CloneTableUtils.getDatatable(worksheet.getDataTable(), factory.getHTable(hnode.getHTableId()), dataTables, selection);
Map<String, String> rowHashToSubjectURI = new HashMap<String, String>();
Map<String, List<String>> SubjectURIToRowId = new HashMap<String, List<String>>();
for(Table t : dataTables) {
for(Row r : t.getRows(0, t.getNumRows(), selection)) {
Node n = r.getNode(hNodeId);
if(n != null && n.getValue() != null && !n.getValue().isEmptyValue() && n.getValue().asString() != null && !n.getValue().asString().trim().isEmpty() ) {
String uri = n.getValue().asString().trim().replace(" ", "");
String baseURI = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(Property.baseURI);
try {
URI t1 = new URI(uri);
if (!t1.isAbsolute() && baseURI != null) {
uri = baseURI + uri;
}
} catch (URISyntaxException e) {
// TODO Auto-generated catch block
}
// n.setValue(uri, n.getStatus(), factory);
rowHashToSubjectURI.put(HashValueManager.getHashValue(r, hNodeIds), uri);
if (SubjectURIToRowId.get(uri) == null)
SubjectURIToRowId.put(uri, new ArrayList<String>());
List<String> rowIds = SubjectURIToRowId.get(uri);
rowIds.add(r.getId());
}
}
}
TripleStoreUtil util = new TripleStoreUtil();
//String modelContext = worksheet.getMetadataContainer().getWorksheetProperties().getPropertyValue(Property.modelContext);
List<String> subjects = new LinkedList<String>();
subjects.addAll(rowHashToSubjectURI.values());
List<String> predicates = new LinkedList<String>();
List<String> otherClasses = new LinkedList<String>();
Map<String, List<String>> results = new HashMap<String, List<String>>();
URIFormatter uriFormatter = new URIFormatter(workspace.getOntologyManager(), new ErrorReport());
if(sameAsPredicate!= null && !sameAsPredicate.trim().isEmpty())
{
sameAsPredicate = uriFormatter.getExpandedAndNormalizedUri(sameAsPredicate);
}
JSONArray predicatesarray = new JSONArray(predicate);
JSONArray otherClassarray = new JSONArray(otherClass);
for(int i = 0; i < predicatesarray.length(); i++) {
predicates.add(predicatesarray.getJSONObject(i).getString("predicate"));
otherClasses.add(otherClassarray.getJSONObject(i).getString("otherClass"));
}
while (subjects.size() > 0) {
ListIterator<String> subjectsIterator = subjects.listIterator();
LinkedList<String> tempSubjects = new LinkedList<String>();
while(tempSubjects.size() < limit && subjects.size() > 0)
{
tempSubjects.add(subjectsIterator.next());
subjectsIterator.remove();
}
try {
Map<String, List<String>> temp = null;
if (!incoming)
temp = util.getObjectsForSubjectsAndPredicates(dataRepoUrl, null, tempSubjects , predicates, otherClasses, sameAsPredicate);
else
temp = util.getSubjectsForPredicatesAndObjects(dataRepoUrl, null, tempSubjects , predicates, otherClasses, sameAsPredicate);
addMappingToResults(results, temp);
// predicates.clear();
// otherClasses.clear();
} catch (KarmaException e) {
LOG.error("Unable to load data to augment: ", e);
return new UpdateContainer(new ErrorUpdate(e.getMessage()));
}
}
List<String> resultSubjects = results.get("resultSubjects");
List<String> resultPredicates = results.get("resultPredicates");
List<String> resultObjects = results.get("resultObjects");
List<String> resultClass = results.get("resultClasses");
AddValuesCommandFactory addFactory = new AddValuesCommandFactory();
for (int i = 0; i < resultPredicates.size(); i++) {
String subject = incoming ? resultObjects.get(i) : resultSubjects.get(i);
List<String> rowIds = SubjectURIToRowId.get(subject);
