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

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This commit is contained in:
Mark H. Wood
2012-08-02 16:48:09 -04:00
parent 925606abe9 ffe1d1a9ff
commit 8bb7a3a50f
10 changed files with 851 additions and 625 deletions
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1
dspace-api/pom.xml
View File

@@ -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>

21
dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java
View File

@@ -87,12 +87,14 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Choic
{
class xmlFilter implements java.io.FilenameFilter
{
@Override
public boolean accept(File dir, String name)
{
return name.endsWith(".xml");
}
}
String vocabulariesPath = ConfigurationManager.getProperty("dspace.dir") + "/config/controlled-vocabularies/";
String vocabulariesPath = ConfigurationManager.getProperty("dspace.dir")
+ "/config/controlled-vocabularies/";
String[] xmlFiles = (new File(vocabulariesPath)).list(new xmlFilter());
List<String> names = new ArrayList<String>();
for (String filename : xmlFiles)
@@ -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();
@@ -162,7 +165,8 @@ 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,
vocabulary, XPathConstants.NODESET);
String[] authorities = new String[results.getLength()];
String[] values = new String[results.getLength()];
String[] labels = new String[results.getLength()];
@@ -186,15 +190,20 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Choic
{
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
authorities[i] = idAttr.getNodeValue();
}
int resultCount = Math.min(labels.length-start, limit);
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++)
{
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) {
@@ -203,6 +212,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Choic
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();

7
dspace-api/src/test/data/dspaceFolder/config/controlled-vocabularies/farm.xml Normal file
View File

@@ -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>

55
dspace-api/src/test/java/org/dspace/MockConfigurationManager.java Normal file
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@@ -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);
}
}

140
dspace-api/src/test/java/org/dspace/content/authority/DSpaceControlledVocabularyTest.java Normal file
View File

@@ -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.");
}
*/
}

38
dspace-stats/src/main/java/org/dspace/statistics/util/ApacheLogRobotsProcessor.java
View File

@@ -45,29 +45,39 @@ 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");
return;
logFileLoc = "-";
}
// Spider IP list
String spiderIpPath;
if (line.hasOption("s"))
{
spiderIpPath = line.getOptionValue("s");
}
else {
System.out.println("We need a spider IP output file");
return;
spiderIpPath = "-";
}
File spiderIpFile = new File(spiderIpPath);
//Get the IPs already added in our file
Set<String> logSpiders;
Writer output;
if ("-".equals(spiderIpPath))
{
logSpiders = new HashSet<String>();
output = new BufferedWriter(new OutputStreamWriter(System.out));
}
else
{
File spiderIpFile = new File(spiderIpPath);
if (spiderIpFile.exists())
{
logSpiders = SpiderDetector.readIpAddresses(spiderIpFile);
@@ -76,9 +86,16 @@ public class ApacheLogRobotsProcessor {
{
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");
}

60
dspace-stats/src/main/java/org/dspace/statistics/util/ClassicDSpaceLogConverter.java
View File

@@ -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("o", "out", true, "destination directory");
options.addOption("i", "in", true, "source file ('-' or omit for standard input)");
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());

27
dspace-stats/src/main/java/org/dspace/statistics/util/StatisticsImporter.java
View File

@@ -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;

1
dspace/modules/additions/pom.xml
View File

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

2
pom.xml
View File

@@ -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>