Health extension implemented

pom.xml

@@ -38,9 +38,9 @@
 	</scm>
 	<dependencies>
 		<dependency>
-			<groupId>org.reflections</groupId>
+			<groupId>io.github.classgraph</groupId>
-			<artifactId>reflections</artifactId>
+			<artifactId>classgraph</artifactId>
-			<version>0.9.10</version>
+			<version>4.8.28</version>
 		</dependency>
 		<dependency>
 			<groupId>org.gcube.common</groupId>

src/main/java/org/gcube/smartgears/context/application/DefaultApplicationContext.java

@@ -6,6 +6,7 @@ import org.gcube.common.events.Hub;
 import org.gcube.smartgears.configuration.application.ApplicationConfiguration;
 import org.gcube.smartgears.context.Properties;
 import org.gcube.smartgears.context.container.ContainerContext;
+import org.gcube.smartgears.health.HealthManager;
 import org.gcube.smartgears.lifecycle.application.ApplicationLifecycle;
 import org.gcube.smartgears.persistence.PersistenceWriter;
 import org.gcube.smartgears.security.AuthorizationProvider;

src/main/java/org/gcube/smartgears/context/container/ContainerContext.java

@@ -51,4 +51,5 @@ public interface ContainerContext {
 
 	
 	AuthorizationProvider authorizationProvider();
+
 }

src/main/java/org/gcube/smartgears/extensions/ApplicationExtension.java

@@ -22,6 +22,8 @@ public interface ApplicationExtension extends Servlet {
 	 */
 	void init(ApplicationContext context) throws Exception;
 	
+	void stop();
+	
 	/**
 	 * Returns the name of this extension.
 	 * @return the name

src/main/java/org/gcube/smartgears/extensions/HttpExtension.java

@@ -76,6 +76,9 @@ public abstract class HttpExtension extends HttpServlet implements ApplicationEx
 		this.context=context;
 	}
 	
+	@Override
+	public void stop() {}
+	
 	@Override
 	public Set<Exclude> excludes() {
 		return new HashSet<Exclude>(); //all managed by default

src/main/java/org/gcube/smartgears/extensions/resource/HealthResource.java

@@ -4,41 +4,108 @@ import static org.gcube.smartgears.Constants.application_json;
 import static org.gcube.smartgears.extensions.HttpExtension.Method.GET;
 
 import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Set;
+import java.util.Timer;
+import java.util.stream.Collectors;
 
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.gcube.common.health.api.response.HealthResponse;
+import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
+import org.gcube.common.health.api.HealthCheck;
+import org.gcube.common.health.api.ReadinessChecker;
+import org.gcube.smartgears.context.application.ApplicationContext;
 import org.gcube.smartgears.extensions.ApiResource;
 import org.gcube.smartgears.extensions.ApiSignature;
+import org.gcube.smartgears.handlers.application.request.RequestError;
+import org.gcube.smartgears.health.HealthManager;
+import org.gcube.smartgears.health.HealthResponse;
+import org.gcube.smartgears.health.HealthTask;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ClassInfo;
+import io.github.classgraph.ClassInfoList;
+import io.github.classgraph.ScanResult;
 
 public class HealthResource extends ApiResource {
 
 	private static final long serialVersionUID = 1L;
 	
+	private static Logger log = LoggerFactory.getLogger(HealthResource.class);
+	
 	public static final String mapping = "/health";
 	
 	private static final ApiSignature signature = handles(mapping).with(method(GET).produces(application_json)); 
 	
+	private HealthManager manager; 
+	
+	private HealthTask task;
+	
+	private Timer timer;
 	
 	HealthResource() {
 		super(signature);
 	}
 	
+	@Override
+	public void init(ApplicationContext context) throws Exception {
+		Set<Class<?>> annotatedReadiness;
+
+		try (ScanResult result = new ClassGraph().enableClassInfo().enableAnnotationInfo().scan()) {
+
+			ClassInfoList classInfos = result.getClassesWithAnnotation(ReadinessChecker.class.getName());
+
+			annotatedReadiness = classInfos.stream().map(ClassInfo::loadClass)
+					.filter(c -> HealthCheck.class.isAssignableFrom(c)).collect(Collectors.toSet());
+		}
+		
+		manager = new HealthManager();
+		for (Class<?> readnessClass : annotatedReadiness)
+			try {
+				manager.register((HealthCheck) readnessClass.getDeclaredConstructor().newInstance());
+				log.info("added class {} to health manager", readnessClass.getCanonicalName());
+			} catch (Throwable e) {
+				log.error("healthChecher class {} cannot be instantiated", readnessClass.getCanonicalName(), e);
+			}
+			
+		task = new HealthTask(manager);
+		
+		timer = new Timer(true);
+		
+		timer.scheduleAtFixedRate(task, 0, 10000); 
+		
+		super.init(context);
+	}
+
+    public void stop() {
+    	timer.cancel();
+    }
 
