@Override
public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
Workspace workspace = vWorkspace.getWorkspace();
alignment = AlignmentManager.Instance().getAlignment(workspace.getId(), worksheetId);
SemanticTypes types = worksheet.getSemanticTypes();
Map<String, ColumnNode> hNodeIdTocolumnNodeMap = createColumnNodeMap();
Map<String, SemanticTypeNode> hNodeIdToDomainNodeMap = createDomainNodeMap();
JSONStringer jsonStr = new JSONStringer();
try {
JSONWriter writer = jsonStr.object();
writer.key("worksheetId").value(worksheetId).key("updateType").value("SemanticTypesUpdate");
writer.key(JsonKeys.Types.name());
writer.array();
// Iterate through all the columns
for (HNodePath path : worksheet.getHeaders().getAllPaths()) {
HNode node = path.getLeaf();
String nodeId = node.getId();
writer.object();
// Check if a semantic type exists for the HNode
SemanticType type = types.getSemanticTypeForHNodeId(nodeId);
if (type != null && type.getConfidenceLevel() != SemanticType.ConfidenceLevel.Low) {
writer
.key(JsonKeys.HNodeId.name())
.value(type.getHNodeId())
.key(JsonKeys.SemanticTypesArray.name())
.array();
ColumnNode alignmentColumnNode = hNodeIdTocolumnNodeMap.get(type.getHNodeId());
SemanticTypeNode domainNode = hNodeIdToDomainNodeMap.get(type.getHNodeId());
if (alignmentColumnNode == null || domainNode == null) {
logger.error(
"Column node or domain node not found in alignment."
+ " (This should not happen conceptually!):"
+ type);
continue;
}
// Add the primary semantic type
writer
.object()
.key(JsonKeys.Origin.name())
.value(type.getOrigin().name())
.key(JsonKeys.ConfidenceLevel.name())
.value(type.getConfidenceLevel().name())
.key(JsonKeys.isPrimary.name())
.value(true);
// Add the RDF literal type to show in the text box
String rdfLiteralType =
alignmentColumnNode.getRdfLiteralType() == null
? ""
: alignmentColumnNode.getRdfLiteralType().getDisplayName();
String language =
alignmentColumnNode.getLanguage() == null ? "" : alignmentColumnNode.getLanguage();
writer.key(JsonKeys.rdfLiteralType.name()).value(rdfLiteralType);
writer.key(JsonKeys.language.name()).value(language);
// String domainDisplayLabel = (domainNode.getLabel().getPrefix() != null &&
// (!domainNode.getLabel().getPrefix().equals(""))) ?
// (domainNode.getLabel().getPrefix() + ":" + domainNode.getLocalId()) :
// domainNode.getLocalId();
if (!type.isClass()) {
writer
.key(JsonKeys.FullType.name())
.value(type.getType().getUri())
.key(JsonKeys.DisplayLabel.name())
.value(type.getType().getDisplayName())
.key(JsonKeys.DisplayRDFSLabel.name())
.value(type.getType().getRdfsLabel())
.key(JsonKeys.DisplayRDFSComment.name())
.value(type.getType().getRdfsComment())
.key(JsonKeys.DomainId.name())
.value(domainNode.getId())
.key(JsonKeys.DomainUri.name())
.value(domainNode.getUri())
.key(JsonKeys.DisplayDomainLabel.name())
.value(domainNode.getDisplayId())
.key(JsonKeys.DomainRDFSLabel.name())
.value(domainNode.getRdfsLabel())
.key(JsonKeys.DomainRDFSComment.name())
.value(domainNode.getRdfsComment());
} else {
writer
.key(JsonKeys.FullType.name())
.value(domainNode.getId())
.key(JsonKeys.DisplayLabel.name())
.value(domainNode.getDisplayId())
.key(JsonKeys.DisplayRDFSLabel.name())
.value(domainNode.getRdfsLabel())
.key(JsonKeys.DisplayRDFSComment.name())
.value(domainNode.getRdfsComment())
.key(JsonKeys.DomainId.name())
.value("")
.key(JsonKeys.DomainUri.name())
