rocker 0.0.8 → 0.0.9

data/Manifest.txt

@@ -9,11 +9,11 @@ script/destroy
 script/generate
 test/test_helper.rb
 test/test_rocker.rb
-ext/rocker/extconf.rb
-ext/rocker/auc_info.h
-ext/rocker/constants.h
-ext/rocker/fetcher.h
-ext/rocker/updater.h
-ext/rocker/line_input_iterator.h
-ext/rocker/rocker.h
-ext/rocker/rocker.cpp
+ext/rockerxx/extconf.rb
+ext/rockerxx/auc_info.h
+ext/rockerxx/constants.h
+ext/rockerxx/fetcher.h
+ext/rockerxx/updater.h
+ext/rockerxx/line_input_iterator.h
+ext/rockerxx/rockerxx.h
+ext/rockerxx/rockerxx.cpp

data/Rakefile

@@ -14,7 +14,6 @@ $hoe = Hoe.spec 'rocker' do
   self.developer 'John Woods', 'john.woods@marcottelab.org'
   self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
   # self.extra_deps         = [['activesupport','>= 2.0.2']]
-
 end
 
 require 'newgem/tasks'

data/ext/{rocker → rockerxx}/extconf.rb

@@ -1,7 +1,7 @@
 require 'rubygems'
 require 'mkmf-rice'
 
-dir_config("rocker")
+dir_config("rockerxx")
 dir_config("boost")
 
 have_library("stdc++")
@@ -12,4 +12,4 @@ if RUBY_VERSION =~ /1.9/ then
   $CPPFLAGS += " -DRUBY_19"
 end
 
-create_makefile('rocker')
+create_makefile('rockerxx')

data/ext/{rocker → rockerxx}/fetcher.h

@@ -1,9 +1,11 @@
 #include <iostream>
 #include <set>
 #include <vector>
+#include <map>
 #include <string>
 #include <sstream>
 #include <pqxx/transactor.hxx>
+#include <pqxx/nontransaction.hxx>
 #include <pqxx/result.hxx>
 
 using std::cout;
@@ -11,42 +13,49 @@ using std::cerr;
 using std::endl;
 using std::set;
 using std::vector;
+using std::map;
 using std::string;
 using std::ostringstream;
 using pqxx::transactor;
+using pqxx::nontransaction;
 using pqxx::result;
 
 typedef unsigned int  uint;
 
 
-class Fetcher : public transactor <> {
+class Fetcher : public transactor<nontransaction> {
 public:
-    Fetcher() : transactor<>("Fetcher") {}
+    Fetcher(uint m_id, map<uint, set<uint> >* known)
+    : transactor<nontransaction>("Fetcher"), matrix_id(m_id), known_correct(known)
+    {
+        cerr << "Constructed" << endl;
+    }
 
-    uint matrix_id;
-    uint experiment_id;
-    vector< set<uint> > known_correct;
-    string query;
+    Fetcher(const Fetcher& rhs)
+    : query(rhs.query), matrix_id(rhs.matrix_id), known_correct(rhs.known_correct)
+    {
+        cerr << "Copy constructed" << endl;
+    }
+
+    ~Fetcher() {
+        cerr << "De-allocate" << endl;
+    }
 
     void operator()(argument_type &T) {
         result R;
-        query = make_known_correct_query().c_str();
+        query = make_known_correct_query();
 
         try {
             R = T.exec(query);
 
-            vector< set<uint> > known(R.size());
-
             // Get the row and add it to the results set
             for (result::const_iterator it = R.begin(); it != R.end(); ++it) {
                 uint i; uint j;
                 (*it)[1].to(j); // Get column
                 (*it)[2].to(i); // Get gene
-                known[j].insert(i);
+                (*known_correct)[j].insert(i);
             }
 
-            known_correct = known;
-
         } catch (pqxx::sql_error e) {
             cerr << "SQL error in Fetcher transactor." << endl;
             cerr << "Query: " << e.query() << endl;
@@ -54,7 +63,20 @@ public:
         }
     }
 
+    set<uint>& operator[](size_t idx) {
+        return (*known_correct)[idx];
+    }
+
+    set<uint> operator[](size_t idx) const {
+        return (*known_correct).find(idx)->second;
+    }
+
 protected:
+    string query;
+    uint matrix_id;
+    
+    map<uint, set<uint> >* known_correct;
+
     string make_known_correct_query() const {
         ostringstream q;
         q << "SELECT id, j, i FROM entries WHERE matrix_id = " << matrix_id

data/ext/{rocker/rocker.cpp → rockerxx/rockerxx.cpp}

@@ -33,7 +33,7 @@ using std::cout;
 using std::endl;
 using namespace Rice;
 
-#include "rocker.h"
+#include "rockerxx.h"
 
 //#include "line_input_iterator.h"
 
