Merge pull request #89 from Novartis/8.7.0

8.7.0

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>com.novartis.opensource</groupId>
 	<artifactId>YADA</artifactId>
-	<version>8.6.2-SNAPSHOT</version>
+	<version>8.7.0-SNAPSHOT</version>
 	<name>YADA</name>
 	<url>http://github.com/Novartis/YADA</url>
 	<description>YADA (Yet Another Data Abstraction) Thin Server Framework</description>

yada-api/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>com.novartis.opensource</groupId>
     <artifactId>YADA</artifactId>
-    <version>8.6.2-SNAPSHOT</version>
+    <version>8.7.0-SNAPSHOT</version>
   </parent>
   <artifactId>yada-api</artifactId>
   <name>yada-api</name>
@@ -849,6 +849,16 @@
     </plugins>
   </reporting>
   <dependencies>
+    <dependency>
+	    <groupId>com.google.oauth-client</groupId>
+	    <artifactId>google-oauth-client</artifactId>
+	    <version>1.22.0</version>
+    </dependency>
+    <dependency>
+      <groupId>com.google.http-client</groupId>
+      <artifactId>google-http-client-jackson2</artifactId>
+      <version>1.11.0-beta</version>
+    </dependency>
     <dependency>
       <groupId>com.novartis.opensource</groupId>
       <artifactId>jsqlparser</artifactId>

yada-api/src/main/java/com/novartis/opensource/yada/Service.java

@@ -47,7 +47,6 @@
 import com.novartis.opensource.yada.plugin.Postprocess;
 import com.novartis.opensource.yada.plugin.Preprocess;
 import com.novartis.opensource.yada.plugin.YADAPluginException;
-import com.novartis.opensource.yada.plugin.YADASecurityException;
 import com.novartis.opensource.yada.util.FileUtils;
 import com.novartis.opensource.yada.util.QueryUtils;
 import com.novartis.opensource.yada.util.YADAUtils;
@@ -308,13 +307,13 @@ public void handleRequest(String referer, Map<String,String[]> paraMap)
   		{
   			getYADARequest().setMethod(paraMap.get(YADARequest.PS_METHOD));
   		}
-  		if (paraMap.get(YADARequest.PL_OVERARGS) != null)
+  		if (paraMap.get(YADARequest.PL_OAUTH) != null)
   		{
-  		  setDeprecatedPlugin(paraMap, YADARequest.PL_OVERARGS);
+  		  getYADARequest().setOAuth(paraMap.get(YADARequest.PL_OAUTH));
   		}
-  		if (paraMap.get(YADARequest.PS_OVERARGS) != null)
+  		if (paraMap.get(YADARequest.PS_OAUTH) != null)
   		{
-  		  setDeprecatedPlugin(paraMap, YADARequest.PS_OVERARGS);
+  			getYADARequest().setOAuth(paraMap.get(YADARequest.PS_OAUTH));
   		}
   		if (paraMap.get(YADARequest.PL_BYPASSARGS) != null)
   		{

yada-api/src/main/java/com/novartis/opensource/yada/YADAQueryResult.java

@@ -36,7 +36,7 @@ public class YADAQueryResult {
 	 */
 	private String       qname;
 	/**
-	 * The app to which the {@link qname} is mapped
+	 * The app to which the {@code qname} is mapped
 	 * @since 8.6.1
 	 */
 	private String       app;

