@Test
public void getMatchingRows() {
Set<ResultRow> rows = new HashSet<ResultRow>();
ResultRow rowOne = new ResultRow();
rowOne.setSubjectAssignment(new StudySubjectAssignment());
rowOne.getSubjectAssignment().setIdentifier("1");
rows.add(rowOne);
ResultRow rowTwo = new ResultRow();
rowTwo.setSubjectAssignment(new StudySubjectAssignment());
rowTwo.getSubjectAssignment().setIdentifier("2");
rows.add(rowTwo);
ResultRow existingRow = new ResultRow();
existingRow.setSubjectAssignment(rowOne.getSubjectAssignment());
ResultRow nonExistentRow = new ResultRow();
nonExistentRow.setSubjectAssignment(new StudySubjectAssignment());
nonExistentRow.getSubjectAssignment().setIdentifier("3");
assertEquals(rowOne, QueryUtil.getMatchingRow(rows, existingRow, false));
assertEquals(rowOne, QueryUtil.getMatchingRow(rows, existingRow, true));
assertNull(QueryUtil.getMatchingRow(rows, nonExistentRow, false));
assertNull(QueryUtil.getMatchingRow(rows, nonExistentRow, true));
}
@Test
public void testAnnotationValueBelongToPermissibleValue() {
StringAnnotationValue stringValue = new StringAnnotationValue();
stringValue.setStringValue("TeSt");
PermissibleValue stringPermissibleValue = new PermissibleValue();
stringPermissibleValue.setValue("tEsT");
assertTrue(
QueryUtil.annotationValueBelongToPermissibleValue(stringValue, stringPermissibleValue));
stringPermissibleValue.setValue("Not Equals");
assertFalse(
QueryUtil.annotationValueBelongToPermissibleValue(stringValue, stringPermissibleValue));
NumericAnnotationValue numericValue = new NumericAnnotationValue();
numericValue.setNumericValue(50.0);
PermissibleValue numericPermissibleValue = new PermissibleValue();
numericPermissibleValue.setValue("50.0");
assertTrue(
QueryUtil.annotationValueBelongToPermissibleValue(numericValue, numericPermissibleValue));
DateAnnotationValue dateValue = new DateAnnotationValue();
long currentTime = System.currentTimeMillis();
dateValue.setDateValue(new Date(currentTime));
PermissibleValue datePermissibleValue = new PermissibleValue();
datePermissibleValue.setValue(DateUtil.toString(new Date(currentTime)));
assertTrue(QueryUtil.annotationValueBelongToPermissibleValue(dateValue, datePermissibleValue));
}
@Test
public void testGetCriterionTypeFromQuery() {
Query query = new Query();
CompoundCriterion compoundCriterion1 = new CompoundCriterion();
CompoundCriterion compoundCriterion2 = new CompoundCriterion();
compoundCriterion1.getCriterionCollection().add(new GeneNameCriterion());
compoundCriterion1.getCriterionCollection().add(compoundCriterion2);
compoundCriterion2.getCriterionCollection().add(new SubjectListCriterion());
compoundCriterion2.getCriterionCollection().add(new SubjectListCriterion());
query.setCompoundCriterion(compoundCriterion1);
assertEquals(1, QueryUtil.getCriterionTypeFromQuery(query, GeneNameCriterion.class).size());
assertEquals(2, QueryUtil.getCriterionTypeFromQuery(query, SubjectListCriterion.class).size());
assertEquals(
0, QueryUtil.getCriterionTypeFromQuery(query, StringComparisonCriterion.class).size());
}
@Test
public void testIsCompoundCriterionGenomic() {
CompoundCriterion compoundCriterion1 = new CompoundCriterion();
compoundCriterion1.setCriterionCollection(new HashSet<AbstractCriterion>());
CompoundCriterion compoundCriterion2 = new CompoundCriterion();
compoundCriterion2.setCriterionCollection(new HashSet<AbstractCriterion>());
compoundCriterion2.getCriterionCollection().add(new StringComparisonCriterion());
compoundCriterion2.getCriterionCollection().add(new StringComparisonCriterion());
compoundCriterion1.getCriterionCollection().add(compoundCriterion2);
assertFalse(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
assertFalse(QueryUtil.isCompoundCriterionCopyNumber(compoundCriterion1));
GeneNameCriterion geneNameCriterion = new GeneNameCriterion();
compoundCriterion1.getCriterionCollection().add(geneNameCriterion);
geneNameCriterion.setGenomicCriterionType(GenomicCriterionTypeEnum.GENE_EXPRESSION);
assertTrue(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
assertFalse(QueryUtil.isCompoundCriterionCopyNumber(compoundCriterion1));
geneNameCriterion.setGenomicCriterionType(GenomicCriterionTypeEnum.COPY_NUMBER);
assertFalse(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
assertTrue(QueryUtil.isCompoundCriterionCopyNumber(compoundCriterion1));
compoundCriterion1.setCriterionCollection(new HashSet<AbstractCriterion>());
compoundCriterion1.getCriterionCollection().add(compoundCriterion2);
compoundCriterion1.getCriterionCollection().add(new StringComparisonCriterion());
assertFalse(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
assertFalse(QueryUtil.isCompoundCriterionCopyNumber(compoundCriterion1));
compoundCriterion2.getCriterionCollection().add(new FoldChangeCriterion());
assertTrue(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
assertFalse(QueryUtil.isCompoundCriterionCopyNumber(compoundCriterion1));
compoundCriterion1 = new CompoundCriterion();
compoundCriterion1.setCriterionCollection(new HashSet<AbstractCriterion>());
compoundCriterion2 = new CompoundCriterion();
compoundCriterion2.setCriterionCollection(new HashSet<AbstractCriterion>());
compoundCriterion1.getCriterionCollection().add(compoundCriterion2);
compoundCriterion1.getCriterionCollection().add(new StringComparisonCriterion());
assertFalse(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
assertFalse(QueryUtil.isCompoundCriterionCopyNumber(compoundCriterion1));
compoundCriterion2.getCriterionCollection().add(new CopyNumberAlterationCriterion());
assertFalse(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
assertTrue(QueryUtil.isCompoundCriterionCopyNumber(compoundCriterion1));
compoundCriterion1 = new CompoundCriterion();
compoundCriterion2 = new CompoundCriterion();
CompoundCriterion compoundCriterion3 = new CompoundCriterion();
compoundCriterion1.getCriterionCollection().add(compoundCriterion2);
compoundCriterion1.getCriterionCollection().add(compoundCriterion3);
compoundCriterion2.getCriterionCollection().add(new StringComparisonCriterion());
compoundCriterion3.getCriterionCollection().add(geneNameCriterion);
geneNameCriterion.setGenomicCriterionType(GenomicCriterionTypeEnum.GENE_EXPRESSION);
assertTrue(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
compoundCriterion1 = new CompoundCriterion();
compoundCriterion1.setCriterionCollection(new HashSet<AbstractCriterion>());
compoundCriterion1.getCriterionCollection().add(new ExpressionLevelCriterion());
assertTrue(QueryUtil.isCompoundCriterionGeneExpression(compoundCriterion1));
}