protected HttpUriRequest createGoodAnnotProfileRequest(int n) throws URISyntaxException {
URIBuilder uriBuilder =
new URIBuilder()
.setScheme("http")
.setHost("localhost")
.setPort(9031)
.setPath("/owlsim/getAttributeInformationProfile/");
List<OWLClass> allClasses = new ArrayList<OWLClass>();
allClasses.addAll(g.getAllOWLClasses());
Collections.shuffle(allClasses);
int i = 0;
for (OWLClass c : allClasses) {
String id = g.getIdentifier(c);
uriBuilder.addParameter("a", id);
i++;
if (i >= n) break;
}
uriBuilder.addParameter("limit", "5");
URI uri = uriBuilder.build();
LOG.info("Getting URL=" + uri);
HttpUriRequest httpUriRequest = new HttpGet(uri);
LOG.info("Got URL=" + uri);
return httpUriRequest;
}
protected OWLGraphWrapper loadOntology(String location) throws Exception {
// load server ontology
ParserWrapper pw = new ParserWrapper();
OWLGraphWrapper g = pw.parseToOWLGraph(location);
// prepare ontology
ABoxUtils.makeDefaultIndividuals(g.getSourceOntology());
return g;
}
@Test
public void testNonCycle3() throws Exception {
ParserWrapper parser = new ParserWrapper();
IRI iri = IRI.create(getResource("verification/self_references.obo").getAbsoluteFile());
OWLGraphWrapper graph = parser.parseToOWLGraph(iri.toString());
OntologyCheck check = new CycleCheck();
Collection<CheckWarning> warnings = check.check(graph, graph.getAllOWLObjects());
assertTrue(warnings.isEmpty());
}
@Test
public void testCycle1() throws Exception {
ParserWrapper parser = new ParserWrapper();
IRI iri = IRI.create(getResource("verification/cycle.obo").getAbsoluteFile());
OWLGraphWrapper graph = parser.parseToOWLGraph(iri.toString());
OntologyCheck check = new CycleCheck();
Collection<CheckWarning> warnings = check.check(graph, graph.getAllOWLObjects());
assertEquals(1, warnings.size());
CheckWarning warning = warnings.iterator().next();
List<IRI> iris = warning.getIris();
assertEquals(3, iris.size());
}
@Test
public void testServerSearchByAttributeSetCommand() throws Exception {
g = loadOntology("../OWLTools-Sim/src/test/resources/sim/mp-subset-1.obo");
ABoxUtils.createRandomClassAssertions(g.getSourceOntology(), 200, 20);
OwlSimFactory owlSimFactory = new FastOwlSimFactory();
OwlSim sos = owlSimFactory.createOwlSim(g.getSourceOntology());
sos.createElementAttributeMapFromOntology();
final HttpUriRequest httppost = createSearchByAttributeSetRequest(5);
runServerCommunication(httppost, sos);
}
@Test
public void testServerGetAnnotationSufficiencyScoreCommandBad() throws Exception {
g = loadOntology("../OWLTools-Sim/src/test/resources/sim/mp-subset-1.obo");
ABoxUtils.createRandomClassAssertions(g.getSourceOntology(), 200, 20);
// set sim
OwlSimFactory owlSimFactory = new FastOwlSimFactory();
OwlSim sos = owlSimFactory.createOwlSim(g.getSourceOntology());
sos.createElementAttributeMapFromOntology();
HttpUriRequest httppost = createBogusAnnotSufRequest(5);
runServerCommunication(httppost, sos);
}
/*
* Add specified closure of OWLObject to annotation and bioentity docs.
* Not the map for bio.
