@Override
public Experiment build() throws InvalidParametersException {
for (Experiment e : experiments) {
e.build();
}
this.exprIt = experiments.iterator();
return this;
}
/**
* Pushes a host back onto the queue of available hosts and attempts to launch a waiting
* experiment (if any).
*
* @param hostNum the index of the host to push back onto the queue of available hosts
*/
protected synchronized void availableHost(int hostNum) {
if (hostNum >= 0) {
if (m_remoteHostFailureCounts[hostNum] < MAX_FAILURES) {
m_remoteHostsQueue.push(new Integer(hostNum));
} else {
notifyListeners(
false,
true,
false,
"Max failures exceeded for host "
+ ((String) m_remoteHosts.elementAt(hostNum))
+ ". Removed from host list.");
m_removedHosts++;
}
}
// check for all sub exp complete or all hosts failed or failed count
// exceeded
if (m_failedCount == (MAX_FAILURES * m_remoteHosts.size())) {
abortExperiment();
notifyListeners(
false, true, true, "Experiment aborted! Max failures " + "exceeded on all remote hosts.");
return;
}
if ((getSplitByDataSet() && (m_baseExperiment.getDatasets().size() == m_finishedCount))
|| (getSplitByProperty() && (m_baseExperiment.getPropertyArrayLength() == m_finishedCount))
|| (!getSplitByDataSet()
&& !getSplitByProperty()
&& (getRunUpper() - getRunLower() + 1) == m_finishedCount)) {
notifyListeners(false, true, false, "Experiment completed successfully.");
notifyListeners(false, true, true, postExperimentInfo());
return;
}
if (checkForAllFailedHosts()) {
return;
}
if (m_experimentAborted
&& (m_remoteHostsQueue.size() + m_removedHosts) == m_remoteHosts.size()) {
notifyListeners(false, true, true, "Experiment aborted. All remote tasks " + "finished.");
}
if (!m_subExpQueue.empty() && !m_experimentAborted) {
if (!m_remoteHostsQueue.empty()) {
int availHost, waitingExp;
try {
availHost = ((Integer) m_remoteHostsQueue.pop()).intValue();
waitingExp = ((Integer) m_subExpQueue.pop()).intValue();
launchNext(waitingExp, availHost);
} catch (Exception ex) {
ex.printStackTrace();
}
}
}
}
@Override
public Simulation next() {
if (exprIt == null) {
throw new RuntimeException("Iterator not initialised, please call build()");
}
if (current == null || !current.hasNext()) {
if (exprIt.hasNext()) current = exprIt.next();
else throw new NoSuchElementException();
}
return current.next();
}
@Override
public void run() {
// gather data from provider
final DataProvider dataProvider = getDataProvider();
checkNotNull(
dataProvider,
"Probable problem: your MASConfiguration/ObjectiveFunction/"
+ "PostProcessor is not fully serializable.");
final Supplier<Scenario> scenario = getDataProvider().getParameter(scenarioId);
final MASConfiguration configuration = getDataProvider().getParameter(configurationId);
final ObjectiveFunction objectiveFunction =
getDataProvider().getParameter(objectiveFunctionId);
final PostProcessor<?> postProcessor = getDataProvider().getParameter(postProcessorId);
final Scenario s = scenario.get();
final SimArgs simArgs =
SimArgs.create(s, configuration, seed, objectiveFunction, false, postProcessor, null);
final Object simResult = Experiment.perform(simArgs);
checkArgument(
simResult instanceof Serializable,
"Your PostProcessor must generate Serializable objects, found %s.",
simResult);
setResult(simResult);
}
@Override
public AbstractMultiConfExperiment clone() throws CloneNotSupportedException {
AbstractMultiConfExperiment e = (AbstractMultiConfExperiment) super.clone();
if (baseExperiment != null) e.baseExperiment = baseExperiment.clone();
return e;
}
@Override
public Set<File> generateFilePath(SequencerPoolPartition partition, Dilution l)
