquire data related to query structure + lazar.fingerprints.each do |uri,matches| + sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar.p_values) + lazar.activities[uri].each do |act| + if sim > 0.3 + neighbors[uri] = {:similarity => sim} + neighbors[uri][:features] = { :activating => [], :deactivating => [] } unless neighbors[uri][:features] + matches.each do |m| + if lazar.effects[m] == 'activating' + neighbors[uri][:features][:activating] << {:smarts => m, :p_value => lazar.p_values[m]} + elsif lazar.effects[m] == 'deactivating' + neighbors[uri][:features][:deactivating] << {:smarts => m, :p_value => lazar.p_values[m]} + end + end + lazar.activities[uri].each do |act| + neighbors[uri][:activities] = [] unless neighbors[uri][:activities] + neighbors[uri][:activities] << act + end + conf += OpenTox::Utils.gauss(sim) + sims << OpenTox::Utils.gauss(sim) + #TODO check for 0 s + acts << Math.log10(act.to_f) + neighbor_matches[i] = matches + i+=1 + end + end + end + conf = conf/neighbors.size + LOGGER.debug "Regression: found " + neighbor_matches.size.to_s + " neighbors." + + + unless neighbor_matches.length == 0 + # gram matrix + (0..(neighbor_matches.length-1)).each do |i| + gram_matrix[i] = [] + # lower triangle + (0..(i-1)).each do |j| + sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(neighbor_matches[i], neighbor_matches[j], lazar.p_values) + gram_matrix[i] << OpenTox::Utils.gauss(sim) + end + # diagonal element + gram_matrix[i][i] = 1.0 + # upper triangle + ((i+1)..(neighbor_matches.length-1)).each do |j| + sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(neighbor_matches[i], neighbor_matches[j], lazar.p_values) + gram_matrix[i] << OpenTox::Utils.gauss(sim) + end + end + + @r = RinRuby.new(false,false) # global R instance leads to Socket errors after a large number of requests + @r.eval "library('kernlab')" # this requires R package "kernlab" to be installed + LOGGER.debug "Setting R data ..." + # set data + @r.gram_matrix = gram_matrix.flatten + @r.n = neighbor_matches.length + @r.y = acts + @r.sims = sims + + LOGGER.debug "Preparing R data ..." + # prepare data + @r.eval "y<-as.vector(y)" + @r.eval "gram_matrix<-as.kernelMatrix(matrix(gram_matrix,n,n))" + @r.eval "sims<-as.vector(sims)" + + # model + support vectors + LOGGER.debug "Creating SVM model ..." + @r.eval "model<-ksvm(gram_matrix, y, kernel=matrix, type=\"nu-svr\", nu=0.8)" + @r.eval "sv<-as.vector(SVindex(model))" + @r.eval "sims<-sims[sv]" + @r.eval "sims<-as.kernelMatrix(matrix(sims,1))" + LOGGER.debug "Predicting ..." + @r.eval "p<-predict(model,sims)[1,1]" + regression = 10**(@r.p.to_f) + LOGGER.debug "Prediction is: '" + regression.to_s + "'." + @r.quit # free R + + end + + if (regression != nil) + feature_uri = lazar.dependentVariables + prediction.compounds << compound_uri + prediction.features << feature_uri + prediction.data[compound_uri] = [] unless prediction.data[compound_uri] + compound_matches.each { |m| features[lazar.effects[m].to_sym] << {:smarts => m, :p_value => lazar.p_values[m] } } + tuple = { + File.join(@@config[:services]["opentox-model"],"lazar#regression") => regression, + File.join(@@config[:services]["opentox-model"],"lazar#confidence") => conf + } + if verbose + tuple[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")] = neighbors + tuple[File.join(@@config[:services]["opentox-model"],"lazar#features")] = features + end + prediction.data[compound_uri] << {feature_uri => tuple} + end + + end + # AM end +=end + + + def classification(compound_uri,prediction,verbose=false) + + lazar = YAML.load self.yaml + compound = OpenTox::Compound.new(:uri => compound_uri) + compound_properties = lazar.properties[compound.uri] + + conf = 0.0 + neighbors = {} + features = [] + classification = nil + + lazar.properties.each do |uri,properties| + + sim = OpenTox::Algorithm::Similarity.euclidean(compound_properties,properties) + if sim and sim > 0.001 + neighbors[uri] = {:similarity => sim} + neighbors[uri][:features] = [] unless neighbors[uri][:features] + properties.each do |p,v| + neighbors[uri][:features] << {p => v} + end + lazar.activities[uri].each do |act| + neighbors[uri][:activities] = [] unless neighbors[uri][:activities] + neighbors[uri][:activities] << act + case act.to_s + when 'true' + conf += OpenTox::Utils.gauss(sim) + when 'false' + conf -= OpenTox::Utils.gauss(sim) + end + end + end + end + + conf = conf/neighbors.size + if conf > 0.0 + classification = true + elsif conf < 0.0 + classification = false + end + if (classification != nil) + feature_uri = lazar.dependentVariables + prediction.compounds << compound_uri + prediction.features << feature_uri + prediction.data[compound_uri] = [] unless prediction.data[compound_uri] + compound_properties.each { |p,v| features << {p => v} } + tuple = { + File.join(@@config[:services]["opentox-model"],"lazar#classification") => classification, + File.join(@@config[:services]["opentox-model"],"lazar#confidence") => conf + } + if verbose + tuple[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")] = neighbors + tuple[File.join(@@config[:services]["opentox-model"],"lazar#features")] = features + end + prediction.data[compound_uri] << {feature_uri => tuple} + end + end + + def database_activity?