Merge pull request #115 from awoods/sprint-search

Update sprint-search to current develop branch

README.md

@@ -1,4 +1,7 @@
 # What is Vitro?
+
+[![Build Status](https://travis-ci.org/vivo-project/Vitro.png?branch=develop)](https://travis-ci.org/vivo-project/Vitro)
+
 Vitro is a general-purpose web-based ontology and instance editor with customizable public browsing. 
 
 Vitro is an integrated ontology editor and semantic web application.
@@ -13,7 +16,7 @@ With Vitro, you can:
 * Search your data with Apache Solr
 
 Vitro was originally developed at Cornell University, and is used as the core of the popular
-research and scholarship portal, [VIVO](http://vivoweb.org) .
+research and scholarship portal, [VIVO](https://duraspace.org/vivo/).
 
-For more information, contact the [VIVO community](http://www.vivoweb.org/support/user-feedback).
+For more information, contact the [VIVO community](https://duraspace.org/vivo/resources/contact/).
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/config/ConfigurationPropertiesSmokeTests.java

@@ -4,6 +4,13 @@ package edu.cornell.mannlib.vitro.webapp.config;
 
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.io.IOException;
+import java.util.List;
+import java.util.Arrays;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.nio.file.Path;
+import java.util.stream.Collectors;
 
 import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;
@@ -25,10 +32,11 @@ public class ConfigurationPropertiesSmokeTests implements
 			.getLog(ConfigurationPropertiesSmokeTests.class);
 
 	private static final String PROPERTY_DEFAULT_NAMESPACE = "Vitro.defaultNamespace";
-	private static final String PROPERTY_LANGUAGE_BUILD = "languages.addToBuild";
 	private static final String PROPERTY_LANGUAGE_SELECTABLE = "languages.selectableLocales";
 	private static final String PROPERTY_LANGUAGE_FORCE = "languages.forceLocale";
 	private static final String PROPERTY_LANGUAGE_FILTER = "RDFService.languageFilter";
+	private static final String VIVO_BUNDLE_PREFIX = "vivo_all_";
+	private static final String VITRO_BUNDLE_PREFIX = "all_";
 	private static final String PROPERTY_ARGON2_TIME = "argon2.time";
 	private static final String PROPERTY_ARGON2_MEMORY = "argon2.memory";
 	private static final String PROPERTY_ARGON2_PARALLELISM = "argon2.parallelism";
@@ -41,8 +49,9 @@ public class ConfigurationPropertiesSmokeTests implements
 
 		checkDefaultNamespace(ctx, props, ss);
 		checkMultipleRPFs(ctx, props, ss);
-		checkLanguages(props, ss);
+		checkLanguages(ctx, props, ss);
 		checkEncryptionParameters(props, ss);
+
 	}
 
 	/**
@@ -110,10 +119,7 @@ public class ConfigurationPropertiesSmokeTests implements
 	 * languages and force language. Shouldn't build with language unless
 	 * language filtering is enabled.
 	 */
-	private void checkLanguages(ConfigurationProperties props, StartupStatus ss) {
+	private void checkLanguages(ServletContext ctx, ConfigurationProperties props, StartupStatus ss) {
-		String buildString = props.getProperty(PROPERTY_LANGUAGE_BUILD);
-		boolean buildWithLanguages = StringUtils.isNotBlank(buildString);
-
 		String selectString = props.getProperty(PROPERTY_LANGUAGE_SELECTABLE);
 		boolean selectableLanguages = StringUtils.isNotBlank(selectString);
 
@@ -121,16 +127,44 @@ public class ConfigurationPropertiesSmokeTests implements
 		boolean forceLanguage = StringUtils.isNotBlank(forceString);
 
 		String filterString = props.getProperty(PROPERTY_LANGUAGE_FILTER,
-				"true");
+				"false");
 		boolean languageFilter = Boolean.valueOf(filterString);
+		String i18nDirPath = ctx.getRealPath("/i18n");
 