yada-api/src/main/java/com/novartis/opensource/yada/YADARequest.java

@@ -423,6 +423,11 @@ public class YADARequest {
 	 * No longer deprecated (4.0.0) as of 8.5.0
 	 */
 	public static final String PS_METHOD      = "m";
+	/**
+	 * a constant equals to: {@value}
+	 * @since 8.7.0
+	 */
+	public static final String PS_OAUTH       = "o";
 	/**
 	 * A constant equal to: {@value}
 	 * @since 4.0.0 (Short param aliases were first added in 4.0.0)
@@ -667,6 +672,12 @@ public class YADARequest {
 	 * No longer deprecated (4.0.0) as of 8.5.0
 	 */
 	public static final String PL_METHOD      = "method";
+	/**
+	 * A constant equals to: {@value}.
+	 * 
+	 * @since 8.7.0
+	 */
+	public static final String PL_OAUTH       = "oauth";
 	/**
 	 * A constant equal to: {@value}.  Use {@link YADARequest#PL_BYPASSARGS} instead.
 	 * @deprecated as of 4.0.0
@@ -723,7 +734,7 @@ public class YADARequest {
 	public static final String PL_PLUGINTYPE  = "plugintype";
 	/**
 	 * A constant equal to: {@value}
-	 * @deprecated
+	 * @deprecated as of 7.1.0
 	 */
 	@Deprecated
 	public static final String PL_POSTARGS    = "postargs";
@@ -833,6 +844,7 @@ public class YADARequest {
 		map.put(PS_JOIN, PL_JOIN);
 		map.put(PS_LEFTJOIN, PL_LEFTJOIN);
 		map.put(PS_METHOD,PL_METHOD);
+		map.put(PS_OAUTH,PL_OAUTH);
 		map.put(PS_OVERARGS,PL_OVERARGS);
 		map.put(PS_PAGE,PL_PAGE);
 		map.put(PS_PAGESIZE,PL_PAGESIZE);
@@ -876,6 +888,7 @@ public class YADARequest {
 		map.put(PL_LABELS,PL_LABELS);
 		map.put(PL_MAIL,PL_MAIL);
 		map.put(PL_METHOD,PL_METHOD);
+		map.put(PL_OAUTH,PL_OAUTH);
 		map.put(PL_OVERARGS,PL_OVERARGS);
 		map.put(PL_PAGE,PL_PAGE);
 		map.put(PL_PAGESIZE,PL_PAGESIZE);
@@ -963,7 +976,7 @@ public class YADARequest {
 	private String     mail;
 	/**
 	 * YADA execution method. Defaults to {@link #METHOD_GET}
-	 * @since 1.0.0, deprecated in v4.0.0, un-deprecated in 8.5.0 to support different HTTP methods for {@link RESTAdaptor}
+	 * @since 1.0.0, deprecated in v4.0.0, un-deprecated in 8.5.0 to support different HTTP methods for {@link com.novartis.opensource.yada.adaptor.RESTAdaptor}
 	 */
 	private String     method 	 	  = METHOD_GET;
 	/**
@@ -1015,6 +1028,11 @@ public class YADARequest {
 	 * The proxy server to use for external REST queries
 	 */
 	private String     proxy        = null;
+	/**
+	 * A JSON object containing oauth key/value pairs needed for authenticated requests
+	 * @since 8.7.0 
+	 */
+	private JSONObject oauth        = null;
 	/**
 	 * The name of the query to be executed, when coupled with {@link #params}, or {@link #plugin}.  Defaults to {@link #DEFAULT_QNAME}
 	 */
@@ -1171,6 +1189,7 @@ public List<YADAParam> getGlobalParamsForQueries() throws YADAQueryConfiguration
 	 *   <li>{@link #PS_FORMAT}</li>
 	 *   <li>{@link #PS_HARMONYMAP}</li>
 	 *   <li>{@link #PS_METHOD} (for backward compatibility)</li>
+	 *   <li>{@link #PS_OAUTH}</li>
 	 *   <li>{@link #PS_PAGESIZE}</li>
 	 *   <li>{@link #PS_PAGESTART}</li>
 	 *   <li>{@link #PS_ROW_DELIMITER}</li>
@@ -1186,6 +1205,7 @@ public List<YADAParam> getRequestParamsForQueries() throws YADAQueryConfiguratio
 		JSONObject jobj = new JSONObject();
 		try
 		{
+			jobj.put(PS_OAUTH, getOAuth());
 			jobj.put(PS_COUNT, getCount());
 			jobj.put(PS_FILTERS, getFilters());
 			jobj.put(PS_PAGESIZE, getPageSize());
@@ -1233,7 +1253,6 @@ public List<YADAParam> getRequestParamsForQueries() throws YADAQueryConfiguratio
 	 */
 	public static String getParamValueForKey(List<YADAParam> q, String frag) throws YADAQueryConfigurationException 
 	{
-		//for (Iterator<YADAParam> iterator = q.iterator(); iterator.hasNext();)
 		for (YADAParam param : q)
 		{
 			try
@@ -2214,23 +2233,21 @@ public void setMethod(String[] method) {
 	}
 