.value("")
.key(JsonKeys.DisplayDomainLabel.name())
.value("")
.key(JsonKeys.DomainRDFSLabel.name())
.value("")
.key(JsonKeys.DomainRDFSComment.name())
.value("");
}
// Mark the special properties
writer
.key(JsonKeys.isMetaProperty.name())
.value(isMetaProperty(type.getType(), alignmentColumnNode));
writer.endObject();
// Iterate through the synonym semantic types
SynonymSemanticTypes synTypes = types.getSynonymTypesForHNodeId(nodeId);
if (synTypes != null) {
for (SemanticType synType : synTypes.getSynonyms()) {
writer
.object()
.key(JsonKeys.HNodeId.name())
.value(synType.getHNodeId())
.key(JsonKeys.FullType.name())
.value(synType.getType().getUri())
.key(JsonKeys.Origin.name())
.value(synType.getOrigin().name())
.key(JsonKeys.ConfidenceLevel.name())
.value(synType.getConfidenceLevel().name())
.key(JsonKeys.DisplayLabel.name())
.value(synType.getType().getDisplayName())
.key(JsonKeys.DisplayRDFSLabel.name())
.value(synType.getType().getRdfsLabel())
.key(JsonKeys.DisplayRDFSComment.name())
.value(synType.getType().getRdfsComment())
.key(JsonKeys.isPrimary.name())
.value(false);
if (!synType.isClass()) {
writer
.key(JsonKeys.DomainUri.name())
.value(synType.getDomain().getUri())
.key(JsonKeys.DomainId.name())
.value("")
.key(JsonKeys.DisplayDomainLabel.name())
.value(synType.getDomain().getDisplayName())
.key(JsonKeys.DomainRDFSLabel.name())
.value(synType.getDomain().getRdfsLabel())
.key(JsonKeys.DomainRDFSComment.name())
.value(synType.getDomain().getRdfsComment());
} else {
writer
.key(JsonKeys.DomainId.name())
.value("")
.key(JsonKeys.DomainUri.name())
.value("")
.key(JsonKeys.DisplayDomainLabel.name())
.value("")
.key(JsonKeys.DomainRDFSLabel.name())
.value("")
.key(JsonKeys.DomainRDFSComment.name())
.value("");
}
writer.endObject();
}
}
writer.endArray();
} else {
writer.key(JsonKeys.HNodeId.name()).value(nodeId);
writer.key(JsonKeys.SemanticTypesArray.name()).array().endArray();
}
writer.endObject();
}
writer.endArray();
writer.endObject();
pw.print(writer.toString());
} catch (JSONException e) {
logger.error("Error occured while writing to JSON!", e);
}
}
private SemanticTypeMapping addSemanticTypeStruct(
ColumnNode sourceColumn, SemanticType semanticType, Set<Node> addedNodes) {
logger.debug("adding semantic type to the graph ... ");
if (addedNodes == null) addedNodes = new HashSet<Node>();
if (semanticType == null) {
logger.error("semantic type is null.");
return null;
}
if (semanticType.getDomain() == null) {
logger.error("semantic type does not have any domain");
return null;
}
if (semanticType.getType() == null) {
logger.error("semantic type does not have any link");
return null;
}
String domainUri = semanticType.getDomain().getUri();
String propertyUri = semanticType.getType().getUri();
Double confidence = semanticType.getConfidenceScore();
Origin origin = semanticType.getOrigin();
if (domainUri == null || domainUri.isEmpty()) {
logger.error("semantic type does not have any domain");
return null;
}
if (propertyUri == null || propertyUri.isEmpty()) {
logger.error("semantic type does not have any link");
return null;
}
logger.debug(
"semantic type: " + domainUri + "|" + propertyUri + "|" + confidence + "|" + origin);
InternalNode source = null;
String nodeId;
nodeId = nodeIdFactory.getNodeId(domainUri);
source = new InternalNode(nodeId, new Label(domainUri));