-		if (selectableLanguages && !buildWithLanguages) {
+		if (i18nDirPath == null) {
-			ss.warning(this, String.format("Problem with Language setup - "
+			throw new IllegalStateException(
-					+ "runtime.properties specifies a "
+					"Application does not have an /i18n directory.");
-					+ "list of selectable languages (%s = %s), but "
+		}
-					+ "build.properties did not include any languages with %s",
+
-					PROPERTY_LANGUAGE_SELECTABLE, selectString,
+		List<String> i18nNames = null;
-					PROPERTY_LANGUAGE_BUILD));
+
+		i18nNames = geti18nNames(i18nDirPath);
+
+		log.debug("i18nNames: " + i18nNames);
+
+		if (i18nNames.isEmpty()) {
+			ss.fatal(this, "The application found no files in '"
+					+ i18nDirPath
+					+ "' .");
+		}
+		else {
+			ss.info(this, "Base language files loaded: " + i18nNames);
+		}
+
+		/* Make sure language files exist for values in the selectableLocales propery.
+		   The prefixes of vitro and vivo are hard coded into the app,
+		   so we can assume the bundle names must have the same file format */
+		if (selectableLanguages) {
+			List<String> selectableLanguagesList = Arrays.asList(selectString.split("\\s*,\\s*"));
+			for (String language : selectableLanguagesList) {
+				String vivoBundle = VIVO_BUNDLE_PREFIX + language + ".properties";
+				String vitroBundle = VITRO_BUNDLE_PREFIX + language + ".properties";
+				if (!i18nNames.contains(vivoBundle) && !i18nNames.contains(vitroBundle)) {
+					ss.warning(this, language + " was found in the value for "
+						+ PROPERTY_LANGUAGE_SELECTABLE + " but no corresponding "
+							+ "language file was found.");
+				}
+			}
 		}
 
 		if (selectableLanguages && forceLanguage) {
@@ -142,17 +176,31 @@ public class ConfigurationPropertiesSmokeTests implements
 					PROPERTY_LANGUAGE_SELECTABLE, selectString));
 		}
 
-		if (buildWithLanguages && !languageFilter) {
+		if (selectableLanguages && !languageFilter) {
 			ss.warning(this, String.format("Problem with Language setup - "
-					+ "build.properties includes one or more additional "
+					+ "languages.selectableLocales in runtime.properties "
+					+ "includes one or more additional "
 					+ "languages (%s = %s), but runtime.properties has "
 					+ "disabled language filtering (%s = %s). This will "
 					+ "likely result in a mix of languages in the "
-					+ "application.", PROPERTY_LANGUAGE_BUILD, buildString,
+					+ "application.", PROPERTY_LANGUAGE_SELECTABLE, selectString,
 					PROPERTY_LANGUAGE_FILTER, filterString));
 		}
 	}
 
+	/** Create a list of the names of available language files. */
+	private List<String> geti18nNames(String i18nBaseDirPath) {
+		try {
+			return Files.walk(Paths.get(i18nBaseDirPath))
+					.filter(Files::isRegularFile)
+					.map(Path::getFileName)
+					.map(p -> {return p.toString();})
+					.collect(Collectors.toList());
+		} catch (IOException e) {
+			throw new RuntimeException("Failed to find language files", e);
+		}
+	}  
+
 	/**
 	 * Fail if there are no config properties for the Argon2 encryption.
 	 */
@@ -170,6 +218,7 @@ public class ConfigurationPropertiesSmokeTests implements
 			ss.fatal(this, "runtime.properties does not contain a value for '"
 					+ name + "'");
 			return;
+
 		}
 	}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/FreemarkerHttpServlet.java

@@ -17,6 +17,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import edu.cornell.mannlib.vitro.webapp.dao.jena.MenuDaoJena;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -461,7 +462,7 @@ public class FreemarkerHttpServlet extends VitroHttpServlet  {
     
     protected MainMenu getDisplayModelMenu(VitroRequest vreq){
         String url = vreq.getRequestURI().substring(vreq.getContextPath().length());
-        return vreq.getWebappDaoFactory().getMenuDao().getMainMenu(url);
+        return vreq.getWebappDaoFactory().getMenuDao().getMainMenu(vreq, url);
     }
     