 	@Override
 	public void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
+		PrintWriter out = resp.getWriter();
+		resp.setContentType("application/json");
+		resp.setCharacterEncoding("UTF-8");
+		Object response = null;
 		
-	}
+		String contextpath = req.getContextPath();
+		log.info("context path is {}", req.getContextPath());
+		if (contextpath.endsWith("/readiness"))
+			response = readiness();
+		else 
+			RequestError.resource_notfound_error.fire();
 		
+		new ObjectMapper().writeValue(out, response);
 		
-	public HealthResponse liveness() {
+		out.flush();
-		return null;
 	}
 	
 	public HealthResponse readiness() {
-		return null;
+		return task.getResponse();
 	}
 	
 }

src/main/java/org/gcube/smartgears/health/HealthManager.java

@@ -0,0 +1,18 @@
+package org.gcube.smartgears.health;
+
+import java.util.List;
+
+import org.gcube.common.health.api.HealthCheck;
+
+public class HealthManager {
+	
+	private List<HealthCheck> checks;
+	
+	public void register(HealthCheck check){
+		checks.add(check);
+	}
+	
+	public List<HealthCheck> getChecks() {
+		return checks;
+	}
+}

src/main/java/org/gcube/smartgears/health/HealthResponse.java

@@ -0,0 +1,35 @@
+package org.gcube.smartgears.health;
+
+import java.util.List;
+
+import org.gcube.com.fasterxml.jackson.annotation.JsonInclude;
+import org.gcube.com.fasterxml.jackson.annotation.JsonInclude.Include;
+import org.gcube.common.health.api.Status;
+import org.gcube.common.health.api.response.HealthCheckResponse;
+import org.gcube.common.validator.annotations.NotNull;
+
+@JsonInclude(Include.NON_NULL)
+public class HealthResponse {
+	
+	@NotNull
+	private Status status;
+	
+	private List<HealthCheckResponse> checks;
+
+	
+	
+	public HealthResponse(Status status, List<HealthCheckResponse> checks) {
+		super();
+		this.status = status;
+		this.checks = checks;
+	}
+
+	public Status getStatus() {
+		return status;
+	}
+
+	public List<HealthCheckResponse> getChecks() {
+		return checks;
+	}
+		
+}

src/main/java/org/gcube/smartgears/health/HealthTask.java

@@ -0,0 +1,43 @@
+package org.gcube.smartgears.health;
+
+import java.util.List;
+import java.util.TimerTask;
+import java.util.stream.Collectors;
+
+import org.gcube.common.health.api.HealthCheck;
+import org.gcube.common.health.api.Status;
+import org.gcube.common.health.api.response.HealthCheckResponse;
+
+public class HealthTask extends TimerTask{
+
+	private HealthResponse response;
+	
+	private HealthManager healthManager;
+	
+	public HealthTask(HealthManager healthManager) {
+		this.healthManager = healthManager;
+	}
+	
+	@Override
+	public void run() {
+		List<HealthCheck> checks = healthManager.getChecks();
+		
+		List<HealthCheckResponse> responses = checks.stream().map(c -> this.wrap(c)).collect(Collectors.toList());
+		Status totalStatus = responses.stream().anyMatch(r -> r.getStatus().equals(Status.DOWN)) ? Status.DOWN : Status.UP;
+		
+		this.response = new HealthResponse(totalStatus, responses);
+	}
+
+	public HealthResponse getResponse() {
+		return response;
+	}
+	
+	private HealthCheckResponse wrap(HealthCheck check){
+		try {
+			return check.check();
+		}catch (Throwable t) {
+			return HealthCheckResponse.builder(check.getName()).down().withMessage("unexpected error executing check").build();
+		}
+		
+	}
+}

src/main/java/org/gcube/smartgears/health/KeyCloakHealthCheck.java

@@ -12,6 +12,10 @@ public class KeyCloakHealthCheck implements HealthCheck{
 
 	private static final String CHECK_NAME = "authorization-check" ;
 	
