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import java.io.Writer; public class GenerateR2RMLModelCommand extends Command { <<<<<<< HEAD private final String worksheetId; private String worksheetName; private String tripleStoreUrl; private String graphContext; private static Logger logger = LoggerFactory.getLogger(GenerateR2RMLModelCommand.class); public enum JsonKeys { updateType, fileUrl, worksheetId } public enum PreferencesKeys { rdfPrefix, rdfNamespace, modelSparqlEndPoint } protected GenerateR2RMLModelCommand(String id, String worksheetId, String url, String context) { super(id); this.worksheetId = worksheetId; this.tripleStoreUrl = url; this.graphContext = context; } public String getTripleStoreUrl() { return tripleStoreUrl; } public void setTripleStoreUrl(String tripleStoreUrl) { this.tripleStoreUrl = tripleStoreUrl; } public String getGraphContext() { return graphContext; } public void setGraphContext(String graphContext) { this.graphContext = graphContext; } @Override public String getCommandName() { return this.getClass().getSimpleName(); } @Override public String getTitle() { return "Generate R2RML Model"; } @Override public String getDescription() { return this.worksheetName; } @Override public CommandType getCommandType() { return CommandType.notUndoable; } @Override public UpdateContainer doIt(Workspace workspace) throws CommandException { //save the preferences savePreferences(workspace); Worksheet worksheet = workspace.getWorksheet(worksheetId); this.worksheetName = worksheet.getTitle(); // Prepare the model file path and names final String modelFileName = workspace.getCommandPreferencesId() + worksheetId + "-" + this.worksheetName + "-model.ttl"; final String modelFileLocalPath = ServletContextParameterMap.getParameterValue( ContextParameter.USER_DIRECTORY_PATH) + "publish/R2RML/" + modelFileName; try { KR2RMLModelGenerator modelGenerator = new KR2RMLModelGenerator(); KR2RMLMappingGenerator mappingGen = modelGenerator.generateModel(workspace, worksheet); // Write the model PrintWriter writer = new PrintWriter(modelFileLocalPath, "UTF-8"); modelGenerator.writeModel(workspace, mappingGen, worksheet, writer); // Write the model to the triple store TripleStoreUtil utilObj = new TripleStoreUtil(); // Get the graph name from properties String graphName = worksheet.getMetadataContainer().getWorksheetProperties() .getPropertyValue(Property.graphName); if (graphName == null \|\| graphName.isEmpty()) { // Set to default worksheet.getMetadataContainer().getWorksheetProperties().setPropertyValue( Property.graphName, WorksheetProperties.createDefaultGraphName(worksheet.getTitle())); graphName = WorksheetProperties.createDefaultGraphName(worksheet.getTitle()); } boolean result = utilObj.saveToStore(modelFileLocalPath, tripleStoreUrl, graphName, true); if (result) { logger.info("Saved model to triple store"); return new UpdateContainer(new AbstractUpdate() { } public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) { JSONObject outputObject = new JSONObject(); try { outputObject.put(JsonKeys.updateType.name(), "PublishR2RMLUpdate"); outputObject.put(JsonKeys.fileUrl.name(), "publish/R2RML/" + modelFileName); outputObject.put(JsonKeys.worksheetId.name(), worksheetId); pw.println(outputObject.toString()); } catch (JSONException e) { logger.error("Error occured while generating JSON!"); } } }); } return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!")); } catch (NullPointerException e) { logger.info("Alignment is NULL for " + worksheet.getId()); return new UpdateContainer(new ErrorUpdate(e.getMessage())); } catch (Exception e) { e.printStackTrace(); logger.error(e.getMessage()); return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!")); } } @Override public UpdateContainer undoIt(Workspace workspace) { // Not required return null; } private void savePreferences(Workspace workspace) { try { JSONObject prefObject = new JSONObject(); prefObject.put(PreferencesKeys.modelSparqlEndPoint.name(), tripleStoreUrl); workspace.getCommandPreferences().setCommandPreferences( "GenerateR2RMLModelCommandPreferences", prefObject); } catch (JSONException e) { e.printStackTrace(); } } ======= private final String worksheetId; private String worksheetName; private String tripleStoreUrl; private String graphContext; private static Logger logger = LoggerFactory.getLogger(GenerateR2RMLModelCommand.class); public enum JsonKeys { updateType, fileUrl, worksheetId } public enum PreferencesKeys { rdfPrefix, rdfNamespace, modelSparqlEndPoint } protected GenerateR2RMLModelCommand(String id, String worksheetId, String url, String context) { super(id); this.worksheetId = worksheetId; this.tripleStoreUrl = url; this.graphContext = context; } public String getTripleStoreUrl() { return tripleStoreUrl; } public void setTripleStoreUrl(String tripleStoreUrl) { this.tripleStoreUrl = tripleStoreUrl; } public String getGraphContext() { return graphContext; } public void setGraphContext(String graphContext) { this.graphContext = graphContext; } @Override public String getCommandName() { return this.getClass().getSimpleName(); } @Override