Merge pull request #6 from dgunda1/master

1.7.12a fix

README.md

@@ -2,12 +2,16 @@
 [Georgia Clinical and Translational Science Alliance (Georgia CTSA)](http://www.georgiactsa.org), [Emory University](http://www.emory.edu), Atlanta, GA
 
 ## What does it do?
-This is a stock i2b2 1.7.09c project management (PM) cell, patched with support for delegating authentication to a server that implements [version 2 of the CAS protocol](https://apereo.github.io/cas/5.0.x/protocol/CAS-Protocol-V2-Specification.html) for single sign-on.
+This is a stock i2b2 1.7.12a project management (PM) cell, patched with support for delegating authentication to a server that implements [version 2 of the CAS protocol](https://apereo.github.io/cas/5.0.x/protocol/CAS-Protocol-V2-Specification.html) for single sign-on.
+
 
 The code is adapted from similar code for an older version of i2b2 by Dan Connolly found at https://bitbucket.org/DanC/i2b2-pm-cas.
 
 ## Version history
 
+### Version 1.3
+Updated i2b2 version to 1.7.12a.
+
 ### Version 1.2
 Updated i2b2 version to 1.7.09c.
 
@@ -17,6 +21,7 @@ Updated i2b2 version to 1.7.08b.
 ### Version 1.0
 Initial release using i2b2 version 1.7.05.
 
+
 ## CAS implementations supported
 We expect any full implementation of version 2 of the CAS protocol to work. In particular, the implementation must support proxying. The following implementations of CAS are known to work:
 * [Eureka! Clinical CAS](https://github.com/eurekaclinical/cas), which is a patched version of [JASIG CAS version 3.5.2](https://wiki.jasig.org/display/CASUM/Home)

build.properties

@@ -1,8 +1,9 @@
 #Ant build property file
 
 ## JBOSS HOME
-jboss.home=/opt/wildfly-10.0.0.Final
+jboss.home=/opt/wildfly-17.0.1.Final
 axis2.war.name=i2b2.war
 
 report=test-reports
 testfiledir=testfiles
+testhost=http://127.0.0.1:9090/i2b2/services

build.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-	$Id: build.xml,v 1.3 2010/02/03 18:19:26 mem61 Exp $
+	$Id: build.xml,v 1.3 2018/01/18 18:19:26 mem61 Exp $
 -->
 <project basedir="." default="all" name="Project Management Cell">
 
@@ -23,6 +23,8 @@
 			<pathelement location="lib/jcifs-1.3.3.jar" />
 			<pathelement location="lib/servlet-api.jar" />
 			<pathelement location="../${i2b2CommonProject}/dist/i2b2Common-core.jar" />
+			<pathelement location="../${i2b2CommonProject}/lib/smbj-0.9.1.jar" />
+
 		</path>
 
 		<taskdef name="xjc" classname="com.sun.tools.xjc.XJCTask">
@@ -43,22 +45,38 @@
 	<!-- 								COMMON JAXB GENERATION 				 -->
 	<!-- =================================================================== -->
 	<target name="jaxb_gen" depends="init" description="Generate JAXB classes for i2b2 and Vocab Data messages">
-				<xjc destdir="${gensrc}" removeOldOutput="no">
+<!--		<exec executable="xjc">
+					        <arg value="-d"/>
+					        <arg value="${gensrc}"/>
+					        <arg value="../${i2b2xmlproject}/xsd/cell/pm_1.1/PM_USER.xsd"/>
+					        <arg value="../${i2b2xmlproject}/xsd/hive/msg_1.1/i2b2_response.xsd"/>
+				        <arg value="../${i2b2xmlproject}/xsd/cell/pm_1.1/i2b2_version_msg.xsd"/>
+				        <arg value="-b"/>
+				        <arg value="./etc/xsd_1.1/i2b2_pm_bindings.xjb"/>
+				        <arg value="-b"/>
+				        <arg value="./etc/xsd_1.1/i2b2_response_message_bindings.xjb"/>
+				        <arg value="-b"/>
+				        <arg value="./etc/xsd_1.1/i2b2_version_bindings.xjb"/>
+
+			</exec>
+-->							<xjc destdir="${gensrc}" removeOldOutput="no">
+
 					<schema dir="../${i2b2xmlproject}/xsd/cell/pm_1.1" includes="PM_USER.xsd" />
 					<schema dir="../${i2b2xmlproject}/xsd/hive/msg_1.1" includes="i2b2_response.xsd" />
 					<schema dir="../${i2b2xmlproject}/xsd/cell/pm_1.1" includes="i2b2_version_msg.xsd" />
 					<binding dir="." includes="etc/xsd_1.1/i2b2_pm_bindings.xjb" />
 					<binding dir="." includes="etc/xsd_1.1/i2b2_response_message_bindings.xjb" />
 					<binding dir="." includes="etc/xsd_1.1/i2b2_version_bindings.xjb" />
 				</xjc>
+
 		</target>
 
