Index: lams_build/3rdParty.userlibraries
===================================================================
diff -u -re30ac38bfa1946e7a5b01c074b54567b0fa30fd5 -r6f45380a036dde6646fa56f2bb825fa5d6650295
--- lams_build/3rdParty.userlibraries	(.../3rdParty.userlibraries)	(revision e30ac38bfa1946e7a5b01c074b54567b0fa30fd5)
+++ lams_build/3rdParty.userlibraries	(.../3rdParty.userlibraries)	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -1,6 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <eclipse-userlibraries version="2">
 <library name="3rdParty" systemlibrary="false">
+<archive path="/lams_build/lib/autopatch/tk-autopatch-1.2.0-b2-cvs.jar"/>
+<archive path="/lams_build/lib/autopatch/tk-discovery-1.0.0.jar"/>
 <archive path="/lams_build/lib/axis/axis.jar"/>
 <archive path="/lams_build/lib/axis/jaxrpc.jar"/>
 <archive path="/lams_build/lib/cglib/cglib_jboss404GA.jar"/>
Index: lams_build/build.xml
===================================================================
diff -u -r88fe2cb40e2b1e5c79ac5bae422decf0f37154de -r6f45380a036dde6646fa56f2bb825fa5d6650295
--- lams_build/build.xml	(.../build.xml)	(revision 88fe2cb40e2b1e5c79ac5bae422decf0f37154de)
+++ lams_build/build.xml	(.../build.xml)	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -118,6 +118,7 @@
 				<patternset id="lib.jars">
 					<!--  the desired jars are nominated explicitly so -->
 					<!--  we don't release a build only one by accident -->
+					<include name="autopatch/*.jar" />
 					<include name="axis/*.jar" />
 					<include name="cglib/*.jar" />
 					<include name="dom4j/*.jar" />
Index: lams_build/conf/j2ee/lams.application.xml
===================================================================
diff -u -re30ac38bfa1946e7a5b01c074b54567b0fa30fd5 -r6f45380a036dde6646fa56f2bb825fa5d6650295
--- lams_build/conf/j2ee/lams.application.xml	(.../lams.application.xml)	(revision e30ac38bfa1946e7a5b01c074b54567b0fa30fd5)
+++ lams_build/conf/j2ee/lams.application.xml	(.../lams.application.xml)	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -76,6 +76,12 @@
 
     <!--  Third Party JAR Files -->
 	<module>
+		<java>tk-autopatch-1.2.0-b2-cvs.jar</java>
+	</module>
+	<module>
+		<java>tk-discovery-1.0.0.jar</java>
+	</module>
+	<module>
 		<java>axis.jar</java>
 	</module>
 	<module>
Index: lams_build/lib/autopatch/tk-autopatch-1.2.0-b2-cvs.jar
===================================================================
diff -u
Binary files differ
Index: lams_build/lib/autopatch/tk-discovery-1.0.0.jar
===================================================================
diff -u
Binary files differ
Index: lams_central/build.xml
===================================================================
diff -u -r9481bb9c6f8c0e4d6fbed6b230a41c77feda64c6 -r6f45380a036dde6646fa56f2bb825fa5d6650295
--- lams_central/build.xml	(.../build.xml)	(revision 9481bb9c6f8c0e4d6fbed6b230a41c77feda64c6)
+++ lams_central/build.xml	(.../build.xml)	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -89,6 +89,12 @@
 						<include name="**/*.properties"/>
 				</fileset>
 		</copy>
+		<!-- Autopatch -->
+		<copy overwrite="yes" todir="${build.classes.java}/">
+					<fileset dir="${src.java.dir}/">
+							<include name="migration.properties"/>
+					</fileset>
+		</copy>
 	</target>
 
 	<target name="compile.test" depends="compile">
@@ -275,8 +281,11 @@
 	<target name="deploy-war" depends="build-war">
 		<copy file="${build.lib}/${product}.jar"
 				todir="${jboss.deploy}"/>
-		<copy file="${build.lib}/${product}.war"
-				todir="${jboss.deploy}"/>
+		<copy todir="${jboss.deploy}/${product}.war">
+			<fileset dir="${build.lib}/${product}.war">
+				<include name="**/*"/>
+			</fileset>
+		</copy>
 		<copy overwrite="yes" todir="${jboss.deploy}/lams-dictionary.jar/org/lamsfoundation/lams/central">
 			<fileset dir="${conf.language.dir}">
 				<include name="**/*.properties"/>
@@ -296,39 +305,6 @@
 	</target>
 
 	
-	<!-- Debug target: Explode tool to ear folder for debug use  -->
-	<target name="delete-exploded-folder" description="delete old tool exploded tool folder">
-		<!-- delete old war folder tree -->
-		<delete quiet="true" includeemptydirs="true">
-			<fileset dir="${jboss.deploy}/${product}.war">
-			    <include name="**"/>
-			</fileset>
-		</delete>
-		<!-- if use explode tool target when jboss is running, explode may be failed and left the the temp folder. Here try to delete the temp folder -->
-		<delete quiet="true" includeemptydirs="true">
-			<fileset dir="${jboss.deploy}/temp-${product}.war">
-			    <include name="**"/>