public String getTitle() { return "Generate R2RML Model"; } @Override public String getDescription() { return this.worksheetName; } @Override public CommandType getCommandType() { return CommandType.notUndoable; @Override public UpdateContainer doIt(Workspace workspace) throws CommandException { //save the preferences savePreferences(workspace); Worksheet worksheet = workspace.getWorksheet(worksheetId); this.worksheetName = worksheet.getTitle(); // Prepare the model file path and names final String modelFileName = workspace.getCommandPreferencesId() + worksheetId + "-" + this.worksheetName + "-model.ttl"; final String modelFileLocalPath = ServletContextParameterMap.getParameterValue( ContextParameter.USER_DIRECTORY_PATH) + "publish/R2RML/" + modelFileName; // Get the alignment for this Worksheet Alignment alignment = AlignmentManager.Instance().getAlignment(AlignmentManager. Instance().constructAlignmentId(workspace.getId(), worksheetId)); if (alignment == null) { logger.info("Alignment is NULL for " + worksheetId); return new UpdateContainer(new ErrorUpdate( "Please align the worksheet before generating R2RML Model!")); } try { // Get the namespace and prefix from the preferences String namespace = ""; String prefix = ""; JSONObject prefObject = workspace.getCommandPreferences().getCommandPreferencesJSONObject( PublishRDFCommand.class.getSimpleName()+"Preferences"); if (prefObject != null) { namespace = prefObject.getString(PreferencesKeys.rdfNamespace.name()); prefix = prefObject.getString(PreferencesKeys.rdfPrefix.name()); namespace = ((namespace == null) \|\| (namespace.equals(""))) ? Namespaces.KARMA_DEV : namespace; prefix = ((prefix == null) \|\| (prefix.equals(""))) ? Prefixes.KARMA_DEV : prefix; } else { namespace = Namespaces.KARMA_DEV; prefix = Prefixes.KARMA_DEV; } // Generate the KR2RML data structures for the RDF generation final ErrorReport errorReport = new ErrorReport(); OntologyManager ontMgr = workspace.getOntologyManager(); KR2RMLMappingGenerator mappingGen = new KR2RMLMappingGenerator(ontMgr, alignment, worksheet.getSemanticTypes(), prefix, namespace, true, errorReport); // Write the model writeModel(workspace, ontMgr, mappingGen, worksheet, modelFileLocalPath); // Write the model to the triple store TripleStoreUtil utilObj = new TripleStoreUtil(); // Get the graph name from properties String graphName = worksheet.getMetadataContainer().getWorksheetProperties() .getPropertyValue(Property.graphName); if (graphName == null \|\| graphName.isEmpty()) { // Set to default worksheet.getMetadataContainer().getWorksheetProperties().setPropertyValue( Property.graphName, WorksheetProperties.createDefaultGraphName(worksheet.getTitle())); graphName = WorksheetProperties.createDefaultGraphName(worksheet.getTitle()); } boolean result = utilObj.saveToStore(modelFileLocalPath, tripleStoreUrl, graphName, true); if (result) { logger.info("Saved model to triple store"); return new UpdateContainer(new AbstractUpdate() { public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) { JSONObject outputObject = new JSONObject(); try { outputObject.put(JsonKeys.updateType.name(), "PublishR2RMLUpdate"); outputObject.put(JsonKeys.fileUrl.name(), "publish/R2RML/" + modelFileName); outputObject.put(JsonKeys.worksheetId.name(), worksheetId); pw.println(outputObject.toString()); } catch (JSONException e) { logger.error("Error occured while generating JSON!"); } } }); } return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!")); } catch (Exception e) { e.printStackTrace(); logger.error(e.getMessage()); return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!")); } } @Override public UpdateContainer undoIt(Workspace workspace) { // Not required return null; } private void writeModel(Workspace workspace, OntologyManager ontMgr, KR2RMLMappingGenerator mappingGen, Worksheet worksheet, String modelFileLocalPath) throws RepositoryException, FileNotFoundException, UnsupportedEncodingException, JSONException { File f = new File(modelFileLocalPath); File parentDir = f.getParentFile(); parentDir.mkdirs(); PrintWriter writer = new PrintWriter(f, "UTF-8"); WorksheetModelWriter modelWriter = new WorksheetModelWriter(writer, workspace.getFactory(), ontMgr, worksheet.getTitle()); // Writer worksheet properties such as Service URL modelWriter.writeWorksheetProperties(worksheet); // Write the worksheet history String historyFilePath = HistoryJsonUtil.constructWorksheetHistoryJsonFilePath( worksheet.getTitle(), workspace.getCommandPreferencesId()); modelWriter.writeCompleteWorksheetHistory(historyFilePath); // Write the R2RML mapping modelWriter.writeR2RMLMapping(ontMgr, mappingGen); modelWriter.close(); writer.flush(); writer.close(); } private void savePreferences(Workspace workspace){ try{ JSONObject prefObject = new JSONObject(); prefObject.put(PreferencesKeys.modelSparqlEndPoint.name(), tripleStoreUrl); workspace.getCommandPreferences().setCommandPreferences( "GenerateR2RMLModelCommandPreferences", prefObject); } catch (JSONException e) { e.printStackTrace(); } } >>>>>>> 99310c12a19df26ef84f4ed4f48909015ebb8809 }

