[Treebase-guts] SF.net SVN: treebase:[487] trunk/treebase-core/src/main

[<vga...@us...>]

Revision: 487
          http://treebase.svn.sourceforge.net/treebase/?rev=487&view=rev
Author:   vgapeyev
Date:     2010-02-09 20:51:58 +0000 (Tue, 09 Feb 2010)

Log Message:
-----------
Split nexusService bean into 2: one for the webapp (init via JNDI) and another for the standalone tools (init from jdbc.properties)

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
    trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml
    trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml
    trunk/treebase-core/src/main/resources/applicationContext-service.xml

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2010-02-09 20:51:58 UTC (rev 487)
@@ -40,6 +40,9 @@
 	private MatrixDataTypeHome mMatrixDataTypeHome;
 	private ItemDefinitionHome mItemDefinitionHome;
 
+	private String mExplicitMesquiteFolder = null;
+	private String mJndiMesquiteFolder = null; 
+
 	/**
 	 * Constructor.
 	 */
@@ -104,24 +107,47 @@
 		return null; // do not need persistence service.
 	}
 	
-	/** Looks up where Mesquite is installed on the host system and informs MesquiteModule of the location.  
+
+	/**  Explicitly set Mesquite folder location that will be passed to mesquite.lib.MesquiteModule. 
+	 *   Only for use in tests and stand-alone tools (the webapp looks up the location in afterPropertiesSet()). 
+	 * 
+	 * @param pMesquiteFolderDir
+	 */
+	public void setMesquiteFolderDir(String pMesquiteFolderDir) {
+		mExplicitMesquiteFolder = pMesquiteFolderDir; 
+		LOGGER.info("Mesquite folder location set explicitly to " + mExplicitMesquiteFolder); 
+		//--
+		//System.setProperty(MESQUITE_FOLDER_DIR_KEY, pMesquiteFolderDir);
+		//MesquiteModule.mesquiteDirectory = new File(pMesquiteFolderDir);
+		//MesquiteModule.mesquiteDirectoryPath = pMesquiteFolderDir;
+	}
+	
+	
+	/** Looks up where Mesquite is installed on the host system and passes the location to mesquite.lib.MesquiteModule.  
         (This is an implementation of a standard Spring bean initialization method, 
          which is invoked after all properties are set.)
    */
 	public void afterPropertiesSet() throws Exception {
-		String mesquiteFolderDir = null; 
-		InitialContext ic;
 		try {
-			ic = new InitialContext();
-			mesquiteFolderDir  = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
+			InitialContext ic = new InitialContext();
+			mJndiMesquiteFolder  = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
 		} catch (NamingException e) {
-			LOGGER.fatal("Error looking up tb/MesquiteFolder via JNDI"); 
+			LOGGER.info("Failure looking up tb/MesquiteFolder via JNDI"); 
 		}
-		mesquiteFolderDir = mesquiteFolderDir + "/foo";   //since the last path element is somehow dropped subsequently... VG 2010-02-07
 
-		System.setProperty(MESQUITE_FOLDER_DIR_KEY, mesquiteFolderDir);
-		MesquiteModule.mesquiteDirectory = new File(mesquiteFolderDir);
-		MesquiteModule.mesquiteDirectoryPath = mesquiteFolderDir;				
+		String mesquiteFolder; 
+		if (mExplicitMesquiteFolder == null) 
+			if (mJndiMesquiteFolder == null) { mesquiteFolder = null; LOGGER.fatal("Failed to determine Mesquite folder location"); }
+			else { mesquiteFolder = mJndiMesquiteFolder; LOGGER.info("Setting mesquite folder location from JNDI: " + mJndiMesquiteFolder); }
+		else 
+			if (mJndiMesquiteFolder == null) { mesquiteFolder = mExplicitMesquiteFolder; LOGGER.info("Using explicitly set Mesquite folder: " + mExplicitMesquiteFolder);}
+			else { mesquiteFolder = mJndiMesquiteFolder; LOGGER.warn("Explicitly set Mesquite folder (" + mExplicitMesquiteFolder + 
+																	 ") is overwritten by the one from JNDI: " + mJndiMesquiteFolder); }
+		
+		mesquiteFolder = mesquiteFolder + "/foo";   //since the last path element is somehow dropped subsequently... VG 2010-02-07
+		System.setProperty(MESQUITE_FOLDER_DIR_KEY, mesquiteFolder);
+		MesquiteModule.mesquiteDirectory = new File(mesquiteFolder);
+		MesquiteModule.mesquiteDirectoryPath = mesquiteFolder;				
 	}
 	
 

Modified: trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml	2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml	2010-02-09 20:51:58 UTC (rev 487)
@@ -28,6 +28,12 @@
 		<property name="numHelperThreads" value="5" />
 	</bean>
 
+	<bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
+                <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+                <property name="taxonLabelHome" ref="taxonLabelHome"/>
+                <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
+                <property name="mesquiteFolderDir" value="${mesquite.folder_dir}"/>
+    </bean>
 
 
 </beans>

Modified: trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml	2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml	2010-02-09 20:51:58 UTC (rev 487)
@@ -13,4 +13,10 @@
 		<property name="jndiName" value="java:comp/env/jdbc/TreebaseDB"/>
 	</bean>
 
+	<bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
+                <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+                <property name="taxonLabelHome" ref="taxonLabelHome"/>
+                <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
+   </bean>
+
 </beans>
\ No newline at end of file

Modified: trunk/treebase-core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-service.xml	2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-service.xml	2010-02-09 20:51:58 UTC (rev 487)
@@ -137,13 +137,14 @@
                 <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
                 <property name="taxonLabelHome" ref="taxonLabelHome"/>
    </bean-->
-	
+
+<!-- VG 2010-02-09 nexusService bean is now set in applicationContext-db-webappp.xml and in applicationContext-db-standalone.xml 	
 	<bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
                 <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
                 <property name="taxonLabelHome" ref="taxonLabelHome"/>
                 <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
    </bean>
-  
+-->  
   	<bean id="nexmlService" class = "org.cipres.treebase.service.nexus.NexusServiceNexml">
                 <!-- property name="domainHome" ref="domainHome"/ -->
                 <property name="taxonLabelHome" ref="taxonLabelHome"/>


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