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wps
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/wps@153272 82a268e6-3cf1-43bd-a215-b396298e98cf

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feature/23107
Lucio Lelii 7 years ago
parent df5b27a4b7
commit 27a8136cdd
8 changed files with 177 additions and 36 deletions
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16
distro/web.xml
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@ -84,6 +84,15 @@
</context-param>
<filter>
<filter-name>ClassLoaderFilter</filter-name>
<filter-class>org.gcube.data.analysis.wps.filter.ClassLoaderFilter</filter-class>
</filter>
<filter>
<filter-name>CORS</filter-name>
<filter-class>com.thetransactioncompany.cors.CORSFilter</filter-class>
<init-param>
@ -111,7 +120,12 @@
<filter-name>CORS</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<filter-mapping>
<filter-name>ClassLoaderFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<!-- <filter> <filter-name>authn</filter-name> -->
<!-- display-name>Authentication Chain Filter</display-name -->
<!-- description> Delegates calls to AuthenticationChainFilter that is defined

2
pom.xml
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@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.gcube.data-analysis</groupId>
<artifactId>wps</artifactId>
<version>1.0.0-SNAPSHOT</version>
<version>1.1.0-SNAPSHOT</version>
<name>WPS</name>
<parent>

6
src/main/java/org/gcube/data/analysis/wps/GetCapabilitiesBuilder.java
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@ -2,6 +2,7 @@ package org.gcube.data.analysis.wps;
import java.io.InputStream;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@ -112,7 +113,10 @@ public class GetCapabilitiesBuilder {
LOGGER.debug("Found {} algorithms in scope {} ",algorithmsInScope.size() ,ScopeProvider.instance.get());
StringBuffer capabilities = new StringBuffer();
for (String algorithmInScope : algorithmsInScope) {
//TO eliminate duplicate coming from IS
Set<String> algorithmsSet = new HashSet<String>(algorithmsInScope);
for (String algorithmInScope : algorithmsSet ) {
String classAlgorithm = allalgorithms.get(algorithmInScope);
if (classAlgorithm != null) {
LOGGER.debug("Approving " + classAlgorithm + " to capabilities ");

34
src/main/java/org/gcube/data/analysis/wps/filter/ClassLoaderFilter.java
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@ -0,0 +1,34 @@
package org.gcube.data.analysis.wps.filter;
import java.io.IOException;
import javax.servlet.Filter;
import javax.servlet.FilterChain;
import javax.servlet.FilterConfig;
import javax.servlet.ServletException;
import javax.servlet.ServletRequest;
import javax.servlet.ServletResponse;
import org.gcube.data.analysis.wps.repository.GcubeAlgorithmRepository;
public class ClassLoaderFilter implements Filter{
@Override
public void init(FilterConfig filterConfig) throws ServletException {
}
@Override
public void doFilter(ServletRequest request, ServletResponse response,
FilterChain chain) throws IOException, ServletException {
Thread.currentThread().setContextClassLoader(GcubeAlgorithmRepository.getUpdater().getLoader());
chain.doFilter(request, response);
}
@Override
public void destroy() {
// TODO Auto-generated method stub
}
}