throws SubmissionException {
Pool<? extends Poolable> pool = partition.getPool();
if (pool != null) {
if (pool.getExperiments() != null) {
Collection<Experiment> experiments = pool.getExperiments();
Experiment experiment = experiments.iterator().next();
StringBuilder filePath = new StringBuilder();
if (!"".equals(basePath)) {
filePath.append(
partition.getSequencerPartitionContainer().getRun().getFilePath()
+ "/Data/Intensities/BaseCalls/PAP/Project_"
+ experiment.getStudy().getProject().getAlias()
+ "/Sample_"
+ l.getLibrary().getName()
+ "/"
+ l.getLibrary().getName());
} else {
filePath.append(
basePath
+ "/"
+ experiment.getStudy().getProject().getAlias()
+ "/Sample_"
+ l.getLibrary().getName()
+ "/"
+ l.getLibrary().getName());
}
if (l.getLibrary().getTagBarcodes() != null && !l.getLibrary().getTagBarcodes().isEmpty()) {
filePath.append("_");
for (TagBarcode tb : l.getLibrary().getTagBarcodes().values()) {
filePath.append(tb.getSequence());
}
}
filePath.append("_L00" + partition.getPartitionNumber() + "*.fastq.gz");
Set<File> files = new HashSet<File>();
files.add(new File(filePath.toString()));
return files;
} else {
throw new SubmissionException("partition.getPool=null!");
}
} else {
throw new SubmissionException("Collection of experiments is empty");
}
}
/** @see ITouchable#handleChanges(IChangesHandler) */
public void handleChanges(IChangesHandler h) {
h.visit(this);
// call handleChanges of all child elementss
experiment.handleChanges(h);
resourceDescription.handleChanges(h);
// manually created alternatives obviously don't have related
// preservation actions
if (action != null) action.handleChanges(h);
}
/**
* Overides toString in Experiment
*
* @return a description of this remote experiment
*/
@Override
public String toString() {
String result = m_baseExperiment.toString();
result += "\nRemote Hosts:\n";
for (int i = 0; i < m_remoteHosts.size(); i++) {
result += ((String) m_remoteHosts.elementAt(i)) + '\n';
}
return result;
}
@Override
public Set<File> generateFilePaths(SequencerPoolPartition partition) throws SubmissionException {
log.debug("Generating filepaths for partition " + partition.getId());
Set<File> filePaths = new HashSet<File>();
Pool pool = partition.getPool();
if (pool == null) {
throw new SubmissionException("partition.getPool=null!");
} else {
Collection<Experiment> experiments = pool.getExperiments();
if (experiments.isEmpty()) {
throw new SubmissionException("Collection or experiments is empty");
} else {
Collection<LibraryDilution> libraryDilutions = pool.getDilutions();
if (libraryDilutions.isEmpty()) {
throw new SubmissionException("Collection or libraryDilutions is empty");
} else {
for (Experiment e : experiments) {
StringBuilder filePath = new StringBuilder();
filePath.append(partition.getSequencerPartitionContainer().getRun().getFilePath());
filePath.append("/Data/Intensities/BaseCalls/PAP/Project_");
filePath.append(e.getStudy().getProject().getAlias());
filePath.append("/Sample_");
for (LibraryDilution l : libraryDilutions) {
// filePath.append(l.getLibrary().getName()+"/");
/*
+l.getLibrary().getName()+"_"+l.getLibrary().getTagBarcode().getSequence());
filePath.append("L00"+lane.getPartitionNumber())
*/
String folder = filePath.toString() + l.getLibrary().getName() + "/*.fastq.gz";
// System.out.println(folder);
File file = new File(folder);
filePaths.add(file);
}
}
}
}
}
return (filePaths);
}
/**
* Set the base experiment. A sub experiment will be created for each run in the base experiment.
*
* @param base the base experiment to use.
