Remove trailing whitespace throughout project

legacy/utilities/buildutils/jarUsageScanner.rb

@@ -11,7 +11,7 @@ The list of JARs should be created by running the jarlist target of the build fi
 That will use JarJar to create a list of JAR file that are not directly referenced
 by the classes in the build. But what about JARs that are needed by a call using
 reflection? Like Class.forName("this.that.theOther"). We know this is how the MySQL
-driver is loaded (so we need mysql-connector-java-5.1.16-bin.jar). Are there any 
+driver is loaded (so we need mysql-connector-java-5.1.16-bin.jar). Are there any
 others? This script will try to find them.
 
 The jarlist target includes a list of JARs that we know are needed, such as the MySQL
@@ -20,7 +20,7 @@ list, and the target run again, in case they depend on other JARs in turn.
 
 --------------------------------------------------------------------------------
 
-One of the tricks that this script uses is to prune the list of packages to 
+One of the tricks that this script uses is to prune the list of packages to
 search for. If a JAR contains both "this.that.other" and "this.that", then we
 only need to search for "this.that", since it will reveal uses of "this.that.other"
 as well.
@@ -28,24 +28,24 @@ as well.
 --------------------------------------------------------------------------------
 
 pass the name of the file that contains the JAR names
-pass the root directory of the combined vitro/vivo distro 
+pass the root directory of the combined vitro/vivo distro
 	(appbase)
-	
+
 --------------------------------------------------------------------------------
 
 Search all of the *.java, *.jsp, *.js, *.tld, *.xml files for mention of these package names
 	For each hit, print the file path, line number, the package name and the JAR name.
-	
+
 To search files:
 	find -X . -name \*.db -or -name \*pot | xargs grep 'org\.package\.name'
 	grep -H -n -f file_with_package_patterns
-	
+
 	or can we do this all with grep on each string?
 		grep -r --include=*.jsp
-		
+
 	grep -H -n -r --include=*.javaxd --include=*.jsp org\.package\.name .
 		and precede the output with a header that lists the package
-	
+
 --------------------------------------------------------------------------------
 --------------------------------------------------------------------------------
 =end
@@ -121,7 +121,7 @@ def print_package_names_for_jars
 		package_array.each do |package_name|
 			puts "      #{package_name}"
 		end
-		puts 
+		puts
 	end
 end
 
@@ -172,9 +172,9 @@ if File.expand_path($0) == File.expand_path(__FILE__)
 	if ARGV.length != 2
 		raise("usage is: ruby jarUsageScanner.rb <jar_names_file> <scan_base_directory>")
 	end
-  
+
 	@jar_names_file, @scan_base_directory = ARGV
-  
+
 	if !File.file?(@jar_names_file)
 		raise "File does not exist: '#{@jar_names_file}'."
 	end
@@ -184,9 +184,9 @@ if File.expand_path($0) == File.expand_path(__FILE__)
 	end
 
 	print_args
-	
+
 	figure_package_names_from_jars
 	print_package_names_for_jars
-	
+
 	show_packages_in_source_files
-end
+end

legacy/utilities/buildutils/src/com/tonicsystems/jarjar/KlugedDepFind.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-/** 
+/**
  * This class is created to work around a known bug in JarJar which did not get fixed in release 1.1.
  * See the comments in edu.cornell.mannlib.vitro.utilities.jarlist.JarLister
  */

legacy/utilities/buildutils/src/edu/cornell/mannlib/vitro/utilities/containerneutral/CheckContainerNeutrality.java

