Merge branch 'master' into master

eurekaclinical · Sep 15, 2020 · ac3a22f · ac3a22f
2 parents 32bc95c + b60a2d6
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diff --git a/README.md b/README.md
@@ -1,14 +1,26 @@
 # i2b2-pm-cas
-[Atlanta Clinical and Translational Science Institute (ACTSI)](http://www.actsi.org), [Emory University](http://www.emory.edu), Atlanta, GA
+[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 1.7.08b 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.
+
+### Version 1.1
+Updated i2b2 version to 1.7.08b.
+
 ### Version 1.0
-Initial release.
+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:

diff --git a/build.xml b/build.xml
@@ -21,6 +21,7 @@
 			<path refid="common-classpath" />
 			<pathelement location="${classes}" />
 			<pathelement location="lib/jcifs-1.3.3.jar" />
+			<pathelement location="lib/servlet-api.jar" />
 			<pathelement location="../${i2b2CommonProject}/dist/i2b2Common-core.jar" />
 			<pathelement location="../${i2b2CommonProject}/lib/smbj-0.9.1.jar" />
 
@@ -190,4 +191,3 @@
 	</target>
 
 </project>
-
diff --git a/lib/servlet-api.jar b/lib/servlet-api.jar
diff --git a/src/edu/harvard/i2b2/pm/delegate/ServicesHandler.java b/src/edu/harvard/i2b2/pm/delegate/ServicesHandler.java
@@ -14,17 +14,18 @@
  */
 package edu.harvard.i2b2.pm.delegate;
 
-
 import java.lang.reflect.Constructor;
 import java.lang.reflect.Field;
 import java.net.InetAddress;
 import java.sql.Connection;
 import java.sql.DriverManager;
+
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
+
 import java.util.Set;
 import java.util.Calendar;
 
@@ -100,11 +101,36 @@
 public class ServicesHandler extends RequestHandler {
 	private ProjectType projectInfo = null;
 	private ServicesMessage getServicesMsg = null;
-
+	private MessageContext context = null;
+
+	protected static final String CONFIG_PATHNAME="/etc/eureka/application.properties";
+	protected static final String CAS_URL_PROPERTY_NAME = "cas.url";
+	protected static final String CAS_DEFAULT_URL = "https://localhost:8443/cas-server/";
+	protected static final Properties appProperties = new Properties();
+	   static {
+	        try {
+	            FileReader fr = new FileReader(CONFIG_PATHNAME);
+	            appProperties.load(fr);
+	            String readCasUrl = appProperties.getProperty(CAS_URL_PROPERTY_NAME);
+	            if (readCasUrl == null) {
+	                appProperties.setProperty(CAS_URL_PROPERTY_NAME, CAS_DEFAULT_URL);
+	            } else if (!readCasUrl.endsWith("/")) {
+	                appProperties.setProperty(CAS_URL_PROPERTY_NAME, readCasUrl + "/");
+	            }
+	            fr.close();
+	            fr = null;
+	        } catch (FileNotFoundException ex) {
+	            appProperties.setProperty(CAS_URL_PROPERTY_NAME, CAS_DEFAULT_URL);
+	        } catch (IOException ex) {
+	            throw new IllegalStateException("Error reading CAS integration configuration file " + CONFIG_PATHNAME, ex);
+	        }
+	    }
 	public ServicesHandler(ServicesMessage servicesMsg) throws I2B2Exception{
 		log.debug("Setting the servicesMsg");
 
 		getServicesMsg = servicesMsg;
+		context = MessageContext.getCurrentMessageContext();
+		System.out.println("+MessageContext+"+context);
 		//setDbInfo(servicesMsg.getRequestMessageType().getMessageHeader());
 	}
 
@@ -114,6 +140,7 @@ private void saveLoginAttempt(PMDbDao pmDb, String username, String attempt)
 		pmDb.setLoginAttempt(username, attempt );
 
 	}
+
 
 
 	protected UserType validateSuppliedPassword (String username, String password, Hashtable param, boolean skipValidation) throws Exception
@@ -732,6 +759,7 @@ else if (name.equals("get_project_request"))
 						// throw new Exception (ee.getMessage());
 						ee.printStackTrace();
 
+
 						MessageHeaderType messageHeader = MessageFactory.createResponseMessageHeader(getServicesMsg.getRequestMessageType().getMessageHeader());
 						responseMessageType = MessageFactory.doBuildErrorResponse(messageHeader,
 								ee.getMessage());
@@ -752,6 +780,7 @@ private String runUserLogin(PMDbDao pmDb, String caller, UserLoginType value) {
 					try {
 
 
+
 						List response = null;
 						try {
 							response = pmDb.getUserLogin(value, caller);
@@ -771,6 +800,7 @@ private String runUserLogin(PMDbDao pmDb, String caller, UserLoginType value) {
 						}
 						//everything is good so just return the same session key and the other info
 
+
 						MessageHeaderType messageHeader = MessageFactory.createResponseMessageHeader(getServicesMsg.getRequestMessageType().getMessageHeader());
 						responseMessageType = MessageFactory.createBuildResponse(messageHeader,users);
 
@@ -786,6 +816,7 @@ private String runUserLogin(PMDbDao pmDb, String caller, UserLoginType value) {
 								ee.getMessage());
 					}
 
