@Test
public void shouldSaveChildForm() {
ArrayList<Map<String, String>> childFormValues = new ArrayList<>();
HashMap<String, String> childFormValue = new HashMap<>();
childFormValue.put("caseId", "94d5374f-290e-409f-bc57-86c2e4bcc43f");
childFormValue.put("xmlns", "http://bihar.commcarehq.org/pregnancy/registration");
childFormValue.put("childName", "suraj");
childFormValue.put("birthStatus", "healthy");
childFormValue.put("instanceId", "ff2eb090-03a9-4f23-afed-cf6012784c55");
childFormValue.put("flw", "89fda0284e008d2e0c980fb13fa0e5bb");
childFormValue.put("timeStart", "2013-03-03T10:31:51.045+05:30");
childFormValue.put("timeEnd", "2013-03-03T10:38:52.804+05:30");
childFormValue.put("dateModified", "2013-03-03T10:38:52.804+05:30");
childFormValues.add(childFormValue);
careService.processAndSaveForms(null, childFormValues);
List<RegistrationChildForm> registrationChildForms =
template.loadAll(RegistrationChildForm.class);
assertEquals(1, registrationChildForms.size());
RegistrationChildForm expectedForm = getExpectedForm("94d5374f-290e-409f-bc57-86c2e4bcc43f");
assertReflectionEqualsWithIgnore(
expectedForm,
registrationChildForms.get(0),
new String[] {"id", "flw", "childCase", "creationTime", "lastModifiedTime"});
List<Flw> flws = template.loadAll(Flw.class);
assertEquals(1, flws.size());
assertEquals("89fda0284e008d2e0c980fb13fa0e5bb", flws.get(0).getFlwId());
}
@Test
public void testWigAndBigWig() throws Exception {
String wigPath = TestUtils.DATA_DIR + "wig/test_fixedStep.wig";
String bigWigPath = TestUtils.DATA_DIR + "wig/test_fixedStep.bigwig";
List<Track> wigtracks = tstLoadFi(wigPath, 1, false);
List<Track> bigWigtracks = tstLoadFi(bigWigPath, 1, false);
String chr = "chr19";
int start = 5930725;
int end = 5930764;
int zoom = 21;
DataSourceTrack wigTrack = (DataSourceTrack) wigtracks.get(0);
DataSourceTrack bigWigTrack = (DataSourceTrack) bigWigtracks.get(0);
int trials = 10;
for (int ii = 0; ii < trials; ii++) {
int strt = start + ii;
List<LocusScore> wigScores = wigTrack.getSummaryScores(chr, strt, end, zoom);
List<LocusScore> bigWigScores = bigWigTrack.getSummaryScores(chr, strt, end, zoom);
assertEquals(wigScores.size(), bigWigScores.size());
int ind = 0;
for (LocusScore ws : wigScores) {
LocusScore bws = bigWigScores.get(ind);
assertEquals(ws.getScore(), bws.getScore());
ind++;
}
}
}
@Test
public void testLoadSIF() throws Exception {
String filepath = TestUtils.DATA_DIR + "sample/BRCA_sif.txt";
List<String> expectedAttributeNames =
Arrays.asList(
"TCGA_EXPERIMENT",
"TCGA_BATCH",
"TUMOR_NORMAL",
"BIRDSEED_GENDER",
"LEVEL2_NOISE",
"LEVEL3_SEGMENT_COUNT",
"PURITY PLOIDY",
"DELTA",
"CANCER_DNA_FRACTION",
"SUBCLONAL_GENOME_FRACTION");
tstLoadFi(filepath, 0, false); // Sample information file, shouldn't have tracks.
