Merge remote-tracking branch 'upstream/master' into DS-861

dspace-api/pom.xml

@@ -111,6 +111,7 @@
                 <configuration>
                     <systemPropertyVariables>
                         <dspace.dir>${project.build.directory}/testing/dspace</dspace.dir>
+                        <dspace.dir.static>${basedir}/src/test/data/dspaceFolder</dspace.dir.static>
                         <dspace.configuration>${project.build.directory}/testing/dspace.cfg.woven</dspace.configuration>
                         <db.schema.path>${project.build.directory}/testing/dspace/etc/h2/database_schema.sql</db.schema.path>
                         <dspace.log.init.disable>true</dspace.log.init.disable>

dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java

@@ -55,7 +55,7 @@ import org.dspace.core.SelfNamedPlugin;
 public class DSpaceControlledVocabulary extends SelfNamedPlugin implements ChoiceAuthority
 {
 
-	private static Logger log = Logger.getLogger(DSpaceControlledVocabulary.class);
+    private static Logger log = Logger.getLogger(DSpaceControlledVocabulary.class);
     private static String xpathTemplate = "//node[contains(translate(@label,'ABCDEFGHIJKLMNOPQRSTUVWXYZ','abcdefghijklmnopqrstuvwxyz'),'%s')]";
     private static String idTemplate = "//node[@id = '%s']";
     private static String pluginNames[] = null;
@@ -85,22 +85,24 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Choic
     {
         if (pluginNames == null)
         {
-        	class xmlFilter implements java.io.FilenameFilter
+            class xmlFilter implements java.io.FilenameFilter
             {
-        		public boolean accept(File dir, String name)
+                @Override
+                public boolean accept(File dir, String name)
                 {
-        			return name.endsWith(".xml");
+                    return name.endsWith(".xml");
-        		}
+                }
-        	}
+            }
-            String vocabulariesPath = ConfigurationManager.getProperty("dspace.dir") + "/config/controlled-vocabularies/";
+            String vocabulariesPath = ConfigurationManager.getProperty("dspace.dir")
-        	String[] xmlFiles = (new File(vocabulariesPath)).list(new xmlFilter());
+                    + "/config/controlled-vocabularies/";
-        	List<String> names = new ArrayList<String>();
+            String[] xmlFiles = (new File(vocabulariesPath)).list(new xmlFilter());
-        	for (String filename : xmlFiles)
+            List<String> names = new ArrayList<String>();
+            for (String filename : xmlFiles)
             {
-        		names.add((new File(filename)).getName().replace(".xml",""));
+                names.add((new File(filename)).getName().replace(".xml", ""));
-        	}
+            }
-        	pluginNames = names.toArray(new String[names.size()]);
+            pluginNames = names.toArray(new String[names.size()]);
-            log.info("Got plugin names = "+Arrays.deepToString(pluginNames));
+            log.info("Got plugin names = " + Arrays.deepToString(pluginNames));
         }
     }
 
@@ -154,6 +156,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Choic
     	}
     }
 
