Merge branch '2023_project_test' into master

code/common/target/maven-archiver/pom.properties

@@ -0,0 +1,3 @@
+artifactId=common
+groupId=ca.sfu.cs
+version=1.0-SNAPSHOT

code/common/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles 2.lst

@@ -0,0 +1 @@
+ca/sfu/cs/common/Configuration/Config.class

code/common/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst

@@ -0,0 +1 @@
+ca/sfu/cs/common/Configuration/Config.class

code/common/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst

@@ -0,0 +1 @@
+/Users/parmis/Desktop/FactorBase/code/common/src/main/java/ca/sfu/cs/common/Configuration/Config.java

code/componentsrunner/target/maven-archiver/pom 2.properties

@@ -0,0 +1,3 @@
+artifactId=componentsrunner
+groupId=ca.sfu.cs
+version=1.0-SNAPSHOT

code/componentsrunner/target/maven-archiver/pom.properties

@@ -0,0 +1,3 @@
+artifactId=componentsrunner
+groupId=ca.sfu.cs
+version=1.0-SNAPSHOT

code/componentsrunner/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles 2.lst

@@ -0,0 +1 @@
+ca/sfu/cs/componentsrunner/app/RunComponent.class

code/componentsrunner/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst

@@ -0,0 +1 @@
+ca/sfu/cs/componentsrunner/app/RunComponent.class

code/componentsrunner/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles 2.lst

@@ -0,0 +1 @@
+/Users/parmis/Desktop/FactorBase/code/componentsrunner/src/main/java/ca/sfu/cs/componentsrunner/app/RunComponent.java

code/componentsrunner/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst

@@ -0,0 +1 @@
+/Users/parmis/Desktop/FactorBase/code/componentsrunner/src/main/java/ca/sfu/cs/componentsrunner/app/RunComponent.java

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

@@ -97,11 +97,13 @@ public static void main(
             databaseCollation,
             countingStrategy
         );
+
         RuntimeLogger.logRunTime(logger, "Running BayesBaseH", bayesBaseHStart, System.currentTimeMillis());
 
         // Now eliminate temporary tables. Keep only the tables for the longest Rchain. Turn this off for debugging.
         long cleanupStart = System.currentTimeMillis();
-        factorBaseDatabase.cleanupDatabase();
+
+        //factorBaseDatabase.cleanupDatabase();
         RuntimeLogger.logRunTime(logger, "Cleanup Database", cleanupStart, System.currentTimeMillis());
 
         // Disconnect from the database.

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

@@ -70,6 +70,7 @@
 import java.sql.SQLException;
 import java.sql.Statement;
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Properties;
 import java.util.StringJoiner;
 import java.util.logging.Logger;
@@ -191,6 +192,30 @@ public static void prepare(String rchain, Connection con1) throws SQLException {
             " FROM Path_BayesNets as FamilyRNodes, FNodes as RNode_check " +
             " where FamilyRNodes.Rchain = '" + rchain + "' and RNode_check.Fid = FamilyRNodes.parent and RNode_check.Type = 'RNode';"
         );
+        // pnaddaf Dec 5ht 2023
+        st.execute("drop view if exists RNodes_inFamily_view;");
+        st.execute(
+            "CREATE VIEW RNodes_inFamily_view AS " +
+            "SELECT distinct child, rnid, short_rnid " + 
+            "from `Final_Path_BayesNets_view` `BN`, `RNodes`, lattice_mapping lm " +
+            "where `RNodes`.`rnid` = `BN`.`parent` AND lm.orig_rnid = BN.parent " +   
+            "union " +
+            "select distinct `BN`.`child` AS `child`, `RNodes`.`rnid` AS rnid, short_rnid " +
+            "from `Final_Path_BayesNets_view` `BN`, `RNodes`, lattice_mapping lm " +
+            "where `RNodes`.`rnid` = `BN`.`child` AND lm.orig_rnid = child " +
+            "union " +
+            "select distinct `BN`.`child` AS `child`, `RNodes_2Nodes`.`rnid` AS `Rnid`,short_rnid " +
+            "from (`Final_Path_BayesNets_view` `BN`, lattice_mapping lm " +
+            "join `RNodes_2Nodes`)  " +
+            "where `RNodes_2Nodes`.`2nid` = `BN`.`parent` and `RNodes_2Nodes`.`rnid`=lm.orig_rnid " + 
+            "union " + 
+            "select distinct `BN`.`child` AS `child`,  `RNodes_2Nodes`.`rnid` AS `Rnid`, short_rnid " +  
+            "from (`Final_Path_BayesNets_view` `BN`, lattice_mapping lm " + 
+            "join `RNodes_2Nodes`) " + 
+            "where `RNodes_2Nodes`.`2nid` = `BN`.`child` and `RNodes_2Nodes`.`rnid` = lm.orig_rnid ; " 
+        );
+
+
 
