Merge branch 'maint-rel-1.6' of https://github.com/vivo-project/Vitro into maint-rel-1.6

This commit is contained in:
hudajkhan 2013-11-19 13:25:46 -05:00
commit 319c495617
37 changed files with 1584 additions and 524 deletions

View file

@ -76,6 +76,8 @@ public class SimplePermission extends Permission {
NAMESPACE + "UseAdvancedDataToolsPages");
public static final SimplePermission USE_SPARQL_QUERY_PAGE = new SimplePermission(
NAMESPACE + "UseSparqlQueryPage");
public static final SimplePermission ENABLE_DEVELOPER_PANEL = new SimplePermission(
NAMESPACE + "EnableDeveloperPanel");
// ----------------------------------------------------------------------

View file

@ -57,7 +57,7 @@ public class Classes2ClassesOperationController extends BaseEditController {
return;
}
VClassDao vcDao = request.getUnfilteredAssertionsWebappDaoFactory().getVClassDao();
VClassDao vcDao = request.getLanguageNeutralWebappDaoFactory().getVClassDao();
String modeStr = request.getParameter("opMode");
modeStr = (modeStr == null) ? "" : modeStr;

View file

@ -38,6 +38,7 @@ public class DelimitingTemplateLoader implements TemplateLoader {
@Override
public Object findTemplateSource(String name) throws IOException {
Object innerTS = innerLoader.findTemplateSource(name);
log.debug("template source for '" + name + "' is '" + innerTS + "'");
if (innerTS == null) {
return null;
} else {

View file

@ -1,162 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import freemarker.cache.TemplateLoader;
/**
* <p>
* A {@link TemplateLoader} that treats a directory and its sub-directories as a
* flat namespace.
* </p>
* <p>
* When a request is made to find a template source, the loader will search its
* base directory and any sub-directories for a file with a matching name. So a
* request for <code>myFile.ftl</code> might return a reference to a file at
* <code>base/myFile.ftl</code> or at <code>base/this/myFile.ftl</code>
* </p>
* <p>
* The order in which the sub-directories are searched is unspecified. The first
* matching file will be returned.
* </p>
* <p>
* A path (absolute or relative) on the source name would be meaningless, so any
* such path will be stripped before the search is made. That is, a request for
* <code>path/file.ftl</code> or <code>/absolute/path/file.ftl</code>is
* functionally identical to a request for <code>file.ftl</code>
* </p>
* <p>
* </p>
*/
public class FlatteningTemplateLoader implements TemplateLoader {
private static final Log log = LogFactory
.getLog(FlatteningTemplateLoader.class);
private final File baseDir;
public FlatteningTemplateLoader(File baseDir) {
if (baseDir == null) {
throw new NullPointerException("baseDir may not be null.");
}
if (!baseDir.exists()) {
throw new IllegalArgumentException("Template directory '"
+ baseDir.getAbsolutePath() + "' does not exist");
}
if (!baseDir.isDirectory()) {
throw new IllegalArgumentException("Template directory '"
+ baseDir.getAbsolutePath() + "' is not a directory");
}
if (!baseDir.canRead()) {
throw new IllegalArgumentException("Can't read template "
+ "directory '" + baseDir.getAbsolutePath() + "'");
}
log.debug("Created template loader - baseDir is '"
+ baseDir.getAbsolutePath() + "'");
this.baseDir = baseDir;
}
/**
* Look for a file by this name in the base directory, or its
* subdirectories, disregarding any path information.
*
* @return a {@link File} that can be used in subsequent calls the template
* loader methods, or <code>null</code> if no template is found.
*/
@Override
public Object findTemplateSource(String name) throws IOException {
if (name == null) {
return null;
}
int lastSlashHere = name.indexOf('/');
String trimmedName = (lastSlashHere == -1) ? name : name
.substring(lastSlashHere + 1);
// start the recursive search.
File source = findFile(trimmedName, baseDir);
if (source == null) {
log.debug("For template name '" + name
+ "', found no template file.");
} else {
log.debug("For template name '" + name + "', template file is "
+ source.getAbsolutePath());
}
return source;
}
/**
* Recursively search for a file of this name.
*/
private File findFile(String name, File dir) {
for (File child : dir.listFiles()) {
if (child.isDirectory()) {
File file = findFile(name, child);
if (file != null) {
return file;
}
} else {
if (child.getName().equals(name)) {
return child;
}
}
}
return null;
}
/**
* Ask the file when it was last modified.
*
* @param templateSource
* a {@link File} that was obtained earlier from
* {@link #findTemplateSource(String)}.
*/
@Override
public long getLastModified(Object templateSource) {
if (!(templateSource instanceof File)) {
throw new IllegalArgumentException("templateSource is not a File: "
+ templateSource);
}
return ((File) templateSource).lastModified();
}
/**
* Get a {@link Reader} on this {@link File}. The framework will see that
* the {@link Reader} is closed when it has been read.
*
* @param templateSource
* a {@link File} that was obtained earlier from
* {@link #findTemplateSource(String)}.
*/
@Override
public Reader getReader(Object templateSource, String encoding)
throws IOException {
if (!(templateSource instanceof File)) {
throw new IllegalArgumentException("templateSource is not a File: "
+ templateSource);
}
return new FileReader(((File) templateSource));
}
/**
* Nothing to do here. No resources to free up.
*
* @param templateSource
* a {@link File} that was obtained earlier from
* {@link #findTemplateSource(String)}.
*/
@Override
public void closeTemplateSource(Object templateSource) throws IOException {
}
}

