Ejemplo n.º 1
0
 @Test
 public void testLeadingSiteCorrect() {
   TrialSite c = factory.getTrialSite();
   validTrial.setLeadingSite(c);
   assertEquals(c, validTrial.getLeadingSite());
   assertValid(validTrial);
 }
Ejemplo n.º 2
0
  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());
  }
Ejemplo n.º 3
0
  @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);
  }
Ejemplo n.º 4
0
 @Test
 public void testLeadingSiteNotNull() {
   validTrial.setLeadingSite(null);
   assertNull(validTrial.getLeadingSite());
   assertInvalid(validTrial);
 }
Ejemplo n.º 5
0
  @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());
  }