/**
* Dumps <code>TRACE</code> data for a given metadata store.
*
* @param store The store to dump <code>TRACE</code> data for.
*/
private void traceMetadataStoreData(OMEROMetadataStoreClient store) {
containerCache = store.getContainerCache();
referenceCache = store.getReferenceCache();
log.trace("Starting container cache...");
for (LSID key : containerCache.keySet()) {
String s =
String.format(
"%s == %s,%s",
key, containerCache.get(key).sourceObject, containerCache.get(key).LSID);
log.trace(s);
}
log.trace("Starting reference cache...");
for (LSID key : referenceCache.keySet()) {
for (LSID value : referenceCache.get(key)) {
String s = String.format("%s == %s", key, value);
log.trace(s);
}
}
log.trace("containerCache contains " + containerCache.size() + " entries.");
log.trace("referenceCache contains " + store.countCachedReferences(null, null) + " entries.");
List<IObjectContainer> imageContainers = store.getIObjectContainers(Image.class);
for (IObjectContainer imageContainer : imageContainers) {
Image image = (Image) imageContainer.sourceObject;
log.trace(
String.format(
"Image indexes:%s name:%s", imageContainer.indexes, image.getName().getValue()));
}
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testLogicalChannelRefs() {
Class<? extends IObject> klass = LogicalChannel.class;
List<IObjectContainer> containers = store.getIObjectContainers(klass);
referenceCache = store.getReferenceCache();
for (IObjectContainer container : containers) {
LSID lsid = new LSID(container.LSID);
if (!referenceCache.containsKey(lsid)) {
continue;
}
List<LSID> references = referenceCache.get(lsid);
assertTrue(references.size() > 0);
for (LSID referenceLSID : references) {
String asString = referenceLSID.toString();
if (asString.endsWith(OMEROMetadataStoreClient.OMERO_EMISSION_FILTER_SUFFIX)
|| asString.endsWith(OMEROMetadataStoreClient.OMERO_EXCITATION_FILTER_SUFFIX)) {
int index = asString.lastIndexOf(':');
referenceLSID = new LSID(asString.substring(0, index));
}
assertNotNull(referenceLSID);
List<Class<? extends IObject>> klasses = new ArrayList<Class<? extends IObject>>();
klasses.add(Filter.class);
klasses.add(FilterSet.class);
String e = String.format("LSID %s not found in container cache", referenceLSID);
assertTrue(e, authoritativeLSIDExists(klasses, referenceLSID));
}
}
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testPlatesExist() {
List<IObjectContainer> containers = store.getIObjectContainers(WellSample.class);
for (IObjectContainer container : containers) {
Map<String, Integer> indexes = container.indexes;
Integer plateIndex = indexes.get(Index.PLATE_INDEX.getValue());
String e = String.format("Plate %d not found in container cache", plateIndex);
assertTrue(e, store.countCachedContainers(Plate.class, plateIndex) > 0);
}
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testPlaneInfoZCT() {
List<IObjectContainer> containers = store.getIObjectContainers(PlaneInfo.class);
for (IObjectContainer container : containers) {
PlaneInfo planeInfo = (PlaneInfo) container.sourceObject;
assertNotNull("theZ is null", planeInfo.getTheZ());
assertNotNull("theC is null", planeInfo.getTheC());
assertNotNull("theT is null", planeInfo.getTheT());
}
}
/**
* Examines the container cache and returns whether or not an LSID is present.
*
* @param klass Instance class of the source object container.
* @param lsid LSID to compare against.
* @return <code>true</code> if the object exists in the container cache, and <code>false</code>
* otherwise.
