@Override
public UpdateContainer doIt(Workspace workspace) throws CommandException {
UpdateContainer uc = new UpdateContainer();
SuperSelection sel = this.getSuperSelection(workspace);
for (int i = 0; i < updates.length(); i++) {
String update = updates.getString(i);
switch (update) {
case "headers":
uc.add(new WorksheetHeadersUpdate(worksheetId));
break;
case "list":
uc.add(new WorksheetListUpdate());
break;
case "data":
uc.add(new WorksheetDataUpdate(worksheetId, sel));
break;
case "alignment":
{
Alignment alignment =
AlignmentManager.Instance()
.getAlignmentOrCreateIt(
workspace.getId(), worksheetId, workspace.getOntologyManager());
uc.add(new AlignmentSVGVisualizationUpdate(worksheetId, alignment));
break;
}
case "semanticTypes":
{
Alignment alignment =
AlignmentManager.Instance()
.getAlignmentOrCreateIt(
workspace.getId(), worksheetId, workspace.getOntologyManager());
uc.add(
new SemanticTypesUpdate(
workspace.getWorksheet(worksheetId), worksheetId, alignment));
break;
}
case "regenerate":
uc.add(new RegenerateWorksheetUpdate(worksheetId));
break;
case "all":
uc = WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId, sel);
break;
case "cleaning":
uc.add(new WorksheetCleaningUpdate(worksheetId, false, sel));
break;
}
}
return uc;
}
@Override
public UpdateContainer doIt(VWorkspace vWorkspace) throws CommandException {
UpdateContainer c = new UpdateContainer();
Worksheet worksheet = vWorkspace.getViewFactory().getVWorksheet(vWorksheetId).getWorksheet();
worksheetName = worksheet.getTitle();
// Generate the semantic types for the worksheet
OntologyManager ontMgr = vWorkspace.getWorkspace().getOntologyManager();
if (ontMgr.isEmpty()) return new UpdateContainer(new ErrorUpdate("No ontology loaded."));
SemanticTypeUtil.computeSemanticTypesForAutoModel(
worksheet, vWorkspace.getWorkspace().getCrfModelHandler(), ontMgr);
String alignmentId =
AlignmentManager.Instance()
.constructAlignmentId(vWorkspace.getWorkspace().getId(), vWorksheetId);
Alignment alignment = AlignmentManager.Instance().getAlignment(alignmentId);
if (alignment == null) {
alignment = new Alignment(ontMgr);
AlignmentManager.Instance().addAlignmentToMap(alignmentId, alignment);
}
try {
// Save the semantic types in the input parameter JSON
saveSemanticTypesInformation(
worksheet, vWorkspace, worksheet.getSemanticTypes().getListOfTypes());
// Add the visualization update
c.add(new SemanticTypesUpdate(worksheet, vWorksheetId, alignment));
c.add(
new SVGAlignmentUpdate_ForceKarmaLayout(
vWorkspace.getViewFactory().getVWorksheet(vWorksheetId), alignment));
} catch (Exception e) {
logger.error("Error occured while generating the model Reason:.", e);
return new UpdateContainer(
new ErrorUpdate("Error occured while generating the model for the source."));
}
c.add(new TagsUpdate());
return c;
}
@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);
}
}
@Override
public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
VWorksheet vWorksheet = vWorkspace.getViewFactory().getVWorksheetByWorksheetId(worksheetId);
List<String> hNodeIdList = new ArrayList<String>();
List<HNodePath> columns = vWorksheet.getColumns();
for (HNodePath path : columns) hNodeIdList.add(path.getLeaf().getId());
String alignmentId =
AlignmentManager.Instance()
.constructAlignmentId(vWorkspace.getWorkspace().getId(), vWorksheet.getWorksheetId());
JSONObject topObj = new JSONObject();
try {
topObj.put(
GenericJsonKeys.updateType.name(), AlignmentSVGVisualizationUpdate.class.getSimpleName());
topObj.put(JsonKeys.alignmentId.name(), alignmentId);
