diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/JobStatistics.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/JobStatistics.java
deleted file mode 100644
index 1e354ee09..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/JobStatistics.java
+++ /dev/null
@@ -1,312 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-
-/**
- * This class implemented methods for the calculation and visualisation of<br>
- * statistics of jobs submitted to an HPC.  
- * 
- * @author msff2
- *
- */
-public class JobStatistics {
-	private int jobsSubmitted = 0;
-	private int jobsCompleted = 0;
-	private int jobsCompleting = 0;
-	private int jobsFailed = 0;
-	private int jobsPending = 0;
-	private int jobsPreempted = 0;
-	private int jobsRunning = 0;
-	private int jobsSuspended = 0;
-	private int jobsStopped = 0;
-	private int jobsErrorTerminated = 0;
-	private int jobsNotStarted = 0;
-	
-	private File jobSpace;
-	
-	/**
-	 * Construct that takes the job workspace folder as the parameter and<br>
-	 * calculates the statistics of jobs submitted to an HPC. 
-	 * 
-	 * @param jobSpace
-	 * @throws IOException
-	 */
-	public JobStatistics(File jobSpace) throws IOException{
-		this.jobSpace = jobSpace;
-		File[] jobs = jobSpace.listFiles();
-		for(File job:jobs){
-			calculateAllStatistics(job);
-		}
-		setJobsSubmitted(getJobsCompleted() + getJobsCompleting() + getJobsFailed() + getJobsPending()
-				+ getJobsPreempted() + getJobsRunning() + getJobsSuspended() + getJobsStopped()
-				+ getJobsErrorTerminated() + getJobsNotStarted());
-	}
-
-	/**
-	 * Calculates statistics of jobs grouped into multiple categories based<br>
-	 * upon their status.
-	 * 
-	 * @param job
-	 * @throws IOException
-	 */
-	private void calculateAllStatistics(File job) throws IOException{
-		if(job!=null && job.isDirectory()){
-			File[] jobFiles = job.listFiles();
-			for(File jobFile:jobFiles){
-				calculateStatistics(jobFile);
-			}
-		}
-	}
-	
-	/**
-	 * Reads the status of single job to calculate the statistics. 
-	 * 
-	 * @param jobFile
-	 * @throws IOException
-	 */
-	private void calculateStatistics(File jobFile) throws IOException{
-		if(!jobFile.isDirectory() && jobFile.getAbsolutePath().endsWith(Status.STATUS_FILE.getName())){
-			calculateStatistics(jobFile.getAbsolutePath());
-		}
-	}
-	/**
-	 * Calculates statistics about all submitted jobs.
-	 * 
-	 * @param statusFilePath
-	 * @throws IOException
-	 */
-	public void calculateStatistics(String statusFilePath) throws IOException{
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName())){
-				if(line.contains(Status.STATUS_JOB_COMPLETED.getName())){
-					setJobsCompleted(getJobsCompleted()+1);
-				} else if(line.contains(Status.STATUS_JOB_COMPLETING.getName())){
-					setJobsCompleting(getJobsCompleting()+1);
-				} else if(line.contains(Status.STATUS_JOB_FAILED.getName())){
-					setJobsFailed(getJobsFailed()+1);
-				} else if(line.contains(Status.STATUS_JOB_PENDING.getName())){
-					setJobsPending(getJobsPending()+1);
-				} else if(line.contains(Status.STATUS_JOB_PREEMPTED.getName())){
-					setJobsPreempted(getJobsPreempted()+1);
-				} else if(line.contains(Status.STATUS_JOB_RUNNING.getName())){
-					setJobsRunning(getJobsRunning()+1);
-				} else if(line.contains(Status.STATUS_JOB_SUSPENDED.getName())){
-					setJobsSuspended(getJobsSuspended()+1);
-				} else if(line.contains(Status.STATUS_JOB_STOPPED.getName())){
-					setJobsStopped(getJobsStopped()+1);
-				} else if(line.contains(Status.STATUS_JOB_ERROR_TERMINATED.getName())){
-					setJobsErrorTerminated(getJobsErrorTerminated()+1);
-				} else if(line.contains(Status.STATUS_JOB_NOT_STARTED.getName())){
-					setJobsNotStarted(getJobsNotStarted()+1);
-				}				
-			}
-		}
-		statusFile.close();
-	}
-	
-	public void setJobSpace(File jobSpace) {
-		this.jobSpace = jobSpace;
-	}
-
-	public int getJobsSubmitted() {
-		return jobsSubmitted;
-	}
-	public void setJobsSubmitted(int jobsSubmitted) {
-		this.jobsSubmitted = jobsSubmitted;
-	}
-	public int getJobsRunning() {
-		return jobsRunning;
-	}
-	public void setJobsRunning(int jobsRunning) {
-		this.jobsRunning = jobsRunning;
-	}
-	public int getJobsCompleted() {
-		return jobsCompleted;
-	}
-	public void setJobsCompleted(int jobsCompleted) {
-		this.jobsCompleted = jobsCompleted;
-	}
-	public int getJobsErrorTerminated() {
-		return jobsErrorTerminated;
-	}
-	public void setJobsErrorTerminated(int jobsErrorTerminated) {
-		this.jobsErrorTerminated = jobsErrorTerminated;
-	}
-	public int getJobsNotStarted() {
-		return jobsNotStarted;
-	}
-	public void setJobsNotStarted(int jobsNotStarted) {
-		this.jobsNotStarted = jobsNotStarted;
-	}
-	
-	public int getJobsCompleting() {
-		return jobsCompleting;
-	}
-
-	public void setJobsCompleting(int jobsCompleting) {
-		this.jobsCompleting = jobsCompleting;
-	}
-
-	public int getJobsFailed() {
-		return jobsFailed;
-	}
-
-	public void setJobsFailed(int jobsFailed) {
-		this.jobsFailed = jobsFailed;
-	}
-
-	public int getJobsPending() {
-		return jobsPending;
-	}
-
-	public void setJobsPending(int jobsPending) {
-		this.jobsPending = jobsPending;
-	}
-
-	public int getJobsPreempted() {
-		return jobsPreempted;
-	}
-
-	public void setJobsPreempted(int jobsPreempted) {
-		this.jobsPreempted = jobsPreempted;
-	}
-
-	public int getJobsSuspended() {
-		return jobsSuspended;
-	}
-
-	public void setJobsSuspended(int jobsSuspended) {
-		this.jobsSuspended = jobsSuspended;
-	}
-
-	public int getJobsStopped() {
-		return jobsStopped;
-	}
-
-	public void setJobsStopped(int jobsStopped) {
-		this.jobsStopped = jobsStopped;
-	}
-
-	/**
-	 * Produces the header for showing the statistics table.
-	 * 
-	 * @return mainly the header of HTML.
-	 */
-	public String getHTMLHeader(){
-		String htmlHead = "<!DOCTYPE html>";     
-		htmlHead = htmlHead.concat("<html>");
-		htmlHead = htmlHead.concat("<head>");
-		htmlHead = htmlHead.concat("<style>");
-		htmlHead = htmlHead.concat("table, th, td {");
-		htmlHead = htmlHead.concat("border: 1px solid black;");
-		htmlHead = htmlHead.concat("border-collapse: collapse;");
-		htmlHead = htmlHead.concat("}");
-		htmlHead = htmlHead.concat("th, td {");
-		htmlHead = htmlHead.concat("padding: 15px;");
-		htmlHead = htmlHead.concat("text-align: left;");
-		htmlHead = htmlHead.concat("}");
-		htmlHead = htmlHead.concat("table#t01 {");
-		htmlHead = htmlHead.concat("width: 100%;");
-		htmlHead = htmlHead.concat("background-color: #f1f1c1;");
-		htmlHead = htmlHead.concat("}");
-		htmlHead = htmlHead.concat("</style>");
-		htmlHead = htmlHead.concat(getResources());
-		htmlHead = htmlHead.concat("</head>");
-		return htmlHead; 
-	}
-	
-	/**
-	 * Adds links to java script libraries and style sheets.
-	 * 
-	 * @return
-	 */
-	private String getResources(){
-		String resourcePath = pathToResource();
-		String headerResource = "<meta charset=\"UTF-8\">";
-		headerResource = headerResource.concat("<script src=\"https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js\"></script>");
-		headerResource = headerResource.concat(getLink("<link rel=\"stylesheet\" type=\"text/css\" href=\"", resourcePath, "css/static/group/bootstrap.min.css\">"));
-		headerResource = headerResource.concat(getLink("<link rel=\"stylesheet\" type=\"text/css\" href=\"", resourcePath, "css/index.css\">"));
-		headerResource = headerResource.concat(getLink("<link rel=\"icon\" href=\"", resourcePath, "css/static/group/favicon.ico\">"));
-		headerResource = headerResource.concat(getLink("<link rel=\"stylesheet\" type=\"text/css\" href=\"", resourcePath, "css/static/group/dftagent.css\">"));
-		headerResource = headerResource.concat("<title>J-Park Simulator</title>");
-		return headerResource;
-	}
-	
-	public String getBodydivStart(){
-		String resourcePath = pathToResource();
-		String startDiv = "<div class=\"jumbotron text-center\" id=\"topBanner\">";
-		startDiv = startDiv.concat("<a id=\"cares-banner\" href=\"http://www.cares.cam.ac.uk\">");
-		startDiv = startDiv.concat("<img id=\"care-banner-img\" src=\"");
-		startDiv = startDiv.concat(resourcePath.concat("images/cam_lang_negativ1%20NEW_0.png\">"));
-		startDiv = startDiv.concat("</a>");
-		startDiv = startDiv.concat("<h1 id=\"title\">A JPS Agent</h1>");
-		startDiv = startDiv.concat("<p id=\"description\">");
-		startDiv = startDiv.concat("An agent developed for performing simulations on HPC servers "
-				+ "to create a living, continuously self-improving and growing "
-				+ "Knowledge Graph of species serving the need for thermochemical data across disciplines.");
-		startDiv = startDiv.concat("</p>");
-		startDiv = startDiv.concat("</div>");
-		return startDiv;
-	}
-	
-	/**
-	 * Converts path specific to a Windows or Linux server.
-	 * 
-	 * @param resourcePath
-	 * @return
-	 */
-	private String pathToResource(){
-		return "/KineticsAgent/assets/";
-	}
-	
-	/**
-	 * Produces a link to a java script library or style sheet using the</br>
-	 * link tag and the path where the resource is located.
-	 *  
-	 * @param link
-	 * @param hrefStartPath
-	 * @param hrefEndPath
-	 * @return
-	 */
-	private String getLink(String link, String hrefStartPath, String hrefEndPath){
-		String linkResource = link;
-		linkResource = linkResource.concat(hrefStartPath);
-		linkResource = linkResource.concat(hrefEndPath);
-		return linkResource;
-	}
-	
-	/**
-	 * Prepares the header of table showing statistics about jobs submitted to DFT Agent.
-	 * 
-	 * @return mainly the header part of the HTML table showing job statistics.
-	 */
-	public String getStatisticsTableHeader(String headerText, String statisticsProperty, String statisticsValue, String tableWidth){
-		String tableHeader = "<h2>"+headerText+"</h2><br>";
-		tableHeader = tableHeader + "<table style=\"width:"+tableWidth+"\">";
-		tableHeader = tableHeader + "<tr>";
-		tableHeader = tableHeader + "<th>"+statisticsProperty+"</th>";
-		tableHeader = tableHeader + "<th>"+statisticsValue+"</th>";
-		tableHeader = tableHeader + "</tr>";
-		return tableHeader;
-	}
-	
-	/**
-	 * Prepares the row of table showing statistics about jobs submitted to DFT Agent.
-	 * 
-	 * @param property
-	 * @param value
-	 * @return
-	 */
-	public String getStatisticsTableRow(String property, String value){
-		String tableRow = "<tr>";
-		tableRow = tableRow + "<td>"+property+"</td>";
-		tableRow = tableRow + "<td>"+value+"</td>";
-		tableRow = tableRow + "</tr>";
-		tableRow = tableRow + "<tr>";
-		return tableRow;
-	}
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/JobSubmission.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/JobSubmission.java
deleted file mode 100644
index 8cf17befa..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/JobSubmission.java
+++ /dev/null
@@ -1,1117 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.UnknownHostException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.json.JSONObject;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
-
-import com.jcraft.jsch.Channel;
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.ChannelSftp;
-import com.jcraft.jsch.IdentityRepository;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-import com.jcraft.jsch.SftpException;
-import com.jcraft.jsch.agentproxy.AgentProxyException;
-import com.jcraft.jsch.agentproxy.Connector;
-import com.jcraft.jsch.agentproxy.RemoteIdentityRepository;
-import com.jcraft.jsch.agentproxy.connector.PageantConnector;
-
-import uk.ac.cam.cares.jps.base.slurm.job.configuration.SlurmJobProperty;
-
-/**
- * This is an API developed for setting-up and running Slurm jobs.
- * 
- * @author msff2
- *
- */
-public class JobSubmission{
-	private Logger LOGGER = LogManager.getLogger(JobSubmission.class);	
-	private String hpcAddress;
-	private String agentClass;
-	private File workspaceDirectory;
-	private String workspaceName;
-	private String workspaceParentPath;
-	boolean isAuthenticated;
-	
-	public SlurmJobProperty slurmJobProperty = new SlurmJobProperty();
-	
-	static Session session;
-	static JSch jsch = new JSch();
-	
-	static int scheduledIteration = 0;
-	static Set<String> jobsRunning = new HashSet<String>();
-	
-	public String getHpcAddress() {
-		return hpcAddress;
-	}
-
-	public void setHpcAddress(String hpcAddress) {
-		this.hpcAddress = hpcAddress;
-	}
-	
-	public String getAgentClass() {
-		return agentClass;
-	}
-	
-	public void setAgentClass(String agentClass) {
-		this.agentClass = agentClass;
-	}
-	
-	public File getWorkspaceDirectory() {
-		return workspaceDirectory;
-	}
-
-	public void setWorkspaceDirectory(File workspaceDirectory) {
-		this.workspaceDirectory = workspaceDirectory;
-	}
-
-	public String getWorkspaceName() {
-		return workspaceName;
-	}
-
-	public void setWorkspaceName(String workspaceName) {
-		this.workspaceName = workspaceName;
-	}
-
-	public static void main(String[] args) throws SlurmJobException{
-//		JobSubmission jobSubmission = new JobSubmission("DFTAgent", new File(System.getProperty("user.home")), "login-skylake.hpc.cam.ac.uk");
-//		jobSubmission.init();
-	}
-	
-	public String getWorkspaceParentPath() {
-		return workspaceParentPath;
-	}
-
-	public void setWorkspaceParentPath(String workspaceParentPath) {
-		this.workspaceParentPath = workspaceParentPath;
-	}
-
-	/**
-	 * Constructor for this class.
-	 * 
-	 * @param agentClass the name of the agent class (e.g. DFTAgent and EBRAgent).
-	 * @param workspaceName the name of workspace<br>
-	 * will be created, e.g. user home directory read by System.getProperty("user.home");
-	 * @param hpcAddress the address of HPC, e.g. login-skylake.hpc.cam.ac.uk for CSD3.
-	 */
-	public JobSubmission(String agentClass, String hpcAddress){
-		this.agentClass = agentClass;
-		this.hpcAddress = hpcAddress;
-		this.workspaceDirectory = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(), agentClass);
-		this.workspaceParentPath = Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName();
-	}
-	
-	/**
-	 * Sets up a Slurm job by creating the job folder and the following files</br>
-	 * under this folder:</br>
-	 * - the input file.</br>
-	 * - the Slurm script file.</br.
-	 * - the Status file.</br>
-	 * - the JSON input file, which comes from the user request.</br>
-	 * 
-	 * @param jsonInput
-	 * @param slurmScript
-	 * @param input
-	 * @param timeStamp
-	 * @return
-	 * @throws IOException
-	 * @throws DFTAgentException
-	 */
-	public String setUpJob(String jsonInput, File slurmScript, File input, long timeStamp) throws IOException, SlurmJobException{
-        String message = setUpJobOnAgentMachine(jsonInput, slurmScript, input, timeStamp);
-        return message;
-    }
-
-	/**
-	 * Sets up a Slurm job by creating the job folder and the following files</br>
-	 * under this folder:</br>
-	 * - the input file.</br>
-	 * - the Slurm script file.</br.
-	 * - the Status file.</br>
-	 * - the JSON input file, which comes from the user request.</br>
-	 * 
-	 * @param jsonInput
-	 * @param slurmScript
-	 * @param input
-	 * @param executable
-	 * @param timeStamp
-	 * @return
-	 * @throws IOException
-	 * @throws DFTAgentException
-	 */
-	public String setUpJob(String jsonInput, File slurmScript, File input, File executable, long timeStamp) throws IOException, SlurmJobException{
-        String message = setUpJobOnAgentMachine(jsonInput, slurmScript, input, executable, timeStamp);
-        JSONObject obj = new JSONObject();
-        obj.put("message", message);
-        return obj.toString();
-    }
-
-	
-	/**
-	 * Sets up the Slurm job for the current input.
-	 *   
-	 * @param jsonString
-	 * @param slurmScript
-	 * @param input
-	 * @param timeStamp
-	 * @return
-	 * @throws IOException
-	 * @throws DFTAgentException
-	 */
-	private String setUpJobOnAgentMachine(String jsonString, File slurmScript, File input, long timeStamp) throws IOException, SlurmJobException{
-		Workspace workspace = new Workspace();
-		if(workspaceDirectory == null){
-            LOGGER.error("Workspace directory has not been set!");
-			return Status.JOB_SETUP_ERROR.getName();
-		}else{
-			return setUpSlurmJob(workspace, workspaceDirectory, jsonString, slurmScript, input, timeStamp);
-		}
-	}
-	
-	/**
-	 * Sets up the Slurm job for the current input.
-	 *   
-	 * @param jsonString
-	 * @param slurmScript
-	 * @param input
-	 * @param executable
-	 * @param timeStamp
-	 * @return
-	 * @throws IOException
-	 * @throws DFTAgentException
-	 */
-	private String setUpJobOnAgentMachine(String jsonString, File slurmScript, File input, File executable, long timeStamp) throws IOException, SlurmJobException{
-		Workspace workspace = new Workspace();
-		if(workspaceDirectory == null){
-            LOGGER.error("Workspace directory has not been set!");
-			return Status.JOB_SETUP_ERROR.getName();
-		}else{
-			return setUpSlurmJob(workspace, workspaceDirectory, jsonString, slurmScript, input, executable, timeStamp);
-		}
-	}
-	
-	/**
-	 * Sets up the Slurm job for the current request.
-	 * 
-	 * @param ws
-	 * @param workspaceFolder
-	 * @param jsonString
-	 * @param slurmScript
-	 * @param input
-	 * @param timeStamp
-	 * @return
-	 * @throws IOException
-	 * @throws DFTAgentException
-	 */
-	private String setUpSlurmJob(Workspace ws, File workspaceFolder, String jsonString, File slurmScript, File input, long timeStamp) throws IOException, SlurmJobException{
-		File jobFolder = ws.createJobFolder(workspaceFolder.getAbsolutePath(), getHpcAddress(), timeStamp);
-        LOGGER.info("Set up slurm job folder at: " + jobFolder);
-
-    	if(createAllFileInJobFolder(ws, workspaceFolder, jobFolder, jsonString, slurmScript, input) == null) {
-            LOGGER.error("Could not create files within the slurm job folder.");
-    		return null;
-    	}
-    	return jobFolder.getName();
-	}
-	
-	/**
-	 * Sets up the Slurm job for the current request.
