Setting the database collation via the configuration file.

- The executable comments found in the SQL files were being removed due to the
  logic in the prepareFile() method.
- Updated areas in the codebase that set the collation to set the collation via
  a value drawn from the configuration file passed to FactorBase.
- Updated the files in the expected-output directory since these appear to be
  the deterministic results when the collation is consistent for all the
  databases.

code/factorbase/src/main/java/ca/sfu/cs/factorbase/app/RunBB.java

@@ -52,12 +52,14 @@ public static void main(
         RuntimeLogger.logRunTime(logger, "Logger + Config Initialization", start, configEnd);
 
         long databaseStart = System.currentTimeMillis();
+        String databaseCollation = config.getProperty("dbcollation");
         FactorBaseDataBase factorBaseDatabase = new MySQLFactorBaseDataBase(
             new FactorBaseDataBaseInfo(config),
             config.getProperty("dbaddress"),
             config.getProperty("dbname"),
             config.getProperty("dbusername"),
             config.getProperty("dbpassword"),
+            databaseCollation,
             countingStrategy
         );
         RuntimeLogger.logRunTime(logger, "Creating Database Connection", databaseStart, System.currentTimeMillis());
@@ -92,6 +94,7 @@ public static void main(
         BayesBaseH.runBBH(
             factorBaseDatabase,
             globalLattice,
+            databaseCollation,
             countingStrategy
         );
         RuntimeLogger.logRunTime(logger, "Running BayesBaseH", bayesBaseHStart, System.currentTimeMillis());

code/factorbase/src/main/java/ca/sfu/cs/factorbase/database/MySQLFactorBaseDataBase.java

@@ -46,6 +46,7 @@ public class MySQLFactorBaseDataBase implements FactorBaseDataBase {
     private Connection dbConnection;
     private FactorBaseDataBaseInfo dbInfo;
     private Map<String, DataExtractor> dataExtractors;
+    private String dbCollation;
     private CountingStrategy countingStrategy;
 
 
@@ -66,10 +67,12 @@ public MySQLFactorBaseDataBase(
         String dbname,
         String username,
         String password,
+        String dbCollation,
         CountingStrategy countingStrategy
     ) throws DataBaseException {
         this.dbInfo = dbInfo;
         this.baseDatabaseName = dbname;
+        this.dbCollation = dbCollation;
         this.countingStrategy = countingStrategy;
         String baseConnectionString = MessageFormat.format(CONNECTION_STRING, dbaddress, dbname);
         Properties connectionProperties = getConnectionStringProperties(username, password);
@@ -89,20 +92,23 @@ public void setupDatabase() throws DataBaseException {
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "initialize_databases.sql",
-                this.baseDatabaseName
+                this.baseDatabaseName,
+                this.dbCollation
             );
 
             // Switch to start using the setup database.
             this.dbConnection.setCatalog(this.dbInfo.getSetupDatabaseName());
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "metadata.sql",
-                this.baseDatabaseName
+                this.baseDatabaseName,
+                this.dbCollation
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "metadata_storedprocedures.sql",
                 this.baseDatabaseName,
+                this.dbCollation,
                 "//"
             );
             MySQLScriptRunner.callSP(this.dbConnection, "find_values");
@@ -111,7 +117,8 @@ public void setupDatabase() throws DataBaseException {
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "latticegenerator_initialize.sql",
-                this.baseDatabaseName
+                this.baseDatabaseName,
+                this.dbCollation
             );
 
             // Switch to start using the BN database.
@@ -120,50 +127,59 @@ public void setupDatabase() throws DataBaseException {
             RuntimeLogger.setupLoggingTable(
                 this.dbConnection,
                 this.baseDatabaseName,
-                this.dbInfo.getBNDatabaseName()
+                this.dbInfo.getBNDatabaseName(),
+                this.dbCollation
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "latticegenerator_initialize_local.sql",
-                this.baseDatabaseName
+                this.baseDatabaseName,
+                this.dbCollation
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "latticegenerator_populate.sql",
                 this.baseDatabaseName,
+                this.dbCollation,
                 "//"
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "transfer_initialize.sql",
-                this.baseDatabaseName
+                this.baseDatabaseName,
+                this.dbCollation
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "transfer_cascade.sql",
                 this.baseDatabaseName,
+                this.dbCollation,
                 "//"
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "modelmanager_initialize.sql",
-                this.baseDatabaseName
+                this.baseDatabaseName,
+                this.dbCollation
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "metaqueries_initialize.sql",
-                this.baseDatabaseName
+                this.baseDatabaseName,
+                this.dbCollation
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "metaqueries_populate.sql",
                 this.baseDatabaseName,
+                this.dbCollation,
                 "//"
             );
             MySQLScriptRunner.runScript(
                 this.dbConnection,
                 Config.SCRIPTS_DIRECTORY + "metaqueries_RChain.sql",
                 this.baseDatabaseName,
+                this.dbCollation,
                 "//"
             );
         } catch (SQLException | IOException e) {