@@ -38,34 +38,34 @@ import org.xml.sax.SAXException;
 /**
  * Look at web.xml, and check for conditions that violate the Servlet 2.4 spec,
  * but that might not be noticed because Tomcat doesn't complain.
- * 
+ *
  * ------
- * 
+ *
  * Values of the <dispatcher/> tag:
- * 
+ *
  * The spec permits only these values: "FORWARD", "REQUEST", "INCLUDE", "ERROR",
  * but Tomcat also allows the lower-case equivalents. GlassFish or WebLogic will
  * barf on lower-case.
- * 
+ *
  * Check to see that only the upper-case values are used.
- * 
+ *
  * ------
- * 
+ *
  * Existence of Servlet classes:
- * 
+ *
  * The spec allows the container to either load all servlets at startup, or to
  * load them when requested. Since Tomcat only loads servlet when requested, it
  * doesn't notice or complain if web.xml cites a <servlet-class/> that doesn't
  * exist, as long as it is never invoked. On the other hand, WebLogic loads all
  * serlvets at startup, and will barf if the class is not found.
- * 
+ *
  * Check each <servlet-class/> to insure that the class can be loaded and
  * instantiated and assigned to HttpServlet.
- * 
+ *
  * ------
- * 
+ *
  * Embedded URIs in taglibs.
- * 
+ *
  * I can't find this definitively in the JSP spec, but some containers complain
  * if web.xml specifies a <taglib-uri/> that conflicts with the <uri/> embedded
  * in the taglib itself. As far as I can see in the spec, the embedded <uri/>
@@ -73,51 +73,51 @@ import org.xml.sax.SAXException;
  * "Implicit Map Entries From TLDs", which in turn is only relevant for TLDs
  * packaged in JAR files. So, I can't find support for this complaint, but it
  * seems a reasonable one.
- * 
+ *
  * Check each <taglib/> specified in web.xml. If the taglib has an embedded
  * <uri/> tag, it should match the <taglib-uri/> from web.xml.
- * 
+ *
  * ------
- * 
+ *
  * Existence of Listener and Filter classes.
- * 
+ *
  * As far as I can tell, there is no ambiguity here, and every container will
  * complain if any of the <listener-class/> or <filter-class/> entries are
  * unsuitable. I check them anyway, since the mechanism was already assembled
  * for checking <servlet-class/> entries.
- * 
+ *
  * Check each <listener-class/> to insure that the class can be loaded and
  * instantiated and assigned to ServletContextListener.
- * 
+ *
  * Check each <filter-class/> to insure that the class can be loaded and
  * instantiated and assigned to Filter.
- * 
+ *
  * ------
- * 
+ *
  * A <servlet/> tag for every <servlet-mapping/> tag
- * 
+ *
  * I can't find a mention of this in the spec, but Tomcat complains and refuses
  * to load the app if there is a <servlet-mapping/> tag whose <servlet-name/> is
  * not matched by a <servlet-name/> in a <servlet/> tag.
- * 
+ *
  * Get sets of all <servlet-name/> tags that are specified in <servlet/> and
  * <servlet-mapping/> tags. There should not be any names in the
  * servlet-mappings that are not in the servlets.
- * 
+ *
  * ---------------------------------------------------------------------
- * 
+ *
  * Although this class is executed as a JUnit test, it doesn't have the usual
  * structure for a unit test.
- * 
+ *
  * In order to produce the most diagnostic information, the test does not abort
  * on the first failure. Rather, failure messages are accumulated until all
  * checks have been performed, and the test list all such messages on failure.
- * 
+ *
  * ---------------------------------------------------------------------
- * 
+ *
  * Since this is not executed as part of the standard Vitro unit tests, it also
  * cannot use the standard logging mechanism. Log4J has not been initialized.
- * 
+ *
  */
 public class CheckContainerNeutrality {
 	private static final String PROPERTY_WEBAPP_DIR = "CheckContainerNeutrality.webapp.dir";

legacy/utilities/buildutils/src/edu/cornell/mannlib/vitro/utilities/jarlist/JarLister.java

@@ -24,23 +24,23 @@ import com.tonicsystems.jarjar.KlugedDepFind;
 