Set<String> attrNames = new HashSet<String>(AttributeManager.getInstance().getAttributeNames());
assertTrue(
attrNames.size()
>= expectedAttributeNames.size()); // Can be larger because of default attributes
for (String name : expectedAttributeNames) {
assertTrue(expectedAttributeNames.contains(name));
}
}
static List<Track> tstLoadFi(
TrackLoader trackLoader,
String filepath,
Integer expected_tracks,
Genome genome,
boolean makeIndex)
throws Exception {
ResourceLocator locator = new ResourceLocator(filepath);
// Try creating an index
// UI would ask for confirmation
if (makeIndex) {
try {
TestUtils.createIndex(filepath);
} catch (Exception e) {
}
}
List<Track> tracks = trackLoader.load(locator, genome);
if (expected_tracks != null) {
assertEquals(expected_tracks.intValue(), tracks.size());
if (expected_tracks == 0) {
return tracks;
}
}
Track track = tracks.get(0);
assertEquals(locator, track.getResourceLocator());
return tracks;
}
@Test
public void shouldNotDeleteEarlierFormIfNewerMotherFormWithSameInstanceIdHasOldDate() {
NewForm persistedForm = new NewForm();
persistedForm.setInstanceId("e34707f8-80c8-4198-bf99-c11c90ba5c98");
final Date oldFormModifiedDate = DateTime.parse("2012-07-20T12:02:59.923+05:30").toDate();
persistedForm.setServerDateModified(oldFormModifiedDate);
persistedForm.setDateModified(oldFormModifiedDate);
template.save(persistedForm);
final String newFormModifiedOn = "2012-07-10T12:02:59.923+05:30";
Map<String, String> motherFormValues =
new HashMap<String, String>() {
{
put("caseId", "94d5374f-290e-409f-bc57-86c2e4bcc43f");
put("dateModified", newFormModifiedOn);
put("serverDateModified", newFormModifiedOn);
put("userId", "89fda0284e008d2e0c980fb13fa0e5bb");
put("xmlns", "http://bihar.commcarehq.org/pregnancy/new");
put("instanceId", "e34707f8-80c8-4198-bf99-c11c90ba5c98");
}
};
careService.processAndSaveForms(motherFormValues, new ArrayList<Map<String, String>>());
List<NewForm> newFormsFromDb = template.loadAll(NewForm.class);
assertEquals(1, newFormsFromDb.size());
assertEquals(oldFormModifiedDate, newFormsFromDb.get(0).getDateModified());
}
@Test
public void shouldDeleteEarlierFormIfBothNewerAndOlderMotherFormWithSameInstanceIdHasNullDate() {
NewForm persistedForm = new NewForm();
persistedForm.setInstanceId("e34707f8-80c8-4198-bf99-c11c90ba5c98");
persistedForm.setCaste("OldCaste");
persistedForm.setServerDateModified(null);
template.save(persistedForm);
final String newCaste = "NewCaste";
Map<String, String> motherFormValues =
new HashMap<String, String>() {
{
put("caseId", "94d5374f-290e-409f-bc57-86c2e4bcc43f");
put("serverDateModified", null);
put("userId", "89fda0284e008d2e0c980fb13fa0e5bb");
put("xmlns", "http://bihar.commcarehq.org/pregnancy/new");
put("instanceId", "e34707f8-80c8-4198-bf99-c11c90ba5c98");
put("caste", newCaste);
}
};
careService.processAndSaveForms(motherFormValues, new ArrayList<Map<String, String>>());
List<NewForm> newFormsFromDb = template.loadAll(NewForm.class);
assertEquals(1, newFormsFromDb.size());
assertNull(newFormsFromDb.get(0).getDateModified());
assertEquals(newCaste, newFormsFromDb.get(0).getCaste());
}
@Test
public void shouldUpdateEntityByExternalPrimaryKeyWhenExists() {
String caseId = "94d5374f-290e-409f-bc57-86c2e4bcc43f";
ChildCase existingChild = new ChildCase();
existingChild.setCaseId(caseId);
existingChild.setName("old Child name");
template.save(existingChild);
HashMap<String, String> updatedValues =
new HashMap<String, String>() {
{
put("caseId", "94d5374f-290e-409f-bc57-86c2e4bcc43f");
put("name", "new child name");
}
};
careService.saveByExternalPrimaryKey(ChildCase.class, updatedValues);
List<ChildCase> childCases = template.loadAll(ChildCase.class);
