Examples with CurieHandler org.geneontology.minerva.curie.CurieHandler used on opensource projects

Example 6 with CurieHandler

use of org.geneontology.minerva.curie.CurieHandler in project minerva by geneontology.

the class CommandLineInterface method legoToAnnotationsSPARQL.

/**
 * Output GPAD files via inference+SPARQL
 * cli --lego-to-gpad-sparql
 *
 * @param modelIdPrefix
 * @param modelIdcurie
 * @param inputDB
 * @param gpadOutputFolder
 * @param ontologyIRI
 * @throws Exception
 */
public static void legoToAnnotationsSPARQL(String modelIdPrefix, String modelIdcurie, String inputDB, String gpadOutputFolder, String ontologyIRI, String catalog, String go_lego_journal_file) throws Exception {
    if (modelIdPrefix == null) {
        modelIdPrefix = "http://model.geneontology.org/";
    }
    if (modelIdcurie == null) {
        modelIdcurie = "gomodel";
    }
    if (inputDB == null) {
        inputDB = "blazegraph.jnl";
    }
    if (gpadOutputFolder == null) {
        gpadOutputFolder = null;
    }
    if (ontologyIRI == null) {
        ontologyIRI = "http://purl.obolibrary.org/obo/go/extensions/go-lego.owl";
    }
    OWLOntologyManager ontman = OWLManager.createOWLOntologyManager();
    if (catalog != null) {
        LOGGER.info("using catalog: " + catalog);
        ontman.setIRIMappers(Sets.newHashSet(new owltools.io.CatalogXmlIRIMapper(catalog)));
    } else {
        LOGGER.info("no catalog, resolving all ontology uris directly");
    }
    OWLOntology ontology = ontman.loadOntology(IRI.create(ontologyIRI));
    CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(modelIdcurie, modelIdPrefix));
    CurieHandler curieHandler = new MappedCurieHandler(DefaultCurieHandler.loadDefaultMappings(), localMappings);
    boolean loadTboxIntoOntJournal = (!(new File(go_lego_journal_file)).exists());
    BlazegraphMolecularModelManager<Void> m3 = new BlazegraphMolecularModelManager<>(ontology, curieHandler, modelIdPrefix, inputDB, null, go_lego_journal_file, false);
    if (loadTboxIntoOntJournal) {
        m3.getGolego_repo().loadRepositoryFromOntology(ontology, "http://example.org/", true);
    }
    final String immutableModelIdPrefix = modelIdPrefix;
    final String immutableGpadOutputFolder = gpadOutputFolder;
    m3.getAvailableModelIds().stream().parallel().forEach(modelIRI -> {
        try {
            // TODO investigate whether changing to a neo-lite model has an impact on this - may need to make use of ontology journal
            String gpad = new GPADSPARQLExport(curieHandler, m3.getLegacyRelationShorthandIndex(), m3.getTboxShorthandIndex(), m3.getGolego_repo().regulatorsToRegulated).exportGPAD(m3.createInferredModel(modelIRI), modelIRI);
            String fileName = StringUtils.replaceOnce(modelIRI.toString(), immutableModelIdPrefix, "") + ".gpad";
            Writer writer = new OutputStreamWriter(new FileOutputStream(Paths.get(immutableGpadOutputFolder, fileName).toFile()), StandardCharsets.UTF_8);
            writer.write(gpad);
            writer.close();
        } catch (InconsistentOntologyException e) {
            LOGGER.error("Inconsistent ontology: " + modelIRI);
        } catch (IOException e) {
            LOGGER.error("Couldn't export GPAD for: " + modelIRI, e);
        }
    });
    m3.dispose();
}

Example 7 with CurieHandler

use of org.geneontology.minerva.curie.CurieHandler in project minerva by geneontology.

the class CommandLineInterface method modelsToOWL.