-	 * 
-	 * @param ws
-	 * @param workspaceFolder
-	 * @param jsonString
-	 * @param slurmScript
-	 * @param input
-	 * @param executable
-	 * @param timeStamp
-	 * @return
-	 * @throws IOException
-	 * @throws DFTAgentException
-	 */
-	private String setUpSlurmJob(Workspace ws, File workspaceFolder, String jsonString, File slurmScript, File input, File executable, long timeStamp) throws IOException, SlurmJobException{
-		File jobFolder = ws.createJobFolder(workspaceFolder.getAbsolutePath(), getHpcAddress(), timeStamp);
-        LOGGER.info("Set up slurm job folder at: " + jobFolder);
-
-    	if(createAllFileInJobFolder(ws, workspaceFolder, jobFolder, jsonString, slurmScript, input, executable) == null) {
-            LOGGER.error("Could not create files within the slurm job folder.");
-    		return null;
-    	}
-    	return Status.JOB_SETUP_SUCCESS_MSG.getName();
-	}
-	
-	/**
-	 * Creates all files relevant for the current job, in particular, it</br>
-	 * creates the following files:</br>
-	 * - the input file in com (.com) format for running the job on an HPC
-	 * - the status file in text (.txt) format
-	 * - the input file in json (.json) format
-	 * - the Slurm script file in shell script (.sh) format 
-	 * 
-	 * @param ws
-	 * @param workspaceFolder
-	 * @param jobFolder
-	 * @param jsonString
-	 * @param slurmScript
-	 * @param input
-	 * @return
-	 * @throws IOException
-	 * @throws DFTAgentException
-	 */
-	private String createAllFileInJobFolder(Workspace ws, File workspaceFolder, File jobFolder, String jsonString, File slurmScript, File input) throws IOException, SlurmJobException{
-		String inputFileMsg = ws.createInputFile(ws.getInputFilePath(jobFolder, getHpcAddress(), ws.getInputFileExtension(input)), input);
-		if(inputFileMsg == null){
-			return Status.JOB_SETUP_INPUT_FILE_ERROR.getName();
-		}
-		String statusFileMsg = ws.createStatusFile(workspaceFolder, ws.getStatusFilePath(jobFolder), getHpcAddress());
-		if(statusFileMsg == null){
-			return null;
-		}
-		String jsonInputFileMsg = ws.createJSONInputFile(workspaceFolder, ws.getJSONInputFilePath(jobFolder), jsonString);
-		if(jsonInputFileMsg == null){
-			return null;
-		}
-		String scriptFileMsg = ws.copyFile(slurmScript.getAbsolutePath(), jobFolder.getAbsolutePath().concat(File.separator).concat(slurmScript.getName()));
-		if(scriptFileMsg == null){
-			return null;
-		}
-		return Status.JOB_SETUP_SUCCESS_MSG.getName();
-	}
-	
-	/**
-	 * Creates all files relevant for the current job, in particular, it</br>
-	 * creates the following files:</br>
-	 * - the input file in zip (.zip) format for running the job on an HPC
-	 * - the status file in text (.txt) format
-	 * - the input file in json (.json) format
-	 * - the Slurm script file in shell script (.sh) format
-	 * - the executable file in java is in jar (.jar) format
-	 * 
-	 * @param ws
-	 * @param workspaceFolder
-	 * @param jobFolder
-	 * @param jsonString
-	 * @param slurmScript
-	 * @param input
-	 * @param executable
-	 * @return
-	 * @throws IOException
-	 * @throws DFTAgentException
-	 */
-	private String createAllFileInJobFolder(Workspace ws, File workspaceFolder, File jobFolder, String jsonString, File slurmScript, File input, File executable) throws IOException, SlurmJobException{
-		String inputFileMsg = ws.createInputFile(ws.getInputFilePath(jobFolder, getHpcAddress(), ws.getInputFileExtension(input)), input);
-		if(inputFileMsg == null){
-			return Status.JOB_SETUP_INPUT_FILE_ERROR.getName();
-		}
-		String statusFileMsg = ws.createStatusFile(workspaceFolder, ws.getStatusFilePath(jobFolder), getHpcAddress());
-		if(statusFileMsg == null){
-			return null;
-		}
-		String jsonInputFileMsg = ws.createJSONInputFile(workspaceFolder, ws.getJSONInputFilePath(jobFolder), jsonString);
-		if(jsonInputFileMsg == null){
-			return null;
-		}
-		String scriptFileMsg = ws.copyFile(slurmScript.getAbsolutePath(), jobFolder.getAbsolutePath().concat(File.separator).concat(slurmScript.getName()));
-		if(scriptFileMsg == null){
-			return null;
-		}
-		String executableFileMsg = ws.copyFile(executable.getAbsolutePath(), jobFolder.getAbsolutePath().concat(File.separator).concat(executable.getName()));
-		if(executableFileMsg == null){
-			return null;
-		}
-		return Status.JOB_SETUP_SUCCESS_MSG.getName();
-	}
-	
-	/**
-     * Shows the following statistics of Slurm jobs.</br>
-     * - Total number of jobs submitted
-     * - Total number of jobs currently running  
-     * - Total number of jobs successfully completed
-     * - Total number of jobs terminated with an error
-     * - Total number of jobs not started yet
-     * 
-     * @param input the JSON string specifying the return data format, e.g. JSON.
-     * @return the statistics in JSON format if requested. 
-     */
-    public String produceStatistics(String input) throws IOException, SlurmJobException{
-		System.out.println("Received a request to send statistics.\n");
-		LOGGER.info("Received a request to send statistics.\n");
-		return "";
-    }
-	
-	/**
-     * Shows the following statistics of Slurm jobs.</br>
-     * - Total number of jobs submitted
-     * - Total number of jobs currently running  
-     * - Total number of jobs successfully completed
-     * - Total number of jobs terminated with an error
-     * - Total number of jobs not started yet
-     * 
-     * @return the statistics in HTML format. 
-     */
-    public String showStatistics() throws IOException, SlurmJobException{
-		System.out.println("Received a request to show statistics.\n");
-		LOGGER.info("Received a request to show statistics.\n");
-		return "";
-    }
-	
-	/**
-	 * Produces the statistics about Slurm jobs.
-	 * 
-	 * @param input in json format containing the format in which the result</br> 
-	 * should be codified, e.g. json. An example input file will look like</br>
-	 * as follows:{"format":"json"}
-	 * @return a JSONObject containing statistics in the user requested format.
-	 * @throws IOException
-	 */
-	public JSONObject getStatistics(String input) throws IOException{
-		JSONObject obj = new JSONObject(input);  
-		String formatAccepts = obj.optString("format"); // json
-		if(formatAccepts!=null && formatAccepts.toLowerCase().contains("json")){
-			JobStatistics jobStatistics = new JobStatistics(workspaceDirectory);
-			obj = new JSONObject();
-			obj.put("Number of jobs currently running", jobStatistics.getJobsRunning());
-			obj.put("Number of jobs successfully completed", jobStatistics.getJobsCompleted());
-			obj.put("Number of jobs completing", jobStatistics.getJobsCompleting());
-			obj.put("Number of jobs failed", jobStatistics.getJobsFailed());
-			obj.put("Number of jobs pending", jobStatistics.getJobsPending());
-			obj.put("Number of jobs preempted", jobStatistics.getJobsPreempted());
-			obj.put("Number of jobs suspended", jobStatistics.getJobsSuspended());
-			obj.put("Number of jobs stopped", jobStatistics.getJobsStopped());
-			obj.put("Number of jobs terminated with an error", jobStatistics.getJobsErrorTerminated());
-			obj.put("Number of jobs to start", jobStatistics.getJobsNotStarted());
-			obj.put("Total number of jobs submitted", jobStatistics.getJobsSubmitted());
-		}
-		return obj;
-	}
-	
-	/**
-	 * Produces the statistics about Slurm jobs.
-	 * 
-	 * @return
-	 * @throws IOException
-	 */
-	public String getStatistics() throws IOException{
-		JobStatistics jobStatistics = new JobStatistics(workspaceDirectory);
-		String statistics = jobStatistics.getHTMLHeader();
-		statistics = statistics + "<body>";
-		statistics = statistics.concat(jobStatistics.getBodydivStart());
-		statistics = statistics + "<center>";
-		String headerText = "Statistics about jobs submitted to this agent are shown in the table below.<p>";
-		statistics = statistics.concat(jobStatistics.getStatisticsTableHeader(headerText, "Property", "Value", "50%"));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs currently running", jobStatistics.getJobsRunning()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs successfully completed", jobStatistics.getJobsCompleted()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs completing", jobStatistics.getJobsCompleting()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs failed", jobStatistics.getJobsFailed()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs pending", jobStatistics.getJobsPending()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs preempted", jobStatistics.getJobsPreempted()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs suspended", jobStatistics.getJobsSuspended()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs stopped", jobStatistics.getJobsStopped()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs terminated with an error", jobStatistics.getJobsErrorTerminated()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("Number of jobs to start", jobStatistics.getJobsNotStarted()+""));
-		statistics = statistics.concat(jobStatistics.getStatisticsTableRow("<i>Total number of jobs submitted</i>", jobStatistics.getJobsSubmitted()+""));
-		statistics = statistics + "</table>";
-		statistics = statistics + "</center>";
-		statistics = statistics + "</body>";
-		statistics = statistics + "</html>";
-		return statistics;
-	}
-	
-	/**
-	 * Monitors the currently running Slurm jobs to allow new jobs to start.</br>
-	 * In doing so, it checks if the number of running jobs is less than the</br>
-	 * maximum number of jobs allowed to run at a time.    
-	 * 
-	 */
-	public void monitorJobs() throws SlurmJobException{
-		try {
-			if(!hostAvailabilityCheck(getHpcAddress(), 22)){
-				System.out.println("The agent cannot connect to the HPC server with address " + getHpcAddress());
-				session = null;
-				return;
-			}
-			scheduledIteration++;
-			if (session == null || scheduledIteration%10==0) {
-				if(session!=null && session.isConnected()){
-					session.disconnect();
-				}
-				System.out.println("Initialising a session.");
-				session = jsch.getSession(slurmJobProperty.getHpcServerLoginUserName(), getHpcAddress(), 22);
-				String pwd = slurmJobProperty.getHpcServerLoginUserPassword();
-				session.setPassword(pwd);
-                                String privateKeyFilename =slurmJobProperty.getHpcServerPrivateKey();
-
-				// Note that session.setConfig("PreferredAuthentications", ...) was removed because it will cause issues
-				// when this code is executed in a container for unknown reasons
-				try {
-                                        if(!privateKeyFilename.isEmpty()){
-                                            jsch.addIdentity(privateKeyFilename);
-                                        }else{
-                                            // Attempt to connect to a running instance of Pageant
-                                            Connector con = new PageantConnector();
-                                            IdentityRepository irepo = new RemoteIdentityRepository(con);
-                                            jsch.setIdentityRepository(irepo);
-                                        }
-				} catch (AgentProxyException e) {
-					LOGGER.info("Failed to detect Pageant, will authenticate using password");
-				}
-
-				session.setConfig("StrictHostKeyChecking", "no");
-				session.connect();
-				scheduledIteration = 0;
-			}
-			if(workspaceDirectory.isDirectory()){
-				File[] jobFolders = workspaceDirectory.listFiles();
-				updateRunningJobSet(jobFolders, jobsRunning);
-
-				for(File jobFolder: jobFolders){
-					if(!Utils.isJobCompleted(jobFolder, slurmJobProperty)){
-						if(Utils.isJobRunning(jobFolder)){
-							if(updateRunningJobsStatus(jobFolder)){
-								if(jobsRunning.contains(jobFolder.getName())){
-									jobsRunning.remove(jobFolder.getName());
-								}
-							}
-						} else if(Utils.isJobNotStarted(jobFolder) && !jobsRunning.contains(jobFolder.getName())){
-
-							if(jobsRunning.size()<slurmJobProperty.getMaxNumberOfHPCJobs()){
-								try{
-                                    LOGGER.info("Attempting to start slurm job in folder: " + jobFolder);
-									boolean flag = runNotStartedJob(jobFolder);
-
-									if(flag){
-										jobsRunning.add(jobFolder.getName());
-									}else{
-										break;
-									}
-								}catch(Exception exception){
-									LOGGER.error("Exception when running new slurm job!", exception);
-								}
-							}else{
-								break;
-							}
-						}
-					}
-				}
-			}
-		} catch (IOException e) {
-			e.printStackTrace();
-			session = null;
-			throw new SlurmJobException(e.getMessage());
-		} catch (InterruptedException e) {
-			e.printStackTrace();
-			session = null;
-			throw new SlurmJobException(e.getMessage());
-		} catch(SftpException e){
-			e.printStackTrace();
-			session = null;
-			throw new SlurmJobException(e.getMessage());
-		} catch(JSchException e){
-			e.printStackTrace();
-			session = null;
-			throw new SlurmJobException(e.getMessage());
-		}
-	}
-
-	/**
-	 * Inserts jobs which are currently running into the list of running jobs.
-	 * 
-	 * @param jobFolders
-	 * @param jobsRunning
-	 * @throws IOException
-	 */
-	private void updateRunningJobSet(File[] jobFolders, Set<String> jobsRunning) throws IOException{
-		for(File jobFolder: jobFolders){
-			if(!(new File(jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName()))).exists()){
-				LOGGER.info("SlurmJobAPI: job status file is not found, so the job folder with ID "+ jobFolder.getName()+" is being moved to the failed job folder.");
-				System.out.println("SlurmJobAPI: job status file is not found, so the job folder with ID "+ jobFolder.getName()+" is being moved to the failed job folder.");
-				try{
-					Utils.moveToFailedJobsFolder(jobFolder, slurmJobProperty);
-				}catch(Exception e){
-					LOGGER.info("SlurmJobAPI: failed to move the job folder with ID "+jobFolder.getName()+" to the failed job folder.");
-					System.out.println("SlurmJobAPI: failed to move the job folder with ID "+jobFolder.getName()+" to the failed job folder.");
-				}
-				continue;
-			}
-			try {
-				if (Utils.isJobRunning(jobFolder)) {
-					jobsRunning.add(jobFolder.getName());
-				}
-			} catch (Exception e) {
-				LOGGER.info("SlurmJobAPI: failed to check the status of the job with ID "+jobFolder.getName()+ " while checking if it was running.");
-				System.out.println("SlurmJobAPI: failed to check the status of the job with ID "+jobFolder.getName()+ " while checking if it was running.");
-			}
-		}
-	}
-	
-	/**
-	 * Starts running Slurm jobs which were set up before. 
-	 * 
-	 * @param jobFolder
-	 * @throws SftpException
-	 * @throws JSchException
-	 * @throws IOException
-	 * @throws UnknownHostException
-	 * @throws InterruptedException
-	 */
-	private boolean runNotStartedJob(File jobFolder)  throws SftpException, JSchException, IOException, UnknownHostException, InterruptedException{
-		// A counter variable to count the number of mandatory files.  
-		int countNumberOfFilesSetInProperties = 0;
-
-		// Checks if the script file (including name and extension) for the current Slurm job is provided.
-		if(slurmJobProperty.getSlurmScriptFileName()==null || slurmJobProperty.getSlurmScriptFileName().isEmpty()){
-			throw new IOException("SlurmJobAPI: Slurm script file name and extension are not provided.");			
-		}else{
-			countNumberOfFilesSetInProperties++;
-		}
-		// Checks if the input file name for the current Slurm job is provided. 
-		if(slurmJobProperty.getInputFileName()==null || slurmJobProperty.getInputFileName().isEmpty()){
-			throw new IOException("SlurmJobAPI: input file name is not provided.");
-		}else{
-			countNumberOfFilesSetInProperties++;
-		}
-		// Checks if input file extension for the current Slurm job is provided.
-		if(slurmJobProperty.getInputFileExtension()==null || slurmJobProperty.getInputFileExtension().isEmpty()){
-			throw new IOException("SlurmJobAPI: input file extension is not provided.");
-		}
-		// Checks if the JSON input file name for the current Slurm job is provided.
-		if(slurmJobProperty.getJsonInputFileName()==null || slurmJobProperty.getJsonInputFileName().isEmpty()){
-			throw new IOException("SlurmJobAPI: JSON input file name is not provided.");
-		}else{
-			countNumberOfFilesSetInProperties++;
-		}
-		// Checks if the JSON input file extension for the current Slurm job is provided.
-		if(slurmJobProperty.getJsonFileExtension()==null || slurmJobProperty.getJsonFileExtension().isEmpty()){
-			throw new IOException("SlurmJobAPI: JSON file extension is not provided.");
-		}
-		// Checks if the executable file (including name and extension) for the current Slurm job is provided.
-		if(slurmJobProperty.getExecutableFile()!=null && !slurmJobProperty.getExecutableFile().isEmpty()){
-			countNumberOfFilesSetInProperties++;
-		}
-		int countNumberOfFilesInJobFolder = 0;
-		// Checks the availability of the following four mandatory files in the current job folder:
-		// 1. Slurm script file (e.g., Slurm.sh)
-		// 2. Input file (e.g., input.zip or input.com)
-		// 3. JSON input file (e.g., input.json)
-		// 4. Status file (e.g., status.txt)
-		for(File file:jobFolder.listFiles()){
-			if(file.getName().equalsIgnoreCase(slurmJobProperty.getSlurmScriptFileName())){
-				countNumberOfFilesInJobFolder++;
-			}
-			if(file.getName().endsWith(slurmJobProperty.getInputFileExtension())){
-				countNumberOfFilesInJobFolder++;
-			}
-			if(file.getName().equalsIgnoreCase(slurmJobProperty.getJsonInputFileName().concat(slurmJobProperty.getJsonFileExtension()))){
-				countNumberOfFilesInJobFolder++;
-			}
-			if(file.getName().equalsIgnoreCase(Status.STATUS_FILE.getName())){
-				countNumberOfFilesInJobFolder++;
-			}
-			if(slurmJobProperty.getExecutableFile()!=null && file.getName().equalsIgnoreCase(slurmJobProperty.getExecutableFile())){
-				countNumberOfFilesInJobFolder++;
-			}
-		}
-		try{
-			// If all files set through properties are not available in a job folder, it
-			// deletes the folder.
-			System.out.println("countNumberOfFilesInJobFolder:"+countNumberOfFilesInJobFolder);
-			System.out.println("countNumberOfFilesSetInProperties:"+countNumberOfFilesSetInProperties);
-			if(!(countNumberOfFilesSetInProperties>=3 && countNumberOfFilesSetInProperties+1==countNumberOfFilesInJobFolder)){
-				LOGGER.info("SlurmJobAPI: all mandatory files are not found, so the job folder with ID "+ jobFolder.getName()+" is deleted.");
-				System.out.println("SlurmJobAPI: all mandatory files are not found, so the job folder with ID "+ jobFolder.getName()+" is deleted.");
-				Utils.moveToFailedJobsFolder(jobFolder, slurmJobProperty);
-				return false;
-			}
-		}catch(Exception e){
-			LOGGER.info("SlurmJobAPI: all mandatory files are not found and an attempt to move the job folder with ID "
-					+jobFolder.getName()+" to the failed job folder is not successful.");
-			System.out.println("SlurmJobAPI: all mandatory files are not found and an attempt to move the job folder with ID "
-					+jobFolder.getName()+" to the failed job folder is not successful.");
-		}
-
-		try{
-			startJob(jobFolder.getName(), Arrays.asList(jobFolder.listFiles()));
-		}catch(Exception e){
-			LOGGER.info("SlurmJobAPI: the Slurm Job with ID "+jobFolder.getName()+" could not be started.", e);
-			System.out.println("SlurmJobAPI: the Slurm Job with ID "+jobFolder.getName()+" could not be started.");
-			return false;
-		}
-		return true;
-	}
-	
-	/**
-	 * Starts a Slurm job.
-	 * 
-	 * @param job
-	 * @param jobFiles
-	 * @throws SftpException
-	 * @throws JSchException
-	 * @throws IOException
-	 * @throws UnknownHostException
-	 * @throws InterruptedException
-	 */
-	private void startJob(String job, List<File> jobFiles) throws SftpException, JSchException, IOException, UnknownHostException, InterruptedException{
-		// On HPC, the job folder and files have the address of machine where DFT Agent runs.
-		// Therefore, the HPC address is replaced with the address of Agent machine.
-		job = job.replace(getHpcAddress(), Utils.getMachineAddress());
-		String jobFolderOnHPC = createJobFolder(job);
-		if(jobFolderOnHPC!=null){
-			uploadFiles(jobFolderOnHPC, jobFiles);
-		}
-	}
-	
-	/**
-	 * For running the current job, it uploads both the input file and</br>
-	 * Slurm script to an HPC.