+	public String getName(){
+		return CHECK_NAME;
+	}
+	
 	@Override
 	public HealthCheckResponse check() {
 		try {

src/main/java/org/gcube/smartgears/managers/ApplicationManager.java

@@ -13,6 +13,7 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.ObjectOutputStream;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map.Entry;
 
@@ -52,6 +53,8 @@ public class ApplicationManager {
 
 	private ApplicationContext context;
 
+	private ApplicationExtensions extensions;
+	
 	/**
 	 * Starts application management.
 	 * 
@@ -80,7 +83,7 @@ public class ApplicationManager {
 
 			ApplicationHandlers handlers = provider().handlersFor(context);
 
-			ApplicationExtensions extensions = provider().extensionsFor(context);
+			extensions = provider().extensionsFor(context);
 			extensions.validate();
 
 			List<ApplicationLifecycleHandler> lifecycleHandlers = handlers.lifecycleHandlers();
@@ -151,6 +154,9 @@ public class ApplicationManager {
 
 			context.events().fire(context, ApplicationLifecycle.stop);
 			
+			if (extensions != null)
+				unregister(extensions);
+			
 			stopLifecycleHandlers();
 
 			log.info("stopping application events for {}", context.name());
@@ -228,6 +234,15 @@ public class ApplicationManager {
 
 	}
 	
+	private void unregister(ApplicationExtensions extensions) {
+
+		for (ApplicationExtension extension : extensions.extensions())
+
+				extension.stop();
+
+	}
+
+
 	private void start(List<ApplicationLifecycleHandler> handlers) {
 
 		try {

src/main/java/org/gcube/smartgears/provider/DefaultProvider.java

@@ -14,12 +14,11 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.InputStream;
 import java.io.ObjectInputStream;
-import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
 import java.util.Set;
 import java.util.UUID;
+import java.util.stream.Collectors;
 
 import javax.servlet.ServletContext;
 
@@ -48,14 +47,14 @@ import org.gcube.smartgears.publishing.SmartgearsProfilePublisher;
 import org.gcube.smartgears.security.AuthorizationProvider;
 import org.gcube.smartgears.security.AuthorizationProviderFactory;
 import org.gcube.smartgears.utils.Utils;
-import org.reflections.Reflections;
-import org.reflections.scanners.SubTypesScanner;
-import org.reflections.scanners.TypeAnnotationsScanner;
-import org.reflections.util.ClasspathHelper;
-import org.reflections.util.ConfigurationBuilder;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ClassInfo;
+import io.github.classgraph.ClassInfoList;
+import io.github.classgraph.ScanResult;
+
 /**
  * Default implementation of the {@link Provider} interface.
  * 
@@ -69,7 +68,6 @@ public class DefaultProvider implements Provider {
 	private ContainerContext containerContext;
 	// TODO: do the same with applicationContext (with a map)
 
-
 	private File configFile = null;
 
 	protected DefaultProvider(File configFile) {
@@ -78,8 +76,8 @@ public class DefaultProvider implements Provider {
 
 	List<Publisher> publishers;
 
-
+	protected DefaultProvider() {
-	protected DefaultProvider(){};
+	};
 
 	@Override
 	public ContainerContext containerContext() {
@@ -109,12 +107,14 @@ public class DefaultProvider implements Provider {
 
 			}
 
-			AuthorizationProviderFactory<?> authfactory = configuration.getauthorizationConfiguration().getAuthProviderFactory();
+			AuthorizationProviderFactory<?> authfactory = configuration.getauthorizationConfiguration()
+					.getAuthProviderFactory();
 			Credentials credentials = configuration.getauthorizationConfiguration().getCredentials();
 
 			AuthorizationProvider authProvider = authfactory.connect(credentials);
 
-			containerContext =  new DefaultContainerContext(id, configuration, hub, lifecycle, authProvider, new Properties());
+			containerContext = new DefaultContainerContext(id, configuration, hub, lifecycle, authProvider,
+					new Properties());
 		}
 		return containerContext;
 	}
@@ -127,7 +127,8 @@ public class DefaultProvider implements Provider {
 			ContainerConfigurationBinder binder = new ContainerConfigurationBinder();
 