Conflicting content

import java.io.Writer;

public class GenerateR2RMLModelCommand extends Command {
<<<<<<< HEAD

    private final String worksheetId;
    private String worksheetName;
    private String tripleStoreUrl;
    private String graphContext;
    private static Logger logger = LoggerFactory.getLogger(GenerateR2RMLModelCommand.class);

    public enum JsonKeys {

        updateType, fileUrl, worksheetId
    }

    public enum PreferencesKeys {

        rdfPrefix, rdfNamespace, modelSparqlEndPoint
    }

    protected GenerateR2RMLModelCommand(String id, String worksheetId, String url, String context) {
        super(id);
        this.worksheetId = worksheetId;
        this.tripleStoreUrl = url;
        this.graphContext = context;
    }

    public String getTripleStoreUrl() {
        return tripleStoreUrl;
    }

    public void setTripleStoreUrl(String tripleStoreUrl) {
        this.tripleStoreUrl = tripleStoreUrl;
    }

    public String getGraphContext() {
        return graphContext;
    }

    public void setGraphContext(String graphContext) {
        this.graphContext = graphContext;
    }

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

    @Override
    public String getTitle() {
        return "Generate R2RML Model";
    }

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

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

    @Override
    public UpdateContainer doIt(Workspace workspace) throws CommandException {

        //save the preferences 
        savePreferences(workspace);

        Worksheet worksheet = workspace.getWorksheet(worksheetId);
        this.worksheetName = worksheet.getTitle();

        // Prepare the model file path and names
        final String modelFileName = workspace.getCommandPreferencesId() + worksheetId + "-"
                + this.worksheetName + "-model.ttl";
        final String modelFileLocalPath = ServletContextParameterMap.getParameterValue(
                ContextParameter.USER_DIRECTORY_PATH) + "publish/R2RML/" + modelFileName;
        

        try {
            KR2RMLModelGenerator modelGenerator = new KR2RMLModelGenerator();
            
            KR2RMLMappingGenerator mappingGen = modelGenerator.generateModel(workspace, worksheet);
            // Write the model
            PrintWriter writer = new PrintWriter(modelFileLocalPath, "UTF-8");
            modelGenerator.writeModel(workspace, mappingGen, worksheet, writer);

            // Write the model to the triple store
            TripleStoreUtil utilObj = new TripleStoreUtil();

            // Get the graph name from properties
            String graphName = worksheet.getMetadataContainer().getWorksheetProperties()
                    .getPropertyValue(Property.graphName);
            if (graphName == null || graphName.isEmpty()) {
                // Set to default
                worksheet.getMetadataContainer().getWorksheetProperties().setPropertyValue(
                        Property.graphName, WorksheetProperties.createDefaultGraphName(worksheet.getTitle()));
                graphName = WorksheetProperties.createDefaultGraphName(worksheet.getTitle());
            }

            boolean result = utilObj.saveToStore(modelFileLocalPath, tripleStoreUrl, graphName, true);
            if (result) {
                logger.info("Saved model to triple store");
                return new UpdateContainer(new AbstractUpdate() {
	}
                    public void generateJson(String prefix, PrintWriter pw,
                            VWorkspace vWorkspace) {
                        JSONObject outputObject = new JSONObject();
                        try {
                            outputObject.put(JsonKeys.updateType.name(), "PublishR2RMLUpdate");
                            outputObject.put(JsonKeys.fileUrl.name(), "publish/R2RML/" + modelFileName);
                            outputObject.put(JsonKeys.worksheetId.name(), worksheetId);
                            pw.println(outputObject.toString());
                        } catch (JSONException e) {
                            logger.error("Error occured while generating JSON!");
                        }
                    }
                });
            }

            return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!"));

        } catch (NullPointerException e) {
            logger.info("Alignment is NULL for " + worksheet.getId());
            return new UpdateContainer(new ErrorUpdate(e.getMessage()));
        } catch (Exception e) {
            e.printStackTrace();
            logger.error(e.getMessage());
            return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!"));
        }
    }

    @Override
    public UpdateContainer undoIt(Workspace workspace) {
        // Not required
        return null;
    }

    

    private void savePreferences(Workspace workspace) {
        try {
            JSONObject prefObject = new JSONObject();
            prefObject.put(PreferencesKeys.modelSparqlEndPoint.name(), tripleStoreUrl);
            workspace.getCommandPreferences().setCommandPreferences(
                    "GenerateR2RMLModelCommandPreferences", prefObject);

        } catch (JSONException e) {
            e.printStackTrace();
        }
    }
=======
	
	private final String worksheetId;
	private String worksheetName;
	private String tripleStoreUrl;
	private String graphContext;
	
	private static Logger logger = LoggerFactory.getLogger(GenerateR2RMLModelCommand.class);
	
	public enum JsonKeys {
		updateType, fileUrl, worksheetId
	}
	
	public enum PreferencesKeys {
		rdfPrefix, rdfNamespace, modelSparqlEndPoint
	}
	
	protected GenerateR2RMLModelCommand(String id, String worksheetId, String url, String context) {
		super(id);
		this.worksheetId = worksheetId;
		this.tripleStoreUrl = url;
		this.graphContext = context;
	}

	public String getTripleStoreUrl() {
		return tripleStoreUrl;
	}

	public void setTripleStoreUrl(String tripleStoreUrl) {
		this.tripleStoreUrl = tripleStoreUrl;
	}
	
	public String getGraphContext() {
		return graphContext;
	}

	public void setGraphContext(String graphContext) {
		this.graphContext = graphContext;
	}

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

	@Override
	public String getTitle() {
		return "Generate R2RML Model";
	}

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

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

	@Override
	public UpdateContainer doIt(Workspace workspace) throws CommandException {
		
		//save the preferences 
		savePreferences(workspace);
				
		Worksheet worksheet = workspace.getWorksheet(worksheetId);
		this.worksheetName = worksheet.getTitle();
		
		// Prepare the model file path and names
		final String modelFileName = workspace.getCommandPreferencesId() + worksheetId + "-" + 
				this.worksheetName +  "-model.ttl"; 
		final String modelFileLocalPath = ServletContextParameterMap.getParameterValue(
				ContextParameter.USER_DIRECTORY_PATH) +  "publish/R2RML/" + modelFileName;

