public static BasicDataSource makeBasicDataSource(
String dbDriverClassname, String jdbcUrl, String username, String password) {
log.debug(
"makeBasicDataSource('"
+ dbDriverClassname
+ "', '"
+ jdbcUrl
+ "', '"
+ username
+ "', '"
+ password
+ "')");
BasicDataSource ds = new BasicDataSource();
ds.setDriverClassName(dbDriverClassname);
ds.setUrl(jdbcUrl);
ds.setUsername(username);
ds.setPassword(password);
int maxActiveInt = DEFAULT_MAXACTIVE;
String maxActiveStr =
ConfigurationProperties.getProperty("VitroConnection.DataSource.pool.maxActive");
if (!StringUtils.isEmpty(maxActiveStr)) {
try {
maxActiveInt = Integer.parseInt(maxActiveStr);
} catch (NumberFormatException nfe) {
log.error(
"Unable to parse connection pool maxActive setting " + maxActiveStr + " as an integer");
}
}
int maxIdleInt = (maxActiveInt > DEFAULT_MAXACTIVE) ? maxActiveInt / 4 : DEFAULT_MAXIDLE;
String maxIdleStr =
ConfigurationProperties.getProperty("VitroConnection.DataSource.pool.maxIdle");
if (!StringUtils.isEmpty(maxIdleStr)) {
try {
maxIdleInt = Integer.parseInt(maxIdleStr);
} catch (NumberFormatException nfe) {
log.error(
"Unable to parse connection pool maxIdle setting " + maxIdleStr + " as an integer");
}
}
ds.setMaxActive(maxActiveInt);
ds.setMaxIdle(maxIdleInt);
ds.setMaxWait(DEFAULT_MAXWAIT);
ds.setValidationQuery(VALIDATIONQUERY);
ds.setTestOnBorrow(DEFAULT_TESTONBORROW);
ds.setTestOnReturn(DEFAULT_TESTONRETURN);
ds.setMinEvictableIdleTimeMillis(DEFAULT_MINEVICTIONIDLETIME);
ds.setNumTestsPerEvictionRun(DEFAULT_TESTSPEREVICTION);
ds.setTimeBetweenEvictionRunsMillis(DEFAULT_TIMEBETWEENEVICTIONS);
try {
ds.getConnection().close();
} catch (Exception e) {
e.printStackTrace();
}
return ds;
}
/** Sets up a BasicDataSource using values from a properties file. */
public final BasicDataSource makeDataSourceFromConfigurationProperties() {
String dbDriverClassname =
ConfigurationProperties.getProperty(
"VitroConnection.DataSource.driver", DB_DRIVER_CLASS_NAME);
String jdbcUrl = getJdbcUrl();
String username = ConfigurationProperties.getProperty("VitroConnection.DataSource.username");
String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
return makeBasicDataSource(dbDriverClassname, jdbcUrl, username, password);
}
/**
* If the {@link ConfigurationProperties} has a name for the initial admin user, create the user
* and add it to the model.
*/
protected void createInitialAdminUser(Model model) {
String initialAdminUsername = ConfigurationProperties.getProperty("initialAdminUser");
if (initialAdminUsername == null) {
return;
}
// A hard-coded MD5 encryption of "defaultAdmin"
String initialAdminPassword = "******";
String vitroDefaultNs = DEFAULT_DEFAULT_NAMESPACE;
Resource user = model.createResource(vitroDefaultNs + "defaultAdminUser");
model.add(
model.createStatement(
user,
model.createProperty(VitroVocabulary.RDF_TYPE),
model.getResource(VitroVocabulary.USER)));
model.add(
model.createStatement(
user,
model.createProperty(VitroVocabulary.USER_USERNAME),
model.createTypedLiteral(initialAdminUsername)));
model.add(
model.createStatement(
user,
model.createProperty(VitroVocabulary.USER_MD5PASSWORD),
model.createTypedLiteral(initialAdminPassword)));
model.add(
model.createStatement(
user,
model.createProperty(VitroVocabulary.USER_ROLE),
model.createTypedLiteral("role:/50")));
}
/** Sets up a Model and DB connection using values from a properties file. */
public final Model makeDBModelFromConfigurationProperties(
String jenaDbModelName, OntModelSpec jenaDbOntModelSpec) {
String jdbcUrl = getJdbcUrl();
String username = ConfigurationProperties.getProperty("VitroConnection.DataSource.username");
String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
BasicDataSource ds = makeBasicDataSource(DB_DRIVER_CLASS_NAME, jdbcUrl, username, password);
String dns = ConfigurationProperties.getProperty("Vitro.defaultNamespace");
defaultNamespace = (dns != null && dns.length() > 0) ? dns : null;