@@ -41,15 +41,15 @@ typedef LineInputIterator<std::string> line_input_iterator;
 
 
 extern "C"
-void Init_rocker() {
+void Init_rockerxx() {
 
     // Expose Rocker class to Ruby
     //database_string dbarg(DBNAME, USER, PASSWORD);
-    Data_Type<Rocker> rb_cRocker =
-            define_class<Rocker>("Rocker")
+    Data_Type<Rocker> rb_cRockerxx =
+            define_class<Rocker>("Rockerxx")
              .define_constructor(Constructor<Rocker,std::string,uint,uint>())
              .define_method("process_results", &Rocker::process_results)
-             .define_method("fetch", &Rocker::fetch, (Arg("j")))
+             .define_method("fetch_column", &Rocker::fetch_column, (Arg("j")))
              .define_method("calculate_statistic",
                             &Rocker::calculate_statistic,
                             (Arg("j"), Arg("threshold") = (double)(0.0)))

data/ext/{rocker/rocker.h → rockerxx/rockerxx.h}

@@ -46,38 +46,39 @@ class Rocker {
 public:
 
     // Connect to the database and create the read transaction
-    Rocker(string dbarg, uint m_id, uint e_id) : c(dbarg), mean_auc_(0.0) {
+    Rocker(string dbarg, uint m_id, uint e_id)
+    : c(dbarg), known_(new map<uint, set<uint> >), fetch(m_id, known_), update(e_id)
+    {
         // Make sure the fetcher knows which matrix to restrict queries to.
-        fetcher.matrix_id = m_id;
+        // fetcher.matrix_id = m_id;
 
         // Set up a transaction
-        action = new pqxx::transaction<>(c, READ_TRANSACTION);
+        // action = new pqxx::transaction<>(c, READ_TRANSACTION);
 
-        fetcher(*action); // Perform the fetch.
+        c.perform(fetch);
+        // fetcher(*action); // Perform the fetch.
 
-        delete action;
+        // delete action;
+        update.aucs = process_results();
 
-        updater.experiment_id = e_id;
-        updater.aucs = process_results();
+        c.perform(update);
+        // action = new pqxx::transaction<>(c, WRITE_TRANSACTION);
 
-        action = new pqxx::transaction<>(c, WRITE_TRANSACTION);
+        // updater(*action);
 
-        updater(*action);
-
-        // Make sure to actually save the results.
-        action->commit();
-
-        delete action;
+        // delete action;
     }
 
 
     //
-    ~Rocker() { }
+    ~Rocker() {
+        delete known_;
+    }
 
 
     // Return the mean AUC calculated -- requires that process_results was called,
     // which happens in the constructor, so it's okay.
-    double mean_auc() { return updater.mean_auc; }
+    double mean_auc() { return update.mean_auc; }
     
     // Go through the results directory
     map<uint,auc_info> process_results() {
@@ -102,24 +103,32 @@ public:
 
         // Calculate the mean AUC
         if (divide_by > 0)
-            updater.mean_auc = temp_auc_accum / (double)(divide_by);
+            update.mean_auc = temp_auc_accum / (double)(divide_by);
         else
-            updater.mean_auc = 0;
+            update.mean_auc = 0;
 
         return rocs;
     }
 
 
     // Get genes with a specific phenotype association (phenotype id = j).
-    set<uint> fetch(uint j) const {
-        return fetcher.known_correct[j];
+    set<uint> fetch_column(uint j) const {
+        return (*known_)[j];
     }
 
 
     // For some phenotype j, determine AUC, fp, tp, fn, tn, etc.
     auc_info calculate_statistic(uint j, double threshold = 0.0) const {
-        set<uint> known_correct = fetch(j);
+        set<uint> known_correct = fetch_column(j);
         gene_score_list candidates = read_candidates(j);
+        auc_info result;
+
+        if (known_correct.size() == 0) {
+            result.auc = 0;
+            return result;
+        }
+
+
         //cerr << "Size of known_correct: " << known_correct.size() << endl;
 
         // Attempted transcription of code from Ruby into C++, after having taken
@@ -129,7 +138,7 @@ public:
         t.reserve(candidates.size()+1); t.push_back(0);
         vector<size_t> f = t;
 
-        auc_info result;
+
 
         for (gene_score_list::const_iterator i = candidates.begin(); i != candidates.end(); ++i) {
             if (known_correct.find(i->first) != known_correct.end()) {
@@ -216,15 +225,8 @@ public:
     
     
 protected:
-
-    uint matrix_id;
-    uint experiment_id;
-    uint current_j;
     pqxx::connection c;
-    pqxx::transaction<>* action;
-
-    double mean_auc_;
-
-    Fetcher fetcher;
-    Updater updater;
+    map<uint, set<uint> >* known_;
+    Fetcher fetch;
+    Updater update;
 };

data/ext/{rocker → rockerxx}/updater.h

@@ -45,12 +45,10 @@ typedef unsigned int  uint;
 
 class Updater : public transactor <> {
 public:
-    Updater() : transactor<>("Updater") {}
+    Updater(uint exp_id) : transactor<>("Updater"), experiment_id(exp_id) {}
 
