@Override
public UpdateContainer undoIt(Workspace workspace) {
Node node = workspace.getFactory().getNode(nodeIdArg);
SuperSelection sel = getSuperSelection(workspace);
node.setValue(previousValue, previousStatus, workspace.getFactory());
UpdateContainer uc =
WorksheetUpdateFactory.createWorksheetHierarchicalAndCleaningResultsUpdates(
worksheetId, sel);
uc.add(new NodeChangedUpdate(worksheetId, nodeIdArg, previousValue, previousStatus));
return uc;
}
private void generateRDFFromWorksheet(
Worksheet wk,
Workspace workspace,
KR2RMLMapping mapping,
List<KR2RMLRDFWriter> writers,
String baseURI)
throws IOException, JSONException, KarmaException {
// Generate RDF for the remaining rows
// Gets all the errors generated during the RDF generation
ErrorReport errorReport = new ErrorReport();
this.applyHistoryToWorksheet(workspace, wk, mapping);
SuperSelection selection = SuperSelectionManager.DEFAULT_SELECTION;
if (selectionName != null && !selectionName.trim().isEmpty())
selection = wk.getSuperSelectionManager().getSuperSelection(selectionName);
if (selection == null) return;
// RDF generation object initialization
KR2RMLWorksheetRDFGenerator rdfGen =
new KR2RMLWorksheetRDFGenerator(
wk,
workspace.getFactory(),
workspace.getOntologyManager(),
writers,
false,
mapping,
errorReport,
selection);
// Generate the rdf
rdfGen.generateRDF(false);
}
@Override
public UpdateContainer doIt(Workspace workspace) throws CommandException {
Node node = workspace.getFactory().getNode(nodeIdArg);
SuperSelection sel = getSuperSelection(workspace);
inputColumns.clear();
outputColumns.clear();
inputColumns.add(node.getHNodeId());
outputColumns.add(node.getHNodeId());
previousValue = node.getValue();
previousStatus = node.getStatus();
if (node.hasNestedTable()) {
throw new CommandException(
this, "Cell " + nodeIdArg + " has a nested table. It cannot be edited.");
}
node.setValue(newValueArg, Node.NodeStatus.edited, workspace.getFactory());
WorksheetUpdateFactory.detectSelectionStatusChange(worksheetId, workspace, this);
UpdateContainer uc =
WorksheetUpdateFactory.createWorksheetHierarchicalAndCleaningResultsUpdates(
worksheetId, sel);
uc.add(new NodeChangedUpdate(worksheetId, nodeIdArg, newValueArg, Node.NodeStatus.edited));
return uc;
}
@Override
public UpdateContainer doIt(Workspace workspace) throws CommandException {
Worksheet worksheet = workspace.getWorksheet(worksheetId);
RepFactory factory = workspace.getFactory();
SuperSelection superSel = getSuperSelection(worksheet);
HTable hTable = factory.getHTable(factory.getHNode(hNodeId).getHTableId());
Selection currentSel = superSel.getSelection(hTable.getId());
if (currentSel != null) {
currentSel.updateSelection();
}
CommandHistory history = workspace.getCommandHistory();
List<Command> tmp =
gatherAllOperateSelectionCommands(
history.getCommandsFromWorksheetId(worksheetId), workspace);
if (tmp.size() > 0) {
JSONArray inputJSON = new JSONArray();
inputJSON.put(
CommandInputJSONUtil.createJsonObject(
"worksheetId", worksheetId, ParameterType.worksheetId));
inputJSON.put(
CommandInputJSONUtil.createJsonObject("hNodeId", hNodeId, ParameterType.hNodeId));
inputJSON.put(
CommandInputJSONUtil.createJsonObject(
"operation", Operation.Intersect.name(), ParameterType.other));
inputJSON.put(
CommandInputJSONUtil.createJsonObject(
"pythonCode", SelectionManager.defaultCode, ParameterType.other));
inputJSON.put(CommandInputJSONUtil.createJsonObject("onError", "false", ParameterType.other));
inputJSON.put(
CommandInputJSONUtil.createJsonObject(
"selectionName", superSel.getName(), ParameterType.other));
Command t = null;
try {
t = new OperateSelectionCommandFactory().createCommand(inputJSON, workspace);
} catch (Exception e) {
}
if (t != null) history._getHistory().add(t);
history._getHistory().addAll(tmp);
}
UpdateContainer uc =
WorksheetUpdateFactory.createWorksheetHierarchicalAndCleaningResultsUpdates(
worksheetId, superSel);
uc.add(new HistoryUpdate(history));
return uc;
}
private JSONArray extractHistoryFromModel(Workspace workspace, UpdateContainer uc)
throws RepositoryException, RDFParseException, IOException, JSONException, KarmaException {
Worksheet ws = workspace.getFactory().getWorksheet(worksheetId);
R2RMLMappingIdentifier id =
new R2RMLMappingIdentifier(ws.getTitle(), r2rmlModelFile.toURI().toURL());
WorksheetR2RMLJenaModelParser parser = new WorksheetR2RMLJenaModelParser(id);
KR2RMLMapping mapping = parser.parse();
KR2RMLVersion version = mapping.getVersion();
if (version.compareTo(KR2RMLVersion.current) < 0) {
uc.add(
new InfoUpdate(
"Model version is "
+ version.toString()
+ ". Current version is "
+ KR2RMLVersion.current.toString()
+ ". Please publish it again."));
}
return mapping.getWorksheetHistory();
}
/*
* Pedro
*
* Return an HNodeId in a nice format for printing on command logs.