		// Get the alignment for this Worksheet
		Alignment alignment = AlignmentManager.Instance().getAlignment(AlignmentManager.
				Instance().constructAlignmentId(workspace.getId(), worksheetId));
		
		if (alignment == null) {
			logger.info("Alignment is NULL for " + worksheetId);
			return new UpdateContainer(new ErrorUpdate(
					"Please align the worksheet before generating R2RML Model!"));
		}
		
		try {
			// Get the namespace and prefix from the preferences
			String namespace = "";
			String prefix = "";
			JSONObject prefObject = workspace.getCommandPreferences().getCommandPreferencesJSONObject(
					PublishRDFCommand.class.getSimpleName()+"Preferences");
			if (prefObject != null) {
				namespace = prefObject.getString(PreferencesKeys.rdfNamespace.name());
				prefix = prefObject.getString(PreferencesKeys.rdfPrefix.name());
				namespace = ((namespace == null) || (namespace.equals(""))) ? 
						Namespaces.KARMA_DEV : namespace;
				prefix = ((prefix == null) || (prefix.equals(""))) ? 
						Prefixes.KARMA_DEV : prefix;
			} else {
				namespace = Namespaces.KARMA_DEV;
				prefix = Prefixes.KARMA_DEV;
			}
			
			// Generate the KR2RML data structures for the RDF generation
			final ErrorReport errorReport = new ErrorReport();
			OntologyManager ontMgr = workspace.getOntologyManager();
			KR2RMLMappingGenerator mappingGen = new KR2RMLMappingGenerator(ontMgr, alignment, 
					worksheet.getSemanticTypes(), prefix, namespace, true, errorReport);
			
			// Write the model
			writeModel(workspace, ontMgr, mappingGen, worksheet, modelFileLocalPath);
			
			// Write the model to the triple store
			TripleStoreUtil utilObj = new TripleStoreUtil();

			// Get the graph name from properties
			String graphName = worksheet.getMetadataContainer().getWorksheetProperties()
					.getPropertyValue(Property.graphName);
			if (graphName == null || graphName.isEmpty()) {
				// Set to default
				worksheet.getMetadataContainer().getWorksheetProperties().setPropertyValue(
						Property.graphName, WorksheetProperties.createDefaultGraphName(worksheet.getTitle()));
				graphName = WorksheetProperties.createDefaultGraphName(worksheet.getTitle());
			}
			
			boolean result = utilObj.saveToStore(modelFileLocalPath, tripleStoreUrl, graphName, true);
			if (result) {
				logger.info("Saved model to triple store");
				return new UpdateContainer(new AbstractUpdate() {
					public void generateJson(String prefix, PrintWriter pw,	
							VWorkspace vWorkspace) {
						JSONObject outputObject = new JSONObject();
						try {
							outputObject.put(JsonKeys.updateType.name(), "PublishR2RMLUpdate");
							outputObject.put(JsonKeys.fileUrl.name(), "publish/R2RML/" + modelFileName);
							outputObject.put(JsonKeys.worksheetId.name(), worksheetId);
							pw.println(outputObject.toString());
						} catch (JSONException e) {
							logger.error("Error occured while generating JSON!");
						}
					}
				});
			} 
			
			return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!"));
			
		} catch (Exception e) {
			e.printStackTrace();
			logger.error(e.getMessage());
			return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!"));
		}
	}

	@Override
	public UpdateContainer undoIt(Workspace workspace) {
		// Not required
		return null;
	}
	
	private void writeModel(Workspace workspace, OntologyManager ontMgr, 
			KR2RMLMappingGenerator mappingGen, Worksheet worksheet, String modelFileLocalPath) 
					throws RepositoryException, FileNotFoundException, 
							UnsupportedEncodingException, JSONException {
		File f = new File(modelFileLocalPath);
		File parentDir = f.getParentFile();
		parentDir.mkdirs();
		PrintWriter writer = new PrintWriter(f, "UTF-8");
		WorksheetModelWriter modelWriter = new WorksheetModelWriter(writer, 
				workspace.getFactory(), ontMgr, worksheet.getTitle());

		// Writer worksheet properties such as Service URL
		modelWriter.writeWorksheetProperties(worksheet);
		
		// Write the worksheet history
		String historyFilePath = HistoryJsonUtil.constructWorksheetHistoryJsonFilePath(
				worksheet.getTitle(), workspace.getCommandPreferencesId());
		modelWriter.writeCompleteWorksheetHistory(historyFilePath);
		
		// Write the R2RML mapping
		modelWriter.writeR2RMLMapping(ontMgr, mappingGen);
		modelWriter.close();
		writer.flush();
		writer.close();
	}

	
	private void savePreferences(Workspace workspace){
		try{
			JSONObject prefObject = new JSONObject();
			prefObject.put(PreferencesKeys.modelSparqlEndPoint.name(), tripleStoreUrl);
			workspace.getCommandPreferences().setCommandPreferences(
					"GenerateR2RMLModelCommandPreferences", prefObject);
			
		} catch (JSONException e) {
			e.printStackTrace();
		}
	}
>>>>>>> 99310c12a19df26ef84f4ed4f48909015ebb8809
}

