Examples with BlazegraphOntologyManager org.geneontology.minerva.BlazegraphOntologyManager used on opensource projects

Example 1 with BlazegraphOntologyManager

use of org.geneontology.minerva.BlazegraphOntologyManager in project minerva by geneontology.

the class ExportExplanation method exportExplanation.

public static String exportExplanation(WorkingMemory wm, BlazegraphOntologyManager go_lego, Map<IRI, String> labelMap) {
    Set<Triple> triples = new HashSet<>();
    Model model = ModelFactory.createDefaultModel();
    model.add(toJava(wm.facts()).stream().map(t -> model.asStatement(Bridge.jenaFromTriple(t))).collect(Collectors.toList()));
    QueryExecution qe = QueryExecutionFactory.create(mainQuery, model);
    ResultSet results = qe.execSelect();
    while (results.hasNext()) {
        QuerySolution qs = results.next();
        triples.add(new Triple(new URI(qs.getResource("s").getURI()), new URI(qs.getResource("p").getURI()), new URI(qs.getResource("o").getURI())));
    }
    qe.close();
    // Make sure all the asserted triples are included, in case they got filtered out as indirect by the first query
    Model assertedModel = ModelFactory.createDefaultModel();
    assertedModel.add(toJava(wm.asserted()).stream().map(t -> assertedModel.asStatement(Bridge.jenaFromTriple(t))).collect(Collectors.toList()));
    QueryExecution aqe = QueryExecutionFactory.create(mainQuery, assertedModel);
    ResultSet assertedResults = aqe.execSelect();
    while (assertedResults.hasNext()) {
        QuerySolution qs = assertedResults.next();
        triples.add(new Triple(new URI(qs.getResource("s").getURI()), new URI(qs.getResource("p").getURI()), new URI(qs.getResource("o").getURI())));
    }
    aqe.close();
    Set<Triple> asserted = triples.stream().filter(t -> wm.asserted().contains(t)).collect(Collectors.toSet());
    Set<Triple> inferred = triples.stream().filter(t -> !wm.asserted().contains(t)).collect(Collectors.toSet());
    Map<Triple, Set<Explanation>> allExplanations = inferred.stream().collect(Collectors.toMap(Function.identity(), s -> toJava(wm.explain(s))));
    Set<Rule> allRules = allExplanations.values().stream().flatMap(es -> es.stream().flatMap(e -> toJava(e.rules()).stream())).collect(Collectors.toSet());
    Stream<URI> subjects = triples.stream().map(t -> (URI) (t.s()));
    Stream<URI> predicates = triples.stream().map(t -> (URI) (t.p()));
    Stream<URI> objects = triples.stream().map(t -> (URI) (t.o()));
    Set<URI> allTerms = new HashSet<>();
    for (Rule rule : allRules) {
        for (TriplePattern tp : toJavaList(rule.body())) {
            if (tp.s() instanceof URI)
                allTerms.add((URI) tp.s());
            if (tp.p() instanceof URI)
                allTerms.add((URI) tp.p());
            if (tp.o() instanceof URI)
                allTerms.add((URI) tp.o());
        }
        for (TriplePattern tp : toJavaList(rule.head())) {
            if (tp.s() instanceof URI)
                allTerms.add((URI) tp.s());
            if (tp.p() instanceof URI)
                allTerms.add((URI) tp.p());
            if (tp.o() instanceof URI)
                allTerms.add((URI) tp.o());
        }
    }
    allTerms.addAll(subjects.collect(Collectors.toSet()));
    allTerms.addAll(predicates.collect(Collectors.toSet()));
    allTerms.addAll(objects.collect(Collectors.toSet()));
    Map<URI, String> labels = findLabels(allTerms, asserted, go_lego, labelMap);
    int currentBlankNode = 0;
    Map<Triple, ExplanationTriple> assertedForJSON = new HashMap<>();
    for (Triple t : asserted) {
        ExplanationTriple et = new ExplanationTriple();
        et.id = "_:" + currentBlankNode++;
        et.subject = ((URI) (t.s())).uri();
        et.predicate = ((URI) (t.p())).uri();
        et.object = ((URI) (t.o())).uri();
        assertedForJSON.put(t, et);
    }
    Map<Rule, ExplanationRule> rulesForJSON = new HashMap<>();
    for (Rule r : allRules) {
        ExplanationRule er = new ExplanationRule();
        er.id = "_:" + currentBlankNode++;
        List<ExplanationTriple> body = new ArrayList<>();
        List<ExplanationTriple> head = new ArrayList<>();
        for (TriplePattern t : toJavaList(r.body())) {
            ExplanationTriple et = new ExplanationTriple();
            et.subject = patternNodeToString(t.s());
            et.predicate = patternNodeToString(t.p());
            et.object = patternNodeToString(t.o());
            body.add(et);
        }
        for (TriplePattern t : toJavaList(r.head())) {
            ExplanationTriple et = new ExplanationTriple();
            et.subject = patternNodeToString(t.s());
            et.predicate = patternNodeToString(t.p());
            et.object = patternNodeToString(t.o());
            head.add(et);
        }
        er.body = body.toArray(new ExplanationTriple[] {});
        er.head = head.toArray(new ExplanationTriple[] {});
        rulesForJSON.put(r, er);
    }
    Map<Triple, ExplanationTriple> inferredForJSON = new HashMap<>();
    for (Triple t : inferred) {
        ExplanationTriple et = new ExplanationTriple();
        et.subject = ((URI) (t.s())).uri();
        et.predicate = ((URI) (t.p())).uri();
        et.object = ((URI) (t.o())).uri();
        Explanation explanation = allExplanations.get(t).iterator().next();
        org.geneontology.minerva.explanation.Explanation ex = new org.geneontology.minerva.explanation.Explanation();
        ex.triples = toJava(explanation.facts()).stream().map(f -> assertedForJSON.get(f).id).toArray(String[]::new);
        ex.rules = toJava(explanation.rules()).stream().map(r -> rulesForJSON.get(r).id).toArray(String[]::new);
        et.explanation = ex;
        inferredForJSON.put(t, et);
    }
    ModelExplanation me = new ModelExplanation();
    me.terms = labels.keySet().stream().map(uri -> {
        ExplanationTerm et = new ExplanationTerm();
        et.id = uri.uri();
        et.label = labels.get(uri);
        return et;
    }).toArray(ExplanationTerm[]::new);
    me.assertions = assertedForJSON.values().toArray(new ExplanationTriple[] {});
    me.rules = rulesForJSON.values().toArray(new ExplanationRule[] {});
    me.inferences = inferredForJSON.values().toArray(new ExplanationTriple[] {});
    GsonBuilder builder = new GsonBuilder();
    builder = builder.setPrettyPrinting();
    Gson gson = builder.create();
    String json = gson.toJson(me);
    return json;
}

Example 2 with BlazegraphOntologyManager

use of org.geneontology.minerva.BlazegraphOntologyManager in project minerva by geneontology.

the class ShexValidatorTest method setUpBeforeClass.

@BeforeClass
public static void setUpBeforeClass() throws Exception {
    go_lego = new BlazegraphOntologyManager(go_lego_journal_file, true);
    CurieHandler curieHandler = DefaultCurieHandler.getDefaultHandler();
    shex = new ShexValidator(schemaFile, mainShapemapFile, go_lego, curieHandler);
    shexMeta = new ShexValidator(metadataSchemaFile, metadataShapemapFile, go_lego, curieHandler);
}