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ThesaurusManager.java
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ThesaurusManager.java
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//=== Copyright (C) 2001-2023 Food and Agriculture Organization of the
//=== United Nations (FAO-UN), United Nations World Food Programme (WFP)
//=== and United Nations Environment Programme (UNEP)
//===
//=== This program is free software; you can redistribute it and/or modify
//=== it under the terms of the GNU General Public License as published by
//=== the Free Software Foundation; either version 2 of the License, or (at
//=== your option) any later version.
//===
//=== This program is distributed in the hope that it will be useful, but
//=== WITHOUT ANY WARRANTY; without even the implied warranty of
//=== MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
//=== General Public License for more details.
//===
//=== You should have received a copy of the GNU General Public License
//=== along with this program; if not, write to the Free Software
//=== Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//===
//=== Contact: Jeroen Ticheler - FAO - Viale delle Terme di Caracalla 2,
//=== Rome - Italy. email: geonetwork@osgeo.org
//==============================================================================
package org.fao.geonet.kernel;
import static com.google.common.io.Files.getNameWithoutExtension;
import java.io.IOException;
import java.io.OutputStream;
import java.nio.file.DirectoryStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.sql.SQLException;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import org.apache.commons.lang.StringUtils;
import org.fao.geonet.Util;
import org.fao.geonet.constants.Geonet;
import org.fao.geonet.domain.AbstractMetadata;
import org.fao.geonet.kernel.datamanager.IMetadataManager;
import org.fao.geonet.kernel.datamanager.IMetadataSchemaUtils;
import org.fao.geonet.kernel.datamanager.IMetadataUtils;
import org.fao.geonet.kernel.oaipmh.Lib;
import org.fao.geonet.kernel.setting.SettingManager;
import org.fao.geonet.kernel.setting.Settings;
import org.fao.geonet.languages.IsoLanguagesMapper;
import org.fao.geonet.utils.IO;
import org.fao.geonet.utils.Log;
import org.fao.geonet.utils.Xml;
import org.jdom.Element;
import org.jdom.JDOMException;
import org.openrdf.sesame.Sesame;
import org.openrdf.sesame.config.ConfigurationException;
import org.openrdf.sesame.config.RepositoryConfig;
import org.openrdf.sesame.config.SailConfig;
import org.openrdf.sesame.constants.RDFFormat;
import org.openrdf.sesame.repository.local.LocalRepository;
import org.openrdf.sesame.repository.local.LocalService;
import org.springframework.beans.factory.annotation.Autowired;
import com.google.common.collect.Maps;
import jeeves.server.context.ServiceContext;
import jeeves.xlink.Processor;
import org.springframework.beans.factory.annotation.Value;
public class ThesaurusManager implements ThesaurusFinder {
@Autowired
private SettingManager settingManager;
@Autowired
private GeonetworkDataDirectory geonetworkDataDirectory;
@Autowired
private IMetadataUtils iMetadataUtils;
@Autowired
private IMetadataManager metadataManager;
@Autowired
private IsoLanguagesMapper isoLanguagesMapper;
@Autowired
private IMetadataSchemaUtils metadataSchemaUtils;
@Autowired
private AllThesaurus allThesaurus;
private ConcurrentHashMap<String, Thesaurus> thesauriMap = new ConcurrentHashMap<>();
private LocalService service = null;
private Path thesauriDirectory = null;
private boolean initialized = false;
@Value("${thesaurus.cache.maxsize:50000}")
private int thesaurusCacheMaxSize = 50000;
public int getThesaurusCacheMaxSize() {
return thesaurusCacheMaxSize;
}
public void setThesaurusCacheMaxSize(int thesaurusCacheMaxSize) {
this.thesaurusCacheMaxSize = thesaurusCacheMaxSize;
}
/**
* Initialize ThesaurusManager.
*
* @param context ServiceContext used to check when servlet is up only
*/
public synchronized void init(boolean isTest, ServiceContext context, String thesauriRepository)
throws Exception {
if (this.initialized) {
return;
}
this.initialized = true;
final String siteURL = this.settingManager.getSiteURL(context);
allThesaurus.init(siteURL);
// Get Sesame interface
service = Sesame.getService();
Path thesauriDir = IO.toPath(thesauriRepository);
if (!Files.exists(thesauriDir)) {
thesauriDir = geonetworkDataDirectory.resolveWebResource(thesauriRepository);
}
thesauriDir = thesauriDir.toAbsolutePath();
thesauriDirectory = thesauriDir.toAbsolutePath();
batchBuildTable(isTest, context, thesauriDir);
}
/**
* Start task to build thesaurus table once the servlet is up.