Solution content
import java.io.Writer; public class GenerateR2RMLModelCommand extends Command { private final String worksheetId; private String worksheetName; private String tripleStoreUrl; private String graphContext; private static Logger logger = LoggerFactory.getLogger(GenerateR2RMLModelCommand.class); public enum JsonKeys { updateType, fileUrl, worksheetId } public enum PreferencesKeys { rdfPrefix, rdfNamespace, modelSparqlEndPoint } protected GenerateR2RMLModelCommand(String id, String worksheetId, String url, String context) { super(id); this.worksheetId = worksheetId; this.tripleStoreUrl = url; this.graphContext = context; } public String getTripleStoreUrl() { return tripleStoreUrl; } public void setTripleStoreUrl(String tripleStoreUrl) { this.tripleStoreUrl = tripleStoreUrl; } public String getGraphContext() { return graphContext; } public void setGraphContext(String graphContext) { this.graphContext = graphContext; } @Override public String getCommandName() { return this.getClass().getSimpleName(); } @Override public String getTitle() { return "Generate R2RML Model"; } @Override public String getDescription() { return this.worksheetName; } @Override public CommandType getCommandType() { return CommandType.notUndoable; } @Override public UpdateContainer doIt(Workspace workspace) throws CommandException { //save the preferences savePreferences(workspace); Worksheet worksheet = workspace.getWorksheet(worksheetId); this.worksheetName = worksheet.getTitle(); // Prepare the model file path and names final String modelFileName = workspace.getCommandPreferencesId() + worksheetId + "-" + this.worksheetName + "-model.ttl"; final String modelFileLocalPath = ServletContextParameterMap.getParameterValue( ContextParameter.USER_DIRECTORY_PATH) + "publish/R2RML/" + modelFileName; // Get the alignment for this Worksheet Alignment alignment = AlignmentManager.Instance().getAlignment(AlignmentManager. Instance().constructAlignmentId(workspace.getId(), worksheetId)); if (alignment == null) { logger.info("Alignment is NULL for " + worksheetId); return new UpdateContainer(new ErrorUpdate( "Please align the worksheet before generating R2RML Model!")); } try { // Get the namespace and prefix from the preferences String namespace = ""; String prefix = ""; JSONObject prefObject = workspace.getCommandPreferences().getCommandPreferencesJSONObject( PublishRDFCommand.class.getSimpleName()+"Preferences"); if (prefObject != null) { namespace = prefObject.getString(PreferencesKeys.rdfNamespace.name()); prefix = prefObject.getString(PreferencesKeys.rdfPrefix.name()); namespace = ((namespace == null) \|\| (namespace.equals(""))) ? Namespaces.KARMA_DEV : namespace; prefix = ((prefix == null) \|\| (prefix.equals(""))) ? Prefixes.KARMA_DEV : prefix; } else { namespace = Namespaces.KARMA_DEV; prefix = Prefixes.KARMA_DEV; } // Generate the KR2RML data structures for the RDF generation final ErrorReport errorReport = new ErrorReport(); OntologyManager ontMgr = workspace.getOntologyManager(); KR2RMLMappingGenerator mappingGen = new KR2RMLMappingGenerator(ontMgr, alignment, worksheet.getSemanticTypes(), prefix, namespace, true, errorReport); // Write the model writeModel(workspace, ontMgr, mappingGen, worksheet, modelFileLocalPath); // Write the model to the triple store TripleStoreUtil utilObj = new TripleStoreUtil(); // Get the graph name from properties String graphName = worksheet.getMetadataContainer().getWorksheetProperties() .getPropertyValue(Property.graphName); if (graphName == null \|\| graphName.isEmpty()) { // Set to default worksheet.getMetadataContainer().getWorksheetProperties().setPropertyValue( Property.graphName, WorksheetProperties.createDefaultGraphName(worksheet.getTitle())); graphName = WorksheetProperties.createDefaultGraphName(worksheet.getTitle()); } boolean result = utilObj.saveToStore(modelFileLocalPath, tripleStoreUrl, graphName, true); if (result) { logger.info("Saved model to triple store"); return new UpdateContainer(new AbstractUpdate() { public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) { JSONObject outputObject = new JSONObject(); try { outputObject.put(JsonKeys.updateType.name(), "PublishR2RMLUpdate"); outputObject.put(JsonKeys.fileUrl.name(), "publish/R2RML/" + modelFileName); outputObject.put(JsonKeys.worksheetId.name(), worksheetId); pw.println(outputObject.toString()); } catch (JSONException e) { logger.error("Error occured while generating JSON!"); } } }); } return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!")); } catch (Exception e) { e.printStackTrace(); logger.error(e.getMessage()); return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!")); } } @Override public UpdateContainer undoIt(Workspace workspace) { // Not required return null; } private void writeModel(Workspace workspace, OntologyManager ontMgr, KR2RMLMappingGenerator mappingGen, Worksheet worksheet, String modelFileLocalPath) throws RepositoryException, FileNotFoundException, UnsupportedEncodingException, JSONException { File f = new File(modelFileLocalPath); File parentDir = f.getParentFile(); parentDir.mkdirs(); PrintWriter writer = new PrintWriter(f, "UTF-8"); WorksheetModelWriter modelWriter = new WorksheetModelWriter(writer, workspace.getFactory(), ontMgr, worksheet.getTitle()); // Writer worksheet properties such as Service URL modelWriter.writeWorksheetProperties(worksheet); // Write the worksheet history String historyFilePath = HistoryJsonUtil.constructWorksheetHistoryJsonFilePath( worksheet.getTitle(), workspace.getCommandPreferencesId()); modelWriter.writeCompleteWorksheetHistory(historyFilePath); // Write the R2RML mapping modelWriter.writeR2RMLMapping(ontMgr, mappingGen); modelWriter.close(); writer.flush(); writer.close(); } private void savePreferences(Workspace workspace) { try { JSONObject prefObject = new JSONObject(); prefObject.put(PreferencesKeys.modelSparqlEndPoint.name(), tripleStoreUrl); workspace.getCommandPreferences().setCommandPreferences( "GenerateR2RMLModelCommandPreferences", prefObject); } catch (JSONException e) { e.printStackTrace(); } } }