Assert.assertEquals(1, childCases.size());
ChildCase expectedChildCase = new ChildCase();
expectedChildCase.setCaseId(caseId);
expectedChildCase.setName("new child name");
assertReflectionEqualsWithIgnore(
expectedChildCase,
childCases.get(0),
new String[] {"id", "creationTime", "lastModifiedTime"});
}
@Test
public void insertMixOfWronglyFormedAndCorrectlyFormedEvents() {
try {
cassandraConnector.saveStreamDefinitionToStore(getCluster(), streamDefinition1);
} catch (StreamDefinitionStoreException e) {
e.printStackTrace();
fail();
}
List<Event> eventList =
EventConverterUtils.convertFromJson(
CassandraTestConstants.properandImproperEvent, streamDefinition1.getStreamId());
List<String> insertedEvents = new ArrayList<String>();
int eventCounter = 0;
for (Event event : eventList) {
try {
String rowKey = insertEvent(cluster, event, eventCounter++);
// inserts row key only if event is valid, i.e. only proper events will add a row key
insertedEvents.add(rowKey);
} catch (Exception e) {
// ignore
}
}
assertEquals(2, insertedEvents.size());
}
/**
* Test that we properly load a vcf file, even though the extension is upper-case. IGV-2012
*
* @throws Exception
*/
@Test
public void testLoadVCFUpperCase() throws Exception {
String filepath = TestUtils.DATA_DIR + "vcf/HC_MOD_CAPS.VCF";
ResourceLocator locator = new ResourceLocator(filepath);
TestUtils.createIndex(filepath);
List<Track> tracks = trackLoader.load(locator, genome);
assertEquals(1, tracks.size());
assertTrue("VCF file loaded incorrect track type", tracks.get(0) instanceof VariantTrack);
}
@Test
public void testLoadGFF() throws Exception {
String filepath = TestUtils.DATA_DIR + "gff/simfeatures.gff3";
List<Track> tracks = trackLoader.load(new ResourceLocator(filepath), genome);
assertEquals(1, tracks.size());
FeatureTrack track = (FeatureTrack) tracks.get(0);
assertEquals("notmeaningful", track.getName());
List<Feature> features = track.getFeatures("chr1", 0, Integer.MAX_VALUE);
assertEquals(2, features.size());
IGVFeature feat0 = (IGVFeature) features.get(0);
IGVFeature feat1 = (IGVFeature) features.get(1);
assertEquals(707 - 1, feat0.getStart());
assertEquals(943, feat0.getEnd());
assertEquals(7563 - 1, feat1.getStart());
assertEquals(7938, feat1.getEnd());
}
@Test
public void shouldSaveMotherFormForExistingCase() {
MotherCase motherCase = new MotherCase();
motherCase.setCaseId("94d5374f-290e-409f-bc57-86c2e4bcc43f");
template.save(motherCase);
Flw flw = new Flw();
flw.setFlwId("89fda0284e008d2e0c980fb13fa0e5bb");
template.save(flw);
Map<String, String> motherForm = motherFormValues(motherCase.getCaseId(), flw.getFlwId());
careService.processAndSaveForms(motherForm, new ArrayList<Map<String, String>>());
List<MotherCase> persistedMotherCases = template.loadAll(MotherCase.class);
assertEquals(1, persistedMotherCases.size());
List<NewForm> newForms = template.loadAll(NewForm.class);
assertEquals(1, newForms.size());
NewForm expectedForm = expectedForm(motherCase, flw);
assertReflectionEqualsWithIgnore(
expectedForm, newForms.get(0), new String[] {"id", "creationTime", "lastModifiedTime"});
}
@Test
public void shouldSaveFlwOnceForMotherAndChild() {
final String flwId = "89fda0284e008d2e0c980fb13fa0e5bb";
Flw flw = new FlwBuilder().flwId(flwId).build();
final String instanceId = "e34707f8-80c8-4198-bf99-c11c90ba5c98";
HashMap<String, String> motherCase =
new HashMap<String, String>() {
{
put("caseId", "3e8998ce-b19f-4fa7-b1a1-721b6951e3cf");
put("userId", flwId);
put("flw", flwId);
put("instanceId", instanceId);
put("xmlns", "http://bihar.commcarehq.org/pregnancy/registration");
}
};
final HashMap<String, String> child1 =
new HashMap<String, String>() {
{
put("caseId", "3e8998ce-b19f-4fa7-b1a1-721b6951e3c1");