-			</fileset>
-		</delete>
-	</target>
-	
-	<target name="explode-war" depends="delete-exploded-folder,deploy-war" description="explode tool jar and war package to a war folder">
-		<!-- rename war file to avoid name conflict -->
-		<move tofile="${jboss.deploy}/temp-${product}.war" file="${jboss.deploy}/${product}.war"/>
-		<!-- explode the ear -->
-		<!-- Don't explode jar file, becuase classes in jar will conflict with those same classes files in war -->
-		<!--<unjar src="${jboss.deploy}/${product}.jar" dest="${jboss.deploy}/${product}.war" />-->
-		<unjar src="${jboss.deploy}/temp-${product}.war" dest="${jboss.deploy}/${product}.war" />
-		<!-- delete war and jar files -->
-		<delete>
-			<fileset dir="${jboss.deploy}">
-			    <include name="temp-${product}.war"/>
-			 <!--   <include name="${product}.jar"/> -->
-			</fileset>
-		</delete>
-	
-	</target>
-	
 	<!-- ================================= -->
 	<!--  target: synchronize-deploy          -->            
 	<!--  ================================= -->
Index: lams_central/conf/xdoclet/web-settings.xml
===================================================================
diff -u -r43dfd9f833c87c58f4dc4a61f386b6c2cf961720 -r6f45380a036dde6646fa56f2bb825fa5d6650295
--- lams_central/conf/xdoclet/web-settings.xml	(.../web-settings.xml)	(revision 43dfd9f833c87c58f4dc4a61f386b6c2cf961720)
+++ lams_central/conf/xdoclet/web-settings.xml	(.../web-settings.xml)	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -15,6 +15,7 @@
 				classpath:/org/lamsfoundation/lams/web/webApplicationContext.xml
 				classpath:/org/lamsfoundation/lams/integrationContext.xml
 				classpath:/org/lamsfoundation/lams/usermanagement/ldapContext.xml
+				classpath:/org/lamsfoundation/lams/dbupdates/autopatchContext.xml
 				<!--  Needed to communicate with the tools -->
 				classpath:/org/lamsfoundation/lams/lesson/lessonApplicationContext.xml
 				classpath:/org/lamsfoundation/lams/learning/learningApplicationContext.xml
Index: lams_central/src/java/migration.properties
===================================================================
diff -u
--- lams_central/src/java/migration.properties	(revision 0)
+++ lams_central/src/java/migration.properties	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -0,0 +1 @@

\ No newline at end of file
Index: lams_common/build.xml
===================================================================
diff -u -r6e4ed3724bd76354c2ee43c88979385c4a162a0e -r6f45380a036dde6646fa56f2bb825fa5d6650295
--- lams_common/build.xml	(.../build.xml)	(revision 6e4ed3724bd76354c2ee43c88979385c4a162a0e)
+++ lams_common/build.xml	(.../build.xml)	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -181,6 +181,8 @@
 		<copy overwrite="yes" todir="${build.classes.java}" verbose="true">
 			<fileset dir="${src.java.dir}">
 				<include name="**/*.properties"/>
+				<!-- Autopatch -->
+				<include name="**/*.sql"/>
 			</fileset>
 		</copy>
 	</target>
Index: lams_common/src/java/org/lamsfoundation/lams/dbupdates/Patch0011Alter21Integration.java
===================================================================
diff -u
--- lams_common/src/java/org/lamsfoundation/lams/dbupdates/Patch0011Alter21Integration.java	(revision 0)
+++ lams_common/src/java/org/lamsfoundation/lams/dbupdates/Patch0011Alter21Integration.java	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -0,0 +1,202 @@
+/****************************************************************
+ * Copyright (C) 2005 LAMS Foundation (http://lamsfoundation.org)
+ * =============================================================
+ * License Information: http://lamsfoundation.org/licensing/lams/2.0/
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License version 2.0
+ * as published by the Free Software Foundation.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 * USA
+ *
+ * http://www.gnu.org/licenses/gpl.txt
+ * ****************************************************************
+ */ 
+ 
+/* $Id$ */ 
+package org.lamsfoundation.lams.dbupdates; 
+
+import java.sql.Connection;
+import java.sql.Date;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.Statement;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+import com.tacitknowledge.util.migration.MigrationContext;
+import com.tacitknowledge.util.migration.MigrationException;
+import com.tacitknowledge.util.migration.MigrationTaskSupport;
+import com.tacitknowledge.util.migration.jdbc.DataSourceMigrationContext;
+ 
+/**
+ * @author jliew
+ *
+ * Update 3rd party integration courses to classes, LDEV-1284.