Solution content

import java.io.Writer;

public class GenerateR2RMLModelCommand extends Command {

    private final String worksheetId;
    private String worksheetName;
    private String tripleStoreUrl;
    private String graphContext;
    private static Logger logger = LoggerFactory.getLogger(GenerateR2RMLModelCommand.class);

    public enum JsonKeys {

        updateType, fileUrl, worksheetId
    }

    public enum PreferencesKeys {

        rdfPrefix, rdfNamespace, modelSparqlEndPoint
    }

    protected GenerateR2RMLModelCommand(String id, String worksheetId, String url, String context) {
        super(id);
        this.worksheetId = worksheetId;
        this.tripleStoreUrl = url;
        this.graphContext = context;
    }

    public String getTripleStoreUrl() {
        return tripleStoreUrl;
    }

    public void setTripleStoreUrl(String tripleStoreUrl) {
        this.tripleStoreUrl = tripleStoreUrl;
    }

    public String getGraphContext() {
        return graphContext;
    }

    public void setGraphContext(String graphContext) {
        this.graphContext = graphContext;
    }

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

    @Override
    public String getTitle() {
        return "Generate R2RML Model";
    }

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

    @Override
    public CommandType getCommandType() {
        return CommandType.notUndoable;
    }
    
    @Override
	public UpdateContainer doIt(Workspace workspace) throws CommandException {
		
		//save the preferences 
		savePreferences(workspace);
				
		Worksheet worksheet = workspace.getWorksheet(worksheetId);
		this.worksheetName = worksheet.getTitle();
		
		// Prepare the model file path and names
		final String modelFileName = workspace.getCommandPreferencesId() + worksheetId + "-" + 
				this.worksheetName +  "-model.ttl"; 
		final String modelFileLocalPath = ServletContextParameterMap.getParameterValue(
				ContextParameter.USER_DIRECTORY_PATH) +  "publish/R2RML/" + modelFileName;

		// Get the alignment for this Worksheet
		Alignment alignment = AlignmentManager.Instance().getAlignment(AlignmentManager.
				Instance().constructAlignmentId(workspace.getId(), worksheetId));
		
		if (alignment == null) {
			logger.info("Alignment is NULL for " + worksheetId);
			return new UpdateContainer(new ErrorUpdate(
					"Please align the worksheet before generating R2RML Model!"));
		}
		
		try {
			// Get the namespace and prefix from the preferences
			String namespace = "";
			String prefix = "";
			JSONObject prefObject = workspace.getCommandPreferences().getCommandPreferencesJSONObject(
					PublishRDFCommand.class.getSimpleName()+"Preferences");
			if (prefObject != null) {
				namespace = prefObject.getString(PreferencesKeys.rdfNamespace.name());
				prefix = prefObject.getString(PreferencesKeys.rdfPrefix.name());
				namespace = ((namespace == null) || (namespace.equals(""))) ? 
						Namespaces.KARMA_DEV : namespace;
				prefix = ((prefix == null) || (prefix.equals(""))) ? 
						Prefixes.KARMA_DEV : prefix;
			} else {
				namespace = Namespaces.KARMA_DEV;
				prefix = Prefixes.KARMA_DEV;
			}
			
			// Generate the KR2RML data structures for the RDF generation
			final ErrorReport errorReport = new ErrorReport();
			OntologyManager ontMgr = workspace.getOntologyManager();
			KR2RMLMappingGenerator mappingGen = new KR2RMLMappingGenerator(ontMgr, alignment, 
					worksheet.getSemanticTypes(), prefix, namespace, true, errorReport);
			
			// Write the model
			writeModel(workspace, ontMgr, mappingGen, worksheet, modelFileLocalPath);
			
			// Write the model to the triple store
			TripleStoreUtil utilObj = new TripleStoreUtil();

			// Get the graph name from properties
			String graphName = worksheet.getMetadataContainer().getWorksheetProperties()
					.getPropertyValue(Property.graphName);
			if (graphName == null || graphName.isEmpty()) {
				// Set to default
				worksheet.getMetadataContainer().getWorksheetProperties().setPropertyValue(
						Property.graphName, WorksheetProperties.createDefaultGraphName(worksheet.getTitle()));
				graphName = WorksheetProperties.createDefaultGraphName(worksheet.getTitle());
			}
			
			boolean result = utilObj.saveToStore(modelFileLocalPath, tripleStoreUrl, graphName, true);
			if (result) {
				logger.info("Saved model to triple store");
				return new UpdateContainer(new AbstractUpdate() {
					public void generateJson(String prefix, PrintWriter pw,	
							VWorkspace vWorkspace) {
						JSONObject outputObject = new JSONObject();
						try {
							outputObject.put(JsonKeys.updateType.name(), "PublishR2RMLUpdate");
							outputObject.put(JsonKeys.fileUrl.name(), "publish/R2RML/" + modelFileName);
							outputObject.put(JsonKeys.worksheetId.name(), worksheetId);
							pw.println(outputObject.toString());
						} catch (JSONException e) {
							logger.error("Error occured while generating JSON!");
						}
					}
				});
			} 
			
			return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!"));
			
		} catch (Exception e) {
			e.printStackTrace();
			logger.error(e.getMessage());
			return new UpdateContainer(new ErrorUpdate("Error occured while generating R2RML model!"));
		}
	}