*
* @param synchRun if false, run the initialization asynchronally
* @param context ServiceContext used to check when servlet is up only
* @param thesauriDir directory containing thesauri
*/
private void batchBuildTable(boolean synchRun, ServiceContext context, Path thesauriDir) {
ExecutorService executor = null;
try {
Runnable worker = new InitThesauriTableTask(context, thesauriDir);
if (synchRun) {
worker.run();
} else {
executor = Executors.newFixedThreadPool(1);
executor.execute(worker);
}
} finally {
if (executor != null) {
executor.shutdown();
}
}
}
/**
*
* @param thesauriDirectory
*/
private void initThesauriTable(Path thesauriDirectory, ServiceContext context) throws IOException {
thesauriMap = new ConcurrentHashMap<>();
Log.info(Geonet.THESAURUS_MAN, "Scanning " + thesauriDirectory);
if (thesauriDirectory != null && Files.isDirectory(thesauriDirectory)) {
String[] types = {Geonet.CodeList.EXTERNAL, Geonet.CodeList.LOCAL, Geonet.CodeList.REGISTER};
for (String type : types) {
// init of external repositories
Path externalThesauriDirectory = thesauriDirectory.resolve(type).resolve(Geonet.CodeList.THESAURUS);
if (Files.isDirectory(externalThesauriDirectory)) {
try (DirectoryStream<Path> paths = Files.newDirectoryStream(externalThesauriDirectory, IO.DIRECTORIES_FILTER)) {
for (Path aRdfDataDirectory : paths) {
loadRepositories(aRdfDataDirectory, type, context);
}
}
}
}
}
}
/**
*
* @param thesauriDirectory
*/
private void loadRepositories(Path thesauriDirectory, String root, ServiceContext context) throws IOException {
final String siteURL = settingManager.getSiteURL(context);
try (DirectoryStream<Path> paths = Files.newDirectoryStream(thesauriDirectory, "*.rdf")) {
for (Path aRdfDataFile : paths) {
final String rdfFileName = aRdfDataFile.getFileName().toString();
final String thesaurusDirName = thesauriDirectory.getFileName().toString();
final Thesaurus gst;
if (root.equals(Geonet.CodeList.REGISTER)) {
if (Log.isDebugEnabled(Geonet.THESAURUS_MAN)) {
Log.debug(Geonet.THESAURUS_MAN, "Creating thesaurus : " + aRdfDataFile);
}
Path outputRdf = thesauriDirectory.resolve(aRdfDataFile);
String uuid = getNameWithoutExtension(rdfFileName);
try (OutputStream outputRdfStream = Files.newOutputStream(outputRdf)) {
getRegisterMetadataAsRdf(uuid, outputRdfStream, context);
} catch (Exception e) {
Log.error(Geonet.THESAURUS_MAN, "Register thesaurus " + aRdfDataFile + " could not be read/converted from ISO19135 "
+ "record in catalog - skipping", e);
continue;
}
gst = new Thesaurus(isoLanguagesMapper, rdfFileName, root, thesaurusDirName, outputRdf, siteURL, thesaurusCacheMaxSize);
} else {
gst = new Thesaurus(isoLanguagesMapper, rdfFileName, root, thesaurusDirName, thesauriDirectory.resolve(aRdfDataFile), siteURL, thesaurusCacheMaxSize);
}
try {
addThesaurus(gst, false);
} catch (Exception e) {
Log.error(Geonet.THESAURUS_MAN, "Error adding thesaurus " + aRdfDataFile + ": " + e.getMessage(), e);
// continue loading
}
}
}
}
/**
* Get ISO19135 Register Metadata from catalog and convert to rdf.
*
* @param uuid Uuid of register (ISO19135) metadata record describing thesaurus
* @param os OutputStream to write rdf to from XSLT conversion
*/
private void getRegisterMetadataAsRdf(String uuid, OutputStream os, ServiceContext context) throws Exception {
AbstractMetadata mdInfo = iMetadataUtils.findOneByUuid(uuid);
Integer id = mdInfo.getId();
Element md = metadataManager.getMetadata("" + id);
Processor.detachXLink(md, context);
final String siteURL = settingManager.getSiteURL(context);
Element env = Lib.prepareTransformEnv(
mdInfo.getUuid(),
mdInfo.getDataInfo().getChangeDate().getDateAndTime(),
"", siteURL, "");
//--- transform the metadata with the created env and specified stylesheet
Element root = new Element("root");
root.addContent(md);
root.addContent(env);
Path styleSheet = metadataSchemaUtils.getSchemaDir("iso19135").resolve("convert").resolve(Geonet.File.EXTRACT_SKOS_FROM_ISO19135);
Xml.transform(root, styleSheet, os);
}
/**
* Build thesaurus file path according to thesaurus configuration (ie. codelist directory
* location). If directory does not exist, it will create it.