 			ClassLoader currentClassLoader = Thread.currentThread().getContextClassLoader();
-			if (currentClassLoader.getParent()!=null && !currentClassLoader.getParent().equals(ClassLoader.getSystemClassLoader())){
+			if (currentClassLoader.getParent() != null
+					&& !currentClassLoader.getParent().equals(ClassLoader.getSystemClassLoader())) {
 				log.trace("probably i'm in a webapp classloader");
 				currentClassLoader = currentClassLoader.getParent();
 			}
@@ -153,28 +154,31 @@ public class DefaultProvider implements Provider {
 		// shouldn't happen: management shouldn't have started at all
 		if (embedded == null && external == null)
 			throw new AssertionError("application @ " + application.getContextPath() + " is not distributed with "
-					+ configuration_file_path+" and there is no external configuration for it in "+container_configuraton_file_path);
+					+ configuration_file_path + " and there is no external configuration for it in "
+					+ container_configuraton_file_path);
 
 		// no embedded configuration
 		if (embedded == null) {
 
 			configuration = external;
 
-			log.info("loaded  configuration for application "+configuration.name()+" from "+container_configuraton_file_path);
+			log.info("loaded  configuration for application " + configuration.name() + " from "
-		}
+					+ container_configuraton_file_path);
-		else  {
+		} else {
 
 			configuration = embedded;
 
 			if (external == null)
 
-				log.info("loaded configuration for application "+configuration.name()+" from "+configuration_file_path);
+				log.info("loaded configuration for application " + configuration.name() + " from "
+						+ configuration_file_path);
 
 			else {
 
 				configuration.merge(external);
 
-				log.info("loaded configuration for application "+configuration.name()+" from "+configuration_file_path+" and "+container_configuraton_file_path);
+				log.info("loaded configuration for application " + configuration.name() + " from "
+						+ configuration_file_path + " and " + container_configuraton_file_path);
 
 			}
 		}
@@ -208,14 +212,13 @@ public class DefaultProvider implements Provider {
 
 		try {
 
-
 			ApplicationConfigurationBinder binder = new ApplicationConfigurationBinder();
 
-
+			// searching for smartegars related application handlers in the common
-
+			// classloader
-			//searching for smartegars related application handlers in the common classloader
 			ClassLoader currentClassLoader = Thread.currentThread().getContextClassLoader();
-			if (currentClassLoader.getParent()!=null && !currentClassLoader.getParent().equals(ClassLoader.getSystemClassLoader())){
+			if (currentClassLoader.getParent() != null
+					&& !currentClassLoader.getParent().equals(ClassLoader.getSystemClassLoader())) {
 				log.trace("probably i'm in a webapp classloader");
 				currentClassLoader = currentClassLoader.getParent();
 			}
@@ -224,15 +227,14 @@ public class DefaultProvider implements Provider {
 
 			return defaultHandlers;
 
-
 		} catch (RuntimeException e) {
 
-			throw new RuntimeException("cannot install handlers for application @ " + context.name()+" (see cause) ", e);
+			throw new RuntimeException("cannot install handlers for application @ " + context.name() + " (see cause) ",
+					e);
 
 		}
 	}
 
-
 	@Override
 	public ApplicationExtensions extensionsFor(ApplicationContext context) {
 
@@ -248,7 +250,8 @@ public class DefaultProvider implements Provider {
 				config = getClass().getResourceAsStream(default_extensions_file_path);
 
 				if (config == null)
-					throw new IllegalStateException("invalid distribution: cannot find " + default_extensions_file_path);
+					throw new IllegalStateException(
+							"invalid distribution: cannot find " + default_extensions_file_path);
 
 			} else
 				log.info("{} uses custom extensions @ {}", context.name(), extensions_file_path);
@@ -259,12 +262,12 @@ public class DefaultProvider implements Provider {
 
 		} catch (RuntimeException e) {
 
-			throw new RuntimeException("cannot install extensions for application @ " + context.name()+" (see cause) ", e);
+			throw new RuntimeException(
+					"cannot install extensions for application @ " + context.name() + " (see cause) ", e);
 
 		}
 	}
 
-
 	@Override
 	public SmartGearsConfiguration smartgearsConfiguration() {
 
@@ -324,22 +327,24 @@ public class DefaultProvider implements Provider {
 			File homeDir = new File(home);
 
 			if (!(homeDir.exists() && homeDir.isDirectory() && homeDir.canRead() && homeDir.canWrite()))
-				throw new IllegalStateException("invalid node configuration: home "+home+" does not exist or is not a directory or cannot be accessed in read/write mode");
+				throw new IllegalStateException("invalid node configuration: home " + home
+						+ " does not exist or is not a directory or cannot be accessed in read/write mode");
 
 			configFile = new File(homeDir, container_configuraton_file_path);
 