(compound_uri,prediction) + # find database activities + lazar = YAML.load self.yaml + db_activities = lazar.activities[compound_uri] + if db_activities + prediction.creator = lazar.trainingDataset + feature_uri = lazar.dependentVariables + prediction.compounds << compound_uri + prediction.features << feature_uri + prediction.data[compound_uri] = [] unless prediction.data[compound_uri] + db_activities.each do |act| + prediction.data[compound_uri] << {feature_uri => act} + end + true + else + false + end + end + + def to_owl + data = YAML.load(yaml) + activity_dataset = YAML.load(RestClient.get(data.trainingDataset, :accept => 'application/x-yaml').to_s) + feature_dataset = YAML.load(RestClient.get(data.feature_dataset_uri, :accept => 'application/x-yaml').to_s) + owl = OpenTox::Owl.create 'Model', uri + owl.set("creator","http://github.com/helma/opentox-model") + owl.set("title", URI.decode(data.dependentVariables.split(/#/).last) ) + #owl.set("title","#{URI.decode(activity_dataset.title)} lazar classification") + owl.set("date",created_at.to_s) + owl.set("algorithm",data.algorithm) + owl.set("dependentVariables",activity_dataset.features.join(', ')) + owl.set("independentVariables",feature_dataset.features.join(', ')) + owl.set("predictedVariables", data.dependentVariables ) + #owl.set("predictedVariables",activity_dataset.features.join(', ') + "_lazar_classification") + owl.set("trainingDataset",data.trainingDataset) + owl.parameters = { + "Dataset URI" => + { :scope => "mandatory", :value => data.trainingDataset }, + "Feature URI for dependent variable" => + { :scope => "mandatory", :value => activity_dataset.features.join(', ')}, + "Feature generation URI" => + { :scope => "mandatory", :value => feature_dataset.creator } + } + + owl.rdf + end + +end + +post '/pl/:id/?' do # create prediction + + lazar = PropertyLazar.get(params[:id]) + LOGGER.debug lazar.to_yaml + halt 404, "Model #{params[:id]} does not exist." unless lazar + halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri] + + @prediction = OpenTox::Dataset.new + @prediction.creator = lazar.uri + dependent_variable = YAML.load(lazar.yaml).dependentVariables + @prediction.title = URI.decode(dependent_variable.split(/#/).last) + case dependent_variable + when /classification/ + prediction_type = "classification" + when /regression/ + prediction_type = "regression" + end + + if compound_uri + # look for cached prediction first + #if cached_prediction = Prediction.first(:model_uri => lazar.uri, :compound_uri => compound_uri) + #@prediction = YAML.load(cached_prediction.yaml) + #else + begin + # AM: switch here between regression and classification + lazar.classification(compound_uri,@prediction,true) #unless lazar.database_activity?(compound_uri,@prediction)" + #eval "lazar.#{prediction_type}(compound_uri,@prediction,true) unless lazar.database_activity?(compound_uri,@prediction)" + #Prediction.create(:model_uri => lazar.uri, :compound_uri => compound_uri, :yaml => @prediction.to_yaml) + rescue + LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} " + halt 500, "Prediction of #{compound_uri} failed." + end + #end + case request.env['HTTP_ACCEPT'] + when /yaml/ + @prediction.to_yaml + when 'application/rdf+xml' + @prediction.to_owl + else + halt 400, "MIME type \"#{request.env['HTTP_ACCEPT']}\" not supported." + end + + elsif dataset_uri + response['Content-Type'] = 'text/uri-list' + task_uri = OpenTox::Task.as_task("Predict dataset",url_for("/#{lazar.id}", :full)) do + input_dataset = OpenTox::Dataset.find(dataset_uri) + input_dataset.compounds.each do |compound_uri| + # AM: switch here between regression and classification + begin + eval "lazar.#{prediction_type}(compound_uri,@prediction) unless lazar.database_activity?(compound_uri,@prediction)" + rescue + LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} " + end + end + begin + uri = @prediction.save.chomp + rescue + halt 500, "Could not save prediction dataset" + end + end + halt 202,task_uri + end + +end -- cgit v1.2.3 From f4b6fcf2b50de0d11e3bcf7986ab9fba4e16208e Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 25 Aug 2010 12:56:05 +0200 Subject: opentox-api-wrapper bumped to 1.6.5 --- application.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/application.rb b/application.rb index 0cec82a..3e80e8b 100644 --- a/application.rb +++ b/application.rb @@ -1,5 +1,5 @@ require 'rubygems' -gem "opentox-ruby-api-wrapper", "= 1.6.4" +gem "opentox-ruby-api-wrapper", "= 1.6.5" require 'opentox-ruby-api-wrapper' class Model -- cgit v1.2.3 From aa9fdad000d45e6ad0fb126704c51fb00c032ea4 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 25 Aug 2010 14:49:33 +0200 Subject: opentox-api-wrapper bumped to 1.6.6 --- application.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/application.rb b/application.rb index 3e80e8b..d0d12af 100644 --- a/application.rb +++ b/application.rb @@ -1,5 +1,5 @@ require 'rubygems' -gem "opentox-ruby-api-wrapper", "= 1.6.5" +gem "opentox-ruby-api-wrapper", "= 1.6.6" require 'opentox-ruby-api-wrapper' class Model -- cgit v1.2.3 From dc7c3474ce544f2f3fa3c23a483f6c24339999de Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Mon, 13 Sep 2010 17:09:37 +0200 Subject: intermediary commit for new owl serializer --- lazar.rb | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/lazar.rb b/lazar.rb index 7d2198a..560a513 100644 --- a/lazar.rb +++ b/lazar.rb @@ -215,17 +215,16 @@ class Lazar < Model data = YAML.load(yaml) activity_dataset = YAML.load(RestClient.get(data.trainingDataset, :accept => 'application/x-yaml').to_s) feature_dataset = YAML.load(RestClient.get(data.feature_dataset_uri, :accept => 'application/x-yaml').to_s) - owl = OpenTox::Owl.create 'Model', uri - owl.set("creator","http://github.com/helma/opentox-model") - owl.set("title", URI.decode(data.dependentVariables.split(/#/).last) ) - #owl.set("title","#{URI.decode(activity_dataset.title)} lazar classification") - owl.set("date",created_at.to_s) - owl.set("algorithm",data.algorithm) - owl.set("dependentVariables",activity_dataset.features.join(', ')) - owl.set("independentVariables",feature_dataset.features.join(', ')) - owl.set("predictedVariables", data.dependentVariables ) - #owl.set("predictedVariables",activity_dataset.features.join(', ') + "_lazar_classification") - owl.set("trainingDataset",data.trainingDataset) + owl = OpenTox::OwlSerializer.create 'Model', uri + owl.annotate("creator","http://github.com/helma/opentox-model") + owl.annotate("title", URI.decode(data.dependentVariables.split(/#/).last) ) + owl.annotate("date",created_at.to_s) + owl.annotate("algorithm",data.algorithm) + owl.annotate("dependentVariables",activity_dataset.features.join(', ')) + owl.annotate("independentVariables",feature_dataset.features.join(', ')) + owl.annotate("predictedVariables", data.dependentVariables ) + owl.annotate("trainingDataset",data.trainingDataset) +=begin owl.parameters = { "Dataset URI" => { :scope => "mandatory", :value => data.trainingDataset }, @@ -234,6 +233,7 @@ class Lazar < Model "Feature generation URI" => { :scope => "mandatory", :value => feature_dataset.creator } } +=end owl.rdf end @@ -257,11 +257,12 @@ get '/:id/?' do case accept when "application/rdf+xml" response['Content-Type'] = 'application/rdf+xml' - unless model.owl # lazy owl creation - model.owl = model.to_owl - model.save - end - model.owl +# unless model.owl # lazy owl creation +# model.owl = model.to_owl +# model.save +# end +# model.owl + model.to_owl when /yaml/ response['Content-Type'] = 'application/x-yaml' model.yaml -- cgit v1.2.3 From 5334912982dd06f61103025504a6f78438847ee0 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 14 Sep 2010 20:52:04 +0200 Subject: simplified version of OwlSerializer, RDF/XML for algorithm/lazar, RDF/XML for annotations,compounds, features in dataset --- lazar.rb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/lazar.rb b/lazar.rb index 560a513..87387df 100644 --- a/lazar.rb +++ b/lazar.rb @@ -216,14 +216,16 @@ class Lazar < Model activity_dataset = YAML.load(RestClient.get(data.trainingDataset, :accept => 'application/x-yaml').to_s) feature_dataset = YAML.load(RestClient.get(data.feature_dataset_uri, :accept => 'application/x-yaml').to_s) owl = OpenTox::OwlSerializer.create 'Model', uri - owl.annotate("creator","http://github.com/helma/opentox-model") + #owl.creator "helma@in-silico.ch" + #owl.contributor "helma@in-silico.ch" + owl.annotate("creator",data.algorithm,XSD.AnyUri) owl.annotate("title", URI.decode(data.dependentVariables.split(/#/).last) ) - owl.annotate("date",created_at.to_s) - owl.annotate("algorithm",data.algorithm) - owl.annotate("dependentVariables",activity_dataset.features.join(', ')) - owl.annotate("independentVariables",feature_dataset.features.join(', ')) - owl.annotate("predictedVariables", data.dependentVariables ) - owl.annotate("trainingDataset",data.trainingDataset) + owl.annotate("date",created_at.to_s,XSD.DateTime) + #owl.annotate("algorithm",data.algorithm) + #owl.annotate("dependentVariables",activity_dataset.features.join(', ')) + #owl.annotate("independentVariables",feature_dataset.features.join(', ')) + #owl.annotate("predictedVariables", data.dependentVariables ) + #owl.annotate("trainingDataset",data.trainingDataset) =begin owl.parameters = { "Dataset URI" => -- cgit v1.2.3 From 6d9653546115e73b732eaadfcb3d1dbe9ab7d99a Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 19 Nov 2010 14:42:29 +0100 Subject: lazar predictions and toxcreate are working --- application.rb | 18 +-- lazar.rb | 361 +++++++++--------------------------------------------- property_lazar.rb | 303 --------------------------------------------- 3 files changed, 68 insertions(+), 614 deletions(-) delete mode 100644 property_lazar.rb diff --git a/application.rb b/application.rb index d0d12af..94c6039 100644 --- a/application.rb +++ b/application.rb @@ -2,28 +2,28 @@ require 'rubygems' gem "opentox-ruby-api-wrapper", "= 1.6.6" require 'opentox-ruby-api-wrapper' -class Model +class ModelStore include DataMapper::Resource + attr_accessor :prediction_dataset property :id, Serial property :uri, String, :length => 255 - property :owl, Text, :length => 2**32-1 property :yaml, Text, :length => 2**32-1 property :created_at, DateTime end -class Prediction +class PredictionCache # cache predictions include DataMapper::Resource property :id, Serial property :compound_uri, String, :length => 255 property :model_uri, String, :length => 255 - property :yaml, Text, :length => 2**32-1 + property :dataset_uri, String, :length => 255 end DataMapper.auto_upgrade! require 'lazar.rb' -require 'property_lazar.rb' +#require 'property_lazar.rb' helpers do @@ -42,12 +42,12 @@ end get '/?' do # get index of models response['Content-Type'] = 'text/uri-list' - Model.all(params).collect{|m| m.uri}.join("\n") + "\n" + ModelStore.all(params).collect{|m| m.uri}.join("\n") + "\n" end delete '/:id/?' do begin - Model.get(params[:id]).destroy! + ModelStore.get(params[:id]).destroy! "Model #{params[:id]} deleted." rescue halt 404, "Model #{params[:id]} does not exist." @@ -57,8 +57,8 @@ end delete '/?' do # TODO delete datasets - Model.auto_migrate! - Prediction.auto_migrate! + ModelStore.auto_migrate! + #Prediction.auto_migrate! response['Content-Type'] = 'text/plain' "All models and cached predictions deleted." end diff --git a/lazar.rb b/lazar.rb index 87387df..3b8a0cf 100644 --- a/lazar.rb +++ b/lazar.rb @@ -4,244 +4,10 @@ R = nil require "rinruby" require "haml" +#require "lazar-helper" -class Lazar < Model - - attr_accessor :prediction_dataset - - # AM begin - # regression function, created 06/10 - # ch: please properly integrate this into the workflow. You will need some criterium for distinguishing regression/classification (hardcoded regression for testing) - def regression(compound_uri,prediction,verbose=false) - - lazar = YAML.load self.yaml - compound = OpenTox::Compound.new(:uri => compound_uri) - - # obtain X values for query compound - compound_matches = compound.match lazar.features - - conf = 0.0 - features = { :activating => [], :deactivating => [] } - neighbors = {} - regression = nil - - regr_occurrences = [] # occurrence vector with {0,1} entries - sims = [] # similarity values between query and neighbors - acts = [] # activities of neighbors for supervised learning - neighbor_matches = [] # as in classification: URIs of matches - gram_matrix = [] # square matrix of similarities between neighbors; implements weighted tanimoto kernel - i = 0 - - # aquire data related to query structure - lazar.fingerprints.each do |uri,matches| - sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar.p_values) - lazar.activities[uri].each do |act| - if sim > 0.3 - neighbors[uri] = {:similarity => sim} - neighbors[uri][:features] = { :activating => [], :deactivating => [] } unless neighbors[uri][:features] - matches.each do |m| - if lazar.effects[m] == 'activating' - neighbors[uri][:features][:activating] << {:smarts => m, :p_value => lazar.p_values[m]} - elsif lazar.effects[m] == 'deactivating' - neighbors[uri][:features][:deactivating] << {:smarts => m, :p_value => lazar.p_values[m]} - end - end - lazar.activities[uri].each do |act| - neighbors[uri][:activities] = [] unless neighbors[uri][:activities] - neighbors[uri][:activities] << act - end - conf += OpenTox::Utils.gauss(sim) - sims << OpenTox::Utils.gauss(sim) - #TODO check for 0 s - acts << Math.log10(act.to_f) - neighbor_matches[i] = matches - i+=1 - end - end - end - conf = conf/neighbors.size - LOGGER.debug "Regression: found " + neighbor_matches.size.to_s + " neighbors." - - - unless neighbor_matches.length == 0 - # gram matrix - (0..