+    @Override
     public Choices getMatches(String field, String text, int collection, int start, int limit, String locale)
     {
     	init();
@@ -162,47 +165,54 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Choic
     	XPath xpath = XPathFactory.newInstance().newXPath();
     	Choice[] choices;
     	try {
-    		NodeList results = (NodeList)xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODESET);
+            NodeList results = (NodeList) xpath.evaluate(xpathExpression,
-    		String[] authorities  = new String[results.getLength()];
+                    vocabulary, XPathConstants.NODESET);
-    		String[] values = new String[results.getLength()];
+            String[] authorities = new String[results.getLength()];
-    		String[] labels  = new String[results.getLength()];
+            String[] values = new String[results.getLength()];
-        	for (int i=0; i<results.getLength(); i++)
+            String[] labels = new String[results.getLength()];
+            for (int i = 0; i < results.getLength(); i++)
             {
-        		Node node = results.item(i);
+                Node node = results.item(i);
-        		String hierarchy = this.buildString(node);
+                String hierarchy = this.buildString(node);
-        		if (this.suggestHierarchy)
+                if (this.suggestHierarchy)
                 {
-        			labels[i] = hierarchy;
+                    labels[i] = hierarchy;
-        		}
+                }
                 else
                 {
-        			labels[i] = node.getAttributes().getNamedItem("label").getNodeValue();
+                    labels[i] = node.getAttributes().getNamedItem("label").getNodeValue();
-        		}
+                }
-        		if (this.storeHierarchy)
+                if (this.storeHierarchy)
                 {
-        			values[i] = hierarchy;
+                    values[i] = hierarchy;
-        		}
+                }
                 else
                 {
-        			values[i] = node.getAttributes().getNamedItem("label").getNodeValue();
+                    values[i] = node.getAttributes().getNamedItem("label").getNodeValue();
-        		}
+                }
-        		authorities[i] = node.getAttributes().getNamedItem("id").getNodeValue();
+                Node idAttr = node.getAttributes().getNamedItem("id");
-        	}
+                if (null != idAttr) // 'id' is optional
-        	int resultCount = Math.min(labels.length-start, limit);
+                    authorities[i] = idAttr.getNodeValue();
-        	choices = new Choice[resultCount];
+            }
-        	if (resultCount > 0)
+            int resultCount = labels.length - start;
+            if ((limit > 0) && (resultCount > limit)) // limit = 0 means no limit
+                resultCount = limit;
+            choices = new Choice[resultCount];
+            if (resultCount > 0)
             {
-            	for (int i=0; i<resultCount; i++)
+                for (int i = 0; i < resultCount; i++)
                 {
-           			choices[i] = new Choice(authorities[start+i],values[start+i],labels[start+i]);
+                    choices[i] = new Choice(authorities[start + i], values[start
-            	}
+                            + i], labels[start + i]);
-        	}
+                }
+            }
     	} catch(XPathExpressionException e) {
     		choices = new Choice[0];
     	}
     	return new Choices(choices, 0, choices.length, Choices.CF_AMBIGUOUS, false);
     }
 
+    @Override
     public Choices getBestMatch(String field, String text, int collection, String locale)
     {
     	init();
@@ -210,6 +220,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Choic
         return getMatches(field, text, collection, 0, 2, locale);
     }
 
+    @Override
     public String getLabel(String field, String key, String locale)
     {
     	init();

dspace-api/src/test/data/dspaceFolder/config/controlled-vocabularies/farm.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<node label='the farm'>
+ <isComposedBy>
+  <node label='north 40'/>
+  <node id='s40' label='south 40'/>
+ </isComposedBy>
+</node>

dspace-api/src/test/java/org/dspace/MockConfigurationManager.java

@@ -0,0 +1,55 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+
+package org.dspace;
+
+import java.util.Properties;
+import mockit.Mock;
+import mockit.MockClass;
+import org.dspace.core.ConfigurationManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Dummy ConfigurationManager with a setter instead of external storage for
+ * values.  Call {@link setProperty} to create configuration.
+ *
+ * <p>Please note that this implementation is incomplete!</p>
+ *
+ * @author mwood
+ */
+@MockClass(realClass=ConfigurationManager.class)
+public class MockConfigurationManager {
+    private static final Properties properties = new Properties();
+    private static final Logger log = LoggerFactory.getLogger(MockConfigurationManager.class);
+
+    /**
+     * Set a value in the configuration map.
+     *
+     * @param key name of the configuration datum.
+     * @param value value to be assigned to the name.
+     */
+    public static void setProperty(String key, String value)
+    {
+        log.info("setProperty({}, {});", key, value);
+        properties.setProperty(key, value);
+    }
+
+    /**
+     * Fetch a value from the map.
+     *
+     * @param key name of the configuration property desired.
+     * @return value bound to that name, or null if not set.
+     */
+    @Mock
+    public static String getProperty(String key)
+    {
+        log.info("getProperty({});", key);
+        return properties.getProperty(key);
+    }
+}

dspace-api/src/test/java/org/dspace/content/authority/DSpaceControlledVocabularyTest.java