+ */
+public class Patch0011Alter21Integration extends MigrationTaskSupport {
+	
+	private static Logger log = Logger.getLogger(Patch0011Alter21Integration.class); 
+	
+	private static final Integer LEVEL = new Integer(11);
+	private static final String NAME = "Alter21Integration";
+	
+	// change integration orgs from classes to courses, with root org as parent.
+	private String updateToCourseType = "UPDATE lams_organisation "
+			+ "SET organisation_type_id=2, "
+			+ "parent_organisation_id=1 "
+			+ "WHERE organisation_id IN ( "
+				+ "SELECT classid " 
+				+ "FROM lams_ext_course_class_map "
+				+ ")";	
+	
+	// we want to give these newly converted courses their own workspaces;
+	private String getCoursesWithoutWorkspaces = "SELECT organisation_id, name "
+		+ "FROM lams_organisation "
+		+ "WHERE organisation_type_id=2 "
+		+ "AND workspace_id IS NULL";
+	
+	// normal folder;
+	private String insertNormalFolder = "INSERT INTO lams_workspace_folder (name, user_id, create_date_time, "
+		+ "last_modified_date_time, lams_workspace_folder_type_id) "
+		+ "VALUES (?, ?, ?, ?, ?)";
+
+	// and run sequence folder
+	private String insertRunSequencesFolder = "INSERT INTO lams_workspace_folder (name, user_id, create_date_time, "
+		+ "last_modified_date_time, lams_workspace_folder_type_id, parent_folder_id) "
+		+ "VALUES (?, ?, ?, ?, ?, ?)";
+	
+	// insert workspace, links to its folders, and link to its org 
+	private String insertWorkspace = "INSERT INTO lams_workspace (name, default_fld_id, def_run_seq_fld_id) "
+		+ "VALUES (?, ?, ?)";
+	
+	private String insertLinks = "INSERT INTO lams_wkspc_wkspc_folder (workspace_id, workspace_folder_id) "
+		+ "VALUES (?, ?)";
+	
+	private String updateOrg = "UPDATE lams_organisation "
+		+ "SET workspace_id=? "
+		+ "WHERE organisation_id=?";
+	
+	public Patch0011Alter21Integration () {
+		setLevel(LEVEL);
+		setName(NAME);
+	}
+	
+	public void migrate(MigrationContext context) throws MigrationException {
+        
+        // assuming we're using data source defined in application container
+        DataSourceMigrationContext ctx = (DataSourceMigrationContext) context;
+        
+        Connection conn = null;
+        
+        try {
+        	conn = ctx.getConnection();
+        	log.debug("Connection.autoCommit=" + conn.getAutoCommit());
+	        conn.setAutoCommit(false);
+			
+			// update classes to courses
+	        PreparedStatement query = conn.prepareStatement(updateToCourseType);
+	        int numUpdatedCourses = query.executeUpdate();
+	        log.debug("Set " + numUpdatedCourses + " integration organisations to courses.");
+	      
+	        // get courses without workspaces
+	        ArrayList<OrgDTO> orgs = new ArrayList<OrgDTO>();
+	        query = conn.prepareStatement(getCoursesWithoutWorkspaces);
+	        ResultSet results = query.executeQuery();  
+	        while (results.next()) {
+				orgs.add(new OrgDTO(results.getLong("organisation_id"), results.getString("name")));
+	        }
+	        
+	        // create workspace and folders for each org
+	        for (OrgDTO org : orgs) {
+	        	// insert normal folder
+	        	query = conn.prepareStatement(insertNormalFolder, Statement.RETURN_GENERATED_KEYS);
+	        	query.setString(1, org.getOrgName());
+	        	query.setLong(2, new Long(1));
+	        	query.setDate(3, new Date(System.currentTimeMillis()));
+	        	query.setDate(4, new Date(System.currentTimeMillis()));
+	        	query.setInt(5, new Integer(1));
+	        	int numInsert = query.executeUpdate();
+	        	results = query.getGeneratedKeys();
+	        	long wkspcFolderId = -1;
+				if (results.next())	wkspcFolderId = results.getLong(1);
+				log.debug("Inserted " + numInsert + " workspace folders, with id " + wkspcFolderId + ".");
+	
+	        	// insert run sequences folder
+	        	query = conn.prepareStatement(insertRunSequencesFolder, Statement.RETURN_GENERATED_KEYS);