    @Override
    public UpdateContainer undoIt(Workspace workspace) {
        // Not required
        return null;
    }

    private void writeModel(Workspace workspace, OntologyManager ontMgr,
            KR2RMLMappingGenerator mappingGen, Worksheet worksheet, String modelFileLocalPath)
            throws RepositoryException, FileNotFoundException,
            UnsupportedEncodingException, JSONException {
        File f = new File(modelFileLocalPath);
        File parentDir = f.getParentFile();
        parentDir.mkdirs();
        PrintWriter writer = new PrintWriter(f, "UTF-8");
        WorksheetModelWriter modelWriter = new WorksheetModelWriter(writer,
                workspace.getFactory(), ontMgr, worksheet.getTitle());

        // Writer worksheet properties such as Service URL
        modelWriter.writeWorksheetProperties(worksheet);

        // Write the worksheet history
        String historyFilePath = HistoryJsonUtil.constructWorksheetHistoryJsonFilePath(
                worksheet.getTitle(), workspace.getCommandPreferencesId());
        modelWriter.writeCompleteWorksheetHistory(historyFilePath);

        // Write the R2RML mapping
        modelWriter.writeR2RMLMapping(ontMgr, mappingGen);
        modelWriter.close();
        writer.flush();
        writer.close();
    }

    private void savePreferences(Workspace workspace) {
        try {
            JSONObject prefObject = new JSONObject();
            prefObject.put(PreferencesKeys.modelSparqlEndPoint.name(), tripleStoreUrl);
            workspace.getCommandPreferences().setCommandPreferences(
                    "GenerateR2RMLModelCommandPreferences", prefObject);

        } catch (JSONException e) {
            e.printStackTrace();
        }
    }
}

File
GenerateR2RMLModelCommand.java

Developer's decision
Version 2

Kind of conflict
Annotation
Attribute
Enum declaration
Method declaration
Method invocation

Chunk

Conflicting content
import edu.isi.karma.controller.command.Command; import edu.isi.karma.controller.command.CommandException; <<<<<<< HEAD import edu.isi.karma.controller.command.WorksheetCommand; import edu.isi.karma.controller.history.WorksheetCommandHistoryReader; ======= >>>>>>> 99310c12a19df26ef84f4ed4f48909015ebb8809 import edu.isi.karma.controller.update.ErrorUpdate; import edu.isi.karma.controller.update.InfoUpdate; import edu.isi.karma.controller.update.UpdateContainer;

Conflicting content

import edu.isi.karma.controller.command.Command;
import edu.isi.karma.controller.command.CommandException;
<<<<<<< HEAD
import edu.isi.karma.controller.command.WorksheetCommand;
import edu.isi.karma.controller.history.WorksheetCommandHistoryReader;
=======
>>>>>>> 99310c12a19df26ef84f4ed4f48909015ebb8809
import edu.isi.karma.controller.update.ErrorUpdate;
import edu.isi.karma.controller.update.InfoUpdate;
import edu.isi.karma.controller.update.UpdateContainer;

Solution content
import edu.isi.karma.controller.command.Command; import edu.isi.karma.controller.command.CommandException; import edu.isi.karma.controller.history.WorksheetCommandHistoryExecutor; import edu.isi.karma.controller.history.WorksheetCommandHistoryReader; import edu.isi.karma.controller.update.ErrorUpdate; import edu.isi.karma.controller.update.InfoUpdate; import edu.isi.karma.controller.update.UpdateContainer;

Solution content

import edu.isi.karma.controller.command.Command;
import edu.isi.karma.controller.command.CommandException;
import edu.isi.karma.controller.history.WorksheetCommandHistoryExecutor;
import edu.isi.karma.controller.history.WorksheetCommandHistoryReader;
import edu.isi.karma.controller.update.ErrorUpdate;
import edu.isi.karma.controller.update.InfoUpdate;
import edu.isi.karma.controller.update.UpdateContainer;

File
ImportCommand.java

Developer's decision
Manual

Kind of conflict
Import

Chunk

Conflicting content
import edu.isi.karma.controller.update.WorksheetListUpdate; import edu.isi.karma.controller.update.WorksheetUpdateFactory; import edu.isi.karma.imp.Import; <<<<<<< HEAD import edu.isi.karma.kr2rml.KR2RMLMappingGenerator; import edu.isi.karma.kr2rml.KR2RMLModelGenerator; import edu.isi.karma.modeling.alignment.Alignment; import edu.isi.karma.modeling.alignment.AlignmentManager; import edu.isi.karma.modeling.semantictypes.SemanticTypeUtil; import edu.isi.karma.rep.Worksheet; import edu.isi.karma.rep.Workspace; import edu.isi.karma.webserver.KarmaException; import java.io.ByteArrayInputStream; import java.io.IOException; import java.io.InputStream; import java.io.PrintWriter; import java.io.StringWriter; import java.sql.SQLException; import org.json.JSONArray; import org.json.JSONException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; ======= import edu.isi.karma.rep.Worksheet; import edu.isi.karma.rep.Workspace; import edu.isi.karma.webserver.KarmaException; >>>>>>> 99310c12a19df26ef84f4ed4f48909015ebb8809 /** * This abstract class in an interface to all Commands that Import data