code/factorbase/src/main/java/ca/sfu/cs/factorbase/learning/BayesBaseH.java

@@ -108,6 +108,7 @@ public class BayesBaseH {
     public static void runBBH(
         FactorBaseDataBase database,
         RelationshipLattice globalLattice,
+        String databaseCollation,
         CountingStrategy countingStrategy
     ) throws SQLException, IOException, DataBaseException, DataExtractionException, ParsingException, ScoringException {
         initProgram(FirstRunning);
@@ -124,6 +125,7 @@ public static void runBBH(
         StructureLearning(
             database,
             con2,
+            databaseCollation,
             countingStrategy,
             globalLattice
         );
@@ -206,6 +208,7 @@ public static void runBBH(
     private static void StructureLearning(
         FactorBaseDataBase database,
         Connection conn,
+        String databaseCollation,
         CountingStrategy countingStrategy,
         RelationshipLattice lattice
     ) throws SQLException, IOException, DataBaseException, DataExtractionException, ParsingException, ScoringException {
@@ -221,7 +224,8 @@ private static void StructureLearning(
         MySQLScriptRunner.runScript(
             conn,
             Config.SCRIPTS_DIRECTORY + "modelmanager_populate.sql",
-            databaseName
+            databaseName,
+            databaseCollation
         );
 
         // Handle rnodes in a bottom-up way following the lattice.

code/factorbase/src/main/java/ca/sfu/cs/factorbase/learning/CountsManager.java

@@ -69,6 +69,7 @@ public class CountsManager {
     private static boolean generatePDPInfo;
     private static String linkCorrelation;
     private static long dbTemporaryTableSize;
+    private static String dbCollation;
     /*
      * cont is Continuous
      * ToDo: Refactor
@@ -93,7 +94,7 @@ public static void buildCT(
         RuntimeLogger.addLogEntry(dbConnection);
         try (Statement statement = dbConnection.createStatement()) {
             statement.execute("DROP SCHEMA IF EXISTS " + dbInfo.getCTDatabaseName() + ";");
-            statement.execute("CREATE SCHEMA " + dbInfo.getCTDatabaseName() + " /*M!100316 COLLATE utf8_general_ci*/;");
+            statement.execute("CREATE SCHEMA " + dbInfo.getCTDatabaseName() + " COLLATE " + dbCollation + ";");
         }
 
         // Propagate metadata based on the FunctorSet.
@@ -492,6 +493,7 @@ private static void setVarsFromConfig() {
         dbPassword = conf.getProperty("dbpassword");
         dbaddress = conf.getProperty("dbaddress");
         dbTemporaryTableSize = Math.round(1024 * 1024 * 1024 * Double.valueOf(conf.getProperty("dbtemporarytablesize")));
+        dbCollation = conf.getProperty("dbcollation");
         linkCorrelation = conf.getProperty("LinkCorrelations");
         cont = conf.getProperty("Continuous");
         String loggingLevel = conf.getProperty("LoggingLevel");