jenaDbOntModelSpec = (jenaDbOntModelSpec != null) ? jenaDbOntModelSpec : DB_ONT_MODEL_SPEC;
return makeDBModel(ds, jenaDbModelName, jenaDbOntModelSpec);
}
protected void makeModelMakerFromConnectionProperties(TripleStoreType type) {
String jdbcUrl = getJdbcUrl();
String username = ConfigurationProperties.getProperty("VitroConnection.DataSource.username");
String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
if (TripleStoreType.RDB.equals(type)) {
vjmm = new VitroJenaModelMaker(jdbcUrl, username, password, DB_TYPE);
} else if (TripleStoreType.SDB.equals(type)) {
StoreDesc storeDesc = new StoreDesc(LayoutType.LayoutTripleNodesHash, DatabaseType.MySQL);
BasicDataSource bds =
JenaDataSourceSetup.makeBasicDataSource(
DB_DRIVER_CLASS_NAME, jdbcUrl, username, password);
try {
vsmm = new VitroJenaSDBModelMaker(storeDesc, bds);
} catch (SQLException sqle) {
log.error("Unable to set up SDB ModelMaker", sqle);
}
}
return;
}
private String getJdbcUrl() {
String jdbcUrl = ConfigurationProperties.getProperty("VitroConnection.DataSource.url");
// Ensure that MySQL handles unicode properly, else all kinds of
// horrible nastiness ensues.
if ("MySQL".equals(DB) && !jdbcUrl.contains("?")) {
jdbcUrl += "?useUnicode=yes&characterEncoding=utf8";
}
return jdbcUrl;
}
public static Model makeDBModel(
BasicDataSource ds,
String jenaDbModelName,
OntModelSpec jenaDbOntModelSpec,
TripleStoreType storeType,
String dbType) {
Model dbModel = null;
try {
// open the db model
try {
Graph g = null;
switch (storeType) {
case RDB:
g = new RegeneratingGraph(new RDBGraphGenerator(ds, dbType, jenaDbModelName));
break;
case SDB:
String layoutStr =
ConfigurationProperties.getProperty(
"VitroConnection.DataSource.sdb.layout", "layout2/hash");
String dbtypeStr =
ConfigurationProperties.getProperty("VitroConnection.DataSource.dbtype", "MySQL");
StoreDesc desc =
new StoreDesc(LayoutType.fetch(layoutStr), DatabaseType.fetch(dbtypeStr));
g = new RegeneratingGraph(new SDBGraphGenerator(ds, desc, jenaDbModelName));
break;
default:
throw new RuntimeException("Unsupported store type " + storeType);
}
dbModel = ModelFactory.createModelForGraph(g);
log.debug("Using database at " + ds.getUrl());
} catch (Throwable t) {
t.printStackTrace();
}
} catch (Throwable t) {
t.printStackTrace();
}
return dbModel;
}
public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
private static final Log log = LogFactory.getLog(JenaDataSourceSetupBase.class);
protected static final int DEFAULT_MAXWAIT = 10000, // ms
DEFAULT_MAXACTIVE = 40,
DEFAULT_MAXIDLE = 10,
DEFAULT_TIMEBETWEENEVICTIONS = 30 * 60 * 1000, // ms
DEFAULT_TESTSPEREVICTION = 3,
DEFAULT_MINEVICTIONIDLETIME = 1000 * 60 * 30; // ms
protected static final String VALIDATIONQUERY =
ConfigurationProperties.getProperty("VitroConnection.DataSource.validationQuery", "SELECT 1");
protected static final boolean DEFAULT_TESTONBORROW = true,
DEFAULT_TESTONRETURN = true,
DEFAULT_TESTWHILEIDLE = true;
protected static String BASE = "/WEB-INF/ontologies/";
protected static String USERPATH = BASE + "user/";
protected static String SYSTEMPATH = BASE + "system/";
protected static String AUTHPATH = BASE + "auth/";
public static String APPPATH = BASE + "app/";
protected static String SUBMODELS = "/WEB-INF/submodels/";
String DB_USER = "******"; // database user id
String DB_PASSWD = "jenatest"; // database password
String DB =
ConfigurationProperties.getProperty( // database type
"VitroConnection.DataSource.dbtype", "MySQL");
String DB_DRIVER_CLASS_NAME =
ConfigurationProperties.getProperty(
"VitroConnection.DataSource.driver", "com.mysql.jdbc.Driver");
// ABox assertions. These are stored in a database (Jena SDB) and the
// application works (queries and updates) with the ABox data from the DB -
// this model is not maintained in memory. For query performance reasons,
// there won't be any submodels for the ABox data.