View file

@ -1048,11 +1048,20 @@ public class VClassDaoJena extends JenaBaseDao implements VClassDao {
try {
OntResource subclass = getOntClass(ontModel,c2c.getSubclassURI());
OntResource superclass = getOntClass(ontModel,c2c.getSuperclassURI());
if(subclass == null || superclass == null) {
log.warn("unable to delete " + c2c.getSubclassURI() +
" rdfs:subClassOf " + c2c.getSuperclassURI());
if (subclass == null) {
log.warn(c2c.getSubclassURI() + " not found in the model.");
}
if (superclass == null) {
log.warn(c2c.getSuperclassURI() + " not found in the model.");
}
return;
}
Model removal = ModelFactory.createDefaultModel();
Model additions = ModelFactory.createDefaultModel(); // to repair any rdf:Lists
if ((subclass != null) && (superclass != null)) {
removal.add(ontModel.listStatements(subclass, RDFS.subClassOf, superclass));
}
removal.add(ontModel.listStatements(subclass, RDFS.subClassOf, superclass));
if (subclass.isAnon()) {
Model[] changeSet = getSmartRemoval(subclass, getOntModel());
removal.add(changeSet[0]);

View file

@ -336,11 +336,11 @@ public class RequestModelsPrep implements Filter {
}
/**
* Language awareness is enabled unless they explicitly disable it.
* Language awareness is disabled unless they explicitly enable it.
*/
private Boolean isLanguageAwarenessEnabled() {
return Boolean.valueOf(props.getProperty("RDFService.languageFilter",
"true"));
"false"));
}
private RDFService addLanguageAwareness(HttpServletRequest req,

View file

@ -3,7 +3,6 @@
package edu.cornell.mannlib.vitro.webapp.freemarker.config;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@ -18,15 +17,16 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.config.RevisionInfoBean;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.DelimitingTemplateLoader;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FlatteningTemplateLoader;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfigurationConstants;
import edu.cornell.mannlib.vitro.webapp.freemarker.loader.FreemarkerTemplateLoader;
import edu.cornell.mannlib.vitro.webapp.i18n.freemarker.I18nMethodModel;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings.Keys;
import edu.cornell.mannlib.vitro.webapp.web.directives.IndividualShortViewDirective;
import edu.cornell.mannlib.vitro.webapp.web.directives.UrlDirective;
import edu.cornell.mannlib.vitro.webapp.web.directives.WidgetDirective;
@ -34,7 +34,6 @@ import edu.cornell.mannlib.vitro.webapp.web.methods.IndividualLocalNameMethod;
import edu.cornell.mannlib.vitro.webapp.web.methods.IndividualPlaceholderImageUrlMethod;
import edu.cornell.mannlib.vitro.webapp.web.methods.IndividualProfileUrlMethod;
import freemarker.cache.ClassTemplateLoader;
import freemarker.cache.FileTemplateLoader;
import freemarker.cache.MultiTemplateLoader;
import freemarker.cache.TemplateLoader;
import freemarker.ext.beans.BeansWrapper;
@ -55,18 +54,17 @@ import freemarker.template.TemplateModelException;
* own locale, etc.
*
* Each time a request asks for the configuration, check to see whether the
* cache is still valid, and whether the theme has changed (needs a new
* TemplateLoader). Store the request info to the ThreadLocal.
* cache is still valid, whether the theme has changed (needs a new
* TemplateLoader), and whether the DeveloperSettings have changed (might need a
* new TemplateLoader). Store the request info to the ThreadLocal.
*/
public abstract class FreemarkerConfiguration {
private static final Log log = LogFactory
.getLog(FreemarkerConfiguration.class);
private static final String PROPERTY_DEFEAT_CACHE = "developer.defeatFreemarkerCache";
private static final String PROPERTY_INSERT_DELIMITERS = "developer.insertFreemarkerDelimiters";
private static volatile FreemarkerConfigurationImpl instance;
private static volatile String previousThemeDir;
private static volatile Map<String, Object> previousSettingsMap;
public static Configuration getConfig(HttpServletRequest req) {
confirmInstanceIsSet();
@ -92,14 +90,12 @@ public abstract class FreemarkerConfiguration {
}
}
/** If the developer doesn't want the cache, it's invalid. */
private static boolean isTemplateCacheInvalid(HttpServletRequest req) {
ConfigurationProperties props = ConfigurationProperties.getBean(req);
// If the developer doesn't want the cache, it's invalid.
if (Boolean.valueOf(props.getProperty(PROPERTY_DEFEAT_CACHE))) {
DeveloperSettings settings = DeveloperSettings.getBean(req);
if (settings.getBoolean(Keys.DEFEAT_FREEMARKER_CACHE)) {
return true;
}
return false;
}
@ -113,7 +109,8 @@ public abstract class FreemarkerConfiguration {
private static void keepTemplateLoaderCurrentWithThemeDirectory(
HttpServletRequest req) {
String themeDir = getThemeDirectory(req);
if (hasThemeDirectoryChanged(themeDir)) {
if (hasThemeDirectoryChanged(themeDir)
|| haveDeveloperSettingsChanged(req)) {
TemplateLoader tl = createTemplateLoader(req, themeDir);
instance.setTemplateLoader(tl);
}
@ -134,44 +131,48 @@ public abstract class FreemarkerConfiguration {
}
}
private static boolean haveDeveloperSettingsChanged(HttpServletRequest req) {
Map<String, Object> settingsMap = DeveloperSettings.getBean(req)
.getSettingsMap();
if (settingsMap.equals(previousSettingsMap)) {
return false;
} else {
previousSettingsMap = settingsMap;
return true;
}
}
private static TemplateLoader createTemplateLoader(HttpServletRequest req,
String themeDir) {
ServletContext ctx = req.getSession().getServletContext();
ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
List<TemplateLoader> loaders = new ArrayList<TemplateLoader>();
// Theme template loader
// Theme template loader - only if the theme has a template directory.
String themeTemplatePath = ctx.getRealPath(themeDir) + "/templates";
File themeTemplateDir = new File(themeTemplatePath);
// A theme need not contain a template directory.
if (themeTemplateDir.exists()) {
try {
FileTemplateLoader themeFtl = new FileTemplateLoader(
themeTemplateDir);
loaders.add(themeFtl);
} catch (IOException e) {
log.error("Error creating theme template loader", e);
}
loaders.add(new FreemarkerTemplateLoader(themeTemplateDir));
}
// Vitro template loader
String vitroTemplatePath = ctx.getRealPath("/templates/freemarker");
loaders.add(new FlatteningTemplateLoader(new File(vitroTemplatePath)));
loaders.add(new FreemarkerTemplateLoader(new File(vitroTemplatePath)));
// TODO VIVO-243 Why is this here?
loaders.add(new ClassTemplateLoader(FreemarkerConfiguration.class, ""));
TemplateLoader[] loaderArray = loaders
.toArray(new TemplateLoader[loaders.size()]);
MultiTemplateLoader mtl = new MultiTemplateLoader(loaderArray);
TemplateLoader tl = new MultiTemplateLoader(loaderArray);
// If requested, add delimiters to the templates.
if (Boolean.valueOf(props.getProperty(PROPERTY_INSERT_DELIMITERS))) {
return new DelimitingTemplateLoader(mtl);
} else {
return mtl;
DeveloperSettings settings = DeveloperSettings.getBean(req);
if (settings.getBoolean(Keys.INSERT_FREEMARKER_DELIMITERS)) {
tl = new DelimitingTemplateLoader(tl);
}
return tl;
}
private static void setThreadLocalsForRequest(HttpServletRequest req) {

