Examples with HPO_Class_Found org.monarchinitiative.loinc2hpo.util.HPO_Class_Found used on opensource projects

Example 6 with HPO_Class_Found

use of org.monarchinitiative.loinc2hpo.util.HPO_Class_Found in project loinc2hpo by monarch-initiative.

the class SparqlQueryTest method testQueryWithOneKey.

@Test
public void testQueryWithOneKey() {
    String key = "Testosterone";
    String looseQueryString = SparqlQuery.buildLooseQueryWithSingleKey(key);
    String standardQueryString = SparqlQuery.buildStandardQueryWithSingleKey(key);
    // System.out.println("loose query:\n" + looseQueryString);
    // System.out.println("\n\nstandard query:\n" + standardQueryString);
    Query looseQuery = QueryFactory.create(looseQueryString);
    Query standardQuery = QueryFactory.create(standardQueryString);
    assertNotNull(model);
    List<HPO_Class_Found> results_loose = SparqlQuery.query(looseQuery, model, null);
    List<HPO_Class_Found> results_standard = SparqlQuery.query(standardQuery, model, null);
    /**
     *        System.out.println(results_loose.size() + " HPO terms are found!");
     *        for(HPO_Class_Found hpo : results_loose) {
     *            System.out.println(hpo.getLabel() + "\t" + hpo.getId() + "\n" + hpo.getDefinition());
     *        }
     */
    // interesting that this program identifies 16 classes;
    assertEquals(14, results_loose.size());
    // while the same query finds 14 in command line
    // reason: command line uses hp.owl; this program builds a model from hp.owl(?)
    // reason: more likely has something to do with what kind of model is generated from hp.owl
    // System.out.println(results_standard.size()+ " HPO terms are found!");
    assertEquals(9, results_standard.size());
}

Example 7 with HPO_Class_Found

use of org.monarchinitiative.loinc2hpo.util.HPO_Class_Found in project loinc2hpo by monarch-initiative.

the class AnnotateTabController method handleCandidateHPODoubleClick.

@FXML
private void handleCandidateHPODoubleClick(MouseEvent e) {
    if (e.getClickCount() == 2 && hpoListView.getSelectionModel().getSelectedItem() != null && hpoListView.getSelectionModel().getSelectedItem() instanceof HPO_Class_Found) {
        HPO_Class_Found hpo_class_found = (HPO_Class_Found) hpoListView.getSelectionModel().getSelectedItem();
        List<HPO_Class_Found> parents = SparqlQuery.getParents(hpo_class_found.getId());
        List<HPO_Class_Found> children = SparqlQuery.getChildren(hpo_class_found.getId());
        // dummy root node
        TreeItem<HPO_TreeView> rootItem = new TreeItem<>(new HPO_TreeView());
        rootItem.setExpanded(true);
        TreeItem<HPO_TreeView> current = new TreeItem<>(new HPO_TreeView(hpo_class_found));
        // add parent terms to root; add current to each parent term
        parents.stream().map(p -> new TreeItem<>(new HPO_TreeView(p))).forEach(p -> {
            rootItem.getChildren().add(p);
            p.getChildren().add(current);
            p.setExpanded(true);
        });
        current.setExpanded(true);
        // add child terms to current
        children.stream().map(p -> new TreeItem<>(new HPO_TreeView(p))).forEach(current.getChildren()::add);
        this.treeView.setRoot(rootItem);
    }
    e.consume();
}

Example 8 with HPO_Class_Found

use of org.monarchinitiative.loinc2hpo.util.HPO_Class_Found in project loinc2hpo by monarch-initiative.

the class SparqlQueryTest method testQueryWithMultiKeys.

@Test
public void testQueryWithMultiKeys() {
    String[] keys = new String[] { "chronic", "kidney", "disease" };
    String looseQueryString = SparqlQuery.buildLooseQueryWithMultiKeys(Arrays.asList(keys));
    String standardQueryString = SparqlQuery.buildStandardQueryWithMultiKeys(Arrays.asList(keys));
    Query looseQuery = QueryFactory.create(looseQueryString);
    Query standardQuery = QueryFactory.create(standardQueryString);
    List<HPO_Class_Found> itr_loose = SparqlQuery.query(looseQuery, model, null);
    List<HPO_Class_Found> itr_standard = SparqlQuery.query(standardQuery, model, null);
    // System.out.println(itr_loose.size() + " HPO terms are found!");
    assertEquals(7, itr_loose.size());
    // System.out.println(itr_standard.size() + " HPO terms are found!");
    assertEquals(5, itr_standard.size());
}