*/
private Map<String, String> addClosureToAnnAndBio(
List<String> relations,
String closureName,
String closureNameLabel,
String closureMap,
OWLObject cls,
OWLGraphWrapper graph,
SolrInputDocument ann_doc,
SolrInputDocument bio_doc,
boolean isNegated) {
// Add closures to doc; label and id.
graph.addPropertyIdsForMaterialization(relations);
final Map<String, String> cmap = graph.getRelationClosureMap(cls, relations);
List<String> idClosure = new ArrayList<String>(cmap.keySet());
List<String> labelClosure = new ArrayList<String>(cmap.values());
ann_doc.addField(closureName, idClosure);
ann_doc.addField(closureNameLabel, labelClosure);
// WARNING this is a side effect for the bio-entity
// only add the class and closure, if it is a non-negated annotation
if (isNegated == false) {
for (String tid : idClosure) {
addFieldUnique(bio_doc, closureName, tid);
}
for (String tlabel : labelClosure) {
addFieldUnique(bio_doc, closureNameLabel, tlabel);
}
}
// Compile closure maps to JSON.
if (!cmap.isEmpty()) {
String jsonized_cmap = gson.toJson(cmap);
ann_doc.addField(closureMap, jsonized_cmap);
// NOTE: This is harder since we'd be adding multiple, so the is done on a collector variable
// elsewhere.
// bio_doc.addField(closureMap, jsonized_cmap);
}
if (isNegated) {
// WARNING this is a side effect for the bio-entity
// only add the class and closure, if it is a non-negated annotation
return Collections.emptyMap();
}
return cmap;
}
protected HttpUriRequest createBadAnnotProfileWithSubgraphsRequest(int n)
throws URISyntaxException {
URIBuilder uriBuilder =
new URIBuilder()
.setScheme("http")
.setHost("localhost")
.setPort(9031)
.setPath("/owlsim/getAttributeInformationProfile/");
List<OWLClass> allClasses = new ArrayList<OWLClass>();
allClasses.addAll(g.getAllOWLClasses());
Collections.shuffle(allClasses);
int i = 0;
for (OWLClass c : allClasses) {
String id = g.getIdentifier(c);
uriBuilder.addParameter("a", id);
// get at least one ancestor of each class
OWLClass r = (OWLClass) g.getAncestors(c).iterator().next();
uriBuilder.addParameter("r", g.getIdentifier(r));
i++;
if (i >= n) break;
}
uriBuilder.addParameter("a", "BOGUS:1234567");
uriBuilder.addParameter("r", "BOGUS:0000003");
Random rand = new Random();
int r = 0;
// get some random classes
for (i = 0; i < n; i++) {
r = rand.nextInt(allClasses.size());
OWLClass c = allClasses.get(r);
String id = g.getIdentifier(c);
uriBuilder.addParameter("r", id);
i++;
if (i >= n) break;
}
uriBuilder.addParameter("limit", "5");
URI uri = uriBuilder.build();
LOG.info("Getting URL=" + uri);
HttpUriRequest httpUriRequest = new HttpGet(uri);
LOG.info("Got URL=" + uri);
return httpUriRequest;
}
protected HttpUriRequest createCompareByAttributeSetsRequest(int nA, int nB)
throws URISyntaxException {
URIBuilder uriBuilder =
new URIBuilder()
.setScheme("http")
.setHost("localhost")
.setPort(9031)
.setPath("/owlsim/compareAttributeSets/");
List<OWLClass> allClasses = new ArrayList<OWLClass>();
allClasses.addAll(g.getAllOWLClasses());
Collections.shuffle(allClasses);
int i = 0;
for (OWLClass c : allClasses) {
String id = g.getIdentifier(c);
uriBuilder.addParameter("a", id);
// get at least one ancestor of each class
i++;
if (i >= nA) break;
}
Collections.shuffle(allClasses);
i = 0;
for (OWLClass c : allClasses) {
String id = g.getIdentifier(c);
uriBuilder.addParameter("b", id);
// get at least one ancestor of each class
i++;