*/
private boolean authoritativeLSIDExists(Class<? extends IObject> klass, LSID lsid) {
List<IObjectContainer> containers = store.getIObjectContainers(klass);
for (IObjectContainer container : containers) {
LSID containerLSID = new LSID(container.LSID);
if (containerLSID.equals(lsid)) {
return true;
}
}
return false;
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testObjectiveSettingsIndexes() {
Class<? extends IObject> klass = ObjectiveSettings.class;
List<IObjectContainer> containers = store.getIObjectContainers(klass);
for (IObjectContainer container : containers) {
Map<String, Integer> indexes = container.indexes;
Integer imageIndex = indexes.get(Index.IMAGE_INDEX.getValue());
int imageCount = store.countCachedContainers(Image.class, null);
String e = String.format("imageIndex %d >= imageCount %d", imageIndex, imageCount);
assertFalse(e, imageIndex >= imageCount);
}
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testOTFIsReferenced() {
Class<? extends IObject> klass = OTF.class;
List<IObjectContainer> containers = store.getIObjectContainers(klass);
referenceCache = store.getReferenceCache();
for (IObjectContainer container : containers) {
LSID lsid = new LSID(container.LSID);
for (LSID target : referenceCache.keySet()) {
for (LSID reference : referenceCache.get(target)) {
if (reference.equals(lsid)) {
return;
}
}
}
fail(String.format("%s %s not referenced by any object.", klass, lsid));
}
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testCreationDateIsReasonable() {
List<IObjectContainer> containers = store.getIObjectContainers(Image.class);
for (IObjectContainer container : containers) {
Image image = (Image) container.sourceObject;
assertNotNull(image.getAcquisitionDate());
Date acquisitionDate = new Date(image.getAcquisitionDate().getValue());
Date now = new Date(System.currentTimeMillis());
Date january1st1995 = new GregorianCalendar(1995, 1, 1).getTime();
if (acquisitionDate.after(now)) {
fail(String.format("%s after %s", acquisitionDate, now));
}
if (acquisitionDate.before(january1st1995)) {
fail(String.format("%s before %s", acquisitionDate, january1st1995));
}
}
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testLightSourceSettingsLightSourceRef() {
Class<? extends IObject> klass = LightSettings.class;
List<IObjectContainer> containers = store.getIObjectContainers(klass);
referenceCache = store.getReferenceCache();
for (IObjectContainer container : containers) {
LSID lsid = new LSID(container.LSID);
String e = String.format("%s %s not found in reference cache", klass, container.LSID);
assertTrue(e, referenceCache.containsKey(lsid));
List<LSID> references = referenceCache.get(lsid);
assertTrue(references.size() > 0);
for (LSID referenceLSID : references) {
assertNotNull(referenceLSID);
klass = LightSource.class;
e = String.format("%s with LSID %s not found in container cache", klass, referenceLSID);
assertTrue(e, authoritativeLSIDExists(klass, referenceLSID));
}
}
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testChannelCount() {
List<IObjectContainer> containers = store.getIObjectContainers(Pixels.class);
for (IObjectContainer container : containers) {
Pixels pixels = (Pixels) container.sourceObject;
assertNotNull(pixels.getSizeC());
int sizeC = pixels.getSizeC().getValue();
Integer imageIndex = container.indexes.get(Index.IMAGE_INDEX.getValue());
int count = store.countCachedContainers(Channel.class, imageIndex);
String e = String.format("Pixels sizeC %d != channel object count %d", sizeC, count);
for (int c = 0; c < sizeC; c++) {
count = store.countCachedContainers(Channel.class, imageIndex, c);
e =
String.format(
"Missing channel object; imageIndex=%d " + "channelIndex=%d", imageIndex, c);
assertEquals(e, 1, count);
}
}
}
@Test(dependsOnMethods = {"testMetadataLevel"})
public void testFilterSetRefs() {
Class<? extends IObject> klass = FilterSet.class;
List<IObjectContainer> containers = store.getIObjectContainers(klass);
referenceCache = store.getReferenceCache();
for (IObjectContainer container : containers) {
LSID lsid = new LSID(container.LSID);
if (!referenceCache.containsKey(lsid)) {
continue;
}
List<LSID> references = referenceCache.get(lsid);
assertTrue(references.size() > 0);
for (LSID referenceLSID : references) {
assertNotNull(referenceLSID);
List<Class<? extends IObject>> klasses = new ArrayList<Class<? extends IObject>>();
klasses.add(Filter.class);
klasses.add(Dichroic.class);
String e = String.format("LSID %s not found in container cache", referenceLSID);
assertTrue(e, authoritativeLSIDExists(klasses, referenceLSID));
}
}
}