 /**
  * This takes the place of the JarJar main routine, in doing a Find operation.
- * 
+ *
  * One thing this lets us do is to call KlugedDepFind instead of DepFind.
  * KlugedDepFind was created because JarJar had a known bug that wasn't fixed in
  * the latest release. (see http://code.google.com/p/jarjar/issues/detail?id=6).
  * I had to put KlugedDepFind into the com.tonicsystems.jarjar package so it
  * wauld have access to DepFindVisitor, which is package-private.
- * 
+ *
  * The other thing we can do is to provide a custom DepHandler which records the
  * dependencies directly instead of writing them to a file which we would need
  * to parse. Since we have the dependencies in a data structure, it's easy to
  * walk the tree and find out what JARs are required, even through several
  * layers of dependency.
- * 
+ *
  * When calling this, pass 2 arguments. The first is the path to the JAR which
  * contains the Vitro (or VIVO) classes. The second is the path to the directory
  * that contains the JARs. (shouldn't end with a slash)
- * 
+ *
  * There is a list of JARs which we know we need but which aren't shown by the
  * analysis. For example, the MySQL driver is loaded dynamically by name, so an
  * analysis of the class files in the JARs won't show that it is used. For now,
@@ -50,9 +50,9 @@ import com.tonicsystems.jarjar.KlugedDepFind;
 public class JarLister {
 	/**
 	 * <pre>
-	 * 
+	 *
 	 * What I originally wanted to do was this:
-	 * 
+	 *
 	 * <target name="jarlist" depends="jar" description="Figure out what JARs are needed">
 	 *   <java classname="com.tonicsystems.jarjar.Main" fork="no" failonerror="true">
 	 *     <classpath refid="utility.run.classpath" />
@@ -62,9 +62,9 @@ public class JarLister {
 	 *     <arg value="${appbase.dir}/lib/*" />
 	 *   </java>
 	 * </target>
-	 * 
+	 *
 	 * I ended up with this instead:
-	 * 
+	 *
 	 * <target name="jarlist" depends="jar" description="Figure out what JARs are needed">
 	 *   <java classname="edu.cornell.mannlib.vitro.utilities.jarlist.JarLister" fork="no" failonerror="true">
 	 *     <classpath refid="utility.run.classpath" />
@@ -73,7 +73,7 @@ public class JarLister {
 	 *     <arg value="${appbase.dir}/config/jarlist/known_dependencies.txt" />
 	 *   </java>
 	 * </target>
-	 * 
+	 *
 	 * </pre>
 	 */
 

legacy/utilities/buildutils/src/edu/cornell/mannlib/vitro/utilities/revisioninfo/ProcessRunner.java

@@ -12,9 +12,9 @@ import java.util.Map;
 
 /**
  * A harness that runs a system-level command.
- * 
+ *
  * No provision is made for standard input.
- * 
+ *
  * The standard output and standard error streams are asynchronously read, so
  * the sub-process will not block on full buffers. Warning: if either of these
  * streams contain more data than can fit into a String, then we will have a
@@ -40,7 +40,7 @@ public class ProcessRunner {
 
 	/**
 	 * Run the command.
-	 * 
+	 *
 	 * @param command
 	 *            a list containing the operating system program and its
 	 *            arguments. See

legacy/utilities/buildutils/src/edu/cornell/mannlib/vitro/utilities/revisioninfo/RevisionInfoBuilder.java

@@ -17,15 +17,15 @@ import edu.cornell.mannlib.vitro.utilities.revisioninfo.ProcessRunner.ProcessExc
 /**
  * Get release and revision information to display on screen. Put this
  * information into a single line and append it to the specified file.
- * 
+ *
  * Ask Git for the information. If Git is available, and if this is a working
  * directory, then we can build the info from the responses we get from
  * "git describe", "git symbolic-ref" and "git log".
- * 
+ *
  * If that doesn't work, read the information from the "revisionInfo" file in
  * the product directory. Presumably, that file was created when the source was
  * exported from Git.
- * 
+ *
  * If that doesn't work either, return something like this:
  * "productName ~ unknown ~ unknown"
  */
@@ -123,7 +123,7 @@ public class RevisionInfoBuilder {
 		if (revision == null) {
 			System.out.println("Couldn't get commit ID from Git");
 		}
-		
+
 		if ((revision == null) && (release == null)) {
 			return null;
 		}

legacy/utilities/buildutils/src/edu/cornell/mannlib/vitro/utilities/testing/VitroTestRunListener.java

