Managed Authorization 2.0

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@131858 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/capabilities/GetCapabilitiesBuilder.java

@@ -61,8 +61,10 @@ public class GetCapabilitiesBuilder {
 		tokenm.getCredentials();
 		String scope = tokenm.getScope();
 		String username = tokenm.getUserName();
+		String token = tokenm.getToken();
 		basicInputs.put(ConfigurationManager.scopeParameter, scope);
 		basicInputs.put(ConfigurationManager.usernameParameter, username);
+		basicInputs.put(ConfigurationManager.tokenParameter, token);
 		
 		configManager.configAlgorithmEnvironment(basicInputs);
 		AnalysisLogger.getLogger().debug("Initializing Capabilities Skeleton in scope " + configManager.getScope() + " with user " + configManager.getUsername());

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/capabilities/GetCapabilitiesChecker.java

@@ -38,9 +38,7 @@ public class GetCapabilitiesChecker {
 		String scannedPath = packageName.replace(".", "/");
 		URL scannedUrl = Thread.currentThread().getContextClassLoader().getResource(scannedPath);
 		String jarPath = scannedUrl.getFile();
-		
+
-		
-		
 		AnalysisLogger.getLogger().debug("Jar Path complete: " + jarPath);
 		jarPath = jarPath.substring(jarPath.indexOf("file:/") + 6, jarPath.lastIndexOf("!"));
 		if (jarPath.startsWith("home"))
@@ -49,33 +47,47 @@ public class GetCapabilitiesChecker {
 
 		JarFile jarFile = null;
 		List<Class<?>> result = new ArrayList<Class<?>>();
-		
+
-		File otherjar = new File(new File(jarPath).getParent(),"dataminer-algorithms.jar");
+		String pathTojars = new File(jarPath).getParent();
-		if (otherjar .exists())
+
-			jarPath =otherjar.getAbsolutePath();
+		File[] jars = new File(pathTojars).listFiles();
-		AnalysisLogger.getLogger().debug("Alternative Jar Path: " + jarPath);
 		try {
-			jarFile = new JarFile(jarPath);
-			Enumeration<JarEntry> en = jarFile.entries();
 
-			while (en.hasMoreElements()) {
+			for (File jar : jars) {
-				JarEntry entry = en.nextElement();
+				// File otherjar = new File(new File(jarPath).getParent(),"dataminer-algorithms.jar");
-				String entryName = entry.getName();
-				packageName = packageName.replace('.', '/');
 
-				if (entryName != null && entryName.endsWith(".class") && entryName.startsWith(packageName)) {
+				if (jar.getName().equals("dataminer-algorithms.jar") || jar.getName().endsWith("_interface.jar")) {
-					try {
-						Class entryClass = Class.forName(entryName.substring(0, entryName.length() - 6).replace('/', '.'));
 
-						if (entryClass != null) {
+					//File otherjar = new File(new File(jarPath).getParent(), "dataminer-algorithms.jar");
-							result.add(entryClass);
+					File otherjar = jar;
+					if (otherjar.exists())
+						jarPath = otherjar.getAbsolutePath();
+				
+					AnalysisLogger.getLogger().debug("Alternative Jar Path: " + jarPath);
+
+					jarFile = new JarFile(jarPath);
+					Enumeration<JarEntry> en = jarFile.entries();
+
+					while (en.hasMoreElements()) {
+						JarEntry entry = en.nextElement();
+						String entryName = entry.getName();
+						packageName = packageName.replace('.', '/');
+
+						if (entryName != null && entryName.endsWith(".class") && entryName.startsWith(packageName)) {
+							try {
+								Class entryClass = Class.forName(entryName.substring(0, entryName.length() - 6).replace('/', '.'));
+
+								if (entryClass != null) {
+									result.add(entryClass);
+								}
+							} catch (Throwable e) {
+								// do nothing, just continue processing classes
+							}
 						}
-					} catch (Throwable e) {
+					}// while
-						// do nothing, just continue processing classes
-					}
-				}
-			}
 
+				}// if jar known
+			}
 			return result;
 		} catch (Exception e) {
 			throw e;
@@ -167,29 +179,22 @@ public class GetCapabilitiesChecker {
 		}
 	}
 
