private String getTemplateTermSetPopulatedWithValues(
Map<String, String> columnValues, TemplateTermSet termSet)
throws ValueNotFoundKarmaException, NoValueFoundInNodeException {
StringBuilder output = new StringBuilder();
for (TemplateTerm term : termSet.getAllTerms()) {
// String template term
if (term instanceof StringTemplateTerm) {
output.append(term.getTemplateTermValue());
}
// Column template term
else if (term instanceof ColumnTemplateTerm) {
String hNodeId = term.getTemplateTermValue();
if (columnValues.containsKey(hNodeId)) {
Node node = factory.getNode(columnValues.get(hNodeId));
if (node != null) {
if (node.getValue().asString() == null || node.getValue().asString().equals("")) {
throw new NoValueFoundInNodeException();
}
output.append(node.getValue().asString());
}
} else {
String columnName = this.factory.getHNode(hNodeId).getColumnName();
throw new ValueNotFoundKarmaException(
"Could not retrieve value from column: " + columnName + ".", hNodeId);
}
}
}
return output.toString();
}
@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 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()));
}
}