diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java
index 515310a6cdf1587d0e3b2f95fe38f7c6d187c4cb..374481004f6c13fb6f4dcccee151dc97b4cb0ab3 100644
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/JobState.java
@@ -1,11 +1,12 @@
package cz.it4i.fiji.haas_java_client;
public enum JobState {
- Configuring ,
- Submitted ,
- Queued ,
- Running ,
- Finished ,
- Failed ,
+ Unknown,
+ Configuring,
+ Submitted,
+ Queued,
+ Running,
+ Finished,
+ Failed,
Canceled;
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
index eeb218aa001c44cdd7fc7cc0655df445de1c33de..473f25510165e0f98d88f9fcc7aeb0a347a9b4dd 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java
@@ -1,6 +1,7 @@
package cz.it4i.fiji.haas_spim_benchmark.core;
import java.io.BufferedReader;
+import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
@@ -9,12 +10,14 @@ import java.nio.file.Files;
import java.nio.file.InvalidPathException;
import java.nio.file.Path;
import java.nio.file.Paths;
+import java.util.ArrayList;
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.Scanner;
import java.util.function.Predicate;
import java.util.stream.Collectors;
@@ -49,20 +52,22 @@ public class BenchmarkJobManager {
private Job job;
- private HaaSOutputHolder outputOfSnakemake;
-
private List<Task> tasks;
private SPIMComputationAccessor computationAccessor = new SPIMComputationAccessor() {
+
+ private HaaSOutputHolder outputOfSnakemake =
+ new HaaSOutputHolderImpl(BenchmarkJob.this, SynchronizableFileType.StandardErrorFile);
+
@Override
public String getActualOutput() {
return outputOfSnakemake.getActualOutput();
}
@Override
- public boolean fileExists(String fileName) {
- // TASK 1011 modify interface of job for checking of file existence
- return false;
+ public boolean fileExists(Path filePath) {
+ File f = new File(filePath.toString());
+ return f.exists() && !f.isDirectory();
}
};
@@ -70,7 +75,6 @@ public class BenchmarkJobManager {
public BenchmarkJob(Job job) {
super();
this.job = job;
- outputOfSnakemake = new HaaSOutputHolderImpl(this, SynchronizableFileType.StandardErrorFile);
}
public void startJob(Progress progress) throws IOException {
@@ -96,7 +100,7 @@ public class BenchmarkJobManager {
setDownloaded(true);
}
- public void downloadStatistics(Progress progress) throws IOException {
+ public void downloadStatistics(Progress progress) throws IOException {
job.download(BenchmarkJobManager.downloadStatistics(), progress);
Path resultFile = job.getDirectory().resolve(Constants.BENCHMARK_RESULT_FILE);
if (resultFile != null)
@@ -135,8 +139,7 @@ public class BenchmarkJobManager {
@Override
public boolean equals(Object obj) {
if (obj instanceof BenchmarkJob) {
- BenchmarkJob job = (BenchmarkJob) obj;
- return job.getId() == getId();
+ return ((BenchmarkJob) obj).getId() == getId();
}
return false;
}
@@ -146,9 +149,8 @@ public class BenchmarkJobManager {
return getDownloaded();
}
- public BenchmarkJob update() {
+ public void update() {
job.updateInfo();
- return this;
}
public Path getDirectory() {
@@ -156,33 +158,39 @@ public class BenchmarkJobManager {
}
public List<Task> getTasks() {
- if(tasks == null) {
+ if (tasks == null) {
fillTasks();
}
return tasks;
- }
-
+ }
private void fillTasks() {
- SPIMComputationAccessor accessor = computationAccessor;
- String snakeMakeoutput = outputOfSnakemake.getActualOutput();
- //TASK 1011 parse snakeOutput, create tasks base part:
-//Job counts:
-// count jobs
-// 1 define_output
-// 1 define_xml_tif
-// 1 done
-// 2 fusion
-// 1 hdf5_xml
-// 1 hdf5_xml_output
-// 2 registration
-// 2 resave_hdf5
-// 2 resave_hdf5_output
-// 1 timelapse
-// 1 xml_merge
-// 15
+ final String OUTPUT_PARSING_JOB_COUNTS = "Job counts:";
+ final String OUTPUT_PARSING_TAB_DELIMITER = "\\t";
+ final int OUTPUT_PARSING_EXPECTED_NUMBER_OF_WORDS_PER_LINE = 2;
+
+ tasks = new ArrayList<>();
+ Scanner scanner = new Scanner(computationAccessor.getActualOutput());