-
 			log.trace("reading container configuration @ {} ", configFile.getAbsolutePath());
 		}
 
 		if (!(configFile.exists() && configFile.canRead()))
-			throw new IllegalStateException("invalid node configuration: file "+configFile.getAbsolutePath()+" does not exist or cannot be accessed");
+			throw new IllegalStateException("invalid node configuration: file " + configFile.getAbsolutePath()
+					+ " does not exist or cannot be accessed");
 
 		ContainerConfiguration configuration;
 		try (InputStream stream = new FileInputStream(configFile)) {
 			configuration = new ContainerConfigurationBinder().load(stream);
 		} catch (Exception e) {
-			throw new IllegalStateException("invalid node configuration: file "+configFile.getAbsolutePath()+" is invalid", e);
+			throw new IllegalStateException(
+					"invalid node configuration: file " + configFile.getAbsolutePath() + " is invalid", e);
 		}
 
 		return configuration;
@@ -348,27 +353,42 @@ public class DefaultProvider implements Provider {
 	@Override
 	public synchronized List<Publisher> publishers() {
 		if (this.publishers == null) {
-			//retrieve from root class loader
-			Collection<URL> urls =  ClasspathHelper.forClassLoader(Thread.currentThread().getContextClassLoader());
-			urls.removeIf(url ->  url.toString().endsWith(".so") || url.toString().endsWith(".zip")  );
 
+			Set<Class<?>> annotatedPublishers;
 
-			ConfigurationBuilder reflectionConf =  new ConfigurationBuilder().addUrls(urls).setScanners(new TypeAnnotationsScanner(), new SubTypesScanner());
+			try (ScanResult result = new ClassGraph().enableClassInfo().enableAnnotationInfo()
+					.addClassLoader(Thread.currentThread().getContextClassLoader()).scan()) {
 
-			Reflections reflection = new Reflections(reflectionConf); 
+				ClassInfoList classInfos = result.getClassesWithAnnotation(SmartgearsProfilePublisher.class.getName());
+
+				annotatedPublishers = classInfos.stream().map(ClassInfo::loadClass)
+						.filter(c -> Publisher.class.isAssignableFrom(c)).collect(Collectors.toSet());
+
+			}
+			/*
+			 * Collection<URL> urls =
+			 * ClasspathHelper.forClassLoader(Thread.currentThread().getContextClassLoader()
+			 * ); urls.removeIf(url -> url.toString().endsWith(".so") ||
+			 * url.toString().endsWith(".zip") );
+			 * 
+			 * 
+			 * ConfigurationBuilder reflectionConf = new
+			 * ConfigurationBuilder().addUrls(urls).setScanners(new
+			 * TypeAnnotationsScanner(), new SubTypesScanner());
+			 * 
+			 * Reflections reflection = new Reflections(reflectionConf);
+			 * 
+			 * = reflection.getTypesAnnotatedWith(SmartgearsProfilePublisher.class);
+			 */
 
-			Set<Class<?>> annotatedPublishers = reflection.getTypesAnnotatedWith(SmartgearsProfilePublisher.class);
 			List<Publisher> foundPublishers = new ArrayList<Publisher>();
 			for (Class<?> annotatedPublisher : annotatedPublishers) {
-				if (Publisher.class.isAssignableFrom(annotatedPublisher))
 				try {
-						foundPublishers.add((Publisher)annotatedPublisher.newInstance());
+					foundPublishers.add((Publisher) annotatedPublisher.getDeclaredConstructor().newInstance());
 					log.info("added class {} to publishers", annotatedPublisher);
-					} catch (Exception e) {
+				} catch (Throwable e) {
 					log.error("publisher class {} cannot be instantiated", annotatedPublisher.getCanonicalName(), e);
 				}
-				else 
-					log.warn("publisher class {} discarded, it doesn't implements Publisher class", annotatedPublisher.getCanonicalName());
 
 			}
 			this.publishers = foundPublishers;
@@ -381,10 +401,8 @@ public class DefaultProvider implements Provider {
 	}
 
 	/*
-	@Override
+	 * @Override public AuthorizationProvider authorizationProvider() { return
-	public AuthorizationProvider authorizationProvider() {
+	 * containerContext.authorizationProvider(); }
-		return containerContext.authorizationProvider();
-	}
 	 */
 
 }