/**
 * Given a blazegraph journal with go-cams in it, write them all out as OWL files.
 * cli --dump-owl-models
 *
 * @param journalFilePath
 * @param outputFolder
 * @param modelIdPrefix
 * @throws Exception
 */
public static void modelsToOWL(String journalFilePath, String outputFolder, String modelIdPrefix) throws Exception {
    if (modelIdPrefix == null) {
        modelIdPrefix = "http://model.geneontology.org/";
    }
    // minimal inputs
    if (journalFilePath == null) {
        System.err.println("No journal file was configured.");
        System.exit(-1);
        return;
    }
    if (outputFolder == null) {
        System.err.println("No output folder was configured.");
        System.exit(-1);
        return;
    }
    OWLOntology dummy = OWLManager.createOWLOntologyManager().createOntology(IRI.create("http://example.org/dummy"));
    CurieHandler curieHandler = new MappedCurieHandler();
    BlazegraphMolecularModelManager<Void> m3 = new BlazegraphMolecularModelManager<>(dummy, curieHandler, modelIdPrefix, journalFilePath, outputFolder, null, false);
    m3.dumpAllStoredModels();
    m3.dispose();
}

Example 8 with CurieHandler

use of org.geneontology.minerva.curie.CurieHandler in project minerva by geneontology.

the class ModelSearchHandler method search.