View file

@ -287,6 +287,7 @@ public class FreemarkerConfigurationImpl extends Configuration {
urls.put("images", UrlBuilder.getUrl("/images"));
urls.put("theme", UrlBuilder.getUrl(themeDir));
urls.put("index", UrlBuilder.getUrl("/browse"));
urls.put("developerAjax", UrlBuilder.getUrl("/admin/developerAjax"));
return urls;
}

View file

@ -0,0 +1,314 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.freemarker.loader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import java.nio.file.FileVisitResult;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.SimpleFileVisitor;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.Comparator;
import java.util.SortedSet;
import java.util.TreeSet;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import freemarker.cache.TemplateLoader;
/**
* Loads Freemarker templates from a given directory.
*
* Different from a file loader in two ways:
*
* 1) Flattens the directory. When it searches for a template, it will look in
* the base directory and in any sub-directories. While doing this, it ignores
* any path that is attached to the template name.
*
* So if you were to ask for 'admin/silly.ftl', it would search for 'silly.ftl'
* in the base directory, and in any sub-directories, until it finds one.
*
* 2) Accepts approximate matches on locales. When asked for a template, it will
* accepts an approximate match that matches the basename and extension, and
* language or region if specifed. So a search for a template with no language
* or region will prefer an exact match, but will accept one with language or
* both language and region.
*
* <pre>
* "this_es_MX.ftl" matches "this_es_MX.ftl"
* "this_es.ftl" matches "this_es.ftl" or "this_es_MX.ftl"
* "this.ftl" matches "this.ftl" or "this_es.ftl" or "this_es_MX.ftl"
* </pre>
*
* This allows Freemarker to mimic the behavior of the language filtering RDF
* service, because if Freemarker does not find a match for "this_es_MX.ftl", it
* will try again with "this_es.ftl" and "this.ftl". So the net effect is that a
* search for "silly_es_MX.ftl" would eventually return any of these, in order
* of preference:
*
* <pre>
* silly_es_MX.ftl
* silly_es.ftl
* silly_es_*.ftl
* silly.ftl
* silly_*.ftl
* </pre>
*
* If more than one template file qualifies, we choose by best fit, shortest
* path, and alphabetical order, to insure that identical requests produce
* identical results.
*/
public class FreemarkerTemplateLoader implements TemplateLoader {
private static final Log log = LogFactory
.getLog(FreemarkerTemplateLoader.class);
private final File baseDir;
public FreemarkerTemplateLoader(File baseDir) {
if (baseDir == null) {
throw new NullPointerException("baseDir may not be null.");
}
String path = baseDir.getAbsolutePath();
if (!baseDir.exists()) {
throw new IllegalArgumentException("Template directory '" + path
+ "' does not exist");
}
if (!baseDir.isDirectory()) {
throw new IllegalArgumentException("Template directory '" + path
+ "' is not a directory");
}
if (!baseDir.canRead()) {
throw new IllegalArgumentException(
"Can't read template directory '" + path + "'");
}
log.debug("Created template loader - baseDir is '" + path + "'");
this.baseDir = baseDir;
}
/**
* Get the best template for this name. Walk the tree finding all possible
* matches, then choose our favorite.
*/
@Override
public Object findTemplateSource(String name) throws IOException {
if (StringUtils.isBlank(name)) {
return null;
}
SortedSet<PathPieces> matches = findAllMatches(new PathPieces(name));
if (matches.isEmpty()) {
return null;
} else {
return matches.last().path.toFile();
}
}
private SortedSet<PathPieces> findAllMatches(PathPieces searchTerm) {
PathPiecesFileVisitor visitor = new PathPiecesFileVisitor(searchTerm);
try {
Files.walkFileTree(baseDir.toPath(), visitor);
} catch (IOException e) {
log.error(e);
}
return visitor.getMatches();
}
/**
* Ask the file when it was last modified.
*
* @param templateSource
* a File that was obtained earlier from findTemplateSource().
*/
@Override
public long getLastModified(Object templateSource) {
return asFile(templateSource).lastModified();
}
/**
* Get a Reader on this File. The framework will close the Reader after
* reading it.
*
* @param templateSource
* a File that was obtained earlier from findTemplateSource().
*/
@Override
public Reader getReader(Object templateSource, String encoding)
throws IOException {
return new FileReader(asFile(templateSource));
}
/**
* Nothing to do here. No resources to free up.
*
* @param templateSource
* a File that was obtained earlier from findTemplateSource().
*/
@Override
public void closeTemplateSource(Object templateSource) throws IOException {
// Nothing to do.
}
/**
* That templateSource is a File, right?
*/
private File asFile(Object templateSource) {
if (templateSource instanceof File) {
return (File) templateSource;
} else {
throw new IllegalArgumentException("templateSource is not a File: "
+ templateSource);
}
}
// ----------------------------------------------------------------------
// Helper classes
// ----------------------------------------------------------------------
/**
* Break a path into handy segments, so we can see whether they match the
* search term, and how well they match.
*/
static class PathPieces {
final Path path;
final String base;
final String language;
final String region;
final String extension;
public PathPieces(String searchTerm) {
this(Paths.get(searchTerm));
}
public PathPieces(Path path) {
this.path = path;
String filename = path.getFileName().toString();
int dotHere = filename.lastIndexOf('.');
String basename;
if (dotHere != -1) {
basename = filename.substring(0, dotHere);
this.extension = filename.substring(dotHere);
} else {
basename = filename;
this.extension = "";
}
int break2 = basename.lastIndexOf('_');
int break1 = basename.lastIndexOf('_', break2 - 1);
if (break1 != -1) {
this.base = basename.substring(0, break1);
this.language = basename.substring(break1, break2);
this.region = basename.substring(break2);
} else if (break2 != -1) {
this.base = basename.substring(0, break2);
this.language = basename.substring(break2);
this.region = "";
} else {
this.base = basename;
this.language = "";
this.region = "";
}
}
/** This is the search term. Does that candidate qualify as a result? */
public boolean matches(PathPieces that) {
return base.equals(that.base) && extension.equals(that.extension)
&& (language.isEmpty() || language.equals(that.language))
&& (region.isEmpty() || region.equals(that.region));
}
public int score(PathPieces that) {
if (matches(that)) {
if (that.language.equals(language)) {
if (that.region.equals(region)) {
return 3; // match language and region
} else {
return 2; // match language, default region.
}
} else {
return 1; // default language.
}
} else {
return -1; // doesn't match.
}
}
@Override
public String toString() {
return "PathPieces[" + base + ", " + language + ", " + region
+ ", " + extension + "]";
}
}
/**
* While walking the file tree, collect all files that match the search
* term, as a sorted set of PathPieces.
*/
static class PathPiecesFileVisitor extends SimpleFileVisitor<Path> {
private final PathPieces searchTerm;
private final SortedSet<PathPieces> matches;
public PathPiecesFileVisitor(PathPieces searchTerm) {
this.searchTerm = searchTerm;
this.matches = new TreeSet<>(new PathPiecesComparator(searchTerm));
}
@Override
public FileVisitResult visitFile(Path path, BasicFileAttributes attrs)
throws IOException {
if (fileQualifies(path)) {
PathPieces found = new PathPieces(path);
if (searchTerm.matches(found)) {
matches.add(found);
}
}
return FileVisitResult.CONTINUE;
}
public boolean fileQualifies(Path path) {
return Files.isRegularFile(path) && Files.isReadable(path);
}
public SortedSet<PathPieces> getMatches() {
return matches;
}
}
/**
* Produce an ordering of paths by desirability. Best match, then shortest
* directory path, and finally alphabetical order.
*/
static class PathPiecesComparator implements Comparator<PathPieces> {
private final PathPieces searchFor;
public PathPiecesComparator(PathPieces searchFor) {
this.searchFor = searchFor;
}
@Override
public int compare(PathPieces p1, PathPieces p2) {
int scoring = searchFor.score(p1) - searchFor.score(p2);
if (scoring != 0) {
return scoring; // prefer matches to region and language
}
int pathLength = p1.path.getNameCount() - p2.path.getNameCount();
if (pathLength != 0) {
return -pathLength; // shorter is better
}
return -p1.path.compareTo(p2.path); // early in alphabet is better
}
}
}

