fix progress

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java

@@ -170,6 +170,8 @@ public class BenchmarkJobManager {
 			if (tasks == null) {
 				fillTasks();
 			}
+			// Carry on in output processing
+			processOutput();
 			return tasks;
 		}		
 
@@ -203,8 +205,7 @@ public class BenchmarkJobManager {
 			List<String> chronologicList = STATISTICS_TASK_NAME_MAP.keySet().stream().collect(Collectors.toList());
 			Collections.sort(tasks, Comparator.comparingInt(task -> chronologicList.indexOf(task.getDescription())));
 			
-			// Carry on in output processing
-			processOutput();
+			
 		}
 		
 		private void processOutput() {

haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java

@@ -10,93 +10,98 @@ public class TaskComputation {
 
 	private final SPIMComputationAccessor computationAccessor;
 	private final int timepoint;
-	
+
 	private JobState state;
 	private int positionInOutput;
-	
+
 	private Collection<String> inputs;
+	@SuppressWarnings("unused")
 	private Collection<String> outputs;
 	private Collection<String> logs;
 	private Long id;
-	
+
 	/**
-	 * Creates a TaskComputation object
-	 * Note: At the time of creation, the job parameters are not populated
-	*/
+	 * Creates a TaskComputation object Note: At the time of creation, the job
+	 * parameters are not populated
+	 */
 	public TaskComputation(SPIMComputationAccessor computationAccessor, int timepoint) {
 		this.computationAccessor = computationAccessor;
 		this.timepoint = timepoint;
 		this.state = JobState.Unknown;
 		updateState();
 	}
-	
+
 	/**
 	 * @return current job state
 	 */
 	public JobState getState() {
+		updateState();
 		return state;
 	}
-	
+
 	/**
 	 * @return job timepoint
 	 */
 	public int getTimepoint() {
 		return timepoint;
 	}
-	
+
 	/**
 	 * @return job id
 	 */
 	public Long getId() {
 		return id;
 	}
-	
+
 	// TODO: Method stub
 	public void update() {
-		
+
 	}
-	
+
 	/**
 	 * Populates parameters of the current object by searching the output
-	 * @param positionInOutput: Index of the output position to search from
+	 * 
+	 * @param positionInOutput:
+	 *            Index of the output position to search from
 	 * @return success flag
 	 */
 	public boolean populateParameters(int positionInOutput) {
-		
-		// Should the state be different than unknown, there is no need to populate parameters
+
+		// Should the state be different than unknown, there is no need to populate
+		// parameters
 		if (state != JobState.Unknown) {
 			return false;
 		}
-		
+
 		this.positionInOutput = positionInOutput;
 		if (!resolveJobParameters()) {
 			return false;
 		}
-		
-		state = JobState.Queued;		
+
+		state = JobState.Queued;
 		updateState();
-		
+
 		return true;
 	}
 
 	private void updateState() {
 
 		// Should the state be queued, try to find out whether a log file exists
-		if (state == JobState.Queued ) {
-			if (!logs.stream().anyMatch(logFile -> computationAccessor.fileExists(logFile))) {
+		if (state == JobState.Queued) {
+			if (null != logs && !logs.stream().anyMatch(logFile -> computationAccessor.fileExists(logFile))) {
 				return; // No log file exists yet
 			}
-			state = JobState.Running;					
+			state = JobState.Running;
 		}
-		
+
 		// Finally, look up any traces that the job has failed or finished
 		if (state == JobState.Running) {
-					
+
 			final String OUTPUT_PARSING_FINISHED_JOB = "Finished job ";
 			final String desiredPatternFinishedJob = OUTPUT_PARSING_FINISHED_JOB + id.toString();
 			final String OUTPUT_PARSING_ERRONEOUS_JOB = "Error job ";
 			final String desiredPatternErroneousJob = OUTPUT_PARSING_ERRONEOUS_JOB + id.toString();
-			
+
 			Scanner scanner = new Scanner(computationAccessor.getActualOutput().substring(positionInOutput));
 			String currentLine;
 			while (scanner.hasNextLine()) {
@@ -112,15 +117,15 @@ public class TaskComputation {
 			scanner.close();
 		}
 	}
-		
+
 	private boolean resolveJobParameters() {
-		
+
 		final String OUTPUT_PARSING_COMMA_SPACE = ", ";
 		final String OUTPUT_PARSING_INPUTS = "input: ";
 		final String OUTPUT_PARSING_OUTPUTS = "output: ";
 		final String OUTPUT_PARSING_LOGS = "log: ";
 		final String OUTPUT_PARSING_JOB_ID = "jobid: ";
-		
+
 		Scanner scanner = new Scanner(computationAccessor.getActualOutput().substring(positionInOutput));
 		String currentLine;
 		while (scanner.hasNextLine()) {
@@ -131,16 +136,15 @@ public class TaskComputation {
 				outputs = Arrays.asList(currentLine.split(OUTPUT_PARSING_OUTPUTS)[1].split(OUTPUT_PARSING_COMMA_SPACE));
 			} else if (currentLine.contains(OUTPUT_PARSING_LOGS)) {
 				logs = Arrays.asList(currentLine.split(OUTPUT_PARSING_LOGS)[1].split(OUTPUT_PARSING_COMMA_SPACE));
-			} else 
-			if (currentLine.contains(OUTPUT_PARSING_JOB_ID)) {
+			} else if (currentLine.contains(OUTPUT_PARSING_JOB_ID)) {
 				id = Long.parseLong(currentLine.split(OUTPUT_PARSING_JOB_ID)[1]);
 			} else if (currentLine.trim().isEmpty()) {
-				break;				
+				break;
 			}
 		}
 		scanner.close();
-		
-		return !(inputs == null || outputs == null || logs == null || id == null);
+
+		return !(inputs == null || id == null);
 	}
-	
+
 }