*/
protected String formatHNodeId(Workspace workspace, String hNodeId) {
return hNodeId + " (" + workspace.getFactory().getColumnName(hNodeId) + ")";
}
private void generateRDF(
String wkname,
String query,
List<KR2RMLRDFWriter> writers,
R2RMLMappingIdentifier id,
String baseURI)
throws IOException, JSONException, KarmaException, SQLException, ClassNotFoundException {
logger.debug("Generating RDF...");
WorksheetR2RMLJenaModelParser parserTest = new WorksheetR2RMLJenaModelParser(id);
KR2RMLMapping mapping = parserTest.parse();
AbstractJDBCUtil dbUtil = JDBCUtilFactory.getInstance(dbType);
Connection conn = dbUtil.getConnection(hostname, portnumber, username, password, dBorSIDName);
conn.setAutoCommit(false);
java.sql.Statement stmt =
conn.createStatement(
java.sql.ResultSet.TYPE_FORWARD_ONLY, java.sql.ResultSet.CONCUR_READ_ONLY);
stmt.setFetchSize(DATABASE_TABLE_FETCH_SIZE);
ResultSet r = stmt.executeQuery(query);
ResultSetMetaData meta = r.getMetaData();
;
// Get the column names
List<String> columnNames = new ArrayList<>();
for (int i = 1; i <= meta.getColumnCount(); i++) {
columnNames.add(meta.getColumnName(i));
}
// Prepare required Karma objects
Workspace workspace = initializeWorkspace();
RepFactory factory = workspace.getFactory();
Worksheet wk = factory.createWorksheet(wkname, workspace, encoding);
List<String> headersList = addHeaders(wk, columnNames, factory);
int counter = 0;
ArrayList<String> rowValues = null;
while ((rowValues = dbUtil.parseResultSetRow(r)) != null) {
// Generate RDF and create a new worksheet for every DATABASE_TABLE_FETCH_SIZE rows
if (counter % DATABASE_TABLE_FETCH_SIZE == 0 && counter != 0) {
generateRDFFromWorksheet(wk, workspace, mapping, writers, baseURI);
logger.debug("Done for " + counter + " rows ...");
removeWorkspace(workspace);
parserTest = new WorksheetR2RMLJenaModelParser(id);
mapping = parserTest.parse();
workspace = initializeWorkspace();
factory = workspace.getFactory();
wk = factory.createWorksheet(wkname, workspace, encoding);
headersList = addHeaders(wk, columnNames, factory);
}
/** Add the data * */
Table dataTable = wk.getDataTable();
Row row = dataTable.addRow(factory);
for (int i = 0; i < rowValues.size(); i++) {
row.setValue(headersList.get(i), rowValues.get(i), factory);
}
counter++;
}
generateRDFFromWorksheet(wk, workspace, mapping, writers, baseURI);
// Releasing all the resources
r.close();
conn.close();
stmt.close();
logger.debug("done");
}
@Override
public UpdateContainer doIt(Workspace workspace) throws CommandException {
ModelingConfiguration modelingConfiguration =
ModelingConfigurationRegistry.getInstance()
.getModelingConfiguration(
WorkspaceKarmaHomeRegistry.getInstance().getKarmaHome(workspace.getId()));
TripleStoreUtil utilObj = new TripleStoreUtil();
boolean showModelsWithoutMatching = modelingConfiguration.isShowModelsWithoutMatching();
try {
HashMap<String, List<String>> metadata =
utilObj.getMappingsWithMetadata(TripleStoreUrl, context);
RepFactory factory = workspace.getFactory();
List<String> model_Names = metadata.get("model_names");
List<String> model_Urls = metadata.get("model_urls");
List<String> model_Times = metadata.get("model_publishtimes");
List<String> model_Contexts = metadata.get("model_contexts");
List<String> model_inputColumns = metadata.get("model_inputcolumns");
final List<JSONObject> list = new ArrayList<>();
Set<String> worksheetcolumns = new HashSet<>();
if (worksheetId != null && !worksheetId.trim().isEmpty()) {
HTable htable = factory.getWorksheet(worksheetId).getHeaders();
getHNodesForWorksheet(htable, worksheetcolumns, factory);
}
Iterator<String> nameitr = model_Names.iterator();
Iterator<String> urlitr = model_Urls.iterator();
Iterator<String> timeitr = model_Times.iterator();
Iterator<String> contextitr = model_Contexts.iterator();
Iterator<String> inputitr = model_inputColumns.iterator();
while (nameitr.hasNext()
&& urlitr.hasNext()
&& timeitr.hasNext()
&& contextitr.hasNext()
&& inputitr.hasNext()) {
JSONObject obj = new JSONObject();
Set<String> inputs = new HashSet<>();
obj.put("name", nameitr.next());
obj.put("url", urlitr.next());
obj.put("publishTime", timeitr.next());