*
* @return the thesaurus file path.
*/
public Path buildThesaurusFilePath(String fname, String type, String dname) throws IOException {
Path dirPath = thesauriDirectory.resolve(type).resolve(Geonet.CodeList.THESAURUS).resolve(dname);
Files.createDirectories(dirPath);
return dirPath.resolve(fname);
}
/**
* @param writeConceptScheme Write the concept scheme and details
* (title, description, ...) in the graph.
* Used when creating local thesaurus.
*/
public void addThesaurus(Thesaurus gst, boolean writeConceptScheme) throws Exception {
String thesaurusName = gst.getKey();
if (Log.isDebugEnabled(Geonet.THESAURUS_MAN)) {
Log.debug(Geonet.THESAURUS_MAN, "Adding thesaurus : " + thesaurusName);
}
if (existsThesaurus(thesaurusName)) {
throw new Exception("A thesaurus exists with code " + thesaurusName);
}
createThesaurusRepository(gst);
thesauriMap.put(thesaurusName, gst);
if (writeConceptScheme) {
gst.createConceptScheme(
gst.getTitle(),
gst.getMultilingualTitles(),
gst.getDescription(),
gst.getMultilingualDescriptions(),
gst.getFname(),
gst.getDname(),
gst.getDefaultNamespace());
}
}
public void addOrReloadThesaurus(Thesaurus gst) throws Exception {
if (thesauriMap.replace(gst.getKey(), gst) != null) {
service.removeRepository(gst.getKey());
}
createThesaurusRepository(gst);
thesauriMap.put(gst.getKey(), gst);
if (Log.isDebugEnabled(Geonet.THESAURUS_MAN)) {
Log.debug(Geonet.THESAURUS_MAN, "Thesaurus " + gst.getKey() + " loaded.");
}
}
/**
*
* @param name
*/
public void remove(String name) {
service.removeRepository(name);
thesauriMap.remove(name);
}
/**
*
* @param gst
*/
private void createThesaurusRepository(Thesaurus gst) throws Exception {
LocalRepository thesaurusRepository;
try {
RepositoryConfig repConfig = new RepositoryConfig(gst.getKey());
SailConfig syncSail = new SailConfig("org.openrdf.sesame.sailimpl.sync.SyncRdfSchemaRepository");
SailConfig memSail = new org.openrdf.sesame.sailimpl.memory.RdfSchemaRepositoryConfig(
gst.getFile().toAbsolutePath().toString(), RDFFormat.RDFXML);
repConfig.addSail(syncSail);
repConfig.addSail(memSail);
repConfig.setWorldReadable(true);
repConfig.setWorldWriteable(true);
thesaurusRepository = service.createRepository(repConfig);
gst.setRepository(thesaurusRepository);
} catch (ConfigurationException e) {
Log.error(Geonet.THESAURUS_MAN, "Create Thesaurus Repository error", e);
throw e;
}
}
public Path getThesauriDirectory() {
return thesauriDirectory;
}
@Override
public Map<String, Thesaurus> getThesauriMap() {
if (this.settingManager.getValueAsBool(Settings.SYSTEM_ENABLE_ALL_THESAURUS)) {
final HashMap<String, Thesaurus> all = Maps.newHashMap(this.thesauriMap);
all.put(this.allThesaurus.getKey(), this.allThesaurus);
return all;
} else {
return Collections.unmodifiableMap(thesauriMap);
}
}
@Override
@Nullable
public Thesaurus getThesaurusByName(@Nonnull String thesaurusName) {
return getThesauriMap().get(thesaurusName);
}
@Override
public Thesaurus getThesaurusByConceptScheme(String uri) {
for (Map.Entry<String, Thesaurus> entry : getThesauriMap().entrySet()) {
try {
Thesaurus thesaurus = entry.getValue();
if (thesaurus.hasConceptScheme(uri)) {
return thesaurus;
}
} catch (Exception e) {
Log.error(Geonet.THESAURUS_MAN, "Get Thesaurus By Concept Scheme error", e);
}
}
return null;
}
public Thesaurus getThesaurusByTitle(String title) {
for (Map.Entry<String, Thesaurus> entry : getThesauriMap().entrySet()) {
try {
Thesaurus thesaurus = entry.getValue();
if (thesaurus.getTitle().equals(title)) {
return thesaurus;
}
} catch (Exception e) {
Log.error(Geonet.THESAURUS_MAN, "Get thesaurus by title error", e);
}
}
return null;
}
/**
* @param name
* @return
*/
@Override
public boolean existsThesaurus(String name) {
return (getThesauriMap().get(name) != null);
}
/**
* Create (or update an existing) rdf thesaurus from the specified ISO19135 register record.