@@ -0,0 +1,140 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.authority;
+
+import java.io.IOException;
+import mockit.UsingMocksAndStubs;
+import org.dspace.MockConfigurationManager;
+import org.dspace.core.PluginManager;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import org.junit.*;
+
+/**
+ * Unit tests for DSpaceControlledVocabulary.
+ *
+ * @author mwood
+ */
+@UsingMocksAndStubs(value=MockConfigurationManager.class)
+public class DSpaceControlledVocabularyTest
+{
+    public DSpaceControlledVocabularyTest()
+    {
+    }
+
+    @BeforeClass
+    public static void setUpClass()
+            throws Exception
+    {
+    }
+
+    @AfterClass
+    public static void tearDownClass()
+            throws Exception
+    {
+    }
+
+    @Before
+    public void setUp()
+    {
+    }
+
+    @After
+    public void tearDown()
+    {
+    }
+
+    /**
+     * Test of getPluginNames method, of class DSpaceControlledVocabulary.
+     */
+/*
+    @Test
+    public void testGetPluginNames()
+    {
+        System.out.println("getPluginNames");
+        String[] expResult = null;
+        String[] result = DSpaceControlledVocabulary.getPluginNames();
+        assertEquals(expResult, result);
+        // TODO review the generated test code and remove the default call to fail.
+        fail("The test case is a prototype.");
+    }
+*/
+
+    /**
+     * Test of getMatches method, of class DSpaceControlledVocabulary.
+     */
+    @Test
+    public void testGetMatches() throws IOException, ClassNotFoundException
+    {
+        System.out.println("getMatches");
+
+        // Set up the PluginManager
+        final String PLUGIN_INTERFACE = "org.dspace.content.authority.ChoiceAuthority";
+        final String PLUGIN_NAME = "org.dspace.content.authority.DSpaceControlledVocabulary";
+
+        MockConfigurationManager.setProperty("dspace.dir",
+                System.getProperty("dspace.dir.static"));
+        MockConfigurationManager.setProperty(
+                "plugin.selfnamed." + PLUGIN_INTERFACE, PLUGIN_NAME);
+
+        // Ensure that 'id' attribute is optional
+        String field = null; // not used
+        String text = "north 40";
+        int collection = 0;
+        int start = 0;
+        int limit = 0;
+        String locale = null;
+        DSpaceControlledVocabulary instance = (DSpaceControlledVocabulary)
+                PluginManager.getNamedPlugin(Class.forName(PLUGIN_INTERFACE), "farm");
+        assertNotNull(instance);
+        Choices result = instance.getMatches(field, text, collection, start,
+                limit, locale);
+        assertEquals("the farm::north 40", result.values[0].value);
+    }
+
+    /**
+     * Test of getBestMatch method, of class DSpaceControlledVocabulary.
+     */
+/*
+    @Test
+    public void testGetBestMatch()
+    {
+        System.out.println("getBestMatch");
+        String field = "";
+        String text = "";
+        int collection = 0;
+        String locale = "";
+        DSpaceControlledVocabulary instance = new DSpaceControlledVocabulary();
+        Choices expResult = null;
+        Choices result = instance.getBestMatch(field, text, collection, locale);
+        assertEquals(expResult, result);
+        // TODO review the generated test code and remove the default call to fail.
+        fail("The test case is a prototype.");
+    }
+*/
+
+    /**
+     * Test of getLabel method, of class DSpaceControlledVocabulary.
+     */
+/*
+    @Test
+    public void testGetLabel()
+    {
+        System.out.println("getLabel");
+        String field = "";
+        String key = "";
+        String locale = "";
+        DSpaceControlledVocabulary instance = new DSpaceControlledVocabulary();
+        String expResult = "";
+        String result = instance.getLabel(field, key, locale);
+        assertEquals(expResult, result);
+        // TODO review the generated test code and remove the default call to fail.
+        fail("The test case is a prototype.");
+    }
+*/
+}

dspace-stats/src/main/java/org/dspace/statistics/util/ApacheLogRobotsProcessor.java

@@ -45,40 +45,57 @@ public class ApacheLogRobotsProcessor {
 
         CommandLine line = parser.parse(options, args);
 
+        // Log source
         String logFileLoc;
-        String spiderIpPath;
         if (line.hasOption("l"))
         {
             logFileLoc = line.getOptionValue("l");
         }
         else {
-            System.out.println("We need our log file");
+            logFileLoc = "-";
-            return;
         }
+
+        // Spider IP list
+        String spiderIpPath;
         if (line.hasOption("s"))
         {
             spiderIpPath = line.getOptionValue("s");
         }
         else {
-            System.out.println("We need a spider IP output file");
+            spiderIpPath = "-";
-            return;
         }
 
-        File spiderIpFile = new File(spiderIpPath);
-
         //Get the IPs already added in our file
         Set<String> logSpiders;
-        if (spiderIpFile.exists())
+        Writer output;
+
+        if ("-".equals(spiderIpPath))
         {
-            logSpiders = SpiderDetector.readIpAddresses(spiderIpFile);
+            logSpiders = new HashSet<String>();
+            output = new BufferedWriter(new OutputStreamWriter(System.out));
         }
         else
         {
-            logSpiders = new HashSet<String>();
+            File spiderIpFile = new File(spiderIpPath);
+
+            if (spiderIpFile.exists())
+            {
+                logSpiders = SpiderDetector.readIpAddresses(spiderIpFile);
+            }
+            else
+            {
+                logSpiders = new HashSet<String>();
+            }
+            output = new BufferedWriter(new FileWriter(spiderIpFile));
         }
 
