BBRC as default descriptors

1 files changed, 142 insertions, 3 deletions

diff --git a/fminer.rb b/fminer.rb
index 9300bac..d48b363 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -1,7 +1,6 @@
 ENV['FMINER_SMARTS'] = 'true'
 ENV['FMINER_NO_AROMATIC'] = 'true'
 ENV['FMINER_PVALUES'] = 'true'
-@@fminer = Bbrc::Bbrc.new 
 
 get '/fminer/?' do
   owl = OpenTox::Owl.create 'Algorithm', url_for('/fminer',:full)
@@ -17,8 +16,148 @@ get '/fminer/?' do
 	rdf
 end
 
-post '/fminer/?' do
-    
+
+['/fminer/bbrc/?','/fminer/?'].each do |path| # AM LAST: set bbrc as default
+  post path do
+    @@fminer = Bbrc::Bbrc.new 
+    halt 404, "Please submit a dataset_uri." unless params[:dataset_uri] and  !params[:dataset_uri].nil?
+    halt 404, "Please submit a feature_uri." unless params[:feature_uri] and  !params[:feature_uri].nil?
+    LOGGER.debug "Dataset: " + params[:dataset_uri]
+    LOGGER.debug "Endpoint: " + params[:feature_uri]
+    feature_uri = params[:feature_uri]
+    begin
+      LOGGER.debug "Retrieving #{params[:dataset_uri]}"
+      training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}"
+    rescue
+      LOGGER.error "Dataset #{params[:dataset_uri]} not found" 
+      halt 404, "Dataset #{params[:dataset_uri]} not found." if training_dataset.nil? 
+    end
+    halt 404, "No feature #{params[:feature_uri]} in dataset #{params[:dataset_uri]}" unless training_dataset.features and training_dataset.features.include?(params[:feature_uri])
+
+    task_uri = OpenTox::Task.as_task("Mine features", url_for('/fminer',:full)) do 
+
+      feature_dataset = OpenTox::Dataset.new
+      title = "BBRC representatives for " + training_dataset.title
+      feature_dataset.title = title
+      feature_dataset.creator = url_for('/fminer',:full)
+      bbrc_uri = url_for("/fminer#BBRC_representative",:full)
+      feature_dataset.features << bbrc_uri
+
+      id = 1 # fminer start id is not 0
+      compounds = []
+
+      g_hash = Hash.new# DV: for effect calculation in regression part
+      @@fminer.Reset
+      #@@fminer.SetChisqSig(0.99)
+      LOGGER.debug "Fminer: initialising ..."
+          training_dataset.data.each do |c,features|
+        begin
+          smiles = OpenTox::Compound.new(:uri => c.to_s).smiles
+        rescue
+          LOGGER.warn "No resource for #{c.to_s}"
+          next
+        end
+        if smiles == '' or smiles.nil?
+          LOGGER.warn "Cannot find smiles for #{c.to_s}."
+        else
+          feature_dataset.compounds << c.to_s
+          features.each do |feature|
+            act = feature[feature_uri]
+            if act.nil? 
+              LOGGER.warn "No #{feature_uri} activiity for #{c.to_s}."
+            else
+              case act.to_s
+              when "true"
+                #LOGGER.debug id.to_s + ' "' + smiles +'"' +  "\t" + true.to_s
+                activity = 1
+              when "false"
+                #LOGGER.debug id.to_s + ' "' + smiles +'"' +  "\t" + false.to_s
+                activity = 0
+              else
+                # AM: add quantitative activity
+                activity = act.to_f
+                @@fminer.SetRegression(true)
+              end
+              compounds[id] = c.to_s
+              begin
+                @@fminer.AddCompound(smiles,id)
+                @@fminer.AddActivity(activity, id)
+                g_hash[id]=activity # DV: insert global information
+              rescue
+                LOGGER.warn "Could not add " + smiles + "\t" + act.to_s + " to fminer"
+              end
+            end
+          end
+          id += 1
+        end
+      end
+      g_array=g_hash.values # DV: calculation of global median for effect calculation
+      g_median=OpenTox::Utils.median(g_array)
+      minfreq = (0.02*id).round
+      #minfreq = 5
+      @@fminer.SetMinfreq(minfreq)
+      LOGGER.debug "Fminer: initialised with #{id} compounds, minimum frequency #{minfreq}"
+
+      raise "no compounds" if compounds.size==0
+
+      values = {}
+      # run @@fminer
+      LOGGER.debug "Fminer: mining ..."
+      (0 .. @@fminer.GetNoRootNodes()-1).each do |j|
+        results = @@fminer.MineRoot(j)
+        results.each do |result|
+          f = YAML.load(result)[0]
+          smarts = f[0]
+          p_value = f[1]
+          # AM: f[3] missing on regression
+          if (!@@fminer.GetRegression) 
+            ids = f[2] + f[3]
+            if f[2].size > f[3].size
+              effect = 'activating'
+            else
+              effect = 'deactivating'
+            end
+          else #regression part
+            ids = f[2]
+                      # DV: effect calculation
+                      f_arr=Array.new
+                      f[2].each do |id|
+                          f_arr.push(g_hash[id]) 
+                      end 
+                      f_median=OpenTox::Utils.median(f_arr)
+                      if g_median >= f_median 
+              effect = 'activating'
+            else
+              effect = 'deactivating'
+                      end
+          end
+
+          tuple = {
+            url_for('/fminer#smarts',:full) => smarts,
+            url_for('/fminer#p_value',:full) => p_value.to_f,
+            url_for('/fminer#effect',:full) => effect
+          }
+          #LOGGER.debug "#{f[0]}\t#{f[1]}\t#{effect}"
+          ids.each do |id|
+            feature_dataset.data[compounds[id]] = [] unless feature_dataset.data[compounds[id]]
+            feature_dataset.data[compounds[id]] << {bbrc_uri => tuple}
+          end
+        end
+      end
+
+      uri = feature_dataset.save 
+      LOGGER.debug "Fminer finished, dataset #{uri} created."
+      uri
+    end
+    LOGGER.debug "Fimer task started: "+task_uri.to_s
+    response['Content-Type'] = 'text/uri-list'
+    halt 202,task_uri.to_s+"\n"
+  end
+end
+
+
+post '/fminer/last/?' do
+  @@fminer = Last::Last.new 
 	halt 404, "Please submit a dataset_uri." unless params[:dataset_uri] and  !params[:dataset_uri].nil?
 	halt 404, "Please submit a feature_uri." unless params[:feature_uri] and  !params[:feature_uri].nil?
 	LOGGER.debug "Dataset: " + params[:dataset_uri]