@@ -25,10 +25,10 @@ import edu.cornell.mannlib.vitro.utilities.testing.VitroTestRunner.ReportLevel;
  * Listen to events as they come from the JUnit test runner. The events from the
  * lifecycle methods are broken down into semantic chunks and executed. Three
  * levels of output are available.
- * 
+ *
  * On the surface, JUnit treats "failures" (failed assertions) the same as
  * "errors" (unexpected exceptions). We're going to distinguish between them.
- * 
+ *
  * @author jeb228
  */
 public class VitroTestRunListener extends RunListener {
@@ -303,10 +303,10 @@ public class VitroTestRunListener extends RunListener {
 	/**
 	 * Trim the stack trace: don't show the line saying "23 more", and don't
 	 * show the lines about org.junit or java.lang.reflect or sun.reflect.
-	 * 
+	 *
 	 * Once we hit some "client code", we won't trim any futher lines even if
 	 * they belong to org.junit, or the others.
-	 * 
+	 *
 	 * If we have nested exceptions, the process repeats for each "Caused by"
 	 * section.
 	 */

legacy/utilities/buildutils/src/edu/cornell/mannlib/vitro/utilities/testing/VitroTestRunner.java

@@ -16,7 +16,7 @@ import org.junit.runner.JUnitCore;
  * It runs the tests with a variety of reporting detail, depending on the level
  * selected. If the level selector is absent or unrecognized, the medium level
  * is used.
- * 
+ *
  * @author jeb228
  */
 public class VitroTestRunner {

legacy/utilities/rdbmigration/src/edu/cornell/mannlib/vivo/utilities/rdbmigration/RdbMigrator.java

@@ -55,7 +55,7 @@ public class RdbMigrator {
 	/**
 	 * Confirm all of the parameters. Ask the user for approval. Do the
 	 * migration.
-	 * 
+	 *
 	 * @throws UserDeclinedException
 	 *             If the user decides not to continue.
 	 */

legacy/utilities/sdb_to_tdb/README.txt

@@ -3,17 +3,17 @@ A tool to convert triples from SDB to TDB.
 Unlike the RDF-migration tool, this tool is not tied to the VIVO
 properties files. Instead, you must provide:
 * The URL for the SDB, including username and password parameters
-* The directory path for the TDB. 
-     The directory must exist. 
+* The directory path for the TDB.
+     The directory must exist.
      The directory must be empty, unless the "force" optiopn is used.
 
 Examples:
 
-   java -jar sdb2tdb.jar \ 
-   		jdbc:mysql://localhost/vitrodb?user=vivoUser&password=vivoPass \ 
+   java -jar sdb2tdb.jar \
+   		jdbc:mysql://localhost/vitrodb?user=vivoUser&password=vivoPass \
    		/usr/local/my/tdb
-   		
+
    java -Xms512m -Xmx4096m -jar .work/sdb2tdb.jar \
         'jdbc:mysql://localhost/weill17?user=vivoUser&password=vivoPass' \
          /Users/jeb228/Testing/instances/weill-develop/vivo_home/contentTdb \
-         force   
+         force

legacy/utilities/sdb_to_tdb/src/edu/cornell/mannlib/vitro/utilities/sdb2tdb/Sdb2Tdb.java