View file

@ -15,8 +15,9 @@ import javax.servlet.http.HttpServletRequest;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings.Keys;
/**
* Provides access to a bundle of text strings, based on the name of the bundle,
@ -31,7 +32,6 @@ public class I18n {
private static final Log log = LogFactory.getLog(I18n.class);
public static final String DEFAULT_BUNDLE_NAME = "all";
private static final String PROPERTY_DEVELOPER_DEFEAT_CACHE = "developer.defeatI18nCache";
/**
* If this attribute is present on the request, then the cache has already
@ -103,6 +103,7 @@ public class I18n {
protected I18nBundle getBundle(String bundleName, HttpServletRequest req) {
log.debug("Getting bundle '" + bundleName + "'");
I18nLogger i18nLogger = new I18nLogger(req);
try {
checkDevelopmentMode(req);
checkForChangeInThemeDirectory(req);
@ -113,13 +114,13 @@ public class I18n {
ResourceBundle.Control control = new ThemeBasedControl(ctx, dir);
ResourceBundle rb = ResourceBundle.getBundle(bundleName,
req.getLocale(), control);
return new I18nBundle(bundleName, rb);
return new I18nBundle(bundleName, rb, i18nLogger);
} catch (MissingResourceException e) {
log.warn("Didn't find text bundle '" + bundleName + "'");
return I18nBundle.emptyBundle(bundleName);
return I18nBundle.emptyBundle(bundleName, i18nLogger);
} catch (Exception e) {
log.error("Failed to create text bundle '" + bundleName + "'", e);
return I18nBundle.emptyBundle(bundleName);
return I18nBundle.emptyBundle(bundleName, i18nLogger);
}
}
@ -127,11 +128,7 @@ public class I18n {
* If we are in development mode, clear the cache on each request.
*/
private void checkDevelopmentMode(HttpServletRequest req) {
ConfigurationProperties bean = ConfigurationProperties.getBean(req);
String flag = bean
.getProperty(PROPERTY_DEVELOPER_DEFEAT_CACHE, "false");
if (Boolean.valueOf(flag.trim())) {
if (DeveloperSettings.getBean(req).getBoolean(Keys.I18N_DEFEAT_CACHE) ) {
log.debug("In development mode - clearing the cache.");
clearCacheOnRequest(req);
}

View file

@ -24,24 +24,28 @@ public class I18nBundle {
private static final String MESSAGE_BUNDLE_NOT_FOUND = "Text bundle ''{0}'' not found.";
private static final String MESSAGE_KEY_NOT_FOUND = "Text bundle ''{0}'' has no text for ''{1}''";
public static I18nBundle emptyBundle(String bundleName) {
return new I18nBundle(bundleName);
public static I18nBundle emptyBundle(String bundleName,
I18nLogger i18nLogger) {
return new I18nBundle(bundleName, i18nLogger);
}
private final String bundleName;
private final ResourceBundle resources;
private final String notFoundMessage;
private final I18nLogger i18nLogger;
private I18nBundle(String bundleName) {
this(bundleName, new EmptyResourceBundle(), MESSAGE_BUNDLE_NOT_FOUND);
private I18nBundle(String bundleName, I18nLogger i18nLogger) {
this(bundleName, new EmptyResourceBundle(), MESSAGE_BUNDLE_NOT_FOUND,
i18nLogger);
}
public I18nBundle(String bundleName, ResourceBundle resources) {
this(bundleName, resources, MESSAGE_KEY_NOT_FOUND);
public I18nBundle(String bundleName, ResourceBundle resources,
I18nLogger i18nLogger) {
this(bundleName, resources, MESSAGE_KEY_NOT_FOUND, i18nLogger);
}
private I18nBundle(String bundleName, ResourceBundle resources,
String notFoundMessage) {
String notFoundMessage, I18nLogger i18nLogger) {
if (bundleName == null) {
throw new IllegalArgumentException("bundleName may not be null");
}
@ -57,22 +61,27 @@ public class I18nBundle {
this.bundleName = bundleName;
this.resources = resources;
this.notFoundMessage = notFoundMessage;
this.i18nLogger = i18nLogger;
}
public String text(String key, Object... parameters) {
String textString;
if (resources.containsKey(key)) {
textString = resources.getString(key);
log.debug("In '" + bundleName + "', " + key + "='" + textString
+ "')");
return formatString(textString, parameters);
} else {
String message = MessageFormat.format(notFoundMessage, bundleName,
key);
log.warn(message);
return "ERROR: " + message;
textString = "ERROR: " + message;
}
String result = formatString(textString, parameters);
if (i18nLogger != null) {
i18nLogger.log(bundleName, key, parameters, textString, result);
}
return result;
}
private static String formatString(String textString, Object... parameters) {

View file

@ -0,0 +1,47 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.i18n;
import java.util.Arrays;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings.Keys;
/**
* If enabled in developer mode, write a message to the log each time someone
* asks for a language string.
*
* The I18nBundle has a life span of one HTTP request, and so does this.
*/
public class I18nLogger {
private static final Log log = LogFactory.getLog(I18nLogger.class);
private final boolean isLogging;
public I18nLogger(HttpServletRequest req) {
DeveloperSettings settings = DeveloperSettings.getBean(req);
this.isLogging = settings.getBoolean(Keys.ENABLED)
&& settings.getBoolean(Keys.I18N_LOG_STRINGS)
&& log.isInfoEnabled();
}
public void log(String bundleName, String key, Object[] parameters,
String rawText, String formattedText) {
if (isLogging) {
String message = String.format(
"Retrieved from %s.%s with %s: '%s'", bundleName, key,
Arrays.toString(parameters), rawText);
if (!rawText.equals(formattedText)) {
message += String.format(" --> '%s'", formattedText);
}
log.info(message);
}
}
}

