more findbugs warnings fixed

Author: Jesse Eichar

code_quality/findbugs-excludes.xml

@@ -8,7 +8,7 @@
 		<Class name="~.*\..*Test" />
 	</Match>
   <Match>
-		<Class name="~org\.fao\.geonet\.[h-zG-Z].*" />
+		<Class name="~org\.fao\.geonet\.[h-zH-Z].*" />
 	</Match>
 	<Match>
 		<Class name="jeeves.server.JeevesEngine" />

web/src/main/java/org/fao/geonet/Geonetwork.java

@@ -185,8 +185,8 @@ public Object start(Element config, ServiceContext context) throws Exception {
 		JeevesJCS.setConfigFilename(path + "WEB-INF/classes/cache.ccf");
 
 		// force caches to be config'd so shutdown hook works correctly
-		JeevesJCS jcsDummy = JeevesJCS.getInstance(Processor.XLINK_JCS);
-		jcsDummy = JeevesJCS.getInstance(XmlResolver.XMLRESOLVER_JCS);
+		JeevesJCS.getInstance(Processor.XLINK_JCS);
+		JeevesJCS.getInstance(XmlResolver.XMLRESOLVER_JCS);
 
 
 
@@ -228,7 +228,6 @@ public Object start(Element config, ServiceContext context) throws Exception {
 
 		boolean z3950Enable    = settingMan.getValueAsBool("system/z3950/enable", false);
 		String  z3950port      = settingMan.getValue("system/z3950/port");
-		String  host           = settingMan.getValue(Geonet.Settings.SERVER_HOST);
 
 		// null means not initialized
 		ApplicationContext app_context = null;
@@ -934,7 +933,9 @@ public void stop() {
 	private DataStore createShapefileDatastore(String indexDir) throws Exception {
 
 		File file = new File(indexDir + "/" + SPATIAL_INDEX_FILENAME + ".shp");
-		file.getParentFile().mkdirs();
+		if(!file.getParentFile().mkdirs() && !file.getParentFile().exists()) {
+		    throw new RuntimeException("Unable to create the spatial index (shapefile) directory: "+file.getParentFile());
+		}
 		if (!file.exists()) {
 			logger.info("Creating shapefile "+file.getAbsolutePath());
 		} else {

web/src/main/java/org/fao/geonet/GeonetworkDataDirectory.java

@@ -10,6 +10,7 @@
 import jeeves.utils.BinaryFile;
 import jeeves.utils.Log;
 
+import org.apache.commons.io.IOUtils;
 import org.fao.geonet.constants.Geonet;
 
 /**
@@ -110,6 +111,8 @@ private static String lookupProperty(JeevesServlet jeevesServlet, ServiceConfig
 //				Instead of looking for geonetwork.dir, get geonetwork_dir
 				value = System.getenv(key.replace('.', '_'));
 				break;
+			default:
+			    throw new IllegalArgumentException("Did not expect value: "+j);
 			}
 
 			if (value == null || value.equalsIgnoreCase("")) {
@@ -259,17 +262,26 @@ private void initDataDirectory(String path, ServiceConfig handlerConfig) {
 		if (!schemaCatFile.exists()) {
 			Log.info(Geonet.DATA_DIRECTORY,
 					"     - Copying schema plugin catalogue ...");
+			FileInputStream in = null;
+			FileOutputStream out = null;
 			try {
-				FileInputStream in = new FileInputStream(path + "WEB-INF"
+                in = new FileInputStream(path + "WEB-INF"
 						+ File.separator + Geonet.File.SCHEMA_PLUGINS_CATALOG);
-				FileOutputStream out = new FileOutputStream(schemaCatFile);
+                out = new FileOutputStream(schemaCatFile);
 
-				BinaryFile.copy(in, out, true, true);
+				BinaryFile.copy(in, out, false, false);
 			} catch (IOException e) {
 				Log.info(
 						Geonet.DATA_DIRECTORY,
 						"      - Error copying schema plugin catalogue: "
 								+ e.getMessage());
+			} finally {
+			    if(in != null) {
+			        IOUtils.closeQuietly(in);
+			    }
+			    if(out != null) {
+			        IOUtils.closeQuietly(out);
+			    }
 			}
 		}
 
@@ -307,8 +319,8 @@ private void setResourceDir(String webappName, ServiceConfig handlerConfig,
 
 		// Create directory if it does not exist
 		File file = new File(dir);
-		if (!file.exists()) {
-			file.mkdirs();
+		if (!file.exists() && !file.mkdirs()) {
+			throw new RuntimeException("Unable to create directory: "+file);
 		}
 
 		Log.info(Geonet.DATA_DIRECTORY, "    - " + envKey + " is " + dir);

web/src/main/java/org/fao/geonet/lib/ServerLib.java

@@ -33,6 +33,8 @@
 import java.util.List;
 import java.util.Properties;
 
+import javax.annotation.CheckForNull;
+import javax.annotation.Nullable;
 import javax.servlet.ServletContext;
 
 import jeeves.server.overrides.ConfigurationOverrides;
@@ -47,19 +49,24 @@ public class ServerLib
 	//---
 	//---------------------------------------------------------------------------
 
-	public ServerLib(ServletContext servletContext, String appPath) throws IOException
+	public ServerLib(@Nullable ServletContext servletContext, String appPath) throws IOException
 	{
 		this.appPath = appPath;
 
 		serverProps = new Properties();
 
-		InputStream stream = servletContext.getResourceAsStream(SERVER_PROPS);
-		if (stream == null) {
-			stream = servletContext.getResourceAsStream(SERVER_PROPS.replace("/",File.separator));
-			if(stream == null) {
-				stream = new FileInputStream(appPath + (SERVER_PROPS.replace("/",File.separator)));
-			}
+		InputStream stream = null;
+		if(servletContext != null) {
+		    stream = servletContext.getResourceAsStream(SERVER_PROPS);
+		    if (stream == null) {
+		        stream = servletContext.getResourceAsStream(SERVER_PROPS.replace("/",File.separator));
+		    }
+		}
+
+		if(stream == null) {
+		    stream = new FileInputStream(appPath + (SERVER_PROPS.replace("/",File.separator)));
 		}
+
 		BufferedReader reader = new BufferedReader(new InputStreamReader(stream, "UTF-8"));
 
 		try {