public static void main(String[] args) { boolean test = false; if (test) { File f = new File("Z:\\workspace"); System.out.println(f.getPath()); File f2 = new File(f.getPath() + "petulant-batman"); System.out.println(f2.getPath()); } if (WINDOWS) { // StudyBuilder sb = new StudyBuilder("C:\\Studies", StudyBuilder.StudyType.local); String root = "C:\\"; StudyFactory.StudyType type = StudyFactory.StudyType.local; List<Study> studies; try { StudyFactory.setRoot(root); studies = Arrays.asList(StudyFactory.getAvailableStudies(type)); for (Study s : studies) { for (String img : s.getImgAddresses()) { System.out.println(img); } } } catch (NoValidStudiesFoundException nvsfe) { System.out.println(nvsfe); } } else { System.err.println("Please write a test for " + OS + "!"); } }
public Interview(Study study) { interview_time = new Date(); study_id = study.getId(); recordings = new ArrayList<Recording>(study.getPhrases().size()); for (Phrase phrase : study.getPhrases()) { Recording recording = new Recording(); recording.setPhrase_id(phrase.getId()); recordings.add(recording); } }
/* * (non-Javadoc) * @see mivc.System.ImageProcurator#getReferenceImage(int, mivc.System.Study) */ @Override public BufferedImage getReferenceImage(int index, Study study) { BufferedImage retVal = new BufferedImage(study.getMaxX(), study.getMaxY(), BufferedImage.TYPE_INT_RGB); for (int x = 0; x < retVal.getWidth(); x++) { for (int y = 0; y < retVal.getHeight(); y++) { // Store the current x, y data into the array retVal.setRGB(x, y, study.getPixel(x, y, index)); } } return retVal; }
private void migrateCourseAgent( CourseAgent caSrc, ExpeditedAdverseEventReport aeReportDest, DomainObjectImportOutcome<ExpeditedAdverseEventReport> outcome) { Study study = aeReportDest.getStudy(); StudyAgent studyAgent = caSrc.getStudyAgent(); if (studyAgent == null || ((studyAgent.getAgent() == null || StringUtils.isEmpty(studyAgent.getAgent().getNscNumber())) && StringUtils.isEmpty(studyAgent.getOtherAgent()))) { outcome.addWarning("ER-CA-1", "Study Agent is missing in the source"); return; } StudyAgent realStudyAgent = studyAgent.getAgent() == null ? study.findStudyAgentByNscOrName(studyAgent.getOtherAgent()) : study.findStudyAgentByNscOrName(studyAgent.getAgent().getNscNumber()); if (realStudyAgent == null) { outcome.addWarning("ER-CA-2", "Given Agent is no longer associated to the study"); return; } CourseAgent caDest = new CourseAgent(); aeReportDest.getTreatmentInformation().addCourseAgent(caDest); // set the study agent caDest.setStudyAgent(realStudyAgent); caDest.setDose(caSrc.getDose()); caDest.setAdministrationDelay(caSrc.getAdministrationDelay()); caDest.setAdministrationDelayAmount(caSrc.getAdministrationDelayAmount()); caDest.setAdministrationDelayUnits(caSrc.getAdministrationDelayUnits()); caDest.setComments(caSrc.getComments()); caDest.setAgentAdjustment(caSrc.getAgentAdjustment()); caDest.setModifiedDose(caSrc.getModifiedDose()); caDest.setLastAdministeredDate(caSrc.getLastAdministeredDate()); caDest.setDurationAndSchedule(caSrc.getDurationAndSchedule()); caDest.setFirstAdministeredDate(caSrc.getFirstAdministeredDate()); caDest.setTotalDoseAdministeredThisCourse(caSrc.getTotalDoseAdministeredThisCourse()); caDest.setFormulation(caSrc.getFormulation()); caDest.setLotNumber(caSrc.getLotNumber()); }
/* * (non-Javadoc) * @see mivc.System.ImageGetter#getReconstructedImage(int, mivc.System.Study, int, int) */ @Override public BufferedImage getReconstructedImage(int index, Study study, int min, int max) { BufferedImage retVal = new BufferedImage(study.getMaxX(), study.getMaxY(), BufferedImage.TYPE_INT_RGB); for (int x = 0; x < retVal.getWidth(); x++) { for (int y = 0; y < retVal.getHeight(); y++) { // Store the current x, y data into the array retVal.setRGB(x, y, study.getPixel(x, y, index)); } } if (min > 0 || max < 255) { return ImageUtil.windowImage(retVal, min, max); } else { return retVal; } }
