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Added UnitTests for getFamilies() and getChildrenWithParents()

This commit is contained in:
Laurent Francioli 2011-12-09 15:57:07 +01:00
parent 5a06170804
commit 72fbfba97d
1 changed files with 62 additions and 0 deletions
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62
public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
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@ -27,11 +27,42 @@ public class SampleDBUnitTest extends BaseTest {
new Sample("dad", "fam1", null, null, Gender.MALE, Affection.UNAFFECTED), new Sample("dad", "fam1", null, null, Gender.MALE, Affection.UNAFFECTED),
new Sample("mom", "fam1", null, null, Gender.FEMALE, Affection.AFFECTED))); new Sample("mom", "fam1", null, null, Gender.FEMALE, Affection.AFFECTED)));
private static final Set<Sample> testPEDFamilyF2 = new HashSet<Sample>(Arrays.asList(
new Sample("s2", "fam2", "d2", "m2", Gender.FEMALE, Affection.AFFECTED),
new Sample("d2", "fam2", null, null, Gender.MALE, Affection.UNKNOWN),
new Sample("m2", "fam2", null, null, Gender.FEMALE, Affection.UNKNOWN)
));
private static final Set<Sample> testPEDFamilyF3 = new HashSet<Sample>(Arrays.asList(
new Sample("s1", "fam3", "d1", "m1", Gender.FEMALE, Affection.AFFECTED),
new Sample("d1", "fam3", null, null, Gender.FEMALE, Affection.UNKNOWN),
new Sample("m1", "fam3", null, null, Gender.FEMALE, Affection.UNKNOWN)
));
private static final Set<Sample> testSAMSamples = new HashSet<Sample>(Arrays.asList( private static final Set<Sample> testSAMSamples = new HashSet<Sample>(Arrays.asList(
new Sample("kid", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN), new Sample("kid", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN),
new Sample("mom", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN), new Sample("mom", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN),
new Sample("dad", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN))); new Sample("dad", null, null, null, Gender.UNKNOWN, Affection.UNKNOWN)));
private static final HashMap<String, Set<Sample>> testGetFamilies = new HashMap<String,Set<Sample>>();
static {
testGetFamilies.put("fam1", testPEDSamples);
testGetFamilies.put("fam2", testPEDFamilyF2);
testGetFamilies.put("fam3", testPEDFamilyF3);
}
private static final Set<Sample> testKidsWithParentsFamilies2 = new HashSet<Sample>(Arrays.asList(
new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED),
new Sample("kid3", "fam5", "dad2", "mom2", Gender.MALE, Affection.AFFECTED),
new Sample("kid2", "fam5", "dad2", "mom2", Gender.MALE, Affection.AFFECTED)));
private static final HashSet<String> testGetPartialFamiliesIds = new HashSet<String>(Arrays.asList("kid","s1"));
private static final HashMap<String, Set<Sample>> testGetPartialFamilies = new HashMap<String,Set<Sample>>();
static {
testGetPartialFamilies.put("fam1", new HashSet<Sample>(Arrays.asList(new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED))));
testGetPartialFamilies.put("fam3", new HashSet<Sample>(Arrays.asList(new Sample("s1", "fam3", "d1", "m1", Gender.FEMALE, Affection.AFFECTED))));
}
private static final String testPEDString = private static final String testPEDString =
String.format("%s%n%s%n%s", String.format("%s%n%s%n%s",
"fam1 kid dad mom 1 2", "fam1 kid dad mom 1 2",
@ -46,6 +77,18 @@ public class SampleDBUnitTest extends BaseTest {
"fam3 s1 d1 m1 2 2", "fam3 s1 d1 m1 2 2",
"fam2 s2 d2 m2 2 2"); "fam2 s2 d2 m2 2 2");
private static final String testPEDMultipleFamilies2 =
String.format("%s%n%s%n%s%n%s%n%s%n%s%n%s%n%s%n%s",
"fam1 kid dad mom 1 2",
"fam1 dad 0 0 1 1",
"fam1 mom 0 0 2 2",
"fam4 kid4 dad4 0 1 2",
"fam4 dad4 0 0 1 1",
"fam5 kid2 dad2 mom2 1 2",
"fam5 kid3 dad2 mom2 1 2",
"fam5 dad2 0 0 1 1",
"fam5 mom2 0 0 2 2");
private static final String testPEDStringInconsistentGender = private static final String testPEDStringInconsistentGender =
"fam1 kid 0 0 2 2"; "fam1 kid 0 0 2 2";
@ -138,6 +181,25 @@ public class SampleDBUnitTest extends BaseTest {
Assert.assertEquals(db.getFamily("fam1"), testPEDSamplesAsSet); Assert.assertEquals(db.getFamily("fam1"), testPEDSamplesAsSet);
} }
@Test()
public void getFamilies(){
builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
SampleDB db = builder.getFinalSampleDB();
Assert.assertEquals(db.getFamilies(),testGetFamilies);
Assert.assertEquals(db.getFamilies(null),testGetFamilies);
Assert.assertEquals(db.getFamilies(testGetPartialFamiliesIds),testGetPartialFamilies);
}
@Test()
public void testGetChildrenWithParents()
{
builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies2));
SampleDB db = builder.getFinalSampleDB();
Assert.assertEquals(db.getChildrenWithParents(), testKidsWithParentsFamilies2);
Assert.assertEquals(db.getChildrenWithParents(false), testKidsWithParentsFamilies2);
Assert.assertEquals(db.getChildrenWithParents(true), new HashSet<Sample>(Arrays.asList(new Sample("kid", "fam1", "dad", "mom", Gender.MALE, Affection.AFFECTED))));
}
@Test() @Test()
public void loadFamilyIDs() { public void loadFamilyIDs() {
builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies)); builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));