* @throws Exception if supplied base experiment is null
*/
public void setBaseExperiment(Experiment base) throws Exception {
if (base == null) {
throw new Exception("Base experiment is null!");
}
m_baseExperiment = base;
setRunLower(m_baseExperiment.getRunLower());
setRunUpper(m_baseExperiment.getRunUpper());
setResultListener(m_baseExperiment.getResultListener());
setResultProducer(m_baseExperiment.getResultProducer());
setDatasets(m_baseExperiment.getDatasets());
setUsePropertyIterator(m_baseExperiment.getUsePropertyIterator());
setPropertyPath(m_baseExperiment.getPropertyPath());
setPropertyArray(m_baseExperiment.getPropertyArray());
setNotes(m_baseExperiment.getNotes());
m_ClassFirst = m_baseExperiment.m_ClassFirst;
m_AdvanceDataSetFirst = m_baseExperiment.m_AdvanceDataSetFirst;
}
/** getXml. */
@Get
public void getXml() {
ExperimentService ss = BeanFactory.getExperimentServiceBean();
Experiment experiment =
(Experiment) testIfNull(ss.findBySWAccession(Integer.parseInt(getId())));
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Experiment> jaxbTool = new JaxbObject<Experiment>();
Experiment dto = copier.hibernate2dto(Experiment.class, experiment);
if (fields.contains("attributes")) {
Set<ExperimentAttribute> eas = experiment.getExperimentAttributes();
if (eas != null && !eas.isEmpty()) {
Set<ExperimentAttribute> newEas = new TreeSet<ExperimentAttribute>();
for (ExperimentAttribute ea : eas) {
newEas.add(copier.hibernate2dto(ExperimentAttribute.class, ea));
}
dto.setExperimentAttributes(newEas);
}
}
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
@Test
public void testExperiments() {
try {
// get row count of experiments in the dataset
int expected = getDataSet().getTable("Experiment").getRowCount();
// get number of experiments from the DAO
int actual = getExperimentDAO().count();
// test data contains 2 experiments, check size of returned list
TestCase.assertEquals("Wrong number of experiments", expected, actual);
System.out.println("Expected number of experiments: " + expected + ", actual: " + actual);
for (Experiment d : random(getExperimentDAO(), actual, 5)) {
TestCase.assertNotNull(d);
TestCase.assertNotNull(d.getId());
}
} catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
public CellLine getCells(Experiment expt) throws SQLException, UnknownRoleException {
java.sql.Connection cxn = loader.getConnection();
PreparedStatement ps = cxn.prepareStatement("select cells from experiment" + " where id=?");
ps.setInt(1, expt.getDBID());
ResultSet rs = ps.executeQuery();
int cellsID = -1;
if (rs.next()) {
cellsID = rs.getInt(1);
}
rs.close();
ps.close();
return chipLoader.loadCellLine(cellsID);
}
@Override
public File generateFilePath(SequencerPoolPartition partition, LibraryDilution l)
throws SubmissionException {
log.debug("Generating filepaths for partition " + partition.getId());
Pool pool = partition.getPool();
if (pool != null) {
if (pool.getExperiments() != null) {
Collection<Experiment> experiments = pool.getExperiments();
Experiment experiment = experiments.iterator().next();
// String filePath =
// lane.getFlowcell().getRun().getFilePath()+"/Data/Intensities/BaseCalls/PAP/Project_"+
String filePath =
partition.getSequencerPartitionContainer().getRun().getFilePath()
+ "/Data/Intensities/BaseCalls/PAP/Project_"
+ experiment.getStudy().getProject().getAlias()
+ "/Sample_"
+ l.getLibrary().getName()
+ "/"
+ l.getLibrary().getName()
+ "_"
+ l.getLibrary().getTagBarcode().getSequence()
+ "_L00"
+ partition.getPartitionNumber()
+ "*.fastq.gz";
// System.out.println(filePath);
File file = new File(filePath);
return (file);
} else {
throw new SubmissionException("partition.getPool=null!");
}
} else {
throw new SubmissionException("Collection of experiments is empty");
}
}
public org.craftsmenlabs.gareth.api.model.Experiment map(final Experiment experiment) {