public static final String JENA_DB_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-2";
// ABox inferences. This is ABox data that is inferred, using VIVO's native
// simple, specific-purpose reasoning based on the combination of the ABox
// (assertion and inferences) data and the TBox (assertions and inferences)
// data.
public static final String JENA_INF_MODEL =
"http://vitro.mannlib.cornell.edu/default/vitro-kb-inf";
// TBox assertions.
// Some of these (the local extensions) are stored and maintained in a Jena
// database and are also maintained in memory while the application is
// running. Other parts of the TBox, the 'VIVO Core,' are also backed by a
// Jena DB, but they are read fresh from files each time the application
// starts. While the application is running, they are kept in memory, as
// submodels of the in memory copy of this named graph.
public static final String JENA_TBOX_ASSERTIONS_MODEL =
"http://vitro.mannlib.cornell.edu/default/asserted-tbox";
// Inferred TBox. This is TBox data that is inferred from the combination of
// VIVO core TBox and any local extension TBox assertions. Pellet computes
// these inferences. These are stored in the DB.
public static final String JENA_TBOX_INF_MODEL =
"http://vitro.mannlib.cornell.edu/default/inferred-tbox";
// Model for tracking edit changes. Obsolete.
static final String JENA_AUDIT_MODEL =
"http://vitro.mannlib.cornell.edu/ns/db/experimental/audit";
// User accounts data
public static final String JENA_USER_ACCOUNTS_MODEL =
"http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccounts";
// This model doesn't exist yet. It's a placeholder for the application
// ontology.
public static final String JENA_APPLICATION_METADATA_MODEL =
"http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadata";
// This is Brian C's application.owl file. We may not have to be concerned
// with this for release 1.2.
static final String JENA_DISPLAY_METADATA_MODEL =
"http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata";
static final String DEFAULT_DEFAULT_NAMESPACE = "http://vitro.mannlib.cornell.edu/ns/default#";
static String defaultNamespace = DEFAULT_DEFAULT_NAMESPACE; // FIXME
// use OWL models with no reasoning
static final OntModelSpec DB_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
static final OntModelSpec MEM_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
private String getJdbcUrl() {
String jdbcUrl = ConfigurationProperties.getProperty("VitroConnection.DataSource.url");
// Ensure that MySQL handles unicode properly, else all kinds of
// horrible nastiness ensues.
if ("MySQL".equals(DB) && !jdbcUrl.contains("?")) {
jdbcUrl += "?useUnicode=yes&characterEncoding=utf8";
}
return jdbcUrl;
}
/** Sets up a Model and DB connection using values from a properties file. */
public final Model makeDBModelFromConfigurationProperties(
String jenaDbModelName, OntModelSpec jenaDbOntModelSpec) {
String jdbcUrl = getJdbcUrl();
String username = ConfigurationProperties.getProperty("VitroConnection.DataSource.username");
String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
BasicDataSource ds = makeBasicDataSource(DB_DRIVER_CLASS_NAME, jdbcUrl, username, password);
String dns = ConfigurationProperties.getProperty("Vitro.defaultNamespace");
defaultNamespace = (dns != null && dns.length() > 0) ? dns : null;
jenaDbOntModelSpec = (jenaDbOntModelSpec != null) ? jenaDbOntModelSpec : DB_ONT_MODEL_SPEC;
return makeDBModel(ds, jenaDbModelName, jenaDbOntModelSpec);
}
/** Sets up a BasicDataSource using values from a properties file. */
public final BasicDataSource makeDataSourceFromConfigurationProperties() {
String dbDriverClassname =
ConfigurationProperties.getProperty(
"VitroConnection.DataSource.driver", DB_DRIVER_CLASS_NAME);
String jdbcUrl = getJdbcUrl();
String username = ConfigurationProperties.getProperty("VitroConnection.DataSource.username");
String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
return makeBasicDataSource(dbDriverClassname, jdbcUrl, username, password);
}
public void setApplicationDataSource(BasicDataSource bds, ServletContext ctx) {
ctx.setAttribute(getDataSourceAttributeName(), bds);
}
public static BasicDataSource getApplicationDataSource(ServletContext ctx) {
return (BasicDataSource) ctx.getAttribute(getDataSourceAttributeName());
