@Test
public final void testNormalizeInoh() {
// there're two Protein objects that have entityReference
// rdf:ID="IMR_0100366_G_alpha_s_Canonical" (in fact a generic ProteinReference inproperly
// defined);
// and that PR has two UniProt UnificationXref: P63092 (human), P63095 (rat).
// Identifiers.org URI for the PR should NOT be generated.
//
// Also, there was a bug when replacing the PR's URI (warning: IllegalBioPAXArgumentException:
// Incompatible type!..)
// The cause is that there was a (weird, invalid) PublicationXref having db:id as UniProt:P63092
// that gets the same URI!
// To avoid such issues altogether (despite illegal pub. xrefs), the Normalizer won't use
// Identifiers.org for PublicationXrefs anymore.
Model model = simpleIO.convertFromOWL(getClass().getResourceAsStream("/test-inoh.owl"));
Normalizer normalizer = new Normalizer();
normalizer.setXmlBase("");
normalizer.normalize(model);
// A weird PublicationXref that uses a UniProt ID won't be normalized:
assertFalse(model.containsID("http://identifiers.org/uniprot/P63092"));
// A PR with two UniProt IDs/unif.xrefs - human, rat - won't be normalized!
assertTrue(model.containsID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical"));
assertEquals(
"ProteinReference",
model
.getByID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical")
.getModelInterface()
.getSimpleName());
}
@Test
public final void testSearch() throws IOException {
SimpleIOHandler reader = new SimpleIOHandler();
Model model =
reader.convertFromOWL(
resourceLoader.getResource("classpath:merge/pathwaydata1.owl").getInputStream());
SearchEngine searchEngine = new SearchEngine(model, indexLocation);
searchEngine.index();
assertTrue(new File(indexLocation).exists());
SearchResponse response = searchEngine.search("ATP", 0, null, null, null);
assertNotNull(response);
assertFalse(response.isEmpty());
assertEquals(7, response.getSearchHit().size());
assertEquals(7, response.getNumHits().intValue());
CPathSettings.getInstance().setDebugEnabled(false);
response = searchEngine.search("ATP", 0, Interaction.class, null, null);
assertNotNull(response);
assertFalse(response.isEmpty());
assertEquals(2, response.getSearchHit().size());
// if cPath2 debugging is disabled, - no score/explain in the excerpt
assertFalse(response.getSearchHit().get(0).getExcerpt().contains("-SCORE-"));
// enable cPath2 debugging...
CPathSettings.getInstance().setDebugEnabled(true);
response = searchEngine.search("ATP", 0, Pathway.class, null, null);
assertNotNull(response);
assertFalse(response.isEmpty());
assertEquals(1, response.getSearchHit().size());
SearchHit hit = response.getSearchHit().get(0);
assertEquals(4, hit.getSize().intValue()); // no. member processes, not counting the hit itself
assertTrue(hit.getExcerpt().contains("-SCORE-"));
CPathSettings.getInstance().setDebugEnabled(false);
// test a special implementation for wildcard queries
response = searchEngine.search("*", 0, Pathway.class, null, null);
assertNotNull(response);
assertFalse(response.isEmpty());
assertEquals(1, response.getSearchHit().size());
// find all objects (this here works with page=0 as long as the
// total no. objects in the test model < max hits per page)
response = searchEngine.search("*", 0, null, null, null);
assertEquals(50, response.getSearchHit().size());
response = searchEngine.search("*", 0, PhysicalEntity.class, null, null);
assertEquals(8, response.getSearchHit().size());
response = searchEngine.search("*", 0, PhysicalEntity.class, null, new String[] {"562"});
assertEquals(2, response.getSearchHit().size());
response =
searchEngine.search("*", 0, PhysicalEntity.class, null, new String[] {"Escherichia"});
assertFalse(response.isEmpty());
assertEquals(2, response.getSearchHit().size());
response =
searchEngine.search("*", 0, PhysicalEntity.class, null, new String[] {"Escherichia coliü"});
assertFalse(response.isEmpty());
assertEquals(2, response.getSearchHit().size());
response = searchEngine.search("*", 0, Provenance.class, null, null);
assertEquals(2, response.getSearchHit().size());
response = searchEngine.search("*", 0, Provenance.class, new String[] {"kegg"}, null);
assertEquals(1, response.getSearchHit().size());
// datasource filter using a URI (required for -update-counts console command and
// datasources.html page to work)
response =
searchEngine.search(
"*", 0, Pathway.class, new String[] {"http://identifiers.org/kegg.pathway/"}, null);
assertFalse(response.isEmpty());
assertEquals(1, response.getSearchHit().size());
response =
searchEngine.search("pathway:glycolysis", 0, SmallMoleculeReference.class, null, null);
assertEquals(5, response.getSearchHit().size());
// test search with pagination
searchEngine.setMaxHitsPerPage(10);
response = searchEngine.search("*", 0, null, null, null);
assertEquals(0, response.getPageNo().intValue());
assertEquals(50, response.getNumHits().intValue());
assertEquals(10, response.getSearchHit().size());
response = searchEngine.search("*", 1, null, null, null);
assertEquals(10, response.getSearchHit().size());
assertEquals(1, response.getPageNo().intValue());
}
static {
simpleIO = new SimpleIOHandler(BioPAXLevel.L3);
simpleIO.mergeDuplicates(true);
}