         //First read in our log file line per line
-        BufferedReader in = new BufferedReader(new FileReader(logFileLoc));
+        BufferedReader in;
+        if ("-".equals(logFileLoc))
+            in = new BufferedReader(new InputStreamReader(System.in));
+        else
+            in = new BufferedReader(new FileReader(logFileLoc));
+
         String logLine;
         while ((logLine = in.readLine()) != null) {
             //Currently only check if robot.txt is present in our line
@@ -92,11 +109,8 @@ public class ApacheLogRobotsProcessor {
         in.close();
 
         //Last but not least add the IPs to our file
-        BufferedWriter output = new BufferedWriter(new FileWriter(spiderIpFile));
-
-        //Second write the new IPs
         for (String ip : logSpiders) {
-            System.out.println("Adding new ip: " + ip);
+            System.err.println("Adding new ip: " + ip);
             //Write each new IP on a separate line
             output.write(ip + "\n");
         }

dspace-stats/src/main/java/org/dspace/statistics/util/ClassicDSpaceLogConverter.java

@@ -85,16 +85,37 @@ public class ClassicDSpaceLogConverter {
         int counter = 0;
         int lines = 0;
         
+        // Figure out input, output
+        BufferedReader input;
+        Writer output;
+        try {
+            if (null == in || in.isEmpty() || "-".equals(in))
+            {
+                input = new BufferedReader(new InputStreamReader(System.in));
+                in = "standard input";
+            }
+            else
+                input = new BufferedReader(new FileReader(in));
+
+            if (null == out || out.isEmpty() || "-".equals(out))
+            {
+                output = new BufferedWriter(new OutputStreamWriter(System.out));
+                out = "standard output";
+            }
+            else
+                output = new BufferedWriter(new FileWriter(out));
+        } catch (IOException ie) {
+            log.error("File access problem", ie);
+            return 0;
+        }
+
         // Say what we're going to do
-        System.out.println(" About to convert '" + in + "' to '" + out + "'");
+        System.err.println(" About to convert '" + in + "' to '" + out + "'");
 
         // Setup the regular expressions for the log file
         LogAnalyser.setRegex(in);
 
         // Open the file and read it line by line
-        BufferedReader input = null;
-        Writer output = null;
-
         try {
             String line;
             LogLine lline;
@@ -107,9 +128,6 @@ public class ClassicDSpaceLogConverter {
             String uid;
             String lastLine = "";
 
-            input =  new BufferedReader(new FileReader(new File(in)));
-            output = new BufferedWriter(new FileWriter(new File(out)));
-
             while ((line = input.readLine()) != null)
             {
                 // Read inthe line and covnert it to a LogLine
@@ -236,7 +254,7 @@ public class ClassicDSpaceLogConverter {
         }
 
         // Tell the user what we have done
-        System.out.println("  Read " + lines + " lines and recorded " + counter + " events");
+        System.err.println("  Read " + lines + " lines and recorded " + counter + " events");
         return counter;
     }
 
@@ -251,7 +269,7 @@ public class ClassicDSpaceLogConverter {
         // print the help message
         HelpFormatter myhelp = new HelpFormatter();
         myhelp.printHelp("ClassicDSpaceLogConverter\n", options);
-        System.out.println("\n\tClassicDSpaceLogConverter -i infilename -o outfilename -v (for verbose output)");
+        System.err.println("\n\tClassicDSpaceLogConverter -i infilename -o outfilename -v (for verbose output)");
         System.exit(exitCode);
     }
 
@@ -266,8 +284,8 @@ public class ClassicDSpaceLogConverter {
 
         Options options = new Options();
 
-        options.addOption("i", "in", true, "source file");
+        options.addOption("i", "in", true, "source file ('-' or omit for standard input)");
-        options.addOption("o", "out", true, "destination directory");
+        options.addOption("o", "out", true, "destination file or directory ('-' or omit for standard output)");
         options.addOption("m", "multiple",false, "treat the input file as having a wildcard ending");
         options.addOption("n", "newformat",false, "process new format log lines (1.6+)");
         options.addOption("v", "verbose", false, "display verbose output (useful for debugging)");
@@ -292,24 +310,6 @@ public class ClassicDSpaceLogConverter {
             printHelp(options, 0);
         }
 
