private void processMergeResourceRequest(VitroRequest vreq) {
String uri1 = vreq.getParameter("uri1"); // get primary uri
String uri2 = vreq.getParameter("uri2"); // get secondary uri
String usePrimaryLabelOnlyStr = vreq.getParameter("usePrimaryLabelOnly");
;
boolean usePrimaryLabelOnly =
usePrimaryLabelOnlyStr != null && !usePrimaryLabelOnlyStr.isEmpty();
if (uri1 != null) {
JenaIngestUtils utils = new JenaIngestUtils();
/*
* get baseOnt and infOnt models
*/
OntModel baseOntModel = ModelAccess.on(getServletContext()).getOntModel(FULL_ASSERTIONS);
OntModel tboxOntModel = ModelAccess.on(getServletContext()).getOntModel(TBOX_UNION);
/*
* calling method that does the merge operation.
*/
MergeResult result =
utils.doMerge(uri1, uri2, baseOntModel, tboxOntModel, usePrimaryLabelOnly);
vreq.getSession().setAttribute("leftoverModel", result.getLeftoverModel());
vreq.setAttribute("result", result);
vreq.setAttribute("title", "Merge Resources");
vreq.setAttribute("bodyJsp", MERGE_RESULT);
} else {
vreq.setAttribute("title", "Merge Resources");
vreq.setAttribute("bodyJsp", MERGE_RESOURCES);
}
}
protected static ModelMaker getModelMaker(HttpServletRequest req) {
ServletContext ctx = req.getSession().getServletContext();
if (isUsingMainStoreForIngest(req)) {
RDFService rdfService = ModelAccess.on(ctx).getRDFService(CONTENT);
return new BlankNodeFilteringModelMaker(
rdfService, ModelAccess.on(ctx).getModelMaker(CONTENT));
} else {
RDFService rdfService = ModelAccess.on(ctx).getRDFService(CONFIGURATION);
return new BlankNodeFilteringModelMaker(
rdfService, ModelAccess.on(ctx).getModelMaker(CONFIGURATION));
}
}
private void processExecuteWorkflowRequest(VitroRequest vreq) {
String workflowURIStr = vreq.getParameter("workflowURI");
String workflowStepURIStr = vreq.getParameter("workflowStepURI");
if (workflowURIStr != null && workflowStepURIStr != null) {
doExecuteWorkflow(vreq);
vreq.setAttribute("title", "IngestMenu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else if (workflowURIStr != null) {
// Select the workflow step at which to start
OntModel jenaOntModel = (OntModel) getModel("vitro:jenaOntModel", vreq);
vreq.setAttribute(
"workflowSteps",
new JenaIngestWorkflowProcessor(
jenaOntModel.getIndividual(workflowURIStr), getModelMaker(vreq))
.getWorkflowSteps(null));
vreq.setAttribute("title", "Choose Workflow Step");
vreq.setAttribute("bodyJsp", WORKFLOW_STEP_JSP);
} else {
OntModel jenaOntModel = ModelAccess.on(getServletContext()).getOntModel();
jenaOntModel.enterCriticalSection(Lock.READ);
List<Individual> savedQueryList = new LinkedList<Individual>();
try {
Resource workflowClassRes = WorkflowOntology.Workflow;
savedQueryList.addAll(jenaOntModel.listIndividuals(workflowClassRes).toList());
} finally {
jenaOntModel.leaveCriticalSection();
}
vreq.setAttribute("workflows", savedQueryList);
vreq.setAttribute("title", "Execute Workflow");
vreq.setAttribute("bodyJsp", EXECUTE_WORKFLOW_JSP);
}
}
private void doDetachModel(String modelName) {
Model m = attachedModels.get(modelName);
if (m == null) {
return;
}
ModelAccess.on(getServletContext()).getOntModel(TBOX_ASSERTIONS).removeSubModel(m);
attachedModels.remove(modelName);
log.info("Detached " + modelName + " (" + m.hashCode() + ") from webapp");
}
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();
}
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 Object getApplicationName() {
String name = "";
try {
WebappDaoFactory wadf = ModelAccess.on(ctx).getWebappDaoFactory();
ApplicationBean app = wadf.getApplicationDao().getApplicationBean();