org.craftsmenlabs.gareth.api.model.Experiment model =
new org.craftsmenlabs.gareth.api.model.Experiment();
model.setExperimentName(experiment.getExperimentName());
AssumptionBlock block = new AssumptionBlock();
block.setBaseline(experiment.getBaselineGlueLine());
block.setAssumption(experiment.getAssumeGlueLine());
block.setFailure(experiment.getFailureGlueLine());
block.setSuccess(experiment.getSuccessGlueLine());
block.setTime(experiment.getTimeGlueLine());
model.setAssumptionBlockList(Arrays.asList(block));
return model;
}
@Override
public void paint(Graphics g) {
super.paint(g);
int size = buffer.getFrames().size();
// int start = size-10;
// System.out.println("Range: "+start+","+(start+10));
g.setColor(new Color(255, 255, 255));
g.fillRect(SCREEN_MINX, SCREEN_MINY, SCREEN_MAXX - SCREEN_MINX, SCREEN_MAXY - SCREEN_MINY);
g.setColor(new Color(0, 0, 0));
g.drawRect(SCREEN_MINX, SCREEN_MINY, SCREEN_MAXX - SCREEN_MINX, SCREEN_MAXY - SCREEN_MINY);
if (size == 0) {
g.drawString("Empty buffer", 10, 50);
return;
}
// if(size<10) {
// start=0;
// }
// punkt w srodku
double xM = Calc.recalcAB(middlePoint[0], coefX[0], coefX[1]);
double yM = Calc.recalcAB(middlePoint[1], coefY[0], coefY[1]);
double xMiddle = Calc.recalc(xM, -screenX, +screenX, SCREEN_MINX, SCREEN_MAXX);
double yMiddle = Calc.recalc(yM, -screenY, +screenY, SCREEN_MINY, SCREEN_MAXY);
yMiddle = SCREEN_MAXY - yMiddle; // ???
Graph.circle(g, (int) xMiddle, (int) yMiddle, 10);
// punkty poprzednie
int frames = (size >= 10) ? 10 : size;
for (int i = 0; i < frames; i++) {
// System.out.println("Reading "+(i+start));
EyeFrame f = buffer.getFrames().get(i + size - frames);
// przeliczenie do zakresu -1000,+1000 - 0,0 jesli na srodek
double xCDeg = Calc.recalcAB(f.eyeX, coefX[0], coefX[1]);
double yCDeg = Calc.recalcAB(f.eyeY, coefY[0], coefY[1]);
// przeliczenie na wspó³rzêdne na ekranie
// TODO wielkoϾ okna ustalona na sztywno... -1000 to lewy brzeg, +1000 to prawy brzeg
double xScreen = Calc.recalc(xCDeg, -screenX, +screenX, SCREEN_MINX, SCREEN_MAXX);
double yScreen = Calc.recalc(yCDeg, -screenY, +screenY, SCREEN_MINY, SCREEN_MAXY);
// wyœwietlenie gaze pointa
yScreen = SCREEN_MAXY - yScreen; // ???
Point pScreen = new Point((int) xScreen, (int) yScreen);
g.drawString(
f.eyeX + "," + f.eyeY + " [" + (int) xScreen + "," + (int) yScreen + "]",
5,
(i * 20) + 50);
int c = 255 - i * 20; // kolor
// System.out.println(c);
g.setColor(new Color(c, c, c));
int s = i + 1;
// rzeczywisty gaze point
Graph.circle(g, pScreen.x, pScreen.y, s);
// jeœli to ostani punkt - dodatkowo ramka
if (i == frames - 1) {
// dwa punkty na osiach
g.fillRect(pScreen.x, getSize().height / 2 /*pScreen.y*/, s, s);
g.fillRect(getSize().height / 2 /*pScreen.x*/, pScreen.y, s, s);
g.drawLine(pScreen.x, getSize().height / 2, getSize().height / 2 /*pScreen.x*/, pScreen.y);
Dimension d = getSize();
g.drawString(
f.eyeX
+ ","
+ f.eyeY
+ " <"
+ (int) xCDeg
+ ","
+ (int) yCDeg
+ "> ["
+ (int) xScreen
+ ","
+ (int) yScreen
+ "]",
d.width / 2,
d.height / 2);
Graph.frame(g, (int) xScreen, (int) yScreen, 50);
}
}
// g.setColor(new Color(255,0,0));
// EyeFrame f = buffer.getFrames().get(size-1);
// double xCDeg = Calc.recalcAB(f.eyeX, coefX[0], coefX[1]);
// double yCDeg = Calc.recalcAB(f.eyeY, coefY[0], coefY[1]);
//
// //TODO: okno powinno byc obliczone w katach
// double xScreen = Calc.recalc(xCDeg, -screenX, +screenX, SCREEN_MINX, SCREEN_MAXX);
// double yScreen = Calc.recalc(yCDeg, -screenY, +screenY, SCREEN_MAXY, SCREEN_MINY);
//
// //yScreen = SCREEN_MAXY-yScreen;
// Dimension d = getSize();
// g.drawString(f.eyeX+","+f.eyeY+" <"+(int)xCDeg+","+(int)yCDeg+">
// ["+(int)xScreen+","+(int)yScreen+"]", d.width/2, d.height/2);
// Graph.frame(g, (int)xScreen, (int)yScreen, 50);
}
/**
* Sets the array of values to set the custom property to.
