Update jsch to 0.1.55

Reviewed-on: #3

.classpath

@@ -15,11 +15,13 @@
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">

.settings/org.eclipse.jdt.core.prefs

@@ -3,6 +3,9 @@ org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
 org.eclipse.jdt.core.compiler.compliance=1.8
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
+org.eclipse.jdt.core.compiler.release=disabled
 org.eclipse.jdt.core.compiler.source=1.8

.settings/org.eclipse.wst.common.component

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
-    <wb-module deploy-name="dataminer-pool-manager-2.7.1-SNAPSHOT">
+    <wb-module deploy-name="dataminer-pool-manager-2.8.0-SNAPSHOT">
         <wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
         <wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>

CHANGELOG.md

@@ -3,8 +3,9 @@
 
 ## [v2.8.0-SNAPSHOT]
 
-- Updated to gcube-smartgears-bom.2.5.0
+- Updated jsch to 0.1.55
-
+- Updated to gcube-smartgears-bom: 2.5.1-SNAPSHOT
+- Updated pom.xml to include configuration resources [#26192]
 
 ## [v2.7.1] - 2022-04-06
 

changelog.xml

@@ -1,6 +1,7 @@
 <ReleaseNotes>
-<Changeset component="org.gcube.dataanalysis.dataminer-pool-manager.2-8-0" date="2023-11-09">
+<Changeset component="org.gcube.dataanalysis.dataminer-pool-manager.2-8-0" date="2024-09-16">
-  <Change>Updated to gcube-smartgears-bom.2.5.0</Change>
+  <Change>Updated to gcube-smartgears-bom: 2.5.1-SNAPSHOT</Change>
+  <Change>Updated pom.xml to include configuration resources [#26192]</Change>
 </Changeset>
 <Changeset component="org.gcube.dataanalysis.dataminer-pool-manager.2-7-1" date="2022-04-06">
   <Change>Updated to gcube-smartgears-bom.2.2.0 [#23133]</Change>

pom.xml

@@ -107,7 +107,7 @@
 		<dependency>
 			<groupId>com.jcraft</groupId>
 			<artifactId>jsch</artifactId>
-			<version>0.1.53</version>
+			<version>0.1.55</version>
 		</dependency>
 
 
@@ -151,7 +151,7 @@
 			<dependency>
 				<groupId>org.gcube.distribution</groupId>
 				<artifactId>gcube-smartgears-bom</artifactId>
-				<version>2.5.0</version>
+				<version>2.5.1-SNAPSHOT</version>
 				<type>pom</type>
 				<scope>import</scope>
 			</dependency>
@@ -191,6 +191,25 @@
 							</resources>
 						</configuration>
 					</execution>
+					<execution>
+						<id>copy-config</id>
+						<goals>
+							<goal>copy-resources</goal>
+						</goals>
+						<phase>process-resources</phase>
+						<configuration>
+							<outputDirectory>${webappDirectory}/classes</outputDirectory>
+							<resources>
+								<resource>
+									<directory>${project.basedir}/src/main/resources/</directory>
+									<filtering>true</filtering>
+									<includes>
+										<include>*/**</include>
+									</includes>
+								</resource>
+							</resources>
+						</configuration>
+					</execution>
 				</executions>
 			</plugin>
 

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/ClientConfigurationCache.java

@@ -97,16 +97,16 @@ public class ClientConfigurationCache
 						
 						if (repositoryPassword != null && repositoryPassword.trim() == "") repositoryPassword = null;
 						
-						this.logger.debug("Repository username "+repositoryUsername);
+						logger.debug("Repository username "+repositoryUsername);
-						this.logger.debug("Repository password "+repositoryPassword);
+						logger.debug("Repository password "+repositoryPassword);
 			
 					} catch (Exception e)
 					{
 						this.logger.debug("SVN Username and password not present");
 					}
 					
-					this.logger.debug("SVN Repository URL: "+repositoryURL);
+					logger.debug("SVN Repository URL: "+repositoryURL);
-					this.logger.debug("SVN Repository path: "+repositoryPath);
+					logger.debug("SVN Repository path: "+repositoryPath);
 				
 					response = new SVNRepository(repositoryURL, repositoryPath,repositoryUsername, repositoryPassword);
 				

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/ConfigurationImpl.java

@@ -30,23 +30,6 @@ public class ConfigurationImpl implements Configuration {
 	}
 	
 	
-//	enum REPOSITORIES {
-//		REPO ("svn.repository"),
-//		MAIN_ALGO ("svn.algo.main.repo");
-//		
-//		private String type;
-//		
-//		private REPOSITORIES(String type) {
-//			this.type = type;
-//		}
-//		
-//		@Override
-//		public String toString() {
-//			return this.type;
-//		}
-//	}
-	
-	
 	private CONFIGURATIONS type;
 	private ClientConfigurationCache cache;
 	

