@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;
}
@Override
public UpdateContainer doIt(Workspace workspace) {
Worksheet worksheet = workspace.getWorksheet(worksheetId);
SuperSelection selection = getSuperSelection(worksheet);
String worksheetName = worksheet.getTitle();
try {
// preparing model file name
final String modelFileName =
workspace.getCommandPreferencesId() + worksheetId + "-" + worksheetName + "-model.ttl";
final String modelFileLocalPath =
ServletContextParameterMap.getParameterValue(ContextParameter.R2RML_PUBLISH_DIR)
+ modelFileName;
File f = new File(modelFileLocalPath);
// preparing the graphUri where the model is published in the triple store
String graphName =
worksheet
.getMetadataContainer()
.getWorksheetProperties()
.getPropertyValue(Property.graphName);
if (graphName == null || graphName.isEmpty()) {
SimpleDateFormat sdf = new SimpleDateFormat("dd-MMM-yyyy-kkmmssS");
String ts = sdf.format(Calendar.getInstance().getTime());
graphName =
"http://localhost/"
+ workspace.getCommandPreferencesId()
+ "/"
+ worksheetId
+ "/model/"
+ ts;
worksheet
.getMetadataContainer()
.getWorksheetProperties()
.setPropertyValue(Property.graphName, graphName);
}
// If the model is not published, publish it!
if (!f.exists() || !f.isFile()) {
GenerateR2RMLModelCommandFactory factory = new GenerateR2RMLModelCommandFactory();
GenerateR2RMLModelCommand cmd =
(GenerateR2RMLModelCommand)
factory.createCommand(
workspace,
worksheetId,
TripleStoreUtil.defaultModelsRepoUrl,
graphName,
selection.getName());
cmd.doIt(workspace);
} else {
// if the model was published 30 min ago, publish it again, just to be sure
long diff = Calendar.getInstance().getTimeInMillis() - f.lastModified();
if ((diff / 1000L / 60L) > 30) {
f.delete();
GenerateR2RMLModelCommandFactory factory = new GenerateR2RMLModelCommandFactory();
GenerateR2RMLModelCommand cmd =
(GenerateR2RMLModelCommand)
factory.createCommand(
workspace,
worksheetId,
TripleStoreUtil.defaultModelsRepoUrl,
graphName,
selection.getName());
cmd.doIt(workspace);
}
}
// TripleStoreUtil tUtil = new TripleStoreUtil();
StringBuffer query =
new StringBuffer(
"prefix rr: <http://www.w3.org/ns/r2rml#> prefix km-dev: <http://isi.edu/integration/karma/dev#> ");
/* ****** this is the query for the list of columns.
PREFIX km-dev: <http://isi.edu/integration/karma/dev#>
PREFIX rr: <http://www.w3.org/ns/r2rml#>
select distinct ?class where {
{
?x1 rr:subjectMap/km-dev:alignmentNodeId "------- The full url of the column/class --------".
?x1 rr:predicateObjectMap/rr:objectMap/rr:column ?column .
?x1 rr:subjectMap/rr:predicate ?class .
}
UNION
{
?x1 rr:subjectMap/km-dev:alignmentNodeId "------- The full url of the column/class --------".
?x1 (rr:predicateObjectMap/rr:objectMap/rr:parentTriplesMap)* ?x2 .
?x2 rr:predicateObjectMap/rr:objectMap/rr:column ?column .
?x2 rr:predicateObjectMap/rr:predicate ?class .
}
}
* */
query.append("select distinct ?class ?column where { ");
if (graphName != null && !graphName.trim().isEmpty()) {
query.append(" graph <" + graphName + "> { ");
}
query
.append("{ ?x1 rr:subjectMap/km-dev:alignmentNodeId \"")
.append(this.nodeId)
.append(
"\" . ?x1 rr:predicateObjectMap/rr:objectMap/rr:column ?column . ?x1 rr:subjectMap/rr:predicate ?class .")
.append(" } UNION { ")
.append("?x1 rr:subjectMap/km-dev:alignmentNodeId \"")
.append(this.nodeId)
.append("\" . ?x1 (rr:predicateObjectMap/rr:objectMap/rr:parentTriplesMap)* ?x2 .")
.append(" ?x2 rr:predicateObjectMap ?x3 . ")
.append(" ?x3 rr:objectMap/rr:column ?column . ?x3 rr:predicate ?class .")
.append(" } }");
if (graphName != null && !graphName.trim().isEmpty()) {
query.append(" } ");
}
logger.info("Query: " + query.toString());
String sData =
TripleStoreUtil.invokeSparqlQuery(
query.toString(), TripleStoreUtil.defaultModelsRepoUrl, "application/json", null);
if (sData == null | sData.isEmpty()) {
logger.error("Empty response object from query : " + query);
}
HashMap<String, String> cols = new HashMap<String, String>();
try {
JSONObject obj1 = new JSONObject(sData);
JSONArray arr = obj1.getJSONObject("results").getJSONArray("bindings");
for (int i = 0; i < arr.length(); i++) {
String colName = arr.getJSONObject(i).getJSONObject("column").getString("value");
String colValue = arr.getJSONObject(i).getJSONObject("class").getString("value");
if (cols.containsKey(colName)) {
logger.error("Duplicate Column <-> property mapping. " + colName + " <=> " + colValue);
} else {
cols.put(colName, colValue);
}
}
} catch (Exception e2) {
logger.error("Error in parsing json response", e2);
}
logger.info("Total Columns fetched : " + cols.size());
final HashMap<String, String> columns = cols;
return new UpdateContainer(
new AbstractUpdate() {
@Override
public void generateJson(String prefix, PrintWriter pw, VWorkspace vWorkspace) {
JSONObject obj = new JSONObject();
try {
Iterator<String> itr = columns.keySet().iterator();
JSONArray colList = new JSONArray();
while (itr.hasNext()) {
JSONObject o = new JSONObject();
String k = itr.next();
o.put("name", k);
o.put("url", columns.get(k));
colList.put(o);
}
obj.put("updateType", "FetchColumnUpdate");
obj.put("columns", colList);
obj.put("rootId", nodeId);
pw.println(obj.toString());
} catch (JSONException e) {
logger.error("Error occurred while fetching worksheet properties!", e);
}
}
});
} catch (Exception e) {
String msg = "Error occured while fetching columns!";
logger.error(msg, e);
return new UpdateContainer(new ErrorUpdate(msg));
}
}