-	 * 
-	 * @param jobFolderOnHPC
-	 * @param jobFiles
-	 * @throws SftpException
-	 * @throws JSchException
-	 * @throws IOException
-	 * @throws UnknownHostException
-	 * @throws InterruptedException
-	 */
-	private void uploadFiles(String jobFolderOnHPC, List<File> jobFiles) throws SftpException, JSchException, IOException, UnknownHostException, InterruptedException{
-		String replacedInputFileName = "";
-		String statusFileAbsolutePath = "";
-		String jobId = "";
-
-		for(File jobFile:jobFiles){
-
-			if(jobFile.getAbsolutePath().endsWith(slurmJobProperty.getInputFileExtension())){
-				replacedInputFileName = getInputFileNameReplaced(jobFile.getAbsolutePath());
-				String inputFileNameOnHPC = jobFolderOnHPC.concat("/").concat(replacedInputFileName);
-				uploadFile(jobFile.getAbsolutePath(), inputFileNameOnHPC);
-				replaceFileContent(jobFolderOnHPC, inputFileNameOnHPC);
-
-			}else if(!jobFile.getAbsolutePath().endsWith(Property.STATUS_FILE_NAME.getPropertyName())){
-				if(jobFile.getAbsolutePath().endsWith(".sh")){
-					Utils.translateLineEndingIntoUnix(new File(jobFile.getAbsolutePath()));
-				}
-				uploadFile(jobFile.getAbsolutePath(), jobFolderOnHPC);				
-			}
-
-			if(jobFile.getAbsolutePath().endsWith(Property.STATUS_FILE_NAME.getPropertyName())){
-				statusFileAbsolutePath = jobFile.getAbsolutePath();
-			}
-		}
-
-        LOGGER.info("Attemping to run job folder on HPC at: " + jobFolderOnHPC);
-		jobId = runSlurmJob(jobFolderOnHPC, replacedInputFileName);
-		if(!jobId.isEmpty()){
-			Utils.addJobId(statusFileAbsolutePath, jobId);
-		}
-	}
-
-	/**
-	 * Produces the command to go to the current job directory and to run</br>
-	 * the job.
-	 * 
-	 * @param jobFolderOnHPC
-	 * @param inputFile
-	 * @return
-	 * @throws JSchException
-	 * @throws IOException
-	 */
-	private String runSlurmJob(String jobFolderOnHPC, String inputFile) throws JSchException, IOException{
-		inputFile = inputFile.replace(slurmJobProperty.getInputFileExtension(), "");
-		String command = "cd "
-            .concat(jobFolderOnHPC)
-            .concat(" && ")
-            .concat("sbatch --job-name=").concat(inputFile)
-            .concat(" ")
-            .concat(Property.SLURM_SCRIPT_FILE_NAME.getPropertyName());
-
-        LOGGER.info("Using command: " + command);
-		return runSlurmJob(command);
-	}
-	
-	/**
-	 * Runs a Slurm job.
-	 * 
-	 * @param command
-	 * @return
-	 * @throws JSchException
-	 * @throws IOException
-	 */
-	private String runSlurmJob(String command) throws JSchException, IOException{
-		ArrayList<String> outputs = executeCommand(command);
-		if (outputs == null) {
-			return null;
-		}
-		String jobId = getJobId(outputs);
-		System.out.println("Job id:" + jobId);
-		return jobId;
-	}
-	
-	/**
-	 * Modifies the names of the check point file and log file provided in</br>
-	 * the input file after copying this into the HPC cluster. 
-	 * 
-	 * @param jobFolderOnHPC
-	 * @param replacedJobFileName
-	 * @throws JSchException
-	 * @throws IOException
-	 * @throws UnknownHostException
-	 */
-	private void replaceFileContent(String jobFolderOnHPC, String replacedJobFileName) throws JSchException, IOException, UnknownHostException{
-		String command = "cd ".concat(jobFolderOnHPC).concat(" && ")
-				.concat("sed -i 's/").concat(getHpcAddress())
-				.concat("/").concat(Utils.getMachineAddress()).concat("/g' ").concat(replacedJobFileName);
-		executeCommand(command);
-	}
-	
-	/**
-	 * Modifies the name of the input file while copying this into the HPC cluster.
-	 * 
-	 * @param inputFile
-	 * @return
-	 * @throws UnknownHostException
-	 */
-	private String getInputFileNameReplaced(String inputFile) throws UnknownHostException{
-		String tokens[];
-		if(inputFile.contains("/")){
-			tokens = inputFile.split("/");
-		}else{
-			tokens = inputFile.split("\\\\");
-		}
-		return tokens[tokens.length-1].replace(getHpcAddress(), Utils.getMachineAddress());
-	}
-	
-	private String createJobFolder(String job) throws JSchException, IOException{
-		// Creates the "mkdir" (make directory) command to create the workspace/jobspace directory.
-		String command = "mkdir /home/".concat(slurmJobProperty.getHpcServerLoginUserName()).concat("/").concat(workspaceDirectory.getName());
-		// Executes the command to create the workspace/jobspace directory.
-		executeCommand(command);
-		// Creates the command to create the job directory.
-		command = "mkdir /home/".concat(slurmJobProperty.getHpcServerLoginUserName()).concat("/").concat(workspaceDirectory.getName()).concat("/").concat(job);
-		// Executes the command for creating the job directory.
-		executeCommand(command);
-		return "/home/".concat(slurmJobProperty.getHpcServerLoginUserName()).concat("/").concat(workspaceDirectory.getName()).concat("/").concat(job);
-	}
-	
-	/**
-	 * Updates the status of a currently running job.
-	 * 
-	 * @param jobFolder
-	 * @return
-	 * @throws JSchException
-	 * @throws SftpException
-	 * @throws IOException
-	 * @throws InterruptedException
-	 */
-	private boolean updateRunningJobsStatus(File jobFolder)
-			throws JSchException, SftpException, IOException, InterruptedException {
-		boolean status = false;
-		try{
-			File statusFile = Utils.getStatusFile(jobFolder);
-			status = updateRunningJobsStatus(jobFolder.getName(), statusFile);
-		}catch(Exception e){
-			LOGGER.info("SlurmJobAPI: failed to update the status of the job with ID "+jobFolder.getName()+" while checking if it was still running.");
-		}
-		return status;
-	}
-	
-	/**
-	 * Updates the latest status of the running jobs. 
-	 * 
-	 * @param runningJob
-	 * @param statusFile
-	 * @return
-	 * @throws JSchException
-	 * @throws SftpException
-	 * @throws IOException
-	 * @throws InterruptedException
-	 */
-	private boolean updateRunningJobsStatus(String runningJob, File statusFile) throws JSchException, SftpException, IOException, InterruptedException{
-		if(statusFile!=null){
-			if(!isJobRunning(statusFile)){
-				if(slurmJobProperty.getOutputFileExtension().trim().toLowerCase().equals(".log")){
-					if(outputFileExist(Utils.getLogFilePathOnHPC(runningJob, slurmJobProperty.getHpcServerLoginUserName(), workspaceDirectory, getHpcAddress()))){
-						try{
-							downloadFile(Utils.getLogFilePathOnHPC(runningJob, slurmJobProperty.getHpcServerLoginUserName(), workspaceDirectory, getHpcAddress()), Utils.getJobOutputFilePathOnAgentPC(runningJob, workspaceDirectory, runningJob, Status.EXTENSION_LOG_FILE.getName()));
-							updateStatusForErrorTermination(statusFile, Utils.getJobOutputFilePathOnAgentPC(runningJob, workspaceDirectory, runningJob, Status.EXTENSION_LOG_FILE.getName()));
-						}catch(Exception e){
-							Utils.modifyStatus(statusFile.getAbsolutePath(), Status.JOB_LOG_MSG_ERROR_TERMINATION.getName());
-						}
-					}else{
-						Utils.modifyStatus(statusFile.getAbsolutePath(), Status.JOB_LOG_MSG_ERROR_TERMINATION.getName());
-					}
-				}else{
-					if(outputFileExist(Utils.getOutputFilePathOnHPC(runningJob, slurmJobProperty.getHpcServerLoginUserName(), workspaceDirectory, getHpcAddress(), slurmJobProperty.getOutputFileName().concat(slurmJobProperty.getOutputFileExtension())))){
-						try{
-							downloadFile(Utils.getOutputFilePathOnHPC(runningJob, slurmJobProperty.getHpcServerLoginUserName(), workspaceDirectory, getHpcAddress(), slurmJobProperty.getOutputFileName().concat(slurmJobProperty.getOutputFileExtension())), Utils.getJobOutputFilePathOnAgentPC(runningJob, workspaceDirectory, slurmJobProperty.getOutputFileName(), slurmJobProperty.getOutputFileExtension()));
-						}catch(Exception e){
-							Utils.modifyStatus(statusFile.getAbsolutePath(), Status.JOB_LOG_MSG_ERROR_TERMINATION.getName());
-						}
-					}else{
-						Utils.modifyStatus(statusFile.getAbsolutePath(), Status.JOB_LOG_MSG_ERROR_TERMINATION.getName());
-					}
-				}
-				deleteJobOnHPC(Utils.getJobFolderPathOnHPC(runningJob, slurmJobProperty.getHpcServerLoginUserName(), workspaceDirectory, getHpcAddress()));
-				return true;
-			}
-		}
-		return false;
-	}
-	
-	/**
-	 * Checks if the output file exists. If it does, it returns true, it returns false otherwise.
-	 * 
-	 * @param fileAbsoultePath
-	 * @return
-	 * @throws JSchException
-	 * @throws IOException
-	 */
-	private boolean outputFileExist(String fileAbsoultePath) throws JSchException, IOException{
-		String command = "[ -f "+fileAbsoultePath+" ] && echo "+Status.JOB_OUTPUT_FILE_EXIST_MESSAGE.getName();
-		ArrayList<String> outputs = executeCommand(command);
-		if(outputs!=null && outputs.size()>0){
-			if(outputs.contains(Status.JOB_OUTPUT_FILE_EXIST_MESSAGE.getName())){
-				return true;
-			}
-		}
-		return false;
-	}
-	
-	/**
-	 * Extracts from the log file if the current job terminated normally or</br>
-	 * with error. In the case of error termination, updates the status of</br>
-	 * the log file accordingly. 
-	 * 
-	 * @param statusFile
-	 * @param jobFolderPathOnAgentPC
-	 */
-	private void updateStatusForErrorTermination(File statusFile, String jobFolderPathOnAgentPC) throws IOException{
-		if(Utils.isErrorTermination(jobFolderPathOnAgentPC)){
-			Utils.modifyStatus(statusFile.getAbsolutePath(), Status.JOB_LOG_MSG_ERROR_TERMINATION.getName());
-		}
-	}
-	
-	/**
-	 * Checks if a job is running using the job id.
-	 * 
-	 * @param statusFile
-	 * @return
-	 * @throws JSchException
-	 * @throws IOException
-	 * @throws InterruptedException
-	 */
-	private boolean isJobRunning(File statusFile) throws JSchException, IOException, InterruptedException{
-		String jobId = Utils.getJobId(statusFile.getAbsolutePath());
-		if(jobId==null){
-			return false;
-		} else{
-			boolean isJobRunning = isJobRunning(jobId , statusFile);
-			if(isJobRunning){
-				return true; 
-			}else{
-				Utils.modifyStatus(statusFile.getAbsolutePath(), Status.STATUS_JOB_COMPLETED.getName());
-				return false;
-			}
-		}
-	}
-	
-	/**
-	 * Checks the status of job on the HPC where it was submitted.
-	 * 
-	 * @param jobId
-	 * @param statusFile 
-	 * @return
-	 * @throws IOException
-	 * @throws InterruptedException
-	 */
-	private boolean isJobRunning(String jobId, File statusFile) throws JSchException, IOException, InterruptedException{
-		String command = "squeue -j " + jobId;
-		ArrayList<String> outputs = executeCommand(command);
-		boolean jobRunning = isJobRunning(outputs, statusFile);
-		return jobRunning;
-	}
-	
-	/**
-	 * Analyses the outputs following the execution of the</br>
-	 * job status check command to understand if the job</br>
-	 * is still running or terminated.
-	 * 
-	 * @param outputs
-	 * @return
-	 */
-	private boolean isJobRunning(ArrayList<String> outputs, File statusFile) throws IOException{
-		if(outputs!=null && outputs.size()<=1){
-			return false;
-		}
-		if(outputs!=null){
-			String[] headers = outputs.get(0).split("\\s+");
-			String[] values = outputs.get(1).split("\\s+");
-			for(int i=0; i<headers.length; i++){
-				if(headers[i].toLowerCase().equals("st")){
-					if(values.length>i){
-//						updateStatus(values[i], statusFile);
-					}
-				}
-			}
-		}
-		return true;
-	}	
-	
-	/**
-	 * Extracts the job id from the 
-	 * 
-	 * @param outputs
-	 * @return
-	 */
-	private String getJobId(ArrayList<String> outputs){
-		for(String output: outputs){
-			if(output.contains("Submitted batch job")){
-				String tokens[] = output.split(" ");
-				if(tokens.length>=4){
-					return tokens[3].trim();
-				}
-			}
-		}
-		return null;
-	}
-	
-	/**
-	 * Deletes the job folder including all files and folders belonging to it.
-	 * 
-	 * @param jobFolder the absolute path to the job folder.
-	 * @throws JSchException
-	 * @throws IOException
-	 * @throws InterruptedException
-	 */
-	private void deleteJobOnHPC(String jobFolder) throws JSchException, IOException, InterruptedException{
-		String command = "rm -r " + jobFolder;
-		executeCommand(command);
-	}
-	
-	/**
-	 * Reads the output of the most recently executed command.
-	 * 
-	 * @param br
-	 * @return
-	 * @throws IOException
-	 */
-	public ArrayList<String> readCommandOutput(BufferedReader br) throws IOException{
-		if(br == null)
-			throw new IOException("The reader is not initialised.");
-		String line;
-		ArrayList<String> outputs = new ArrayList<>();
-		while((line=br.readLine())!=null){
-			outputs.add(line);
-		}
-		br.close();
-		return outputs;
-	}
-	
-	/**
-	 * Displays every item in a list of string array.
-	 * 
-	 * @param list
-	 */
-	public void displayArray(ArrayList<String> list){
-		for(String item:list){
-			System.out.println(item);
-		}
-	}
-	
-	/**
-	 * Uploads a file from the source folder belonging to any machine to</br> 
-	 * the destination folder on the same machine or any other machine.
-	 *   
-	 * @param src
-	 * @param dest
-	 * @throws JSchException
-	 * @throws SftpException
-	 */
-	public void uploadFile(String src, String dest) throws JSchException, SftpException{
-        System.out.println("Establishing a channel to transfer "+src+" to "+dest);
-		ChannelSftp sftpChannel = (ChannelSftp) session.openChannel("sftp");
-		sftpChannel.connect();
-
-		sftpChannel.put(src, dest);
-		sftpChannel.disconnect();
-		System.out.println("Closing the channel.");
-	}
-	
-	/**
-	 * Downloads the log file.
-	 * 
-	 * @param src the file to be downloaded 
-	 * @param dest the path under which the source file will be downloaded</br>
-	 * 	or the absolute path containing the path and the file name.  
-	 * @throws JSchException
-	 * @throws SftpException
-	 */
-	public void downloadFile(String src, String dest) throws JSchException, SftpException{
-        System.out.println("Establishing a channel to transfer "+src+" to "+dest);
-		ChannelSftp sftpChannel = (ChannelSftp) session.openChannel("sftp");
-		sftpChannel.connect();
-		sftpChannel.get(src, dest);
-		sftpChannel.disconnect();
-		System.out.println("Closing the channel.");
-	}
-
-	/**
-	 * Deletes a folder or file name from an HPC, if the complete path is provided.</br>
-	 * For example, to delete a folder called "test", user needs to provide "rds/.../test"
-	 * 
-	 * @param folderOrFileName 
-	 * @throws JSchException
-	 * @throws SftpException
-	 */
-	public void deleteFolderOrFile(String folderOrFileName) throws JSchException, SftpException, IOException{
-		executeCommand("rm -r "+folderOrFileName);
-	}
-	
-	/**
-	 * Executes any command that can be run on the Linux console.
-	 * 
-	 * @param Command
-	 * @return
-	 * @throws JSchException
-	 * @throws IOException
-	 */
-	public ArrayList<String> executeCommand(String Command) throws JSchException, IOException{
-		ArrayList<String> outputs = null;
-		System.out.println("Establishing a channel to perform the following command:" + Command);
-		Channel execChannel = session.openChannel("exec");
-		((ChannelExec) execChannel).setCommand(Command);
-		execChannel.setInputStream(null);
-		((ChannelExec) execChannel).setErrStream(System.err);
-		BufferedReader stdInput = new BufferedReader(new InputStreamReader(execChannel.getInputStream()));
-		execChannel.connect();
-		outputs = readCommandOutput(stdInput);
-		execChannel.disconnect();
-		System.out.println("Closing the channel.");
-		return outputs;
-	}
-
-	/**
-	 * Indicates if a server is online.
-	 * 
-	 * @param server refers to the server address
-	 * @param port refers to the port number
-	 * @return
-	 */
-	public boolean hostAvailabilityCheck(String server, int port) throws IOException {
-		boolean available = true;
-//		try (final Socket dummy = new Socket(server, port)){
-//		} catch (UnknownHostException | IllegalArgumentException e) {
-//			available = false;
-//		}
-		return available;
-	}
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/PostProcessing.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/PostProcessing.java
deleted file mode 100644
index 1f97fa416..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/PostProcessing.java
+++ /dev/null
@@ -1,77 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.SftpException;
-
-import uk.ac.cam.cares.jps.base.util.FileUtil;
-
-
-public class PostProcessing {
-	/**
-	 * Updates the output status of a completed job.
-	 * 
-	 * @param jobFolder
-	 * @return
-	 * @throws JSchException
-	 * @throws SftpException
-	 * @throws IOException
-	 * @throws InterruptedException
-	 */
-	public static boolean updateJobOutputStatus(File jobFolder)
-			throws IOException {
-			File statusFile = Utils.getStatusFile(jobFolder);
-			return updateJobOutputStatus(statusFile, Status.OUTPUT_PROCESSED.getName());
-	}
-	
-	/**
-	 * Updates the latest status of the running jobs. 
-	 * 
-	 * @param runningJob
-	 * @param statusFile
-	 * @return
-	 * @throws JSchException
-	 * @throws SftpException
-	 * @throws IOException
-	 * @throws InterruptedException
-	 */
-	private static boolean updateJobOutputStatus(File statusFile, String status) throws IOException{
-		if(statusFile!=null){
-			modifyOutputStatus(statusFile.getAbsolutePath(), Status.OUTPUT_PROCESSED.getName());
-			return true;
-		}
-		return false;
-	}
-	
-	/**
-	 * Modifies the output to processed in the status file. 
-	 * 
-	 * @param filePath the path to the status file.
-	 * @param status can be empty ("") or "processed".
-	 * @throws IOException
-	 */
-	public static void modifyOutputStatus(String filePath, String status) throws IOException{
-		List<String> fileContent = new ArrayList<>();
-		BufferedReader br = FileUtil.openSourceFile(filePath);
-		String line;
-		while((line=br.readLine())!=null){
-		    if (line.trim().startsWith(Status.ATTRIBUTE_JOB_OUTPUT.getName())) {
-		        line = Status.ATTRIBUTE_JOB_OUTPUT.getName().concat(" ").concat(status);
-		    }
-		    fileContent.add(line);
-		}
-		br.close();
-		BufferedWriter bw = FileUtil.openBufferedWriter(filePath);
-		for(String lineContent:fileContent){
-			bw.write(lineContent.concat("\n"));
-		}
-		bw.flush();
-		bw.close();
-	}
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Property.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Property.java
deleted file mode 100644
index 1ee69f85c..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Property.java
+++ /dev/null
@@ -1,38 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-/**
- * This enumerated list defines the name of important properties of</br>
- * Slurm jobs. Some example properties are:</br>
- * - the name of the agent class</br>
- * - the name of the workspace folder on the machine where the agent runs</br>
- * - the name of the workspace folder on HPC where DFT calculations run</br>
- *  
- * @author Feroz Farazi(msff2@cam.ac.uk)
- *
- */
-public enum Property {
-
-	JOB_WORKSPACE_PARENT_DIR(System.getProperty("user.home")),
-	CHK_POINT_FILE_EXTENSION(".chk"),
-	STATUS_FILE_NAME("status.txt"),
-	JSON_INPUT_FILE_NAME("input.json"),
-	SLURM_SCRIPT_FILE_NAME("Slurm.sh");
-	
-	private String propertyName;
-	private int value;
-	private Property(String propertyName){
-		this.propertyName = propertyName;
-	}
-	
-	public String getPropertyName(){
-		return propertyName;
-	}
-	
-	private Property(final int newValue){
-		value = newValue;
-	}
-	
-	public int getValue(){
-		return value;
-	}
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJob.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJob.java
deleted file mode 100644
index 75d29c2f0..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJob.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-public class SlurmJob {
-	private String jobFolderName;
-	
-	public String getJobFolderName() {
-		return jobFolderName;
-	}
-
-	public void setJobFolderName(String jobFolderName) {
-		this.jobFolderName = jobFolderName;
-	}
-	/**
-	 * To create a new job folder name, this method is used. 