 	<!-- =================================================================== -->
 	<!-- 								COMPILE 							 -->
 	<!-- =================================================================== -->
 	<target name="compile" depends="init,jaxb_gen" description="Compile files without cleaning">
 		<mkdir dir="${classes}" />
-		<javac destdir="${classes}" optimize="${javac.opt}" debug="${javac.debug}">
+		<javac destdir="${classes}" optimize="${javac.opt}" debug="true">
 			<src path="${src}" />
 			<src path="${gensrc}" />
 			<src path="test" /> 
@@ -150,6 +168,7 @@
 			<formatter type="xml" />
 			<jvmarg value="-Dtestfiledir=${testfiledir}" />
 			<jvmarg value="-Djava.endorsed.dirs=endorsed_lib" />
+			<jvmarg value="-Dtesthost=${testhost}" />
 			<!--<test name="AllTests" todir="${report.dir}"/>-->
 			<batchtest fork="yes" todir="${reports.dir}">
 				<fileset dir="test">

etc/axis2/services.xml

@@ -1,4 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
+<!--
+  Copyright (c) 2006-2018 Massachusetts General Hospital 
+  All rights reserved. This program and the accompanying materials 
+  are made available under the terms of the Mozilla Public License,
+  v. 2.0. If a copy of the MPL was not distributed with this file, You can
+  obtain one at http://mozilla.org/MPL/2.0/. I2b2 is also distributed under
+  the terms of the Healthcare Disclaimer.
+-->
 <service name="PMService" scope="request">
     <description>
         Project Management Processing Service
@@ -10,4 +18,4 @@
         <messageReceiver class="org.apache.axis2.receivers.RawXMLINOutMessageReceiver"/>
     </operation>
     <parameter name="ServiceClass">edu.harvard.i2b2.pm.ws.PMService</parameter>
-</service>
+</service>

etc/jboss/pm-ds.xml

@@ -1,63 +1,105 @@
 <?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+  _____  __  __    _____        _         _____                          
+ |  __ \|  \/  |  |  __ \      | |       / ____|                         
+ | |__) | \  / |  | |  | | __ _| |_ __ _| (___   ___  _   _ _ __ ___ ___ 
+ |  ___/| |\/| |  | |  | |/ _` | __/ _` |\___ \ / _ \| | | | '__/ __/ _ \
+ | |    | |  | |  | |__| | (_| | || (_| |____) | (_) | |_| | | | (_|  __/
+ |_|    |_|  |_|  |_____/ \__,_|\__\__,_|_____/ \___/ \__,_|_|  \___\___|
+                                                                         
+                                                                         
+-->
 <datasources xmlns="http://www.jboss.org/ironjacamar/schema">
+<!-- 
+
+   _____ ______ _____ _______ _____ ____  _   _    __   
+  / ____|  ____/ ____|__   __|_   _/ __ \| \ | |  /_ |  
+ | (___ | |__ | |       | |    | || |  | |  \| |   | |  
+  \___ \|  __|| |       | |    | || |  | | . ` |   | |  
+  ____) | |___| |____   | |   _| || |__| | |\  |   | |   
+ |_____/|______\_____|  |_|  |_____\____/|_| \_|   |_|  
+                                                                               
+								                                         
+ The bootstrap points to the data source for your database lookup table which is a hivedata table, this is required.
+ 
+ 1)	This database defaults to Oracle, uncomment SQL Server or PostgreSQL and comment out the Oracle one.					                                         
+ 2) Update the <connection-url> with the location of your hostname, port  and SID (Oracle Only).   
+ 2) Update the <user-name> with the database user
+ 3) Update the <password> with the database password
+
+-->
 	<datasource jta="false" jndi-name="java:/PMBootStrapDS"
 		pool-name="PMBootStrapDS" enabled="true" use-ccm="false">
 		<connection-url>jdbc:oracle:thin:@localhost:1521:xe</connection-url>
 		<driver-class>oracle.jdbc.OracleDriver</driver-class>
-		<driver>ojdbc6.jar</driver>
+		<driver>ojdbc8.jar</driver>
 		<security>
 			<user-name>i2b2pm</user-name>
 			<password>demouser</password>
 		</security>
 		<validation>
+			<valid-connection-checker class-name="org.jboss.jca.adapters.jdbc.extensions.oracle.OracleValidConnectionChecker"/>
 			<validate-on-match>false</validate-on-match>
-			<background-validation>false</background-validation>
-		</validation>
+			<background-validation>true</background-validation>
+			<background-validation-millis>60000</background-validation-millis>
+			<use-fast-fail>true</use-fast-fail>
+			<check-valid-connection-sql>SELECT 1 FROM DUAL</check-valid-connection-sql>
+		</validation> 
 		<statement>
 			<share-prepared-statements>false</share-prepared-statements>
 		</statement>
 	</datasource>
 