*
* @param newPropArray a value of type Object which should be an array of the appropriate values.
*/
@Override
public void setPropertyArray(Object newPropArray) {
super.setPropertyArray(newPropArray);
m_baseExperiment.setPropertyArray(newPropArray);
}
/**
* Prepares a remote experiment for running, creates sub experiments
*
* @throws Exception if an error occurs
*/
@Override
public void initialize() throws Exception {
if (m_baseExperiment == null) {
throw new Exception("No base experiment specified!");
}
m_experimentAborted = false;
m_finishedCount = 0;
m_failedCount = 0;
m_RunNumber = getRunLower();
m_DatasetNumber = 0;
m_PropertyNumber = 0;
m_CurrentProperty = -1;
m_CurrentInstances = null;
m_Finished = false;
if (m_remoteHosts.size() == 0) {
throw new Exception("No hosts specified!");
}
// initialize all remote hosts to available
m_remoteHostsStatus = new int[m_remoteHosts.size()];
m_remoteHostFailureCounts = new int[m_remoteHosts.size()];
m_remoteHostsQueue = new Queue();
// prime the hosts queue
for (int i = 0; i < m_remoteHosts.size(); i++) {
m_remoteHostsQueue.push(new Integer(i));
}
// set up sub experiments
m_subExpQueue = new Queue();
int numExps;
if (getSplitByDataSet()) {
numExps = m_baseExperiment.getDatasets().size();
} else if (getSplitByProperty()) {
numExps = m_baseExperiment.getPropertyArrayLength();
} else {
numExps = getRunUpper() - getRunLower() + 1;
}
m_subExperiments = new Experiment[numExps];
m_subExpComplete = new int[numExps];
// create copy of base experiment
SerializedObject so = new SerializedObject(m_baseExperiment);
if (getSplitByDataSet()) {
for (int i = 0; i < m_baseExperiment.getDatasets().size(); i++) {
m_subExperiments[i] = (Experiment) so.getObject();
// one for each data set
DefaultListModel temp = new DefaultListModel();
temp.addElement(m_baseExperiment.getDatasets().get(i));
m_subExperiments[i].setDatasets(temp);
m_subExpQueue.push(new Integer(i));
}
} else if (getSplitByProperty()) {
for (int i = 0; i < m_baseExperiment.getPropertyArrayLength(); i++) {
m_subExperiments[i] = (Experiment) so.getObject();
Object[] a = new Object[1];
a[0] = m_baseExperiment.getPropertyArrayValue(i);
m_subExperiments[i].setPropertyArray(a);
m_subExpQueue.push(new Integer(i));
}
} else {
for (int i = getRunLower(); i <= getRunUpper(); i++) {
m_subExperiments[i - getRunLower()] = (Experiment) so.getObject();
// one run for each sub experiment
m_subExperiments[i - getRunLower()].setRunLower(i);
m_subExperiments[i - getRunLower()].setRunUpper(i);
m_subExpQueue.push(new Integer(i - getRunLower()));
}
}
}
protected Element asXMLElement(Document document, Element OME_element) {
// Creating XML block for OME
if (OME_element == null) {
OME_element = document.createElementNS(NAMESPACE, "OME");
}
if (uuid != null) {
// Attribute property UUID
OME_element.setAttribute("UUID", uuid.toString());
}
if (creator != null) {
// Attribute property Creator
OME_element.setAttribute("Creator", creator.toString());
}
if (projects != null) {
// Element property Project which is complex (has
// sub-elements) and occurs more than once
for (Project projects_value : projects) {
OME_element.appendChild(projects_value.asXMLElement(document));
}
}
if (datasets != null) {
// Element property Dataset which is complex (has
// sub-elements) and occurs more than once
for (Dataset datasets_value : datasets) {
OME_element.appendChild(datasets_value.asXMLElement(document));
}
}
if (experiments != null) {
// Element property Experiment which is complex (has
// sub-elements) and occurs more than once
for (Experiment experiments_value : experiments) {