+ while (scanner.hasNextLine()) {
+ if (!scanner.nextLine().equals(OUTPUT_PARSING_JOB_COUNTS)) {
+ continue;
+ }
+ scanner.nextLine();
+
+ while (true) {
+ List<String> lineWords = Arrays.stream(scanner.nextLine().split(OUTPUT_PARSING_TAB_DELIMITER))
+ .filter(word -> word.length() > 0).collect(Collectors.toList());
+ if (lineWords.size() != OUTPUT_PARSING_EXPECTED_NUMBER_OF_WORDS_PER_LINE) {
+ break;
+ }
+ tasks.add(new Task(computationAccessor, lineWords.get(1), Integer.parseInt(lineWords.get(0))));
+ }
+ break;
+ }
+ scanner.close();
}
+
private void setDownloaded(boolean b) {
job.setProperty(JOB_HAS_DATA_TO_DOWNLOAD_PROPERTY, b + "");
}
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;
- }
- };
- }
-}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java
index 0ba6590109e4406f0d99e247ac8757d25af4e908..39151ca434b506f873741dae844360934863ffbb 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/SPIMComputationAccessor.java
@@ -1,7 +1,9 @@
package cz.it4i.fiji.haas_spim_benchmark.core;
+import java.nio.file.Path;
+
import cz.it4i.fiji.haas.HaaSOutputHolder;
public interface SPIMComputationAccessor extends HaaSOutputHolder {
- boolean fileExists(String fileName);
+ boolean fileExists(Path fileName);
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java
index 285a579ff2e7d0d91dbdebb594485e0ece3f3965..38f42ad8a8f74d6a6172399c814fd2852e1445b4 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/Task.java
@@ -4,38 +4,28 @@ import java.util.LinkedList;
import java.util.List;
public class Task {
- private SPIMComputationAccessor outputHolder;
- private String description;
- private List<TaskComputation> computations;
- private int numComputations;
+ private final String description;
+ private final List<TaskComputation> computations;
public Task(SPIMComputationAccessor outputHolder, String description, int numComputations) {
this.description = description;
- this.outputHolder = outputHolder;
- this.numComputations = numComputations;
- }
-
- public List<TaskComputation> getComputations() {
- if (computations == null) {
- fillComputations();
+ this.computations = new LinkedList<>();
+
+ for (int i = 0; i < numComputations; i++) {
+ computations.add(new TaskComputation(outputHolder, this, i + 1));
}
- return computations;
}
public String getDescription() {
return description;
}
-
- private void fillComputations() {
- computations = new LinkedList<>();
- for (int i = 0; i < numComputations; i++) {
- computations.add(new TaskComputation(outputHolder, this, i + 1));
- }
+
+ public List<TaskComputation> getComputations() {
+ return computations;
}
public void update() {
// TODO Auto-generated method stub
}
-
}
diff --git a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
index c0fc812c89d4e0601ec441af204ecedc53458156..af869e56765636d16a861800e6a58341e7449fe5 100644
--- a/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
+++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/TaskComputation.java
@@ -1,78 +1,119 @@
package cz.it4i.fiji.haas_spim_benchmark.core;
+import java.util.Arrays;
import java.util.Collection;
import java.util.LinkedList;
+import java.util.Scanner;
import cz.it4i.fiji.haas_java_client.JobState;
-
public class TaskComputation {
+
+ // A single-purpose class dedicated to help with TaskComputation members initialization
+ private class ParsedTaskComputationValues {
+ private final Collection<String> logs;
+ private final Collection<String> inputs;
+ private final Collection<String> outputs;
+ private final Long id;
+
+ public ParsedTaskComputationValues(Collection<String> inputs, Collection<String> outputs, Collection<String> logs, Long id) {
+ this.inputs = inputs;
+ this.outputs = outputs;
+ this.logs = logs;
+ this.id = id;
+ }
+ }
- private SPIMComputationAccessor outputHolder;
- private int timepoint;
- private Long id;
+ private final Task task;
+ private final int timepoint;
+ private final Collection<String> inputs;
