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);
}
}
private void processCleanLiteralsRequest(VitroRequest vreq) {
String modelNameStr = vreq.getParameter("modelName");
Model model = getModel(modelNameStr, vreq);
doCleanLiterals(model);
vreq.setAttribute("title", "Ingest Menu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
}
private void processCreateModelRequest(
VitroRequest vreq, ModelMaker maker, WhichService modelType) {
String modelName = vreq.getParameter("modelName");
if (modelName != null) {
try {
URI graphURI = new URI(modelName);
if (graphURI.getScheme() == null) {
String origName = modelName;
modelName = CREATED_GRAPH_BASE_URI + modelName;
log.info("The model name has been changed from " + origName + " to " + modelName);
}
doCreateModel(modelName, maker);
showModelList(vreq, maker, modelType);
} catch (URISyntaxException e) {
throw new RuntimeException("the model name must be a valid URI");
}
} else {
vreq.setAttribute("modelType", modelType.toString());
vreq.setAttribute("title", "Create New Model");
vreq.setAttribute("bodyJsp", CREATE_MODEL_JSP);
}
}
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);
}
}
private void processProcessStringsRequest(VitroRequest vreq) {
String className = vreq.getParameter("className");
if (className != null) {
doProcessStrings(vreq);
vreq.setAttribute("title", "IngestMenu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else {
vreq.setAttribute("title", "Process Strings");
vreq.setAttribute("bodyJsp", PROCESS_STRINGS_JSP);
}
}
private void processSubtractModelRequest(VitroRequest vreq) {
String modela = vreq.getParameter("modela");
if (modela != null) {
doSubtractModels(vreq);
vreq.setAttribute("title", "IngestMenu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else {
vreq.setAttribute("title", "Subtract Models");
vreq.setAttribute("bodyJsp", SUBTRACT_MODELS_JSP);
}
}
private void processSmushSingleModelRequest(VitroRequest vreq) {
String propertyURIStr = vreq.getParameter("propertyURI");
if (propertyURIStr != null) {
doSmushSingleModel(vreq);
vreq.setAttribute("title", "Ingest Menu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else {
vreq.setAttribute("title", "Smush Resources");
vreq.setAttribute("bodyJsp", SMUSH_JSP);
}
}
private void processGenerateTBoxRequest(VitroRequest vreq) {
String testParam = vreq.getParameter("sourceModelName");
if (testParam != null) {
doGenerateTBox(vreq);
vreq.setAttribute("title", "Ingest Menu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else {
vreq.setAttribute("title", "Generate TBox from Assertions Data");
vreq.setAttribute("bodyJsp", GENERATE_TBOX_JSP);
}
}
private void processSplitPropertyValuesRequest(VitroRequest vreq) {
String splitRegex = vreq.getParameter("splitRegex");
if (splitRegex != null) {
doSplitPropertyValues(vreq);
vreq.setAttribute("title", "IngestMenu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else {
vreq.setAttribute("title", "Split PropertyValues");
vreq.setAttribute("bodyJsp", SPLIT_PROPERTY_VALUES_JSP);
}
}
private void processCsv2rdfRequest(VitroRequest vreq) {
String csvUrl = vreq.getParameter("csvUrl");
if (csvUrl != null) {
/*doExecuteCsv2Rdf(vreq);*/
vreq.setAttribute("title", "IngestMenu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else {
vreq.setAttribute("title", "Convert CSV to RDF");
vreq.setAttribute("bodyJsp", CSV2RDF_JSP);
}
}
private void processLoadRDFDataRequest(VitroRequest vreq, ModelMaker maker) {
String docLoc = vreq.getParameter("docLoc");
String filePath = vreq.getParameter("filePath");
String modelName = vreq.getParameter("modelName");
String languageParam = null;
String language =
((languageParam = vreq.getParameter("language")) != null) ? languageParam : "RDF/XML";
if (docLoc != null && modelName != null) {
doLoadRDFData(modelName, docLoc, filePath, language, maker);
vreq.setAttribute("title", "Ingest Menu");
vreq.setAttribute("bodyJsp", INGEST_MENU_JSP);
} else {
vreq.setAttribute("title", "Load RDF Data");
vreq.setAttribute("bodyJsp", LOAD_RDF_DATA_JSP);
}
}
private void processRenameResourceRequest(VitroRequest vreq) {
String oldNamespace = vreq.getParameter("oldNamespace");
String newNamespace = vreq.getParameter("newNamespace");
String errorMsg = "";
if (oldNamespace != null) {
if (oldNamespace.isEmpty() && !newNamespace.isEmpty()) {
errorMsg = "Please enter the old namespace to be changed.";
} else if (!oldNamespace.isEmpty() && newNamespace.isEmpty()) {