+	        	query.setString(1, org.getOrgName()+" Run Sequences");
+	        	query.setLong(2, new Long(1));
+	        	query.setDate(3, new Date(System.currentTimeMillis()));
+	        	query.setDate(4, new Date(System.currentTimeMillis()));
+	        	query.setInt(5, new Integer(2));
+	        	query.setLong(6, wkspcFolderId);
+	        	numInsert = query.executeUpdate();
+	        	results = query.getGeneratedKeys();
+	        	long wkspcRunFolderId = -1;
+				if (results.next()) wkspcRunFolderId = results.getLong(1);
+				log.debug("Inserted " + numInsert + " workspace folders, with id " + wkspcRunFolderId + ".");
+	
+	        	// insert workspace
+	        	query = conn.prepareStatement(insertWorkspace, Statement.RETURN_GENERATED_KEYS);
+	        	query.setString(1, org.getOrgName());
+	        	query.setLong(2, wkspcFolderId);
+	        	query.setLong(3, wkspcRunFolderId);
+	        	numInsert = query.executeUpdate();
+	        	results = query.getGeneratedKeys();
+	        	long wkspcId = -1;
+				if (results.next()) wkspcId = results.getLong(1);
+	        	log.debug("Inserted " + numInsert + " workspaces, with id " + wkspcId + ".");
+	
+	        	// insert wkspc_wkspc_folder links
+	        	query = conn.prepareStatement(insertLinks);
+	        	query.setLong(1, wkspcId);
+	        	query.setLong(2, wkspcFolderId);
+	        	numInsert = query.executeUpdate();
+	        	log.debug("Inserted " + numInsert + " wkspc_wkspc_folder links.");
+	        	query.setLong(1, wkspcId);
+	        	query.setLong(2, wkspcRunFolderId);
+	        	numInsert = query.executeUpdate();
+	        	log.debug("Inserted " + numInsert + " wkspc_wkspc_folder links.");
+	
+	        	// update organisation with this workspace
+	        	query = conn.prepareStatement(updateOrg);
+	        	query.setLong(1, wkspcId);
+	        	query.setLong(2, org.getOrgId());
+	        	numInsert = query.executeUpdate();
+	        	log.debug("Updated " + org.getOrgName() + " with workspace_id " + wkspcId + ".");
+	        }
+	
+			ctx.commit();
+			
+	        //conn.close(); // container managed data source
+        } catch (Exception e) {
+        	ctx.rollback();
+        	throw new MigrationException("Problem running update; ");
+        }
+	}
+	
+	public class OrgDTO {
+		private Long orgId;
+		private String orgName;
+		public OrgDTO(Long orgId, String orgName) {
+			this.orgId = orgId;
+			this.orgName = orgName;
+		}
+		public Long getOrgId() {
+			return orgId;
+		}
+		public String getOrgName() {
+			return orgName;
+		}
+	}
+	
+}
+ 
\ No newline at end of file
Index: lams_common/src/java/org/lamsfoundation/lams/dbupdates/autopatchContext.xml
===================================================================
diff -u
--- lams_common/src/java/org/lamsfoundation/lams/dbupdates/autopatchContext.xml	(revision 0)
+++ lams_common/src/java/org/lamsfoundation/lams/dbupdates/autopatchContext.xml	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
+<beans>
+	<!-- Autopatch service -->
+	<bean id="autopatchService" init-method="patch" class="com.tacitknowledge.util.migration.jdbc.AutoPatchService">
+		<property name="systemName" value="lams"/> 
+		<property name="databaseType" value="mysql"/> 
+		<property name="patchPath" value="org/lamsfoundation/lams/dbupdates" /> 
+		<property name="dataSource" ref="dataSource"/> 
+	</bean>
+</beans>
\ No newline at end of file
Index: lams_common/src/java/org/lamsfoundation/lams/dbupdates/patch0013_updateFrom21.sql
===================================================================
diff -u
--- lams_common/src/java/org/lamsfoundation/lams/dbupdates/patch0013_updateFrom21.sql	(revision 0)
+++ lams_common/src/java/org/lamsfoundation/lams/dbupdates/patch0013_updateFrom21.sql	(revision 6f45380a036dde6646fa56f2bb825fa5d6650295)
@@ -0,0 +1 @@
+-- SQL statements to update from LAMS 2.1/2.1.1
\ No newline at end of file