(neighbor_matches.length-1)).each do |i| - gram_matrix[i] = [] - # lower triangle - (0..(i-1)).each do |j| - sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(neighbor_matches[i], neighbor_matches[j], lazar.p_values) - gram_matrix[i] << OpenTox::Utils.gauss(sim) - end - # diagonal element - gram_matrix[i][i] = 1.0 - # upper triangle - ((i+1)..(neighbor_matches.length-1)).each do |j| - sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(neighbor_matches[i], neighbor_matches[j], lazar.p_values) - gram_matrix[i] << OpenTox::Utils.gauss(sim) - end - end - - @r = RinRuby.new(false,false) # global R instance leads to Socket errors after a large number of requests - @r.eval "library('kernlab')" # this requires R package "kernlab" to be installed - LOGGER.debug "Setting R data ..." - # set data - @r.gram_matrix = gram_matrix.flatten - @r.n = neighbor_matches.length - @r.y = acts - @r.sims = sims - - LOGGER.debug "Preparing R data ..." - # prepare data - @r.eval "y<-as.vector(y)" - @r.eval "gram_matrix<-as.kernelMatrix(matrix(gram_matrix,n,n))" - @r.eval "sims<-as.vector(sims)" - - # model + support vectors - LOGGER.debug "Creating SVM model ..." - @r.eval "model<-ksvm(gram_matrix, y, kernel=matrix, type=\"nu-svr\", nu=0.8)" - @r.eval "sv<-as.vector(SVindex(model))" - @r.eval "sims<-sims[sv]" - @r.eval "sims<-as.kernelMatrix(matrix(sims,1))" - LOGGER.debug "Predicting ..." - @r.eval "p<-predict(model,sims)[1,1]" - regression = 10**(@r.p.to_f) - LOGGER.debug "Prediction is: '" + regression.to_s + "'." - @r.quit # free R - - end - - if (regression != nil) - feature_uri = lazar.dependentVariables - prediction.compounds << compound_uri - prediction.features << feature_uri - prediction.data[compound_uri] = [] unless prediction.data[compound_uri] - compound_matches.each { |m| features[lazar.effects[m].to_sym] << {:smarts => m, :p_value => lazar.p_values[m] } } - tuple = { - File.join(@@config[:services]["opentox-model"],"lazar#regression") => regression, - File.join(@@config[:services]["opentox-model"],"lazar#confidence") => conf - } - if verbose - tuple[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")] = neighbors - tuple[File.join(@@config[:services]["opentox-model"],"lazar#features")] = features - end - prediction.data[compound_uri] << {feature_uri => tuple} - end - - end - # AM end - - - def classification(compound_uri,prediction,verbose=false) - - lazar = YAML.load self.yaml - compound = OpenTox::Compound.new(:uri => compound_uri) - compound_matches = compound.match lazar.features - - conf = 0.0 - features = { :activating => [], :deactivating => [] } - neighbors = {} - classification = nil - - lazar.fingerprints.each do |uri,matches| - - sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar.p_values) - if sim > 0.3 - neighbors[uri] = {:similarity => sim} - neighbors[uri][:features] = { :activating => [], :deactivating => [] } unless neighbors[uri][:features] - matches.each do |m| - if lazar.effects[m] == 'activating' - neighbors[uri][:features][:activating] << {:smarts => m, :p_value => lazar.p_values[m]} - elsif lazar.effects[m] == 'deactivating' - neighbors[uri][:features][:deactivating] << {:smarts => m, :p_value => lazar.p_values[m]} - end - end - lazar.activities[uri].each do |act| - neighbors[uri][:activities] = [] unless neighbors[uri][:activities] - neighbors[uri][:activities] << act - case act.to_s - when 'true' - conf += OpenTox::Utils.gauss(sim) - when 'false' - conf -= OpenTox::Utils.gauss(sim) - end - end - end - end - - conf = conf/neighbors.size - if conf > 0.0 - classification = true - elsif conf < 0.0 - classification = false - end - if (classification != nil) - feature_uri = lazar.dependentVariables - prediction.compounds << compound_uri - prediction.features << feature_uri - prediction.data[compound_uri] = [] unless prediction.data[compound_uri] - compound_matches.each { |m| features[lazar.effects[m].to_sym] << {:smarts => m, :p_value => lazar.p_values[m] } } - tuple = { - File.join(@@config[:services]["opentox-model"],"lazar#classification") => classification, - File.join(@@config[:services]["opentox-model"],"lazar#confidence") => conf - } - if verbose - tuple[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")] = neighbors - tuple[File.join(@@config[:services]["opentox-model"],"lazar#features")] = features - end - prediction.data[compound_uri] << {feature_uri => tuple} - end - end - - def database_activity?(compound_uri,prediction) - # find database activities - lazar = YAML.load self.yaml - db_activities = lazar.activities[compound_uri] - if db_activities - prediction.creator = lazar.trainingDataset - feature_uri = lazar.dependentVariables - prediction.compounds << compound_uri - prediction.features << feature_uri - prediction.data[compound_uri] = [] unless prediction.data[compound_uri] - db_activities.each do |act| - prediction.data[compound_uri] << {feature_uri => act} - end - true - else - false - end - end - - def to_owl - data = YAML.load(yaml) - activity_dataset = YAML.load(RestClient.get(data.trainingDataset, :accept => 'application/x-yaml').to_s) - feature_dataset = YAML.load(RestClient.get(data.feature_dataset_uri, :accept => 'application/x-yaml').to_s) - owl = OpenTox::OwlSerializer.create 'Model', uri - #owl.creator "helma@in-silico.ch" - #owl.contributor "helma@in-silico.ch" - owl.annotate("creator",data.algorithm,XSD.AnyUri) - owl.annotate("title", URI.decode(data.dependentVariables.split(/#/).last) ) - owl.annotate("date",created_at.to_s,XSD.DateTime) - #owl.annotate("algorithm",data.algorithm) - #owl.annotate("dependentVariables",activity_dataset.features.join(', ')) - #owl.annotate("independentVariables",feature_dataset.features.join(', ')) - #owl.annotate("predictedVariables", data.dependentVariables ) - #owl.annotate("trainingDataset",data.trainingDataset) -=begin - owl.parameters = { - "Dataset URI" => - { :scope => "mandatory", :value => data.trainingDataset }, - "Feature URI for dependent variable" => - { :scope => "mandatory", :value => activity_dataset.features.join(', ')}, - "Feature generation URI" => - { :scope => "mandatory", :value => feature_dataset.creator } - } -=end - - owl.rdf - end - -end - +# Get model representation +# @return [application/rdf+xml,application/x-yaml] Model representation get '/:id/?' do accept = request.env['HTTP_ACCEPT'] accept = "application/rdf+xml" if accept == '*/*' or accept == '' or accept.nil? @@ -254,17 +20,14 @@ get '/:id/?' do params[:id].sub!(/.rdf$/,'') accept = 'application/rdf+xml' end - model = Lazar.get(params[:id]) - halt 404, "Model #{params[:id]} not found." unless model + halt 404, "Model #{params[:id]} not found." unless model = ModelStore.get(params[:id]) + lazar = YAML.load model.yaml case accept - when "application/rdf+xml" - response['Content-Type'] = 'application/rdf+xml' -# unless model.owl # lazy owl creation -# model.owl = model.to_owl -# model.save -# end -# model.owl - model.to_owl + when /application\/rdf\+xml/ + s = OpenTox::Serializer::Owl.new + s.add_model(url_for('/lazar',:full),lazar.metadata) + response['Content-Type'] = 'application/rdf+xml' + s.to_rdfxml when /yaml/ response['Content-Type'] = 'application/x-yaml' model.yaml @@ -273,88 +36,82 @@ get '/:id/?' do end end +=begin get '/:id/algorithm/?' do response['Content-Type'] = 'text/plain' - YAML.load(Lazar.get(params[:id]).yaml).algorithm + YAML.load(ModelStore.get(params[:id]).yaml).algorithm end get '/:id/trainingDataset/?' do response['Content-Type'] = 'text/plain' - YAML.load(Lazar.get(params[:id]).yaml).trainingDataset + YAML.load(ModelStore.get(params[:id]).yaml).trainingDataset end get '/:id/feature_dataset/?' do response['Content-Type'] = 'text/plain' - YAML.load(Lazar.get(params[:id]).yaml).feature_dataset_uri + YAML.load(ModelStore.get(params[:id]).yaml).feature_dataset_uri end +=end +# Store a lazar model. This method should not be called directly, use OpenTox::Algorithm::Lazr to create a lazar model +# @param [Body] lazar Model representation in YAML format +# @return [String] Model URI post '/?' do # create model halt 400, "MIME type \"#{request.content_type}\" not supported." unless request.content_type.match(/yaml/) - model = Lazar.new - model.save + model = ModelStore.create model.uri = url_for("/#{model.id}", :full) - model.yaml = request.env["rack.input"].read + lazar = YAML.load request.env["rack.input"].read + lazar.uri = model.uri + model.yaml = lazar.to_yaml model.save model.uri end -post '/:id/?' do # create prediction - - lazar = Lazar.get(params[:id]) - halt 404, "Model #{params[:id]} does not exist." unless lazar +# Make a lazar prediction. Predicts either a single compound or all compounds from a dataset +# @param [optional,String] dataset_uri URI of the dataset to be predicted +# @param [optional,String] compound_uri URI of the compound to be predicted +# @param [optional,Header] Accept Content-type of prediction, can be either `application/rdf+xml or application/x-yaml` +# @return [text/uri-list,application/rdf+xml,application/x-yaml] URI of prediction task (dataset prediction) or prediction in requested representation +post '/:id/?' do + + start = Time.now + @lazar = YAML.load ModelStore.get(params[:id]).yaml + + halt 404, "Model #{params[:id]} does not exist." unless @lazar halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri] - @prediction = OpenTox::Dataset.new - @prediction.creator = lazar.uri - dependent_variable = YAML.load(lazar.yaml).dependentVariables - @prediction.title = URI.decode(dependent_variable.split(/#/).last) - case dependent_variable - when /classification/ - prediction_type = "classification" - when /regression/ - prediction_type = "regression" - end - + s = Time.now if compound_uri - # look for cached prediction first - if cached_prediction = Prediction.first(:model_uri => lazar.uri, :compound_uri => compound_uri) - @prediction = YAML.load(cached_prediction.yaml) - else - begin - # AM: switch here between regression and classification - eval "lazar.#{prediction_type}(compound_uri,@prediction,true) unless lazar.database_activity?(compound_uri,@prediction)" - Prediction.create(:model_uri => lazar.uri, :compound_uri => compound_uri, :yaml => @prediction.to_yaml) - rescue - LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} " - halt 500, "Prediction of #{compound_uri} failed." - end - end - case request.env['HTTP_ACCEPT'] - when /yaml/ - @prediction.to_yaml - when 'application/rdf+xml' - @prediction.to_owl - else - halt 400, "MIME type \"#{request.env['HTTP_ACCEPT']}\" not supported." - end + #begin + @prediction = @lazar.predict(compound_uri,true) + #rescue + #LOGGER.error "Lazar prediction failed for #{compound_uri} with #{$!} " + #halt 500, "Prediction of #{compound_uri} with #{@lazar.uri} failed." + #end + #accept = request.env['HTTP_ACCEPT'] + #accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil? + LOGGER.debug "Total: #{Time.now - start} seconds" + #case accept + #when /yaml/ + @prediction.uri + #else # RestClientWrapper does not send accept header + #when /application\/rdf\+xml/ + #@prediction.to_rdfxml + #else + #halt 400, "MIME type \"#{request.env['HTTP_ACCEPT']}\" not supported." + #end elsif dataset_uri response['Content-Type'] = 'text/uri-list' task_uri = OpenTox::Task.as_task("Predict dataset",url_for("/#{lazar.id}", :full)) do - input_dataset = OpenTox::Dataset.find(dataset_uri) - input_dataset.compounds.each do |compound_uri| - # AM: switch here between regression and classification - begin - eval "lazar.#{prediction_type}(compound_uri,@prediction) unless lazar.database_activity?