}
private static String getDataSourceAttributeName() {
return JenaDataSourceSetupBase.class.getName() + ".dataSource";
}
public static BasicDataSource makeBasicDataSource(
String dbDriverClassname, String jdbcUrl, String username, String password) {
log.debug(
"makeBasicDataSource('"
+ dbDriverClassname
+ "', '"
+ jdbcUrl
+ "', '"
+ username
+ "', '"
+ password
+ "')");
BasicDataSource ds = new BasicDataSource();
ds.setDriverClassName(dbDriverClassname);
ds.setUrl(jdbcUrl);
ds.setUsername(username);
ds.setPassword(password);
int maxActiveInt = DEFAULT_MAXACTIVE;
String maxActiveStr =
ConfigurationProperties.getProperty("VitroConnection.DataSource.pool.maxActive");
if (!StringUtils.isEmpty(maxActiveStr)) {
try {
maxActiveInt = Integer.parseInt(maxActiveStr);
} catch (NumberFormatException nfe) {
log.error(
"Unable to parse connection pool maxActive setting " + maxActiveStr + " as an integer");
}
}
int maxIdleInt = (maxActiveInt > DEFAULT_MAXACTIVE) ? maxActiveInt / 4 : DEFAULT_MAXIDLE;
String maxIdleStr =
ConfigurationProperties.getProperty("VitroConnection.DataSource.pool.maxIdle");
if (!StringUtils.isEmpty(maxIdleStr)) {
try {
maxIdleInt = Integer.parseInt(maxIdleStr);
} catch (NumberFormatException nfe) {
log.error(
"Unable to parse connection pool maxIdle setting " + maxIdleStr + " as an integer");
}
}
ds.setMaxActive(maxActiveInt);
ds.setMaxIdle(maxIdleInt);
ds.setMaxWait(DEFAULT_MAXWAIT);
ds.setValidationQuery(VALIDATIONQUERY);
ds.setTestOnBorrow(DEFAULT_TESTONBORROW);
ds.setTestOnReturn(DEFAULT_TESTONRETURN);
ds.setMinEvictableIdleTimeMillis(DEFAULT_MINEVICTIONIDLETIME);
ds.setNumTestsPerEvictionRun(DEFAULT_TESTSPEREVICTION);
ds.setTimeBetweenEvictionRunsMillis(DEFAULT_TIMEBETWEENEVICTIONS);
try {
ds.getConnection().close();
} catch (Exception e) {
e.printStackTrace();
}
return ds;
}
public enum TripleStoreType {
RDB,
SDB
}
protected Model makeDBModel(
BasicDataSource ds, String jenaDbModelname, OntModelSpec jenaDbOntModelSpec) {
return makeDBModel(ds, jenaDbModelname, jenaDbOntModelSpec, TripleStoreType.RDB);
}
protected Model makeDBModel(
BasicDataSource ds,
String jenaDbModelName,
OntModelSpec jenaDbOntModelSpec,
TripleStoreType storeType) {
return makeDBModel(ds, jenaDbModelName, jenaDbOntModelSpec, storeType, DB);
}
public static Model makeDBModel(
BasicDataSource ds,
String jenaDbModelName,
OntModelSpec jenaDbOntModelSpec,
TripleStoreType storeType,
String dbType) {
Model dbModel = null;
try {
// open the db model
try {
Graph g = null;
switch (storeType) {
case RDB:
g = new RegeneratingGraph(new RDBGraphGenerator(ds, dbType, jenaDbModelName));
break;
case SDB:
String layoutStr =
ConfigurationProperties.getProperty(
"VitroConnection.DataSource.sdb.layout", "layout2/hash");
String dbtypeStr =
ConfigurationProperties.getProperty("VitroConnection.DataSource.dbtype", "MySQL");
StoreDesc desc =
new StoreDesc(LayoutType.fetch(layoutStr), DatabaseType.fetch(dbtypeStr));
g = new RegeneratingGraph(new SDBGraphGenerator(ds, desc, jenaDbModelName));
break;
default:
throw new RuntimeException("Unsupported store type " + storeType);
}
dbModel = ModelFactory.createModelForGraph(g);
log.debug("Using database at " + ds.getUrl());
} catch (Throwable t) {
t.printStackTrace();
}
} catch (Throwable t) {
t.printStackTrace();
}
return dbModel;
}
public static void readOntologyFilesInPathSet(String path, ServletContext ctx, Model model) {
log.debug("Reading ontology files from '" + path + "'");
Set<String> paths = ctx.getResourcePaths(path);
if (paths != null) {
for (String p : paths) {
String format = getRdfFormat(p);
log.info("Loading ontology file at " + p + " as format " + format);
InputStream ontologyInputStream = ctx.getResourceAsStream(p);
try {
model.read(ontologyInputStream, null, format);
log.debug("...successful");
} catch (Throwable t) {
log.error("Failed to load ontology file at '" + p + "' as format " + format, t);
}
}
}
}
private static String getRdfFormat(String filename) {
String defaultformat = "RDF/XML";
if (filename == null) return defaultformat;
else if (filename.endsWith("n3")) return "N3";
else if (filename.endsWith("ttl")) return "TURTLE";
else return defaultformat;
}
/**
* If the {@link ConfigurationProperties} has a name for the initial admin user, create the user
* and add it to the model.