View file

@ -207,6 +207,14 @@ public class KnowledgeBaseUpdater {
StmtIterator sit = anonModel.listStatements();
while (sit.hasNext()) {
Statement stmt = sit.nextStatement();
// Skip statements with blank nodes (unsupported) to avoid
// excessive deletion. In the future, the whole updater
// could be modified to change whole graphs at once through
// the RDFService, but right now this whole thing is statement
// based.
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
continue;
}
Iterator<String> graphIt = dataset.listNames();
while(graphIt.hasNext()) {
String graph = graphIt.next();
@ -223,8 +231,9 @@ public class KnowledgeBaseUpdater {
//log.info("removed " + anonModel.size() + " statements from SPARQL CONSTRUCTs");
} else {
Model writeModel = dataset.getNamedModel(JenaDataSourceSetupBase.JENA_DB_MODEL);
Model dedupeModel = dataset.getDefaultModel();
Model additions = jiu.renameBNodes(
anonModel, settings.getDefaultNamespace() + "n", writeModel);
anonModel, settings.getDefaultNamespace() + "n", dedupeModel);
Model actualAdditions = ModelFactory.createDefaultModel();
StmtIterator stmtIt = additions.listStatements();
while (stmtIt.hasNext()) {

View file

@ -217,6 +217,9 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic
private List<Statement> sort(List<Statement> stmts) {
List<Statement> output = new ArrayList<Statement>();
int originalSize = stmts.size();
if(originalSize == 1) {
return stmts;
}
List <Statement> remaining = stmts;
ConcurrentLinkedQueue<Resource> subjQueue = new ConcurrentLinkedQueue<Resource>();
for(Statement stmt : remaining) {

View file

@ -15,7 +15,8 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings;
import edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings.Keys;
/**
* Writes the log message for the LoggingRDFService.
@ -41,10 +42,6 @@ import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
public class RDFServiceLogger implements AutoCloseable {
private static final Log log = LogFactory.getLog(RDFServiceLogger.class);
private static final String PROPERTY_ENABLED = "developer.loggingRDFService.enable";
private static final String PROPERTY_STACK_TRACE = "developer.loggingRDFService.stackTrace";
private static final String PROPERTY_RESTRICTION = "developer.loggingRDFService.restriction";
private final ServletContext ctx;
private final Object[] args;
@ -72,18 +69,21 @@ public class RDFServiceLogger implements AutoCloseable {
}
private void getProperties() {
ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
isEnabled = Boolean.valueOf(props.getProperty(PROPERTY_ENABLED));
traceRequested = Boolean.valueOf(props
.getProperty(PROPERTY_STACK_TRACE));
DeveloperSettings settings = DeveloperSettings.getBean(ctx);
isEnabled = settings.getBoolean(Keys.LOGGING_RDF_ENABLE);
traceRequested = settings.getBoolean(Keys.LOGGING_RDF_STACK_TRACE);
String restrictionString = props.getProperty(PROPERTY_RESTRICTION);
if (StringUtils.isNotBlank(restrictionString)) {
String restrictionString = settings
.getString(Keys.LOGGING_RDF_RESTRICTION);
if (StringUtils.isBlank(restrictionString)) {
restriction = null;
} else {
try {
restriction = Pattern.compile(restrictionString);
} catch (Exception e) {
log.error("Failed to compile the pattern for "
+ PROPERTY_RESTRICTION + " = " + restriction + " " + e);
+ Keys.LOGGING_RDF_RESTRICTION + " = " + restriction
+ " " + e);
isEnabled = false;
}
}

View file

@ -744,6 +744,8 @@ public class RDFServiceSparql extends RDFServiceImpl implements RDFService {
private List<Statement> sort(List<Statement> stmts) {
List<Statement> output = new ArrayList<Statement>();
int originalSize = stmts.size();
if (originalSize == 1)
return stmts;
List <Statement> remaining = stmts;
ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource> subjQueue =
new ConcurrentLinkedQueue<com.hp.hpl.jena.rdf.model.Resource>();

View file

@ -3,6 +3,7 @@
package edu.cornell.mannlib.vitro.webapp.reasoner;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
@ -295,14 +296,35 @@ public class ABoxRecomputer {
*/
protected Collection<String> getAllIndividualURIs() {
String queryString = "SELECT DISTINCT ?s WHERE { GRAPH ?g { ?s a ?type } " +
" FILTER (!bound(?g) || !regex(str(?g),\"tbox\")) } ORDER BY ?s";
return getIndividualURIs(queryString);
HashSet<String> individualURIs = new HashSet<String>();
List<String> classList = new ArrayList<String>();
tboxModel.enterCriticalSection(Lock.READ);
try {
StmtIterator classIt = tboxModel.listStatements(
(Resource) null, RDF.type, OWL.Class);
while(classIt.hasNext()) {
Statement stmt = classIt.nextStatement();
if(stmt.getSubject().isURIResource()
&& stmt.getSubject().getURI() != null
&& !stmt.getSubject().getURI().isEmpty()) {
classList.add(stmt.getSubject().getURI());
}
}
} finally {
tboxModel.leaveCriticalSection();
}
for (String classURI : classList) {
String queryString = "SELECT ?s WHERE { ?s a <" + classURI + "> } ";
getIndividualURIs(queryString, individualURIs);
}
return individualURIs;
}
protected Collection<String> getIndividualURIs(String queryString) {
Set<String> individuals = new HashSet<String>();
protected void getIndividualURIs(String queryString, Set<String> individuals) {
int batchSize = 50000;
int offset = 0;
@ -342,7 +364,6 @@ public class ABoxRecomputer {
offset += batchSize;
}
return individuals;
}
protected void addedABoxTypeAssertion(Resource individual, Model inferenceModel, HashSet<String> unknownTypes) {
@ -410,6 +431,11 @@ public class ABoxRecomputer {
while (iter.hasNext()) {
Statement stmt = iter.next();
// skip statements with blank nodes to avoid excessive deletion
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
continue;
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
inferenceModel.remove(stmt);

