diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java.orig b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java.orig
deleted file mode 100644
index 4dbef62b7c09997dcd9d4da19b0bcc8a421cd616..0000000000000000000000000000000000000000
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java.orig
+++ /dev/null
@@ -1,420 +0,0 @@
-package cz.it4i.fiji.haas_spim_benchmark.core;
-
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.InvalidPathException;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.Arrays;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.function.Predicate;
-import java.util.stream.Collectors;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.yaml.snakeyaml.Yaml;
-
-<<<<<<< HEAD
-import cz.it4i.fiji.haas.HaaSOutputHolder;
-import cz.it4i.fiji.haas.HaaSOutputSource;
-=======
-import cz.it4i.fiji.haas.Job;
->>>>>>> master
-import cz.it4i.fiji.haas.JobManager;
-import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile;
-import cz.it4i.fiji.haas.UploadingFileFromResource;
-import cz.it4i.fiji.haas_java_client.HaaSClient;
-import cz.it4i.fiji.haas_java_client.JobState;
-import cz.it4i.fiji.haas_java_client.Settings;
-import cz.it4i.fiji.haas_java_client.SynchronizableFileType;
-import javafx.beans.value.ObservableValueBase;
-import net.imagej.updater.util.Progress;
-
-public class BenchmarkJobManager {
-
- private static final String JOB_HAS_DATA_TO_DOWNLOAD_PROPERTY = "job.needDownload";
-
- private static Logger log = LoggerFactory
- .getLogger(cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager.class);
-
-<<<<<<< HEAD
- public final class Job extends ObservableValueBase<Job> implements HaaSOutputSource {
- private JobInfo jobInfo;
-
-=======
- public final class BenchmarkJob extends ObservableValueBase<BenchmarkJob> {
-
- private Job job;
->>>>>>> master
- private JobState oldState;
-
- private HaaSOutputHolder outputOfSnakemake;
-
- private Collection<Task> tasks;
-
- public BenchmarkJob(Job job) {
- super();
-<<<<<<< HEAD
- this.jobInfo = ji;
- outputOfSnakemake = new HaaSOutputHolder(getValue(), SynchronizableFileType.StandardErrorFile);
-=======
- this.job = job;
->>>>>>> master
- }
-
- public void startJob(Progress progress) throws IOException {
- job.uploadFilesByName(Arrays.asList(Constants.CONFIG_YAML), progress);
- String outputName = getOutputName(job.openLocalFile(Constants.CONFIG_YAML));
- job.submit();
- job.setProperty(Constants.SPIM_OUTPUT_FILENAME_PATTERN, outputName);
- fireValueChangedEvent();
- setDownloaded(false);
- }
-
- public JobState getState() {
- return oldState = job.getState();
- }
-
- public void downloadData(Progress progress) throws IOException {
- if (job.getState() == JobState.Finished) {
- String filePattern = job.getProperty(Constants.SPIM_OUTPUT_FILENAME_PATTERN);
- job.download(downloadFinishedData(filePattern), progress);
- } else if (job.getState() == JobState.Failed) {
- job.download(downloadFailedData(), progress);
- }
- fireValueChangedEvent();
- setDownloaded(true);
- }
-
- public void downloadStatistics(Progress progress) throws IOException {
- job.download(BenchmarkJobManager.downloadStatistics(), progress);
- fireValueChangedEvent();
- Path resultFile = job.getDirectory().resolve(Constants.BENCHMARK_RESULT_FILE);
- if (resultFile != null)
- BenchmarkJobManager.formatResultFile(resultFile);
- }
-
- public List<String> getOutput(List<JobSynchronizableFile> files) {
- return job.getOutput(files);
- }
-
- public long getId() {
- return job.getId();
- }
-
- public String getCreationTime() {
- return getStringFromTimeSafely(job.getCreationTime());
- }
-
- public String getStartTime() {
- return getStringFromTimeSafely(job.getStartTime());
- }
-
- public String getEndTime() {
