private DirectedWeightedMultigraph<Node, LabeledLink> computeSteinerTree(Set<Node> steinerNodes) { if (steinerNodes == null || steinerNodes.size() == 0) { logger.error("There is no steiner node."); return null; } // System.out.println(steinerNodes.size()); List<Node> steinerNodeList = new ArrayList<Node>(steinerNodes); long start = System.currentTimeMillis(); UndirectedGraph<Node, DefaultLink> undirectedGraph = new AsUndirectedGraph<Node, DefaultLink>(this.graphBuilder.getGraph()); logger.debug("computing steiner tree ..."); SteinerTree steinerTree = new SteinerTree(undirectedGraph, steinerNodeList); DirectedWeightedMultigraph<Node, LabeledLink> tree = new TreePostProcess(this.graphBuilder, steinerTree.getDefaultSteinerTree(), null, false) .getTree(); // (DirectedWeightedMultigraph<Node, // LabeledLink>)GraphUtil.asDirectedGraph(steinerTree.getDefaultSteinerTree()); logger.debug(GraphUtil.labeledGraphToString(tree)); long steinerTreeElapsedTimeMillis = System.currentTimeMillis() - start; logger.debug("total number of nodes in steiner tree: " + tree.vertexSet().size()); logger.debug("total number of edges in steiner tree: " + tree.edgeSet().size()); logger.debug("time to compute steiner tree: " + (steinerTreeElapsedTimeMillis / 1000F)); return tree; // long finalTreeElapsedTimeMillis = System.currentTimeMillis() - steinerTreeElapsedTimeMillis; // DirectedWeightedMultigraph<Node, Link> finalTree = buildOutputTree(tree); // logger.info("time to build final tree: " + (finalTreeElapsedTimeMillis/1000F)); // GraphUtil.printGraph(finalTree); // return finalTree; }
@Override public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) { JSONObject topObj = new JSONObject(); try { topObj.put( GenericJsonKeys.updateType.name(), SVGAlignmentUpdate_ForceKarmaLayout.class.getSimpleName()); topObj.put(JsonKeys.alignmentId.name(), alignmentId); topObj.put(JsonKeys.worksheetId.name(), vWorksheetId); @SuppressWarnings("unchecked") DirectedWeightedMultigraph<Vertex, LabeledWeightedEdge> treeClone = (DirectedWeightedMultigraph<Vertex, LabeledWeightedEdge>) tree.clone(); // Reversing the inverse links alignment.updateLinksDirections(this.root, null, treeClone); /** * Add the nodes and the links from the Steiner tree ** */ List<String> hNodeIdsAdded = new ArrayList<String>(); JSONArray vertArr = new JSONArray(); JSONArray linksArr = new JSONArray(); int maxTreeHeight = 0; if (tree != null && tree.vertexSet().size() != 0) { /** * Add the nodes ** */ Set<Vertex> vertices = tree.vertexSet(); HashMap<Vertex, Integer> verticesIndex = new HashMap<Vertex, Integer>(); int nodesIndexcounter = 0; for (Vertex vertex : vertices) { JSONObject vertObj = new JSONObject(); vertObj.put(JsonKeys.label.name(), vertex.getLocalID()); vertObj.put(JsonKeys.id.name(), vertex.getID()); vertObj.put(JsonKeys.nodeType.name(), vertex.getNodeType().name()); List<Vertex> nodesWithSemTypesCovered = new ArrayList<Vertex>(); int height = getHeight(vertex, nodesWithSemTypesCovered, treeClone); if (height >= maxTreeHeight) { maxTreeHeight = height; } vertObj.put(JsonKeys.height.name(), height); JSONArray hNodeIdsCoveredByVertex = new JSONArray(); for (Vertex v : nodesWithSemTypesCovered) hNodeIdsCoveredByVertex.put(v.getSemanticType().getHNodeId()); vertObj.put(JsonKeys.hNodesCovered.name(), hNodeIdsCoveredByVertex); // Add