// examples
// http://127.0.0.1:6800/search/?
// ?gp=http://identifiers.org/uniprot/P15822-3
// ?term=http://purl.obolibrary.org/obo/GO_0003677
// 
// 
// ?gp=http://identifiers.org/mgi/MGI:1328355
// &gp=http://identifiers.org/mgi/MGI:87986
// &term=http://purl.obolibrary.org/obo/GO_0030968
// &title=mouse
// &pmid=PMID:19911006
// &state=development&state=review {development, production, closed, review, delete} or operator
// &count
// 127.0.0.1:6800/search/?contributor=http://orcid.org/0000-0002-1706-4196
public ModelSearchResult search(Set<String> taxa, Set<String> gene_product_ids, Set<String> terms, String expand, Set<String> pmids, String title_search, Set<String> state_search, Set<String> contributor_search, Set<String> group_search, String exactdate, String date_search, String datend, int offset, int limit, String count, String debug, Set<String> id) {
    ModelSearchResult r = new ModelSearchResult();
    Set<String> go_type_ids = new HashSet<String>();
    Set<String> gene_type_ids = new HashSet<String>();
    if (gene_product_ids != null) {
        gene_type_ids.addAll(gene_product_ids);
    }
    if (terms != null) {
        go_type_ids.addAll(terms);
    }
    CurieHandler curie_handler = m3.getCuriHandler();
    Set<String> go_type_uris = new HashSet<String>();
    Set<String> gene_type_uris = new HashSet<String>();
    for (String curi : go_type_ids) {
        if (curi.startsWith("http")) {
            go_type_uris.add(curi);
        } else {
            try {
                IRI iri = curie_handler.getIRI(curi);
                if (iri != null) {
                    go_type_uris.add(iri.toString());
                }
            } catch (UnknownIdentifierException e) {
                r.error += e.getMessage() + " \n ";
                e.printStackTrace();
                return r;
            }
        }
    }
    for (String curi : gene_type_ids) {
        if (curi.startsWith("http")) {
            gene_type_uris.add(curi);
        } else {
            try {
                IRI iri = curie_handler.getIRI(curi);
                if (iri != null) {
                    gene_type_uris.add(iri.toString());
                }
            } catch (UnknownIdentifierException e) {
                r.error += e.getMessage() + " \n ";
                e.printStackTrace();
                return r;
            }
        }
    }
    Map<String, ModelMeta> id_model = new LinkedHashMap<String, ModelMeta>();
    String sparql = "";
    try {
        sparql = IOUtils.toString(ModelSearchHandler.class.getResourceAsStream("/ModelSearchQueryTemplate.rq"), StandardCharsets.UTF_8);
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    Map<String, String> ind_return = new HashMap<String, String>();
    // <ind_return_list>
    String ind_return_list = "";
    // <types>
    String types = "";
    int n = 0;
    for (String type_uri : gene_type_uris) {
        n++;
        ind_return.put("?ind" + n, type_uri);
        ind_return_list = ind_return_list + " (GROUP_CONCAT(?ind" + n + " ; separator=\" \") AS ?inds" + n + ")";
        types = types + "?ind" + n + " rdf:type <" + type_uri + "> . \n";
    }
    if (expand != null) {
        for (String go_type_uri : go_type_uris) {
            n++;
            ind_return.put("?ind" + n, go_type_uri);
            ind_return_list = ind_return_list + " (GROUP_CONCAT(?ind" + n + " ; separator=\" \") AS ?inds" + n + ")";
            String expansion = "VALUES ?term" + n + " { ";
            try {
                Set<String> subclasses = go_lego.getAllSubClasses(go_type_uri);
                for (String sub : subclasses) {
                    expansion += "<" + sub + "> \n";
                }
                expansion += "} . \n";
                types = types + " " + expansion + " ?ind" + n + " rdf:type ?term" + n + " . \n";
            } catch (IOException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
        }
    } else {
        for (String go_type_uri : go_type_uris) {
            n++;
            ind_return.put("?ind" + n, go_type_uri);
            ind_return_list = ind_return_list + " (GROUP_CONCAT(?ind" + n + " ; separator=\" \") AS ?inds" + n + ")";
            types = types + "?ind" + n + " rdf:type <" + go_type_uri + "> . \n";
        }
    }
    String id_constraint = "";
    if (id != null && id.size() > 0) {
        String id_list = "";
        for (String mid : id) {
            if (!mid.contains("http")) {
                String[] curie = mid.split(":");
                if (curie != null && curie.length == 2) {
                    mid = "http://model.geneontology.org/" + curie[1];
                }
            // TODO figure this out and add it to standard curie collection
            // try {
            // IRI iri = curie_handler.getIRI(id);
            // id = iri.toString();
            // } catch (UnknownIdentifierException e) {
            // // TODO Auto-generated catch block
            // e.printStackTrace();
            // }
            }
            id_list += "<" + mid + "> ";
        }
        id_constraint = " values ?id { " + id_list + " } ";
    }
    // <pmid_constraints>
    String pmid_constraints = "";
    if (pmids != null) {
        for (String pmid : pmids) {
            n++;
            ind_return.put("?ind" + n, pmid);
            ind_return_list = ind_return_list + " (GROUP_CONCAT(?ind" + n + " ; separator=\" \") AS ?inds" + n + ")";