OME_element.appendChild(experiments_value.asXMLElement(document));
}
}
if (plates != null) {
// Element property Plate which is complex (has
// sub-elements) and occurs more than once
for (Plate plates_value : plates) {
OME_element.appendChild(plates_value.asXMLElement(document));
}
}
if (screens != null) {
// Element property Screen which is complex (has
// sub-elements) and occurs more than once
for (Screen screens_value : screens) {
OME_element.appendChild(screens_value.asXMLElement(document));
}
}
if (experimenters != null) {
// Element property Experimenter which is complex (has
// sub-elements) and occurs more than once
for (Experimenter experimenters_value : experimenters) {
OME_element.appendChild(experimenters_value.asXMLElement(document));
}
}
if (experimenterGroups != null) {
// Element property ExperimenterGroup which is complex (has
// sub-elements) and occurs more than once
for (ExperimenterGroup experimenterGroups_value : experimenterGroups) {
OME_element.appendChild(experimenterGroups_value.asXMLElement(document));
}
}
if (instruments != null) {
// Element property Instrument which is complex (has
// sub-elements) and occurs more than once
for (Instrument instruments_value : instruments) {
OME_element.appendChild(instruments_value.asXMLElement(document));
}
}
if (images != null) {
// Element property Image which is complex (has
// sub-elements) and occurs more than once
for (Image images_value : images) {
OME_element.appendChild(images_value.asXMLElement(document));
}
}
if (structuredAnnotations != null) {
// Element property StructuredAnnotations which is complex (has
// sub-elements)
OME_element.appendChild(structuredAnnotations.asXMLElement(document));
}
if (roIs != null) {
// Element property ROI which is complex (has
// sub-elements) and occurs more than once
for (ROI roIs_value : roIs) {
OME_element.appendChild(roIs_value.asXMLElement(document));
}
}
if (binaryOnly != null) {
// Element property BinaryOnly which is complex (has
// sub-elements)
OME_element.appendChild(binaryOnly.asXMLElement(document));
}
return super.asXMLElement(document, OME_element);
}
/**
* test method used to generate output for data about fifo. The assert is just to make webcat
* happy about the test having at least one assert. I'm using the tests to collect data about
* runtime and path size.
*/
public void testFIFISol() {
tester.testFIFO();
assertNotNull(tester);
}
public static ExperimentBuilder aCopyOf(Experiment experiment) {
return anExperiment()
.withExperimentSnapshot(experiment.getExperimentSnapshot())
.withId(experiment.getId())
.withLastUpdated(experiment.getLastUpdated());
}
public Experiment addParameter(String name, Iterable<String> values) {
for (Experiment e : experiments) {
e.addParameter(name, values);
}
return this;
}
/**
* Sets whether the custom property iterator should be used.
*
* @param newUsePropertyIterator true if so
*/
@Override
public void setUsePropertyIterator(boolean newUsePropertyIterator) {
super.setUsePropertyIterator(newUsePropertyIterator);
m_baseExperiment.setUsePropertyIterator(newUsePropertyIterator);
}
@Override
public boolean hasNext() {
return exprIt.hasNext() || (current != null && current.hasNext());
}
public static ExperimentModule forExperiment(Experiment experiment) {
Method benchmarkMethod = experiment.instrumentation().benchmarkMethod();
return new ExperimentModule(benchmarkMethod, experiment.userParameters());
}
/**
* test method used to generate output for data about the pq. The assert is just to make webcat
* happy about the test having at least one assert. I'm using the tests to collect data about
* runtime and path size.