-	 * 
-	 * @param hpcAddress
-	 * @return
-	 */
-	public String getNewJobFolderName(String hpcAddress){
-		setJobFolderName(hpcAddress.concat("_").concat("" + Utils.getTimeStamp()));
-		return getJobFolderName();
-	}
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobException.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobException.java
deleted file mode 100644
index 82ae1fc9e..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobException.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-/**
- * The exception class to catch all possible exceptions within the<br>
- * Slurm Job API. 
- * 
- * @author msff2
- *
- */
-public class SlurmJobException extends Exception{
-    public SlurmJobException() {
-        super();
-    }
-
-    public SlurmJobException(String message) {
-        super(message);
-    }
-
-    public SlurmJobException(String message, Throwable cause) {
-        super(message, cause);
-    }
-
-    public SlurmJobException(Throwable cause) {
-        super(cause);
-    }
-
-    protected SlurmJobException(String message, Throwable cause,
-            boolean enableSuppression,
-            boolean writableStackTrace) {
-        super(message, cause, enableSuppression, writableStackTrace);
-    }
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Status.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Status.java
deleted file mode 100644
index a06eaed83..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Status.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-/**
- * Starting from the submission to the completion a Slurm job goes through<br>
- * different statuses, e.g. pending, running and completed. This java class<br>
- * contains all possible statuses and corresponding messages as constants.   
- * 
- * @author msff2
- *
- */
-public enum Status {
-	STATUS_FILE("status.txt"),
-	ATTRIBUTE_JOB_STATUS("JobStatus:"),
-	STATUS_JOB_NOT_STARTED("not started"),
-	STATUS_JOB_COMPLETED("completed"),
-	STATUS_JOB_COMPLETING("completing"),
-	STATUS_JOB_FAILED("failed"),
-	STATUS_JOB_PENDING("pending"),
-	STATUS_JOB_PREEMPTED("preempted"),
-	STATUS_JOB_RUNNING("running"),
-	STATUS_JOB_SUSPENDED("suspended"),
-	STATUS_JOB_STOPPED("stopped"),
-	STATUS_JOB_ERROR_TERMINATED("error termination"),
-	ATTRIBUTE_JOB_ID("JobId:"),
-	ATTRIBUTE_AGENT_ID("AgentId:"),
-	ATTRIBUTE_HPC_ADDRESS("HPCAddress:"),
-	ATTRIBUTE_JOB_OUTPUT("JobOutput:"),
-	OUTPUT_PROCESSED("processed"),
-	EXTENSION_SLURM_FILE(".sh"),
-	EXTENSION_LOG_FILE(".log"),
-	EXTENSION_JSON_FILE(".json"),
-	JOB_SETUP_SUCCESS_MSG("The job request has been processed successfully."),
-	JOB_SETUP_JSON_ERROR("The JSON request is ill formatted."),
-	JOB_SETUP_SLURM_SCRIPT_ERROR("The Slurm script could not be downloaded."),
-	JOB_SETUP_INPUT_FILE_ERROR("The input file for the job could not be created."),
-	JOB_SETUP_ERROR("The requested job could not be set up, therefore, resubmit the job."),
-	JOB_LOG_MSG_ERROR_TERMINATION("error termination"),
-	JOB_LOG_MSG_NORMAL_TERMINATION("normal termination"),
-	JOB_OUTPUT_FILE_EXIST_MESSAGE("The file exist."),
-	JOB_SQUEUE_STATUS_COMPLETED("CD"),
-	JOB_SQUEUE_STATUS_COMPLETING("CG"),
-	JOB_SQUEUE_STATUS_FAILED("F"),
-	JOB_SQUEUE_STATUS_PENDING("PD"),
-	JOB_SQUEUE_STATUS_PREEMPTED("PR"),
-	JOB_SQUEUE_STATUS_RUNNING("R"),
-	JOB_SQUEUE_STATUS_SUSPENDED("S"),
-	JOB_SQUEUE_STATUS_STOPPED("ST");
-	
-	private String property;
-	private Status(String property){
-		this.property = property;
-	}
-	
-	public String getName(){
-		return property;
-	}
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Utils.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Utils.java
deleted file mode 100644
index 02f83ecb6..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Utils.java
+++ /dev/null
@@ -1,626 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.InetAddress;
-import java.net.UnknownHostException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
-
-import uk.ac.cam.cares.jps.base.slurm.job.configuration.SlurmJobProperty;
-
-public class Utils{
-	private static Logger LOGGER = LogManager.getLogger(Utils.class);	
-	public static long previousTimeStamp;
-	
-	/**
-	 * Generate unique time stamp to be used in naming Slurm jobs.
-	 * 
-	 * @return
-	 */
-	public static long getTimeStamp(){
-		long currentTimeStamp = System.nanoTime();
-		while(!(currentTimeStamp > previousTimeStamp)){
-			currentTimeStamp = System.nanoTime();
-		}
-		previousTimeStamp = currentTimeStamp;
-		return currentTimeStamp;
-	}
-	
-	/**
-	 * Creates an instance of the BufferedWriter class.
-	 * 
-	 * @param filePathPlusName the path plus name of the file being written
-	 * @return
-	 * @throws IOException
-	 */
-	public static BufferedWriter openBufferedWriter(String filePathPlusName) throws IOException{
-		return new BufferedWriter(new FileWriter(filePathPlusName));
-	}
-	
-	/**
-	 * Creates and returns an instance of the BufferedReader class.
-	 * 
-	 * @param filePathPlusName
-	 *            the path plus name of the file being read
-	 * @return
-	 * @throws IOException
-	 */
-	public static BufferedReader openSourceFile(String filePathPlusName)
-			throws IOException {
-		return new BufferedReader(new InputStreamReader(new FileInputStream(
-				filePathPlusName), "UTF-8"));
-	}
-	
-	/**
-	 * Check if a job is completed.
-	 * 
-	 * @param jobFolder
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobCompleted(File jobFolder) throws IOException{
-		return isJobFinished(jobFolder, jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName()));
-	}
-	
-	/**
-	 * Check if a job is completed.
-	 * 
-	 * @param jobFolder
-	 * @param slurmJobProperty
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobCompleted(File jobFolder, SlurmJobProperty slurmJobProperty) throws IOException{
-		boolean status = false;
-		try {
-			status = isJobFinished(jobFolder, jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName()), slurmJobProperty);
-		} catch (Exception e) {
-			LOGGER.info("SlurmJobAPI: failed to check the status of the job with ID " + jobFolder.getName());
-		}
-		return status;
-	}
-	
-	/**
-	 * Check if a job is completed with erroneous or incomplete output.
-	 * 
-	 * @param jobFolder
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobErroneouslyCompleted(File jobFolder) throws IOException{
-		return isJobErroneouslyCompleted(jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName()));
-	}
-	
-	/**
-	 * Checks if a job is still running.
-	 * 
-	 * @param jobFolder
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobRunning(File jobFolder) throws IOException{
-		boolean status = false;
-		try{
-			status = isJobRunning(jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName()));
-		}catch(Exception e){
-			LOGGER.info("SlurmJobAPI: failed to check the status of the job with ID "+jobFolder.getName());
-		}
-		return status;
-	}
-	
-	/**
-	 * Checks if a job is not started yet. 
-	 * 
-	 * @param jobFolder
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobNotStarted(File jobFolder) throws IOException{
-		return isJobNotStarted(jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName()));
-	}
-	
-	/**
-	 * Check the status if a job finished.
-	 * 
-	 * @param jobFolder the folder that contains the job.
-	 * @param statusFilePath the file that contains the status of the job. 
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobFinished(File jobFolder, String statusFilePath) throws IOException{
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName())){
-				if(line.contains(Status.STATUS_JOB_COMPLETED.getName())){
-					statusFile.close();
-					return true;
-				}
-				if(line.contains(Status.STATUS_JOB_ERROR_TERMINATED.getName())){
-					statusFile.close();
-					return true;
-				}
-			}
-		}
-		statusFile.close();
-		return false;
-	}
-
-	
-	/**
-	 * Check the status if a job finished.
-	 * 
-	 * @param jobFolder the folder that contains the job.
-	 * @param statusFilePath the file that contains the status of the job.
-	 * @param slurmJobProperty the variable that allows to read different<br>
-	 * properties including agentClass, completed jobs folder prefix, etc.
-	 * 
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobFinished(File jobFolder, String statusFilePath, SlurmJobProperty slurmJobProperty) throws IOException{
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName())){
-				if(line.contains(Status.STATUS_JOB_COMPLETED.getName())){
-					statusFile.close();
-					if(isJobPostProcessed(jobFolder, statusFilePath)){
-						moveToCompletedJobsFolder(jobFolder, slurmJobProperty);
-					}
-					return true;
-				}
-				if(line.contains(Status.STATUS_JOB_ERROR_TERMINATED.getName())){
-					statusFile.close();
-					moveToFailedJobsFolder(jobFolder, slurmJobProperty);
-					return true;
-				}
-			}
-		}
-		statusFile.close();
-		return false;
-	}
-	
-	/**
-	 * Check the status if a job post-processed.
-	 * 
-	 * @param jobFolder the folder that contains the job.
-	 * @param statusFilePath the file that contains the status of the job.
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobPostProcessed(File jobFolder, String statusFilePath) throws IOException{
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().startsWith(Status.ATTRIBUTE_JOB_OUTPUT.getName())){
-				if(line.contains(Status.OUTPUT_PROCESSED.getName())){
-					statusFile.close();
-					return true;
-				}
-			}
-		}
-		statusFile.close();
-		return false;
-	}
-	
-	/**
-	 * Check the status if a job produced erroneous or incomplete output.
-	 * 
-	 * @param statusFilePath
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobErroneouslyCompleted(String statusFilePath) throws IOException{
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName())){
-				if(line.contains(Status.STATUS_JOB_ERROR_TERMINATED.getName())){
-					statusFile.close();
-					return true;
-				}
-			}
-		}
-		statusFile.close();
-		return false;
-	}
-	
-	public static boolean isJobOutputProcessed(File jobFolder) throws IOException{
-		return isJobOutputProcessed(jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName()));
-	}
-	
-	/**
-	 * Check the status if a job is currently running.
-	 * 
-	 * @param statusFilePath the absolute path to the status file.
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobOutputProcessed(String statusFilePath) throws IOException{
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().startsWith(Status.ATTRIBUTE_JOB_OUTPUT.getName())){
-				if(line.contains(Status.OUTPUT_PROCESSED.getName())){
-					statusFile.close();
-					return true;
-				}
-			}
-		}
-		statusFile.close();
-		return false;
-	}
-	
-	/**
-	 * Check the status if a job is currently running.
-	 * 
-	 * @param statusFilePath the absolute path to the status file.
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobRunning(String statusFilePath) throws IOException{
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName())){
-				if(line.contains(Status.STATUS_JOB_RUNNING.getName()) 
-						|| line.contains(Status.STATUS_JOB_COMPLETING.getName()) 
-						|| line.contains(Status.STATUS_JOB_PENDING.getName())){
-					statusFile.close();
-					return true;
-				}
-			}
-		}
-		statusFile.close();
-		return false;
-	}
-	
-	protected static boolean isStatusFileOpen = false;
-	
-	/**
-	 * Check the status if a job is not started yet.
-	 * 
-	 * @param statusFilePath the absolute path to the status file.
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isJobNotStarted(String statusFilePath) throws IOException{
-		if(isStatusFileOpen){
-			return false;
-		}
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		isStatusFileOpen = true;
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName())){
-				if(line.contains(Status.STATUS_JOB_NOT_STARTED.getName())){
-					statusFile.close();
-					isStatusFileOpen = false;
-					return true;
-				}
-			}
-		}
-		statusFile.close();
-		isStatusFileOpen = false;
-		return false;
-	}
-	
-	/**
-	 * Reads the job id from the status file.
-	 * 
-	 * @param statusFilePath the absolute path to the status file.
-	 * @return
-	 * @throws IOException
-	 */
-	public static String getJobId(String statusFilePath) throws IOException{
-		BufferedReader statusFile = Utils.openSourceFile(statusFilePath);
-		String line;
-		while((line=statusFile.readLine())!=null){
-			if(line.trim().toLowerCase().startsWith(Status.ATTRIBUTE_JOB_ID.getName().toLowerCase())){
-				String tokens[] = line.trim().split(":");
-				if(tokens.length>=2 && tokens[1].trim().length()>0){
-					statusFile.close();
-					return tokens[1].trim();
-				}
-			}
-		}
-		statusFile.close();
-		return null;
-	}
-	/**
-	 * Adds the job id to the status file. 
-	 * 
-	 * @param filePath the path to the status file.
-	 * @param jobId the job id generated following the sbatch submission. 
-	 * @throws IOException
-	 */
-	public static void addJobId(String filePath, String jobId) throws IOException{
-		List<String> fileContent = new ArrayList<>();
-		BufferedReader br = openSourceFile(filePath);
-		String line;
-		while((line=br.readLine())!=null){
-		    if (line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName())) {
-		        line = Status.ATTRIBUTE_JOB_STATUS.getName().concat(" ").concat(Status.STATUS_JOB_RUNNING.getName());
-		    }
-		    if (line.trim().startsWith(Status.ATTRIBUTE_JOB_ID.getName())) {
-		        line = Status.ATTRIBUTE_JOB_ID.getName().concat(" ").concat(jobId);
-		    }
-		    fileContent.add(line);
-		}
-		br.close();
-		BufferedWriter bw = openBufferedWriter(filePath);
-		for(String lineContent:fileContent){
-			bw.write(lineContent.concat("\n"));
-		}
-		bw.flush();
-		bw.close();
-	}
-	
-	/**
-	 * Modifies the status of job in the status file. 
-	 * 
-	 * @param filePath the path to the status file.
-	 * @param status can be "running" or "completed".
-	 * @throws IOException
-	 */
-	public static void modifyStatus(String filePath, String status) throws IOException{
-		List<String> fileContent = new ArrayList<>();
-		BufferedReader br = openSourceFile(filePath);
-		String line;
-		while((line=br.readLine())!=null){
-		    if (line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName())) {
-		        line = Status.ATTRIBUTE_JOB_STATUS.getName().concat(" ").concat(status);
-		    }
-		    fileContent.add(line);
-		}
-		br.close();
-		BufferedWriter bw = openBufferedWriter(filePath);
-		for(String lineContent:fileContent){
-			bw.write(lineContent.concat("\n"));
-		}
-		bw.flush();
-		bw.close();
-	}
-
-	/**
-	 * Returns the status file if the job folder is provided.
-	 *  
-	 * @param jobFolder path to the job folder.
-	 * @return
-	 */
-	public static File getStatusFile(File jobFolder){
-		if(jobFolder.isDirectory()){
-			if((new File(jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName())).isFile())){
-				return new File(jobFolder.getAbsolutePath().concat(File.separator).concat(Status.STATUS_FILE.getName()));
-			}
-		}
-		return null;
-	}
-	
-	/**
-	 * Returns the log file path (absolute path) on a HPC server where the<br> 
-	 * Slurm job is running.
-	 * 
-	 * @param runningJob
-	 * @param userName
-	 * @param taskSpace
-	 * @param hpcAddress
-	 * @return
-	 * @throws UnknownHostException
-	 */
-	public static String getLogFilePathOnHPC(String runningJob, String userName, File taskSpace, String hpcAddress) throws UnknownHostException{
-		String jobFolderOnHPC = runningJob.replace(hpcAddress, getMachineAddress());
-		String logFilePath = getJobFolderPathOnHPC(runningJob, userName, taskSpace, hpcAddress).concat("/").concat(jobFolderOnHPC)
-				.concat(Status.EXTENSION_LOG_FILE.getName());
-		return logFilePath;
-	}
-
-	/**
-	 * Returns the output file path (absolute path) on a HPC server where the<br> 
-	 * Slurm job is running.
-	 * 
-	 * @param runningJob
-	 * @param userName
-	 * @param taskSpace
-	 * @param hpcAddress
-	 * @param outputFileNameWithExtension
-	 * @return
-	 * @throws UnknownHostException
-	 */
-	public static String getOutputFilePathOnHPC(String runningJob, String userName, File taskSpace, String hpcAddress, String outputFileNameWithExtension) throws UnknownHostException{
-		String outputFilePath = getJobFolderPathOnHPC(runningJob, userName, taskSpace, hpcAddress).concat("/").concat(outputFileNameWithExtension);
-		return outputFilePath;
-	}
-	
-	/**
-	 * Returns the job folder path (absolute path) on a HPC where the job is running. 
-	 * 
-	 * @param runningJob
-	 * @param userName
-	 * @param taskSpace
-	 * @param hpcAddress
-	 * @return
-	 * @throws UnknownHostException
-	 */
-	public static String getJobFolderPathOnHPC(String runningJob, String userName, File taskSpace, String hpcAddress) throws UnknownHostException{
-		String jobFolderOnHPC = runningJob.replace(hpcAddress, getMachineAddress());
-		String jobFolderPath = "/home/".concat(userName).concat("/")
-				.concat(taskSpace.getName()).concat("/")
-				.concat(jobFolderOnHPC);
-		return jobFolderPath;
-	}
-	
-	/**
-	 * Returns the absolute path to the output file on the machine where the Agent is running.
-	 * 
-	 * @param runningJob
-	 * @param taskSpace
-	 * @param outputFileName
-	 * @param outputFileExtension
-	 * @return
-	 */
-	public static String getJobOutputFilePathOnAgentPC(String runningJob, File taskSpace, String outputFileName, String outputFileExtension){
-		return taskSpace.getAbsolutePath().concat(File.separator).concat(runningJob).concat(File.separator)
-				.concat(outputFileName).concat(outputFileExtension);
-	}
-	
-	/**
-	 * Checks the log file, in the case of the Gaussian software, if it is an<br>
-	 * error termination.
-	 * 
-	 * @param logFileOnAgentPC
-	 * @return
-	 * @throws IOException
-	 */
-	public static boolean isErrorTermination(String logFileOnAgentPC)throws IOException{
-		BufferedReader logFile = openSourceFile(logFileOnAgentPC);
-		String line;
-		while((line=logFile.readLine())!=null){
-			if(line.trim().toLowerCase().startsWith(Status.JOB_LOG_MSG_ERROR_TERMINATION.getName().toLowerCase())){
-				logFile.close();
-				return true;
-			}
-		}
-		logFile.close();
-		return false;
-	}
-	
-	/**
-	 * Reads the address of the machine where an instance of the agent<br>
-	 * running Slurm jobs is hosted.
-	 * 
-	 * @return
-	 * @throws UnknownHostException
-	 */
-	public static String getMachineAddress() throws UnknownHostException{
-		try {
-		   InetAddress address;
-		   address = InetAddress.getLocalHost();
-		   return address.toString().replace("/", "_");
-		} catch (UnknownHostException e){
-		    e.printStackTrace();
-		    LOGGER.error("SlurmJobAPI: The host address is unknown as InetAddress.getLocalHost() threw an exception.");
-		}
-		return null;
-	}
-	
-	/**
-	 * Windows uses both carriage return (\r) and line feed (\n) as a line<br> 
-	 * ending (\r\n). Unix uses line feed (\n) as a line ending.<br>
-	 * This method translates all line endings codified with "\r\n" in a<br>
-	 * file into "\n".
-	 * 
-	 * @param file
-	 */
-	public static void translateLineEndingIntoUnix(File file) throws IOException{
-		File recreatedFile = new File(System.getProperty("user.home").replace("\\", "/").concat("/").concat(file.getName()));
-		copyModifiedContentForUnix(file, recreatedFile);
-		copyModifiedContentForUnix(recreatedFile, file);
-	}
-	
-	/**
-	 * Copies file from the source path to the destination path with the<br>
-	 * line ending modified to format in Unix.
-	 * 
-	 * @param source
-	 * @param destination
-	 * @throws IOException
-	 */
-	private static void copyModifiedContentForUnix(File source, File destination) throws IOException{
-		BufferedReader receivedFile = openSourceFile(source.getAbsolutePath());
-		BufferedWriter recreatedFile = openBufferedWriter(destination.getAbsolutePath());
-		String line;
-		while((line=receivedFile.readLine())!=null){
-				recreatedFile.write(line.concat("\n"));
-		}
-		recreatedFile.close();
-		receivedFile.close();
-	}
-	
-	/**
-	 * Moves the provided job folder to the folder that contains completed<br>
-	 * and post-processed jobs of the agent. 