View file

@ -187,8 +187,7 @@ public class FileGraphSetup implements ServletContextListener {
} else {
baseModel.add(model);
}
log.info("Attached file graph as " + type + " submodel " + p.getFileName());
log.debug("Attached file graph as " + type + " submodel " + p.getFileName());
}
modelChanged = modelChanged | updateGraphInDB(dataset, model, type, p);

View file

@ -221,7 +221,7 @@ public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
int[] maxActiveAndIdle = getMaxActiveAndIdle(ctx);
cpds.setMaxPoolSize(maxActiveAndIdle[0]);
cpds.setMinPoolSize(maxActiveAndIdle[1]);
cpds.setMaxIdleTime(3600); // ms
cpds.setMaxIdleTime(43200); // s
cpds.setMaxIdleTimeExcessConnections(300);
cpds.setAcquireIncrement(5);
cpds.setNumHelperThreads(6);

View file

@ -0,0 +1,305 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.utils.developer;
import java.io.File;
import java.io.FileReader;
import java.nio.file.Paths;
import java.util.Arrays;
import java.util.EnumMap;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import javax.servlet.ServletContext;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
/**
* Hold the global developer settings. Render to JSON when requested.
*
* On first request, the "developer.properties" file is loaded from the Vitro
* home directory. If the file doesn't exist, or doesn't contain values for
* certain properties, those propertiew will keep their default values.
*
* An AJAX request can be used to update the properties. If the request has
* multiple values for a property, the first value will be used. If the request
* does not contain a value for a property, that property will keep its current
* value.
*/
public class DeveloperSettings {
private static final Log log = LogFactory.getLog(DeveloperSettings.class);
public enum Keys {
/**
* Developer mode and developer panel is enabled.
*/
ENABLED("developer.enabled", true),
/**
* Users don't need authority to use the developer panel. But they still
* can't enable it without authority.
*/
PERMIT_ANONYMOUS_CONTROL("developer.permitAnonymousControl", true),
/**
* Load Freemarker templates every time they are requested.
*/
DEFEAT_FREEMARKER_CACHE("developer.defeatFreemarkerCache", true),
/**
* Show where each Freemarker template starts and stops.
*/
INSERT_FREEMARKER_DELIMITERS("developer.insertFreemarkerDelimiters",
true),
/**
* Load language property files every time they are requested.
*/
I18N_DEFEAT_CACHE("developer.i18n.defeatCache", true),
/**
* Enable the I18nLogger to log each string request.
*/
I18N_LOG_STRINGS("developer.i18n.logStringRequests", true),
/**
* Enable the LoggingRDFService
*/
LOGGING_RDF_ENABLE("developer.loggingRDFService.enable", true),
/**
* When logging with the LoggingRDFService, include a stack trace
*/
LOGGING_RDF_STACK_TRACE("developer.loggingRDFService.stackTrace", true),
/**
* Don't log with the LoggingRDFService unless the calling stack meets
* this restriction.
*/
LOGGING_RDF_RESTRICTION("developer.loggingRDFService.restriction",
false);
private final String propertyName;
private final String elementId;
private final boolean bool;
private Keys(String propertyName, boolean bool) {
this.propertyName = propertyName;
this.elementId = produceElementId();
this.bool = bool;
}
public String propertyName() {
return propertyName;
}
public String elementId() {
return elementId;
}
boolean isBoolean() {
return bool;
}
/**
* The element ID is camel-case instead of period-delimited. So
* "developer.enabled" becomes "developerEnabled".
*/
String produceElementId() {
StringBuilder id = new StringBuilder(propertyName.length());
boolean capitalize = false;
for (int i = 0; i < propertyName.length(); i++) {
char c = propertyName.charAt(i);
if (c == '.') {
capitalize = true;
} else if (capitalize) {
id.append(Character.toUpperCase(c));
capitalize = false;
} else {
id.append(c);
}
}
return id.toString();
}
@Override
public String toString() {
return propertyName;
}
static Keys fromElementId(String id) {
for (Keys k : Keys.values()) {
if (k.elementId.equals(id)) {