(compound_uri,@prediction)" - rescue - LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} " - end - end - begin - uri = @prediction.save.chomp - rescue - halt 500, "Could not save prediction dataset" + OpenTox::Dataset.find(dataset_uri).compounds.each do |compound_uri| + #begin + predict(compound_uri,true) + #rescue + #LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} " + #end end + @prediction.save end halt 202,task_uri end diff --git a/property_lazar.rb b/property_lazar.rb deleted file mode 100644 index 6e68718..0000000 --- a/property_lazar.rb +++ /dev/null @@ -1,303 +0,0 @@ -# R integration -# workaround to initialize R non-interactively (former rinruby versions did this by default) -# avoids compiling R with X -R = nil -require "rinruby" -require "haml" - -class PropertyLazar < Model - - attr_accessor :prediction_dataset - -=begin - # AM begin - # regression function, created 06/10 - def regression(compound_uri,prediction,verbose=false) - - lazar = YAML.load self.yaml - compound = OpenTox::Compound.new(:uri => compound_uri) - - # obtain X values for query compound - compound_matches = compound.match lazar.features - - conf = 0.0 - features = { :activating => [], :deactivating => [] } - neighbors = {} - regression = nil - - regr_occurrences = [] # occurrence vector with {0,1} entries - sims = [] # similarity values between query and neighbors - acts = [] # activities of neighbors for supervised learning - neighbor_matches = [] # as in classification: URIs of matches - gram_matrix = [] # square matrix of similarities between neighbors; implements weighted tanimoto kernel - i = 0 - - # aquire data related to query structure - lazar.fingerprints.each do |uri,matches| - sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar.p_values) - lazar.activities[uri].each do |act| - if sim > 0.3 - neighbors[uri] = {:similarity => sim} - neighbors[uri][:features] = { :activating => [], :deactivating => [] } unless neighbors[uri][:features] - matches.each do |m| - if lazar.effects[m] == 'activating' - neighbors[uri][:features][:activating] << {:smarts => m, :p_value => lazar.p_values[m]} - elsif lazar.effects[m] == 'deactivating' - neighbors[uri][:features][:deactivating] << {:smarts => m, :p_value => lazar.p_values[m]} - end - end - lazar.activities[uri].each do |act| - neighbors[uri][:activities] = [] unless neighbors[uri][:activities] - neighbors[uri][:activities] << act - end - conf += OpenTox::Utils.gauss(sim) - sims << OpenTox::Utils.gauss(sim) - #TODO check for 0 s - acts << Math.log10(act.to_f) - neighbor_matches[i] = matches - i+=1 - end - end - end - conf = conf/neighbors.size - LOGGER.debug "Regression: found " + neighbor_matches.size.to_s + " neighbors." - - - unless neighbor_matches.length == 0 - # gram matrix - (0..(neighbor_matches.length-1)).each do |i| - gram_matrix[i] = [] - # lower triangle - (0..(i-1)).each do |j| - sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(neighbor_matches[i], neighbor_matches[j], lazar.p_values) - gram_matrix[i] << OpenTox::Utils.gauss(sim) - end - # diagonal element - gram_matrix[i][i] = 1.0 - # upper triangle - ((i+1)..(neighbor_matches.length-1)).each do |j| - sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(neighbor_matches[i], neighbor_matches[j], lazar.p_values) - gram_matrix[i] << OpenTox::Utils.gauss(sim) - end - end - - @r = RinRuby.new(false,false) # global R instance leads to Socket errors after a large number of requests - @r.eval "library('kernlab')" # this requires R package "kernlab" to be installed - LOGGER.debug "Setting R data ..." - # set data - @r.gram_matrix = gram_matrix.flatten - @r.n = neighbor_matches.length - @r.y = acts - @r.sims = sims - - LOGGER.debug "Preparing R data ..." - # prepare data - @r.eval "y<-as.vector(y)" - @r.eval "gram_matrix<-as.kernelMatrix(matrix(gram_matrix,n,n))" - @r.eval "sims<-as.vector(sims)" - - # model + support vectors - LOGGER.debug "Creating SVM model ..." - @r.eval "model<-ksvm(gram_matrix, y, kernel=matrix, type=\"nu-svr\", nu=0.8)" - @r.eval "sv<-as.vector(SVindex(model))" - @r.eval "sims<-sims[sv]" - @r.eval "sims<-as.kernelMatrix(matrix(sims,1))" - LOGGER.debug "Predicting ..." - @r.eval "p<-predict(model,sims)[1,1]" - regression = 10**(@r.p.to_f) - LOGGER.debug "Prediction is: '" + regression.to_s + "'." - @r.quit # free R - - end - - if (regression != nil) - feature_uri = lazar.dependentVariables - prediction.compounds << compound_uri - prediction.features << feature_uri - prediction.data[compound_uri] = [] unless prediction.data[compound_uri] - compound_matches.each { |m| features[lazar.effects[m].to_sym] << {:smarts => m, :p_value => lazar.p_values[m] } } - tuple = { - File.join(@@config[:services]["opentox-model"],"lazar#regression") => regression, - File.join(@@config[:services]["opentox-model"],"lazar#confidence") => conf - } - if verbose - tuple[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")] = neighbors - tuple[File.join(@@config[:services]["opentox-model"],"lazar#features")] = features - end - prediction.data[compound_uri] << {feature_uri => tuple} - end - - end - # AM end -=end - - - def classification(compound_uri,prediction,verbose=false) - - lazar = YAML.load self.yaml - compound = OpenTox::Compound.new(:uri => compound_uri) - compound_properties = lazar.properties[compound.uri] - - conf = 0.0 - neighbors = {} - features = [] - classification = nil - - lazar.properties.each do |uri,properties| - - sim = OpenTox::Algorithm::Similarity.euclidean(compound_properties,properties) - if sim and sim > 0.001 - neighbors[uri] = {:similarity => sim} - neighbors[uri][:features] = [] unless neighbors[uri][:features] - properties.each do |p,v| - neighbors[uri][:features] << {p => v} - end - lazar.activities[uri].each do |act| - neighbors[uri][:activities] = [] unless neighbors[uri][:activities] - neighbors[uri][:activities] << act - case act.to_s - when 'true' - conf += OpenTox::Utils.gauss(sim) - when 'false' - conf -= OpenTox::Utils.gauss(sim) - end - end - end - end - - conf = conf/neighbors.size - if conf > 0.0 - classification = true - elsif conf < 0.0 - classification = false - end - if (classification != nil) - feature_uri = lazar.dependentVariables - prediction.compounds << compound_uri - prediction.features << feature_uri - prediction.data[compound_uri] = [] unless prediction.data[compound_uri] - compound_properties.each { |p,v| features << {p => v} } - tuple = { - File.join(@@config[:services]["opentox-model"],"lazar#classification") => classification, - File.join(@@config[:services]["opentox-model"],"lazar#confidence") => conf - } - if verbose - tuple[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")] = neighbors - tuple[File.join(@@config[:services]["opentox-model"],"lazar#features")] = features - end - prediction.data[compound_uri] << {feature_uri => tuple} - end - end - - def database_activity?