            pmid_constraints = pmid_constraints + "?ind" + n + " <http://purl.org/dc/elements/1.1/source> ?pmid FILTER (?pmid=\"" + pmid + "\"^^xsd:string) .\n";
        }
    }
    String taxa_constraint = "";
    if (taxa != null && !taxa.isEmpty()) {
        for (String taxon : taxa) {
            if (taxon.startsWith("NCBITaxon:")) {
                taxon = taxon.replace(":", "_");
                taxon = "http://purl.obolibrary.org/obo/" + taxon;
            } else if (!taxon.startsWith("http://purl.obolibrary.org/obo/NCBITaxon_")) {
                taxon = "http://purl.obolibrary.org/obo/NCBITaxon_" + taxon;
            }
            taxa_constraint += "?id <" + BlazegraphOntologyManager.in_taxon_uri + "> <" + taxon + "> . \n";
        }
    }
    // if(taxa!=null&&!taxa.isEmpty()) {
    // String model_filter =  " VALUES ?id { \n";
    // for(String taxon : taxa) {
    // if(taxon.startsWith("NCBITaxon:")) {
    // taxon = taxon.replace(":", "_");
    // taxon = "http://purl.obolibrary.org/obo/"+taxon;
    // }
    // else if(!taxon.startsWith("http://purl.obolibrary.org/obo/NCBITaxon_")) {
    // taxon = "http://purl.obolibrary.org/obo/NCBITaxon_"+taxon;
    // }
    // Set<String> models = taxon_models.get(taxon);
    // if(models!=null) {
    // for(String model : models) {
    // model_filter+="<"+model+"> \n";
    // }
    // }
    // }
    // model_filter += "} . \n";
    // taxa_constraint = model_filter;
    // }
    String title_search_constraint = "";
    if (title_search != null) {
        title_search_constraint = "?title <http://www.bigdata.com/rdf/search#search> \"" + title_search + "\" .\n";
        if (!title_search.contains("*")) {
            title_search_constraint += " ?title <http://www.bigdata.com/rdf/search#matchAllTerms> \"" + "true" + "\" . \n";
        }
    // if(exact_match) {
    // title_search_constraint+=" ?title <http://www.bigdata.com/rdf/search#matchExact>  \""+"true"+"\" . \n";
    // }
    }
    String state_search_constraint = "";
    if (state_search != null && state_search.size() > 0) {
        String allowed_states = "";
        int c = 0;
        for (String s : state_search) {
            c++;
            allowed_states += "\"" + s + "\"";
            if (c < state_search.size()) {
                allowed_states += ",";
            }
        }
        // FILTER (?state IN ("production", , "development", "review", "closed", "delete" ))
        state_search_constraint = "FILTER (?state IN (" + allowed_states + ")) . \n";
    }
    String contributor_search_constraint = "";
    if (contributor_search != null && contributor_search.size() > 0) {
        String allowed_contributors = "";
        int c = 0;
        for (String contributor : contributor_search) {
            c++;
            allowed_contributors += "\"" + contributor + "\"";
            if (c < contributor_search.size()) {
                allowed_contributors += ",";
            }
        }
        contributor_search_constraint = " ?id <http://purl.org/dc/elements/1.1/contributor> ?test_contributor . \n" + " FILTER (?test_contributor IN (" + allowed_contributors + ")) . \n";
    }
    String group_search_constraint = "";
    if (group_search != null && group_search.size() > 0) {
        String allowed_group = "";
        int c = 0;
        for (String group : group_search) {
            c++;
            allowed_group += "\"" + group + "\"";
            if (c < group_search.size()) {
                allowed_group += ",";
            }
        }
        group_search_constraint = " ?id <http://purl.org/pav/providedBy> ?test_group . \n" + "FILTER (?test_group IN (" + allowed_group + ")) . \n";
    }
    String date_constraint = "";
    if (exactdate != null && exactdate.length() == 10) {
        date_constraint = "FILTER (?date = '" + exactdate + "') \n";
    } else if (date_search != null && date_search.length() == 10) {
        // e.g. 2019-06-26
        date_constraint = "FILTER (?date > '" + date_search + "') \n";
        if (datend != null && datend.length() == 10) {
            date_constraint = "FILTER (?date > '" + date_search + "' && ?date < '" + datend + "') \n";
        }
    }
    String offset_constraint = "";
    if (offset != 0) {
        offset_constraint = "OFFSET " + offset + "\n";
    }
    String limit_constraint = "";
    if (limit != 0) {
        limit_constraint = "LIMIT " + limit + "\n";
    }
    if (offset == 0 && limit == 0) {
        limit_constraint = "LIMIT 1000\n";
    }
    // default group by
    String group_by_constraint = "GROUP BY ?id";
    // default return block
    // TODO investigate need to add DISTINCT to GROUP_CONCAT here
    String return_block = "?id (MIN(?date) AS ?mindate) (MIN(?title) AS ?mintitle) (MIN(?state) AS ?minstate) <ind_return_list> (GROUP_CONCAT(DISTINCT ?contributor;separator=\";\") AS ?contributors) (GROUP_CONCAT(DISTINCT ?group;separator=\";\") AS ?groups)";
    if (count != null) {
        return_block = "(count(distinct ?id) as ?count)";
        limit_constraint = "";
        offset_constraint = "";
        group_by_constraint = "";
    }
    sparql = sparql.replaceAll("<return_block>", return_block);
    sparql = sparql.replaceAll("<id_constraint>", id_constraint);
    sparql = sparql.replaceAll("<group_by_constraint>", group_by_constraint);
