@Test
public void testLeadingSiteCorrect() {
TrialSite c = factory.getTrialSite();
validTrial.setLeadingSite(c);
assertEquals(c, validTrial.getLeadingSite());
assertValid(validTrial);
}
private void randomizeInValidTrialTwoYears()
throws IllegalArgumentException, TrialStateException {
authenticatAsPrincipalInvestigator();
validTrial.setStartDate(new GregorianCalendar(2009, 0, 1));
validTrial.setEndDate(new GregorianCalendar(2010, 11, 1));
int blocksize = 4;
int randomizations = 240;
TreatmentArm arm1 = new TreatmentArm();
arm1.setPlannedSubjects(randomizations / 2);
arm1.setName("arm1");
arm1.setTrial(validTrial);
TreatmentArm arm2 = new TreatmentArm();
arm2.setPlannedSubjects(randomizations / 2);
arm2.setName("arm2");
arm2.setTrial(validTrial);
List<TreatmentArm> arms = new ArrayList<TreatmentArm>();
arms.add(arm1);
arms.add(arm2);
trialService.create(validTrial);
validTrial.setTreatmentArms(arms);
BlockRandomizationConfig config = new BlockRandomizationConfig();
config.setMaximum(blocksize);
config.setMinimum(blocksize);
validTrial.setRandomizationConfiguration(config);
trialService.update(validTrial);
assertTrue(validTrial.getId() > 0);
assertEquals(2, validTrial.getTreatmentArms().size());
authenticatAsInvestigator();
for (int i = 0; i < randomizations; i++) {
TrialSubject subject = new TrialSubject();
subject.setIdentification("identification" + i);
subject.setTrialSite(validTrial.getLeadingSite());
trialService.randomize(validTrial, subject);
subject.setCreatedAt(new GregorianCalendar(2009 + (i >= 120 ? 1 : 0), i % 12, 1));
sessionFactory.getCurrentSession().update(subject);
if ((i % blocksize) == (blocksize - 1)) {
assertEquals(
validTrial.getTreatmentArms().get(0).getSubjects().size(),
validTrial.getTreatmentArms().get(1).getSubjects().size());
}
int diff =
validTrial.getTreatmentArms().get(0).getSubjects().size()
- validTrial.getTreatmentArms().get(1).getSubjects().size();
assertTrue((blocksize / 2) >= diff && (-1) * (blocksize / 2) <= diff);
}
Trial dbTrial = trialService.getObject(validTrial.getId());
assertNotNull(dbTrial);
assertEquals(validTrial.getName(), dbTrial.getName());
assertEquals(2, dbTrial.getTreatmentArms().size());
assertEquals(
randomizations,
dbTrial.getTreatmentArms().get(0).getSubjects().size()
+ dbTrial.getTreatmentArms().get(1).getSubjects().size());
assertEquals(randomizations / 2, dbTrial.getTreatmentArms().get(0).getSubjects().size());
assertEquals(randomizations / 2, dbTrial.getTreatmentArms().get(1).getSubjects().size());
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void logTrialChange(
LogEntry.ActionType action, String username, Trial oldTrial, Trial changedTrial) {
LogEntry entry = new LogEntry();
entry.setAction(action);
entry.setUsername(username);
entry.setClazz(Trial.class);
entry.setIdentifier(changedTrial.getId());
StringBuilder sb = new StringBuilder();
if (!oldTrial.getName().equals(changedTrial.getName())) {
sb.append("Name: ")
.append(oldTrial.getName())
.append(" -> ")
.append(changedTrial.getName())
.append(" | ");
}
if (!oldTrial.getAbbreviation().equals(changedTrial.getAbbreviation())) {
sb.append("Abbreviation: ")
.append(oldTrial.getAbbreviation())
.append(" -> ")
.append(changedTrial.getAbbreviation())
.append(" | ");
}
if (!oldTrial.getDescription().equals(changedTrial.getDescription())) {
sb.append("Description: ")
.append(oldTrial.getDescription())
.append(" -> ")
.append(changedTrial.getDescription())
.append(" | ");
}
if (!oldTrial.getStartDate().equals(changedTrial.getStartDate())) {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
sb.append("Start-Date: ")
.append(sdf.format(oldTrial.getStartDate().getTime()))
.append(" -> ")
.append(sdf.format(changedTrial.getStartDate().getTime()))
.append(" | ");
}
if (!oldTrial.getEndDate().equals(changedTrial.getEndDate())) {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
sb.append("End-Date: ")
.append(sdf.format(oldTrial.getEndDate().getTime()))
.append(" -> ")
.append(sdf.format(changedTrial.getEndDate().getTime()))
.append(" | ");
}
if (!oldTrial.getLeadingSite().equals(changedTrial.getLeadingSite())) {
sb.append("Leading Site: ")
.append(oldTrial.getLeadingSite().getName())
.append(" -> ")