@Test public void testStudies() { try { // get row count of experiments in the dataset int expected = getDataSet().getTable("Study").getRowCount(); // get number of experiments from the DAO int actual = getStudyDAO().count(); // test data contains 2 experiments, check size of returned list TestCase.assertEquals("Wrong number of Study", expected, actual); System.out.println("Expected number of Study: " + expected + ", actual: " + actual); for (Study d : random(getStudyDAO(), actual, 5)) { TestCase.assertNotNull(d); TestCase.assertNotNull(d.getId()); } } catch (Exception e) { e.printStackTrace(); TestCase.fail(); } }
public void testRemoveDetachedNodesWhileIterating() { Study s = Fixtures.createReleasedTemplate(); Delta pc = Delta.createDeltaFor(s.getPlannedCalendar()); Delta epoch2 = Delta.createDeltaFor(s.getPlannedCalendar().getEpochs().get(0)); StudySegment segment1 = s.getPlannedCalendar().getEpochs().get(0).getStudySegments().get(1); Delta ss1 = Delta.createDeltaFor(segment1); Delta ss2 = Delta.createDeltaFor(s.getPlannedCalendar().getEpochs().get(0).getStudySegments().get(2)); List<Delta<?>> deltaList = new ArrayList<Delta<?>>(); deltaList.add(ss1); deltaList.add(epoch2); deltaList.add(pc); deltaList.add(ss2); expect(templateService.findEquivalentChild(s, pc.getNode())).andReturn(pc.getNode()); expect(templateService.findEquivalentChild(s, epoch2.getNode())).andReturn(epoch2.getNode()); expect(templateService.findEquivalentChild(s, ss1.getNode())).andReturn(ss1.getNode()); expect(templateService.findEquivalentChild(s, ss2.getNode())).andReturn(ss2.getNode()); replayMocks(); DeltaIterator di = new DeltaIterator(deltaList, s, templateService, false); List<Delta> encountered = new LinkedList<Delta>(); while (di.hasNext()) { Delta delta = di.next(); encountered.add(delta); if (delta == epoch2) { segment1.setParent(null); } } assertEquals("Wrong number of deltas encountered: " + encountered, 3, encountered.size()); assertEquals("Wrong delta 0", pc, encountered.get(0)); assertEquals("Wrong delta 1", epoch2, encountered.get(1)); assertEquals("Wrong delta 2", ss2, encountered.get(2)); verifyMocks(); }
@Test public void testRoundtripVersionInfo() throws MalformedURLException { Study study = new Study(); Assert.assertNull(study.getVersionInfo()); study.setVersionInfo("1"); URL resource = StudyClient.upload(study, new URL(TEST_SERVER)); Study roundtripped = StudyClient.download(resource); Assert.assertNotNull(roundtripped.getVersionInfo()); Assert.assertEquals("1", roundtripped.getVersionInfo()); }
@Test public void testRoundtripAbstract() throws MalformedURLException { Study study = new Study(); Assert.assertNull(study.getAbstract()); study.setAbstract("This is an abstract"); URL resource = StudyClient.upload(study, new URL(TEST_SERVER)); Study roundtripped = StudyClient.download(resource); Assert.assertNotNull(roundtripped.getAbstract()); Assert.assertEquals(19, roundtripped.getAbstract().length()); }
@Test public void testRoundtripKeywords() throws MalformedURLException { Study study = new Study(); Assert.assertEquals(0, study.getKeywords().size()); study.addKeyword("foo"); URL resource = StudyClient.upload(study, new URL(TEST_SERVER)); Study roundtripped = StudyClient.download(resource); Assert.assertEquals(1, roundtripped.getKeywords().size()); Assert.assertTrue(roundtripped.getKeywords().contains("foo")); }
/** {@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; }
public Meeting(Study study) { this(); this.study = study; this.maximum = study.getMaximum(); }
