/**
* Creates a scenario where the fetcher always throws a bridge failure exception. Shows that the
* query does not repeat infinitely.
*
* @throws psidev.psi.mi.jami.enricher.exception.EnricherException
*/
@Test(expected = EnricherException.class)
public void test_bridgeFailure_throws_exception_when_persistent() throws EnricherException {
persistentBioactiveEntity = new DefaultBioactiveEntity(TEST_SHORTNAME, TEST_FULLNAME);
persistentBioactiveEntity.setChebi(CHEBI_ID);
int timesToTry = -1;
FailingBioactiveEntityFetcher fetcher = new FailingBioactiveEntityFetcher(timesToTry);
fetcher.addEntry(CHEBI_ID, Collections.singleton(persistentBioactiveEntity));
enricher = new FullBioactiveEntityUpdater(fetcher);
enricher.enrich(persistentBioactiveEntity);
fail("Exception should be thrown before this point");
}
/**
* Creates a scenario where the fetcher does not retrieve an entry on its first attempt. If the
* enricher re-queries the fetcher, it will eventually receive the entry.
*
* @throws EnricherException
*/
@Test
public void test_bridgeFailure_does_not_throw_exception_when_not_persistent()
throws EnricherException {
persistentBioactiveEntity = new DefaultBioactiveEntity(TEST_SHORTNAME, TEST_FULLNAME);
persistentBioactiveEntity.setChebi(CHEBI_ID);
int timesToTry = 3;
assertTrue(
"The test can not be applied as the conditions do not invoke the required response. "
+ "Change the timesToTry.",
timesToTry < 5);
FailingBioactiveEntityFetcher fetcher = new FailingBioactiveEntityFetcher(timesToTry);
fetcher.addEntry(CHEBI_ID, Collections.singleton(persistentBioactiveEntity));
enricher = new FullBioactiveEntityUpdater(fetcher);
enricher.enrich(persistentBioactiveEntity);
assertEquals(TEST_FULLNAME, persistentBioactiveEntity.getFullName());
}
@Test
public void test_enrichment_completes_as_failed_when_no_entry_fetched() throws EnricherException {
persistentBioactiveEntity = new DefaultBioactiveEntity(TEST_SHORTNAME, TEST_FULLNAME);
fetcher.clearEntries();
enricher.setListener(
new BioactiveEntityEnricherListenerManager(
new BioactiveEntityEnricherLogger(),
new BioactiveEntityEnricherListener() {
public void onEnrichmentComplete(
BioactiveEntity object, EnrichmentStatus status, String message) {
assertTrue(object == persistentBioactiveEntity);
assertEquals(EnrichmentStatus.FAILED, status);
persistentInt++;
}
public void onChebiUpdate(BioactiveEntity bioactiveEntity, String oldId) {
fail("failed");
}
public void onSmileUpdate(BioactiveEntity bioactiveEntity, String oldSmile) {
fail("failed");
}
public void onStandardInchiKeyUpdate(BioactiveEntity bioactiveEntity, String oldKey) {
fail("failed");
}
public void onStandardInchiUpdate(BioactiveEntity bioactiveEntity, String oldInchi) {
fail("failed");
}
public void onShortNameUpdate(BioactiveEntity interactor, String oldShortName) {
fail("failed");
}
public void onFullNameUpdate(BioactiveEntity interactor, String oldFullName) {
fail("failed");
}
public void onOrganismUpdate(BioactiveEntity interactor, Organism oldOrganism) {
fail("failed");
}
public void onInteractorTypeUpdate(BioactiveEntity interactor, CvTerm oldType) {
fail("failed");
}
public void onAddedIdentifier(BioactiveEntity interactor, Xref added) {
fail("failed");
}
public void onRemovedIdentifier(BioactiveEntity interactor, Xref removed) {
fail("failed");
}
public void onAddedXref(BioactiveEntity interactor, Xref added) {
fail("failed");
}
public void onRemovedXref(BioactiveEntity interactor, Xref removed) {
fail("failed");
}
public void onAddedAlias(BioactiveEntity interactor, Alias added) {
fail("failed");
}
public void onRemovedAlias(BioactiveEntity interactor, Alias removed) {
fail("failed");
}
public void onAddedChecksum(BioactiveEntity interactor, Checksum added) {
fail("failed");
}
public void onRemovedChecksum(BioactiveEntity interactor, Checksum removed) {
fail("failed");
}
public void onAddedAnnotation(BioactiveEntity o, Annotation added) {
Assert.fail();
}
public void onRemovedAnnotation(BioactiveEntity o, Annotation removed) {
Assert.fail();
}
public void onEnrichmentError(BioactiveEntity object, String message, Exception e) {
Assert.fail();
}
}));
enricher.enrich(persistentBioactiveEntity);
assertEquals(1, persistentInt);
}
/**
* Attempts to enrich a null CvTerm. This should always cause an illegal argument exception
*
* @throws EnricherException
*/
@Test(expected = IllegalArgumentException.class)
public void test_enriching_with_null_CvTerm() throws EnricherException {
BioactiveEntity nullBioactiveEntity = null;
enricher.enrich(nullBioactiveEntity);
fail("Exception should be thrown before this point");
}