.append(changedTrial.getLeadingSite().getName())
.append(" | ");
}
if (!oldTrial.getSponsorInvestigator().equals(changedTrial.getSponsorInvestigator())) {
sb.append("Sponsor investigator: ")
.append(oldTrial.getSponsorInvestigator().getUIName())
.append(" -> ")
.append(changedTrial.getSponsorInvestigator().getUIName())
.append(" | ");
}
if (!(oldTrial.getStatus() == changedTrial.getStatus())) {
sb.append("Status: ")
.append(oldTrial.getStatus())
.append(" -> ")
.append(changedTrial.getStatus());
}
if (sb.length() == 0) {
sb.append(changedTrial.getAbbreviation());
}
entry.setUiName(sb.toString());
entry.setValue(sb.toString());
entityManager.persist(entry);
}
@Test
public void testLeadingSiteNotNull() {
validTrial.setLeadingSite(null);
assertNull(validTrial.getLeadingSite());
assertInvalid(validTrial);
}
@Test
public void testChartSubGroups() {
authenticatAsPrincipalInvestigator();
validTrial.setStartDate(new GregorianCalendar(2009, 0, 1));
validTrial.setEndDate(new GregorianCalendar(2010, 11, 1));
int blocksize = 4;
int randomizations = 240;
TreatmentArm arm1 = new TreatmentArm();
arm1.setPlannedSubjects(randomizations / 2);
arm1.setName("arm1");
arm1.setTrial(validTrial);
TreatmentArm arm2 = new TreatmentArm();
arm2.setPlannedSubjects(randomizations / 2);
arm2.setName("arm2");
arm2.setTrial(validTrial);
List<TreatmentArm> arms = new ArrayList<TreatmentArm>();
arms.add(arm1);
arms.add(arm2);
validTrial.setTreatmentArms(arms);
DichotomousCriterion cr = new DichotomousCriterion();
cr.setOption1("1");
cr.setOption2("2");
DichotomousCriterion cr1 = new DichotomousCriterion();
cr1.setOption1("1");
cr1.setOption2("2");
DichotomousCriterion cr2 = new DichotomousCriterion();
cr2.setOption1("1");
cr2.setOption2("2");
try {
cr.addStrata(new DichotomousConstraint(Arrays.asList(new String[] {"1"})));
cr.addStrata(new DichotomousConstraint(Arrays.asList(new String[] {"2"})));
cr1.addStrata(new DichotomousConstraint(Arrays.asList(new String[] {"1"})));
cr1.addStrata(new DichotomousConstraint(Arrays.asList(new String[] {"2"})));
cr2.addStrata(new DichotomousConstraint(Arrays.asList(new String[] {"1"})));
cr2.addStrata(new DichotomousConstraint(Arrays.asList(new String[] {"2"})));
validTrial.addCriterion(cr);
validTrial.addCriterion(cr1);
validTrial.addCriterion(cr2);
} catch (ContraintViolatedException e) {
BoxedException.throwBoxed(e);
}
BlockRandomizationConfig config = new BlockRandomizationConfig();
config.setMaximum(blocksize);
config.setMinimum(blocksize);
validTrial.setRandomizationConfiguration(config);
trialService.create(validTrial);
assertTrue(validTrial.getId() > 0);
assertEquals(2, validTrial.getTreatmentArms().size());
authenticatAsInvestigator();
for (int i = 0; i < randomizations; i++) {
TrialSubject subject = new TrialSubject();
subject.setIdentification("identification" + i);
subject.setTrialSite(validTrial.getLeadingSite());
SubjectProperty<Serializable> subprob =
new SubjectProperty<Serializable>(validTrial.getCriteria().get(0));
SubjectProperty<Serializable> subprob1 =
new SubjectProperty<Serializable>(validTrial.getCriteria().get(1));
SubjectProperty<Serializable> subprob2 =
new SubjectProperty<Serializable>(validTrial.getCriteria().get(2));
try {
if ((new Random()).nextInt(2) == 0) {
subprob.setValue(cr.getOption1());
} else {
subprob.setValue(cr.getOption2());
}
if ((new Random()).nextInt(2) == 0) {
subprob1.setValue(cr1.getOption1());
} else {
subprob1.setValue(cr1.getOption2());
}
if ((new Random()).nextInt(2) == 0) {
subprob2.setValue(cr2.getOption1());
} else {
subprob2.setValue(cr2.getOption2());
}
} catch (ContraintViolatedException e) {
BoxedException.throwBoxed(e);
}
Set<SubjectProperty<?>> proberties = new HashSet<SubjectProperty<?>>();
proberties.add(subprob);
proberties.add(subprob1);
proberties.add(subprob2);
subject.setProperties(proberties);
trialService.randomize(validTrial, subject);
subject.setCreatedAt(new GregorianCalendar(2009 + (i >= 120 ? 1 : 0), i % 12, 1));
sessionFactory.getCurrentSession().update(subject);
}
ChartData data = chartsService.generateRecruitmentChartFactors(validTrial);
assertEquals(8, data.getData().size());
assertEquals(8, data.getData().get(0).length);
assertEquals(8, data.getXLabels().size());
}
