private void doLoadRDFData(
String modelName, String docLoc, String filePath, String language, ModelMaker modelMaker) {
Model m = modelMaker.getModel(modelName);
m.enterCriticalSection(Lock.WRITE);
try {
if ((docLoc != null) && (docLoc.length() > 0)) {
m.read(docLoc, language);
} else if ((filePath != null) && (filePath.length() > 0)) {
File file = new File(filePath);
File[] files;
if (file.isDirectory()) {
files = file.listFiles();
} else {
files = new File[1];
files[0] = file;
}
for (int i = 0; i < files.length; i++) {
File currentFile = files[i];
log.info("Reading file " + currentFile.getName());
FileInputStream fis;
try {
fis = new FileInputStream(currentFile);
m.read(fis, null, language);
fis.close();
} catch (IOException ioe) {
throw new RuntimeException(ioe);
}
}
}
} finally {
m.leaveCriticalSection();
}
}
private void doAttachModel(String modelName, ModelMaker modelMaker) {
if (attachedModels.containsKey(modelName)) {
doDetachModel(modelName);
}
Model m = ModelFactory.createDefaultModel();
m.add(modelMaker.getModel(modelName));
ModelAccess.on(getServletContext()).getOntModel(TBOX_ASSERTIONS).addSubModel(m);
attachedModels.put(modelName, m);
log.info("Attached " + modelName + " (" + m.hashCode() + ") to webapp");
}
private void doClearModel(String modelName, ModelMaker modelMaker) {
Model m = modelMaker.getModel(modelName);
OntModel o = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, m);
o.enterCriticalSection(Lock.WRITE);
try {
o.removeAll(null, null, null);
} finally {
o.leaveCriticalSection();
}
// removeAll() doesn't work with the listeners!
}
protected void showModelList(VitroRequest vreq, ModelMaker maker, WhichService modelType) {
vreq.setAttribute("modelType", modelType.toString());
if (modelType == CONTENT) {
vreq.setAttribute("infoLine", "Main Store models");
} else {
vreq.setAttribute("infoLine", "Configuration models");
}
vreq.setAttribute("modelNames", maker.listModels().toList());
vreq.setAttribute("bodyAttr", "onLoad=\"init()\"");
vreq.setAttribute("title", "Available Models");
vreq.setAttribute("bodyJsp", LIST_MODELS_JSP);
}
public static void main(String[] args) {
try {
String className = args[0];
Class.forName(className);
String DB_URL = args[1]; // URL of database
String DB_NAME = args[2]; // DB name
String DB_USER = args[3]; // database user id
String DB_PASSWD = args[4]; // database password
String DB = args[5]; // database type
IDBConnection conn = new PagedDBConnection(DB_URL + DB_NAME, DB_USER, DB_PASSWD, DB);
ModelMaker maker = ExtendedModelFactory.createPagedModelRDBMaker(conn);
PagedModelRDB model = (PagedModelRDB) maker.createModel(args[6]);
model.setDoDuplicateCheck(false);
long startTime = System.currentTimeMillis();
model.read(new FileInputStream(args[7]), null, "N3");
long endTime = System.currentTimeMillis();
System.out.println(
"time to read in the model = " + (endTime - startTime) / 1000 + " seconds.\n");
startTime = System.currentTimeMillis();
long count = 0L;
String queryString = " SELECT ?x ?y ?z " + " WHERE { ?x ?y ?z } ";
QueryExecution qexec = QueryExecutionFactory.create(queryString, model);
ResultSet rs = qexec.execSelect();
while (rs.hasNext()) {
count++;
rs.nextSolution();
}
qexec.close();
endTime = System.currentTimeMillis();
System.out.println("count of found statements = " + count);
System.out.println("time to query for results = " + (endTime - startTime) + " milliseconds.");
conn.cleanDB();
conn.close();
} catch (Exception e) {
e.printStackTrace();
}
}
private void processPermanentURIRequest(VitroRequest vreq, ModelMaker maker) {
String modelName = vreq.getParameter("modelName");
String oldModel = vreq.getParameter("oldModel");
String newModel = vreq.getParameter("newModel");
String oldNamespace = vreq.getParameter("oldNamespace");
String newNamespace = vreq.getParameter("newNamespace");
String dNamespace = vreq.getParameter("defaultNamespace");
newNamespace = (newNamespace == null || newNamespace.isEmpty()) ? oldNamespace : newNamespace;
newNamespace = (dNamespace != null) ? dNamespace : newNamespace;
if (modelName != null) {
Model m = maker.getModel(modelName);
List<String> namespaceList = new ArrayList<>();
ResIterator resItr = m.listResourcesWithProperty((Property) null);
if (resItr != null) {
while (resItr.hasNext()) {
String namespace = resItr.nextResource().getNameSpace();
if (!namespaceList.contains(namespace)) {
namespaceList.add(namespace);
}
}
} else {
namespaceList.add("no resources present");
}
String defaultNamespace = vreq.getUnfilteredWebappDaoFactory().getDefaultNamespace();
vreq.setAttribute("modelName", modelName);
vreq.setAttribute("defaultNamespace", defaultNamespace);
vreq.setAttribute("namespaceList", namespaceList);
vreq.setAttribute("title", "Permanent URI");
vreq.setAttribute("bodyJsp", PERMANENT_URI);