-	
-	
 	public static Charset getConnectionCharset(URLConnection connection) {
 		String contentType = null;
 		try {
 			contentType = connection.getContentType();
-		}
+		} catch (Exception e) {
-		catch (Exception e) {
 			// specified charset is not found,
 			// skip it to return the default one
 			return Charset.defaultCharset();
 		}
-		if (contentType != null && contentType.length() > 0)
+		if (contentType != null && contentType.length() > 0) {
-		{
 			contentType = contentType.toLowerCase();
 			String charsetName = extractCharsetName(contentType);
-			if (charsetName != null && charsetName.length() > 0)
+			if (charsetName != null && charsetName.length() > 0) {
-			{
+				try {
-				try
-				{
 					return Charset.forName(charsetName);
-				}
+				} catch (Exception e) {
-				catch (Exception e) {
 					// specified charset is not found,
 					// skip it to return the default one
 				}
@@ -199,27 +204,25 @@ public class GetCapabilitiesChecker {
 		// return the default charset
 		return Charset.defaultCharset();
 	}
+
 	/**
-	 * Extract the charset name form the content type string.
+	 * Extract the charset name form the content type string. Content type string is received from Content-Type header.
-	 * Content type string is received from Content-Type header.
+	 * 
-	 *
+	 * @param contentType
-	 * @param contentType the content type string, must be not null.
+	 *            the content type string, must be not null.
 	 * @return the found charset name or null if not found.
 	 */
 	private static String extractCharsetName(String contentType) {
 		// split onto media types
 		final String[] mediaTypes = contentType.split(":");
-		if (mediaTypes.length > 0)
+		if (mediaTypes.length > 0) {
-		{
 			// use only the first one, and split it on parameters
 			final String[] params = mediaTypes[0].split(";");
 
 			// find the charset parameter and return it's value
-			for (String each : params)
+			for (String each : params) {
-			{
 				each = each.trim();
-				if (each.startsWith("charset="))
+				if (each.startsWith("charset=")) {
-				{
 					// return the charset name
 					return each.substring(8).trim();
 				}
@@ -229,65 +232,63 @@ public class GetCapabilitiesChecker {
 		return null;
 	}
 
-
 	private static String RUNTIME_RESOURCE_NAME = "ReportsStoreGateway";
 	private static String CATEGORY_NAME = "Service";
-		
-	public static String readPageNoHttpClient(URL url) throws Exception{
-			URLConnection conn = url.openConnection();
-			//pretend you're a browser (make my request from Java more browsery-like.) 
-			conn.addRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11");
-			conn.setDoOutput(true);
-			conn.setAllowUserInteraction(true);
-			conn.setConnectTimeout(25*60000);
-			conn.setReadTimeout(25*60000);
 
-			Charset charset = getConnectionCharset(conn);
+	public static String readPageNoHttpClient(URL url) throws Exception {
-			
-			BufferedReader dis = new BufferedReader(new InputStreamReader(conn.getInputStream(), charset));
-			String inputLine;
-			StringBuffer pageBuffer = new StringBuffer();
-
-			// Loop through each line, looking for the closing head element
-			while ((inputLine = dis.readLine()) != null) {	
-				pageBuffer.append(inputLine + "\r\n");
-			}
-			
-			String page = pageBuffer.toString();
-			System.out.println(page);
-			conn.getInputStream().close();
-			return page;
-	}
-	
-	
-	public static String readPageHTTPHeader(URL url,String token) throws Exception{
 		URLConnection conn = url.openConnection();
-		//pretend you're a browser (make my request from Java more browsery-like.) 
+		// pretend you're a browser (make my request from Java more browsery-like.)
 		conn.addRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11");
 		conn.setDoOutput(true);
 		conn.setAllowUserInteraction(true);
-		conn.setConnectTimeout(25*60000);
+		conn.setConnectTimeout(25 * 60000);
-		conn.setReadTimeout(25*60000);
+		conn.setReadTimeout(25 * 60000);
-		conn.setRequestProperty("gcube-token", token);
+
-		
 		Charset charset = getConnectionCharset(conn);
-		
+
 		BufferedReader dis = new BufferedReader(new InputStreamReader(conn.getInputStream(), charset));
 		String inputLine;
 		StringBuffer pageBuffer = new StringBuffer();
 