public void testDetailOrder() { Study s = Fixtures.createReleasedTemplate(); Period period = Fixtures.createPeriod("period1", 1, 10, 2); PlannedActivity plannedActivity = Fixtures.createPlannedActivity("activity", 3); PlannedActivityLabel plannedActivityLabel = Fixtures.createPlannedActivityLabel("label"); period.addPlannedActivity(plannedActivity); plannedActivity.addPlannedActivityLabel(plannedActivityLabel); s.getPlannedCalendar().getEpochs().get(0).getStudySegments().get(0).getPeriods().add(period); Delta studyDelta = Delta.createDeltaFor(s.getPlannedCalendar().getStudy()); Delta epochDelta = Delta.createDeltaFor(s.getPlannedCalendar().getEpochs().get(0)); Delta studySegmentDelta = Delta.createDeltaFor(s.getPlannedCalendar().getEpochs().get(0).getStudySegments().get(1)); Delta periodDelta = Delta.createDeltaFor( s.getPlannedCalendar() .getEpochs() .get(0) .getStudySegments() .get(0) .getPeriods() .last()); Delta plannedActivityDelta = Delta.createDeltaFor( s.getPlannedCalendar() .getEpochs() .get(0) .getStudySegments() .get(0) .getPeriods() .first() .getPlannedActivities() .get(0)); Delta plannedActivityLabelDelta = Delta.createDeltaFor( s.getPlannedCalendar() .getEpochs() .get(0) .getStudySegments() .get(0) .getPeriods() .first() .getPlannedActivities() .get(0) .getPlannedActivityLabels() .first()); List<Delta<?>> listOfDeltas = new ArrayList<Delta<?>>(); listOfDeltas.add(plannedActivityDelta); listOfDeltas.add(periodDelta); listOfDeltas.add(epochDelta); listOfDeltas.add(studyDelta); listOfDeltas.add(studySegmentDelta); listOfDeltas.add(plannedActivityLabelDelta); expect(templateService.findEquivalentChild(s, studyDelta.getNode())).andReturn(s); expect(templateService.findEquivalentChild(s, periodDelta.getNode())).andReturn(null); expect(templateService.findEquivalentChild(s, epochDelta.getNode())) .andReturn(epochDelta.getNode()); expect(templateService.findEquivalentChild(s, studySegmentDelta.getNode())) .andReturn(studySegmentDelta.getNode()); expect(templateService.findEquivalentChild(s, plannedActivityDelta.getNode())).andReturn(null); expect(templateService.findEquivalentChild(s, plannedActivityLabelDelta.getNode())) .andReturn(plannedActivityLabelDelta.getNode()); replayMocks(); DeltaIterator di = new DeltaIterator(listOfDeltas, s, templateService, false); assertSame("studyDelta is not the first element", studyDelta, di.next()); assertSame("epochDelta is not the second element", epochDelta, di.next()); assertSame("studySegmentDelta is not the third element", studySegmentDelta, di.next()); assertSame("periodDelta is not the forth element", plannedActivityLabelDelta, di.next()); assertFalse("deltaIterator has more elements ", di.hasNext()); verifyMocks(); }
public void resolveNames(Long batchSize) { StopWatch watchForEntireRun = new StopWatch(); watchForEntireRun.start(); StopWatch watchForBatch = new StopWatch(); watchForBatch.start(); Long count = 0L; Index<Node> studyIndex = graphService.index().forNodes("studies"); IndexHits<Node> studies = studyIndex.query("title", "*"); for (Node studyNode : studies) { final Study study1 = new Study(studyNode); final Iterable<Relationship> specimens = study1.getSpecimens(); for (Relationship collected : specimens) { Specimen specimen = new Specimen(collected.getEndNode()); final Relationship classifiedAs = specimen .getUnderlyingNode() .getSingleRelationship(RelTypes.CLASSIFIED_AS, Direction.OUTGOING); if (classifiedAs == null) { final Relationship describedAs = specimen .getUnderlyingNode() .getSingleRelationship(RelTypes.ORIGINALLY_DESCRIBED_AS, Direction.OUTGOING); final TaxonNode describedAsTaxon = new TaxonNode(describedAs.getEndNode()); try { if (taxonFilter.shouldInclude(describedAsTaxon)) { TaxonNode resolvedTaxon = taxonIndex.getOrCreateTaxon(describedAsTaxon); if (resolvedTaxon != null) { specimen.classifyAs(resolvedTaxon); } } } catch (NodeFactoryException e) { LOG.warn( "failed to create taxon with name [" + describedAsTaxon.getName() + "] and id [" + describedAsTaxon.getExternalId() + "]", e); } finally { count++; if (count % batchSize == 0) { watchForBatch.stop(); final long duration = watchForBatch.getTime(); if (duration > 0) { LOG.info( "resolved batch of [" + batchSize + "] names in " + getProgressMsg(batchSize, duration)); } watchForBatch.reset(); watchForBatch.start(); } } } } } studies.close(); watchForEntireRun.stop(); LOG.info( "resolved [" + count + "] names in " + getProgressMsg(count, watchForEntireRun.getTime())); }