[Demonstration 1]

[Buggy Method]
@Test
public void contextLoads() {
    Assert.assertNotNull(null);
}

[Buggy Hunk]
Assert.assertNotNull(null);

[Patch]
Assert.assertNotNull("Test");

[Demonstration 2]

[Buggy Method]
@Override
public String runQuery(BioPortalAnnotatorQuery query) throws IOException {
    /*
         * Request parameters
         */
    Map<String, String> requestProperties = new HashMap<>();
    requestProperties.put("Authorization", String.format("apikey token=%s", apiKey));
    requestProperties.put("Accept", "application/rdf+xml");
    RequestGenerator requestGenerator = new RequestGenerator(baseURI, "POST", requestProperties);
    requestGenerator.put("text", query.getText());
    requestGenerator.put("apikey", apiKey);
    String ontologyString = query.generateOntologyString();
    if (!ontologyString.isEmpty()) {
        requestGenerator.put("ontologies", ontologyString);
    }
    String semanticTypesString = query.generateSemanticTypesString();
    if (!semanticTypesString.isEmpty()) {
        requestGenerator.put("semantic_types", semanticTypesString);
    }
    String semanticGroupsString = query.generateSemanticGroupsString();
    if (!semanticTypesString.isEmpty()) {
        requestGenerator.put("semantic_groups", semanticGroupsString);
    }
    if (query.isExcludeNumbers()) {
        requestGenerator.put("exclude_numbers", "true");
    }
    if (query.isWholeWordOnly()) {
        requestGenerator.put("whole_word_only", "true");
    }
    if (query.isExcludeSynonyms()) {
        requestGenerator.put("exclude_synonyms", "true");
    }
    if (query.isExpandMappings()) {
        requestGenerator.put("expand_mappings", "true");
    }
    if (query.isExpandClassHierarchy()) {
        requestGenerator.put("expand_class_hierarchy", "true");
    }
    if (!query.getScore().isEmpty()) {
        requestGenerator.put("score", query.getScore());
    }
    if (query.getClassHierarchyMaxLevel() > 0) {
        requestGenerator.put("class_hierarchy_max_level", Integer.toString(query.getClassHierarchyMaxLevel()));
    }
    if (query.isNegation()) {
        requestGenerator.put("negation", Boolean.toString(query.isNegation()));
    }
    if (query.isTemporality()) {
        requestGenerator.put("temporality", Boolean.toString(query.isTemporality()));
    }
    if (query.isExperiencer()) {
        requestGenerator.put("experiencer", Boolean.toString(query.isExperiencer()));
    }
    if (query.isLemmatize()) {
        requestGenerator.put("lemmatize", Boolean.toString(query.isLemmatize()));
    }
    requestGenerator.put("format", query.getFormat());
    //logger.error(connection.toString());
    return RestfulRequest.queryAnnotator(requestGenerator);
}

[Buggy Hunk]
if (!semanticTypesString.isEmpty()) {

[Patch]
if (!semanticGroupsString.isEmpty()) {

[Demonstration 3]

[Buggy Method]
public List<Membership> getNetworkUserMemberships(UUID networkId, Permissions permission, int skipBlocks, int blockSize) throws ObjectNotFoundException, NdexException, SQLException {
    Preconditions.checkArgument(!Strings.isNullOrEmpty(networkId.toString()), "A network UUID is required");
    if (permission != null)
        Preconditions.checkArgument((permission.equals(Permissions.ADMIN)) || (permission.equals(Permissions.WRITE)) || (permission.equals(Permissions.READ)), "Valid permission required");
    List<Membership> memberships = new ArrayList<>();
    String sql = "select owneruuid as user_id, owner as user_name,name, 'ADMIN' from network where \"UUID\"=? and is_deleted=false";
    if (permission == null) {
        sql += " union select un.user_id, u.user_name, n.name, un.permission_type from user_network_membership un, network n, ndex_user u where u.\"UUID\" = un.user_id and " + "n.\"UUID\" = un.network_id and network_id = '" + networkId.toString() + "'";
    } else if (permission != Permissions.ADMIN)
        sql = "select user_id, u.user_name, n.name, un.permission_type from user_network_membership un, network n, ndex_user u where u.\"UUID\" = un.user_id and n.\"UUID\" = un.network_id " + "and network_id = '" + networkId + "' and ndex_permission_type = '" + permission.toString() + "'";
    if (skipBlocks >= 0 && blockSize > 0) {
        sql += " limit " + blockSize + " offset " + skipBlocks * blockSize;
    }
    try (PreparedStatement p = db.prepareStatement(sql)) {
        p.setObject(1, networkId);
        try (ResultSet rs = p.executeQuery()) {
            while (rs.next()) {
                Membership membership = new Membership();
                membership.setMembershipType(MembershipType.NETWORK);
                membership.setMemberAccountName(rs.getString(2));
                membership.setMemberUUID((UUID) rs.getObject(1));
                membership.setPermissions(Permissions.valueOf(rs.getString(4)));
                membership.setResourceName(rs.getString(3));
                membership.setResourceUUID(networkId);
                memberships.add(membership);
            }
        }
    }
    logger.info("Successfuly retrieved network-user memberships");
    return memberships;
}

[Buggy Hunk]
+ "and network_id = '" + networkId+ "' and ndex_permission_type = '" + permission.toString() + "'";

[Patch]
+ "and network_id = ? and un.permission_type = '" + permission.toString() + "'";