if (!this.graphBuilder.addNodeAndUpdate(source, addedNodes)) return null;
nodeId = new RandomGUID().toString();
ColumnNode target = new ColumnNode(nodeId, nodeId, sourceColumn.getColumnName(), null);
if (!this.graphBuilder.addNode(target)) return null;
addedNodes.add(target);
String linkId = LinkIdFactory.getLinkId(propertyUri, source.getId(), target.getId());
LabeledLink link;
if (propertyUri.equalsIgnoreCase(ClassInstanceLink.getFixedLabel().getUri()))
link = new ClassInstanceLink(linkId);
else {
Label label = this.ontologyManager.getUriLabel(propertyUri);
link = new DataPropertyLink(linkId, label);
}
if (!this.graphBuilder.addLink(source, target, link)) return null;
SemanticTypeMapping mappingStruct =
new SemanticTypeMapping(sourceColumn, semanticType, source, link, target);
return mappingStruct;
}
private CandidateSteinerSets getCandidateSteinerSets(
List<ColumnNode> columnNodes,
boolean useCorrectTypes,
int numberOfCRFCandidates,
Set<Node> addedNodes) {
if (columnNodes == null || columnNodes.isEmpty()) return null;
int maxNumberOfSteinerNodes = columnNodes.size() * 2;
CandidateSteinerSets candidateSteinerSets =
new CandidateSteinerSets(maxNumberOfSteinerNodes, ontologyManager.getContextId());
if (addedNodes == null) addedNodes = new HashSet<Node>();
Set<SemanticTypeMapping> tempSemanticTypeMappings;
HashMap<ColumnNode, List<SemanticType>> columnSemanticTypes =
new HashMap<ColumnNode, List<SemanticType>>();
HashMap<String, Integer> semanticTypesCount = new HashMap<String, Integer>();
List<SemanticType> candidateSemanticTypes;
String domainUri = "", propertyUri = "";
for (ColumnNode n : columnNodes) {
candidateSemanticTypes = n.getTopKLearnedSemanticTypes(numberOfCRFCandidates);
columnSemanticTypes.put(n, candidateSemanticTypes);
for (SemanticType semanticType : candidateSemanticTypes) {
if (semanticType == null
|| semanticType.getDomain() == null
|| semanticType.getType() == null) continue;
domainUri = semanticType.getDomain().getUri();
propertyUri = semanticType.getType().getUri();
Integer count = semanticTypesCount.get(domainUri + propertyUri);
if (count == null) semanticTypesCount.put(domainUri + propertyUri, 1);
else semanticTypesCount.put(domainUri + propertyUri, count.intValue() + 1);
}
}
int numOfMappings = 1;
for (ColumnNode n : columnNodes) {
candidateSemanticTypes = columnSemanticTypes.get(n);
if (candidateSemanticTypes == null) continue;
logger.info("===== Column: " + n.getColumnName());
Set<SemanticTypeMapping> semanticTypeMappings = new HashSet<SemanticTypeMapping>();
for (SemanticType semanticType : candidateSemanticTypes) {
logger.info("\t===== Semantic Type: " + semanticType.getModelLabelString());
if (semanticType == null
|| semanticType.getDomain() == null
|| semanticType.getType() == null) continue;
domainUri = semanticType.getDomain().getUri();
propertyUri = semanticType.getType().getUri();
Integer countOfSemanticType = semanticTypesCount.get(domainUri + propertyUri);
// logger.info("count of semantic type: " + countOfSemanticType);
tempSemanticTypeMappings =
findSemanticTypeInGraph(n, semanticType, semanticTypesCount, addedNodes);
// logger.info("number of matches for semantic type: " +
// + (tempSemanticTypeMappings == null ? 0 : tempSemanticTypeMappings.size()));
if (tempSemanticTypeMappings != null) semanticTypeMappings.addAll(tempSemanticTypeMappings);
int countOfMatches = tempSemanticTypeMappings == null ? 0 : tempSemanticTypeMappings.size();