+ private final Collection<String> outputs;
+ private final Collection<String> logs;
+ private final Long id;
+
//TASK 1011 what states will be defined and how it will be defined
- private JobState state;
- private Task task;
- private Collection<String> logs = new LinkedList<>();
- private Collection<String> outputs = new LinkedList<>();
- private Collection<String> inputs = new LinkedList<>();
-
+ private JobState state = JobState.Unknown;
- public TaskComputation(SPIMComputationAccessor outputHolder,Task task, int timepoint) {
- this.outputHolder = outputHolder;
- this.timepoint = timepoint;
+ public TaskComputation(SPIMComputationAccessor outputHolder, Task task, int timepoint) {
this.task = task;
+ this.timepoint = timepoint;
+ ParsedTaskComputationValues parsedValues = parseStuff(outputHolder);
+ this.inputs = parsedValues.inputs;
+ this.outputs = parsedValues.outputs;
+ this.logs = parsedValues.logs;
+ this.id = parsedValues.id;
}
public JobState getState() {
updateState();//TASK 1011 it is not good idea update every time when state is requested
- return state != null?state:JobState.Configuring;
+ return state;
}
+ public void update() {
+ }
+
public int getTimepoint() {
return timepoint;
}
private void updateState() {
- String snakeOutput = outputHolder.getActualOutput();
- Long id = getId();
- if(id == null) {
+ //TASK 1011 This should never happen, add some error handling to resolveId()
+ if (id == null) {
return;
}
+
+ //String snakeOutput = outputHolder.getActualOutput();
+
//TASK 1011
//resolve if job is queued (defined id), started (exists log file), finished (in log is Finished job 10.) or
//or failed (some error in log)
}
private Long getId() {
- if(id == null) {
- fillId();
- }
return id;
}
- private void fillId() {
- //TASK 1011
- //find timepoint-th occurence of
-//rule resave_hdf5:
-// input: HisRFP_test-01-00.h5_xml, HisRFP_test_first.xml
-// output: HisRFP_test-01-00.h5, HisRFP_test-01-00.h5_hdf5
-// log: logs/b2_resave_hdf5-01.log
-// jobid: 7
-// wildcards: xml_base=HisRFP_test, file_id=01
+ private ParsedTaskComputationValues parseStuff(SPIMComputationAccessor outputHolder) {
- //resave_hdf5 == task.getDescription()
- //jobid -> id
- //input->inputs
- //...
- //
- //or return
- }
-
- public void update() {
- // TODO Auto-generated method stub
+ final String OUTPUT_PARSING_RULE = "rule ";
+ final String OUTPUT_PARSING_COLON = ":";
+ final String OUTPUT_PARSING_COMMA_SPACE = ", ";
+ final String desiredPattern = OUTPUT_PARSING_RULE + task.getDescription() + OUTPUT_PARSING_COLON;
- }
-
+ 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(outputHolder.getActualOutput());
+ int jobsToSkip = timepoint;
+ while (scanner.hasNextLine() && jobsToSkip > 0) {
+ if (scanner.nextLine().equals(desiredPattern)) {
+ jobsToSkip--;
+ }
+ }
+
+ String currentLine;
+ Collection<String> resolvedInputs = new LinkedList<>();
+ Collection<String> resolvedOutputs = new LinkedList<>();
+ Collection<String> resolvedLogs = new LinkedList<>();
+ Long resolvedId = null;
+ while (scanner.hasNextLine()) {
+ currentLine = scanner.nextLine();
+ if (currentLine.contains(OUTPUT_PARSING_INPUTS)) {
+ resolvedInputs = Arrays.asList(currentLine.split(OUTPUT_PARSING_INPUTS)[1].split(OUTPUT_PARSING_COMMA_SPACE));
+ } else if (currentLine.contains(OUTPUT_PARSING_OUTPUTS)) {
+ resolvedOutputs = Arrays.asList(currentLine.split(OUTPUT_PARSING_OUTPUTS)[1].split(OUTPUT_PARSING_COMMA_SPACE));
+ } else if (currentLine.contains(OUTPUT_PARSING_LOGS)) {
+ resolvedLogs = Arrays.asList(currentLine.split(OUTPUT_PARSING_LOGS)[1].split(OUTPUT_PARSING_COMMA_SPACE));
+ } else if (currentLine.contains(OUTPUT_PARSING_JOB_ID)) {
+ resolvedId = Long.parseLong(currentLine.split(OUTPUT_PARSING_JOB_ID)[1]);
+ } else if (currentLine.trim().isEmpty()) {
+ break;
+ }
+ }
+ scanner.close();
+
+ return new ParsedTaskComputationValues(resolvedInputs, resolvedOutputs, resolvedLogs, resolvedId);
+ }
}