     // NIHVIVO-3307: we need this here instead of FreemarkerConfiguration.java so that updates to

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/MenuDao.java

@@ -3,10 +3,19 @@ package edu.cornell.mannlib.vitro.webapp.dao;
 
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.menu.MainMenu;
 
+import javax.servlet.ServletRequest;
+
 public interface MenuDao {
     /**
      * @param url - url of request for setting active menu items. This should start with a / and not have the context path.
      * These values will be checked against urlMapping. ex. /people or /home 
      */
     public MainMenu getMainMenu( String url);
+
+    /**
+     * @param req - the ServletRequest for the current request
+     * @param url - url of request for setting active menu items. This should start with a / and not have the context path.
+     * These values will be checked against urlMapping. ex. /people or /home
+     */
+    public MainMenu getMainMenu(ServletRequest req, String url);
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/MenuDaoJena.java

@@ -5,9 +5,11 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
 import java.util.HashSet;
 import java.util.Set;
 
+import edu.cornell.mannlib.vitro.webapp.rdfservice.filter.LanguageFilteringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import org.apache.jena.ontology.OntModel;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryExecution;
 import org.apache.jena.query.QueryExecutionFactory;
@@ -23,6 +25,8 @@ import edu.cornell.mannlib.vitro.webapp.dao.MenuDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.menu.MainMenu;
 
+import javax.servlet.ServletRequest;
+
 public class MenuDaoJena extends JenaBaseDao implements MenuDao {
 
     private static final Log log = LogFactory.getLog(MenuDaoJena.class);
@@ -68,6 +72,10 @@ public class MenuDaoJena extends JenaBaseDao implements MenuDao {
         return getMenu( getOntModelSelector().getDisplayModel(), url );
     }
 
+    public MainMenu getMainMenu( ServletRequest req, String url ) {
+        OntModel displayModel = LanguageFilteringUtils.wrapOntModelInALanguageFilter(getOntModelSelector().getDisplayModel(), req );
+        return getMenu(displayModel,  url) ;
+    }
 
     protected MainMenu getMenu(Model displayModel, String url){
         //setup query parameters

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/WebappDaoFactoryJena.java

@@ -365,10 +365,8 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     @Override
 	public ObjectPropertyStatementDao getObjectPropertyStatementDao() {
         if( objectPropertyStatementDao == null )
-            // TODO supply a valid RDFService as the first argument if we keep this
-            // implementation
             objectPropertyStatementDao = new ObjectPropertyStatementDaoJena(
-                    null, dwf, this);
+                    rdfService, dwf, this);
         return objectPropertyStatementDao;
     }
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/sparql/RDFServiceSparql.java

@@ -19,6 +19,7 @@ import java.util.concurrent.ConcurrentLinkedQueue;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.apache.http.Consts;
 import org.apache.http.HttpResponse;
 import org.apache.http.auth.AuthScope;
 import org.apache.http.auth.AuthenticationException;
@@ -495,8 +496,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 	protected void executeUpdate(String updateString) throws RDFServiceException {
 		try {
 			HttpPost meth = new HttpPost(updateEndpointURI);
-			meth.addHeader("Content-Type", "application/x-www-form-urlencoded");
+			meth.addHeader("Content-Type", "application/x-www-form-urlencoded; charset="+Consts.UTF_8);
-			meth.setEntity(new UrlEncodedFormEntity(Arrays.asList(new BasicNameValuePair("update", updateString))));
+			meth.setEntity(new UrlEncodedFormEntity(Arrays.asList(new BasicNameValuePair("update", updateString)),Consts.UTF_8));
 			HttpContext context = getContext(meth);
 			HttpResponse response = context != null ? httpClient.execute(meth, context) : httpClient.execute(meth);
 			try {
@@ -510,6 +511,7 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
 				EntityUtils.consume(response.getEntity());
 			}
 		} catch (Exception e) {
+			log.debug("update string: \n" + updateString);
 			throw new RDFServiceException("Unable to perform change set update", e);
 		}
 	}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/searchindex/tasks/UpdateDocumentWorkUnit.java