topObj.put(JsonKeys.worksheetId.name(), worksheetId);
// Using Mohsen's GraphUtils method for graph traversal
HashMap<Node, Integer> nodeHeightsMap = GraphUtil.levelingCyclicGraph(alignmentGraph);
HashMap<Node, Set<ColumnNode>> nodeCoverage =
GraphUtil.getNodesCoverage(alignmentGraph, nodeHeightsMap);
/** Identify the max height * */
int maxTreeHeight = 0;
for (Node node : nodeHeightsMap.keySet()) {
if (nodeHeightsMap.get(node) >= maxTreeHeight) {
maxTreeHeight = nodeHeightsMap.get(node);
}
}
/** * Add the nodes and the links from the Steiner tree ** */
List<String> hNodeIdsAdded = new ArrayList<String>();
JSONArray nodesArr = new JSONArray();
JSONArray linksArr = new JSONArray();
if (alignmentGraph != null && alignmentGraph.vertexSet().size() != 0) {
/** Add the nodes * */
Set<Node> nodes = alignmentGraph.vertexSet();
HashMap<Node, Integer> verticesIndex = new HashMap<Node, Integer>();
int nodesIndexcounter = 0;
for (Node node : nodes) {
/** Get info about the nodes that this node covers or sits above * */
int height = maxTreeHeight - nodeHeightsMap.get(node);
/** Add the hnode ids of the columns that this vertex covers * */
JSONArray hNodeIdsCoveredByVertex = new JSONArray();
for (Node v : nodeCoverage.get(node)) {
if (v instanceof ColumnNode) {
ColumnNode cNode = (ColumnNode) v;
hNodeIdsCoveredByVertex.put(cNode.getHNodeId());
}
}
String hNodeId = "";
/** Add the semantic type information * */
if (node instanceof ColumnNode) {
ColumnNode cNode = (ColumnNode) node;
hNodeId = cNode.getHNodeId();
hNodeIdsAdded.add(cNode.getHNodeId());
}
JSONObject nodeObj =
getNodeJsonObject(
node.getLocalId(),
node.getId(),
node.getType().name(),
height,
hNodeIdsCoveredByVertex,
hNodeId);
nodesArr.put(nodeObj);
verticesIndex.put(node, nodesIndexcounter++);
}
/** * Add the links ** */
Set<Link> links = alignmentGraph.edgeSet();
for (Link link : links) {
Node source = link.getSource();
Integer sourceIndex = verticesIndex.get(source);
Node target = link.getTarget();
Integer targetIndex = verticesIndex.get(target);
Set<Link> outEdges = alignmentGraph.outgoingEdgesOf(target);
if (sourceIndex == null || targetIndex == null) {
logger.error("Edge vertex index not found!");
continue;
}
JSONObject linkObj = new JSONObject();
linkObj.put(JsonKeys.source.name(), sourceIndex);
linkObj.put(JsonKeys.target.name(), targetIndex);
linkObj.put(JsonKeys.sourceNodeId.name(), source.getId());
linkObj.put(JsonKeys.targetNodeId.name(), target.getId());
linkObj.put(JsonKeys.label.name(), link.getLabel().getLocalName());
linkObj.put(JsonKeys.id.name(), link.getId() + "");
linkObj.put(JsonKeys.linkStatus.name(), link.getStatus().name());
linkObj.put(JsonKeys.linkUri.name(), link.getLabel().getUri());
if (target.getType() == NodeType.ColumnNode && outEdges.isEmpty()) {
linkObj.put(JsonKeys.linkType.name(), JsonValues.holderLink.name());
if (link.getKeyType() == LinkKeyInfo.PartOfKey)
linkObj.put(JsonKeys.label.name(), link.getLabel().getLocalName() + "*");
}
linksArr.put(linkObj);
if (link.getType() == LinkType.ClassInstanceLink
&& link.getKeyType() == LinkKeyInfo.PartOfKey
&& target instanceof ColumnNode) {
ColumnNode cNode = (ColumnNode) target;
// Add the holder vertex object and the link that attaches nodes to the columns
JSONArray hNodeIdsCoveredByVertex_holder = new JSONArray();
hNodeIdsCoveredByVertex_holder.put(cNode.getHNodeId());
JSONObject vertObj_holder =
getNodeJsonObject(
JsonValues.key.name(),
source.getId() + "_holder",
NodeType.ColumnNode.name(),
0,
hNodeIdsCoveredByVertex_holder,