(compound_uri,prediction) - # find database activities - lazar = YAML.load self.yaml - db_activities = lazar.activities[compound_uri] - if db_activities - prediction.creator = lazar.trainingDataset - feature_uri = lazar.dependentVariables - prediction.compounds << compound_uri - prediction.features << feature_uri - prediction.data[compound_uri] = [] unless prediction.data[compound_uri] - db_activities.each do |act| - prediction.data[compound_uri] << {feature_uri => act} - end - true - else - false - end - end - - def to_owl - data = YAML.load(yaml) - activity_dataset = YAML.load(RestClient.get(data.trainingDataset, :accept => 'application/x-yaml').to_s) - feature_dataset = YAML.load(RestClient.get(data.feature_dataset_uri, :accept => 'application/x-yaml').to_s) - owl = OpenTox::Owl.create 'Model', uri - owl.set("creator","http://github.com/helma/opentox-model") - owl.set("title", URI.decode(data.dependentVariables.split(/#/).last) ) - #owl.set("title","#{URI.decode(activity_dataset.title)} lazar classification") - owl.set("date",created_at.to_s) - owl.set("algorithm",data.algorithm) - owl.set("dependentVariables",activity_dataset.features.join(', ')) - owl.set("independentVariables",feature_dataset.features.join(', ')) - owl.set("predictedVariables", data.dependentVariables ) - #owl.set("predictedVariables",activity_dataset.features.join(', ') + "_lazar_classification") - owl.set("trainingDataset",data.trainingDataset) - owl.parameters = { - "Dataset URI" => - { :scope => "mandatory", :value => data.trainingDataset }, - "Feature URI for dependent variable" => - { :scope => "mandatory", :value => activity_dataset.features.join(', ')}, - "Feature generation URI" => - { :scope => "mandatory", :value => feature_dataset.creator } - } - - owl.rdf - end - -end - -post '/pl/:id/?' do # create prediction - - lazar = PropertyLazar.get(params[:id]) - LOGGER.debug lazar.to_yaml - halt 404, "Model #{params[:id]} does not exist." unless lazar - halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri] - - @prediction = OpenTox::Dataset.new - @prediction.creator = lazar.uri - dependent_variable = YAML.load(lazar.yaml).dependentVariables - @prediction.title = URI.decode(dependent_variable.split(/#/).last) - case dependent_variable - when /classification/ - prediction_type = "classification" - when /regression/ - prediction_type = "regression" - end - - if compound_uri - # look for cached prediction first - #if cached_prediction = Prediction.first(:model_uri => lazar.uri, :compound_uri => compound_uri) - #@prediction = YAML.load(cached_prediction.yaml) - #else - begin - # AM: switch here between regression and classification - lazar.classification(compound_uri,@prediction,true) #unless lazar.database_activity?(compound_uri,@prediction)" - #eval "lazar.#{prediction_type}(compound_uri,@prediction,true) unless lazar.database_activity?(compound_uri,@prediction)" - #Prediction.create(:model_uri => lazar.uri, :compound_uri => compound_uri, :yaml => @prediction.to_yaml) - rescue - LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} " - halt 500, "Prediction of #{compound_uri} failed." - end - #end - case request.env['HTTP_ACCEPT'] - when /yaml/ - @prediction.to_yaml - when 'application/rdf+xml' - @prediction.to_owl - else - halt 400, "MIME type \"#{request.env['HTTP_ACCEPT']}\" not supported." - end - - elsif dataset_uri - response['Content-Type'] = 'text/uri-list' - task_uri = OpenTox::Task.as_task("Predict dataset",url_for("/#{lazar.id}", :full)) do - input_dataset = OpenTox::Dataset.find(dataset_uri) - input_dataset.compounds.each do |compound_uri| - # AM: switch here between regression and classification - begin - eval "lazar.#{prediction_type}(compound_uri,@prediction) unless lazar.database_activity?(compound_uri,@prediction)" - rescue - LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} " - end - end - begin - uri = @prediction.save.chomp - rescue - halt 500, "Could not save prediction dataset" - end - end - halt 202,task_uri - end - -end -- cgit v1.2.3 From 2d0c76b7838f5f31552a09c54a81e621d1618d2d Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 19 Nov 2010 16:51:14 +0100 Subject: working predictions for toxcreate --- lazar.rb | 65 +++++++++++++--------------------------------------------------- 1 file changed, 13 insertions(+), 52 deletions(-) diff --git a/lazar.rb b/lazar.rb index 3b8a0cf..8ad9fed 100644 --- a/lazar.rb +++ b/lazar.rb @@ -1,8 +1,3 @@ -# R integration -# workaround to initialize R non-interactively (former rinruby versions did this by default) -# avoids compiling R with X -R = nil -require "rinruby" require "haml" #require "lazar-helper" @@ -36,23 +31,6 @@ get '/:id/?' do end end -=begin -get '/:id/algorithm/?' do - response['Content-Type'] = 'text/plain' - YAML.load(ModelStore.get(params[:id]).yaml).algorithm -end - -get '/:id/trainingDataset/?' do - response['Content-Type'] = 'text/plain' - YAML.load(ModelStore.get(params[:id]).yaml).trainingDataset -end - -get '/:id/feature_dataset/?' do - response['Content-Type'] = 'text/plain' - YAML.load(ModelStore.get(params[:id]).yaml).feature_dataset_uri -end -=end - # Store a lazar model. This method should not be called directly, use OpenTox::Algorithm::Lazr to create a lazar model # @param [Body] lazar Model representation in YAML format # @return [String] Model URI @@ -71,47 +49,30 @@ end # @param [optional,String] dataset_uri URI of the dataset to be predicted # @param [optional,String] compound_uri URI of the compound to be predicted # @param [optional,Header] Accept Content-type of prediction, can be either `application/rdf+xml or application/x-yaml` -# @return [text/uri-list,application/rdf+xml,application/x-yaml] URI of prediction task (dataset prediction) or prediction in requested representation +# @return [text/uri-list] URI of prediction task (dataset prediction) or prediction dataset (compound prediction) post '/:id/?' do - start = Time.now @lazar = YAML.load ModelStore.get(params[:id]).yaml halt 404, "Model #{params[:id]} does not exist." unless @lazar halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri] - s = Time.now + response['Content-Type'] = 'text/uri-list' if compound_uri - #begin - @prediction = @lazar.predict(compound_uri,true) - #rescue - #LOGGER.error "Lazar prediction failed for #{compound_uri} with #{$!