 		// Loop through each line, looking for the closing head element
-		while ((inputLine = dis.readLine()) != null) {	
+		while ((inputLine = dis.readLine()) != null) {
 			pageBuffer.append(inputLine + "\r\n");
 		}
-		
+
 		String page = pageBuffer.toString();
 		System.out.println(page);
 		conn.getInputStream().close();
 		return page;
-}
+	}
-	
+
-	//build config.xml
+	public static String readPageHTTPHeader(URL url, String token) throws Exception {
+		URLConnection conn = url.openConnection();
+		// pretend you're a browser (make my request from Java more browsery-like.)
+		conn.addRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11");
+		conn.setDoOutput(true);
+		conn.setAllowUserInteraction(true);
+		conn.setConnectTimeout(25 * 60000);
+		conn.setReadTimeout(25 * 60000);
+		conn.setRequestProperty("gcube-token", token);
+
+		Charset charset = getConnectionCharset(conn);
+
+		BufferedReader dis = new BufferedReader(new InputStreamReader(conn.getInputStream(), charset));
+		String inputLine;
+		StringBuffer pageBuffer = new StringBuffer();
+
+		// Loop through each line, looking for the closing head element
+		while ((inputLine = dis.readLine()) != null) {
+			pageBuffer.append(inputLine + "\r\n");
+		}
+
+		String page = pageBuffer.toString();
+		System.out.println(page);
+		conn.getInputStream().close();
+		return page;
+	}
+
+	// build config.xml
 	public static void main(String[] args) throws Exception {
 		String packageS = "org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses";
 		List<Class<?>> classes = GetCapabilitiesChecker.find(packageS);
@@ -302,7 +303,7 @@ public class GetCapabilitiesChecker {
 		System.out.println(classes.size() + " algorithms");
 
 	}
-	
+
 	public static void main1(String[] args) throws Exception {
 		String packageS = "org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses";
 		List<Class<?>> classes = GetCapabilitiesChecker.find(packageS);
@@ -340,9 +341,5 @@ public class GetCapabilitiesChecker {
 		System.out.println("Checked " + counter + " algorithms");
 
 	}
-	
-	
-	
-	
 
 }

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/infrastructure/InfrastructureDialoguer.java

@@ -18,7 +18,7 @@ public class InfrastructureDialoguer {
 	public String scope;
 	
 	public InfrastructureDialoguer(String scope){
-		ScopeProvider.instance.set(scope);
+		//ScopeProvider.instance.set(scope);
 		this.scope = scope;
 	}
 	

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/AbstractEcologicalEngineMapper.java

@@ -314,19 +314,40 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
 		updateComputationOnWS(status, exception, null, null);
 	}
 
-	public void updateComputationOnWS(float status, String exception, List<StoredData> inputData, List<File> generatedData) {
+	class RunDataspaceManager implements Runnable{
-		if (currentComputation != null) {
+		List<StoredData> inputData;
-			currentComputation.setStatus("" + status);
+		List<File> generatedData;
-			if (exception != null && exception.length() > 0)
+		public RunDataspaceManager(List<StoredData> inputData,		List<File> generatedData){
-				currentComputation.setException(exception);
+			this.inputData=inputData;
+			this.generatedData=generatedData;
+		}
+		
+		public void run() {
 			DataspaceManager manager = new DataspaceManager(config, currentComputation, inputData, null, generatedData);
 			try {
+				AnalysisLogger.getLogger().debug("Dataspace->Status updater->Writing computational info on the WS asyncronously");
 				manager.writeRunningComputationData();
 			} catch (Exception ez) {
 				AnalysisLogger.getLogger().debug("Dataspace->Status updater->Impossible to write computation information on the Workspace");
 				AnalysisLogger.getLogger().debug(ez);
 			}
 		}
+	};
+
+	public void updateComputationOnWS(float status, String exception, List<StoredData> inputData, List<File> generatedData) {
+		if (currentComputation != null) {
+			currentComputation.setStatus("" + status);
+			if (exception != null && exception.length() > 0)
+				currentComputation.setException(exception);
+			
+			RunDataspaceManager rundm = new RunDataspaceManager(inputData,generatedData);
+			rundm.run();
+			
+			/*
+			Thread t = new Thread(rundm);
+			t.start();
+			*/
+		}
 	}
 