@@ -176,8 +176,6 @@ public class UpdateDocumentWorkUnit implements Runnable {
 					classGroupUris.add(classGroupUri);
 				}
 
-				addToAlltext(doc, clz.getName());
-
 				Float boost = clz.getSearchBoost();
 				if (boost != null) {
 					doc.setDocumentBoost(doc.getDocumentBoost() + boost);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/web/templatemodels/customlistview/CustomListViewConfigFile.java

@@ -197,7 +197,12 @@ public class CustomListViewConfigFile {
 		 */
 		NodeList doomed = element.getElementsByTagName(tagName);
 		for (int i = doomed.getLength() - 1; i >= 0; i--) {
-			element.removeChild(doomed.item(i));
+			/*
+			 * As the node to be removed may be at an arbitrary depth in the DOM tree,
+			 * we need to get the parent of the node that we are trying to remove,
+			 * and then remove the child from there.
+			 */
+			doomed.item(i).getParentNode().removeChild(doomed.item(i));
 		}
 	}
 

api/src/test/java/edu/cornell/mannlib/vitro/webapp/controller/edit/AuthenticateTest.java

@@ -10,15 +10,18 @@ import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.fail;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
 import org.apache.log4j.Level;
 import org.junit.Before;
+import org.junit.BeforeClass;
 import org.junit.Ignore;
 import org.junit.Test;
 
@@ -119,16 +122,33 @@ public class AuthenticateTest extends AbstractTestClass {
 	private static final String NO_USER = "";
 	private static final String NO_MSG = "";
 
+	/**
+	 * Due to increased overhead of password hashing, create a list of UserAccount objects once
+	 * when the class is cloaded.
+	 *
+	 * These prepared user accounts will then be (re)used to populate the authenticator stubs prior to each test
+	 */
+	private static List<UserAccount> userAccounts = new ArrayList<>();
+
+	@BeforeClass
+	public static void prepareUserAccounts() {
+		userAccounts.add(createUserFromUserInfo(NEW_DBA));
+		userAccounts.add(createUserFromUserInfo(OLD_DBA));
+		userAccounts.add(createUserFromUserInfo(OLD_SELF));
+		userAccounts.add(createUserFromUserInfo(OLD_STRANGER));
+	}
+
 	@Before
 	public void setup() throws Exception {
 		I18nStub.setup();
 
 		authenticatorFactory = new AuthenticatorStub.Factory();
 		authenticator = authenticatorFactory.getInstance(request);
-		authenticator.addUser(createUserFromUserInfo(NEW_DBA));
+
-		authenticator.addUser(createUserFromUserInfo(OLD_DBA));
+		for (UserAccount account : userAccounts) {
-		authenticator.addUser(createUserFromUserInfo(OLD_SELF));
+			authenticator.addUser(account);
-		authenticator.addUser(createUserFromUserInfo(OLD_STRANGER));
+		}
+
 		authenticator.setAssociatedUri(OLD_SELF.username,
 				"old_self_associated_uri");
 
@@ -143,10 +163,9 @@ public class AuthenticateTest extends AbstractTestClass {
 		
 		userAccountsDao = new UserAccountsDaoStub();
 		userAccountsDao.addPermissionSet(adminPermissionSet);
-		userAccountsDao.addUser(createUserFromUserInfo(NEW_DBA));
+		for (UserAccount account : userAccounts) {
-		userAccountsDao.addUser(createUserFromUserInfo(OLD_DBA));
+			userAccountsDao.addUser(account);
-		userAccountsDao.addUser(createUserFromUserInfo(OLD_SELF));
+		}
-		userAccountsDao.addUser(createUserFromUserInfo(OLD_STRANGER));
 
 		individualDao = new IndividualDaoStub();
 
@@ -186,7 +205,7 @@ public class AuthenticateTest extends AbstractTestClass {
 				new HasPermissionFactory(servletContext));
 	}
 
