Exemplo n.º 1
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());
  }
Exemplo n.º 2
0
 @Test
 public void testTreatmentArmsCorrect() {
   TreatmentArm arm1 = new TreatmentArm();
   arm1.setName("arm1");
   TreatmentArm arm2 = new TreatmentArm();
   arm2.setName("arm2");
   List<TreatmentArm> arms = new ArrayList<TreatmentArm>();
   arms.add(arm1);
   arms.add(arm2);
   validTrial.setTreatmentArms(arms);
   assertEquals(arms, validTrial.getTreatmentArms());
   assertEquals(2, validTrial.getTreatmentArms().size());
   assertTrue(validTrial.getTreatmentArms().containsAll(arms));
   assertValid(validTrial);
 }
Exemplo n.º 3
0
 @Test
 public void testTreatmentArmsNull() {
   validTrial.setTreatmentArms(null);
   assertNull(validTrial.getTreatmentArms());
   assertValid(validTrial);
 }
Exemplo n.º 4
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());
  }
Exemplo n.º 5
0
  private void randomizeInValidTrialTwoTrialSites31()
      throws IllegalArgumentException, TrialStateException {
    authenticatAsAdmin();
    Person cp1 = new Person();
    cp1.setFirstname("Contact");
    cp1.setSurname("Person");
    cp1.setEmail("*****@*****.**");
    cp1.setPhone("1234567");
    cp1.setSex(Gender.MALE);
    TrialSite trialSite1 = new TrialSite();
    trialSite1.setCity("Heidelberg");
    trialSite1.setCountry("Germany");
    trialSite1.setName("NCT");
    trialSite1.setPostcode("69120");
    trialSite1.setStreet("INF");
    trialSite1.setPassword("1$heidelberg");
    trialSite1.setContactPerson(cp1);
    trialSiteService.create(trialSite1);

    Person cp2 = new Person();
    cp2.setFirstname("Contact");
    cp2.setSurname("Person");
    cp2.setEmail("*****@*****.**");
    cp2.setPhone("1234567");
    cp2.setSex(Gender.MALE);
    TrialSite trialSite2 = new TrialSite();
    trialSite2.setCity("Heidelberg");
    trialSite2.setCountry("Germany");
    trialSite2.setName("NCT2");
    trialSite2.setPostcode("69120");
    trialSite2.setStreet("INF");
    trialSite2.setPassword("1$heidelberg");
    trialSite2.setContactPerson(cp2);
    trialSiteService.create(trialSite2);

    validTrial.addParticipatingSite(trialSite1);
    validTrial.addParticipatingSite(trialSite2);
    validTrial.setStartDate(new GregorianCalendar(2009, 0, 1));
    validTrial.setEndDate(new GregorianCalendar(2009, 11, 1));

    authenticatAsPrincipalInvestigator();
    int blocksize = 4;
    int randomizations = 120;
    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());
    Iterator<TrialSite> it = validTrial.getParticipatingSites().iterator();
    TrialSite site1 = it.next();
    TrialSite site2 = it.next();
    authenticatAsInvestigator();
    for (int i = 0; i < randomizations; i++) {
      TrialSubject subject = new TrialSubject();
      subject.setIdentification("identification" + i);
      if (i < 90) {
        subject.setTrialSite(site1);
      } else {
        subject.setTrialSite(site2);
      }
      trialService.randomize(validTrial, subject);
      subject.setCreatedAt(new GregorianCalendar(2009, 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());
  }