130
src/main/java/org/gcube/data/analysis/wps/repository/AlgorithmUpdater.java
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@ -1,19 +1,23 @@
package org.gcube.data.analysis.wps.repository;
import static java.nio.file.StandardWatchEventKinds.ENTRY_CREATE;
import static java.nio.file.StandardWatchEventKinds.ENTRY_MODIFY;
import static java.nio.file.StandardWatchEventKinds.OVERFLOW;
import java.io.IOException;
import java.lang.reflect.Method;
import java.net.URL;
import java.net.URLClassLoader;
import java.nio.file.DirectoryIteratorException;
import java.nio.file.DirectoryStream;
import java.nio.file.FileSystems;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.WatchEvent;
import java.nio.file.WatchKey;
import java.nio.file.WatchService;
import java.util.ArrayList;
import java.util.List;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -21,13 +25,13 @@ import org.slf4j.LoggerFactory;
public final class AlgorithmUpdater {
private static final Logger log = LoggerFactory.getLogger(AlgorithmUpdater.class);
private String algorithmDirectory;
private boolean mustUpdate = false;
private WatcherThread watcherThread = null;
public AlgorithmUpdater(String algorithmDirectory) {
super();
this.algorithmDirectory = algorithmDirectory;
@ -36,43 +40,62 @@ public final class AlgorithmUpdater {
protected synchronized boolean mustUpdate(){
return mustUpdate;
}
protected synchronized void reset(){
mustUpdate = false;
}
public boolean isStarted(){
return watcherThread!=null;
}
protected void startWhatcher(){
protected void init(){
watcherThread = new WatcherThread(Thread.currentThread().getContextClassLoader(), algorithmDirectory);
}
protected void startWhatcher(){
watcherThread.start();
}
protected void init(){
public ClassLoader getLoader() {
return this.watcherThread.getLoader();
}
private class WatcherThread extends Thread {
/*private Map<String, Long> justCreated = new WeakHashMap<String, Long>();
private static final long ENTRY_MAX_TIME = 300000;*/
private WatchService watcher;
private ClassLoader loader;
private ClassLoader parentLoader;
private Path dir;
public WatcherThread(ClassLoader loader, String algorithmDirectory) {
private List<String> installedURLS;
public WatcherThread(ClassLoader parentLoader, String algorithmDirectory) {
super();
try {
log.debug("Watcher Thread created");
watcher = FileSystems.getDefault().newWatchService();
this.loader = loader;
//TODO: change with something from configuration
this.parentLoader = parentLoader;
log.debug("parent class loader is {}", parentLoader.getClass().getSimpleName());
dir = Paths.get(algorithmDirectory);
dir.register(watcher, ENTRY_CREATE, ENTRY_MODIFY);
installedURLS = updateClassLoader();
dir.register(watcher, ENTRY_CREATE);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
protected ClassLoader getLoader() {
return loader;
}
@SuppressWarnings("unchecked")
public void run(){
for (;;) {
@ -88,7 +111,7 @@ public final class AlgorithmUpdater {
for (WatchEvent<?> event: key.pollEvents()) {
WatchEvent.Kind<?> kind = event.kind();
log.trace("new event thrown for directory watcher");
// This key is registered only
// for ENTRY_CREATE events,
// but an OVERFLOW event can
@ -102,21 +125,41 @@ public final class AlgorithmUpdater {
// context of the event.
WatchEvent<Path> ev = (WatchEvent<Path>)event;
Path filename = ev.context();
if (filename.toString().endsWith(".jar")){
log.debug("found filename {} ",filename.toString());
log.trace("new event thrown for directory watcher with filename {} and kind {}", filename, kind);
if (filename.toString().endsWith("_interface.jar") ){
try{
final Class<URLClassLoader> sysclass = URLClassLoader.class;
// TODO some kind of a hack. Need to invent better solution.
final Method method = sysclass.getDeclaredMethod("addURL", new Class[] { URL.class });
method.setAccessible(true);
method.invoke(loader, new URL[] { dir.resolve(filename).toFile().toURI().toURL() });
log.info("filename added is {} in loader {}",filename, loader.getClass().getName());
if (installedURLS.contains(filename.getFileName().toString())){
log.debug("modifying an already installed algorithm");
installedURLS = updateClassLoader();
} else {
log.debug("installing new algorithm");
final Class<URLClassLoader> sysclass = URLClassLoader.class;
// TODO some kind of a hack. Need to invent better solution.
final Method method = sysclass.getDeclaredMethod("addURL", new Class[] { URL.class });
method.setAccessible(true);
URL realjarURL = null;
URL[] jarURLS ;
try{
realjarURL = dir.resolve(filename.toString().replaceFirst("_interface", "")).getFileName().toUri().toURL();
jarURLS = new URL[] {realjarURL,
dir.resolve(filename).toFile().toURI().toURL() };
log.debug("found {} ",realjarURL);
}catch(Exception ipe){
jarURLS = new URL[] {dir.resolve(filename).toFile().toURI().toURL() };
log.warn("only {} have been found",filename);
}
method.invoke(loader, jarURLS );
log.info("filename added in loader {}",filename, loader.getClass().getName());
installedURLS.add(filename.getFileName().toString());
}
mustUpdate = true;
}catch(Exception e){
log.error("filename {} cannot be added to classpath",e,filename);
}
} else log.info("filename {} is not a jar",filename);
} else log.info("filename {} is not an algorithm interface",filename);
}
@ -126,8 +169,35 @@ public final class AlgorithmUpdater {
}
}
}
private List<String> updateClassLoader(){
log.debug("getting the stream from directoy {}",dir.getFileName());
List<URL> urls = new ArrayList<URL>();
List<String> toReturn = new ArrayList<String>(urls.size());
DirectoryStream.Filter<Path> filter = new DirectoryStream.Filter<Path>() {
public boolean accept(Path file) throws IOException {
return (file.getFileName().toString().endsWith(".jar"));
}
};
try (DirectoryStream<Path> stream = Files.newDirectoryStream(dir, filter )){
for (Path file: stream) {
log.debug("loading url {}",file.getFileName());
urls.add(file.toUri().toURL());
toReturn.add(file.getFileName().toString());
}
} catch (IOException | DirectoryIteratorException x) {
log.error("error reading config dir",x);
}
this.loader = new URLClassLoader(urls.toArray(new URL[urls.size()]), parentLoader);
log.debug("loader object is {}", loader);
return toReturn;
}
}
protected void shutdown(){
if (isStarted()){
//TODO : kill the watcherThread