- return getStringFromTimeSafely(job.getEndTime());
- }
-
- private String getStringFromTimeSafely(Calendar time) {
- return time != null ? time.getTime().toString() : "N/A";
- }
-
- @Override
- public BenchmarkJob getValue() {
- return this;
- }
-
- @Override
- public int hashCode() {
- return Long.hashCode(job.getId());
- }
-
- @Override
- public boolean equals(Object obj) {
- if (obj instanceof BenchmarkJob) {
- BenchmarkJob job = (BenchmarkJob) obj;
- return job.getId() == getId();
- }
- return false;
- }
-
- public void update(BenchmarkJob benchmarkJob) {
- job = benchmarkJob.job;
- if (benchmarkJob.job.getState() != oldState)
- fireValueChangedEvent();
- }
-
- public boolean downloaded() {
- return getDownloaded();
- }
-
- public BenchmarkJob update() {
- job.updateInfo();
- if (!job.getState().equals(oldState))
- fireValueChangedEvent();
- return this;
- }
-
- public Path getDirectory() {
- return job.getDirectory();
- }
-
-<<<<<<< HEAD
- public Collection<Task> getTasks() {
- if(tasks == null) {
- fillTasks();
- }
- return tasks;
- }
-
-
- private void fillTasks() {
- String snakeMakeoutput = outputOfSnakemake.getActualOutput();
-
- }
-
-=======
->>>>>>> master
- private void setDownloaded(boolean b) {
- job.setProperty(JOB_HAS_DATA_TO_DOWNLOAD_PROPERTY, b + "");
- }
-
- private boolean getDownloaded() {
- String downloadedStr = job.getProperty(JOB_HAS_DATA_TO_DOWNLOAD_PROPERTY);
- return downloadedStr != null && Boolean.parseBoolean(downloadedStr);
- }
- }
-
- private JobManager jobManager;
-
- public BenchmarkJobManager(BenchmarkSPIMParameters params) throws IOException {
- jobManager = new JobManager(params.workingDirectory(), constructSettingsFromParams(params));
- }
-
- public BenchmarkJob createJob() throws IOException {
- Job job = jobManager.createJob();
- job.storeDataInWorkdirectory(getUploadingFile());
- return convertJob(job);
- }
-
- public Collection<BenchmarkJob> getJobs() throws IOException {
- return jobManager.getJobs().stream().map(this::convertJob).collect(Collectors.toList());
- }
-
-
- private HaaSClient.UploadingFile getUploadingFile() {
- return new UploadingFileFromResource("", Constants.CONFIG_YAML);
- }
-
- private BenchmarkJob convertJob(Job job) {
- return new BenchmarkJob(job);
- }
-
- private String getOutputName(InputStream openLocalFile) throws IOException {
- try (InputStream is = openLocalFile) {
- Yaml yaml = new Yaml();
-
- Map<String, Map<String, String>> map = yaml.load(is);
- String result = map.get("common").get("hdf5_xml_filename");
- if (result == null) {
- throw new IllegalArgumentException("hdf5_xml_filename not found");
- }
- if (result.charAt(0) == '"' || result.charAt(0) == '\'') {
- if (result.charAt(result.length() - 1) != result.charAt(0)) {
- throw new IllegalArgumentException(result);
- }
- result = result.substring(1, result.length() - 1);
- }
-
- return result;
- }
-
- }
-
- private static Predicate<String> downloadFinishedData(String filePattern) {
- return name -> {
- Path path = getPathSafely(name);
- if (path == null)
- return false;
-
- String fileName = path.getFileName().toString();
- return fileName.startsWith(filePattern) && fileName.endsWith("h5") || fileName.equals(filePattern + ".xml")
- || fileName.equals(Constants.BENCHMARK_RESULT_FILE);
- };
- }
-
- private static Predicate<String> downloadStatistics() {
- return name -> {
- Path path = getPathSafely(name);
- if (path == null)
- return false;
-
- String fileName = path.getFileName().toString();
- return fileName.equals(Constants.BENCHMARK_RESULT_FILE);
- };
- }
-
- private static Predicate<String> downloadFailedData() {
- return name -> {
- Path path = getPathSafely(name);
- if (path == null)
- return false;
-
- return path.getFileName().toString().startsWith("snakejob.")