-	 * 
-	 * @param jobFolder the folder that contains a job
-	 * @param slurmJobProperty
-	 */
-	public static void moveToCompletedJobsFolder(File jobFolder, SlurmJobProperty slurmJobProperty) {
-		try {
-			File destDir = getCompletedJobsDirectory(jobFolder, slurmJobProperty);
-			if(destDir!=null){
-				FileUtils.copyDirectory(jobFolder, destDir);
-				FileUtils.deleteDirectory(jobFolder);
-			}
-		} catch (IOException e) {
-		    e.printStackTrace();
-		}
-	}
-	
-	/**
-	 * Returns the folder where completed jobs are saved.
-	 * 
-	 * @param jobFolder
-	 * @param slurmJobProperty
-	 * @return
-	 * @throws IOException
-	 */
-	public static File getCompletedJobsDirectory(File jobFolder, SlurmJobProperty slurmJobProperty) throws IOException{
-		File workspace = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(), slurmJobProperty.getAgentClass());
-		String completedJobsDirectory = Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName().concat(File.separator).concat(slurmJobProperty.getAgentCompletedJobsSpacePrefix()).concat(workspace.getName()).concat(File.separator).concat(jobFolder.getName());
-		File jobFolderInCompletedJobs = new File(completedJobsDirectory);
-		jobFolderInCompletedJobs.mkdirs();
-		if(jobFolderInCompletedJobs.exists()){
-			return jobFolderInCompletedJobs;
-		}
-		return null;
-	}
-	
-	/**
-	 * Moves the provided job folder to the folder that contains failed<br>
-	 * jobs of the agent.
-	 * 
-	 * @param jobFolder the folder that contains a job
-	 * @param slurmJobProperty
-	 */
-	public static void moveToFailedJobsFolder(File jobFolder, SlurmJobProperty slurmJobProperty) {
-		try {
-			File destDir = getFailedJobsDirectory(jobFolder, slurmJobProperty);
-			if(destDir!=null){
-				FileUtils.copyDirectory(jobFolder, destDir);
-				FileUtils.deleteDirectory(jobFolder);
-			}
-		} catch (IOException e) {
-		    e.printStackTrace();
-		}
-	}
-	
-	/**
-	 * Returns the folder where failed jobs are saved.
-	 * 
-	 * @param jobFolder
-	 * @param slurmJobProperty
-	 * @return
-	 * @throws IOException
-	 */
-	public static File getFailedJobsDirectory(File jobFolder, SlurmJobProperty slurmJobProperty) throws IOException{
-		File workspace = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(), slurmJobProperty.getAgentClass());
-		String failedJobsDirectory = Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName().concat(File.separator).concat(slurmJobProperty.getAgentFailedJobsSpacePrefix()).concat(workspace.getName()).concat(File.separator).concat(jobFolder.getName());
-		File jobFolderInFailedJobs = new File(failedJobsDirectory);
-		jobFolderInFailedJobs.mkdirs();
-		if(jobFolderInFailedJobs.exists()){
-			return jobFolderInFailedJobs;
-		}
-		return null;
-	}
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Workspace.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Workspace.java
deleted file mode 100644
index 6d3e62963..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/Workspace.java
+++ /dev/null
@@ -1,263 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Paths;
-
-import org.apache.commons.lang.math.NumberUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-import com.google.common.io.Files;
-
-/**
- * All functionalities for creating the workspace, job folder, status file,<br>
- * json input file, script file and input file for Slurm jobs.
- * 
- * @author msff2
- *
- */
-public class Workspace {
-	private Logger LOGGER = LogManager.getLogger(Workspace.class); 
-	public long previousTimeStamp = System.nanoTime();
-
-	/**
-	 * Receives both the agent class (e.g. DFTAgent) and folder (absolute path)<br>
-	 * where the workspace for the agent will be created, and returns the name<br>
-	 * of workspace. 
-	 *  
-	 * @param workspaceParentPath specific to the OS. For example,<br>
-	 * - on Windows an example path will be 'C:/Users/<username>', and<br>
-	 * - on Linux the path '/home/<username>'.
-	 * 
-	 * @param agentClass
-	 * @return
-	 */
-	public static File getWorkspace(String workspaceParentPath, String agentClass) {
-		File dir = new File(workspaceParentPath);
-		for (File file : dir.listFiles()) {
-			if (file.isDirectory()) {
-				if (file.getName().toLowerCase().startsWith(agentClass.toLowerCase())) {
-					String[] tokens = file.getName().split("_");
-					if (tokens.length >= 2 && tokens[tokens.length - 1].length() > 6
-							&& NumberUtils.isNumber(tokens[tokens.length - 1])) {
-						return file;
-					}
-				}
-			}
-		}
-		return createWorkspaceName(workspaceParentPath, agentClass);
-	}
-	
-	private static File createWorkspaceName(String workspaceParentPath, String agentClass) {
-		String workspaceName = agentClass.concat("_").concat("" + System.nanoTime());
-		File workspace = Paths.get(workspaceParentPath, workspaceName).toFile();
-		if (workspace.mkdir()) {
-			return workspace;
-		}
-		return null;
-	}
-	
-	protected boolean isWorkspaceAvailable(File dir, String agentClass) {
-		for (File file : dir.listFiles()) {
-			if (file.isDirectory()) {
-				if (file.getName().toLowerCase().startsWith(agentClass.toLowerCase())) {
-					return true;
-				}
-			}
-		}
-		return false;
-	}
-	
-	/**
-	 * Creates the JSON formatted input file in the current job folder. 
-	 *  
-	 * @param workspaceFolder
-	 * @param jsonInputFilePath the path where the JSON formatted input<br>
-	 * file will be stored.
-	 * @param jsonString the string that contains the the whole content<br>
-	 * of the JSON formatted input.
-	 * @return success message if the file JSON file can be created, null<br>
-	 * otherwise. 
-	 * @throws IOException
-	 */
-	public String createJSONInputFile(File workspaceFolder, String jsonInputFilePath, String jsonString) throws IOException{
-		BufferedWriter jsonInputFile = Utils.openBufferedWriter(jsonInputFilePath);
-		if(jsonInputFile == null){
-			return null;
-		}
-		jsonInputFile.write(jsonString);
-		jsonInputFile.close();
-		return Status.JOB_SETUP_SUCCESS_MSG.getName();
-	}
-	
-	/**
-	 * Returns the absolute path to an input file identified by its extension.<br>
-	 * For example, .com, .g09, .csv, .jar, etc.
-	 * 
-	 * @param jobFolder
-	 * @param hpcAddress
-	 * @param inputFileExtension
-	 * @return
-	 */
-	public String getInputFilePath(File jobFolder, String hpcAddress, String inputFileExtension){
-		return jobFolder.getAbsolutePath()
-		.concat(File.separator)
-		.concat(hpcAddress)
-		.concat("_").concat(getTimeStampPart(jobFolder.getName()))
-		.concat(inputFileExtension);
-	}
-	
-	public String getInputFileExtension(File input) throws SlurmJobException{
-		
-		if(input.isFile()){
-			
-			return input.getAbsolutePath().substring(input.getAbsolutePath().lastIndexOf("."));
-			
-		}else{
-			
-			LOGGER.error("SlurmJobAPI: The provided input file is not a file.");
-			
-			throw new SlurmJobException("SlurmJobAPI: The provided input file is not a file.");
-		}
-	}
-	
-	/**
-	 * Creates the job folder on the host machine where the current agent runs.
-	 * 
-	 * @param workspacePath
-	 * @param hpcAddress
-	 * @param timeStamp
-	 * @return
-	 */
-	public File createJobFolder(String workspacePath, String hpcAddress, long timeStamp){
-		String jobFolder = hpcAddress.concat("_").concat("" + timeStamp);
-		File workspace = new File(workspacePath.concat(File.separator).concat(jobFolder));
-		if(workspace.mkdir()){
-			return workspace;
-		}
-		return null;
-	}
-	
-	public String createInputFile(String inputFileDestinationPath, File input) throws IOException{
-		copyFile(input, new File(inputFileDestinationPath));
-		return Status.JOB_SETUP_SUCCESS_MSG.getName();
-	}
-	
-	public String createStatusFile(File workspaceFolder, String statusFilePath, String hpcAddress) throws IOException{
-		BufferedWriter statusFile = Utils.openBufferedWriter(statusFilePath);
-		if(statusFile == null){
-			return null;
-		}
-		statusFile.write(Status.ATTRIBUTE_JOB_STATUS.getName().concat(" "));
-		statusFile.write(Status.STATUS_JOB_NOT_STARTED.getName().concat("\n"));
-		statusFile.write(Status.ATTRIBUTE_JOB_ID.getName().concat("\n"));
-		statusFile.write(Status.ATTRIBUTE_AGENT_ID.getName().concat(" "));
-		statusFile.write(workspaceFolder.getName().concat("\n"));
-		statusFile.write(Status.ATTRIBUTE_HPC_ADDRESS.getName().concat(" "));
-		statusFile.write(hpcAddress.concat("\n"));
-		statusFile.write(Status.ATTRIBUTE_JOB_OUTPUT.getName().concat("\n"));
-		statusFile.close();
-		return Status.JOB_SETUP_SUCCESS_MSG.getName();
-	}
-	
-	public String copyFile(String source, String destination) throws IOException{
-		try{
-		copyFile(new File(source),
-				new File(destination));
-		if(destination.endsWith(".sh")){
-			Utils.translateLineEndingIntoUnix(new File(destination));
-		}
-		return Status.JOB_SETUP_SUCCESS_MSG.getName();
-		}catch(IOException e){
-			e.printStackTrace();
-			return null;
-		}
-	}
-	
-	/**
-	 * Extracts the time stamp part from the job folder. For example,<br>
-	 * if the job folder is named login-skylake.hpc.cam.ac.uk_428109593378500,<br>
-	 * the method will return 428109593378500.
-	 *  
-	 * @param folder
-	 * @return
-	 */
-	public String getTimeStampPart(String folder){
-		if(folder.contains("_")){
-			String[] tokens = folder.split("_");
-			if(tokens.length==2 && tokens[1]!=null && StringUtils.isNumeric(tokens[1])){
-				return tokens[1];
-			}
-		}
-		return null;
-	}
-	
-	/**
-	 * Receives the jobFolder as the input and returns the absolute path to<br>
-	 * to the job status file.
-	 *  
-	 * @param jobFolder
-	 * @return
-	 */
-	public String getStatusFilePath(File jobFolder){
-		return jobFolder.getAbsolutePath().concat(File.separator).concat(Property.STATUS_FILE_NAME.getPropertyName());
-	}
-	
-	/**
-	 * Receives the jobFolder as the input and returns the absolute path to<br>
-	 * to the JSON input file.
-	 * 
-	 * @param jobFolder
-	 * @param jsonInputFileName
-	 * @return
-	 */
-	public String getJSONInputFilePath(File jobFolder){
-		return jobFolder.getAbsolutePath().concat(File.separator).concat(Property.JSON_INPUT_FILE_NAME.getPropertyName());
-	}
-	
-
-	
-	/**
-	 * Copy the Slurm script to the job folder to set up the current<br>
-	 * job. If the method can copy the script, it returns a job set up<br>
-	 * success message. Otherwise, it returns null.  
-	 *  
-	 *  
-	 * @param source
-	 * @param destination
-	 * @param slurmScriptFileName
-	 * @return
-	 * @throws IOException
-	 */
-	public String copyScriptFile(String source, String destination, String slurmScriptFileName) throws IOException{
-		try{
-		copyFile(new File(source),
-				new File(destination.concat(File.separator)
-						.concat(slurmScriptFileName)));
-		Utils.translateLineEndingIntoUnix(new File(destination.concat(File.separator)
-				.concat(slurmScriptFileName)));
-		return Status.JOB_SETUP_SUCCESS_MSG.getName();
-		}catch(IOException e){
-			e.printStackTrace();
-			return null;
-		}
-	}
-	
-	/**
-	 * Copy any file from the source path to the destination path.
-	 * 
-	 * @param from the absolute path to the file which will be copied.
-	 * @param to the absolute path to the folder where the file will be<br>
-	 * copied. If user provides absolute path including the file name,<br>
-	 * probably renamed or the same as the one in the from path, the method<br>
-	 * will keep the same name. 
-	 * 
-	 * @throws IOException
-	 */
-	private void copyFile(File from, File to) throws IOException{
-		Files.copy(from, to);
-	}
-}
diff --git a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/configuration/SlurmJobProperty.java b/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/configuration/SlurmJobProperty.java
deleted file mode 100644
index fb2cf4fdd..000000000
--- a/src/main/java/uk/ac/cam/cares/jps/base/slurm/job/configuration/SlurmJobProperty.java
+++ /dev/null
@@ -1,181 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job.configuration;
-
-/**
- * These properties must be set by all agents that will run Slurm jobs<br>
- * with this API.
- * 
- * @author Feroz Farazi (msff2@cam.ac.uk)
- *
- */
-public class SlurmJobProperty {
-	private String hpcServerLoginUserName;
-	private String hpcServerLoginUserPassword;
-        private String hpcServerPrivateKey;
-	private String agentClass;
-	private String agentWorkspacePrefix;
-	private String agentCompletedJobsSpacePrefix;
-	private String agentFailedJobsSpacePrefix;
-	private String hpcAddress;
-	private String inputFileName;
-	private String inputFileExtension;
-	private String jsonInputFileName;
-	private String jsonFileExtension;
-	private String slurmScriptFileName;
-	private String executableFile;
-	private String outputFileName;
-	private String outputFileExtension;
-	private int maxNumberOfHPCJobs;
-	private int agentInitialDelayToStartJobMonitoring;
-	private int agentPeriodicActionInterval;
-	
-	public String getHpcServerLoginUserName() {
-		return hpcServerLoginUserName;
-	}
-
-	public void setHpcServerLoginUserName(String hpcServerLoginUserName) {
-		this.hpcServerLoginUserName = hpcServerLoginUserName;
-	}
-
-	public String getHpcServerLoginUserPassword() {
-		return hpcServerLoginUserPassword;
-	}
-
-	public void setHpcServerLoginUserPassword(String hpcServerLoginUserPassword) {
-		this.hpcServerLoginUserPassword = hpcServerLoginUserPassword;
-	}
-        
-        public String getHpcServerPrivateKey() {
-            return this.hpcServerPrivateKey;
-        }
-        public void setHpcServerPrivateKey(String hpcServerPrivateKey) {
-            this.hpcServerPrivateKey = hpcServerPrivateKey;
-        }
-        
-	public String getAgentClass() {
-		return agentClass;
-	}
-
-	public String getAgentWorkspacePrefix() {
-		return agentWorkspacePrefix;
-	}
-	
-	public String getAgentCompletedJobsSpacePrefix() {
-		return agentCompletedJobsSpacePrefix;
-	}
-
-	public String getHpcAddress() {
-		return hpcAddress;
-	}
-
-	public String getInputFileName() {
-		return inputFileName;
-	}
-
-	public String getInputFileExtension() {
-		return inputFileExtension;
-	}
-
-	public String getJsonFileExtension() {
-		return jsonFileExtension;
-	}
-
-	public String getJsonInputFileName() {
-		return jsonInputFileName;
-	}
-
-	public String getSlurmScriptFileName() {
-		return slurmScriptFileName;
-	}
-
-	public String getOutputFileName() {
-		return outputFileName;
-	}
-
-	public String getOutputFileExtension() {
-		return outputFileExtension;
-	}
-
-	public String getExecutableFile() {
-		return executableFile;
-	}
-
-	public void setExecutableFile(String executableFile) {
-		this.executableFile = executableFile;
-	}
-
-	public int getMaxNumberOfHPCJobs() {
-		return maxNumberOfHPCJobs;
-	}
-
-	public int getAgentInitialDelayToStartJobMonitoring() {
-		return agentInitialDelayToStartJobMonitoring;
-	}
-
-	public int getAgentPeriodicActionInterval() {
-		return agentPeriodicActionInterval;
-	}
-
-	public void setAgentClass(String agentClass) {
-		this.agentClass = agentClass;
-	}
-
-	public void setAgentWorkspacePrefix(String agentWorkspacePrefix) {
-		this.agentWorkspacePrefix = agentWorkspacePrefix;
-	}
-
-	public void setAgentCompletedJobsSpacePrefix(String agentCompletedJobsSpacePrefix) {
-		this.agentCompletedJobsSpacePrefix = agentCompletedJobsSpacePrefix;
-	}
-
-	public void setHpcAddress(String hpcAddress) {
-		this.hpcAddress = hpcAddress;
-	}
-
-	public void setInputFileName(String inputFileName) {
-		this.inputFileName = inputFileName;
-	}
-
-	public void setInputFileExtension(String inputFileExtension) {
-		this.inputFileExtension = inputFileExtension;
-	}
-
-	public void setJsonFileExtension(String jsonFileExtension) {
-		this.jsonFileExtension = jsonFileExtension;
-	}
-
-	public void setJsonInputFileName(String jsonInputFileName) {
-		this.jsonInputFileName = jsonInputFileName;
-	}
-
-	public void setSlurmScriptFileName(String slurmScriptFileName) {
-		this.slurmScriptFileName = slurmScriptFileName;
-	}
-
-	public void setOutputFileName(String outputFileName) {
-		this.outputFileName = outputFileName;
-	}
-
-	public void setOutputFileExtension(String outputFileExtension) {
-		this.outputFileExtension = outputFileExtension;
-	}
-
-	public void setMaxNumberOfHPCJobs(int maxNumberOfHPCJobs) {
-		this.maxNumberOfHPCJobs = maxNumberOfHPCJobs;
-	}
-
-	public void setAgentInitialDelayToStartJobMonitoring(int agentInitialDelayToStartJobMonitoring) {
-		this.agentInitialDelayToStartJobMonitoring = agentInitialDelayToStartJobMonitoring;
-	}
-
-	public void setAgentPeriodicActionInterval(int agentPeriodicActionInterval) {
-		this.agentPeriodicActionInterval = agentPeriodicActionInterval;
-	}
-
-	public String getAgentFailedJobsSpacePrefix() {
-		return agentFailedJobsSpacePrefix;
-	}
-
-	public void setAgentFailedJobsSpacePrefix(String agentFailedJobsSpacePrefix) {
-		this.agentFailedJobsSpacePrefix = agentFailedJobsSpacePrefix;
-	}
-}
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/JobStatisticsTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/JobStatisticsTest.java
deleted file mode 100644
index 8e4800ba6..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/JobStatisticsTest.java
+++ /dev/null
@@ -1,115 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.DisplayName;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.io.TempDir;
-
-class JobStatisticsTest {
-    @TempDir()
-    static Path tempFolder;
-    private static Path fileloc;
-
-    // Create JobstatisticsTestInputstatus.txt. This file will be deleted at the end
-    // of the unit test.
-    @BeforeAll
-    static void generatefile() throws IOException {
-        Files.createDirectories(tempFolder);
-        fileloc = tempFolder.resolve("jobFolder").resolve("JobStatisticsTestInputstatus.txt");
-        File tempInputStatus = fileloc.toFile();
-        tempInputStatus.getParentFile().mkdirs();
-        try (FileWriter writer = new FileWriter(tempInputStatus)) {
-
-            // Fill JobStatisticsTestInputstatus.txt with text. We have one JobStatus:
-            // completed, two JobStatus: completing, etc.
-            for (int i = 0; i < 1; i++) {
-                writer.write("JobStatus: completed\n");
-            }
-
-            for (int i = 0; i < 2; i++) {
-                writer.write("JobStatus: completing\n");
-            }
-
-            for (int i = 0; i < 3; i++) {
-                writer.write("JobStatus: failed\n");
-            }
-
-            for (int i = 0; i < 4; i++) {
-                writer.write("JobStatus: pending\n");
-            }
-
-            for (int i = 0; i < 5; i++) {
-                writer.write("JobStatus: preempted\n");
-            }
-
-            for (int i = 0; i < 6; i++) {
-                writer.write("JobStatus: running\n");
-            }
-
-            for (int i = 0; i < 7; i++) {
-                writer.write("JobStatus: suspended\n");
-            }
-
-            for (int i = 0; i < 8; i++) {
-                writer.write("JobStatus: stopped\n");
-            }
-
-            for (int i = 0; i < 9; i++) {
-                writer.write("JobStatus: error termination\n");
-            }
-
-            for (int i = 0; i < 10; i++) {
-                writer.write("JobStatus: not started\n");
-            }
-        }
-    }
-
-    @Test
-    @DisplayName("Testing calculateStatistics")
-    void calculateStatistics() throws IOException, URISyntaxException {
-        // Call JobstatisticsTestInputstatus.txt, which was created by generatefile().