    sparql = sparql.replaceAll("<ind_return_list>", ind_return_list);
    sparql = sparql.replaceAll("<types>", types);
    sparql = sparql.replaceAll("<pmid_constraints>", pmid_constraints);
    sparql = sparql.replaceAll("<title_constraint>", title_search_constraint);
    sparql = sparql.replaceAll("<state_constraint>", state_search_constraint);
    sparql = sparql.replaceAll("<contributor_constraint>", contributor_search_constraint);
    sparql = sparql.replaceAll("<group_constraint>", group_search_constraint);
    sparql = sparql.replaceAll("<date_constraint>", date_constraint);
    sparql = sparql.replaceAll("<limit_constraint>", limit_constraint);
    sparql = sparql.replaceAll("<offset_constraint>", offset_constraint);
    sparql = sparql.replaceAll("<taxa_constraint>", taxa_constraint);
    if (debug != null) {
        r.sparql = sparql;
    } else {
        r.sparql = "add 'debug' parameter to see sparql request";
    }
    TupleQueryResult result;
    try {
        result = (TupleQueryResult) m3.executeSPARQLQuery(sparql, 1000);
    } catch (MalformedQueryException | QueryEvaluationException | RepositoryException e) {
        if (e instanceof MalformedQueryException) {
            r.message = "Malformed Query";
        } else if (e instanceof QueryEvaluationException) {
            r.message = "Query Evaluation Problem - probably a time out";
        } else if (e instanceof RepositoryException) {
            r.message = "Repository Exception";
        }
        r.error = e.getMessage();
        e.printStackTrace();
        return r;
    }
    String n_count = null;
    try {
        while (result.hasNext()) {
            BindingSet bs = result.next();
            if (count != null) {
                n_count = bs.getBinding("count").getValue().stringValue();
            } else {
                // model meta
                String model_iri_string = bs.getBinding("id").getValue().stringValue();
                IRI model_iri = IRI.create(model_iri_string);
                String model_curie = null;
                try {
                    model_curie = curie_handler.getCuri(IRI.create(model_iri_string));
                    if (model_curie == null) {
                        model_curie = model_iri_string;
                    }
                } catch (Exception e) {
                    r.error += e.getMessage() + " \n ";
                    e.printStackTrace();
                    return r;
                }
                String date = bs.getBinding("mindate").getValue().stringValue();
                String title = bs.getBinding("mintitle").getValue().stringValue();
                String contribs = bs.getBinding("contributors").getValue().stringValue();
                // optional values (some are empty)
                Binding state_binding = bs.getBinding("minstate");
                String state = "";
                if (state_binding != null) {
                    state = state_binding.getValue().stringValue();
                }
                Binding group_binding = bs.getBinding("groups");
                String groups_ = "";
                if (group_binding != null) {
                    groups_ = group_binding.getValue().stringValue();
                }
                Set<String> contributors = new HashSet<String>(Arrays.asList(contribs.split(";")));
                Set<String> groups = new HashSet<String>();
                if (groups_ != null) {
                    groups.addAll(Arrays.asList(groups_.split(";")));
                }
                ModelMeta mm = id_model.get(model_curie);
                if (mm == null) {
                    // look up model in in-memory cache to check edit state
                    boolean is_modified = m3.isModelModified(model_iri);
                    mm = new ModelMeta(model_curie, date, title, state, contributors, groups, is_modified);
                }
                // matching
                for (String ind : ind_return.keySet()) {
                    String bindingName = ind.replace("?ind", "inds");
                    String[] ind_class_matches = bs.getBinding(bindingName).getValue().stringValue().split(" ", -1);
                    for (String ind_class_match : ind_class_matches) {
                        Set<String> matching_inds = mm.query_match.get(ind_return.get(ind));
                        if (matching_inds == null) {
                            matching_inds = new HashSet<String>();
                        }
                        matching_inds.add(ind_class_match);
                        mm.query_match.put(ind_return.get(ind), matching_inds);
                    }
                }
                id_model.put(model_curie, mm);
            }
        }
    } catch (QueryEvaluationException e) {
        r.message = "Query Evaluation Problem - probably a time out";
        r.error = e.getMessage();
        e.printStackTrace();
        return r;
    }
    if (n_count != null) {
        r.n = Integer.parseInt(n_count);
    } else {
        r.n = id_model.size();
        r.models = new LinkedHashSet<ModelMeta>(id_model.values());
    }
    try {
        result.close();
    } catch (QueryEvaluationException e) {
        r.message = "Query Evaluation Problem - can't close result set";
        r.error = e.getMessage();
        e.printStackTrace();
        return r;
    }
    // http://127.0.0.1:6800/modelsearch/?query=bla
    return r;
}