*/
public void testPQSol() {
System.out.println("PQ:");
tester.testPQ();
assertNotNull(tester);
}
/**
* Sets the path of properties taken to get to the custom property to iterate over.
*
* @param newPropertyPath an array of PropertyNodes
*/
@Override
public void setPropertyPath(PropertyNode[] newPropertyPath) {
super.setPropertyPath(newPropertyPath);
m_baseExperiment.setPropertyPath(newPropertyPath);
}
/**
* Configures/Runs the Experiment from the command line.
*
* @param args command line arguments to the Experiment.
*/
public static void main(String[] args) {
try {
weka.core.WekaPackageManager.loadPackages(false, true, false);
RemoteExperiment exp = null;
// get options from XML?
String xmlOption = Utils.getOption("xml", args);
if (!xmlOption.equals("")) {
args = new XMLOptions(xmlOption).toArray();
}
Experiment base = null;
String expFile = Utils.getOption('l', args);
String saveFile = Utils.getOption('s', args);
boolean runExp = Utils.getFlag('r', args);
ArrayList<String> remoteHosts = new ArrayList<String>();
String runHost = " ";
while (runHost.length() != 0) {
runHost = Utils.getOption('h', args);
if (runHost.length() != 0) {
remoteHosts.add(runHost);
}
}
if (expFile.length() == 0) {
base = new Experiment();
try {
base.setOptions(args);
Utils.checkForRemainingOptions(args);
} catch (Exception ex) {
ex.printStackTrace();
String result =
"Usage:\n\n"
+ "-l <exp file>\n"
+ "\tLoad experiment from file (default use cli options)\n"
+ "-s <exp file>\n"
+ "\tSave experiment to file after setting other options\n"
+ "\t(default don't save)\n"
+ "-h <remote host name>\n"
+ "\tHost to run experiment on (may be specified more than once\n"
+ "\tfor multiple remote hosts)\n"
+ "-r \n"
+ "\tRun experiment on (default don't run)\n"
+ "-xml <filename | xml-string>\n"
+ "\tget options from XML-Data instead from parameters\n"
+ "\n";
Enumeration<Option> enm = ((OptionHandler) base).listOptions();
while (enm.hasMoreElements()) {
Option option = enm.nextElement();
result += option.synopsis() + "\n";
result += option.description() + "\n";
}
throw new Exception(result + "\n" + ex.getMessage());
}
} else {
Object tmp;
// KOML?
if ((KOML.isPresent()) && (expFile.toLowerCase().endsWith(KOML.FILE_EXTENSION))) {
tmp = KOML.read(expFile);
} else
// XML?
if (expFile.toLowerCase().endsWith(".xml")) {
XMLExperiment xml = new XMLExperiment();
tmp = xml.read(expFile);
}
// binary
else {
FileInputStream fi = new FileInputStream(expFile);
ObjectInputStream oi = new ObjectInputStream(new BufferedInputStream(fi));
tmp = oi.readObject();
oi.close();
}
if (tmp instanceof RemoteExperiment) {
exp = (RemoteExperiment) tmp;
} else {
base = (Experiment) tmp;
}
}
if (base != null) {
exp = new RemoteExperiment(base);
}
for (int i = 0; i < remoteHosts.size(); i++) {
exp.addRemoteHost(remoteHosts.get(i));
}
System.err.println("Experiment:\n" + exp.toString());
if (saveFile.length() != 0) {
// KOML?
if ((KOML.isPresent()) && (saveFile.toLowerCase().endsWith(KOML.FILE_EXTENSION))) {
KOML.write(saveFile, exp);
} else
// XML?