7
src/main/java/org/gcube/data/analysis/wps/repository/GcubeAlgorithmRepository.java
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@ -29,6 +29,7 @@ public class GcubeAlgorithmRepository implements IAlgorithmRepository {
public GcubeAlgorithmRepository(){
log.info("gcube algorithm repository started");
if (updater==null) throw new RuntimeException("GcubeAlgorithmRepository cannot be initialized: updater is null");
updater.init();
updateRepository();
updater.startWhatcher();
}
@ -85,11 +86,12 @@ public class GcubeAlgorithmRepository implements IAlgorithmRepository {
private static synchronized void updateRepository(){
if (reflection==null || updater.mustUpdate()){
Thread.currentThread().setContextClassLoader(updater.getLoader());
log.info("updating repository ({}) ",updater.mustUpdate());
updater.reset();
ConfigurationBuilder confBuilder = new ConfigurationBuilder()
.filterInputsBy(new FilterBuilder().include(FilterBuilder.prefix(PACKAGE_TO_FIND)))
.setUrls(((URLClassLoader)Thread.currentThread().getContextClassLoader()).getURLs());
.setUrls(((URLClassLoader)updater.getLoader()).getURLs());
reflection = new Reflections(confBuilder);
}
}
@ -117,4 +119,7 @@ public class GcubeAlgorithmRepository implements IAlgorithmRepository {
} else return false;
}
public static AlgorithmUpdater getUpdater(){
return updater;
}
}

2
src/main/webapp/WEB-INF/README
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@ -25,7 +25,7 @@ no. 654119), SoBigData (grant no. 654024);
Version
--------------------------------------------------
1.0.0-SNAPSHOT (${maven.build.timestamp})
1.0.0-SNAPSHOT (2017-09-19)
Please see the file named "changelog.xml" in this directory for the release notes.

16
src/main/webapp/WEB-INF/web.xml
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@ -84,6 +84,15 @@
</context-param>
<filter>
<filter-name>ClassLoaderFilter</filter-name>
<filter-class>org.gcube.data.analysis.wps.filter.ClassLoaderFilter</filter-class>
</filter>
<filter>
<filter-name>CORS</filter-name>
<filter-class>com.thetransactioncompany.cors.CORSFilter</filter-class>
<init-param>
@ -111,7 +120,12 @@
<filter-name>CORS</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<filter-mapping>
<filter-name>ClassLoaderFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<!-- <filter> <filter-name>authn</filter-name> -->
<!-- display-name>Authentication Chain Filter</display-name -->
<!-- description> Delegates calls to AuthenticationChainFilter that is defined

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