Completed integration of LAST-PM

4 files changed, 32 insertions, 17 deletions

diff --git a/Rakefile b/Rakefile
index 588236b..0c72015 100644
--- a/Rakefile
+++ b/Rakefile
@@ -9,7 +9,11 @@ namespace "fminer" do
     puts `git submodule init`
     puts `git submodule update`
     Dir.chdir('libfminer/libbbrc')
-    puts `git checkout master`
+    puts `git checkout Makefile`
+    #puts `git checkout master`
+    puts `git fetch`
+    puts `git checkout -f -b refactor origin/refactor`
+    puts `git checkout refactor`
     puts `git pull`
     puts `./configure`
     if $? == 0
@@ -20,7 +24,11 @@ namespace "fminer" do
     end
     puts `make ruby`
     Dir.chdir('../liblast')
-    puts `git checkout master`
+    puts `git checkout Makefile`
+    #puts `git checkout master`
+    puts `git fetch`
+    puts `git checkout -f -b refactor origin/refactor`
+    puts `git checkout refactor`
     puts `git pull`
     puts `./configure`
     if $? == 0
@@ -32,7 +40,7 @@ namespace "fminer" do
     puts `make ruby`
     Dir.chdir('../../last-utils')
     puts `git fetch`
-    puts `git checkout -b experimental origin/experimental`
+    puts `git checkout -f -b experimental origin/experimental`
     puts `git pull`
   end
 
@@ -40,7 +48,11 @@ namespace "fminer" do
   task :update do
     puts `git submodule update`
     Dir.chdir('libfminer/libbbrc')
-    puts `git checkout master`
+    puts `git checkout Makefile`
+    #puts `git checkout master`
+    puts `git fetch`
+    puts `git checkout -f -b refactor origin/refactor`
+    puts `git checkout refactor`
     puts `git pull`
     puts `./configure`
     if $? == 0
@@ -51,7 +63,11 @@ namespace "fminer" do
     end
     puts `make ruby`
     Dir.chdir('../liblast')
-    puts `git checkout master`
+    puts `git checkout Makefile`
+    #puts `git checkout master`
+    puts `git fetch`
+    puts `git checkout -f -b refactor origin/refactor`
+    puts `git checkout refactor`
     puts `git pull`
     puts `./configure`
     if $? == 0
@@ -63,7 +79,7 @@ namespace "fminer" do
     puts `make ruby`
     Dir.chdir('../../last-utils')
     puts `git fetch`
-    puts `git checkout -b experimental origin/experimental`
+    puts `git checkout -f -b experimental origin/experimental`
     puts `git pull`
   end
 end
diff --git a/application.rb b/application.rb
index 5aecfbb..3d511d1 100644
--- a/application.rb
+++ b/application.rb
@@ -1,4 +1,6 @@
 require 'rubygems'
+require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/libbbrc/bbrc') # has to be included before openbabel, otherwise we have strange SWIG overloading problems
+require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/liblast/last') # has to be included before openbabel, otherwise we have strange SWIG overloading problems
 require File.join(File.expand_path(File.dirname(__FILE__)), 'last-utils/lu.rb') # AM LAST
 gem "opentox-ruby-api-wrapper", "= 1.6.5"
 require 'opentox-ruby-api-wrapper'
diff --git a/fminer.rb b/fminer.rb
index 8cbf490..b706fb0 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -19,7 +19,6 @@ end
 
 ['/fminer/bbrc/?','/fminer/?'].each do |path| # AM LAST: set bbrc as default
   post path do
-    require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/libbbrc/bbrc') # has to be included before openbabel, otherwise we have strange SWIG overloading problems
     @@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?
@@ -150,7 +149,7 @@ end
       LOGGER.debug "Fminer finished, dataset #{uri} created."
       uri
     end
-    LOGGER.debug "Fimer task started: "+task_uri.to_s
+    LOGGER.debug "Fminer task started: "+task_uri.to_s
     response['Content-Type'] = 'text/uri-list'
     halt 202,task_uri.to_s+"\n"
   end
@@ -158,7 +157,6 @@ end
 
 
 post '/fminer/last/?' do
-  require File.join(File.expand_path(File.dirname(__FILE__)), 'libfminer/liblast/last') # has to be included before openbabel, otherwise we have strange SWIG overloading problems
   @@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?
@@ -187,7 +185,7 @@ post '/fminer/last/?' do
     compounds = []
     smi = [] # AM LAST: needed for matching the patterns back
 
-    g_hash = Hash.new# DV: for effect calculation in regression part
+    all_hash = Hash.new# DV: for effect calculation in regression part
     @@fminer.Reset
     #@@fminer.SetChisqSig(0.99)
     LOGGER.debug "Fminer: initialising ..."
@@ -224,7 +222,7 @@ post '/fminer/last/?' do
             begin
               @@fminer.AddCompound(smiles,id)
               @@fminer.AddActivity(activity, id)
-              g_hash[id]=activity # DV: insert global information
+              all_hash[id]=activity # DV: insert global information
             rescue
               LOGGER.warn "Could not add " + smiles + "\t" + act.to_s + " to fminer"
             end
@@ -233,8 +231,6 @@ post '/fminer/last/?' do
         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)
@@ -254,12 +250,13 @@ post '/fminer/last/?' do
     dom=lu.read(xml)                        # AM LAST: parse GraphML (needs hpricot, @ch: to be included in wrapper!)
     smarts=lu.smarts_rb(dom,'msa')          # AM LAST: converts patterns to LAST-SMARTS using msa variant (see last-pm.maunz.de)
     instances=lu.match_rb(smi,smarts)       # AM LAST: creates instantiations
-
     instances.each do |smarts, ids|
+      feat_hash = Hash[*(all_hash.select { |k,v| ids.include?(k) }.flatten)] # AM LAST: get activities of feature occurrences; see http://www.softiesonrails.com/2007/9/18/ruby-201-weird-hash-syntax
+      @@fminer.GetRegression() ? p_value = @@fminer.KSTest(all_hash.values, feat_hash.values).to_f : p_value = @@fminer.ChisqTest(all_hash.values, feat_hash.values).to_f
       tuple = {
         url_for('/fminer#smarts',:full) => smarts,
-        url_for('/fminer#p_value',:full) => nil, # AM LAST: TODO
-        url_for('/fminer#effect',:full) => nil   # AM LAST: TODO
+        url_for('/fminer#p_value',:full) => p_value.abs,
+        url_for('/fminer#effect',:full) => ((p_value>0)?'activating':'deactivating')
       }
       ids.each do |id|
         feature_dataset.data[compounds[id]] = [] unless feature_dataset.data[compounds[id]]
@@ -271,7 +268,7 @@ post '/fminer/last/?' do
     LOGGER.debug "Fminer finished, dataset #{uri} created."
     uri
   end
-  LOGGER.debug "Fimer task started: "+task_uri.to_s
+  LOGGER.debug "Fminer task started: "+task_uri.to_s
   response['Content-Type'] = 'text/uri-list'
   halt 202,task_uri.to_s+"\n"
 end
diff --git a/libfminer b/libfminer
-Subproject 00ce7e88f4f1ca16030a9b7bdabf216b5402f9c
+Subproject e0eee431ecb954328ff64e3cc48840c7003a276