if (saveFile.toLowerCase().endsWith(".xml")) {
XMLExperiment xml = new XMLExperiment();
xml.write(saveFile, exp);
}
// binary
else {
FileOutputStream fo = new FileOutputStream(saveFile);
ObjectOutputStream oo = new ObjectOutputStream(new BufferedOutputStream(fo));
oo.writeObject(exp);
oo.close();
}
}
if (runExp) {
System.err.println("Initializing...");
exp.initialize();
System.err.println("Iterating...");
exp.runExperiment();
System.err.println("Postprocessing...");
exp.postProcess();
}
} catch (Exception ex) {
ex.printStackTrace();
System.err.println(ex.getMessage());
}
}
/** {@inheritDoc} */
@Override
@Put
public Representation put(Representation entity) {
authenticate();
Representation representation = null;
Experiment newObj = null;
JaxbObject<Experiment> jo = new JaxbObject<Experiment>();
try {
String text = entity.getText();
newObj = (Experiment) XmlTools.unMarshal(jo, new Experiment(), text);
} catch (SAXException ex) {
ex.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
} catch (IOException e) {
e.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e);
}
try {
ExperimentService service = BeanFactory.getExperimentServiceBean();
Experiment exp = (Experiment) testIfNull(service.findByID(newObj.getExperimentId()));
exp.givesPermission(registration);
// simple types
String title = newObj.getTitle();
String name = newObj.getName();
String desc = newObj.getDescription();
String alias = newObj.getAlias();
String accession = newObj.getAccession();
String status = newObj.getStatus();
String centerName = newObj.getCenterName();
String sequencerSpace = newObj.getSequenceSpace();
String baseCaller = newObj.getBaseCaller();
String qualityScorer = newObj.getQualityScorer();
Integer qualityNumberLevels = newObj.getQualityNumberOfLevels();
Integer qualityMultiplier = newObj.getQualityMultiplier();
Long expectedNumberSpots = newObj.getExpectedNumberSpots();
Long expectedNumberReads = newObj.getExpectedNumberReads();
// foreign keys
Study study = newObj.getStudy();
Registration owner = newObj.getOwner();
// sets
Set<ExperimentAttribute> expAttributes = newObj.getExperimentAttributes();
if (title != null) {
exp.setTitle(title);
}
if (name != null) {
exp.setName(name);
}
if (desc != null) {
exp.setDescription(desc);
}
if (alias != null) {
exp.setAlias(alias);
}
if (accession != null) {
exp.setAccession(accession);
}
if (status != null) {
exp.setStatus(status);
}
if (centerName != null) {
exp.setCenterName(centerName);
}
if (sequencerSpace != null) {
exp.setSequenceSpace(sequencerSpace);
}
if (baseCaller != null) {
exp.setBaseCaller(baseCaller);
}
if (qualityScorer != null) {
exp.setQualityScorer(qualityScorer);
}
if (qualityNumberLevels != null) {
exp.setQualityNumberOfLevels(qualityNumberLevels);
}
if (qualityMultiplier != null) {
exp.setQualityMultiplier(qualityMultiplier);
}
if (expectedNumberSpots != null) {
exp.setExpectedNumberSpots(expectedNumberSpots);
}
if (expectedNumberReads != null) {
exp.setExpectedNumberReads(expectedNumberReads);
}
if (study != null) {
StudyService ss = BeanFactory.getStudyServiceBean();
Study newStudy = ss.findByID(study.getStudyId());
if (newStudy != null && newStudy.givesPermission(registration)) {
exp.setStudy(newStudy);
} else if (newStudy == null) {
Log.info("Could not be found " + study);
}
}
if (owner != null) {
RegistrationService rs = BeanFactory.getRegistrationServiceBean();
Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
if (newReg != null) {
exp.setOwner(newReg);
} else {
Log.info("Could not be found " + owner);
}
} else if (exp.getOwner() == null) {
exp.setOwner(registration);
}
if (null != expAttributes) {
exp.getExperimentAttributes().clear();
for (ExperimentAttribute ea : expAttributes) {
ea.setExperiment(exp);
exp.getExperimentAttributes().add(ea);
}
}
service.update(registration, exp);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Experiment detachedLane = copier.hibernate2dto(Experiment.class, exp);
Document line = XmlTools.marshalToDocument(jo, detachedLane);
representation = XmlTools.getRepresentation(line);
getResponse().setEntity(representation);
getResponse()
.setLocationRef(
getRequest().getRootRef() + "/experiments/" + detachedLane.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
}
return representation;
}
/** runs before every test and sets up the testing environment */
public void setUp() {
tester = new Experiment();
tester.moveN(5);
}