Example #1
0
  @Test
  public void testSubjectCriteriaCorrect() {
    DichotomousCriterion criterion1 = new DichotomousCriterion();
    criterion1.setName("criterion1");
    DichotomousCriterion criterion2 = new DichotomousCriterion();
    criterion2.setName("criterion2");
    List<
            AbstractCriterion<
                ? extends Serializable, ? extends AbstractConstraint<? extends Serializable>>>
        criteria =
            new ArrayList<
                AbstractCriterion<
                    ? extends Serializable,
                    ? extends AbstractConstraint<? extends Serializable>>>();
    criteria.add(criterion1);
    criteria.add(criterion2);
    validTrial.setCriteria(criteria);
    assertEquals(2, validTrial.getCriteria().size());
    assertTrue(DichotomousCriterion.class.isInstance(validTrial.getCriteria().get(0)));
    assertEquals("criterion1", validTrial.getCriteria().get(0).getName());
    assertTrue(DichotomousCriterion.class.isInstance(validTrial.getCriteria().get(1)));
    assertEquals("criterion2", validTrial.getCriteria().get(1).getName());

    List<
            AbstractCriterion<
                ? extends Serializable, ? extends AbstractConstraint<? extends Serializable>>>
        list =
            new ArrayList<
                AbstractCriterion<
                    ? extends Serializable,
                    ? extends AbstractConstraint<? extends Serializable>>>();
    validTrial.setCriteria(list);
    assertEquals(list, validTrial.getCriteria());
  }
Example #2
0
 @Test
 public void testAddSubjectCriteria() {
   DichotomousCriterion criterion1 = new DichotomousCriterion();
   criterion1.setName("criterion1");
   DichotomousCriterion criterion2 = new DichotomousCriterion();
   criterion2.setName("criterion2");
   validTrial.addCriterion(criterion1);
   validTrial.addCriterion(criterion2);
   assertEquals(2, validTrial.getCriteria().size());
   assertTrue(DichotomousCriterion.class.isInstance(validTrial.getCriteria().get(0)));
   assertEquals("criterion1", validTrial.getCriteria().get(0).getName());
   assertTrue(DichotomousCriterion.class.isInstance(validTrial.getCriteria().get(1)));
   assertEquals("criterion2", validTrial.getCriteria().get(1).getName());
   assertValid(validTrial);
 }
Example #3
0
  @Test
  public void testStrataNamesAndIdsStrataCriterionsTrialSite() {

    TrialSite site1 = new TrialSite();
    site1.setId(1);
    site1.setName("site1");

    TrialSite site2 = new TrialSite();
    site2.setId(2);
    site2.setName("site2");

    validTrial.addParticipatingSite(site1);
    validTrial.addParticipatingSite(site2);

    validTrial.setStratifyTrialSite(true);

    DichotomousCriterion criterion1 = new DichotomousCriterion();
    criterion1.setId(1);
    criterion1.setName("criterion1");
    criterion1.setOption1("option1");
    criterion1.setOption2("option2");
    try {
      DichotomousConstraint d1 = new DichotomousConstraint(Arrays.asList(new String[] {"option1"}));
      d1.setId(1);
      criterion1.addStrata(d1);
      DichotomousConstraint d2 = new DichotomousConstraint(Arrays.asList(new String[] {"option2"}));
      d2.setId(2);
      criterion1.addStrata(d2);
    } catch (ContraintViolatedException e) {
      fail();
    }
    DichotomousCriterion criterion2 = new DichotomousCriterion();
    criterion2.setId(2);
    criterion2.setName("criterion2");
    criterion2.setOption1("option1");
    criterion2.setOption2("option2");
    try {
      DichotomousConstraint d1 = new DichotomousConstraint(Arrays.asList(new String[] {"option1"}));
      d1.setId(1);
      criterion2.addStrata(d1);
      DichotomousConstraint d2 = new DichotomousConstraint(Arrays.asList(new String[] {"option2"}));
      d2.setId(2);
      criterion2.addStrata(d2);
    } catch (ContraintViolatedException e) {
      fail();
    }
    validTrial.addCriterion(criterion1);
    validTrial.addCriterion(criterion2);

    Pair<List<String>, List<String>> pair = validTrial.getAllStrataIdsAndNames();

    assertEquals(8, pair.first().size());
    assertEquals(8, pair.last().size());

    Collections.sort(pair.first());
    assertEquals("1__1_1;2_1;", pair.first().get(0));
    assertEquals("1__1_1;2_2;", pair.first().get(1));
    assertEquals("1__1_2;2_1;", pair.first().get(2));
    assertEquals("1__1_2;2_2;", pair.first().get(3));
    assertEquals("2__1_1;2_1;", pair.first().get(4));
    assertEquals("2__1_1;2_2;", pair.first().get(5));
    assertEquals("2__1_2;2_1;", pair.first().get(6));
    assertEquals("2__1_2;2_2;", pair.first().get(7));

    Collections.sort(pair.last());
    assertEquals("site1 | criterion1_option1;criterion2_option1;", pair.last().get(0));
    assertEquals("site1 | criterion1_option1;criterion2_option2;", pair.last().get(1));
    assertEquals("site1 | criterion1_option2;criterion2_option1;", pair.last().get(2));
    assertEquals("site1 | criterion1_option2;criterion2_option2;", pair.last().get(3));
    assertEquals("site2 | criterion1_option1;criterion2_option1;", pair.last().get(4));
    assertEquals("site2 | criterion1_option1;criterion2_option2;", pair.last().get(5));
    assertEquals("site2 | criterion1_option2;criterion2_option1;", pair.last().get(6));
    assertEquals("site2 | criterion1_option2;criterion2_option2;", pair.last().get(7));
  }
Example #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());
  }