*
* @param uuid Uuid of iso19135 register metadata record to update thesaurus
* @param type Type of thesaurus (theme, etc)
* @return id of thesaurus created/updated
*/
public String createUpdateThesaurusFromRegister(String uuid, String type, ServiceContext context) throws Exception {
String root = Geonet.CodeList.REGISTER;
// check whether we have created a thesaurus for this register already
String aRdfDataFile = uuid + ".rdf";
Path thesaurusFile = buildThesaurusFilePath(aRdfDataFile, root, type);
final String siteURL = settingManager.getSiteURL(context);
Thesaurus gst = new Thesaurus(isoLanguagesMapper, aRdfDataFile, root, type, thesaurusFile, siteURL, thesaurusCacheMaxSize);
try (OutputStream outputRdfStream = Files.newOutputStream(thesaurusFile)) {
getRegisterMetadataAsRdf(uuid, outputRdfStream, context);
} catch (Exception e) {
Log.error(Geonet.THESAURUS_MAN, "Register thesaurus " + aRdfDataFile + " could not be read/converted from ISO19135 record in catalog - skipping", e);
}
String theKey = gst.getKey();
gst.retrieveThesaurusInformation();
addOrReloadThesaurus(gst);
return theKey;
}
/**
* @return {@link org.jdom.Element}
*/
public Element buildResultfromThTable(ServiceContext context) throws SQLException, JDOMException, IOException {
Element elRoot = new Element("thesauri");
Collection<Thesaurus> e = getThesauriMap().values();
for (Thesaurus currentTh : e) {
Element elLoop = new Element("thesaurus");
Element elKey = new Element("key");
String key = currentTh.getKey();
elKey.addContent(key);
Element elDname = new Element("dname");
String dname = currentTh.getDname();
elDname.addContent(dname);
Element description = new Element("description");
description.addContent(currentTh.getDescription());
Element elFname = new Element("filename");
String fname = currentTh.getFname();
elFname.addContent(fname);
Element elTitle = new Element("title");
String title = currentTh.getTitles(context.getApplicationContext()).get(context.getLanguage());
if (title == null) {
title = currentTh.getTitle();
}
elTitle.addContent(title);
//add multilingual titles in to response
// "multilingualTitles": [
// { "lang": "fr","title": "Data Usage Scope FR"},
// {"lang": "en","title": "Data Usage Scope EN"}
// ],
Element elMultilingualTitles = new Element("multilingualTitles");
for (Map.Entry<String, String> entry : currentTh.getMultilingualTitles().entrySet()) {
if (StringUtils.isNotBlank(entry.getValue())) {
Element elMultilingualTitle = new Element("multilingualTitle");
Element elMultilingualTitleLang = new Element("lang");
elMultilingualTitleLang.setText(entry.getKey());
Element elMultilingualTitleTitle = new Element("title");
elMultilingualTitleTitle.setText(entry.getValue());
elMultilingualTitle.addContent(elMultilingualTitleLang);
elMultilingualTitle.addContent(elMultilingualTitleTitle);
elMultilingualTitles.addContent(elMultilingualTitle);
}
}
//add dublin core items to the response
// "dublinCoreMultilingual": [
// { "lang": "fr","tag":"title","value": "Data Usage Scope FR"},
// {"lang": "en","tag":"title","value": "Data Usage Scope EN"}
//]
Element elDublinCoreMultilingual = new Element("dublinCoreMultilinguals");
for (Map.Entry<String, Map<String,String>> entryLang : currentTh.getDublinCoreMultilingual().entrySet()) {
String lang = entryLang.getKey();
for (Map.Entry<String, String> entryItem : entryLang.getValue().entrySet()) {
if (StringUtils.isNotBlank(entryItem.getValue())) {
Element elItem = new Element("dublinCoreMultilingual");
Element elLang = new Element("lang");
elLang.setText(lang);
Element elTag = new Element("tag");
elTag.setText(entryItem.getKey());
Element elValue = new Element("value");
