SuggestAutoModelCommand.java

/*******************************************************************************
 * Copyright 2012 University of Southern California
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 * 	http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 * 
 * This code was developed by the Information Integration Group as part 
 * of the Karma project at the Information Sciences Institute of the 
 * University of Southern California.  For more information, publications, 
 * and related projects, please see: http://www.isi.edu/integration
 ******************************************************************************/
package edu.isi.karma.controller.command.alignment;

import java.util.ArrayList;
import java.util.Collection;
import java.util.List;

import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import edu.isi.karma.controller.command.CommandException;
import edu.isi.karma.controller.command.CommandType;
import edu.isi.karma.controller.command.WorksheetCommand;
import edu.isi.karma.controller.history.HistoryJsonUtil.ClientJsonKeys;
import edu.isi.karma.controller.history.HistoryJsonUtil.ParameterType;
import edu.isi.karma.controller.update.ErrorUpdate;
import edu.isi.karma.controller.update.TagsUpdate;
import edu.isi.karma.controller.update.UpdateContainer;
import edu.isi.karma.modeling.Namespaces;
import edu.isi.karma.modeling.alignment.Alignment;
import edu.isi.karma.modeling.alignment.AlignmentManager;
import edu.isi.karma.modeling.ontology.OntologyManager;
import edu.isi.karma.rep.HNode;
import edu.isi.karma.rep.Worksheet;
import edu.isi.karma.rep.Workspace;
import edu.isi.karma.rep.alignment.ColumnNode;
import edu.isi.karma.rep.alignment.Label;
import edu.isi.karma.rep.alignment.LabeledLink;
import edu.isi.karma.rep.alignment.Node;
import edu.isi.karma.rep.alignment.SemanticType;


public class SuggestAutoModelCommand extends WorksheetCommand {

	private String worksheetName;

	private static Logger logger = LoggerFactory
			.getLogger(SuggestAutoModelCommand.class);

	protected SuggestAutoModelCommand(String id, String model, String worksheetId)
			{
		super(id, model, worksheetId);
		
		/** NOTE Not saving this command in history for now since we are 
		 * not letting CRF model assign semantic types automatically. This command 
		 * was being saved in history to keep track of the semantic types 
		 * that were assigned by the CRF Model **/ 
		// addTag(CommandTag.Modeling);
	}

	@Override
	public String getCommandName() {
		return this.getClass().getSimpleName();
	}

	@Override
	public String getTitle() {
		return "Suggest AutoModel";
	}

	@Override
	public String getDescription() {
		return worksheetName;
	}

	@Override
	public CommandType getCommandType() {
		return CommandType.notUndoable;
	}

	@Override
	public UpdateContainer doIt(Workspace workspace) throws CommandException {
		UpdateContainer c = new UpdateContainer();
		Worksheet worksheet = workspace.getWorksheet(worksheetId);

		worksheetName = worksheet.getTitle();

		// Generate the semantic types for the worksheet
		OntologyManager ontMgr = workspace.getOntologyManager();
		if(ontMgr.isEmpty())
			return new UpdateContainer(new ErrorUpdate("No ontology loaded."));


		String alignmentId = AlignmentManager.Instance().constructAlignmentId(workspace.getId(), worksheetId);
		Alignment alignment = AlignmentManager.Instance().getAlignment(alignmentId);
		if (alignment == null) {
			alignment = new Alignment(ontMgr);
			AlignmentManager.Instance().addAlignmentToMap(alignmentId, alignment);
		}
		
		String ns = Namespaces.KARMA;
		// Create the internal node for worksheet
		Label internalNodeLabel = new Label(ns + worksheet.getTitle().trim().replaceAll(" ", "_"), ns, "karma");
		Node classNode = alignment.addInternalNode(internalNodeLabel);
		
		// Create column nodes for all columns 
		List<HNode> sortedLeafHNodes = new ArrayList<>();
		worksheet.getHeaders().getSortedLeafHNodes(sortedLeafHNodes);
		for (HNode hNode : sortedLeafHNodes){
			String columnName = hNode.getColumnName().trim().replaceAll(" ", "_");
			ColumnNode columnNode = alignment.getColumnNodeByHNodeId(hNode.getId());
			
			List<LabeledLink> columnNodeIncomingLinks = alignment.getGraphBuilder().getIncomingLinks(columnNode.getId());
			if (columnNodeIncomingLinks == null || columnNodeIncomingLinks.isEmpty()) { // SemanticType not yet assigned
				Label propertyLabel = new Label(ns + columnName, ns, "karma");
				alignment.addDataPropertyLink(classNode, columnNode, propertyLabel, false);
				
				// Create a semantic type object
				SemanticType type = new SemanticType(hNode.getId(), propertyLabel, internalNodeLabel, classNode.getId(), false, SemanticType.Origin.User, 1.0);
				worksheet.getSemanticTypes().addType(type);
				
				List<SemanticType> userSemanticTypes = columnNode.getUserSemanticTypes();
				boolean duplicateSemanticType = false;
				if (userSemanticTypes != null) {
					for (SemanticType st : userSemanticTypes) {
						if (st.getModelLabelString().equalsIgnoreCase(type.getModelLabelString())) {
							duplicateSemanticType = true;
							break;
						}
					}
				}
				if (!duplicateSemanticType)
					columnNode.assignUserType(type);
			} else {
				// User-defined: do nothing
			}
		}
		if(!this.isExecutedInBatch())
			alignment.align();
		
		try {
			// Save the semantic types in the input parameter JSON
			saveSemanticTypesInformation(worksheet, workspace, worksheet.getSemanticTypes().getListOfTypes());
			// Add the visualization update
			c.append(this.computeAlignmentAndSemanticTypesAndCreateUpdates(workspace));

		} 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;
	}

	private void saveSemanticTypesInformation(Worksheet worksheet, Workspace workspace
			, Collection<SemanticType> semanticTypes) throws JSONException {
		JSONArray typesArray = new JSONArray();
		
		// Add the vworksheet information
		JSONObject vwIDJObj = new JSONObject();
		vwIDJObj.put(ClientJsonKeys.name.name(), ParameterType.worksheetId.name());
		vwIDJObj.put(ClientJsonKeys.type.name(), ParameterType.worksheetId.name());
		vwIDJObj.put(ClientJsonKeys.value.name(), worksheetId);
		typesArray.put(vwIDJObj);
	
		for (SemanticType type: semanticTypes) {
			// Add the hNode information
			JSONObject hNodeJObj = new JSONObject();
			hNodeJObj.put(ClientJsonKeys.name.name(), ParameterType.hNodeId.name());
			hNodeJObj.put(ClientJsonKeys.type.name(), ParameterType.hNodeId.name());
			hNodeJObj.put(ClientJsonKeys.value.name(), type.getHNodeId());
			typesArray.put(hNodeJObj);
			
			// Add the semantic type information
			JSONObject typeJObj = new JSONObject();
			typeJObj.put(ClientJsonKeys.name.name(), ClientJsonKeys.SemanticType.name());
			typeJObj.put(ClientJsonKeys.type.name(), ParameterType.other.name());
			typeJObj.put(ClientJsonKeys.value.name(), type.getJSONArrayRepresentation());
			typesArray.put(typeJObj);
		}
		setInputParameterJson(typesArray.toString(4));
	}

	@Override
	public UpdateContainer undoIt(Workspace workspace) {
		return null;
	}
}