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/DMPMClientConfiguratorManager.java

@@ -14,7 +14,7 @@ import org.slf4j.LoggerFactory;
 import org.tmatesoft.svn.core.SVNException;
 
 public class DMPMClientConfiguratorManager {
-	private final Logger logger;
+	private final Logger logger=LoggerFactory.getLogger(DMPMClientConfiguratorManager.class);
 	private Properties defaultAdmins;
 
 	static DMPMClientConfiguratorManager instance;
@@ -22,28 +22,27 @@ public class DMPMClientConfiguratorManager {
 	private ScopedCacheMap cacheMap;
 
 	private DMPMClientConfiguratorManager() {
-		this.cacheMap = new ScopedCacheMap();
+		cacheMap = new ScopedCacheMap();
-		this.logger = LoggerFactory.getLogger(DMPMClientConfiguratorManager.class);
+		defaultAdmins = new Properties();
-		this.defaultAdmins = new Properties();
 
 		try {
-			this.defaultAdmins.load(this.getClass().getResourceAsStream("/default.admins"));
+			defaultAdmins.load(this.getClass().getResourceAsStream("/default.admins"));
-			this.logger.debug("Default users successfully loaded");
+			logger.debug("Default users successfully loaded");
 		} catch (Exception e) {
-			this.logger.error("Unable to get default users", e);
+			logger.error("Unable to get default users", e);
 		}
 	}
 
 	private ClientConfigurationCache getCurrentCache() {
 		String currentScope = ScopeProvider.instance.get();
-		this.logger.debug("Current scope = " + currentScope);
+		logger.debug("Current scope = " + currentScope);
-		this.logger.debug("Getting current configuration cache");
+		logger.debug("Getting current configuration cache");
-		ClientConfigurationCache cache = this.cacheMap.get(currentScope);
+		ClientConfigurationCache cache = cacheMap.get(currentScope);
 
 		if (cache == null) {
-			this.logger.debug("Cache not created yet, creating...");
+			logger.debug("Cache not created yet, creating...");
 			cache = new ClientConfigurationCache();
-			this.cacheMap.put(currentScope, cache);
+			cacheMap.put(currentScope, cache);
 
 		}
 
@@ -88,8 +87,8 @@ public class DMPMClientConfiguratorManager {
 
 	public static void main(String[] args) throws IOException, SVNException {
 		DMPMClientConfiguratorManager a = new DMPMClientConfiguratorManager();
-		ScopeProvider.instance.set("/gcube/devNext/NextNext");
+		ScopeProvider.instance.set("/gcube/devsec/devVRE");
-		// SecurityTokenProvider.instance.set("708e7eb8-11a7-4e9a-816b-c9ed7e7e99fe-98187548");
+		// SecurityTokenProvider.instance.set("xxx-xxx-xxx-xxx");
 
 		System.out.println("RESULT 1" + a.getStagingConfiguration().getSVNCRANDepsList());
 		System.out.println("RESULT 2" + a.getProductionConfiguration().getRepository());

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckMethod.java

@@ -9,6 +9,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 import java.util.Properties;
 
 import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration;
@@ -186,9 +187,18 @@ public abstract class CheckMethod {
 			
 			
 			this.logger.debug("session created.");
+			this.logger.debug("Session Config:");
+			for (Object key: sshConfig.keySet()) {
+			    this.logger.debug("{} = {} ", key, sshConfig.get(key));
+			}
+			
+			
+			this.logger.debug("SSH Config: {}",sshConfig);
 			session.setConfig(this.sshConfig);
 			session.connect();
 
+			this.logger.debug("Open Channel SFTP");
+			this.logger.debug("Protocol: "+SFTP_PROTOCOL);
 			Channel channel = session.openChannel(SFTP_PROTOCOL);
 			channel.connect();
 			this.logger.debug("shell channel connected....");
@@ -207,6 +217,7 @@ public abstract class CheckMethod {
 			session.disconnect();
 		} catch (Exception e)
 		{
+			this.logger.error("Error in deleteFiles(): {} ",e.getLocalizedMessage(),e);
 			throw new GenericException(e);
 		}
 		

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SVNRepositoryManager.java

@@ -14,11 +14,10 @@ public class SVNRepositoryManager {
 
 	private SVNRepository svnRepository;
 	private static  SVNRepositoryManager instance;
-	private Logger logger;
+	private Logger logger=LoggerFactory.getLogger(SVNRepositoryManager.class);
 	
 	private SVNRepositoryManager (Configuration configuration) throws SVNException
 	{
-		this.logger = LoggerFactory.getLogger(SVNRepositoryManager.class);
 		org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.SVNRepository repository = configuration.getSVNRepository();
 		this.svnRepository = SVNRepositoryFactory.create(SVNURL.parseURIEncoded(repository.getBaseUrl()));
 		ISVNAuthenticationManager authManager = null;