-	<!--  
+
+	<!--   SQL SERVER EXAMPLE    -->
+	<!-- 
 	<datasource jta="false" jndi-name="java:/PMBootStrapDS"
 		pool-name="PMBootStrapDS" enabled="true" use-ccm="false">
-		<connection-url>jdbc:postgresql://localhost:5432/i2b2</connection-url>
-		<driver-class>org.postgresql.Driver</driver-class>
-		<driver>postgresql-9.2-1002.jdbc4.jar</driver>
+		<connection-url>jdbc:sqlserver://localhost:1433</connection-url>
+		<driver-class>com.microsoft.sqlserver.jdbc.SQLServerDriver</driver-class>
+		<driver>mssql-jdbc-7.4.1.jre8.jar</driver>
 		<security>
 			<user-name>i2b2pm</user-name>
 			<password>demouser</password>
 		</security>
 		<validation>
+			<valid-connection-checker class-name="org.jboss.jca.adapters.jdbc.extensions.mssql.MSSQLValidConnectionChecker"/>
 			<validate-on-match>false</validate-on-match>
-			<background-validation>false</background-validation>
+			<background-validation>true</background-validation>
+			<background-validation-millis>60000</background-validation-millis>
+			<use-fast-fail>true</use-fast-fail>
+			<check-valid-connection-sql>SELECT 1</check-valid-connection-sql>
 		</validation>
 		<statement>
 			<share-prepared-statements>false</share-prepared-statements>
 		</statement>
 	</datasource>
 	-->
 
+	<!--  POSTGRESQL EXAMPLE -->
 	<!-- 
-	
 	<datasource jta="false" jndi-name="java:/PMBootStrapDS"
 		pool-name="PMBootStrapDS" enabled="true" use-ccm="false">
-		<connection-url>jdbc:sqlserver://localhost:1433</connection-url>
-		<driver-class>com.microsoft.sqlserver.jdbc.SQLServerDriver</driver-class>
-		<driver>sqljdbc4.jar</driver>
+		<connection-url>jdbc:postgresql://localhost:5432/i2b2</connection-url>
+		<driver-class>org.postgresql.Driver</driver-class>
+		<driver>postgresql-42.2.8.jar</driver>
 		<security>
 			<user-name>i2b2pm</user-name>
 			<password>demouser</password>
 		</security>
 		<validation>
-			<valid-connection-checker class-name="org.jboss.jca.adapters.jdbc.extensions.mssql.MSSQLValidConnectionChecker"></valid-connection-checker>
-            <validate-on-match>false</validate-on-match>
+			<valid-connection-checker class-name="org.jboss.jca.adapters.jdbc.extensions.postgres.PostgreSQLValidConnectionChecker"/>		
+			<validate-on-match>false</validate-on-match>
+			<background-validation>true</background-validation>
+			<background-validation-millis>60000</background-validation-millis>
+			<use-fast-fail>true</use-fast-fail>
+    		<check-valid-connection-sql>SELECT 1</check-valid-connection-sql>
 		</validation>
 		<statement>
 			<share-prepared-statements>false</share-prepared-statements>
 		</statement>
 	</datasource>
-	
-	 -->
+	-->
 </datasources>