-	private UserAccount createUserFromUserInfo(UserInfo userInfo) {
+	private static UserAccount createUserFromUserInfo(UserInfo userInfo) {
 		UserAccount user = new UserAccount();
 		user.setEmailAddress(userInfo.username);
 		user.setUri(userInfo.uri);

api/src/test/java/stubs/edu/cornell/mannlib/vitro/webapp/dao/MenuDaoStub.java

@@ -5,6 +5,8 @@ package stubs.edu.cornell.mannlib.vitro.webapp.dao;
 import edu.cornell.mannlib.vitro.webapp.dao.MenuDao;
 import edu.cornell.mannlib.vitro.webapp.web.templatemodels.menu.MainMenu;
 
+import javax.servlet.ServletRequest;
+
 /**
  * A minimal implementation of the MenuDao.
  * 
@@ -35,6 +37,11 @@ public class MenuDaoStub implements MenuDao {
 		return this.mainMenu;
 	}
 
+	@Override
+	public MainMenu getMainMenu(ServletRequest req, String url) {
+		return this.mainMenu;
+	}
+
 	// ----------------------------------------------------------------------
 	// Un-implemented methods
 	// ----------------------------------------------------------------------

installer/pom.xml

@@ -64,7 +64,7 @@
                 </plugin>
                 <plugin>
                     <artifactId>maven-compiler-plugin</artifactId>
-                    <version>3.5.1</version>
+                    <version>3.8.0</version>
                 </plugin>
                 <plugin>
                     <artifactId>maven-dependency-plugin</artifactId>

pom.xml

@@ -193,6 +193,30 @@
                 </plugins>
             </build>
         </profile>
+        <profile>
+            <!-- JDK 8 profile for the Error Prone plugin -->
+            <id>jdk8</id>
+            <activation>
+                <jdk>1.8</jdk>
+            </activation>
+            <properties>
+                <javac.version>9+181-r4173-1</javac.version>
+            </properties>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-compiler-plugin</artifactId>
+                        <configuration>
+                            <fork>true</fork>
+                            <compilerArgs combine.children="append">
+                                <arg>-J-Xbootclasspath/p:${settings.localRepository}/com/google/errorprone/javac/${javac.version}/javac-${javac.version}.jar</arg>
+                            </compilerArgs>
+                        </configuration>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
     </profiles>
 
     <build>
@@ -204,23 +228,18 @@
                     <source>1.8</source>
                     <target>1.8</target>
                     <encoding>UTF-8</encoding>
-                    <compilerId>javac-with-errorprone</compilerId>
+                    <compilerArgs>
-                    <forceJavacCompilerUse>true</forceJavacCompilerUse>
+                        <arg>-XDcompilePolicy=simple</arg>
+                        <arg>-Xplugin:ErrorProne</arg>
+                    </compilerArgs>
+                    <annotationProcessorPaths>
+                        <path>
+                            <groupId>com.google.errorprone</groupId>
+                            <artifactId>error_prone_core</artifactId>
+                            <version>2.3.2</version>
+                        </path>
+                    </annotationProcessorPaths>
                 </configuration>
-                <dependencies>
-                    <dependency>
-                        <groupId>org.codehaus.plexus</groupId>
-                        <artifactId>plexus-compiler-javac-errorprone</artifactId>
-                        <version>2.8</version>
-                    </dependency>
-                    <!-- override plexus-compiler-javac-errorprone's dependency on
-                         Error Prone with the latest version -->
-                    <dependency>
-                        <groupId>com.google.errorprone</groupId>
-                        <artifactId>error_prone_core</artifactId>
-                        <version>2.1.1</version>
-                    </dependency>
-                </dependencies>
             </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
@@ -267,7 +286,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-compiler-plugin</artifactId>
-                    <version>3.5.1</version>
+                    <version>3.8.0</version>
                 </plugin>
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>

webapp/src/main/webapp/templates/freemarker/page/page.ftl

@@ -24,7 +24,7 @@
         <hr class="hidden" />
 
         <div id="contentwrap">
-            <#include "flash.html">
+            <#include "flash.ftl">
 
             <div id="content">                      
                 ${body}