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SVNUpdater.java

@@ -45,12 +45,11 @@ public abstract class SVNUpdater {
 
 	private SVNRepository svnRepository;
 	private Configuration configuration;
-	private Logger logger;
+	private Logger logger=LoggerFactory.getLogger(SVNUpdater.class);
 
 	public SVNUpdater(Configuration configuration) throws SVNException {
 		this.configuration = configuration;
 		this.svnRepository = SVNRepositoryManager.getInstance(configuration).getSvnRepository();
-		this.logger = LoggerFactory.getLogger(SVNUpdater.class);
 	}
 
 //	public void updateRPRotoDeps(Algorithm algorithm) {
@@ -72,7 +71,7 @@ public abstract class SVNUpdater {
 	
 	private String getDependencyFile (Configuration configuration, String language)
 	{
-		this.logger.debug("Getting dependency file for language "+language);
+		logger.debug("Getting dependency file for language "+language);
 		
 		switch (language) 
 		{
@@ -123,7 +122,7 @@ public abstract class SVNUpdater {
 	
 	private void updateAlgorithmList(String svnMainAlgoRepo, File algorithmsFile) throws SVNException, SVNCommitException
 	{
-		this.logger.debug("Adding .jar file: " + algorithmsFile + " to repository " + svnMainAlgoRepo);
+		logger.debug("Adding .jar file: " + algorithmsFile + " to repository " + svnMainAlgoRepo);
 		
 		try
 		{
@@ -137,7 +136,7 @@ public abstract class SVNUpdater {
 		} 
 		catch (FileNotFoundException e)
 		{
-			this.logger.error("Temporary algorithm file not found: this exception should not happen",e);
+			logger.error("Temporary algorithm file not found: this exception should not happen",e);
 		}
 		finally
 		{
@@ -149,7 +148,7 @@ public abstract class SVNUpdater {
 	
 	public void putFile(FileInputStream fileInputSreeam, String destinationFolder, String fileName) throws SVNException, SVNCommitException 
 	{
-		this.logger.debug("Putting new file on the SVN repository");
+		logger.debug("Putting new file on the SVN repository");
 		final ISVNEditor commitEditor = svnRepository.getCommitEditor("Add algorithm to list", null);
 		commitEditor.openRoot(-1);
 		commitEditor.openDir(destinationFolder, -1);
@@ -166,17 +165,17 @@ public abstract class SVNUpdater {
 		
 		if (errorMessage != null)
 		{
-			this.logger.error("Operation failed: "+errorMessage.getFullMessage());
+			logger.error("Operation failed: "+errorMessage.getFullMessage());
 			throw new SVNCommitException(errorMessage,fileName);
 		}
 		
-		this.logger.debug("Operation completed");
+		logger.debug("Operation completed");
 	}
 	
 	
 	public void updateFile(FileInputStream fileInputStream, String destinationFolder, String fileName) throws SVNException, SVNCommitException  {
 		
-		this.logger.debug("Updating existing file on the SVN repository");		
+		logger.debug("Updating existing file on the SVN repository");		
 		final ISVNEditor commitEditor = svnRepository.getCommitEditor("Updating algorithm", null);
 		commitEditor.openRoot(-1);
 		commitEditor.openDir(destinationFolder, -1);
@@ -197,12 +196,12 @@ public abstract class SVNUpdater {
 		
 		if (errorMessage != null)
 		{
-			this.logger.error("Operation failed: "+errorMessage.getFullMessage());
+			logger.error("Operation failed: "+errorMessage.getFullMessage());
 
 			throw new SVNCommitException(errorMessage,fileName+" to be updated");
 		}
 		
-		this.logger.debug("Operation completed");
+		logger.debug("Operation completed");
 	}
 	
 	
@@ -231,7 +230,7 @@ public abstract class SVNUpdater {
 		boolean response = false;
 		
 		try {
-			this.logger.debug("Updating algorithm list: " + file);
+			logger.debug("Updating algorithm list: " + file);
 			final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
 			svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
 			String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
@@ -277,7 +276,7 @@ public abstract class SVNUpdater {
 			
 			if (errorMessage != null)
 			{
-				this.logger.error("Operation failed: "+errorMessage.getFullMessage());
+				logger.error("Operation failed: "+errorMessage.getFullMessage());
 				response = false;
 			}
 			else response = true;
@@ -286,7 +285,7 @@ public abstract class SVNUpdater {
 		} 
 		catch (Exception ex) 
 		{
-			this.logger.error("Unable to commit algorithm list",ex);
+			logger.error("Unable to commit algorithm list",ex);
 			response = false;
 		}
 