 	/**
-	 * @deprecated As of YADA 4.0.0
-	 * @param args bypass plugin arguments
+	 * @since 8.7.0
+	 * @param oauth oauth parameters
+	 * @throws YADARequestException if the parameter string is not malformed
 	 */
-	@Deprecated
-	public void setOverArgs(List<String> args) {
-		this.bypassArgs = args;
-		l.debug(getFormattedDebugString("bypassArgs", args.toString()));
-	}
-
-	/**
-	 * @since 4.0.0
-	 * @param argArr bypass plugin arguments
-   * @deprecated as of 7.1.0
-   */
-  @Deprecated
-	public void setOverargs(String[] argArr) {
-		this.setBypassargs(argArr);
+	public void setOAuth(String[] oauth) throws YADARequestException
+	{
+		try
+		{
+			this.oauth = new JSONObject(oauth[0]);
+		}
+		catch(JSONException e)
+		{
+			String msg = "The OAuth parameter JSON string appears to be malformed.";
+			throw new YADARequestException(msg, e);
+		}
 	}
 
 	/**
@@ -3038,6 +3055,17 @@ public int getPageSize() {
 		return this.pageSize;
 	}
 
+	/**
+	 * Returns an {@link JSONObject} containing oauth parameters such as <code>consumer_key</code>, 
+	 * <code>secret</code>, etc. See the YADA OAuth 1.0a specification or YADA parameter documentation
+	 * for details. 
+	 * @return the oauth parameters object
+	 * @since 8.7.0
+	 */
+	//TODO Add link to YADA OAuth 1.0a spec 
+	public JSONObject getOAuth() {
+		return this.oauth;
+	}
 
 	/**
 	 * Returns the results from page {@code pageStart}, using {@link #getPageSize()} to determine which row should

yada-api/src/main/java/com/novartis/opensource/yada/plugin/YADASecurityException.java → yada-api/src/main/java/com/novartis/opensource/yada/YADASecurityException.java

@@ -15,10 +15,13 @@
 /**
  * 
  */
-package com.novartis.opensource.yada.plugin;
+package com.novartis.opensource.yada;
+
+import com.novartis.opensource.yada.plugin.YADAPluginException;
 
 /**
- * Throw from a security preprocessor when authentication fails.
+ * Throw from a security preprocessor or adaptor when authentication or authorization fails. 
+ * Moved to main package from {@code plugin} for {@code 8.7.0}
  * @author Dave Varon
  * @since 7.0.0
  *

yada-api/src/main/java/com/novartis/opensource/yada/adaptor/Adaptor.java

@@ -22,6 +22,7 @@
 import com.novartis.opensource.yada.YADAQuery;
 import com.novartis.opensource.yada.YADAQueryResult;
 import com.novartis.opensource.yada.YADARequest;
+import com.novartis.opensource.yada.YADASecurityException;
 
 /**
  * The abstract Adaptor class is at the root of the package hierarchy. Adaptors
@@ -79,8 +80,9 @@ public Adaptor(YADARequest yadaReq)
 	 * 
 	 * @param yq the {@link YADAQuery} containing the code to execute
 	 * @throws YADAAdaptorExecutionException if exception is thrown during query execution 
+	 * @throws YADASecurityException if there is authentication or authorization error in preparation for or during execution
 	 */
-	public void execute(YADAQuery yq) throws YADAAdaptorExecutionException
+	public void execute(YADAQuery yq) throws YADAAdaptorExecutionException, YADASecurityException
 	{
 		//
 	}
@@ -130,7 +132,7 @@ protected YADARequest getServiceParameters()
 	 * @param yq the query to which to apply the new settings
 	 */
 	protected void resetCountParameter(YADAQuery yq) {
-		//TODO run this through the debugger to check the distinction betwen these 2 instances of yadaReq
+		//TODO run this through the debugger to check the distinction between these 2 instances of yadaReq
 		this.yadaReq.setCount(new String[] {"false"});
 		yq.replaceParam(YADARequest.PS_COUNT, "false");
 	}

yada-api/src/main/java/com/novartis/opensource/yada/adaptor/FileSystemAdaptor.java

@@ -52,7 +52,7 @@ public class FileSystemAdaptor extends Adaptor
    */
 	protected final static String  PARAM_SYMBOL_RX = "([\\/=:<])(\\?[idvn])";
 	/**
-   * Constant equal to: {@code &lt;{1,2}.*}
+   * Constant equal to: {@code &lt;&lcub;1,2&rcub;.*}
    */
 	protected final static String  NON_READ_SFX_RX = "<{1,2}.*";
 	/**