         st.execute("drop table if exists 2Nodes_inFamily;");
         st.execute(
@@ -285,24 +310,83 @@ public static void nopar(String rchain, Connection con1) throws SQLException {
             logger.fine("noparent node: " + rst.getString(1));
             noparent_tables.add(rst.getString(1));
         }
-        // zqian Nov 13, computing sum(mult) from biggest CT table
-        // and close the connections
-        java.sql.Statement st2 = con1.createStatement();
-        String sql2 =
-            "SELECT SUM(MULT) " +
-            "FROM " + databaseName2 + ".`" + bigTable + "`;"; // Only need to do this query once, Nov 12 zqian.
-        logger.fine(sql2 + "\n");
-        ResultSet deno = st2.executeQuery(sql2);
-        deno.absolute(1);
-        double mydeno = deno.getDouble(1);
-        logger.fine("SUM(mult) in bigCTTable : "+mydeno + "\n");
-        for(int i = 0; i < noparent_tables.size(); i++) {
+        // pnaddaf Dec 5th 2023        
+        for (int i = 0; i < noparent_tables.size(); i++) {
+            ResultSet rst_short_rnids = st.executeQuery("SELECT short_rnid FROM RNodes_inFamily_view where child = '" + noparent_tables.get(i) + "' ORDER BY short_rnid;");
+            logger.fine("*************************************************");
+            logger.fine("SELECT short_rnid FROM RNodes_inFamily_view where child = '" + noparent_tables.get(i) + "';");
+            // Initialize a StringBuilder to concatenate the elements
+            StringBuilder concatenated_rnids = new StringBuilder();
+            boolean isFirst = true;
+            if (rst_short_rnids.next()) {        
+                do{
+                    // Add a comma if it's not the first value
+                    if (!isFirst) {
+                        concatenated_rnids.append(",");
+                    } else {
+                        isFirst = false;
+                    }
+                    // Retrieve data from the result set
+                    String short_rnid = rst_short_rnids.getString("short_rnid");
+
+                    // Append the value to the StringBuilder
+                    concatenated_rnids.append(short_rnid);
+
+                } while(rst_short_rnids.next());
+
+                bigTable = concatenated_rnids.toString() + "_CT";
+                logger.fine("tableName for " +  noparent_tables.get(i) + " is: " + bigTable);
+
+
+            } else {
+                // ResultSet is empty
+
+                logger.fine("ResultSet is empty");
+                ResultSet rst_pvid = st.executeQuery("SELECT distinct pvid FROM Pvars_Family WHERE child = '" + noparent_tables.get(i) + "' ;");
+                if (rst_pvid.next()) {
+                    do {
+                            // Add a comma if it's not the first value
+                        if (!isFirst) {
+                            concatenated_rnids.append(",");
+                        } else {
+                            isFirst = false;
+                        }
+                        // Retrieve data from the result set
+                        String short_rnid = rst_pvid.getString("pvid");
+
+                        // Append the value to the concatenated_rnids
+                        concatenated_rnids.append(short_rnid);
+                    } while (rst_pvid.next());
+
+                }
+                bigTable = concatenated_rnids.toString() + "_counts";
+                logger.fine("tableName is: " + bigTable);
+
+                // Close the ResultSet when you're done with it
+                rst_pvid.close();
+            }
+
+            // Close the ResultSet when you're done with it
+            rst_short_rnids.close();
+
+
+            // zqian Nov 13, computing sum(mult) from biggest CT table
+            // and close the connections
+            java.sql.Statement st2 = con1.createStatement();
+            String sql2 =
+                "SELECT SUM(MULT) " +
+                "FROM " + databaseName2 + ".`" + bigTable + "`;"; 
+            logger.fine(sql2 + "\n");
+            ResultSet deno = st2.executeQuery(sql2);
+            deno.absolute(1);
+            double mydeno = deno.getDouble(1);
+            logger.fine("SUM(mult) in bigTable : "+mydeno + "\n");
             nopar_update(rchain, bigTable, noparent_tables.get(i), con1, mydeno);
-        }
+            st2.close();
+        } 
+    st.close();
+}
 