put("userId", flwId);
put("flw", flwId);
put("instanceId", instanceId);
put("xmlns", "http://bihar.commcarehq.org/pregnancy/registration");
}
};
final HashMap<String, String> child2 =
new HashMap<String, String>() {
{
put("caseId", "3e8998ce-b19f-4fa7-b1a1-721b6951e3c2");
put("userId", flwId);
put("flw", flwId);
put("instanceId", instanceId);
put("xmlns", "http://bihar.commcarehq.org/pregnancy/registration");
}
};
careService.processAndSaveForms(
motherCase,
new ArrayList<Map<String, String>>() {
{
add(child1);
add(child2);
}
});
List<Flw> actualFlws = template.loadAll(Flw.class);
assertEquals(1, actualFlws.size());
assertReflectionEqualsWithIgnore(
flw, actualFlws.get(0), new String[] {"id", "creationTime", "lastModifiedTime"});
}
@Test
public void testLoadGFFAliasedChrs() throws Exception {
String filepath = TestUtils.DATA_DIR + "gff/aliased.unsorted.gff";
Genome genome =
IgvTools.loadGenome(TestUtils.DATA_DIR + "genomes/hg18_truncated_aliased.genome");
List<Track> tracks = trackLoader.load(new ResourceLocator(filepath), genome);
assertEquals(1, tracks.size());
FeatureTrack track = (FeatureTrack) tracks.get(0);
assertEquals("aliased.unsorted.gff", track.getName());
List<Feature> features = track.getFeatures("chr1", 0, Integer.MAX_VALUE);
assertEquals(56, features.size());
features = track.getFeatures("chr5", 0, Integer.MAX_VALUE);
assertEquals(16, features.size());
// Non-aliased
features = track.getFeatures("NC_007072.3", 0, Integer.MAX_VALUE);
assertEquals(30, features.size());
}
@Test
public void shouldSaveMotherFormAndCreateNewCase() {
Map<String, String> motherForm =
motherFormValues(
"94d5374f-290e-409f-bc57-86c2e4bcc43f", "89fda0284e008d2e0c980fb13fa0e5bb");
careService.processAndSaveForms(motherForm, new ArrayList<Map<String, String>>());
List<MotherCase> persistedMotherCases = template.loadAll(MotherCase.class);
assertEquals(1, persistedMotherCases.size());
List<NewForm> newForms = template.loadAll(NewForm.class);
assertEquals(1, newForms.size());
NewForm expectedForm =
expectedForm(
new MotherCaseBuilder().caseId("94d5374f-290e-409f-bc57-86c2e4bcc43f").build(),
new FlwBuilder().flwId("89fda0284e008d2e0c980fb13fa0e5bb").build());
assertReflectionEqualsWithIgnore(
expectedForm, newForms.get(0), new String[] {"id", "creationTime", "flw", "motherCase"});
assertEquals(
"94d5374f-290e-409f-bc57-86c2e4bcc43f", newForms.get(0).getMotherCase().getCaseId());
assertEquals("89fda0284e008d2e0c980fb13fa0e5bb", newForms.get(0).getFlw().getFlwId());
}
@Test
public void shouldCreateNewFlw() {
Flw newFlw =
flw(
"5ba9a0928dde95d187544babf6c0ad24",
"FirstName1",
flwGroupWithNameAndId("64a9a0928dde95d187544babf6c0ad38", "oldGroupName"));
careService.saveOrUpdateAllByExternalPrimaryKey(Flw.class, Arrays.asList(newFlw));
List<Flw> flwsFromDb = template.loadAll(Flw.class);
assertEquals(1, flwsFromDb.size());
assertReflectionContains(newFlw, flwsFromDb, new String[] {"id"});
}
/**
* Test loading sample information file from a sql database, using a profile
*
* @throws Exception
*/
@Test
public void testLoadSampleInfoProfile() throws Exception {
AttributeManager.getInstance().clearAllAttributes();
String path = TestUtils.DATA_DIR + "sql/sampleinfo_brca_sif_profile.dbxml";
int expectedTracks = 0;
List<Track> tracks = trackLoader.load(new ResourceLocator(path), genome);
assertEquals(expectedTracks, tracks.size());
String[] attrNames =
"TCGA_EXPERIMENT TCGA_BATCH TUMOR_NORMAL BIRDSEED_GENDER LEVEL2_NOISE LEVEL3_SEGMENT_COUNT PURITY PLOIDY DELTA CANCER_DNA_FRACTION SUBCLONAL_GENOME_FRACTION"
.split("\\s+");
Set<String> expAttrNames = new HashSet<String>(Arrays.asList(attrNames));
List<String> actAttrNames = AttributeManager.getInstance().getAttributeNames();
actAttrNames.remove("NAME");