cNode.getHNodeId());
nodesArr.put(vertObj_holder);
nodesIndexcounter++;
// Add the holder link
JSONObject linkObj_holder =
getLinkJsonObject(
JsonValues.key.name(),
"",
nodesIndexcounter,
nodesIndexcounter - 1,
"",
"",
"",
"");
linksArr.put(linkObj_holder);
}
if (link.getType() == LinkType.DataPropertyOfColumnLink) {
DataPropertyOfColumnLink dpLink = (DataPropertyOfColumnLink) link;
String startHNodeId = dpLink.getSpecializedColumnHNodeId();
// Get height of the class instance node
int height = maxTreeHeight - nodeHeightsMap.get(link.getSource());
// Add 2 more holder nodes
// Start node
JSONArray hNodeIdsCoveredByVertex_holder = new JSONArray();
hNodeIdsCoveredByVertex_holder.put(startHNodeId);
JSONObject startNode =
getNodeJsonObject(
"",
source.getId() + "_holder",
JsonValues.DataPropertyOfColumnHolder.name(),
height - 0.35,
hNodeIdsCoveredByVertex_holder,
startHNodeId);
nodesArr.put(startNode);
nodesIndexcounter++;
// End node
String endHNodeId = ((ColumnNode) link.getTarget()).getHNodeId();
JSONArray hNodeIdsCoveredByVertex_holder_2 = new JSONArray();
hNodeIdsCoveredByVertex_holder_2.put(endHNodeId);
JSONObject endNode =
getNodeJsonObject(
"",
target.getId() + "_holder",
JsonValues.DataPropertyOfColumnHolder.name(),
height - 0.35,
hNodeIdsCoveredByVertex_holder_2,
endHNodeId);
nodesArr.put(endNode);
nodesIndexcounter++;
// Add the horizontal link
JSONObject linkObj_holder =
getLinkJsonObject(
"",
"",
nodesIndexcounter - 2,
nodesIndexcounter - 1,
JsonValues.horizontalDataPropertyLink.name(),
"",
"",
"");
linksArr.put(linkObj_holder);
} else if (link.getType() == LinkType.ObjectPropertySpecializationLink) {
ObjectPropertySpecializationLink opLink = (ObjectPropertySpecializationLink) link;
Link specializedLink = opLink.getSpecializedLink();
// Get height of the class instance node
int height = nodeHeightsMap.get(specializedLink.getTarget());
// Add 2 more holder nodes
// Start node
JSONArray hNodeIdsCoveredByVertex_holder = new JSONArray();
for (Node v : nodeCoverage.get(specializedLink.getTarget())) {
if (v instanceof ColumnNode) {
ColumnNode cNode = (ColumnNode) v;
hNodeIdsCoveredByVertex_holder.put(cNode.getHNodeId());
}
}
JSONObject startNode =
getNodeJsonObject(
"",
source.getId() + "_holder",
JsonValues.DataPropertyOfColumnHolder.name(),
height + 0.65,
hNodeIdsCoveredByVertex_holder,
"");
nodesArr.put(startNode);
nodesIndexcounter++;
// End node
String endHNodeId = ((ColumnNode) link.getTarget()).getHNodeId();
JSONArray hNodeIdsCoveredByVertex_holder_2 = new JSONArray();
hNodeIdsCoveredByVertex_holder_2.put(endHNodeId);
JSONObject endNode =
getNodeJsonObject(
"",
target.getId() + "_holder",
JsonValues.DataPropertyOfColumnHolder.name(),
height + 0.65,
hNodeIdsCoveredByVertex_holder_2,
endHNodeId);
nodesArr.put(endNode);
nodesIndexcounter++;
// Add the horizontal link
JSONObject linkObj_holder =
getLinkJsonObject(
"",
"",
nodesIndexcounter - 2,
nodesIndexcounter - 1,
JsonValues.horizontalDataPropertyLink.name(),
"",
"",
"");
linksArr.put(linkObj_holder);
}
linkObj.put(JsonKeys.linkType.name(), link.getType());
}
}
// Add the vertices for the columns that were not in Steiner tree
hNodeIdList.removeAll(hNodeIdsAdded);
for (String hNodeId : hNodeIdList) {
JSONArray hNodeIdsCoveredByVertex = new JSONArray();
hNodeIdsCoveredByVertex.put(hNodeId);
JSONObject vertObj =
getNodeJsonObject(
"", hNodeId, JsonValues.Unassigned.name(), 0, hNodeIdsCoveredByVertex, hNodeId);
nodesArr.put(vertObj);
}
topObj.put(JsonKeys.maxTreeHeight.name(), maxTreeHeight);