if (countOfMatches
< countOfSemanticType) // No struct in graph is matched with the semantic type, we add a
// new struct to the graph
{
for (int i = 0; i < countOfSemanticType - countOfMatches; i++) {
SemanticTypeMapping mp = addSemanticTypeStruct(n, semanticType, addedNodes);
if (mp != null) semanticTypeMappings.add(mp);
}
}
}
// System.out.println("number of matches for column " + n.getColumnName() +
// ": " + (semanticTypeMappings == null ? 0 : semanticTypeMappings.size()));
logger.info(
"number of matches for column "
+ n.getColumnName()
+ ": "
+ (semanticTypeMappings == null ? 0 : semanticTypeMappings.size()));
numOfMappings *=
semanticTypeMappings == null || semanticTypeMappings.isEmpty()
? 1
: semanticTypeMappings.size();
candidateSteinerSets.updateSteinerSets(semanticTypeMappings);
}
// System.out.println("number of possible mappings: " + numOfMappings);
logger.info("number of possible mappings: " + numOfMappings);
return candidateSteinerSets;
}
private Set<SemanticTypeMapping> findSemanticTypeInGraph(
ColumnNode sourceColumn,
SemanticType semanticType,
HashMap<String, Integer> semanticTypesCount,
Set<Node> addedNodes) {
logger.debug("finding matches for semantic type in the graph ... ");
if (addedNodes == null) addedNodes = new HashSet<Node>();
Set<SemanticTypeMapping> mappings = new HashSet<SemanticTypeMapping>();
if (semanticType == null) {
logger.error("semantic type is null.");
return mappings;
}
if (semanticType.getDomain() == null) {
logger.error("semantic type does not have any domain");
return mappings;
}
if (semanticType.getType() == null) {
logger.error("semantic type does not have any link");
return mappings;
}
String domainUri = semanticType.getDomain().getUri();
String propertyUri = semanticType.getType().getUri();
Double confidence = semanticType.getConfidenceScore();
Origin origin = semanticType.getOrigin();
Integer countOfSemanticType = semanticTypesCount.get(domainUri + propertyUri);
if (countOfSemanticType == null) {
logger.error("count of semantic type should not be null or zero");
return mappings;
}
if (domainUri == null || domainUri.isEmpty()) {
logger.error("semantic type does not have any domain");
return mappings;
}
if (propertyUri == null || propertyUri.isEmpty()) {
logger.error("semantic type does not have any link");
return mappings;
}
logger.debug(
"semantic type: " + domainUri + "|" + propertyUri + "|" + confidence + "|" + origin);
// add dataproperty to existing classes if sl is a data node mapping
// Set<Node> foundInternalNodes = new HashSet<Node>();
Set<SemanticTypeMapping> semanticTypeMatches =
this.graphBuilder.getSemanticTypeMatches().get(domainUri + propertyUri);
if (semanticTypeMatches != null) {
for (SemanticTypeMapping stm : semanticTypeMatches) {
SemanticTypeMapping mp =
new SemanticTypeMapping(
sourceColumn, semanticType, stm.getSource(), stm.getLink(), stm.getTarget());
mappings.add(mp);
// foundInternalNodes.add(stm.getSource());
}
}
logger.debug("adding data property to the found internal nodes ...");
Integer count;
boolean allowMultipleSamePropertiesPerNode =
ModelingConfigurationRegistry.getInstance()
.getModelingConfiguration(
ContextParametersRegistry.getInstance()
.getContextParameters(ontologyManager.getContextId())
.getKarmaHome())
.isMultipleSamePropertyPerNode();