-        // This file will be deleted at the end of the unit test.
-        File tempInputStatus = fileloc.toFile();
-        File input = tempInputStatus.getParentFile();
-
-        // Create new object And feed JobStatisticsTestInputstatus.txt as the input. The
-        // file has 1 job completed, 2 jobs completing, etc, hence all of the
-        // assertEquals must be true for the test to be successful
-        JobStatistics result = new JobStatistics(input);
-        result.calculateStatistics(fileloc.toString());
-
-        assertEquals(1, result.getJobsCompleted());
-        assertEquals(2, result.getJobsCompleting());
-        assertEquals(3, result.getJobsFailed());
-        assertEquals(4, result.getJobsPending());
-        assertEquals(5, result.getJobsPreempted());
-        assertEquals(6, result.getJobsRunning());
-        assertEquals(7, result.getJobsSuspended());
-        assertEquals(8, result.getJobsStopped());
-        assertEquals(9, result.getJobsErrorTerminated());
-        assertEquals(10, result.getJobsNotStarted());
-    }
-
-    @Test
-    @DisplayName("Testing JobStatistics")
-    void JobStatistics() throws IOException {
-
-        File tempInputStatus = fileloc.toFile();
-        File input = tempInputStatus.getParentFile().getParentFile();
-
-        JobStatistics result = new JobStatistics(input);
-        // There are 55 jobs total (= 1 + 2 + 3 + 4 + ... + 10). 1 completed, 2
-        // completing, 3 failed, 4 pending, etc. getJobsSubmitted should therefore
-        // return 55.
-        assertEquals(55, result.getJobsSubmitted());
-    }
-}
\ No newline at end of file
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/PostProcessingTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/PostProcessingTest.java
deleted file mode 100644
index 6278e1680..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/PostProcessingTest.java
+++ /dev/null
@@ -1,59 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-
-import org.apache.commons.io.FileUtils;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-
-class PostProcessingTest {
-    private Path tempDir;
-
-    @BeforeEach
-    void createTempDir() throws IOException {
-        // This directory will be deleted at the end of each test.
-        tempDir = Files.createTempDirectory("PostProcessingTest");
-    }
-
-    @AfterEach
-    void deleteTempDir() throws IOException {
-        if (null != tempDir) {
-            FileUtils.forceDelete(tempDir.toFile());
-        }
-    }
-
-    @Test
-    void testupdateJobOutputStatus() throws IOException {
-        // Create the status.txt file.
-        Path tempStatusFile = tempDir.resolve("jobDir").resolve("status.txt");
-        Files.createDirectories(tempStatusFile.getParent());
-        Files.write(tempStatusFile, "JobOutput: processed".getBytes());
-
-        // Not a valid job folder as not "status.txt" file.
-        File falseDir = tempDir.toFile();
-        assertFalse(PostProcessing.updateJobOutputStatus(falseDir));
-        // "status.txt" file should be detected.
-        File trueDir = tempStatusFile.toFile().getParentFile();
-        assertTrue(PostProcessing.updateJobOutputStatus(trueDir));
-    }
-
-    @Test
-    void testmodifyOutputStatus() throws IOException {
-        // Create the status.txt file.
-        Path tempStatusFile = tempDir.resolve("jobDir").resolve("status.txt");
-        Files.createDirectories(tempStatusFile.getParent());
-        Files.write(tempStatusFile, "JobOutput: processed".getBytes());
-
-        String status = "Try!!";
-        PostProcessing.modifyOutputStatus(tempStatusFile.toString(), status);
-        Files.readAllLines(tempStatusFile).forEach(line -> assertEquals("JobOutput: " + status, line));
-    }
-}
\ No newline at end of file
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/PropertyTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/PropertyTest.java
deleted file mode 100644
index 442a1a232..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/PropertyTest.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-import junit.framework.TestCase;
-
-public class PropertyTest extends TestCase{
-
-	// test getPropertyName
-	public void testgetPropertyName() {
-		String userhome = System.getProperty("user.home");
-		
-		assertEquals(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(), userhome);
-		assertEquals(Property.CHK_POINT_FILE_EXTENSION.getPropertyName(),".chk");
-		assertEquals(Property.STATUS_FILE_NAME.getPropertyName(),"status.txt");
-		assertEquals(Property.JSON_INPUT_FILE_NAME.getPropertyName(),"input.json");
-		assertEquals(Property.SLURM_SCRIPT_FILE_NAME.getPropertyName(),"Slurm.sh");
-	}
-	
-	// test getValue
-	public void testgetValue() {
-		assertEquals(Property.JOB_WORKSPACE_PARENT_DIR.getValue(), 0);
-		assertEquals(Property.CHK_POINT_FILE_EXTENSION.getValue(), 0);
-		assertEquals(Property.STATUS_FILE_NAME.getValue(),0);
-		assertEquals(Property.JSON_INPUT_FILE_NAME.getValue(), 0);
-		assertEquals(Property.SLURM_SCRIPT_FILE_NAME.getValue(), 0);
-	}
-	
-}
\ No newline at end of file
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobExceptionTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobExceptionTest.java
deleted file mode 100644
index a87f39b54..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobExceptionTest.java
+++ /dev/null
@@ -1,76 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
-
-import org.junit.jupiter.api.Test;
-
-public class SlurmJobExceptionTest {
-
-	// Create arbitrary Throwable cause (ArithmeticException: / by zero)
-	public Throwable createExceptionCause(int a, int b) {
-		try {
-			int c = a / b;
-		} catch (ArithmeticException e) {
-			return e;
-		}
-		return null;
-	}
-
-	// Set arbitrary inputs
-	String message = "test message";
-	Throwable cause = createExceptionCause(1, 0);
-	boolean enableSuppression = false;
-	boolean writableStackTrace = false;
-	
-	@Test
-	// Test SlurmJobException() should give same results as Exception()
-	public void testSlurmJobException_None() {
-		SlurmJobException testNone = new SlurmJobException();
-		Exception expectedNone = new Exception();
-		assertEquals(expectedNone.getMessage(), testNone.getMessage());
-	}
-	
-	@Test
-	// Test SlurmJobException(message) should give same results as Exception(message)
-	public void testSlurmJobException_Message() {
-		SlurmJobException testMessage = new SlurmJobException(message);
-		Exception expectedMessage = new Exception(message);
-		assertEquals(expectedMessage.getMessage(), testMessage.getMessage());
-	}
-	
-	@Test
-	// Test SlurmJobException(message, cause) should give same results as Exception(message, cause)
-	public void testSlurmJobException_MessageandCause() {
-		SlurmJobException testMessageandCause = new SlurmJobException(message, cause);
-		Exception expectedMessageandCause = new Exception(message, cause);
-		assertEquals(expectedMessageandCause.getMessage(), testMessageandCause.getMessage());
-		assertEquals(expectedMessageandCause.getCause(), testMessageandCause.getCause());
-	}
-	
-	@Test
-	// Test SlurmJobException(cause) should give same results as Exception(cause)
-	public void testSlurmJobException_Cause() {
-		SlurmJobException testCause = new SlurmJobException(cause);
-		Exception expectedCause = new Exception(cause);
-		assertEquals(expectedCause.getCause(), testCause.getCause());
-	}
-	
-	@Test
-	// Test SlurmJobException(message, cause, enableSuppression, writableStackTrace)
-	public void testAll() throws NoSuchMethodException, IllegalAccessException, InvocationTargetException, InstantiationException {
-		Constructor<SlurmJobException> constrct = SlurmJobException.class.getDeclaredConstructor(String.class, Throwable.class, boolean.class, boolean.class);
-		constrct.setAccessible(true);
-		SlurmJobException testAll = constrct.newInstance(message, cause, enableSuppression, writableStackTrace);
-		
-		assertEquals("test message", testAll.getMessage());
-		assertEquals(cause, testAll.getCause());
-
-		// enableSuppression and writableStackTrace are false, should return zero length array
-		assertEquals(0, testAll.getSuppressed().length);
-		assertEquals(0, testAll.getStackTrace().length);
-	}
-
-}
\ No newline at end of file
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobTest.java
deleted file mode 100644
index 29df87f8f..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/SlurmJobTest.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import org.junit.Assert;
-import org.junit.Test;
-import org.mockito.MockedStatic;
-import org.mockito.Mockito;
-
-public class SlurmJobTest {
-	
-	SlurmJob test = new SlurmJob();
-	
-	//Test setJobFolderName() and getJobFolderName()
-	@Test
-	public void testSetJobFolderName() {
-		test.setJobFolderName("Example_One");
-		Assert.assertEquals("Example_One", test.getJobFolderName());
-	}
-
-	//Test getNewJobFolderName()
-	@Test
-	public void testGetNewJobFolderName() {
-		String folderName = "Example_Two_1234567";
-		try (MockedStatic<Utils> theMock = Mockito.mockStatic(Utils.class)) {
-			theMock.when(Utils::getTimeStamp).thenReturn(1234567L);
-			Assert.assertEquals(folderName, test.getNewJobFolderName("Example_Two"));
-		}
-		//Assert.assertEquals("Example_Two_".concat("" + Utils.getTimeStamp()), test.getNewJobFolderName("Example_Two"));
-	}
-}
-
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/StatusTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/StatusTest.java
deleted file mode 100644
index dc6b826ca..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/StatusTest.java
+++ /dev/null
@@ -1,49 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import junit.framework.TestCase;
-
-public class StatusTest extends TestCase{
-	
-	
-	public void testStatus() {
-		
-		
-		assertEquals(Status.STATUS_FILE.getName(),"status.txt");
-		assertEquals(Status.ATTRIBUTE_JOB_STATUS.getName(),"JobStatus:");
-		assertEquals(Status.STATUS_JOB_NOT_STARTED.getName(),"not started");
-		assertEquals(Status.STATUS_JOB_COMPLETED.getName(),"completed");
-		assertEquals(Status.STATUS_JOB_COMPLETING.getName(),"completing");
-		assertEquals(Status.STATUS_JOB_FAILED.getName(),"failed");
-		assertEquals(Status.STATUS_JOB_PENDING.getName(),"pending");
-		assertEquals(Status.STATUS_JOB_PREEMPTED.getName(),"preempted");
-		assertEquals(Status.STATUS_JOB_RUNNING.getName(),"running");
-		assertEquals(Status.STATUS_JOB_SUSPENDED.getName(),"suspended");
-		assertEquals(Status.STATUS_JOB_STOPPED.getName(),"stopped");
-		assertEquals(Status.STATUS_JOB_ERROR_TERMINATED.getName(),"error termination");
-		assertEquals(Status.ATTRIBUTE_JOB_ID.getName(),"JobId:");
-		assertEquals(Status.ATTRIBUTE_AGENT_ID.getName(),"AgentId:");
-		assertEquals(Status.ATTRIBUTE_HPC_ADDRESS.getName(),"HPCAddress:");
-		assertEquals(Status.ATTRIBUTE_JOB_OUTPUT.getName(),"JobOutput:");
-		assertEquals(Status.OUTPUT_PROCESSED.getName(),"processed");
-		assertEquals(Status.EXTENSION_SLURM_FILE.getName(),".sh");
-		assertEquals(Status.EXTENSION_LOG_FILE.getName(),".log");
-		assertEquals(Status.EXTENSION_JSON_FILE.getName(),".json");
-		assertEquals(Status.JOB_SETUP_SUCCESS_MSG.getName(),"The job request has been processed successfully.");
-		assertEquals(Status.JOB_SETUP_JSON_ERROR.getName(),"The JSON request is ill formatted.");
-		assertEquals(Status.JOB_SETUP_SLURM_SCRIPT_ERROR.getName(),"The Slurm script could not be downloaded.");
-		assertEquals(Status.JOB_SETUP_INPUT_FILE_ERROR.getName(),"The input file for the job could not be created.");
-		assertEquals(Status.JOB_SETUP_ERROR.getName(),"The requested job could not be set up, therefore, resubmit the job.");
-		assertEquals(Status.JOB_LOG_MSG_ERROR_TERMINATION.getName(),"error termination");
-		assertEquals(Status.JOB_LOG_MSG_NORMAL_TERMINATION.getName(),"normal termination");
-		assertEquals(Status.JOB_OUTPUT_FILE_EXIST_MESSAGE.getName(),"The file exist.");
-		assertEquals(Status.JOB_SQUEUE_STATUS_COMPLETED.getName(),"CD");
-		assertEquals(Status.JOB_SQUEUE_STATUS_COMPLETING.getName(),"CG");
-		assertEquals(Status.JOB_SQUEUE_STATUS_FAILED.getName(),"F");
-		assertEquals(Status.JOB_SQUEUE_STATUS_PENDING.getName(),"PD");
-		assertEquals(Status.JOB_SQUEUE_STATUS_PREEMPTED.getName(),"PR");
-		assertEquals(Status.JOB_SQUEUE_STATUS_RUNNING.getName(),"R");
-		assertEquals(Status.JOB_SQUEUE_STATUS_SUSPENDED.getName(),"S");
-		assertEquals(Status.JOB_SQUEUE_STATUS_STOPPED.getName(),"ST");
-	}
-
-}
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/UtilsTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/UtilsTest.java
deleted file mode 100644
index 91d924090..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/UtilsTest.java
+++ /dev/null
@@ -1,986 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertNotEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.lang.reflect.Field;
-import java.net.InetAddress;
-import java.net.UnknownHostException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.List;
-import java.util.stream.Stream;
-
-import org.apache.commons.io.FileUtils;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-
-import uk.ac.cam.cares.jps.base.slurm.job.configuration.SlurmJobProperty;
-
-class UtilsTest {
-
-	private static final String TEST_TEXT = "Lorem ipsum dolor sit amet\nconsectetur adipisci elit,\nsed eiusmod tempor incidunt\n minim veniam, quis nostrum exercitationem ullam corporis suscipit\n";
-	private Path TEMP_DIR;
-
-	@BeforeEach
-	void createFolder() throws IOException {
-		TEMP_DIR = Files.createTempDirectory("UtilsTest");
-	}
-
-	@AfterEach
-	void cleanUp() throws IOException {
-		try (Stream<Path> pathTree = Files.walk(TEMP_DIR)) {
-			pathTree.sorted(Comparator.reverseOrder())
-					.map(Path::toFile)
-					.forEach(File::delete);
-		}
-	}
-
-	@Test
-	void getTimeStampTest() {
-		assertNotEquals(Utils.getTimeStamp(), Utils.getTimeStamp());
-	}
-
-	@Test
-	void openBufferedWriterTest() throws IOException {
-
-		File tempfile = File.createTempFile("test_file", ".txt", TEMP_DIR.toFile());
-
-		try (BufferedWriter bw = Utils.openBufferedWriter(tempfile.getAbsolutePath())) {
-			assertNotNull(bw);
-		} finally {
-			Files.deleteIfExists(tempfile.toPath());
-		}
-	}
-
-	@Test
-	void openSourceFileTest() throws IOException {
-		File tempfile = File.createTempFile("test_file", ".txt", TEMP_DIR.toFile());
-
-		try (BufferedReader br = Utils.openSourceFile(tempfile.getAbsolutePath())) {
-			assertNotNull(br);
-		} finally {
-			Files.deleteIfExists(tempfile.toPath());
-		}
-
-	}
-
-	@Test
-	void isJobCompletedOneTest() throws IOException {
-
-		Path jobFolder = TEMP_DIR.resolve("login-skylake.hpc.cam.ac.uk_110761971919363");
-		Files.createDirectories(jobFolder);
-		Path statusFile = jobFolder.resolve(Status.STATUS_FILE.getName());
-
-		// prepare status file for JobStatus:completed
-		Files.write(statusFile,
-				(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_COMPLETED.getName()).getBytes());
-		// test
-		assertTrue(Utils.isJobCompleted(jobFolder.toFile()));
-		Files.delete(statusFile);
-
-		// prepare status file for JobStatus:error termination
-		Files.write(statusFile,
-				(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_ERROR_TERMINATED.getName()).getBytes());
-		// test
-		assertTrue(Utils.isJobCompleted(jobFolder.toFile()));
-		Files.delete(statusFile);
-
-		// prepare status file for fail
-		Files.write(statusFile, " ".getBytes());
-		// test
-		assertFalse(Utils.isJobCompleted(jobFolder.toFile()));
-		Files.delete(statusFile);
-	}
-
-	@Test
-	public void isJobCompletedTwoTest() throws IOException {
-
-		SlurmJobProperty slurmJobProperty = new SlurmJobProperty();
-		slurmJobProperty.setAgentClass("UnitTestAgent");
-		slurmJobProperty.setAgentCompletedJobsSpacePrefix("CompletedJobs");
-		slurmJobProperty.setAgentFailedJobsSpacePrefix("FailedJobs");
-
-		File taskspace = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(),
-				slurmJobProperty.getAgentClass());
-		Path jobFolder_path = taskspace.toPath().resolve("login-skylake.hpc.cam.ac.uk_110761971919363");
-		Path status_path = jobFolder_path.resolve(Status.STATUS_FILE.getName());
-
-		// JobStatus:completed and JobOutput:processed
-		Files.createDirectories(jobFolder_path);
-
-		Files.write(status_path, (Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_COMPLETED.getName() + "\n"
-				+ Status.ATTRIBUTE_JOB_OUTPUT.getName() + Status.OUTPUT_PROCESSED.getName()).getBytes());
-		File jobFolder = jobFolder_path.toFile();
-		String[] src1 = jobFolder.list();
-		File completedJobsDir = Paths.get(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(),
-				slurmJobProperty.getAgentCompletedJobsSpacePrefix() + taskspace.getName(),
-				jobFolder.getName())
-				.toFile();
-
-		assertTrue(Utils.isJobCompleted(jobFolder, slurmJobProperty));
-		assertTrue(completedJobsDir.isDirectory());
-		List<String> completedFiles = Arrays.asList(completedJobsDir.list());
-		for (String file : src1) {
-			assertTrue(completedFiles.contains(file));
-		}
-		assertFalse(jobFolder.exists());
-
-		// JobStatus:completed
-		Files.createDirectories(jobFolder_path);
-		Files.write(status_path,
-				(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_COMPLETED.getName() + "\n").getBytes());
-
-		assertTrue(Utils.isJobCompleted(jobFolder, slurmJobProperty));
-		Files.delete(status_path);
-
-		// JobStatus: error termination
-		Files.write(status_path,
-				(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_ERROR_TERMINATED.getName()).getBytes());
-		String[] src2 = jobFolder.list();
-
-		File FailedJobsDir = Paths.get(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(),
-				slurmJobProperty.getAgentFailedJobsSpacePrefix() + taskspace.getName(),
-				jobFolder.getName())
-				.toFile();
-
-		assertTrue(Utils.isJobCompleted(jobFolder, slurmJobProperty));
-		assertTrue(FailedJobsDir.isDirectory());
-		List<String> failedFiles = Arrays.asList(FailedJobsDir.list());
-		for (String file : src2) {
-			assertTrue(failedFiles.contains(file));
-		}
-		assertFalse(jobFolder.exists());
-
-		// false scenario
-		Files.createDirectories(jobFolder_path);
-		Files.write(status_path, " ".getBytes());
-		assertFalse(Utils.isJobCompleted(jobFolder, slurmJobProperty));
-
-		FileUtils.forceDelete(taskspace);
-		FileUtils.forceDelete(completedJobsDir.getParentFile());
-		FileUtils.forceDelete(FailedJobsDir.getParentFile());
-	}
-
-	@Test
-	void isJobErroneouslyCompletedOneTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for Jobstatus:error termination
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_ERROR_TERMINATED.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobErroneouslyCompleted(jobFolder));
-		statusfile1.delete();
-
-		// prepare status file for fail
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(" ");
-		bw2.close();
-		// test
-		assertFalse(Utils.isJobErroneouslyCompleted(jobFolder));
-
-		FileUtils.forceDelete(taskspace);
-
-	}
-
-	@Test
-	void isJobErroneouslyCompletedTwoTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for Jobstatus:error termination