-        st2.close();
-        st.close();
-    }
 
     /**
      * Similar simpler computation for nodes without parents.
@@ -322,6 +406,10 @@ public static void nopar_update(String rchain, String bigTable, String nodeName,
                 "local_mult DECIMAL(65)" +
             ");"
         );
+        logger.fine("tableName : "+ tableName + "\n");
+        logger.fine("nodeName : "+ nodeName + "\n");
+        logger.fine("databaseName2 : "+ databaseName2 + "\n");
+        logger.fine("bigTable : "+ bigTable + "\n");
         st.execute(
             "INSERT INTO `" + tableName + "` (`" + nodeName + "`) " +
             "SELECT DISTINCT `" + nodeName + "` " +
@@ -370,13 +458,13 @@ public static void nopar_update(String rchain, String bigTable, String nodeName,
             while(rs.next()) {
                 local = Long.parseLong (rs.getString("Tuples"));
                 logger.fine("local is " + local);
-                mynume = mynume / local;
+                // mynume = mynume / local;   set local_mult = mult OS Dec 5, 2023
 //                logger.fine("set local_mult = mult, May 21, 2014 zqian ");
                 // set local_mult = mult, May 21, 2014 zqian
             }
             if (!rs.first()) {
                 logger.fine("local is 1, ******");
-                mynume = mynume / local;
+               // mynume = mynume / local;   set local_mult = mult OS Dec 5, 2023
             }
             // updating the local_mult = mult / local , Dec 3rd
             String sql4 =
@@ -460,10 +548,71 @@ public static void haspar(String rchain, Connection con1) throws SQLException {
             logger.fine("hasparent node: " + rst.getString(1));
             hasparent_tables.add(rst.getString(1));
         }
-        for(int i = 0; i < hasparent_tables.size(); i++) {
+
+
+        // pnaddaf Dec 8th 2023        
+        for (int i = 0; i < hasparent_tables.size(); i++) {
+            ResultSet rst_short_rnids = st.executeQuery("SELECT short_rnid FROM RNodes_inFamily_view where child = '" + hasparent_tables.get(i) + "' ORDER BY short_rnid ;");
+            logger.fine("*************************************************");
+            logger.fine("SELECT short_rnid FROM RNodes_inFamily_view where child = '" + hasparent_tables.get(i) + "';");
+            // Initialize a StringBuilder to concatenate the elements
+            StringBuilder concatenated_rnids = new StringBuilder();
+            boolean isFirst = true;
+            if (rst_short_rnids.next()) {        
+                do{
+                    // Add a comma if it's not the first value
+                    if (!isFirst) {
+                        concatenated_rnids.append(",");
+                    } else {
+                        isFirst = false;
+                    }
+                    // Retrieve data from the result set
+                    String short_rnid = rst_short_rnids.getString("short_rnid");
+
+                    // Append the value to the StringBuilder
+                    concatenated_rnids.append(short_rnid);
+
+                } while(rst_short_rnids.next());
+
+                bigTable = concatenated_rnids.toString() + "_CT";
+                logger.fine("tableName for " +  hasparent_tables.get(i) + " is: " + bigTable);
+
+
+            } else {
+                // ResultSet is empty
+
+                logger.fine("ResultSet is empty");
+                ResultSet rst_pvid = st.executeQuery("SELECT distinct pvid FROM Pvars_Family WHERE child = '" + hasparent_tables.get(i) + "';");
+                if (rst_pvid.next()) {
+                    do {
+                            // Add a comma if it's not the first value
+                        if (!isFirst) {
+                            concatenated_rnids.append(",");
+                        } else {
+                            isFirst = false;
+                        }
+                        // Retrieve data from the result set
+                        String short_rnid = rst_pvid.getString("pvid");
+
+                        // Append the value to the concatenated_rnids
+                        concatenated_rnids.append(short_rnid);
+                    } while (rst_pvid.next());
+
+                }
+                bigTable = concatenated_rnids.toString() + "_counts";
+                logger.fine("tableName is: " + bigTable);
+
+                // Close the ResultSet when you're done with it
+                rst_pvid.close();
+            }
+
+            // Close the ResultSet when you're done with it
+            rst_short_rnids.close();
             haspar_update(rchain, bigTable, hasparent_tables.get(i), con1, databaseName2);
+
+
         }
-        st.close();
+        st.close(); 
     }
 