Example 9 with CurieHandler

use of org.geneontology.minerva.curie.CurieHandler in project minerva by geneontology.

the class GoCamModelTest method testRootTypesForComplements.

@Test
public void testRootTypesForComplements() throws Exception {
    String ontologyJournalFile = "/tmp/test-go-lego-blazegraph-complements.jnl";
    OWLOntologyManager man = OWLManager.createOWLOntologyManager();
    OWLOntology tboxOntology = man.loadOntologyFromOntologyDocument(new File("src/test/resources/go-basic.obo"));
    CurieHandler curieHandler = new MappedCurieHandler();
    String inputDB = "/tmp/test-blazegraph-models-complements.jnl";
    UndoAwareMolecularModelManager m3 = null;
    m3 = new UndoAwareMolecularModelManager(tboxOntology, curieHandler, "gomodel", inputDB, null, ontologyJournalFile, true);
    m3.importModelToDatabase(new File("src/test/resources/test-complement-roots.ttl"), true);
    ModelContainer mc = m3.getModel(IRI.create("http://model.geneontology.org/61f3310500000003"));
    OWLOntology gocam_via_mc = mc.getAboxOntology();
    GoCamModel g = new GoCamModel(gocam_via_mc, m3);
    assertTrue("Can get roots for classes and complements", g.ind_types.get(man.getOWLDataFactory().getOWLNamedIndividual(IRI.create("http://model.geneontology.org/61f3310500000003/61f3310500000004"))).contains("http://purl.obolibrary.org/obo/GO_0008150"));
    assertTrue("Can get roots for classes and complements", g.ind_types.get(man.getOWLDataFactory().getOWLNamedIndividual(IRI.create("http://model.geneontology.org/61f3310500000003/61f3310500000005"))).contains("http://purl.obolibrary.org/obo/GO_0008150"));
    m3.getGolego_repo().dispose();
}

Example 10 with CurieHandler

use of org.geneontology.minerva.curie.CurieHandler in project minerva by geneontology.

the class GoCamModelTest method testGoModelStats.

@Test
public void testGoModelStats() throws Exception {
    OWLOntologyManager man = OWLManager.createOWLOntologyManager();
    OWLOntology tbox_ontology = man.loadOntology(IRI.create("http://purl.obolibrary.org/obo/go/extensions/go-lego.owl"));
    CurieHandler curieHandler = new MappedCurieHandler();
    String inputDB = "/tmp/test-blazegraph-models.jnl";
    // load it into a journal and launch an m3
    UndoAwareMolecularModelManager m3 = null;
    File f = new File(gocam_dir);
    if (f.isDirectory()) {
        // remove anything that existed from previous runs
        File bgdb = new File(inputDB);
        if (bgdb.exists()) {
            bgdb.delete();
        }
        // set it up with empty db
        m3 = new UndoAwareMolecularModelManager(tbox_ontology, curieHandler, "gomodel", inputDB, null, ontology_journal_file, true);
        onto_repo = m3.getGolego_repo();
        // load the db
        for (File file : f.listFiles()) {
            if (file.getName().endsWith("ttl")) {
                m3.importModelToDatabase(file, true);
            }
        }
    }
    // read it back out and check on stats
    for (IRI modelIRI : m3.getAvailableModelIds()) {
        ModelContainer mc = m3.getModel(modelIRI);
        OWLOntology gocam_via_mc = mc.getAboxOntology();
        GoCamModel g = new GoCamModel(gocam_via_mc, m3);
        // testing for an issue with the OWL blazegraph loader
        assertFalse("title not read out of M3 retrieved model " + modelIRI, (g.getTitle() == null));
        // these reactions are not counted as activities, but causal relations coming from them are counted.
        if (modelIRI.toString().contains("R-HSA-5654719")) {
            // SHC-mediated cascade:FGFR4
            assertTrue("wrong n activities " + g.getStats().n_activity_units, g.getStats().n_activity_units == 4);
            assertTrue("wrong n complete activities " + g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units == 2);
            assertTrue("wrong n unenabled activities " + g.getStats().n_no_enabler, g.getStats().n_no_enabler == 2);
            assertTrue("wrong n causal relations " + g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions == 6);
        } else if (modelIRI.toString().contains("R-HSA-201688")) {
            // WNT mediated activation of DVL
            assertTrue("wrong n activities " + g.getStats().n_activity_units, g.getStats().n_activity_units == 4);
            assertTrue("wrong n complete activities " + g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units == 3);
            assertTrue("wrong n unenabled activities " + g.getStats().n_no_enabler, g.getStats().n_no_enabler == 1);
            assertTrue("wrong n causal relations " + g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions == 3);
        } else if (modelIRI.toString().contains("R-HSA-5654733")) {
            // Negative regulation of FGFR4 signaling
            assertTrue("wrong n activities " + g.getStats().n_activity_units, g.getStats().n_activity_units == 3);
            assertTrue("wrong n complete activities " + g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units == 2);
            assertTrue("wrong n unenabled activities " + g.getStats().n_no_enabler, g.getStats().n_no_enabler == 1);
            assertTrue("wrong n causal relations " + g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions == 3);
        }
    }
}