name = app.getApplicationName();
} catch (Exception e) {
// deal with problems below
}
if ((name != null) && (!name.isEmpty())) {
return name;
} else {
return getContextPath();
}
}
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);
}
}
private void processContentModelsRequest(VitroRequest vreq) {
ModelMaker vsmm = ModelAccess.on(getServletContext()).getModelMaker(CONTENT);
vreq.getSession().setAttribute(WHICH_MODEL_MAKER, CONTENT);
showModelList(vreq, vsmm, CONTENT);
}
private String doRename(String oldNamespace, String newNamespace) {
String uri = null;
String result = null;
Integer counter = 0;
Boolean namespacePresent = false;
RDFService rdfService = ModelAccess.on(getServletContext()).getRDFService();
try {
Model baseOntModel =
RDFServiceGraph.createRDFServiceModel(new RDFServiceGraph(rdfService, ABOX_ASSERTIONS));
OntModel ontModel = ModelAccess.on(getServletContext()).getOntModel();
List<String> urisToChange = new LinkedList<String>();
ontModel.enterCriticalSection(Lock.READ);
try {
Iterator<Individual> indIter = ontModel.listIndividuals();
while (indIter.hasNext()) {
Individual ind = indIter.next();
String namespace = ind.getNameSpace();
if (namespace != null) {
if (oldNamespace.equals(namespace)) {
uri = ind.getURI();
urisToChange.add(uri);
namespacePresent = true;
}
}
}
} finally {
ontModel.leaveCriticalSection();
}
if (!namespacePresent) {
result = "no resources renamed";
return result;
}
for (String oldURIStr : urisToChange) {
long time1 = System.currentTimeMillis();
Resource res = baseOntModel.getResource(oldURIStr);
long time2 = System.currentTimeMillis();
String newURIStr = null;
Pattern p = Pattern.compile(oldNamespace);
String candidateString = res.getURI();
Matcher matcher = p.matcher(candidateString);
newURIStr = matcher.replaceFirst(newNamespace);
long time3 = System.currentTimeMillis();
log.debug("time to get new uri: " + Long.toString(time3 - time2));
log.debug("Renaming " + oldURIStr + " to " + newURIStr);
String whereClause =
"} WHERE { \n"
+ " GRAPH <"
+ ABOX_ASSERTIONS
+ "> { \n"
+ " { <"
+ oldURIStr
+ "> ?p <"
+ oldURIStr
+ "> } \n "
+ " UNION \n"
+ " { <"
+ oldURIStr
+ "> ?q ?o } \n "
+ " UNION \n"
+ " { ?s ?r <"
+ oldURIStr
+ "> } \n"
+ " } \n"
+ "}";
String removeQuery =
"CONSTRUCT { \n"
+ " <"
+ oldURIStr
+ "> ?p <"
+ oldURIStr
+ "> . \n "
+ " <"
+ oldURIStr
+ "> ?q ?o . \n "
+ " ?s ?r <"
+ oldURIStr
+ "> \n"
+ whereClause;
String addQuery =
"CONSTRUCT { \n"
+ " <"
+ newURIStr
+ "> ?p <"
+ newURIStr
+ "> . \n "
+ " <"
+ newURIStr
+ "> ?q ?o . \n "
+ " ?s ?r <"
+ newURIStr
+ "> \n"
+ whereClause;
try {
ChangeSet cs = rdfService.manufactureChangeSet();
cs.addAddition(
rdfService.sparqlConstructQuery(addQuery, RDFService.ModelSerializationFormat.N3),
RDFService.ModelSerializationFormat.N3,
ABOX_ASSERTIONS);
cs.addRemoval(
rdfService.sparqlConstructQuery(removeQuery, RDFService.ModelSerializationFormat.N3),
RDFService.ModelSerializationFormat.N3,
ABOX_ASSERTIONS);
rdfService.changeSetUpdate(cs);
} catch (RDFServiceException e) {
throw new RuntimeException(e);
}
long time4 = System.currentTimeMillis();
log.debug(" time to rename : " + Long.toString(time4 - time3));
log.debug(" time for one resource: " + Long.toString(time4 - time1));
counter++;
}
result = counter.toString() + " resources renamed";
return result;
} finally {
if (rdfService != null) {
rdfService.close();
}
}
}
protected WebappDaoFactory getWebappDaoFactory() {
return ModelAccess.on(getServletContext()).getWebappDaoFactory(ASSERTIONS_ONLY);
}