code/factorbase/src/main/java/ca/sfu/cs/factorbase/util/MySQLScriptRunner.java

@@ -32,9 +32,14 @@ private MySQLScriptRunner() {
      *
      * @param fileName - the file to create a copy of with the variables filled in.
      * @param databaseName - the name of the database to replace instances of "@database@" with.
+     * @param databaseCollation - the collation to use for the tables created.
      * @throws IOException if there is an issue reading from the script.
      */
-    private static String prepareFile(String fileName, String databaseName) throws IOException {
+    private static String prepareFile(
+        String fileName,
+        String databaseName,
+        String databaseCollation
+    ) throws IOException {
         InputStream inputStream = MySQLScriptRunner.class.getClassLoader().getResourceAsStream(fileName);
         if (inputStream == null) {
             throw new FileNotFoundException("Unable to read the file: " + fileName);
@@ -59,6 +64,7 @@ private static String prepareFile(String fileName, String databaseName) throws I
         String finalOutput = "";
         while (line != null) {
             line = line.replace("@database@", databaseName);
+            line = line.replace("@dbcollation@", databaseCollation);
             finalOutput += line + System.getProperty("line.separator");
             line = input.readLine();
         }
@@ -94,11 +100,17 @@ public static void callSP(Connection dbConnection, String spName) throws SQLExce
      * @param dbConnection - connection to the database to execute the script on.
      * @param scriptFileName - the path to the MySQL script to execute.
      * @param databaseName - the name of the database to replace instances of "@database@" with.
+     * @param databaseCollation - the collation to use for the tables created.
      * @throws SQLException if there is an issue executing the command(s).
      * @throws IOException if there is an issue reading from the script.
      */
-    public static void runScript(Connection dbConnection, String scriptFileName, String databaseName) throws SQLException, IOException {
-        runScript(dbConnection, scriptFileName, databaseName, ";");
+    public static void runScript(
+        Connection dbConnection,
+        String scriptFileName,
+        String databaseName,
+        String databaseCollation
+    ) throws SQLException, IOException {
+        runScript(dbConnection, scriptFileName, databaseName, databaseCollation, ";");
     }
 
 
@@ -110,12 +122,19 @@ public static void runScript(Connection dbConnection, String scriptFileName, Str
      * @param dbConnection - connection to the database to execute the script on.
      * @param scriptFileName - the path to the MySQL script to execute.
      * @param databaseName - the name of the database to replace instances of "@database@" with.
+     * @param databaseCollation - the collation to use for the tables created.
      * @param delimiter - the delimiter to use when reading the commands from the given script.
      * @throws SQLException if there is an issue executing the command(s).
      * @throws IOException if there is an issue reading from the script.
      */
-    public static void runScript(Connection dbConnection, String scriptFileName, String databaseName, String delimiter) throws SQLException, IOException {
-        String newScriptFileName = prepareFile(scriptFileName, databaseName);
+    public static void runScript(
+        Connection dbConnection,
+        String scriptFileName,
+        String databaseName,
+        String databaseCollation,
+        String delimiter
+    ) throws SQLException, IOException {
+        String newScriptFileName = prepareFile(scriptFileName, databaseName, databaseCollation);
 
         ScriptRunner runner = new ScriptRunner(dbConnection);
         try (

code/factorbase/src/main/java/ca/sfu/cs/factorbase/util/RuntimeLogger.java

@@ -94,13 +94,15 @@ public static void logExecutedQuery(Logger logger, String query) {
     public static void setupLoggingTable(
         Connection dbConnection,
         String baseDatabaseName,
-        String loggingTableDatabaseName
+        String loggingTableDatabaseName,
+        String databaseCollation
     ) throws SQLException, IOException {
         dbName = loggingTableDatabaseName;
         MySQLScriptRunner.runScript(
             dbConnection,
             Config.SCRIPTS_DIRECTORY + "logging.sql",
-            baseDatabaseName
+            baseDatabaseName,
+            databaseCollation
         );
     }
 

code/factorbase/src/main/resources/scripts/initialize_databases.sql

@@ -1,7 +1,5 @@
 -- Initialize the databases required by FactorBase.
-/*M!100316 SET collation_server = 'utf8_general_ci';*/
-
-SET collation_server = 'utf8_general_ci';
+SET collation_server = @dbcollation@;
 
 DROP SCHEMA IF EXISTS @database@_setup;
 CREATE SCHEMA @database@_setup;

config.cfg

@@ -4,6 +4,7 @@ dbname = name_of_database
 dbusername = database_username
 dbpassword = database_password
 dbtemporarytablesize = 4
+dbcollation = utf8_general_ci
 
 # FactorBase Configurations
 AutomaticSetup = 1

travis-resources/config.cfg

@@ -4,6 +4,7 @@ dbname = unielwin
 dbusername = root
 dbpassword = 123456
 dbtemporarytablesize = 4
+dbcollation = utf8_general_ci
 