} else if (oldModel != null) {
JenaIngestUtils utils = new JenaIngestUtils();
utils.doPermanentURI(oldModel, newModel, oldNamespace, newNamespace, maker, vreq);
vreq.setAttribute("title", "Ingest Menu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
}
}
private void processRenameBNodesRequest(VitroRequest vreq, ModelMaker maker) {
String[] sourceModel = vreq.getParameterValues("sourceModelName");
JenaIngestUtils utils = new JenaIngestUtils();
if (sourceModel != null && sourceModel.length != 0) {
List<Model> sourceModelList = new ArrayList<Model>();
for (int i = 0; i < sourceModel.length; i++) {
Model m = maker.getModel(sourceModel[i]);
if (m != null) {
sourceModelList.add(m);
}
}
Map<String, LinkedList<String>> propertyMap =
utils.generatePropertyMap(sourceModelList, maker);
List<String> sourceModelNameList = Arrays.asList(sourceModel);
vreq.setAttribute("sourceModel", sourceModelNameList);
vreq.setAttribute("propertyMap", propertyMap);
vreq.setAttribute("enablePropertyPatternURIs", !propertyMap.isEmpty());
vreq.setAttribute("title", "URI Select");
vreq.setAttribute("bodyJsp", RENAME_BNODES_URI_SELECT_JSP);
} else {
vreq.setAttribute("title", "Rename Blank Nodes");
vreq.setAttribute("bodyJsp", RENAME_BNODES_JSP);
}
}
private void doRemoveModel(String modelName, ModelMaker modelMaker) {
// Try to detach first since it cause problems to remove an attached model.
doDetachModel(modelName);
log.debug("Removing " + modelName + " from webapp");
modelMaker.removeModel(modelName);
}
private void doCreateModel(String modelName, ModelMaker modelMaker) {
modelMaker.createModel(modelName);
}
@Override
public void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
if (!isAuthorizedToDisplayPage(
request, response, SimplePermission.USE_ADVANCED_DATA_TOOLS_PAGES.ACTION)) {
return;
}
VitroRequest vreq = new VitroRequest(request);
ModelMaker maker = getModelMaker(vreq);
WhichService modelType = getModelType(vreq);
String actionStr = vreq.getParameter("action");
actionStr = (actionStr != null) ? actionStr : "";
if ("listModels".equals(actionStr)) {
processListModelsRequest(vreq, maker, modelType);
} else if ("configModels".equals(actionStr)) {
processConfigModelsRequest(vreq);
} else if ("contentModels".equals(actionStr)) {
processContentModelsRequest(vreq);
} else if ("createModel".equals(actionStr)) {
processCreateModelRequest(vreq, maker, modelType);
} else if ("removeModel".equals(actionStr)) {
processRemoveModelRequest(vreq, maker, modelType);
} else if ("loadRDFData".equals(actionStr)) {
processLoadRDFDataRequest(vreq, maker);
} else if ("cleanLiterals".equals(actionStr)) {
processCleanLiteralsRequest(vreq);
} else if ("outputModel".equals(actionStr)) {
processOutputModelRequest(vreq, response);
return; // don't attempt to display a JSP
} else if ("clearModel".equals(actionStr)) {
processClearModelRequest(vreq, maker, modelType);
} else if ("attachModel".equals(actionStr)) {
processAttachModelRequest(vreq, maker, modelType);
} else if ("detachModel".equals(actionStr)) {
processDetachModelRequest(vreq, maker, modelType);
} else if ("renameBNodes".equals(actionStr)) {
processRenameBNodesRequest(vreq, maker);
} else if ("renameBNodesURISelect".equals(actionStr)) {
processRenameBNodesURISelectRequest(vreq, maker);
} else if ("smushSingleModel".equals(actionStr)) {
processSmushSingleModelRequest(vreq);
} else if ("csv2rdf".equals(actionStr)) {
processCsv2rdfRequest(vreq);
} else if ("processStrings".equals(actionStr)) {
processProcessStringsRequest(vreq);
} else if ("splitPropertyValues".equals(actionStr)) {
processSplitPropertyValuesRequest(vreq);
} else if ("subtractModels".equals(actionStr)) {
processSubtractModelRequest(vreq);
} else if ("executeWorkflow".equals(actionStr)) {
processExecuteWorkflowRequest(vreq);
} else if ("executeSparql".equals(actionStr)) {
processExecuteSparqlRequest(vreq);
} else if ("generateTBox".equals(actionStr)) {
processGenerateTBoxRequest(vreq);
} else if ("permanentURI".equals(actionStr)) {
processPermanentURIRequest(vreq, maker);
} else if ("mergeResources".equals(actionStr)) {
processMergeResourceRequest(vreq);
} else if ("renameResource".equals(actionStr)) {
processRenameResourceRequest(vreq);
} else if ("mergeResult".equals(actionStr)) {
processMergeResultRequest(vreq, response);
return;
} else if ("dumpRestore".equals(actionStr)) {
processDumpRestore(vreq, response);
return;
} else {
request.setAttribute("title", "Ingest Menu");
request.setAttribute("bodyJsp", INGEST_MENU_JSP);
}
maker = getModelMaker(vreq);
request.setAttribute("modelNames", maker.listModels().toList());
RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
try {
rd.forward(request, response);
} catch (Exception e) {
log.error(e, e);
throw new ServletException(e);
}
}
/**
* Gets the Jena graph using options.