topObj.put(JsonKeys.nodes.name(), nodesArr);
topObj.put(JsonKeys.links.name(), linksArr);
pw.write(topObj.toString());
} catch (JSONException e) {
logger.error("Error occured while writing JSON!", e);
}
}
@Override
public UpdateContainer doIt(Workspace workspace) throws CommandException {
final OntologyManager ontMgr = workspace.getOntologyManager();
Set<LabeledLink> properties = new HashSet<>();
logger.debug(
"GetPropertiesCommand:"
+ propertiesRange
+ ":"
+ classURI
+ ","
+ domainURI
+ ", "
+ rangeURI);
if (propertiesRange == INTERNAL_PROP_RANGE.allObjectProperties) {
HashMap<String, Label> linkList = ontMgr.getObjectProperties();
if (linkList != null) {
for (Label label : linkList.values()) {
properties.add(new DataPropertyLink(label.getUri(), label));
}
}
} else if (propertiesRange == INTERNAL_PROP_RANGE.allDataProperties) {
HashMap<String, Label> linkList = ontMgr.getDataProperties();
for (Label label : linkList.values()) {
properties.add(new DataPropertyLink(label.getUri(), label));
}
} else if (propertiesRange == INTERNAL_PROP_RANGE.propertiesWithDomainRange) {
Map<String, Label> linkList =
ontMgr.getObjectPropertiesByDomainRange(domainURI, rangeURI, true);
for (Label label : linkList.values()) {
properties.add(new DataPropertyLink(label.getUri(), label));
}
} else if (propertiesRange == INTERNAL_PROP_RANGE.dataPropertiesForClass) {
Map<String, Label> linkList = ontMgr.getDataPropertiesByDomain(classURI, true);
for (Label label : linkList.values()) {
properties.add(new DataPropertyLink(label.getUri(), label));
}
} else if (propertiesRange == INTERNAL_PROP_RANGE.existingProperties) {
Alignment alignment =
AlignmentManager.Instance()
.getAlignmentOrCreateIt(workspace.getId(), worksheetId, ontMgr);
Set<String> steinerTreeNodeIds = new HashSet<String>();
if (alignment != null && !alignment.isEmpty()) {
DirectedWeightedMultigraph<Node, LabeledLink> steinerTree = alignment.getSteinerTree();
for (Node node : steinerTree.vertexSet()) {
if (node.getType() == NodeType.InternalNode) {
steinerTreeNodeIds.add(node.getId());
}
}
List<LabeledLink> specializedLinks = new ArrayList<LabeledLink>();
Set<LabeledLink> temp = null;
temp = alignment.getLinksByType(LinkType.DataPropertyLink);
if (temp != null) specializedLinks.addAll(temp);
for (LabeledLink link : steinerTree.edgeSet())
if (link instanceof ObjectPropertyLink) specializedLinks.add(link);
// Store the data property links for specialized edge link options
properties.addAll(specializedLinks);
}
}
logger.debug("Got back " + properties.size() + " results");
final Set<LabeledLink> finalProperties = properties;
UpdateContainer upd =
new UpdateContainer(
new AbstractUpdate() {
@Override
public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
JSONObject obj = new JSONObject();
JSONArray resultArray = new JSONArray();
try {
obj.put(JsonKeys.updateType.name(), "PropertyList");
for (LabeledLink link : finalProperties) {
Label linkLabel = link.getLabel();
String edgeLabelStr = linkLabel.getDisplayName();
JSONObject edgeObj = new JSONObject();
if (linkLabel.getUri() != null
&& linkLabel.getNs() != null
&& linkLabel.getUri().equalsIgnoreCase(linkLabel.getNs())) {
edgeLabelStr = linkLabel.getUri();
}
edgeObj.put(JsonKeys.label.name(), edgeLabelStr);
edgeObj.put(JsonKeys.uri.name(), linkLabel.getUri());
edgeObj.put(JsonKeys.id.name(), link.getId());
resultArray.put(edgeObj);
}
obj.put(JsonKeys.properties.name(), resultArray);
pw.println(obj.toString());
} catch (Exception e) {
logger.error("Exception:", e);
e.printStackTrace();
}
}
});
return upd;
}