 # FactorBase Configurations
 AutomaticSetup = 1

travis-resources/expected-output/Bif_unielwin.xml

@@ -95,7 +95,7 @@ xsi:schemaLocation="http://www.cs.ubc.ca/labs/lci/fopi/ve/XMLBIFv0_3 http://www.
 	<FOR>capability(prof0,student0)</FOR>
 	<GIVEN>RA(prof0,student0)</GIVEN>
 	<GIVEN>salary(prof0,student0)</GIVEN>
-	<TABLE> 0.166667 0.166667 0.166667 0.166667 0.166665 0.166667 0.166667 0.166667 0.166667 0.166667 0.166665 0.166667 0.166667 0.166667 0.166667 0.166667 0.166665 0.166667 0.000491 0.000491 0.000491 0.000491 0.000491 0.997545 0.008621 0.008621 0.181034 0.439655 0.353448 0.008621 0.375 0.375 0.196429 0.017857 0.017857 0.017857 0.322917 0.21875 0.427082 0.010417 0.010417 0.010417 0.166667 0.166667 0.166667 0.166667 0.166665 0.166667</TABLE>
+	<TABLE> 0.166665 0.166667 0.166667 0.166667 0.166667 0.166667 0.166665 0.166667 0.166667 0.166667 0.166667 0.166667 0.166665 0.166667 0.166667 0.166667 0.166667 0.166667 0.000491 0.000491 0.000491 0.000491 0.000491 0.997545 0.008621 0.008621 0.181034 0.439655 0.353448 0.008621 0.375 0.375 0.196429 0.017857 0.017857 0.017857 0.322917 0.21875 0.427082 0.010417 0.010417 0.010417 0.166665 0.166667 0.166667 0.166667 0.166667 0.166667</TABLE>
 </DEFINITION>
 <DEFINITION>
 	<FOR>intelligence(student0)</FOR>

travis-resources/expected-output/mysql-extraction.txt

@@ -951,12 +951,12 @@ Table: capability(prof0,student0)_CP_pairs
 0	N/A	T	N/A
 MULT	capability(prof0,student0)	RA(prof0,student0)	salary(prof0,student0)
 Table: capability(prof0,student0)_CP_smoothed
-1	1	F	high	6	NULL	0.166667	NULL	NULL
-1	1	F	low	6	NULL	0.166667	NULL	NULL
-1	1	F	med	6	NULL	0.166667	NULL	NULL
+1	1	F	high	6	NULL	0.166665	NULL	NULL
+1	1	F	low	6	NULL	0.166665	NULL	NULL
+1	1	F	med	6	NULL	0.166665	NULL	NULL
 1	1	F	N/A	2036	NULL	0.000491	NULL	NULL
 1	1	T	high	116	NULL	0.008621	NULL	NULL
-1	1	T	N/A	6	NULL	0.166667	NULL	NULL
+1	1	T	N/A	6	NULL	0.166665	NULL	NULL
 1	2	F	high	6	NULL	0.166667	NULL	NULL
 1	2	F	low	6	NULL	0.166667	NULL	NULL
 1	2	F	med	6	NULL	0.166667	NULL	NULL
@@ -975,13 +975,13 @@ Table: capability(prof0,student0)_CP_smoothed
 1	4	T	low	56	NULL	0.017857	NULL	NULL
 1	4	T	med	96	NULL	0.010417	NULL	NULL
 1	4	T	N/A	6	NULL	0.166667	NULL	NULL
-1	5	F	high	6	NULL	0.166665	NULL	NULL
-1	5	F	low	6	NULL	0.166665	NULL	NULL
-1	5	F	med	6	NULL	0.166665	NULL	NULL
+1	5	F	high	6	NULL	0.166667	NULL	NULL
+1	5	F	low	6	NULL	0.166667	NULL	NULL
+1	5	F	med	6	NULL	0.166667	NULL	NULL
 1	5	F	N/A	2036	NULL	0.000491	NULL	NULL
 1	5	T	low	56	NULL	0.017857	NULL	NULL
 1	5	T	med	96	NULL	0.010417	NULL	NULL
-1	5	T	N/A	6	NULL	0.166665	NULL	NULL
+1	5	T	N/A	6	NULL	0.166667	NULL	NULL
 1	N/A	F	high	6	NULL	0.166667	NULL	NULL
 1	N/A	F	low	6	NULL	0.166667	NULL	NULL
 1	N/A	F	med	6	NULL	0.166667	NULL	NULL