*
* <p>The Jena "Convenient" reification style is used when opening models: it allows to ignore
* reification quadlets when calling the statements list.
*
* @param forceReload boolean stating if the jena graph has to be reloaded using options
* @return the Jena graph (model)
*/
protected synchronized GraphConnection openGraph(boolean forceReload) {
// create model given backend
if (backend.equals("memory")) {
if (memoryGraph == null || forceReload) {
memoryGraph = ModelFactory.createDefaultModel(ModelFactory.Convenient);
memoryGraph.setNsPrefixes(namespaces);
}
return new GraphConnection((Connection) null, memoryGraph);
} else if (backend.equals("sql")) {
if (datasource == null) {
throw new IllegalArgumentException("Missing datasource for sql graph : " + name);
}
// create a database connection
Connection baseConnection;
try {
// try single-datasource non-XA mode
baseConnection = ConnectionHelper.getConnection(datasource);
if (baseConnection == null) {
// standard datasource usage
DataSource ds = DataSourceHelper.getDataSource(datasource);
baseConnection = ds.getConnection();
}
} catch (NamingException e) {
throw new IllegalArgumentException(String.format("Datasource %s not found", datasource), e);
} catch (SQLException e) {
throw new IllegalArgumentException(
String.format("SQLException while opening %s", datasource), e);
}
/*
* We have to wrap the connection to disallow any commit() or setAutoCommit() on it. Jena calls these
* methods without regard to the fact that the connection may be managed by an external transaction.
*/
Connection wrappedConnection =
(Connection)
Proxy.newProxyInstance(
Connection.class.getClassLoader(),
new Class[] {Connection.class},
new ConnectionFixInvocationHandler(baseConnection));
DBConnection connection = new DBConnection(wrappedConnection, databaseType);
// check if named model already exists
Model graph;
if (connection.containsModel(name)) {
ModelMaker m = ModelFactory.createModelRDBMaker(connection, ModelFactory.Convenient);
graph = m.openModel(name);
} else {
// create it
// check if other models already exist for that connection.
if (connection.getAllModelNames().hasNext()) {
// other models already exist => do not set parameters
// on driver.
if (databaseDoCompressUri != connection.getDriver().getDoCompressURI()) {
log.warn(
String.format(
"Cannot set databaseDoCompressUri attribute to %s "
+ "for model %s, other models already "
+ "exist with value %s",
databaseDoCompressUri, name, connection.getDriver().getDoCompressURI()));
}
if (databaseTransactionEnabled != connection.getDriver().getIsTransactionDb()) {
log.warn(
String.format(
"Cannot set databaseTransactionEnabled attribute to %s "
+ "for model %s, other models already "
+ "exist with value %s",
databaseTransactionEnabled, name, connection.getDriver().getIsTransactionDb()));
}
} else {
if (databaseDoCompressUri) {
connection.getDriver().setDoCompressURI(true);
}
if (databaseTransactionEnabled) {
connection.getDriver().setIsTransactionDb(true);
}
}
ModelMaker m = ModelFactory.createModelRDBMaker(connection, ModelFactory.Convenient);
graph = m.createModel(name);
}
graph.setNsPrefixes(namespaces);
// use baseConnection so that it is closed instead of the jena one
// (to let the pool handled closure).
if (baseConnection != null) {
return new GraphConnection(baseConnection, graph);
}
return new GraphConnection(connection, graph);
} else {
throw new IllegalArgumentException("Unknown backend type " + backend);
}
}