@@ -314,7 +313,7 @@ public abstract class SVNUpdater {
 		sb.append("none | ");
 		sb.append(this.getTimeZone() + " | ");
 		
-		this.logger.info("Algo details: "+sb.toString());
+		logger.info("Algo details: "+sb.toString());
 		
 		return sb.toString();
 	}
@@ -337,7 +336,7 @@ public abstract class SVNUpdater {
 			}
 			
 			
-			this.logger.debug("Checking dependencies list: " + file);
+			logger.debug("Checking dependencies list: " + file);
 			
 
 			List<String> validDependencies = new LinkedList<String>();
@@ -351,7 +350,7 @@ public abstract class SVNUpdater {
 				validDependencies.add(l.trim());
 			}}
 
-			this.logger.debug("Valid dependencies are: "+validDependencies);
+			logger.debug("Valid dependencies are: "+validDependencies);
 			for(Dependency d: deps){
 				String depName = d.getName();
 				if(!validDependencies.contains(depName)){
@@ -410,6 +409,7 @@ public abstract class SVNUpdater {
 //			return check;
 		} catch (SVNException e)
 		{
+			logger.error(e.getLocalizedMessage(),e);
 			throw new GenericException(e);
 		}
 		
@@ -423,7 +423,7 @@ public abstract class SVNUpdater {
 
 		boolean check = false;
 		try {
-			this.logger.info("Checking dependencies list: " + file);
+			logger.info("Checking dependencies list: " + file);
 			final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
 			svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
 			String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
@@ -454,7 +454,7 @@ public abstract class SVNUpdater {
 			// }
 		} catch (Exception a) 
 		{
-			this.logger.error(a.getMessage(),a);
+			logger.error(a.getMessage(),a);
 			
 		}
 
@@ -464,7 +464,7 @@ public abstract class SVNUpdater {
 
 	public void updateSVN(String file, Collection<Dependency> deps) {
 		try {
-			this.logger.info("Updating dependencies list: " + file);
+			logger.info("Updating dependencies list: " + file);
 
 			final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
 			svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
@@ -543,7 +543,7 @@ public abstract class SVNUpdater {
 		Date fromDate = formatter.parse(cal.getTime().toString());
 	    TimeZone central = TimeZone.getTimeZone("UTC");
 	    formatter.setTimeZone(central);
-	    this.logger.info(formatter.format(fromDate));
+	    logger.info(formatter.format(fromDate));
 		return formatter.format(fromDate);
 	}
 	

src/main/resources/service.properties

@@ -6,7 +6,7 @@ svn.algo.main.repo = /trunk/data-analysis/DataMinerConfiguration/algorithms
 
 
 #STAGE
-STAGE_GHOST = dataminer-ghost-d.dev.d4science.org
+STAGE_GHOST = dataminer-ghost.cloud-dev.d4science.org
 svn.stage.algorithms-list = /trunk/data-analysis/DataMinerConfiguration/algorithms/dev/algorithms
 
 svn.stage.deps-linux-compiled = /trunk/data-analysis/RConfiguration/RPackagesManagement/r_deb_pkgs.txt

src/main/resources/static/gcube-algorithm-installer/meta/main.yaml

@@ -1,4 +1,4 @@
 dependencies:
 #  - { role: gcube-dataminer }
 #  - { role: os-unzip }
-#  - { role: os-java-1.7.0 }
+#  - { role: os-java-1.8.0 }

src/main/resources/static/os-java-1.8.0/tasks/main.yaml

@@ -1,7 +1,7 @@
 ---
 
-- name: adding OS Package java-1.7.0
+- name: adding OS Package java-1.8.0
   package: 
-    name: java-1.7.0-openjdk
+    name: java-1.8.0-openjdk
     state: "{{os_package_state}}"
   become: true

src/main/webapp/WEB-INF/.gitignore

@@ -3,3 +3,4 @@
 /changelog.xml
 /gcube-app.xml
 /profile.xml
+/classes/

src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/SVNTests.java

@@ -24,7 +24,7 @@ public class SVNTests {
     //algo.setClazz(algo.getClazz() + "TEST");
     algo.setAlgorithmType("transducerers");
     algo.setCategory("NLP");
-    algo.setFullname("Ondřej Košarko");
+    algo.setFullname("Master Test");
     //System.out.println(algo.getCategory());
     //System.out.println(algo.getSkipJava());