} " - #halt 500, "Prediction of #{compound_uri} with #{@lazar.uri} failed." - #end - #accept = request.env['HTTP_ACCEPT'] - #accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil? - LOGGER.debug "Total: #{Time.now - start} seconds" - #case accept - #when /yaml/ - @prediction.uri - #else # RestClientWrapper does not send accept header - #when /application\/rdf\+xml/ - #@prediction.to_rdfxml - #else - #halt 400, "MIME type \"#{request.env['HTTP_ACCEPT']}\" not supported." - #end + begin + cache = PredictionCache.first(:model_uri => @lazar.uri, :compound_uri => compound_uri) + return cache.dataset_uri if cache + prediction_uri = @lazar.predict(compound_uri,true).uri + PredictionCache.create(:model_uri => @lazar.uri, :compound_uri => compound_uri, :dataset_uri => prediction_uri) + prediction_uri + rescue + LOGGER.error "Lazar prediction failed for #{compound_uri} with #{$!} " + halt 500, "Prediction of #{compound_uri} with #{@lazar.uri} failed." + end elsif dataset_uri - response['Content-Type'] = 'text/uri-list' task_uri = OpenTox::Task.as_task("Predict dataset",url_for("/#{lazar.id}", :full)) do - OpenTox::Dataset.find(dataset_uri).compounds.each do |compound_uri| - #begin - predict(compound_uri,true) - #rescue - #LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} " - #end - end - @prediction.save + @lazar.predict(dataset_uri).uri end halt 202,task_uri end -- cgit v1.2.3 From 40d607c935e27ab26a2f2dd1d641717c9d6a5e31 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 23 Nov 2010 16:45:21 +0100 Subject: dataset prediction fixed --- lazar.rb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/lazar.rb b/lazar.rb index 8ad9fed..0a9dddf 100644 --- a/lazar.rb +++ b/lazar.rb @@ -59,9 +59,9 @@ post '/:id/?' do response['Content-Type'] = 'text/uri-list' if compound_uri + #cache = PredictionCache.first(:model_uri => @lazar.uri, :compound_uri => compound_uri) + #return cache.dataset_uri if cache begin - cache = PredictionCache.first(:model_uri => @lazar.uri, :compound_uri => compound_uri) - return cache.dataset_uri if cache prediction_uri = @lazar.predict(compound_uri,true).uri PredictionCache.create(:model_uri => @lazar.uri, :compound_uri => compound_uri, :dataset_uri => prediction_uri) prediction_uri @@ -71,10 +71,10 @@ post '/:id/?' do end elsif dataset_uri - task_uri = OpenTox::Task.as_task("Predict dataset",url_for("/#{lazar.id}", :full)) do - @lazar.predict(dataset_uri).uri + task = OpenTox::Task.create("Predict dataset",url_for("/#{@lazar.id}", :full)) do + @lazar.predict_dataset(dataset_uri).uri end - halt 202,task_uri + halt 202,task.uri end end -- cgit v1.2.3 From 6e5aa1678e7d0380de77e462347ae2260fd3051b Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 24 Nov 2010 11:48:32 +0100 Subject: status 503 for rejected tasks --- lazar.rb | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/lazar.rb b/lazar.rb index 0a9dddf..e543802 100644 --- a/lazar.rb +++ b/lazar.rb @@ -1,5 +1,13 @@ require "haml" -#require "lazar-helper" + +helpers do + def uri_available?(urlStr) + url = URI.parse(urlStr) + Net::HTTP.start(urlStr.host, urlStr.port) do |http| + return http.head(urlStr.request_uri).code == "200" + end + end +end # Get model representation # @return [application/rdf+xml,application/x-yaml] Model representation @@ -59,8 +67,8 @@ post '/:id/?' do response['Content-Type'] = 'text/uri-list' if compound_uri - #cache = PredictionCache.first(:model_uri => @lazar.uri, :compound_uri => compound_uri) - #return cache.dataset_uri if cache + cache = PredictionCache.first(:model_uri => @lazar.uri, :compound_uri => compound_uri) + return cache.dataset_uri if cache and uri_available?(cache.dataset_uri) begin prediction_uri = @lazar.predict(compound_uri,true).uri PredictionCache.create(:model_uri => @lazar.uri, :compound_uri => compound_uri, :dataset_uri => prediction_uri) @@ -74,6 +82,7 @@ post '/:id/?' do task = OpenTox::Task.create("Predict dataset",url_for("/#{@lazar.id}", :full)) do @lazar.predict_dataset(dataset_uri).uri end + halt 503,task.uri+"\n" if task.status == "Cancelled" halt 202,task.uri end -- cgit v1.2.3 From 61ba09a60cd00c8e8f54ba6766cabe56e658051e Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 24 Nov 2010 13:10:52 +0100 Subject: opentox-ruby-api-wrapper renamed to opentox-ruby --- application.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/application.rb b/application.rb index 94c6039..eb7db12 100644 --- a/application.rb +++ b/application.rb @@ -1,6 +1,6 @@ require 'rubygems' -gem "opentox-ruby-api-wrapper", "= 1.6.6" -require 'opentox-ruby-api-wrapper' +gem "opentox-ruby", "~> 0" +require 'opentox-ruby' class ModelStore include DataMapper::Resource -- cgit v1.2.3 From 12220a1cc4b37fda3a6776c4d0fd787d90a16882 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 24 Nov 2010 14:43:20 +0100 Subject: opentox-ruby gem in config.ru --- config.ru | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/config.ru b/config.ru index 6f5db40..1616a96 100644 --- a/config.ru +++ b/config.ru @@ -1,6 +1,5 @@ require 'rubygems' -require 'opentox-ruby-api-wrapper' +require 'opentox-ruby' require 'config/config_ru' set :app_file, __FILE__ # to get the view path right run Sinatra::Application - -- cgit v1.2.3