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_ERROR_TERMINATED.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobErroneouslyCompleted(status_path));
-		statusfile1.delete();
-
-		// prepare status file for fail
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(" ");
-		bw2.close();
-		// test
-		assertFalse(Utils.isJobErroneouslyCompleted(status_path));
-
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void isJobRunningOneTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for JobStatus:running
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_RUNNING.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobRunning(jobFolder));
-		statusfile1.delete();
-
-		// prepare status file for JobStatus:completing
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_COMPLETING.getName());
-		bw2.close();
-		// test
-		assertTrue(Utils.isJobRunning(jobFolder));
-		statusfile2.delete();
-
-		// prepare status file for JobStatus:pending
-		File statusfile3 = new File(status_path);
-		BufferedWriter bw3 = new BufferedWriter(new FileWriter(statusfile3));
-		bw3.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_PENDING.getName());
-		bw3.close();
-		// test
-		assertTrue(Utils.isJobRunning(jobFolder));
-		statusfile3.delete();
-
-		// prepare status file for fail
-		File statusfile4 = new File(status_path);
-		BufferedWriter bw4 = new BufferedWriter(new FileWriter(statusfile4));
-		bw4.write(" ");
-		bw4.close();
-		// test
-		assertFalse(Utils.isJobRunning(jobFolder));
-
-		FileUtils.forceDelete(taskspace);
-
-	}
-
-	@Test
-	void isJobRunningTwoTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for JobStatus:running
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_RUNNING.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobRunning(status_path));
-		statusfile1.delete();
-
-		// prepare status file for JobStatus:completing
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_COMPLETING.getName());
-		bw2.close();
-		// test
-		assertTrue(Utils.isJobRunning(status_path));
-		statusfile2.delete();
-
-		// prepare status file for JobStatus:pending
-		File statusfile3 = new File(status_path);
-		BufferedWriter bw3 = new BufferedWriter(new FileWriter(statusfile3));
-		bw3.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_PENDING.getName());
-		bw3.close();
-		// test
-		assertTrue(Utils.isJobRunning(status_path));
-		statusfile3.delete();
-
-		// prepare status file for fail
-		File statusfile4 = new File(status_path);
-		BufferedWriter bw4 = new BufferedWriter(new FileWriter(statusfile4));
-		bw4.write(" ");
-		bw4.close();
-		// test
-		assertFalse(Utils.isJobRunning(status_path));
-
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void isJobNotStartedOneTest() throws IOException, NoSuchFieldException, IllegalAccessException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for JobStatus:not started
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_NOT_STARTED.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobNotStarted(jobFolder));
-		statusfile1.delete();
-
-		// False scenario - 1
-		Utils utils = new Utils();
-		Field isStatusFileOpen = utils.getClass().getDeclaredField("isStatusFileOpen");
-		isStatusFileOpen.setAccessible(true);
-		isStatusFileOpen.setBoolean(isStatusFileOpen, true);
-		assertFalse(Utils.isJobNotStarted(jobFolder));
-		isStatusFileOpen.setBoolean(isStatusFileOpen, false);
-
-		// False scenario - 2
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(" ");
-		bw2.close();
-		// test
-		assertFalse(Utils.isJobNotStarted(jobFolder));
-
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void isJobNotStartedTwoTest() throws IOException, NoSuchFieldException, IllegalAccessException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for JobStatus:not started
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_NOT_STARTED.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobNotStarted(status_path));
-		statusfile1.delete();
-
-		// False scenario 1
-		Utils utils = new Utils();
-		Field isStatusFileOpen = utils.getClass().getDeclaredField("isStatusFileOpen");
-		isStatusFileOpen.setAccessible(true);
-		isStatusFileOpen.setBoolean(isStatusFileOpen, true);
-		assertFalse(Utils.isJobNotStarted(status_path));
-		isStatusFileOpen.setBoolean(isStatusFileOpen, false);
-
-		// False scenario 2
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(" ");
-		bw2.close();
-		// test
-		assertFalse(Utils.isJobNotStarted(status_path));
-
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void isJobFinishedOneTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for JobStatus:completed
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_COMPLETED.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobFinished(jobFolder, status_path));
-		statusfile1.delete();
-
-		// prepare status file for JobStatus:error termination
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_ERROR_TERMINATED.getName());
-		bw2.close();
-		// test
-		assertTrue(Utils.isJobFinished(jobFolder, status_path));
-		statusfile2.delete();
-
-		// prepare status file for fail
-		File statusfile3 = new File(status_path);
-		BufferedWriter bw3 = new BufferedWriter(new FileWriter(statusfile3));
-		bw3.write(" ");
-		bw3.close();
-		// test
-		assertFalse(Utils.isJobFinished(jobFolder, status_path));
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void isJobFinishedTwoTest() throws IOException {
-
-		SlurmJobProperty slurmJobProperty = new SlurmJobProperty();
-		slurmJobProperty.setAgentClass("UnitTestAgent");
-		slurmJobProperty.setAgentCompletedJobsSpacePrefix("CompletedJobs");
-		slurmJobProperty.setAgentFailedJobsSpacePrefix("FailedJobs");
-
-		File taskspace = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(),
-				slurmJobProperty.getAgentClass());
-		;
-		String jobFolder_path = taskspace.getAbsolutePath() + File.separator
-				+ "login-skylake.hpc.cam.ac.uk_110761971919363";
-		String status_path = jobFolder_path + File.separator + Status.STATUS_FILE.getName();
-
-		// JobStatus:completed and JobOutput:processed
-		File jobFolder1 = new File(jobFolder_path);
-		jobFolder1.mkdirs();
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_COMPLETED.getName() + "\n"
-				+ Status.ATTRIBUTE_JOB_OUTPUT.getName() + Status.OUTPUT_PROCESSED.getName());
-		bw1.close();
-		String[] src1 = jobFolder1.list();
-
-		File completedJobsDir_parent = new File(
-				Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName().concat(File.separator)
-						.concat(slurmJobProperty.getAgentCompletedJobsSpacePrefix()).concat(taskspace.getName()));
-		File completedJobsDir = new File(completedJobsDir_parent + File.separator + jobFolder1.getName());
-
-		assertTrue(Utils.isJobFinished(jobFolder1, status_path, slurmJobProperty));
-		assertTrue(completedJobsDir.isDirectory());
-		for (String file : src1) {
-			assertTrue(Arrays.asList(completedJobsDir.list()).contains(file));
-		}
-		assertFalse(jobFolder1.exists());
-
-		// JobStatus:completed
-		File jobFolder2 = new File(jobFolder_path);
-		jobFolder2.mkdirs();
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_COMPLETED.getName() + "\n");
-		bw2.close();
-
-		assertTrue(Utils.isJobFinished(jobFolder2, status_path, slurmJobProperty));
-		statusfile2.delete();
-
-		// JobStatus: error termination
-		File statusfile3 = new File(status_path);
-		BufferedWriter bw3 = new BufferedWriter(new FileWriter(statusfile3));
-		bw3.write(Status.ATTRIBUTE_JOB_STATUS.getName() + Status.STATUS_JOB_ERROR_TERMINATED.getName());
-		bw3.close();
-		String[] src2 = jobFolder2.list();
-
-		File FailedJobsDir_parent = new File(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName().concat(File.separator)
-				.concat(slurmJobProperty.getAgentFailedJobsSpacePrefix()).concat(taskspace.getName()));
-		File FailedJobsDir = new File(FailedJobsDir_parent + File.separator + jobFolder2.getName());
-
-		assertTrue(Utils.isJobFinished(jobFolder2, status_path, slurmJobProperty));
-		assertTrue(FailedJobsDir.isDirectory());
-		for (String file : src2) {
-			assertTrue(Arrays.asList(FailedJobsDir.list()).contains(file));
-		}
-		assertFalse(jobFolder2.exists());
-
-		// false scenario
-		File jobFolder3 = new File(jobFolder_path);
-		jobFolder3.mkdirs();
-		File statusfile4 = new File(status_path);
-		BufferedWriter bw4 = new BufferedWriter(new FileWriter(statusfile4));
-		bw4.write(" ");
-		bw4.close();
-		assertFalse(Utils.isJobFinished(jobFolder3, status_path, slurmJobProperty));
-
-		FileUtils.forceDelete(taskspace);
-		FileUtils.forceDelete(completedJobsDir_parent);
-		FileUtils.forceDelete(FailedJobsDir_parent);
-
-	}
-
-	@Test
-	void isJobPostProcessedTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for Jobstatus:error termination
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_OUTPUT.getName() + Status.OUTPUT_PROCESSED.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobPostProcessed(jobFolder, status_path));
-		statusfile1.delete();
-
-		// prepare status file for fail
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(" ");
-		bw2.close();
-		// test
-		assertFalse(Utils.isJobPostProcessed(jobFolder, status_path));
-
-		FileUtils.forceDelete(taskspace);
-
-	}
-
-	@Test
-	void isJobOutputProcessedOneTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for JobOutput:processed
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_OUTPUT.getName() + Status.OUTPUT_PROCESSED.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobOutputProcessed(jobFolder));
-		statusfile1.delete();
-
-		// prepare status file for fail
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(" ");
-		bw2.close();
-		// test
-		assertFalse(Utils.isJobOutputProcessed(jobFolder));
-
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void isJobOutputProcessedTwoTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		// prepare status file for JobOutput:processed
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_OUTPUT.getName() + Status.OUTPUT_PROCESSED.getName());
-		bw1.close();
-		// test
-		assertTrue(Utils.isJobOutputProcessed(status_path));
-		statusfile1.delete();
-
-		// prepare status file for fail
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(" ");
-		bw2.close();
-		// test
-		assertFalse(Utils.isJobOutputProcessed(status_path));
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void getJobIdTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-		String tmpstr = Status.ATTRIBUTE_JOB_ID.getName() + " 28082086";
-
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(tmpstr);
-		bw1.close();
-
-		String tmpid = null;
-		// extract job id
-		String tokens[] = tmpstr.trim().toLowerCase().split(":");
-		if (tokens.length >= 2 && tokens[1].trim().length() > 0)
-			tmpid = tokens[1].trim();
-
-		assertEquals(tmpid, Utils.getJobId(status_path));
-		statusfile1.delete();
-
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(Status.ATTRIBUTE_JOB_ID.getName());
-		bw2.close();
-
-		assertNull(Utils.getJobId(status_path));
-
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void addJobIdTest() throws IOException {
-
-		Path taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609");
-		File jobFolder = taskspace.resolve("login-skylake.hpc.cam.ac.uk_110761971919363").toFile();
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-		String jobid = "28082086";
-
-		// prepare status file for addobId method with JobStatus and JobId
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + "\n" + Status.ATTRIBUTE_JOB_ID.getName());
-		bw1.close();
-
-		Utils.addJobId(status_path, jobid);
-
-		// test contents of status file
-		BufferedReader br1 = new BufferedReader(new InputStreamReader(new FileInputStream(status_path), "UTF-8"));
-		String line;
-		while ((line = br1.readLine()) != null) {
-			if (line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName()))
-				assertEquals(Status.ATTRIBUTE_JOB_STATUS.getName() + " " + Status.STATUS_JOB_RUNNING.getName(), line);
-			if (line.trim().startsWith(Status.ATTRIBUTE_JOB_ID.getName()))
-				assertEquals(Status.ATTRIBUTE_JOB_ID.getName() + " " + jobid, line);
-
-		}
-		br1.close();
-		statusfile1.delete();
-
-		// prepare status file for addobId method with only JobId
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(Status.ATTRIBUTE_JOB_ID.getName());
-		bw2.close();
-
-		Utils.addJobId(status_path, jobid);
-
-		// test contents of status file
-		BufferedReader br2 = new BufferedReader(new InputStreamReader(new FileInputStream(status_path), "UTF-8"));
-		while ((line = br2.readLine()) != null) {
-			if (line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName()))
-				assertEquals(Status.ATTRIBUTE_JOB_STATUS.getName() + " " + Status.STATUS_JOB_RUNNING.getName(), line);
-			if (line.trim().startsWith(Status.ATTRIBUTE_JOB_ID.getName()))
-				assertEquals(Status.ATTRIBUTE_JOB_ID.getName() + " " + jobid, line);
-		}
-		br2.close();
-		statusfile2.delete();
-
-		// prepare status file for addobId method without anything
-		File statusfile3 = new File(status_path);
-		BufferedWriter bw3 = new BufferedWriter(new FileWriter(statusfile3));
-		bw3.close();
-
-		Utils.addJobId(status_path, jobid);
-
-		// test contents of status file
-		BufferedReader br3 = new BufferedReader(new InputStreamReader(new FileInputStream(status_path), "UTF-8"));
-		while ((line = br3.readLine()) != null) {
-			if (line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName()))
-				assertEquals(Status.ATTRIBUTE_JOB_STATUS.getName() + " " + Status.STATUS_JOB_RUNNING.getName(), line);
-			if (line.trim().startsWith(Status.ATTRIBUTE_JOB_ID.getName()))
-				assertEquals(Status.ATTRIBUTE_JOB_ID.getName() + " " + jobid, line);
-		}
-		br3.close();
-	}
-
-	@Test
-	void modifyStatusTest() throws IOException {
-
-		Path taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609");
-		File jobFolder = taskspace.resolve("login-skylake.hpc.cam.ac.uk_110761971919363").toFile();
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-		String status1 = Status.STATUS_JOB_RUNNING.getName();
-		String status2 = Status.STATUS_JOB_COMPLETED.getName();
-
-		// test for modifyStatus completed -> running
-		File statusfile1 = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile1));
-		bw1.write(Status.ATTRIBUTE_JOB_STATUS.getName() + status2 + "\n");
-		bw1.close();
-
-		Utils.modifyStatus(status_path, status1);
-
-		BufferedReader br1 = new BufferedReader(new InputStreamReader(new FileInputStream(status_path), "UTF-8"));
-		String line;
-		while ((line = br1.readLine()) != null) {
-			if (line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName()))
-				assertEquals(Status.ATTRIBUTE_JOB_STATUS.getName() + " " + status1, line);
-
-		}
-		br1.close();
-		statusfile1.delete();
-
-		// test for modifyStatus running -> completed
-		File statusfile2 = new File(status_path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(statusfile2));
-		bw2.write(Status.ATTRIBUTE_JOB_STATUS.getName() + status1 + "\n");
-		bw2.close();
-
-		Utils.modifyStatus(status_path, status2);
-
-		BufferedReader br2 = new BufferedReader(new InputStreamReader(new FileInputStream(status_path), "UTF-8"));
-		while ((line = br2.readLine()) != null) {
-			if (line.trim().startsWith(Status.ATTRIBUTE_JOB_STATUS.getName()))
-				assertEquals(Status.ATTRIBUTE_JOB_STATUS.getName() + " " + status2, line);
-
-		}
-		br2.close();
-	}
-
-	@Test
-	void getStatusFileTest() throws IOException {
-
-		Path taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609");
-		File jobFolder = taskspace.resolve("login-skylake.hpc.cam.ac.uk_110761971919363").toFile();
-		jobFolder.mkdirs();
-		File jobFolder_null = new File("");
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		File statusfile = new File(status_path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(statusfile));
-		bw1.close();
-		assertEquals(status_path, Utils.getStatusFile(jobFolder).getAbsolutePath());
-		assertNull(Utils.getStatusFile(jobFolder_null));
-	}
-
-	@Test
-	void getLogFilePathOnHPCTest() throws UnknownHostException {
-
-		String runningJob = "login-skylake.hpc.cam.ac.uk_110761971919363";
-		String userName = "hpcServerUserName";
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		String hpcAddress = "login-skylake.hpc.cam.ac.uk";
-		InetAddress address;
-		address = InetAddress.getLocalHost();
-		String MachineAddress = address.toString().replace("/", "_");
-
-		assertEquals("/home/".concat(userName).concat("/").concat(taskspace.getName()).concat("/")
-				.concat(runningJob.replace(hpcAddress, MachineAddress)).concat("/")
-				.concat(runningJob.replace(hpcAddress, MachineAddress)).concat(Status.EXTENSION_LOG_FILE.getName()),
-				Utils.getLogFilePathOnHPC(runningJob, userName, taskspace, hpcAddress));
-	}
-
-	@Test
-	void getOutputFilePathOnHPCTest() throws UnknownHostException {
-
-		String runningJob = "login-skylake.hpc.cam.ac.uk_110761971919363";
-		String userName = "hpcServerUserName";
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		String hpcAddress = "login-skylake.hpc.cam.ac.uk";
-		String outputFileNameWithExtension = "output.log";
-		InetAddress address;
-		address = InetAddress.getLocalHost();
-		String MachineAddress = address.toString().replace("/", "_");
-
-		assertEquals("/home/".concat(userName).concat("/").concat(taskspace.getName()).concat("/")
-				.concat(runningJob.replace(hpcAddress, MachineAddress)).concat("/").concat(outputFileNameWithExtension),
-				Utils.getOutputFilePathOnHPC(runningJob, userName, taskspace, hpcAddress,
-						outputFileNameWithExtension));
-	}
-
-	@Test
-	void getJobFolderPathOnHPCTest() throws UnknownHostException {
-		String runningJob = "login-skylake.hpc.cam.ac.uk_110761971919363";
-		String userName = "hpcServerUserName";
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		String hpcAddress = "login-skylake.hpc.cam.ac.uk";
-		InetAddress address;
-		address = InetAddress.getLocalHost();
-		String MachineAddress = address.toString().replace("/", "_");
-		assertEquals("/home/".concat(userName).concat("/").concat(taskspace.getName()).concat("/")
-				.concat(runningJob.replace(hpcAddress, MachineAddress)),
-				Utils.getJobFolderPathOnHPC(runningJob, userName, taskspace, hpcAddress));
-
-	}
-
-	@Test
-	void getJobOutputFilePathOnAgentPCTest() {
-
-		String runningJob = "login-skylake.hpc.cam.ac.uk_110761971919363";
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		String outputFileName = "output";
-		String outputFileExtension = ".log";
-		assertEquals(taskspace.getAbsolutePath().concat(File.separator).concat(runningJob).concat(File.separator)
-				.concat(outputFileName).concat(outputFileExtension),
-				Utils.getJobOutputFilePathOnAgentPC(runningJob, taskspace, outputFileName, outputFileExtension));
-	}
-
-	@Test
-	void isErrorTerminationTest() throws IOException {
-
-		File taskspace = TEMP_DIR.resolve("UnitTestAgent_435827288195609").toFile();
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String path = jobFolder.getAbsolutePath() + File.separator + "logFileOnAgentPC";
-
-		File logfile1 = new File(path);
-		BufferedWriter bw1 = new BufferedWriter(new FileWriter(logfile1));
