private void processRenameBNodesURISelectRequest(VitroRequest vreq, ModelMaker maker) {
String namespaceEtcStr = vreq.getParameter("namespaceEtcStr");
String pattern = vreq.getParameter("pattern");
String concatenate = vreq.getParameter("concatenate");
String[] sourceModel = vreq.getParameterValues("sourceModelName");
if (namespaceEtcStr != null) {
if (namespaceEtcStr.isEmpty()) {
if ("true".equals(vreq.getParameter("csv2rdf"))) {
processCsv2rdfRequest(vreq);
return;
} else {
vreq.setAttribute("errorMsg", "Please enter a value.");
processRenameBNodesRequest(vreq, maker);
return;
}
}
if (concatenate.equals("integer")) {
doRenameBNodes(vreq, namespaceEtcStr, false, null, sourceModel);
} else {
pattern = pattern.trim();
doRenameBNodes(vreq, namespaceEtcStr, true, pattern, sourceModel);
}
vreq.setAttribute("title", "Ingest Menu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else {
vreq.setAttribute("title", "URI Select");
vreq.setAttribute("bodyJsp", RENAME_BNODES_URI_SELECT_JSP);
}
}
protected Collection<String> getStringParameters(String key) {
String[] values = vreq.getParameterValues(key);
if (values == null) {
return Collections.emptySet();
} else {
return new HashSet<String>(Arrays.asList(values));
}
}
private long doExecuteSparql(VitroRequest vreq) {
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getOntModel();
OntModel source = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
String[] sourceModel = vreq.getParameterValues("sourceModelName");
for (int i = 0; i < sourceModel.length; i++) {
Model m = getModel(sourceModel[i], vreq);
source.addSubModel(m);
}
Model destination = getModel(vreq.getParameter("destinationModelName"), vreq);
String sparqlQueryStr = vreq.getParameter("sparqlQueryStr");
String savedQueryURIStr = vreq.getParameter("savedQuery");
String queryStr;
if (savedQueryURIStr.length() == 0) {
log.debug("Using entered query");
queryStr = sparqlQueryStr;
} else {
Property queryStrProp = ResourceFactory.createProperty(SPARQL_QUERYSTR_PROP);
jenaOntModel.enterCriticalSection(Lock.READ);
try {
Individual ind = jenaOntModel.getIndividual(savedQueryURIStr);
log.debug("Using query " + savedQueryURIStr);
queryStr = ((Literal) ind.getPropertyValue(queryStrProp)).getLexicalForm();
queryStr =
StringEscapeUtils.unescapeHtml(
queryStr); // !!! We need to turn off automatic HTML-escaping for data property
// editing.
} finally {
jenaOntModel.leaveCriticalSection();
}
}
Model tempModel = ModelFactory.createDefaultModel();
Query query = SparqlQueryUtils.create(queryStr);
QueryExecution qexec = QueryExecutionFactory.create(query, source);
try {
qexec.execConstruct(tempModel);
} catch (QueryExecException qee) {
qexec.execDescribe(tempModel);
}
destination.enterCriticalSection(Lock.WRITE);
try {
if (destination instanceof OntModel) {
((OntModel) destination).getBaseModel().notifyEvent(new EditEvent(null, true));
} else {
destination.notifyEvent(new EditEvent(null, true));
}
destination.add(tempModel);
} finally {
if (destination instanceof OntModel) {
((OntModel) destination).getBaseModel().notifyEvent(new EditEvent(null, false));
} else {
destination.notifyEvent(new EditEvent(null, false));
}
destination.leaveCriticalSection();
}
return tempModel.size();
}
public void doGenerateTBox(VitroRequest vreq) {
OntModel source = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
String[] sourceModel = vreq.getParameterValues("sourceModelName");
for (int i = 0; i < sourceModel.length; i++) {
Model m = getModel(sourceModel[i], vreq);
source.addSubModel(m);
}
String destinationModelStr = vreq.getParameter("destinationModelName");
Model destination = getModel(destinationModelStr, vreq);
destination.add((new JenaIngestUtils()).generateTBox(source));
}
@Override
protected void doRequest(VitroRequest vreq, HttpServletResponse response) {
String errorMsg = null;
String rankPredicate = vreq.getParameter(RANK_PREDICATE_PARAMETER_NAME);
if (rankPredicate == null) {
errorMsg = "No rank parameter specified";
log.error(errorMsg);
doError(response, errorMsg, HttpServletResponse.SC_BAD_REQUEST);
return;
}
String[] individualUris = vreq.getParameterValues(INDIVIDUAL_PREDICATE_PARAMETER_NAME);
if (individualUris == null || individualUris.length == 0) {
errorMsg = "No individuals specified";
log.error(errorMsg);
doError(response, errorMsg, HttpServletResponse.SC_BAD_REQUEST);
return;
}
WebappDaoFactory wadf = vreq.getWebappDaoFactory();
if (vreq.getWebappDaoFactory() == null) {
errorMsg = "No WebappDaoFactory available";
log.error(errorMsg);
doError(response, errorMsg, HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
return;
}
DataPropertyStatementDao dpsDao = wadf.getDataPropertyStatementDao();
if (dpsDao == null) {
errorMsg = "No DataPropertyStatementDao available";
log.error(errorMsg);
doError(response, errorMsg, HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
return;
}
// check permissions
// TODO: (bdc34)This is not yet implemented, must check the IDs against the policies for
// permissons before doing an edit!