 	@Execute
@@ -533,6 +554,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
 		ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(), agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(), config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(), this.getClass().getCanonicalName());
 		// post on WS
 		DataspaceManager manager = new DataspaceManager(config, computation, inputData, outputData, generatedFiles);
+		
 		Thread t = new Thread(manager);
 		t.start();
 		AnalysisLogger.getLogger().debug("Provenance manager running");

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/ConfigurationManager.java

@@ -19,6 +19,7 @@ public class ConfigurationManager {
 	public static String webPersistencePathVariable = "";
 	public static String usernameParameter = "user.name";
 	public static String scopeParameter = "scope";
+	public static String tokenParameter = "usertoken";
 	public static String defaultScope= "/gcube/devsec";
 	public static String defaultUsername= "statistical.wps";
 	
@@ -57,6 +58,7 @@ public class ConfigurationManager {
 	private AlgorithmConfiguration config;
 	private String scope;
 	private String username;
+	private String token;
 
 	public String getScope() {
 		return scope;
@@ -122,11 +124,20 @@ public class ConfigurationManager {
 			scope = "/" + scope;
 
 		username = (String) inputs.get(usernameParameter);
+		token = (String) inputs.get(tokenParameter);
+		
 		AnalysisLogger.getLogger().debug("User name used by the client: " + username);
+		AnalysisLogger.getLogger().debug("User token used by the client: " + token);
+		
 		if (username == null || username.trim().length() == 0)
 			throw new Exception("Error: user name parameter (user.name) not set! This violates e-Infrastructure security policies");
 		
+		if (token == null || token.trim().length() == 0)
+			throw new Exception("Error: token parameter not set! This violates e-Infrastructure security policies");
+
 		config.setGcubeScope(scope);
+		config.setGcubeUserName(username);
+		config.setGcubeToken(token);
 		// DONE get username from request
 		config.setParam(serviceUserNameParameterVariable, username);
 		config.setParam(processingSessionVariable, "" + UUID.randomUUID());

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/TokenManager.java

@@ -1,15 +1,18 @@
 package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping;
 
+import static org.gcube.common.authorization.client.Constants.authorizationService;
+
+import org.gcube.common.authorization.library.AuthorizationEntry;
 import org.gcube.common.authorization.library.provider.AuthorizationProvider;
 import org.gcube.common.authorization.library.provider.ClientInfo;
+import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
 import org.gcube.common.authorization.library.provider.UserInfo;
-import org.gcube.common.scope.api.ScopeProvider;
 
 public class TokenManager {
 
 	String username;
 	String scope;
-	
+	String token;
 	
 	public String getScope(){
 		return scope;
@@ -19,26 +22,35 @@ public class TokenManager {
 		return username;
 	}
 	
+	public String getToken(){
+		return token;
+	}
+	
 	public void getCredentials() {
 		try{
 			System.out.println("Retrieving token credentials");
-			scope = ScopeProvider.instance.get();
+			//scope = ScopeProvider.instance.get();
 			System.out.println("Credentials from the GHN: scope: "+scope);
 			//get username from SmartGears
-			ClientInfo token = (UserInfo) AuthorizationProvider.instance.get().getClient();
+			ClientInfo tokenInfo = (UserInfo) AuthorizationProvider.instance.get().getClient();
-			username = token.getId();
+			username = tokenInfo.getId();
-			System.out.println("Credentials from the GHN: user: "+username);
+			token = SecurityTokenProvider.instance.get();
+			AuthorizationEntry entry = authorizationService().get(token);
+			scope = entry.getContext();
+			
+			System.out.println("Credentials from the GHN: user: "+username+" , "+scope+" , "+token);
 			}catch(Exception e){
 				e.printStackTrace();
 				System.out.println("Error Retrieving token credentials: "+e.getLocalizedMessage());
 				scope = null;
 				username= null;
+				
 			}
 			if ((scope==null || username==null) && ConfigurationManager.isSimulationMode()){
 				scope = ConfigurationManager.defaultScope;
 				username = ConfigurationManager.defaultUsername;
 			}
-			System.out.println("Retrieved scope: "+scope+" Username: "+username +" SIMULATION MODE: "+ConfigurationManager.isSimulationMode());
+			System.out.println("Retrieved scope: "+scope+" Username: "+username +" Token "+token+" SIMULATION MODE: "+ConfigurationManager.isSimulationMode());
 