-		bw1.write(Status.JOB_LOG_MSG_ERROR_TERMINATION.getName().toLowerCase());
-		bw1.close();
-		assertTrue(Utils.isErrorTermination(path));
-		logfile1.delete();
-
-		File logfile2 = new File(path);
-		BufferedWriter bw2 = new BufferedWriter(new FileWriter(logfile2));
-		bw2.write(" ");
-		bw2.close();
-		assertFalse(Utils.isErrorTermination(path));
-
-		FileUtils.forceDelete(taskspace);
-	}
-
-	@Test
-	void getMachineAddressTest() throws UnknownHostException {
-		InetAddress address;
-		address = InetAddress.getLocalHost();
-		String MachineAddress = address.toString().replace("/", "_");
-		assertEquals(MachineAddress, Utils.getMachineAddress());
-	}
-
-	@Test
-	void translateLineEndingIntoUnixTest() throws IOException {
-		Path src = TEMP_DIR.resolve("src.txt");
-		Path dest = TEMP_DIR.resolve("dest.txt");
-
-		Files.write(src, TEST_TEXT.replace("\n", "\r\n").getBytes());
-		Files.write(dest, TEST_TEXT.getBytes());
-
-		Utils.translateLineEndingIntoUnix(src.toFile());
-
-		assertTrue(FileUtils.contentEquals(dest.toFile(), src.toFile()));
-	}
-
-	@Test
-	void moveToCompletedJobsFolderTest() throws IOException {
-
-		SlurmJobProperty slurmJobProperty = new SlurmJobProperty();
-		slurmJobProperty.setAgentClass("UnitTestAgent");
-		slurmJobProperty.setAgentCompletedJobsSpacePrefix("CompletedJobs");
-		slurmJobProperty.setAgentFailedJobsSpacePrefix("FailedJobs");
-
-		File taskspace = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(),
-				slurmJobProperty.getAgentClass());
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		File statusfile = new File(status_path);
-		BufferedWriter bw = new BufferedWriter(new FileWriter(statusfile));
-		bw.write("XYZ");
-		bw.close();
-		String[] src = jobFolder.list();
-
-		File completedJobsDir_parent = new File(
-				Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName().concat(File.separator)
-						.concat(slurmJobProperty.getAgentCompletedJobsSpacePrefix()).concat(taskspace.getName()));
-		File completedJobsDir = new File(completedJobsDir_parent + File.separator + jobFolder.getName());
-
-		Utils.moveToCompletedJobsFolder(jobFolder, slurmJobProperty);
-		assertTrue(completedJobsDir.isDirectory());
-		for (String file : src) {
-			assertTrue(Arrays.asList(completedJobsDir.list()).contains(file));
-		}
-		assertFalse(jobFolder.exists());
-
-		FileUtils.forceDelete(taskspace);
-		FileUtils.forceDelete(completedJobsDir_parent);
-	}
-
-	@Test
-	void getCompletedJobsDirectoryTest() throws IOException {
-
-		SlurmJobProperty slurmJobProperty = new SlurmJobProperty();
-		slurmJobProperty.setAgentClass("UnitTestAgent");
-		slurmJobProperty.setAgentCompletedJobsSpacePrefix("CompletedJobs");
-		slurmJobProperty.setAgentFailedJobsSpacePrefix("FailedJobs");
-
-		File taskspace = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(),
-				slurmJobProperty.getAgentClass());
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		File completedJobsDir_parent = new File(
-				Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName().concat(File.separator)
-						.concat(slurmJobProperty.getAgentCompletedJobsSpacePrefix()).concat(taskspace.getName()));
-		File completedJobsDir = new File(completedJobsDir_parent + File.separator + jobFolder.getName());
-
-		assertEquals(completedJobsDir, Utils.getCompletedJobsDirectory(jobFolder, slurmJobProperty));
-		FileUtils.forceDelete(taskspace);
-		FileUtils.forceDelete(completedJobsDir_parent);
-	}
-
-	@Test
-	void moveToFailedJobsFolderTest() throws IOException {
-
-		SlurmJobProperty slurmJobProperty = new SlurmJobProperty();
-		slurmJobProperty.setAgentClass("UnitTestAgent");
-		slurmJobProperty.setAgentCompletedJobsSpacePrefix("CompletedJobs");
-		slurmJobProperty.setAgentFailedJobsSpacePrefix("FailedJobs");
-
-		File taskspace = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(),
-				slurmJobProperty.getAgentClass());
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		String status_path = jobFolder.getAbsolutePath() + File.separator + Status.STATUS_FILE.getName();
-
-		File statusfile = new File(status_path);
-		BufferedWriter bw = new BufferedWriter(new FileWriter(statusfile));
-		bw.write("XYZ");
-		bw.close();
-		String[] src = jobFolder.list();
-
-		File FailedJobsDir_parent = new File(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName().concat(File.separator)
-				.concat(slurmJobProperty.getAgentFailedJobsSpacePrefix()).concat(taskspace.getName()));
-		File FailedJobsDir = new File(FailedJobsDir_parent + File.separator + jobFolder.getName());
-
-		Utils.moveToFailedJobsFolder(jobFolder, slurmJobProperty);
-		assertTrue(FailedJobsDir.isDirectory());
-		for (String file : src) {
-			assertTrue(Arrays.asList(FailedJobsDir.list()).contains(file));
-		}
-		assertFalse(jobFolder.exists());
-
-		FileUtils.forceDelete(taskspace);
-		FileUtils.forceDelete(FailedJobsDir_parent);
-
-	}
-
-	@Test
-	void getFailedJobsDirectoryTest() throws IOException {
-
-		SlurmJobProperty slurmJobProperty = new SlurmJobProperty();
-		slurmJobProperty.setAgentClass("UnitTestAgent");
-		slurmJobProperty.setAgentCompletedJobsSpacePrefix("CompletedJobs");
-		slurmJobProperty.setAgentFailedJobsSpacePrefix("FailedJobs");
-
-		File taskspace = Workspace.getWorkspace(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName(),
-				slurmJobProperty.getAgentClass());
-		File jobFolder = new File(taskspace + File.separator + "login-skylake.hpc.cam.ac.uk_110761971919363");
-		jobFolder.mkdirs();
-		File FailedJobsDir_parent = new File(Property.JOB_WORKSPACE_PARENT_DIR.getPropertyName().concat(File.separator)
-				.concat(slurmJobProperty.getAgentFailedJobsSpacePrefix()).concat(taskspace.getName()));
-		File FailedJobsDir = new File(FailedJobsDir_parent + File.separator + jobFolder.getName());
-
-		assertEquals(FailedJobsDir, Utils.getFailedJobsDirectory(jobFolder, slurmJobProperty));
-		FileUtils.forceDelete(taskspace);
-		FileUtils.forceDelete(FailedJobsDir_parent);
-
-	}
-}
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/WorkspaceTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/WorkspaceTest.java
deleted file mode 100644
index 299d143b7..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/WorkspaceTest.java
+++ /dev/null
@@ -1,248 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.Comparator;
-import java.util.stream.Stream;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-
-class WorkspaceTest {
-
-	private static final String TEST_TEXT = "Lorem ipsum dolor sit amet\nconsectetur adipisci elit,\nsed eiusmod tempor incidunt\n minim veniam, quis nostrum exercitationem ullam corporis suscipit\n";
-	private Path TEMP_DIR;
-
-	@BeforeEach
-	void createFolder() throws IOException {
-		TEMP_DIR = Files.createTempDirectory("WorkspaceTest");
-	}
-
-	@AfterEach
-	void cleanUp() throws IOException {
-		try (Stream<Path> pathTree = Files.walk(TEMP_DIR)) {
-			pathTree.sorted(Comparator.reverseOrder())
-					.map(Path::toFile)
-					.forEach(File::delete);
-		}
-	}
-
-	@Test
-	void getExistingWorkspaceTest() throws IOException {
-		String agentClass = "UnitTestAgent";
-		Path workspace = TEMP_DIR.resolve(agentClass + "_" + System.nanoTime());
-		Files.createDirectories(workspace);
-
-		assertEquals(workspace.toAbsolutePath(),
-				Workspace.getWorkspace(TEMP_DIR.toString(), agentClass).toPath().toAbsolutePath());
-
-		Files.delete(workspace);
-	}
-
-	@Test
-	void getNewWorkspaceTest() throws IOException {
-		String agentClass = "UnitTestAgent";
-		assertEquals(TEMP_DIR.resolve(agentClass).toString(),
-				Workspace.getWorkspace(TEMP_DIR.toString(), agentClass).getAbsolutePath().split("_")[0]);
-	}
-
-	@Test
-	void isWorkspaceAvailableTestTwo()
-			throws IllegalAccessException, InvocationTargetException, NoSuchMethodException, IOException {
-
-		String agentClass = "UnitTestAgent";
-		Path ws = TEMP_DIR.resolve(agentClass + "_" + System.nanoTime());
-		Files.createDirectories(ws);
-
-		Workspace workspace = new Workspace();
-
-		assertTrue(workspace.isWorkspaceAvailable(TEMP_DIR.toFile(), agentClass));
-		Files.delete(ws);
-		assertFalse(workspace.isWorkspaceAvailable(TEMP_DIR.toFile(), agentClass));
-	}
-
-	@Test
-	void createJSONInputFileTest() throws IOException {
-
-		Path workspaceFolder = TEMP_DIR;
-		Path jsonInputFilePath = workspaceFolder.resolve("input.json").toAbsolutePath();
-		Path jsonInputFilePath_temp = workspaceFolder.resolve("input_temp.json").toAbsolutePath();
-		Workspace workspace = new Workspace();
-
-		Files.write(jsonInputFilePath_temp, TEST_TEXT.getBytes());
-
-		assertEquals(Status.JOB_SETUP_SUCCESS_MSG.getName(),
-				workspace.createJSONInputFile(workspaceFolder.toFile(), jsonInputFilePath.toString(), TEST_TEXT));
-		assertTrue(FileUtils.contentEquals(jsonInputFilePath.toFile(), jsonInputFilePath_temp.toFile()));
-	}
-
-	@Test
-	void getInputFilePathTest() throws IOException {
-
-		Path taskSpace = TEMP_DIR.resolve("UnitTestAgent_435827288195609");
-		Path jobFolder = taskSpace.resolve("login-skylake.hpc.cam.ac.uk_110761971919363");
-		Files.createDirectories(jobFolder);
-		String hpcAddress = "login-skylake.hpc.cam.ac.uk";
-		String inputFileExtension = ".com";
-		String[] tokens = jobFolder.getFileName().toString().split("_");
-		String timeStampPart = null;
-		if (tokens.length == 2 && tokens[1] != null && StringUtils.isNumeric(tokens[1]))
-			timeStampPart = tokens[1];
-		Workspace workspace = new Workspace();
-		assertEquals(
-				jobFolder.resolve(hpcAddress + "_" + timeStampPart + inputFileExtension).toAbsolutePath().toString(),
-				workspace.getInputFilePath(jobFolder.toFile(), hpcAddress, inputFileExtension));
-	}
-
-	@Test
-	void getInputFileExtension() throws SlurmJobException, IOException {
-
-		Path input = TEMP_DIR.resolve("input.csv");
-
-		Files.createFile(input);
-
-		Workspace workspace = new Workspace();
-
-		assertEquals(input.toString().substring(input.toString().lastIndexOf('.')),
-				workspace.getInputFileExtension(input.toFile()));
-	}
-
-	@Test
-	void createJobFolderTest() throws IOException {
-		Path workspacePath = TEMP_DIR;
-		String hpcAddress = "login-skylake.hpc.cam.ac.uk";
-		long timeStamp = System.nanoTime();
-		Workspace workspace = new Workspace();
-		Path jobFolder = workspacePath.resolve(hpcAddress + "_" + timeStamp);
-
-		assertEquals(jobFolder.toAbsolutePath(),
-				workspace.createJobFolder(workspacePath.toString(), hpcAddress, timeStamp).toPath().toAbsolutePath());
-		assertNull(workspace.createJobFolder(workspacePath.toString(), hpcAddress, timeStamp));
-	}
-
-	@Test
-	void createInputFileTest() throws IOException {
-
-		Path inputFileDestinationPath = TEMP_DIR.resolve("input_dest");
-		Path input = TEMP_DIR.resolve("input_src");
-		Workspace workspace = new Workspace();
-
-		Files.write(input, TEST_TEXT.getBytes());
-
-		assertEquals(Status.JOB_SETUP_SUCCESS_MSG.getName(),
-				workspace.createInputFile(inputFileDestinationPath.toString(), input.toFile()));
-		assertTrue(FileUtils.contentEquals(input.toFile(), inputFileDestinationPath.toFile()));
-	}
-
-	@Test
-	void createStatusFileTest() throws IOException {
-
-		Path workspaceFolder = TEMP_DIR;
-		Path statusFilePath = workspaceFolder.resolve(Status.STATUS_FILE.getName());
-		String hpcAddress = "login-skylake.hpc.cam.ac.uk";
-		Path tempFile = workspaceFolder.resolve("temp.txt");
-		Workspace workspace = new Workspace();
-
-		try (BufferedWriter bw = new BufferedWriter(new FileWriter(tempFile.toFile()))) {
-			bw.write(Status.ATTRIBUTE_JOB_STATUS.getName() + " ");
-			bw.write(Status.STATUS_JOB_NOT_STARTED.getName() + "\n");
-			bw.write(Status.ATTRIBUTE_JOB_ID.getName() + "\n");
-			bw.write(Status.ATTRIBUTE_AGENT_ID.getName() + " ");
-			bw.write(workspaceFolder.getFileName() + "\n");
-			bw.write(Status.ATTRIBUTE_HPC_ADDRESS.getName() + " ");
-			bw.write(hpcAddress + "\n");
-			bw.write(Status.ATTRIBUTE_JOB_OUTPUT.getName() + "\n");
-		}
-
-		assertEquals(Status.JOB_SETUP_SUCCESS_MSG.getName(),
-				workspace.createStatusFile(workspaceFolder.toFile(), statusFilePath.toString(), hpcAddress));
-		assertTrue(FileUtils.contentEquals(statusFilePath.toFile(), tempFile.toFile()));
-	}
-
-	@Test
-	void copyFileTestOne() throws IOException {
-
-		Path destination = TEMP_DIR.resolve("dest");
-		Path source = TEMP_DIR.resolve("src");
-		Path temp = TEMP_DIR.resolve("temp");
-		Workspace workspace = new Workspace();
-
-		Files.write(source, TEST_TEXT.getBytes());
-
-		assertEquals(Status.JOB_SETUP_SUCCESS_MSG.getName(),
-				workspace.copyFile(source.toString(), destination.toString()));
-		assertTrue(FileUtils.contentEquals(source.toFile(), destination.toFile()));
-
-		Files.delete(destination);
-
-		Path destination_sh = TEMP_DIR.resolve("dest.sh");
-		Files.write(temp, TEST_TEXT.getBytes());
-
-		assertEquals(Status.JOB_SETUP_SUCCESS_MSG.getName(),
-				workspace.copyFile(source.toString(), destination_sh.toString()));
-		assertTrue(FileUtils.contentEquals(temp.toFile(), destination_sh.toFile()));
-	}
-
-	@Test
-	void getTimeStampPartTest() {
-
-		String folder = "login-skylake.hpc.cam.ac.uk_428109593378500";
-		String folder_null = "";
-		Workspace workspace = new Workspace();
-		String[] tokens = folder.split("_");
-		assertEquals(tokens[1], workspace.getTimeStampPart(folder));
-		assertNull(workspace.getTimeStampPart(folder_null));
-	}
-
-	@Test
-	void getStatusFilePathTest() {
-
-		Path jobFolder = TEMP_DIR;
-		Workspace workspace = new Workspace();
-		String expected = jobFolder.resolve(Property.STATUS_FILE_NAME.getPropertyName()).toAbsolutePath().toString();
-		assertEquals(expected, workspace.getStatusFilePath(jobFolder.toFile()));
-	}
-
-	@Test
-	void getJSONInputFilePathTest() {
-
-		Path jobFolder = TEMP_DIR;
-		Workspace workspace = new Workspace();
-		String expected = jobFolder.resolve(Property.JSON_INPUT_FILE_NAME.getPropertyName()).toAbsolutePath()
-				.toString();
-		assertEquals(expected, workspace.getJSONInputFilePath(jobFolder.toFile()));
-	}
-
-	@Test
-	void copyScriptFileTest() throws IOException {
-
-		Path source = TEMP_DIR.resolve("source");
-		Path dest = TEMP_DIR.resolve("dest");
-		Files.createDirectories(dest);
-
-		String slurmScriptFileName = "slurmscript.sh";
-		Path temp = TEMP_DIR.resolve("temp");
-		Workspace workspace = new Workspace();
-
-		Files.write(source, TEST_TEXT.getBytes());
-		Files.write(temp, TEST_TEXT.getBytes());
-
-		assertEquals(Status.JOB_SETUP_SUCCESS_MSG.getName(),
-				workspace.copyScriptFile(source.toString(), dest.toString(), slurmScriptFileName));
-		Path slurmScriptPath = dest.resolve(slurmScriptFileName);
-		assertTrue(FileUtils.contentEquals(temp.toFile(), slurmScriptPath.toFile()));
-	}
-}
diff --git a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/configuration/SlurmJobPropertyTest.java b/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/configuration/SlurmJobPropertyTest.java
deleted file mode 100644
index 892a813a0..000000000
--- a/src/test/java/uk/ac/cam/cares/jps/base/slurm/job/configuration/SlurmJobPropertyTest.java
+++ /dev/null
@@ -1,142 +0,0 @@
-package uk.ac.cam.cares.jps.base.slurm.job.configuration;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import org.junit.Test;
-
-public class SlurmJobPropertyTest {
-	
-	SlurmJobProperty test = new SlurmJobProperty();
-	
-	@Test
-	public void getHpcServerLoginUserNameTest() {
-		// Default value
-		assertNull(test.getHpcServerLoginUserName());
-		// Set specific value and check whether it is set correctly
-		test.setHpcServerLoginUserName("user");
-		assertEquals("user", test.getHpcServerLoginUserName());
-	}
-	
-	@Test
-	public void getHpcServerLoginUserPasswordTest() {
-		assertNull(test.getHpcServerLoginUserPassword());
-		test.setHpcServerLoginUserPassword("user");
-		assertEquals("user", test.getHpcServerLoginUserPassword());
-	}
-	
-	@Test
-	public void getAgentClassTest() {
-		assertNull(test.getAgentClass());
-		test.setAgentClass("user");
-		assertEquals("user", test.getAgentClass());
-	}
-	
-	@Test
-	public void getAgentWorkspacePrefixTest() {
-		assertNull(test.getAgentWorkspacePrefix());
-		test.setAgentWorkspacePrefix("user");
-		assertEquals("user", test.getAgentWorkspacePrefix());
-	}
-	
-	@Test
-	public void getAgentCompletedJobsSpacePrefixTest() {
-		assertNull(test.getAgentCompletedJobsSpacePrefix());
-		test.setAgentCompletedJobsSpacePrefix("user");
-		assertEquals("user", test.getAgentCompletedJobsSpacePrefix());
-	}
-	
-	@Test
-	public void getHpcAddressTest() {
-		assertNull(test.getHpcAddress());
-		test.setHpcAddress("user");
-		assertEquals("user", test.getHpcAddress());
-	}
-	
-	@Test
-	public void getInputFileNameTest() {
-		assertNull(test.getInputFileName());
-		test.setInputFileName("user");
-		assertEquals("user", test.getInputFileName());
-	}
-	
-	@Test
-	public void getInputFileExtensionTest() {
-		assertNull(test.getInputFileExtension());
-		test.setInputFileName("user");
-		assertEquals("user", test.getInputFileName());
-	}
-	
-	@Test
-	public void getJsonInputFileNameTest() {
-		assertNull(test.getJsonInputFileName());
-		test.setJsonInputFileName("user");
-		assertEquals("user", test.getJsonInputFileName());
-	}
-	
-	@Test
-	public void getJsonFileExtensionTest() {
-		assertNull(test.getJsonFileExtension());
-		test.setJsonFileExtension("user");
-		assertEquals("user", test.getJsonFileExtension());
-	}
-	
-	@Test
-	public void getSlurmScriptFileNameTest() {
-		assertNull(test.getSlurmScriptFileName());
-		test.setSlurmScriptFileName("user");
-		assertEquals("user", test.getSlurmScriptFileName());
-	}
-	
-	@Test
-	public void getOutputFileNameTest() {
-		assertNull(test.getOutputFileName());
-		test.setOutputFileName("user");
-		assertEquals("user", test.getOutputFileName());
-	}
-	
-	@Test
-	public void getOutputFileExtensionTest() {
-		assertNull(test.getOutputFileExtension());
-		test.setOutputFileExtension("user");
-		assertEquals("user", test.getOutputFileExtension());
-	}
-	
-	@Test
-	public void getExecutableFileTest() {
-		assertNull(test.getExecutableFile());
-		test.setExecutableFile("user");
-		assertEquals("user", test.getExecutableFile());
-	}
-	
-	@Test
-	public void getAgentFailedJobsSpacePrefixTest() {
-		assertNull(test.getAgentFailedJobsSpacePrefix());
-		test.setAgentFailedJobsSpacePrefix("user");
-		assertEquals("user", test.getAgentFailedJobsSpacePrefix());
-	}
-	
-	
-	@Test
-	public void getMaxNumberOfHPCJobsTest() {
-		assertEquals(test.getMaxNumberOfHPCJobs(), 0);
-		test.setMaxNumberOfHPCJobs(123);
-		assertEquals(123, test.getMaxNumberOfHPCJobs());
-	}
-	
-	@Test
-	public void getAgentInitialDelayToStartJobMonitoringTest() {
-		assertEquals(test.getAgentInitialDelayToStartJobMonitoring(), 0);
-		test.setAgentInitialDelayToStartJobMonitoring(123);
-		assertEquals(123, test.getAgentInitialDelayToStartJobMonitoring());
-	}
-	
-	@Test
-	public void getAgentPeriodicActionIntervalTest() {
-		assertEquals(test.getAgentPeriodicActionInterval(), 0);
-		test.setAgentPeriodicActionInterval(123);
-		assertEquals(123, test.getAgentPeriodicActionInterval());
-		
-	}
-
-}
\ No newline at end of file