-    uint experiment_id;
     map<uint,auc_info> aucs;
     double mean_auc;
-    string insert_query, update_query;
 
     void operator()(argument_type &T) {
         result R;
@@ -60,19 +58,16 @@ public:
             return;
         }
 
-        insert_query = make_insertion_sql().c_str();
-        update_query = make_update_total_auc_sql().c_str();
+        query = make_insertion_sql() + "\n" + make_update_total_auc_sql();
 
         try {
             // Insert the AUCs
-            R = T.exec(insert_query);
-            cout << "Query:" << endl;
-            cout << insert_query << endl;
-
             // Update the average AUC
-            R = T.exec(update_query);
+            R = T.exec(query);
             cout << "Query:" << endl;
-            cout << update_query << endl;
+            cout << query << endl;
+
+            T.commit();
         } catch (pqxx::sql_error e) {
             cerr << "SQL error in Updater transactor." << endl;
             cerr << "Query: " << e.query() << endl;
@@ -82,14 +77,17 @@ public:
     }
 
 protected:
+    uint experiment_id;
+    string query;
+
     string make_insertion_sql() const {
         ostringstream q;
-        q << "INSERT INTO rocs " << AUC_COLUMNS << " VALUES \n";
+        q << "INSERT INTO rocs " << AUC_COLUMNS << " VALUES ";
         list<string> insertions;
         for (map<uint,auc_info>::const_iterator i = aucs.begin(); i != aucs.end(); ++i) {
             insertions.push_back( i->second.entry(experiment_id, i->first) );
         }
-        q << join(insertions, ",\n") << ';';
+        q << join(insertions, ", ") << ';';
         return q.str();
     }
 
@@ -97,6 +95,6 @@ protected:
         ostringstream q;
         q << "UPDATE experiments SET total_auc = " << mean_auc
           << " WHERE experiments.id = " << experiment_id << ';';
-
+        return q.str();
     }
 };

data/lib/rocker.rb

@@ -1,8 +1,18 @@
 $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
-require 'rocker.so'
+# STDERR.puts("__FILE__=#{__FILE__}\ndirname=#{File.dirname(__FILE__)}")
+# $:.unshift(File.join(File.dirname(__FILE__),'..','ext','rocker'))
+# STDERR.puts($:)
 
-class Rocker
-  VERSION = '0.0.8'
+#require 'rockerxx'
+
+module Rocker
+  VERSION = '0.0.9'
+  DBARGS  = "dbname=crossval_development user=jwoods password=youwish1"
+
+  # Calculate AUCs in the current working directory
+  def self.calculate(matrix_id, experiment_id)
+    Rockerxx.new(DBARGS, matrix_id, experiment_id)
+  end
 end

data/test/test_rocker_extn.rb

@@ -1,15 +1,14 @@
 require "test/unit"
 
-$:.unshift File.dirname(__FILE__) + "/../ext/rocker"
-require "rocker.so"
-
-def database_string dbn = "crossval_development", u = "jwoods", p = "youwish1"
-  "dbname=#{dbn} user=#{u} password=#{p}"
-end
+$:.unshift File.dirname(__FILE__) + "/../ext/rockerxx"
+require "rockerxx.so"
 
 class TestRockerExtn < Test::Unit::TestCase
   def test_working
-    t = Rocker.new(database_string, 1, 167)
+    t = nil
+    #Dir.chdir("../crossval/tmp/work/matrix_1/experiment_167/results.20100318222010/") do
+      t = Rocker.calculate(1, 167)
+    #end
     x = t.mean_auc
     puts "Mean AUC was #{x}"
   end

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 8
-  version: 0.0.8
+  - 9
+  version: 0.0.9
 platform: ruby
 authors: 
 - John Woods
@@ -59,7 +59,7 @@ email:
 executables: []
 
 extensions: 
-- ext/rocker/extconf.rb
+- ext/rockerxx/extconf.rb
 extra_rdoc_files: 
 - History.txt
 - Manifest.txt
@@ -76,14 +76,14 @@ files:
 - script/generate
 - test/test_helper.rb
 - test/test_rocker.rb
-- ext/rocker/extconf.rb
-- ext/rocker/auc_info.h
-- ext/rocker/constants.h
-- ext/rocker/fetcher.h
-- ext/rocker/updater.h
-- ext/rocker/line_input_iterator.h
-- ext/rocker/rocker.h
-- ext/rocker/rocker.cpp
+- ext/rockerxx/extconf.rb
+- ext/rockerxx/auc_info.h
+- ext/rockerxx/constants.h
+- ext/rockerxx/fetcher.h
+- ext/rockerxx/updater.h
+- ext/rockerxx/line_input_iterator.h
+- ext/rockerxx/rockerxx.h
+- ext/rockerxx/rockerxx.cpp
 has_rdoc: true
 homepage: http://github.com/MarcotteLabGit/rocker
 licenses: []
@@ -94,7 +94,7 @@ rdoc_options:
 - README.rdoc
 require_paths: 
 - lib
-- ext/rocker
+- ext/rockerxx
 required_ruby_version: !ruby/object:Gem::Requirement 
   requirements: 
   - - ">="