return k;
}
}
log.error("Can't find key for element id: '" + id + "'");
return null;
}
static Keys fromPropertyName(String name) {
for (Keys k : Keys.values()) {
if (k.propertyName.equals(name)) {
return k;
}
}
log.error("Can't find key for property name: '" + name + "'");
return null;
}
}
// ----------------------------------------------------------------------
// The factory
// ----------------------------------------------------------------------
private static final String ATTRIBUTE_NAME = DeveloperSettings.class
.getName();
public static DeveloperSettings getBean(HttpServletRequest req) {
return getBean(req.getSession().getServletContext());
}
public static DeveloperSettings getBean(ServletContext ctx) {
Object o = ctx.getAttribute(ATTRIBUTE_NAME);
if (o instanceof DeveloperSettings) {
return (DeveloperSettings) o;
} else {
DeveloperSettings ds = new DeveloperSettings(ctx);
ctx.setAttribute(ATTRIBUTE_NAME, ds);
return ds;
}
}
// ----------------------------------------------------------------------
// The instance
// ----------------------------------------------------------------------
private final Map<Keys, Object> settings = new EnumMap<>(Keys.class);
private DeveloperSettings(ServletContext ctx) {
updateFromFile(ctx);
}
/**
* Read the initial settings from "developer.properties" in the Vitro home
* directory.
*
* This method is "protected" so we can override it for unit tests.
*/
protected void updateFromFile(ServletContext ctx) {
Map<Keys, String> fromFile = new HashMap<>();
ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
String home = props.getProperty("vitro.home");
File dsFile = Paths.get(home, "developer.properties").toFile();
if (dsFile.isFile()) {
try (FileReader reader = new FileReader(dsFile)) {
Properties dsProps = new Properties();
dsProps.load(reader);
for (String key : dsProps.stringPropertyNames()) {
fromFile.put(Keys.fromPropertyName(key),
dsProps.getProperty(key));
}
} catch (Exception e) {
log.warn("Failed to load 'developer.properties' file.", e);
}
} else {
log.debug("No developer.properties file.");
}
log.debug("Properties from file: " + fromFile);
update(fromFile);
}
/** Provide the parameter map from the HttpServletRequest */
public void updateFromRequest(Map<String, String[]> parameterMap) {
if (log.isDebugEnabled()) {
dumpParameterMap(parameterMap);
}
Map<Keys, String> fromRequest = new HashMap<>();
for (String key : parameterMap.keySet()) {
fromRequest.put(Keys.fromElementId(key), parameterMap.get(key)[0]);
}
update(fromRequest);
}
private void update(Map<Keys, String> changedSettings) {
for (Keys key : Keys.values()) {
String s = changedSettings.get(key);
if (s != null) {
if (key.isBoolean()) {
settings.put(key, Boolean.valueOf(s));
} else {
settings.put(key, s);
}
}
}
log.debug("DeveloperSettings: " + this);
}
public Object get(Keys key) {
if (key.isBoolean()) {
return getBoolean(key);
} else {
return getString(key);
}
}
public boolean getBoolean(Keys key) {
if (!key.isBoolean()) {
throw new IllegalArgumentException("Key '" + key
+ "' does not take a boolean value.");
}
if (settings.containsKey(key)) {
if (Boolean.TRUE.equals(settings.get(Keys.ENABLED))) {
return (Boolean) settings.get(key);
}
}
return false;
}
public String getString(Keys key) {
if (key.isBoolean()) {
throw new IllegalArgumentException("Key '" + key
+ "' takes a boolean value.");
}
if (settings.containsKey(key)) {
if (Boolean.TRUE.equals(settings.get(Keys.ENABLED))) {
return (String) settings.get(key);
}
}
return "";
}
public Map<String, Object> getSettingsMap() {
Map<String, Object> map = new HashMap<>();
for (Keys key : Keys.values()) {
map.put(key.elementId(), get(key));
}
return map;
}
@Override
public String toString() {
return "DeveloperSettings" + settings;
}
/* For debugging. */
private void dumpParameterMap(Map<String, String[]> parameterMap) {
Map<String, List<String>> map = new HashMap<>();
for (String key : parameterMap.keySet()) {
map.put(key, Arrays.asList(parameterMap.get(key)));
}
log.debug("Parameter map: " + map);
}
}