actAttrNames.remove("DATA TYPE");
actAttrNames.remove("DATA FILE");
assertEquals(actAttrNames.size(), expAttrNames.size());
for (String attrName : actAttrNames) {
assertTrue(expAttrNames.contains(attrName));
}
}
/**
* Test loading segmented data file from a sql database, using a profile
*
* @throws Exception
*/
@Test
public void testLoadSegProfile() throws Exception {
String path = TestUtils.DATA_DIR + "sql/seg_canFam2_profile.dbxml";
int expectedTracks = 6;
List<Track> tracks = trackLoader.load(new ResourceLocator(path), genome);
assertEquals(expectedTracks, tracks.size());
Set<String> expSampleIds =
new HashSet<String>(
Arrays.asList("0123-A", "0123-B-1", "0123-C-1", "0123-C-2", "0123-C-3"));
Set<String> actSampleIds = new HashSet<String>(5);
for (Track track : tracks) {
if (track instanceof DataSourceTrack) {
actSampleIds.add(track.getName());
}
}
assertEquals(expSampleIds, actSampleIds);
}
@Test
public void shouldSaveNewGroup() throws Exception {
FlwGroup newGroup =
new FlwGroupBuilder()
.groupId("5ba9a0928dde95d187544babf6c0ad24")
.name("amir team 1")
.domain("care-mp")
.awcCode("007")
.caseSharing(true)
.reporting(true)
.build();
careService.saveOrUpdateAllByExternalPrimaryKey(FlwGroup.class, Arrays.asList(newGroup));
List<FlwGroup> flwGroupsFromDb = template.loadAll(FlwGroup.class);
assertEquals(1, flwGroupsFromDb.size());
assertReflectionContains(newGroup, flwGroupsFromDb, new String[] {"id"});
}
@Test
public void
shouldSaveChildFormByDeletingOlderFormIfFormWithSameInstanceIdAndCaseIdExistsAlready() {
final String instanceId = "e34707f8-80c8-4198-bf99-c11c90ba5c98";
final String caseId = "3e8998ce-b19f-4fa7-b1a1-721b6951e3cf";
final Date oldFormModifiedDate = DateTime.parse("2012-07-10T12:02:59.923+05:30").toDate();
ChildCase persistedChildCase = new ChildCase();
persistedChildCase.setCaseId(caseId);
final DeathChildForm persistedForm = new DeathChildForm();
persistedForm.setInstanceId(instanceId);
persistedForm.setChildCase(persistedChildCase);
persistedForm.setDateModified(oldFormModifiedDate);
persistedForm.setServerDateModified(oldFormModifiedDate);
template.save(persistedForm);
final String newFormModifiedOn = "2012-07-20T12:02:59.923+05:30";
final Date newFormModifiedDate = DateTime.parse(newFormModifiedOn).toDate();
final HashMap<String, String> deathChildFormValues =
new HashMap<String, String>() {
{
put("caseId", caseId);
put("dateModified", newFormModifiedOn);
put("serverDateModified", newFormModifiedOn);
put("userId", "89fda0284e008d2e0c980fb13fa0e5bb");
put("close", "true");
put("instanceId", instanceId);
put("xmlns", "http://bihar.commcarehq.org/pregnancy/death");
}
};
careService.processAndSaveForms(
null,
new ArrayList<Map<String, String>>() {
{
add(deathChildFormValues);
}
});
List<DeathChildForm> deathChildForms = template.loadAll(DeathChildForm.class);
assertEquals(1, deathChildForms.size());
assertEquals(newFormModifiedDate, deathChildForms.get(0).getDateModified());
}
@Test
public void shouldInsertAnEntityByExternalPrimaryKeyWhenDoesNotExists() throws Exception {
HashMap<String, String> flwValues =
new HashMap<String, String>() {
{
put("flwId", "5ba9a0928dde95d187544babf6c0ad24");
put("firstName", "FirstName1");
}
};
careService.saveByExternalPrimaryKey(Flw.class, flwValues);
List<Flw> flws = template.loadAll(Flw.class);
Flw expectedFlw = flw("5ba9a0928dde95d187544babf6c0ad24", "FirstName1", null);
assertEquals(1, flws.size());
assertReflectionEqualsWithIgnore(
expectedFlw,
flws.get(0),
new String[] {"id", "flwGroups", "creationTime", "lastModifiedTime"});
}
@Test
public void testDataConsumption() throws Exception {
List<SampleData> ginzburg = create("ginzburg", 10, 10);
assertEquals(ginzburg.size(), 10);
}