Conflicting content

import edu.isi.karma.controller.update.WorksheetListUpdate;
import edu.isi.karma.controller.update.WorksheetUpdateFactory;
import edu.isi.karma.imp.Import;
<<<<<<< HEAD
import edu.isi.karma.kr2rml.KR2RMLMappingGenerator;
import edu.isi.karma.kr2rml.KR2RMLModelGenerator;
import edu.isi.karma.modeling.alignment.Alignment;
import edu.isi.karma.modeling.alignment.AlignmentManager;
import edu.isi.karma.modeling.semantictypes.SemanticTypeUtil;
import edu.isi.karma.rep.Worksheet;
import edu.isi.karma.rep.Workspace;
import edu.isi.karma.webserver.KarmaException;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.sql.SQLException;
import org.json.JSONArray;
import org.json.JSONException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
=======
import edu.isi.karma.rep.Worksheet;
import edu.isi.karma.rep.Workspace;
import edu.isi.karma.webserver.KarmaException;
>>>>>>> 99310c12a19df26ef84f4ed4f48909015ebb8809

/**
 * This abstract class in an interface to all Commands that Import data

Solution content
import edu.isi.karma.controller.update.WorksheetListUpdate; import edu.isi.karma.controller.update.WorksheetUpdateFactory; import edu.isi.karma.imp.Import; import edu.isi.karma.kr2rml.ErrorReport; import edu.isi.karma.kr2rml.KR2RMLMappingGenerator; import edu.isi.karma.kr2rml.R2RMLMapping; import edu.isi.karma.modeling.Uris; import edu.isi.karma.modeling.alignment.Alignment; import edu.isi.karma.modeling.alignment.AlignmentManager; import edu.isi.karma.modeling.semantictypes.SemanticTypeUtil; import edu.isi.karma.rep.Worksheet; import edu.isi.karma.rep.Workspace; import edu.isi.karma.webserver.KarmaException; import java.io.ByteArrayInputStream; import java.io.IOException; import java.io.InputStream; import java.io.PrintWriter; import java.io.StringWriter; import org.json.JSONArray; import org.json.JSONException; import org.openrdf.model.Statement; import org.openrdf.model.URI; import org.openrdf.model.Value; import org.openrdf.model.ValueFactory; import org.openrdf.repository.Repository; import org.openrdf.repository.RepositoryConnection; import org.openrdf.repository.RepositoryException; import org.openrdf.repository.RepositoryResult; import org.openrdf.repository.sail.SailRepository; import org.openrdf.rio.RDFFormat; import org.openrdf.rio.RDFParseException; import org.openrdf.sail.memory.MemoryStore; import org.slf4j.Logger; import org.slf4j.LoggerFactory; /** * This abstract class in an interface to all Commands that Import data

Solution content

import edu.isi.karma.controller.update.WorksheetListUpdate;
import edu.isi.karma.controller.update.WorksheetUpdateFactory;
import edu.isi.karma.imp.Import;
import edu.isi.karma.kr2rml.ErrorReport;
import edu.isi.karma.kr2rml.KR2RMLMappingGenerator;
import edu.isi.karma.kr2rml.R2RMLMapping;
import edu.isi.karma.modeling.Uris;
import edu.isi.karma.modeling.alignment.Alignment;
import edu.isi.karma.modeling.alignment.AlignmentManager;
import edu.isi.karma.modeling.semantictypes.SemanticTypeUtil;
import edu.isi.karma.rep.Worksheet;
import edu.isi.karma.rep.Workspace;
import edu.isi.karma.webserver.KarmaException;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import org.json.JSONArray;
import org.json.JSONException;
import org.openrdf.model.Statement;
import org.openrdf.model.URI;
import org.openrdf.model.Value;
import org.openrdf.model.ValueFactory;
import org.openrdf.repository.Repository;
import org.openrdf.repository.RepositoryConnection;
import org.openrdf.repository.RepositoryException;
import org.openrdf.repository.RepositoryResult;
import org.openrdf.repository.sail.SailRepository;
import org.openrdf.rio.RDFFormat;
import org.openrdf.rio.RDFParseException;
import org.openrdf.sail.memory.MemoryStore;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * This abstract class in an interface to all Commands that Import data

File
ImportCommand.java

Developer's decision
Manual

Kind of conflict
Import

Chunk

Conflicting content
@Override public UpdateContainer doIt(Workspace workspace) throws CommandException { <<<<<<< HEAD WorksheetCommandHistoryReader histReader = new WorksheetCommandHistoryReader( worksheetId, workspace); KR2RMLModelGenerator modelGenerator = new KR2RMLModelGenerator(); ======= UpdateContainer c = WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId); >>>>>>> 99310c12a19df26ef84f4ed4f48909015ebb8809 try { FileInputStream fis = new FileInputStream(r2rmlModelFile); String historyStr = modelGenerator.extractHistoryFromModel(fis);

Conflicting content

	@Override
	public UpdateContainer doIt(Workspace workspace) throws CommandException {
<<<<<<< HEAD
		WorksheetCommandHistoryReader histReader = new WorksheetCommandHistoryReader(
				worksheetId, workspace);
                
                KR2RMLModelGenerator modelGenerator = new KR2RMLModelGenerator();
=======
		UpdateContainer c = WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId);
		
>>>>>>> 99310c12a19df26ef84f4ed4f48909015ebb8809
		try {
                        FileInputStream fis = new FileInputStream(r2rmlModelFile);
			String historyStr = modelGenerator.extractHistoryFromModel(fis);

Solution content
@Override public UpdateContainer doIt(Workspace workspace) throws CommandException { UpdateContainer c = WorksheetUpdateFactory.createRegenerateWorksheetUpdates(worksheetId); try {

File
ApplyHistoryFromR2RMLModelCommand.java

Developer's decision
Version 2

Kind of conflict
Method invocation
Variable

Projects >> Web-Karma >>8663d2cc4b58cdb9ba84599013372aba0f88da65