- || path.getParent().getFileName().toString().equals("logs");
- };
- }
-
- private static Path getPathSafely(String name) {
- try {
- return Paths.get(name);
- } catch(InvalidPathException ex) {
- return null;
- }
- }
-
- private static void formatResultFile(Path filename) throws FileNotFoundException {
-
- List<ResultFileTask> identifiedTasks = new LinkedList<ResultFileTask>();
-
- final String newLineSeparator = "\n";
- final String delimiter = ";";
- final String summaryFileHeader = "Task;MemoryUsage;WallTime;JobCount";
-
- try {
- String line = null;
-
- ResultFileTask processedTask = null;
- List<ResultFileJob> jobs = new LinkedList<>();
-
- BufferedReader reader = Files.newBufferedReader(filename);
- while (null != (line = reader.readLine())) {
-
- line = line.trim();
- if (line.isEmpty()) {
- continue;
- }
-
- String[] columns = line.split(delimiter);
-
- if (columns[0].equals(Constants.STATISTICS_TASK_NAME)) {
-
- // If there is a task being processed, add all cached jobs to it and wrap it up
- if (null != processedTask ) {
- processedTask.jobs.addAll(jobs);
- identifiedTasks.add(processedTask);
- }
-
- // Start processing a new task
- processedTask = new ResultFileTask(columns[1]);
- jobs.clear();
-
- } else if (columns[0].equals(Constants.STATISTICS_JOB_IDS)) {
-
- // Cache all found jobs
- for (int i = 1; i < columns.length; i++) {
- jobs.add(new ResultFileJob(columns[i]));
- }
-
- } else if (!columns[0].equals(Constants.STATISTICS_JOB_COUNT)) {
-
- // Save values of a given property to cached jobs
- for (int i = 1; i < columns.length; i++) {
- jobs.get(i - 1).setValue(columns[0], columns[i]);
- }
-
- }
- }
-
- // If there is a task being processed, add all cached jobs to it and wrap it up
- if (null != processedTask ) {
- processedTask.jobs.addAll(jobs);
- identifiedTasks.add(processedTask);
- }
-
- } catch (IOException e) {
- log.error(e.getMessage(), e);
- }
-
- FileWriter fileWriter = null;
- try {
- fileWriter = new FileWriter(filename.getParent().toString() + "/" + Constants.STATISTICS_SUMMARY_FILENAME);
- fileWriter.append(summaryFileHeader).append(newLineSeparator);
-
- for (ResultFileTask task : identifiedTasks) {
- fileWriter.append(Constants.STATISTICS_TASK_NAME_MAP.get(task.name)).append(delimiter);
- fileWriter.append(Double.toString(task.getAverageMemoryUsage())).append(delimiter);
- fileWriter.append(Double.toString(task.getAverageWallTime())).append(delimiter);
- fileWriter.append(Integer.toString(task.getJobCount()));
- fileWriter.append(newLineSeparator);
- }
- } catch (Exception e) {
- log.error(e.getMessage(), e);
- } finally {
- try {
- fileWriter.flush();
- fileWriter.close();
- } catch (Exception e) {
- log.error(e.getMessage(), e);
- }
- }
- }
-
- private static Settings constructSettingsFromParams(BenchmarkSPIMParameters params) {
- // TODO Auto-generated method stub
- return new Settings() {
-
- @Override
- public String getUserName() {
- return params.username();
- }
-
- @Override
- public int getTimeout() {
- return Constants.HAAS_TIMEOUT;
- }
-
- @Override
- public long getTemplateId() {
- return Constants.HAAS_TEMPLATE_ID;
- }
-
- @Override
- public String getProjectId() {
- return Constants.HAAS_PROJECT_ID;
- }
-
- @Override
- public String getPhone() {
- return params.phone();
- }
-
- @Override
- public String getPassword() {
- return params.password();
- }
-
- @Override
- public String getJobName() {
- return Constants.HAAS_JOB_NAME;
- }
-
- @Override
- public String getEmail() {
- return params.email();
- }
-
- @Override
- public long getClusterNodeType() {
- return Constants.HAAS_CLUSTER_NODE_TYPE;
- }
- };
- }
-}