@@ -40,25 +40,25 @@ import org.apache.jena.tdb.TDBFactory;
 /**
  * Copy all of the data from an SDB triple-store to a TDB triple-store. See
  * README.txt for more details.
- * 
+ *
  * Examples of invoking it:
- * 
+ *
  * <pre>
- *    java -jar sdb2tdb.jar \ 
- *    		'jdbc:mysql://localhost/vitrodb?user=vivoUser&password=vivoPass'\ 
+ *    java -jar sdb2tdb.jar \
+ *    		'jdbc:mysql://localhost/vitrodb?user=vivoUser&password=vivoPass'\
  *    		/usr/local/my/tdb
- *    
+ *
  *    java -Xms2048m -Xmx2048m -jar .work/sdb2tdb.jar \
  *          'jdbc:mysql://localhost/weill17?user=vivoUser&password=vivoPass' \
  *          /Users/jeb228/Testing/instances/weill-develop/vivo_home/contentTdb \
  *          force
  * </pre>
- * 
+ *
  * Each graph is copied separately. Small graphs are simply loaded into memory
  * and transferred. Large graphs are read to produce a streaming result set
  * which is written to a temporary file. That file is then read into a TDB
  * model.
- * 
+ *
  * This has been tested with graphs up to 6 million triples without crashing.
  */
 public class Sdb2Tdb {

legacy/utilities/solrtester/src/edu/cornell/mannlib/vitro/utilities/solrtest/SolrConfigTester.java

@@ -226,22 +226,22 @@ public class SolrConfigTester {
 
 /**
  * TODO
- * 
+ *
  * <pre>
  * // ** Let's index a document into our embedded server
- * 
+ *
  * SolrInputDocument newDoc = new SolrInputDocument();
  * newDoc.addField(&quot;title&quot;, &quot;Test Document 1&quot;);
  * newDoc.addField(&quot;id&quot;, &quot;doc-1&quot;);
  * newDoc.addField(&quot;text&quot;, &quot;Hello world!&quot;);
  * server.add(newDoc);
  * server.commit();
- * 
+ *
  * // ** And now let's query for it
- * 
+ *
  * params.set(&quot;q&quot;, &quot;title:test&quot;);
  * QueryResponse qResp = server.query(params);
- * 
+ *
  * SolrDocumentList docList = qResp.getResults();
  * System.out.println(&quot;Num docs: &quot; + docList.getNumFound());
  * SolrDocument doc = docList.get(0);

legacy/utilities/testrunner/test-user-model.owl

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
          xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
          xmlns:owl="http://www.w3.org/2002/07/owl#"
          xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
@@ -14,8 +14,8 @@
     <auth:lastName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Admin</auth:lastName>
     <auth:md5password rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DC647EB65E6711E155375218212B3964</auth:md5password>
     <auth:status rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVE</auth:status>
-    <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>  
-    <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>  
+    <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>
+    <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>
     <auth:hasPermissionSet rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/authorization#ADMIN"/>
 </auth:UserAccount>
 
@@ -26,8 +26,8 @@
     <auth:lastName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Curator</auth:lastName>
     <auth:md5password rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DC647EB65E6711E155375218212B3964</auth:md5password>
     <auth:status rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVE</auth:status>
-    <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>  
-    <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>  
+    <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>
+    <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>
     <auth:hasPermissionSet rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/authorization#CURATOR"/>
 </auth:UserAccount>
 
@@ -38,8 +38,8 @@
     <auth:lastName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Editor</auth:lastName>
     <auth:md5password rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DC647EB65E6711E155375218212B3964</auth:md5password>
     <auth:status rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVE</auth:status>
-    <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>  
-    <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>  
+    <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>
+    <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>
     <auth:hasPermissionSet rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/authorization#EDITOR"/>
 </auth:UserAccount>
 
@@ -50,8 +50,8 @@
     <auth:lastName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">User</auth:lastName>
     <auth:md5password rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DC647EB65E6711E155375218212B3964</auth:md5password>
     <auth:status rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ACTIVE</auth:status>
-    <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>  
-    <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>  
+    <auth:loginCount rdf:datatype="http://www.w3.org/2001/XMLSchema#int">1</auth:loginCount>
+    <auth:passwordLinkExpires rdf:datatype="http://www.w3.org/2001/XMLSchema#long">0</auth:passwordLinkExpires>
     <auth:hasPermissionSet rdf:resource="http://vitro.mannlib.cornell.edu/ns/vitro/authorization#SELF_EDITOR"/>
 </auth:UserAccount>