View file

@ -0,0 +1,93 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.utils.developer;
import static edu.cornell.mannlib.vitro.webapp.utils.developer.DeveloperSettings.Keys.PERMIT_ANONYMOUS_CONTROL;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.ajax.VitroAjaxController;
import edu.cornell.mannlib.vitro.webapp.services.freemarker.FreemarkerProcessingService.TemplateProcessingException;
import edu.cornell.mannlib.vitro.webapp.services.freemarker.FreemarkerProcessingServiceSetup;
/**
* Accept an AJAX request to update the developer settings. Return an HTML
* representation of the developer panel from the settings and a Freemarker
* template.
*
* If developer mode is not enabled, the HTML response is empty.
*
* You may only control the panel if you are logged in with sufficient
* authorization, or if anonymous control is permitted by the settings.
*
* If you are not allowed to control the panel, then the HTML response
* is only a statement that developer mode is enabled. Otherwise, it
* is a full panel (collapsed at first).
*/
public class DeveloperSettingsServlet extends VitroAjaxController {
private static final Log log = LogFactory
.getLog(DeveloperSettingsServlet.class);
@Override
protected void doRequest(VitroRequest vreq, HttpServletResponse resp)
throws ServletException, IOException {
DeveloperSettings settings = DeveloperSettings.getBean(vreq);
/*
* Are they allowed to control the panel?
*/
if (isAuthorized(vreq)) {
// Update the settings.
settings.updateFromRequest(vreq.getParameterMap());
} else {
log.debug("Not authorized to update settings.");
}
/*
* Build the response.
*/
try {
Map<String, Object> bodyMap = buildBodyMap(isAuthorized(vreq),
settings);
String rendered = renderTemplate(vreq, bodyMap);
resp.getWriter().write(rendered);
} catch (Exception e) {
doError(resp, e.toString(), 500);
}
}
private Map<String, Object> buildBodyMap(boolean authorized,
DeveloperSettings settings) {
Map<String, Object> settingsMap = new HashMap<>();
settingsMap.putAll(settings.getSettingsMap());
settingsMap.put("mayControl", authorized);
Map<String, Object> bodyMap = new HashMap<>();
bodyMap.put("settings", settingsMap);
return bodyMap;
}
private String renderTemplate(VitroRequest vreq, Map<String, Object> bodyMap)
throws TemplateProcessingException {
return FreemarkerProcessingServiceSetup.getService(getServletContext())
.renderTemplate("developerPanel.ftl", bodyMap, vreq);
}
private boolean isAuthorized(VitroRequest vreq) {
boolean authBySetting = DeveloperSettings.getBean(vreq).getBoolean(
PERMIT_ANONYMOUS_CONTROL);
boolean authByPolicy = PolicyHelper.isAuthorizedForActions(vreq,
SimplePermission.ENABLE_DEVELOPER_PANEL.ACTION);
return authBySetting || authByPolicy;
}
}