elValue.setText(entryItem.getValue());
elItem.addContent(elLang);
elItem.addContent(elTag);
elItem.addContent(elValue);
elDublinCoreMultilingual.addContent(elItem);
}
}
}
//add multilingual descriptions in to response
// "multilingualDescriptions": [
// { "lang": "fr","title": "Data Usage Scope FR"},
// {"lang": "en","title": "Data Usage Scope EN"}
// ],
Element elMultilingualDescriptions = new Element("multilingualDescriptions");
for (Map.Entry<String, String> entry : currentTh.getMultilingualDescriptions().entrySet()) {
if (StringUtils.isNotBlank(entry.getValue())) {
Element elMultilingualDescription = new Element("multilingualDescription");
Element elMultilingualDescLang = new Element("lang");
elMultilingualDescLang.setText(entry.getKey());
Element elMultilingualDescDesc = new Element("description");
elMultilingualDescDesc.setText(entry.getValue());
elMultilingualDescription.addContent(elMultilingualDescLang);
elMultilingualDescription.addContent(elMultilingualDescDesc);
elMultilingualDescriptions.addContent(elMultilingualDescription);
}
}
Element elType = new Element("type");
String type = currentTh.getType();
elType.addContent(type);
Element elDate = new Element("date");
String date = currentTh.getDate();
elDate.addContent(date);
Element elCreatedDate = new Element("createdDate");
String createdDate = currentTh.getCreatedDate();
elCreatedDate.addContent(createdDate);
Element elIssuedDate = new Element("issuedDate");
String issuedDate = currentTh.getIssuedDate();
elIssuedDate.addContent(issuedDate);
Element elModifiedDate = new Element("modifiedDate");
String modifiedDate = currentTh.getModifiedDate();
elModifiedDate.addContent(modifiedDate);
Element elUrl = new Element("url");
String url = currentTh.getDownloadUrl();
elUrl.addContent(url);
Element elDefaultURI = new Element("defaultNamespace");
String defaultURI = currentTh.getDefaultNamespace();
elDefaultURI.addContent(defaultURI);
elLoop.addContent(elKey);
elLoop.addContent(elDname);
elLoop.addContent(description);
elLoop.addContent(elFname);
elLoop.addContent(elTitle);
elLoop.addContent(elMultilingualTitles);
elLoop.addContent(elDublinCoreMultilingual);
elLoop.addContent(elMultilingualDescriptions);
elLoop.addContent(elDate);
elLoop.addContent(elCreatedDate);
elLoop.addContent(elIssuedDate);
elLoop.addContent(elModifiedDate);
elLoop.addContent(elUrl);
elLoop.addContent(elDefaultURI);
elLoop.addContent(elType);
elRoot.addContent(elLoop);
}
return elRoot;
}
/**
* A Task to build the thesaurus table once the servlet is up.
*
* Since <b>thesauri can be metadata records</b> (registers) they can also have xlinks. These
* may not be resolveable until the servlet is up. Hence we start a thread that waits until the
* servlet is up before reading the thesauri and creating the thesaurus table.
*/
final class InitThesauriTableTask implements Runnable {
private final ServiceContext context;
private final Path thesauriDir;
InitThesauriTableTask(ServiceContext context, Path thesauriDir) {
this.context = context;
this.thesauriDir = thesauriDir;
}
public void run() {
context.setAsThreadLocal();
try {
// poll context to see whether servlet is up yet
while (!context.isServletInitialized()) {
if (Log.isDebugEnabled(Geonet.THESAURUS_MAN)) {
Log.debug(Geonet.THESAURUS_MAN, "Waiting for servlet to finish initializing..");
}
Thread.sleep(10000); // sleep 10 seconds
}
try {
initThesauriTable(thesauriDir, context);
} catch (Exception e) {
Log.error(Geonet.THESAURUS_MAN, "Error rebuilding thesaurus table : " + e.getMessage() + "\n" + Util.getStackTrace(e));
}
} catch (Exception e) {
Log.debug(Geonet.THESAURUS_MAN, "Thesaurus table rebuilding thread threw exception", e);
}
}
}
}