boolean isNewNode = false;
for (String RowId : rowIds) {
String predicate = resultPredicates.get(i);
String otherClass = resultClass.get(i);
JSONArray array = new JSONArray();
JSONObject obj = new JSONObject();
JSONObject obj2 = new JSONObject();
if (otherClass != null && !otherClass.trim().isEmpty())
obj.put("URIs", incoming ? resultSubjects.get(i) : resultObjects.get(i));
else
obj.put("values", incoming ? resultSubjects.get(i) : resultObjects.get(i));
obj2.put("rowId", RowId);
obj2.put("rowIdHash", "");
obj2.put("values", obj);
array.put(obj2);
JSONArray input = new JSONArray();
JSONObject obj3 = new JSONObject();
obj3.put("name", "AddValues");
obj3.put("value", array.toString());
obj3.put("type", "other");
input.put(obj3);
try {
OntologyManager ontMgr = workspace.getOntologyManager();
Label label = ontMgr.getUriLabel(incoming ? otherClass : predicate);
AddValuesCommand command = (AddValuesCommand) addFactory.createCommand(input, workspace, hNodeId, worksheetId, hnode.getHTableId(), label.getDisplayName(), HNodeType.AugmentData, selection.getName());
command.doIt(workspace);
outputColumns.addAll(command.getOutputColumns());
isNewNode |= command.isNewNode();
if (command.isNewNode())
appliedCommands.push(command);
newhNodeId = command.getNewHNodeId();
} catch(Exception e) {
e.printStackTrace();
return new UpdateContainer(new ErrorUpdate(e.getMessage()));
}
}
if (isNewNode && alignment.GetTreeRoot() != null) {
HNode tableHNode =workspace.getFactory().getHNode(newhNodeId);
String nestedHNodeId = tableHNode.getNestedTable().getHNodeIdFromColumnName("values");
if (nestedHNodeId == null)
nestedHNodeId = tableHNode.getNestedTable().getHNodeIdFromColumnName("URIs");
SetSemanticTypeCommandFactory sstFactory = new SetSemanticTypeCommandFactory();
JSONArray semanticTypesArray = new JSONArray();
JSONObject semanticType = new JSONObject();
edu.isi.karma.rep.alignment.Node n = alignment.getNodeById(columnUri);
semanticType.put(ClientJsonKeys.isPrimary.name(), "true");
Set<edu.isi.karma.rep.alignment.Node> oldNodes = new HashSet<edu.isi.karma.rep.alignment.Node>();
if(resultClass.get(i).trim().isEmpty())
{
semanticType.put(ClientJsonKeys.DomainId.name(), n.getId());
semanticType.put(ClientJsonKeys.FullType.name(), resultPredicates.get(i));
semanticType.put(ClientJsonKeys.DomainUri.name(), n.getUri());
}
else
{
if (alignment.getNodesByUri(resultClass.get(i)) != null)
oldNodes.addAll( alignment.getNodesByUri(resultClass.get(i)));
semanticType.put(ClientJsonKeys.DomainId.name(), resultClass.get(i));
semanticType.put(ClientJsonKeys.FullType.name(), Uris.CLASS_INSTANCE_LINK_URI);
}
semanticTypesArray.put(semanticType);
Command sstCommand = sstFactory.createCommand(workspace, worksheetId, nestedHNodeId, false, semanticTypesArray, false, "", selection.getName());
appliedCommands.push(sstCommand);
sstCommand.doIt(workspace);
if(!resultClass.get(i).trim().isEmpty())
{
ChangeInternalNodeLinksCommandFactory cinlcf = new ChangeInternalNodeLinksCommandFactory();
SetMetaPropertyCommandFactory smpcf = new SetMetaPropertyCommandFactory();
JSONArray newEdges = new JSONArray();
JSONObject newEdge = new JSONObject();
String sourceId = n.getId();
Set<edu.isi.karma.rep.alignment.Node> tempnodes = new HashSet<edu.isi.karma.rep.alignment.Node>();
tempnodes.addAll(alignment.getNodesByUri(resultClass.get(i)));
tempnodes.removeAll(oldNodes);
edu.isi.karma.rep.alignment.Node target = tempnodes.iterator().next();