if (i >= nB) break;
}
URI uri = uriBuilder.build();
LOG.info("Getting URL=" + uri);
HttpUriRequest httpUriRequest = new HttpGet(uri);
LOG.info("Got URL=" + uri);
return httpUriRequest;
}
protected HttpUriRequest createPartiallyBogusAnnotSufRequest(int n) throws URISyntaxException {
URIBuilder uriBuilder =
new URIBuilder()
.setScheme("http")
.setHost("localhost")
.setPort(9031)
.setPath("/owlsim/getAnnotationSufficiencyScore/");
int i = 0;
for (OWLClass c : g.getAllOWLClasses()) {
String id = g.getIdentifier(c);
uriBuilder.addParameter("a", id);
uriBuilder.addParameter("a", "BOGUS:000000" + i);
i++;
if (i >= n) break;
}
uriBuilder.addParameter("limit", "5");
URI uri = uriBuilder.build();
LOG.info("Getting URL=" + uri);
HttpUriRequest httpUriRequest = new HttpGet(uri);
LOG.info("Got URL=" + uri);
return httpUriRequest;
}
@Test
public void testServerGetCoAnnotationSuggestions() throws Exception {
g = loadOntology("../OWLTools-Sim/src/test/resources/sim/mp-subset-1.obo");
String file = "../OWLTools-Sim/src/test/resources/sim/mgi-gene2mp-subset-1.tbl";
// g = loadOntology("/Users/Nicole/work/MONARCH/phenotype-ontologies/src/ontology/hp.obo");
// String
// file="/Users/Nicole/work/MONARCH/phenotype-ontologies/data/Homo_sapiens/Hs-disease-to-phenotype-O.txt";
TableToAxiomConverter ttac = new TableToAxiomConverter(g);
ttac.config.axiomType = AxiomType.CLASS_ASSERTION;
ttac.config.isSwitchSubjectObject = true;
ttac.parse(file);
OwlSimFactory owlSimFactory = new FastOwlSimFactory();
OwlSim sos = owlSimFactory.createOwlSim(g.getSourceOntology());
sos.createElementAttributeMapFromOntology();
// sos.populateFullCoannotationMatrix();
LOG.info("Finished populating the big matrix");
HttpUriRequest httppost = createGoodCoAnnotationRequest(1);
runServerCommunication(httppost, sos);
}
public static void main(String[] args) throws Exception {
String catalog = args[0];
String file = args[1];
final ParserWrapper pw = new ParserWrapper();
pw.addIRIMapper(new CatalogXmlIRIMapper(catalog));
final OWLOntology ontology = pw.parse(file);
final OWLGraphWrapper g = new OWLGraphWrapper(ontology);
OWLObjectProperty part_of = g.getOWLObjectPropertyByIdentifier("part_of");
OWLObjectProperty has_part = g.getOWLObjectPropertyByIdentifier("has_part");
OWLObjectProperty regulates = g.getOWLObjectPropertyByIdentifier("regulates");
OWLObjectProperty negatively_regulates =
g.getOWLObjectPropertyByIdentifier("negatively_regulates");
OWLObjectProperty positively_regulates =
g.getOWLObjectPropertyByIdentifier("positively_regulates");
final OWLClassFilter filter =
new OWLClassFilter() {
@Override
public boolean use(OWLClass cls) {
String id = g.getIdentifier(cls.getIRI());
return id.startsWith("GO:");
}
};
Set<OWLObjectProperty> props = Sets.newHashSet(part_of);
Map<OWLClass, Set<OWLObjectSomeValuesFrom>> expressions =
getExpressions(ontology, props, filter);
List<OWLClass> classes = new ArrayList<OWLClass>(expressions.keySet());
Collections.sort(classes);
OWLPrettyPrinter pp = new OWLPrettyPrinter(g);
int count = 0;
for (OWLClass cls : classes) {
Set<OWLObjectSomeValuesFrom> svfs = expressions.get(cls);
for (OWLObjectSomeValuesFrom svf : svfs) {
StringBuilder sb = new StringBuilder();
sb.append(pp.render(cls)).append("\t");
sb.append(pp.render(svf.getProperty())).append("\t");
sb.append(pp.render(svf.getFiller()));
System.out.println(sb);
count += 1;
}
}
System.out.println("Count: " + count);
}