+
 					String responseVdo = "DONE";
 					try {
 						responseVdo = MessageFactory.convertToXMLString(responseMessageType);
@@ -803,6 +834,7 @@ private String runGetAllDatasource(PMDbDao pmDb, String project, String caller)
 
 						List<DataSource> response = new ArrayList<DataSource>();
 
+
 						//List<DataSource> availableDatasources = new ArrayList<DataSource>();
 						try {
 
@@ -2447,7 +2479,101 @@ private String runGetUserConfiguration(PMDbDao pmDb, GetUserConfigurationType us
 
 			}
 
-
+	/*private String getUsername()
+	{
+		String username = null;
+		try{
+		System.out.println("Inside user name");
+		//stub._getServiceContext().getCurrentOperationContext().getMessageContext("In");
+		//context = MessageContext.getCurrentMessageContext();
+		System.out.println("context:"+context);
+		HttpServletRequest  request = (HttpServletRequest) context.getProperty("transport.http.servletRequest");
+		String ticketVal = null ;
+		
+		if(request != null)
+		{
+			ticketVal = request.getParameter("ticket");
+			System.out.println("ticketVal++"+ticketVal);
+		}
+		System.out.println("+++request+++"+request);
+		log.debug("+++request+++"+request);
+		log.info("+++request+++"+request);
+		String addr = "";
+		
+		 addr = appProperties.getProperty(CAS_URL_PROPERTY_NAME) + "proxyValidate?"
+		    + "service=" + URLEncoder.encode("http://localhost:9090"+request.getRequestURI().toString(), "UTF-8")
+		    + "&ticket="+ticketVal;
+		
+		log.debug("CAS validation address: " + addr);
+		System.out.println("FORWARD ADDRESS++++++++:"+addr);
+		log.debug("FORWARD ADDRESS++++++++:"+addr);
+		log.info("FORWARD ADDRESS++++++++:"+addr);
+		BufferedReader body = URLOpener.open(addr);
+	        try {
+		    StringBuilder builder = new StringBuilder();
+		    String line;
+		    while ((line = body.readLine()) != null) {
+			builder.append(line);
+		    }
+		    String response = builder.toString();
+		    System.out.println("+++++response+++:"+response);
+		    int start = response.indexOf("<cas:authenticationSuccess");
+		    
+		    if (start > -1) {
+		    	start = response.indexOf(">", start);
+		    	if (start < 0) {
+		    	    log.error("Unexpected response from CAS: " + response);
+		    	    throw new Exception("EINTERNAL");
+		    	}
+			start += 1;
+			start = response.indexOf("<cas:user", start);
+			if (start < 0) {
+			    log.error("Unexpected response from CAS: " + response);
+			    throw new Exception("EINTERNAL");
+			} else {
+			    start = response.indexOf(">", start);
+			    if (start < 0) {
+		    	        log.error("Unexpected response from CAS: " + response);
+		    	        throw new Exception("EINTERNAL");
+		    	    }
+			    start += 1;
+			    int finish = response.indexOf("</cas:user", start);
+			    if (finish < 0) {
+				log.error("Unexpected response from CAS: " + response);
+				throw new Exception("EINTERNAL");
+			    } else {
+				username = response.substring(start, finish).trim();
+			    }
+			}
+		    } else {
+			if (response.contains("<cas:authenticationFailure")) {
+			    log.debug("CAS authentication result negative");
+			    throw new Exception("EAUTHENTICATION");
+			} else {
+			    log.error("Unexpected response from CAS: " + response);
+			    throw new Exception("EINTERNAL");
+			}
+		    }
+
+	            log.debug("CAS authenticated user:" + username);
+
+	        }finally {
+	            if (body != null) {
+	                try {
+	                    body.close();
+	                } catch (IOException e) 
+	                {
+	                	e.printStackTrace();
+	                }
+	            }
+	        }
+		}catch(Exception e)
+		{
+			e.printStackTrace();
+		}
+		return username;
+	}*/
+
 
 
 
@@ -2459,3 +2585,4 @@ private String runGetUserConfiguration(PMDbDao pmDb, GetUserConfigurationType us
 
 
 
+
diff --git a/src/edu/harvard/i2b2/pm/ws/PMService.java b/src/edu/harvard/i2b2/pm/ws/PMService.java
@@ -222,7 +222,7 @@ public OMElement getServices(OMElement getPMDataElement)
 		 */
 
 		OMElement returnElement = null;
-
+		
 
 		if (getPMDataElement == null) {
 			log.error("Incoming PM request is null");
@@ -264,6 +264,7 @@ public OMElement getServices(OMElement getPMDataElement)
 			log.debug("middle setRequestHandler");
 
 
+
 			log.debug("end setRequestHandler");
 
 
@@ -290,6 +291,7 @@ public OMElement getServices(OMElement getPMDataElement)
 						} else { 
 							t.wait(); 
 						} 
+
 					} 
 					pmDataResponse = er.getOutputString();
 

diff --git a/src/edu/harvard/i2b2/pm/ws/ServicesMessage.java b/src/edu/harvard/i2b2/pm/ws/ServicesMessage.java
@@ -54,7 +54,7 @@ public ServicesMessage(String requestPdo) throws I2B2Exception {
 
             log.debug("Finished unmarshall of XML");
             this.reqMessageType = (RequestMessageType) jaxbElement.getValue();
-            
+	    
         } catch (JAXBUtilException e) {
             e.printStackTrace();
             log.error(e.getMessage(), e);