-        // Check we have an input and output file
-        if ((!line.hasOption('i')) && (!line.hasOption('o')))
-        {
-            System.err.println("-i and -o input and output file names are required");
-            printHelp(options, 1);
-        }
-        else if (!line.hasOption('i'))
-        {
-            System.err.println("-i input file name is required");
-            printHelp(options, 1);
-        }
-
-        if (!line.hasOption('o'))
-        {
-            System.err.println("-o output file names is required");
-            printHelp(options, 1);
-        }
-
         // Whether or not to include event created by org.dspace.usage.LoggerUsageEventListener
         boolean newEvents = line.hasOption('n');
 
@@ -357,7 +357,7 @@ public class ClassicDSpaceLogConverter {
             String[] children = dir.list(filter);
             for (String in : children)
             {
-                System.out.println(in);
+                System.err.println(in);
                 String out = line.getOptionValue('o') +
                              (dir.getAbsolutePath() +
                               System.getProperty("file.separator") + in).substring(line.getOptionValue('i').length());

dspace-stats/src/main/java/org/dspace/statistics/util/StatisticsImporter.java

@@ -13,7 +13,6 @@ import org.apache.log4j.Logger;
 import org.apache.solr.common.SolrInputDocument;
 import org.apache.solr.client.solrj.impl.CommonsHttpSolrServer;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.*;
 import org.dspace.content.Collection;
 import org.dspace.core.Context;
@@ -22,7 +21,6 @@ import org.dspace.core.ConfigurationManager;
 import org.dspace.eperson.EPerson;
 import org.dspace.statistics.SolrLogger;
 
-import java.sql.SQLException;
 import java.text.*;
 import java.io.*;
 import java.util.*;
@@ -135,7 +133,7 @@ public class StatisticsImporter
     }
 
     /**
-     * Method to load the lines from the statics file and load them into solr
+     * Read lines from the statistics file and load their data into solr.
      *
      * @param filename The filename of the file to load
      * @param context The DSpace Context
@@ -143,9 +141,6 @@ public class StatisticsImporter
      */
     private void load(String filename, Context context, boolean verbose)
     {
-        // Print out the filename for confirmation
-        System.out.println("Processing file: " + filename);
-
         // Item counter
         int counter = 0;
         int errors = 0;
@@ -153,7 +148,17 @@ public class StatisticsImporter
 
         try
         {
-            BufferedReader input =  new BufferedReader(new FileReader(new File(filename)));
+            BufferedReader input;
+            if (null == filename || "-".equals(filename))
+            {
+                input = new BufferedReader(new InputStreamReader(System.in));
+                filename = "standard input";
+            }
+            else
+                input = new BufferedReader(new FileReader(new File(filename)));
+
+            // Print out the filename for confirmation
+            System.out.println("Processing file: " + filename);
 
             String line;
 //            String uuid;
@@ -426,7 +431,7 @@ public class StatisticsImporter
 
 		Options options = new Options();
 
-        options.addOption("i", "in", true, "the inpout file");
+        options.addOption("i", "in", true, "the input file ('-' or omit for standard input)");
         options.addOption("l", "local", false, "developers tool - map external log file to local handles");
         options.addOption("m", "multiple", false, "treat the input file as having a wildcard ending");
         options.addOption("s", "skipdns", false, "skip performing reverse DNS lookups on IP addresses");
@@ -441,12 +446,6 @@ public class StatisticsImporter
             printHelp(options, 0);
         }
 
-        if (!line.hasOption('i'))
-        {
-            System.err.println("You must specify an input file using the -i flag");
-            printHelp(options, 1);
-        }
-
         if (line.hasOption('s'))
         {
             skipReverseDNS = true;

dspace/modules/additions/pom.xml

@@ -94,7 +94,6 @@
       <dependency>
          <groupId>javax.servlet</groupId>
          <artifactId>servlet-api</artifactId>
-         <scope>provided</scope>
       </dependency>
       <dependency>
          <groupId>ant-contrib</groupId>

pom.xml

@@ -844,7 +844,7 @@
          <dependency>
             <groupId>postgresql</groupId>
             <artifactId>postgresql</artifactId>
-            <version>8.1-408.jdbc3</version>
+            <version>9.1-901-1.jdbc4</version>
          </dependency>
          <dependency>
             <groupId>com.oracle</groupId>