Set<Node> nodesWithSameUriOfDomain = this.graphBuilder.getUriToNodesMap().get(domainUri);
if (nodesWithSameUriOfDomain != null) {
for (Node source : nodesWithSameUriOfDomain) {
count = this.graphBuilder.getNodeDataPropertyCount().get(source.getId() + propertyUri);
if (count != null) {
if (allowMultipleSamePropertiesPerNode) {
if (count >= countOfSemanticType.intValue()) continue;
} else {
if (count >= 1) continue;
}
}
String nodeId = new RandomGUID().toString();
ColumnNode target = new ColumnNode(nodeId, nodeId, sourceColumn.getColumnName(), null);
if (!this.graphBuilder.addNode(target)) continue;
;
addedNodes.add(target);
String linkId = LinkIdFactory.getLinkId(propertyUri, source.getId(), target.getId());
LabeledLink link = new DataPropertyLink(linkId, new Label(propertyUri));
if (!this.graphBuilder.addLink(source, target, link)) continue;
;
SemanticTypeMapping mp =
new SemanticTypeMapping(
sourceColumn, semanticType, (InternalNode) source, link, target);
mappings.add(mp);
}
}
return mappings;
}
public void run() {
long start = System.currentTimeMillis();
// Find the corresponding hNodePath. Used to find examples for training the CRF Model.
HNodePath currentColumnPath = null;
List<HNodePath> paths = worksheet.getHeaders().getAllPaths();
for (HNodePath path : paths) {
if (path.getLeaf().getId().equals(newType.getHNodeId())) {
currentColumnPath = path;
break;
}
}
Map<ColumnFeature, Collection<String>> columnFeatures =
new HashMap<ColumnFeature, Collection<String>>();
// Prepare the column name for training
String columnName = currentColumnPath.getLeaf().getColumnName();
Collection<String> columnNameList = new ArrayList<String>();
columnNameList.add(columnName);
columnFeatures.put(ColumnFeature.ColumnHeaderName, columnNameList);
// Train the model with the new type
ArrayList<String> trainingExamples =
SemanticTypeUtil.getTrainingExamples(worksheet, currentColumnPath);
boolean trainingResult = false;
String newTypeString =
(newType.getDomain() == null)
? newType.getType().getUri()
: newType.getDomain().getUri() + "|" + newType.getType().getUri();
trainingResult =
crfModelHandler.addOrUpdateLabel(newTypeString, trainingExamples, columnFeatures);
if (!trainingResult) {
logger.error("Error occured while training CRF Model.");
}
// logger.debug("Using type:" + newType.getDomain().getUri() + "|" +
// newType.getType().getUri());
// Add the new CRF column model for this column
ArrayList<String> labels = new ArrayList<String>();
ArrayList<Double> scores = new ArrayList<Double>();
trainingResult =
crfModelHandler.predictLabelForExamples(
trainingExamples, 4, labels, scores, null, columnFeatures);
if (!trainingResult) {
logger.error("Error occured while predicting labels");
}
CRFColumnModel newModel = new CRFColumnModel(labels, scores);
worksheet.getCrfModel().addColumnModel(newType.getHNodeId(), newModel);
long elapsedTimeMillis = System.currentTimeMillis() - start;
float elapsedTimeSec = elapsedTimeMillis / 1000F;
logger.info("Time required for training the semantic type: " + elapsedTimeSec);
// long t2 = System.currentTimeMillis();
// Identify the outliers for the column
// SemanticTypeUtil.identifyOutliers(worksheet, newTypeString,currentColumnPath,
// vWorkspace.getWorkspace().getTagsContainer()
// .getTag(TagName.Outlier), columnFeatures, crfModelHandler);
// long t3 = System.currentTimeMillis();
// logger.info("Identify outliers: "+ (t3-t2));
}