the semantic type information if required. if (vertex.getSemanticType() != null) { SemanticType type = vertex.getSemanticType(); vertObj.put(JsonKeys.hNodeId.name(), type.getHNodeId()); hNodeIdsAdded.add(type.getHNodeId()); if (vertex.getNodeType() == NodeType.Class) { if (type.isPartOfKey()) { vertObj.put(JsonKeys.label.name(), vertex.getLocalID() + "*"); } // Add the holder vertex object and the link that // attaches nodes to the columns JSONObject vertObj_holder = new JSONObject(); vertObj_holder.put(JsonKeys.label.name(), JsonValues.key.name()); vertObj_holder.put(JsonKeys.id.name(), vertex.getID() + "_holder"); vertObj_holder.put(JsonKeys.nodeType.name(), NodeType.DataProperty.name()); vertObj_holder.put(JsonKeys.hNodeId.name(), type.getHNodeId()); JSONArray hNodeIdsCoveredByVertex_holder = new JSONArray(); hNodeIdsCoveredByVertex_holder.put(vertex.getSemanticType().getHNodeId()); vertObj_holder.put(JsonKeys.hNodesCovered.name(), hNodeIdsCoveredByVertex_holder); vertObj_holder.put(JsonKeys.height.name(), 0); vertArr.put(vertObj_holder); nodesIndexcounter++; // Add the holder link JSONObject linkObj = new JSONObject(); linkObj.put(JsonKeys.source.name(), nodesIndexcounter); linkObj.put(JsonKeys.target.name(), nodesIndexcounter - 1); linkObj.put(JsonKeys.label.name(), JsonValues.key.name()); linkObj.put(JsonKeys.id.name(), ""); linksArr.put(linkObj); } } vertArr.put(vertObj); verticesIndex.put(vertex, nodesIndexcounter++); } /** * Add the links ** */ Set<LabeledWeightedEdge> edges = tree.edgeSet(); for (LabeledWeightedEdge edge : edges) { Vertex source = edge.getSource(); Integer sourceIndex = verticesIndex.get(source); Vertex target = edge.getTarget(); Integer targetIndex = verticesIndex.get(target); Set<LabeledWeightedEdge> outEdges = tree.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(), edge.getLocalLabel()); linkObj.put(JsonKeys.id.name(), edge.getID() + ""); linkObj.put(JsonKeys.linkStatus.name(), edge.getLinkStatus().name()); if (target.getSemanticType() != null && outEdges.isEmpty()) { linkObj.put(JsonKeys.linkType.name(), JsonValues.holderLink.name()); if (target.getSemanticType().isPartOfKey()) linkObj.put(JsonKeys.label.name(), edge.getLocalLabel() + "*"); } linksArr.put(linkObj); if (source.getNodeType() == NodeType.Class && target.getNodeType() == NodeType.Class) { linkObj.put(JsonKeys.linkType.name(), JsonValues.objPropertyLink.name()); } } } // Add the vertices for the columns that were not in Steiner tree hNodeIdList.removeAll(hNodeIdsAdded); for (String hNodeId : hNodeIdList) { JSONObject vertObj = new JSONObject(); vertObj.put(JsonKeys.id.name(), hNodeId); vertObj.put(JsonKeys.hNodeId.name(), hNodeId); vertObj.put(JsonKeys.nodeType.name(), JsonValues.Unassigned.name()); vertArr.put(vertObj); vertObj.put(JsonKeys.height.name(), 0); JSONArray hNodeIdsCoveredByVertex = new JSONArray(); hNodeIdsCoveredByVertex.put(hNodeId); vertObj.put(JsonKeys.hNodesCovered.name(), hNodeIdsCoveredByVertex); } topObj.put(JsonKeys.maxTreeHeight.name(), maxTreeHeight); topObj.put(JsonKeys.nodes.name(), vertArr); topObj.put(JsonKeys.links.name(), linksArr); pw.write(topObj.toString(4)); } catch (JSONException e) { logger.error("Error occured while writing 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; }