     /**
@@ -573,18 +722,20 @@ public static void haspar_update(String rchain, String bigTable, String nodeName
         while(rs.next()) {
             local = Long.parseLong (rs.getString("Tuples"));
             logger.fine("local is " + local);
-            String sql = "UPDATE " + escapedTableName + " SET local_mult = MULT / " + local + ";";
+            // String sql = "UPDATE " + escapedTableName + " SET local_mult = MULT / " + local + ";"; OS Dec 5 make local_mult = mult
+            String sql = "UPDATE " + escapedTableName + " SET local_mult = MULT;"; 
 //            String sql = "update " + table_name + " set local_mult = mult;";
             logger.fine(sql);
             // set local_mult = mult, May 21, 2014 zqian
             st1.execute(sql);
         }
         if (!rs.first()) {
             logger.fine("local is 1, ******" );
-            String sql = "UPDATE " + escapedTableName + " SET local_mult = MULT / " + local + ";";
+            String sql = "UPDATE " + escapedTableName + " SET local_mult = MULT; ";
+          //  String sql = "UPDATE " + escapedTableName + " SET local_mult = MULT / " + local + ";"; OS Dec 5 make local_mult = mult
             st1.execute(sql);
         }
-
+        logger.fine("UPDATE " + escapedTableName + " SET likelihood = LOG(CP) * local_mult;");
         st.execute("UPDATE " + escapedTableName + " SET likelihood = LOG(CP) * local_mult;");
         st.execute("drop table if exists temp;");
 

code/factorbase/src/main/java/edu/cmu/tetrad/data/Knowledge.java

@@ -698,12 +698,13 @@ public final void setEdgeForbidden(String var1, String var2,
                 throw new IllegalStateException("The edge " + var1 + "-->" + var2 +
                         " is required by a knowledge group. Please remove that requirement first.");
             }
-
+        /*
             if (edgeRequired(var1, var2)) {
                 throw new IllegalStateException("The edge " + var1 + "-->" +
                         var2 +
                         " is already required. Please first remove that requirement.");
             }
+        */
 
             explicitlyForbiddenEdges.add(new KnowledgeEdge(var1, var2));
             this.forbiddenEdges = null;

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

@@ -1,5 +1,6 @@
 -- Initialize the databases required by FactorBase.
-SET collation_server = @dbcollation@;
+
+SET collation_server = 'utf8_general_ci';
 
 DROP SCHEMA IF EXISTS @database@_setup;
 CREATE SCHEMA @database@_setup;

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

@@ -2,29 +2,29 @@
 SET storage_engine=INNODB;
 
 CREATE TABLE lattice_membership (
-    name VARCHAR(398),
-    member VARCHAR(398),
+    name VARCHAR(300),
+    member VARCHAR(300),
     PRIMARY KEY(name, member)
 );
 
 
 CREATE TABLE lattice_rel (
-    parent VARCHAR(398),
-    child VARCHAR(398),
-    removed VARCHAR(199),
+    parent VARCHAR(300),
+    child VARCHAR(300),
+    removed VARCHAR(300),
     PRIMARY KEY(parent, child)
 );
 
 
 CREATE TABLE lattice_set (
-    name VARCHAR(398),
+    name VARCHAR(300),
     length INT(11),
     PRIMARY KEY(name, length)
 );
 
 
 CREATE TABLE lattice_mapping (
-    orig_rnid VARCHAR(398),
+    orig_rnid VARCHAR(300),
     short_rnid VARCHAR(20),
     PRIMARY KEY(orig_rnid, short_rnid)
 );

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

@@ -2,22 +2,22 @@
 SET storage_engine=MEMORY;
 
 CREATE TABLE lattice_membership (
-    name VARCHAR(398),
-    member VARCHAR(398),
+    name VARCHAR(300),
+    member VARCHAR(300),
     PRIMARY KEY(name, member)
 );
 
 
 CREATE TABLE lattice_rel (
-    parent VARCHAR(398),
-    child VARCHAR(398),
-    removed VARCHAR(199),
+    parent VARCHAR(300),
+    child VARCHAR(300),
+    removed VARCHAR(300),
     PRIMARY KEY(parent, child)
 );
 
 
 CREATE TABLE lattice_set (
-    name VARCHAR(398),
+    name VARCHAR(300),
     length INT(11),
     PRIMARY KEY(name, length)
 );