errorMsg = "Please enter the new namespace.";
} else if (oldNamespace.isEmpty() && newNamespace.isEmpty()) {
errorMsg = "Please enter the namespaces.";
} else if (oldNamespace.equals(newNamespace)) {
errorMsg = "Please enter two different namespaces.";
}
if (!errorMsg.isEmpty()) {
vreq.setAttribute("errorMsg", errorMsg);
vreq.setAttribute("oldNamespace", oldNamespace);
vreq.setAttribute("newNamespace", newNamespace);
vreq.setAttribute("title", "Rename Resource");
vreq.setAttribute("bodyJsp", RENAME_RESOURCE);
} else {
String result = doRename(oldNamespace, newNamespace);
vreq.setAttribute("result", result);
vreq.setAttribute("title", "Rename Resources");
vreq.setAttribute("bodyJsp", RENAME_RESULT);
}
} else {
vreq.setAttribute("title", "Rename Resource");
vreq.setAttribute("bodyJsp", RENAME_RESOURCE);
}
}
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 ResponseValues doValidationErrors(
VitroRequest vreq,
EditConfigurationVTwo editConfiguration,
MultiValueEditSubmission submission) {
Map<String, String> errors = submission.getValidationErrors();
if (errors != null && !errors.isEmpty()) {
String form = editConfiguration.getFormUrl();
vreq.setAttribute("formUrl", form);
vreq.setAttribute("view", vreq.getParameter("view"));
// Need to ensure that edit key is set so that the correct
// edit configuration and edit submission are retrieved
// This can also be set as a parameter instead
String formUrl = editConfiguration.getFormUrl();
formUrl += "&editKey=" + editConfiguration.getEditKey();
return new RedirectResponseValues(formUrl);
}
return null; // no errors
}
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);
}
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 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);
}
}
@Override
public void doPost(HttpServletRequest req, HttpServletResponse response) {
if (!isAuthorizedToDisplayPage(req, response, new Actions(new EditOntology()))) {
return;
}
VitroRequest request = new VitroRequest(req);
EditProcessObject epo = super.createEpo(request);
request.setAttribute("epoKey", epo.getKey());
OntologyDao oDao = request.getFullWebappDaoFactory().getOntologyDao();
Ontology o = null;
if (request.getParameter("uri") == null) {
log.error("doPost() expects non-null uri parameter");
} else {
o = oDao.getOntologyByURI(request.getParameter("uri"));
if (o == null) {
if (!VitroVocabulary.vitroURI.equals(request.getParameter("uri"))) {
log.debug(
"doPost(): no ontology object found for the namespace "
+ request.getParameter("uri"));
}
} else {
request.setAttribute("Ontology", o);
}
}
ArrayList<String> results = new ArrayList<String>();
results.add("Ontology");
results.add("Namespace");
results.add("Prefix");
String name = o == null ? "" : (o.getName() == null) ? "" : o.getName();
results.add(name);
String namespace = o == null ? "" : (o.getURI() == null) ? "" : o.getURI();
results.add(namespace);
String prefix = o == null ? "" : (o.getPrefix() == null) ? "" : o.getPrefix();
results.add(prefix);
request.setAttribute("results", results);
request.setAttribute("columncount", 3);
request.setAttribute("suppressquery", "true");
epo.setDataAccessObject(oDao);
FormObject foo = new FormObject();
HashMap<String, List<Option>> OptionMap = new HashMap<String, List<Option>>();
HashMap formSelect =
new HashMap(); // tells the JSP what select lists are populated, and thus should be
// displayed
request.setAttribute("formSelect", formSelect);
// add the options
foo.setOptionLists(OptionMap);
epo.setFormObject(foo);
// funky hack because Ontology.getURI() will append a hash for a hash namespace
// See OntologyDaoJena.ontologyFromOntologyResource() comments
String realURI = OntologyDaoJena.adjustOntologyURI(o.getURI());
request.setAttribute("realURI", realURI);
request.setAttribute("exportURL", request.getContextPath() + Controllers.EXPORT_RDF);
RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
request.setAttribute("epoKey", epo.getKey());
request.setAttribute("bodyJsp", "/templates/edit/specific/ontologies_edit.jsp");
request.setAttribute("title", "Ontology Control Panel");
request.setAttribute(
"css",
"<link rel=\"stylesheet\" type=\"text/css\" href=\""
+ request.getAppBean().getThemeDir()
+ "css/edit.css\"/>");
try {
rd.forward(request, response);
} catch (Exception e) {
log.error("OntologyEditController could not forward to view.");
log.error(e.getMessage());
log.error(e.getStackTrace());
}
}
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);
}
}