obj.put("context", contextitr.next());
String columns = inputitr.next();
if (columns != null && !columns.isEmpty()) {
JSONArray array = new JSONArray(columns);
for (int i = 0; i < array.length(); i++) inputs.add(array.get(i).toString());
} else if (showModelsWithoutMatching) {
list.add(obj);
}
if (worksheetId != null && !worksheetId.isEmpty()) {
inputs.retainAll(worksheetcolumns);
obj.put("inputColumns", inputs.size());
} else obj.put("inputColumns", 0);
if (!inputs.isEmpty() || (worksheetId == null || worksheetId.trim().isEmpty()))
list.add(obj);
}
Collections.sort(
list,
new Comparator<JSONObject>() {
@Override
public int compare(JSONObject a, JSONObject b) {
return b.getInt("inputColumns") - a.getInt("inputColumns");
}
});
return new UpdateContainer(
new AbstractUpdate() {
@Override
public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
try {
JSONArray array = new JSONArray();
for (JSONObject obj : list) {
array.put(obj);
}
pw.print(array.toString());
} catch (Exception e) {
logger.error("Error generating JSON!", e);
}
}
});
} catch (Exception e) {
return new UpdateContainer(
new ErrorUpdate("Unable to get mappings with metadata: " + e.getMessage()));
}
}
private boolean isSamehTableId(String hNodeId1, String hNodeId2, Workspace workspace) {
HNode hNode1 = workspace.getFactory().getHNode(hNodeId1);
HNode hNode2 = workspace.getFactory().getHNode(hNodeId2);
if (hNode1 == null || hNode2 == null) return false;
return hNode1.getHTableId().equals(hNode2.getHTableId());
}
@Override
public UpdateContainer doIt(Workspace workspace) throws CommandException {
Worksheet worksheet = workspace.getWorksheet(worksheetId);
SuperSelection selection = getSuperSelection(worksheet);
HNodePath selectedPath = null;
List<HNodePath> columnPaths = worksheet.getHeaders().getAllPaths();
for (HNodePath path : columnPaths) {
if (path.getLeaf().getId().equals(hNodeId)) {
selectedPath = path;
}
}
Collection<Node> nodes = new ArrayList<Node>();
workspace
.getFactory()
.getWorksheet(worksheetId)
.getDataTable()
.collectNodes(selectedPath, nodes, selection);
try {
JSONArray requestJsonArray = new JSONArray();
for (Node node : nodes) {
String id = node.getId();
String originalVal = node.getValue().asString();
JSONObject jsonRecord = new JSONObject();
jsonRecord.put("id", id);
originalVal = originalVal == null ? "" : originalVal;
jsonRecord.put("value", originalVal);
requestJsonArray.put(jsonRecord);
}
String jsonString = null;
jsonString = requestJsonArray.toString();
// String url =
// "http://localhost:8080/cleaningService/IdentifyData";
// String url = "http://localhost:8070/myWS/IdentifyData";
String url =
ServletContextParameterMap.getParameterValue(ContextParameter.CLEANING_SERVICE_URL);
HttpClient httpclient = new DefaultHttpClient();
HttpPost httppost = null;
HttpResponse response = null;
HttpEntity entity;
StringBuffer out = new StringBuffer();
URI u = null;
u = new URI(url);
List<NameValuePair> formparams = new ArrayList<NameValuePair>();
formparams.add(new BasicNameValuePair("json", jsonString));
httppost = new HttpPost(u);
httppost.setEntity(new UrlEncodedFormEntity(formparams, "UTF-8"));
response = httpclient.execute(httppost);
entity = response.getEntity();
if (entity != null) {
BufferedReader buf = new BufferedReader(new InputStreamReader(entity.getContent()));
String line = buf.readLine();
while (line != null) {
out.append(line);
line = buf.readLine();
}
}
// logger.trace(out.toString());
// logger.info("Connnection success : " + url + " Successful.");
final JSONObject data1 = new JSONObject(out.toString());
// logger.trace("Data--->" + data1);
return new UpdateContainer(
new AbstractUpdate() {
@Override
public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
JSONObject response = new JSONObject();
// logger.trace("Reached here");
try {
response.put("updateType", "CleaningServiceOutput");
response.put("chartData", data1);
response.put("hNodeId", hNodeId);
// logger.trace(response.toString(4));
} catch (JSONException e) {
pw.print("Error");
}
pw.print(response.toString());
}
});
} catch (Exception e) {
e.printStackTrace();
return new UpdateContainer(new ErrorUpdate("Error!"));
}
}