*/
protected void createInitialAdminUser(Model model) {
String initialAdminUsername = ConfigurationProperties.getProperty("initialAdminUser");
if (initialAdminUsername == null) {
return;
}
// A hard-coded MD5 encryption of "defaultAdmin"
String initialAdminPassword = "******";
String vitroDefaultNs = DEFAULT_DEFAULT_NAMESPACE;
Resource user = model.createResource(vitroDefaultNs + "defaultAdminUser");
model.add(
model.createStatement(
user,
model.createProperty(VitroVocabulary.RDF_TYPE),
model.getResource(VitroVocabulary.USER)));
model.add(
model.createStatement(
user,
model.createProperty(VitroVocabulary.USER_USERNAME),
model.createTypedLiteral(initialAdminUsername)));
model.add(
model.createStatement(
user,
model.createProperty(VitroVocabulary.USER_MD5PASSWORD),
model.createTypedLiteral(initialAdminPassword)));
model.add(
model.createStatement(
user,
model.createProperty(VitroVocabulary.USER_ROLE),
model.createTypedLiteral("role:/50")));
}
protected static final String DB_TYPE = "MySQL";
private static VitroJenaModelMaker vjmm = null;
private static VitroJenaSDBModelMaker vsmm = null;
private static final String sdbModelMaker = "vitroJenaSDBModelMaker";
private static final String rdbModelMaker = "vitroJenaModelMaker";
protected void makeModelMakerFromConnectionProperties(TripleStoreType type) {
String jdbcUrl = getJdbcUrl();
String username = ConfigurationProperties.getProperty("VitroConnection.DataSource.username");
String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
if (TripleStoreType.RDB.equals(type)) {
vjmm = new VitroJenaModelMaker(jdbcUrl, username, password, DB_TYPE);
} else if (TripleStoreType.SDB.equals(type)) {
StoreDesc storeDesc = new StoreDesc(LayoutType.LayoutTripleNodesHash, DatabaseType.MySQL);
BasicDataSource bds =
JenaDataSourceSetup.makeBasicDataSource(
DB_DRIVER_CLASS_NAME, jdbcUrl, username, password);
try {
vsmm = new VitroJenaSDBModelMaker(storeDesc, bds);
} catch (SQLException sqle) {
log.error("Unable to set up SDB ModelMaker", sqle);
}
}
return;
}
public static void setVitroJenaModelMaker(VitroJenaModelMaker vjmm, ServletContextEvent sce) {
sce.getServletContext().setAttribute(rdbModelMaker, vjmm);
}
public static void setVitroJenaSDBModelMaker(
VitroJenaSDBModelMaker vsmm, ServletContextEvent sce) {
sce.getServletContext().setAttribute(sdbModelMaker, vsmm);
}
public static boolean isSDBActive() {
String tripleStoreTypeStr =
ConfigurationProperties.getProperty("VitroConnection.DataSource.tripleStoreType", "RDB");
return ("SDB".equals(tripleStoreTypeStr));
}
protected VitroJenaModelMaker getVitroJenaModelMaker() {
return vjmm;
}
protected VitroJenaSDBModelMaker getVitroJenaSDBModelMaker() {
return vsmm;
}
}
public static boolean isSDBActive() {
String tripleStoreTypeStr =
ConfigurationProperties.getProperty("VitroConnection.DataSource.tripleStoreType", "RDB");
return ("SDB".equals(tripleStoreTypeStr));
}