 	}
 

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/dataspace/DataspaceManager.java

@@ -176,7 +176,7 @@ public class DataspaceManager implements Runnable {
 				//fileItem.getProperties().addProperties(properties);
 				AnalysisLogger.getLogger().debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
 				
-				url = fileItem.getPublicLink(true);
+				url = fileItem.getPublicLink(false);
 				AnalysisLogger.getLogger().debug("Dataspace->WS OP url produced for the file " + url);
 				
 				data.payload = url;
@@ -184,7 +184,7 @@ public class DataspaceManager implements Runnable {
 					in.close();
 				} catch (Exception e) {
 					AnalysisLogger.getLogger().debug("Dataspace->Error creating file " + e.getMessage());
-					AnalysisLogger.getLogger().debug(e);
+					//AnalysisLogger.getLogger().debug(e);
 				}
 				AnalysisLogger.getLogger().debug("Dataspace->File created " + filenameonwsString);
 			} else {
@@ -194,7 +194,7 @@ public class DataspaceManager implements Runnable {
 		} catch (Throwable e) {
 			e.printStackTrace();
 			AnalysisLogger.getLogger().debug("Dataspace->Could not retrieve input payload " + data.payload+" - "+e.getLocalizedMessage());
-			AnalysisLogger.getLogger().debug(e);
+			//AnalysisLogger.getLogger().debug(e);
 			url = "payload was not made available for this dataset";
 			data.payload = url;
 		}

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/test/CreateTestTableFromFile.java

@@ -0,0 +1,35 @@
+package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.test;
+
+import java.io.File;
+
+import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
+import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
+import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
+import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.infrastructure.DatabaseInfo;
+import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.infrastructure.InfrastructureDialoguer;
+import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.InputsManager;
+
+public class CreateTestTableFromFile {
+	public static void main(String[] args) throws Exception{
+		Regressor regressor = new Regressor();
+		AlgorithmConfiguration config = regressor.getConfig();
+		
+		String tableName = "spread_test";
+		File tableFile = new File("C:\\Users\\coro\\Desktop\\DATABASE e NOTE\\spread_input_dataset .csv");
+		String inputTableTemplate = TableTemplates.GENERIC.name();
+		String scope = "/gcube/devsec/devVRE";
+		System.out.println("Asking the infra for database in scope: "+scope);
+		InfrastructureDialoguer dialoguer = new InfrastructureDialoguer(scope);
+		DatabaseInfo supportDatabaseInfo = dialoguer.getDatabaseInfo("StatisticalManagerDataBase");
+		InputsManager manager = new InputsManager(null, config, "test");
+		manager.configSupportDatabaseParameters(supportDatabaseInfo);
+		System.out.println("Database retrieved: "+supportDatabaseInfo.url);
+		
+		System.out.println("Creating: "+tableName);
+		
+		manager.createTable(tableName, tableFile,manager.getConfig(), supportDatabaseInfo, inputTableTemplate);
+		
+		System.out.println("DB coordinates: \nURL "+supportDatabaseInfo.url+"\n user "+supportDatabaseInfo.username+"\n password "+supportDatabaseInfo.password+"\n driver "+supportDatabaseInfo.driver+"\n dialect "+supportDatabaseInfo.dialect);
+		System.out.println("All done");
+	}
+}

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/web/ExecuteRequest.java

@@ -795,6 +795,7 @@ public class ExecuteRequest extends Request implements IObserver {
 		try {
 			is = executeDocument.newInputStream();
 			DatabaseFactory.getDatabase().insertRequest(wpsid, is, true);
+			//DatabaseFactory.getDatabase().insertRequest(wpsid, is, false);
 		} catch (Exception e) {
 			LOGGER.error("Exception storing ExecuteRequest", e);
 		} finally {