// rjy7 This should be inherited from the superclass
boolean hasPermission = true;
if (!hasPermission) {
// if not okay, send error message
doError(response, "Insufficent permissions", HttpStatus.SC_UNAUTHORIZED);
return;
}
// This may not be the most efficient way. Should we instead build up a Model of retractions and
// additions, so
// we only hit the database once?
reorderIndividuals(individualUris, vreq, rankPredicate);
response.setStatus(HttpServletResponse.SC_OK);
}
private void doSmushSingleModel(VitroRequest vreq) {
OntModel source = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
String[] sourceModel = vreq.getParameterValues("sourceModelName");
for (int i = 0; i < sourceModel.length; i++) {
Model m = getModel(sourceModel[i], vreq);
source.addSubModel(m);
}
Model destination = getModel(vreq.getParameter("destinationModelName"), vreq);
String propertyURIStr = vreq.getParameter("propertyURI");
Property prop = ResourceFactory.createProperty(propertyURIStr);
JenaIngestUtils utils = new JenaIngestUtils();
destination.enterCriticalSection(Lock.WRITE);
try {
destination.add(utils.smushResources(source, prop));
} finally {
destination.leaveCriticalSection();
}
}
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 processExecuteSparqlRequest(VitroRequest vreq) {
String sparqlQueryStr = vreq.getParameter("sparqlQueryStr");
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getOntModel();
jenaOntModel.enterCriticalSection(Lock.READ);
List<Individual> savedQueryList = new LinkedList<Individual>();
try {
Resource sparqlConstructClassRes = ResourceFactory.createResource(SPARQL_CONSTRUCT_CLASS);
savedQueryList.addAll(jenaOntModel.listIndividuals(sparqlConstructClassRes).toList());
} finally {
jenaOntModel.leaveCriticalSection();
}
/*ass92*/
OntologyDao daoObj = vreq.getUnfilteredWebappDaoFactory().getOntologyDao();
List<Ontology> ontologiesObj = daoObj.getAllOntologies();
List<String> prefixList = new ArrayList<>();
if (ontologiesObj != null && ontologiesObj.size() > 0) {
Iterator<Ontology> ontItr = ontologiesObj.iterator();
while (ontItr.hasNext()) {
Ontology ont = ontItr.next();
prefixList.add(ont.getPrefix() == null ? "(not yet specified)" : ont.getPrefix());
prefixList.add(ont.getURI() == null ? "" : ont.getURI());
}
} else {
prefixList.add("<strong>" + "No Ontologies added" + "</strong>");
prefixList.add("<strong>" + "Load Ontologies" + "</strong>");
}
vreq.setAttribute("prefixList", prefixList);
/*complete*/
if (sparqlQueryStr != null) {
String validationMessage = "";
if (vreq.getParameterValues("sourceModelName") == null) {
validationMessage += "<p>Please select one or more source models.</p>";
}
if (vreq.getParameter("destinationModelName") == null) {
validationMessage += "<p>Please select a destination model</p>";
}
if (validationMessage.length() > 0) {
vreq.setAttribute("validationMessage", validationMessage);
} else {
long constructedStmtCount = 0;
try {
constructedStmtCount = doExecuteSparql(vreq);
} catch (QueryParseException qpe) {
String errorMsg = "<p>Unable to parse query:</p>";
if (qpe.getMessage() != null) {
errorMsg += "<p>" + qpe.getMessage() + "</p>";
}
vreq.setAttribute("errorMsg", errorMsg);
} catch (InconsistentOntologyException ioe) {
String errorMsg = "<p>Inconsistent source ontology:</p>";
if (ioe.getMessage() != null) {
errorMsg += "<p>" + ioe.getMessage() + "</p>";
}
vreq.setAttribute("errorMsg", errorMsg);
}
vreq.setAttribute("constructedStmtCount", constructedStmtCount);
}
vreq.setAttribute("savedQueries", savedQueryList);
vreq.setAttribute("title", "SPARQL CONSTRUCT result");
vreq.setAttribute("bodyJsp", EXECUTE_SPARQL_JSP);
} else {
vreq.setAttribute("savedQueries", savedQueryList);
vreq.setAttribute("title", "Execute SPARQL Construct");
vreq.setAttribute("bodyJsp", EXECUTE_SPARQL_JSP);
}
}
