public void map(LongWritable key, Text value, Context context)
throws IOException, InterruptedException {
String strId = "";
String strBody = "";
// Parse the xml and read data (page id and article body)
// Using XOM library
Builder builder = new Builder();
try {
Document doc = builder.build(value.toString(), null);
Nodes nodeId = doc.query("//eecs485_article_id");
strId = nodeId.get(0).getChild(0).getValue();
Nodes nodeBody = doc.query("//eecs485_article_body");
strBody = nodeBody.get(0).getChild(0).getValue();
} catch (ParsingException ex) {
System.out.println("Not well-formed.");
System.out.println(ex.getMessage());
} catch (IOException ex) {
System.out.println("io exception");
}
// Tokenize document body
Pattern pattern = Pattern.compile("\\w+");
Matcher matcher = pattern.matcher(strBody);
while (matcher.find()) {
// Write the parsed token
// key = term, docid value = 1
context.write(new Text(matcher.group() + "," + strId), one);
}
}
private Collection<ConnectableDefinition> loadConnectableDefs(File connectableDefs) {
Collection<ConnectableDefinition> defs = new HashSet<ConnectableDefinition>();
try {
Builder parser = new Builder();
Document doc = parser.build(connectableDefs);
Element root = doc.getRootElement();
Elements definitions = root.getChildElements();
for (int i = 0; i < definitions.size(); i++) {
Element definition = definitions.get(i);
String id = definition.getAttributeValue("id");
String pinCount = definition.getAttributeValue("pins");
String type = definition.getAttributeValue("type");
ConnectableDefinition d = new ConnectableDefinition(id, type, Integer.parseInt(pinCount));
Elements pins = definition.getChildElements();
for (int j = 0; j < pins.size(); j++) {
Element pinElement = pins.get(j);
String pinNumber = pinElement.getAttributeValue("number");
String pinName = pinElement.getAttributeValue("name");
d.addPin(Integer.parseInt(pinNumber), pinName);
}
defs.add(d);
}
} catch (ParsingException ex) {
System.err.println("malformed XML file : " + ex.getMessage());
} catch (IOException ex) {
System.err.println("io error : " + ex.getMessage());
}
return defs;
}
private FogBugzCommunicationException parsingError(ParsingException e, String url) {
// XOM catches runtime exceptions and wraps them as parsing errors. OperationCanceledException
// isn't error though,
// so we ignore parsing exception, and rethrow original operation cancelled
if (e.getCause() instanceof OperationCanceledException) {
throw (OperationCanceledException) e.getCause();
}
return new FogBugzCommunicationException("Cannot parse FogBugz response", e, url);
}
protected ComponentSet loadSet(File componentsDef, File connectionsDef) {
ComponentSet set = null;
// for collecting all connectables
Map<String, Connectable> connectables = new HashMap<String, Connectable>();
try {
// open the components.xml file
Builder builder = new Builder();
Document doc = builder.build(componentsDef);
Element componentsRoot = doc.getRootElement();
int rows = Integer.parseInt(componentsRoot.getAttributeValue("rows"));
int cols = Integer.parseInt(componentsRoot.getAttributeValue("cols"));
boolean autoLocate = Boolean.parseBoolean(componentsRoot.getAttributeValue("autoLocate"));
// add connectables (components need to be located in the set,
// endpoints are not so they are just added to the connectables map
Elements componentElements = componentsRoot.getChildElements();
if (autoLocate) {
set = addComponentsWithAutoLocate(connectables, rows, cols, componentElements);
} else {
set = addComponents(connectables, rows, cols, componentElements);
}
doc = builder.build(connectionsDef);
Element connectionsRoot = doc.getRootElement();
// add connections
Elements connections = connectionsRoot.getChildElements();
for (int i = 0; i < connections.size(); i++) {
Element c = connections.get(i);
String from = c.getAttributeValue("from");
String to = c.getAttributeValue("to");
String fromPinLabel = c.getAttributeValue("fromPin");
String toPinLabel = c.getAttributeValue("toPin");
Connectable fromComp = connectables.get(from);
Connectable toComp = connectables.get(to);
Collection<Pin> fromPins = fromComp.getPins(fromPinLabel);
Collection<Pin> toPins = toComp.getPins(toPinLabel);
Connection con = new Connection(fromComp, fromPins, toComp, toPins);
set.addConnection(con);
}
} catch (ParsingException ex) {
System.err.println("malformed XML file : " + ex.getMessage());
} catch (IOException ex) {
System.err.println("io error : " + ex.getMessage());
}
return set;
}
@Override
protected List<AlignmentFile> getAlignmentFiles(int currentIter) {
// sort input file alphabetically to look nicer
File inputDirectory = new File(this.inputDirectory);
File[] listOfFiles = inputDirectory.listFiles();
Arrays.sort(listOfFiles, new NaturalOrderFilenameComparator());
List<AlignmentFile> alignmentDataList = new ArrayList<AlignmentFile>();
List<Feature> allFeatures = new ArrayList<Feature>();
// load feature data
for (int i = 0; i < listOfFiles.length; i++) {
if (listOfFiles[i].isFile()) {
File myFile = listOfFiles[i];
String filename = myFile.getName();
String path = myFile.getPath();
String extension = filename.substring(filename.lastIndexOf('.') + 1);
// ignore other crap files in the directory
if (!"txt".equals(extension)) {
continue;
}
List<Feature> features = new ArrayList<Feature>();
try {
features = this.loadFeatures(path);
} catch (ValidityException e) {
e.printStackTrace();
} catch (ParsingException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
AlignmentFile alignmentData = new AlignmentFile(i, myFile, features);
if (verbose) {
System.out.println(
"Load " + filename + " with " + alignmentData.getFeaturesCount() + " features");
}
alignmentDataList.add(alignmentData);
allFeatures.addAll(alignmentData.getFeatures());
}
}
this.alignmentFiles = alignmentDataList;
return alignmentDataList;
}
public static void main(String[] args) {
if (args.length <= 0) {
System.out.println("Usage: java nu.xom.samples.PureValidator URL");
return;
}
try {
Builder parser = new Builder(true, new MinimalNodeFactory());
parser.build(args[0]);
System.out.println(args[0] + " is valid.");
} catch (ValidityException ex) {
System.out.println(args[0] + " is not valid.");
System.out.println(ex.getMessage());
System.out.println(" at line " + ex.getLineNumber() + ", column " + ex.getColumnNumber());
} catch (ParsingException ex) {
System.out.println(args[0] + " is not well-formed.");
System.out.println(ex.getMessage());
System.out.println(" at line " + ex.getLineNumber() + ", column " + ex.getColumnNumber());
} catch (IOException ex) {
System.out.println("Due to an IOException, the parser could not check " + args[0]);
}
}
public static SaxonXQueryExpression.Result evaluateXQuery(
final SaxonXQueryExpression xquery,
Object context,
Map<String, Object> parameterValues,
final RowProcessor processor,
CommandContext commandContext)
throws TeiidProcessingException, TeiidComponentException {
DynamicQueryContext dynamicContext = new DynamicQueryContext(xquery.config);
SaxonXQueryExpression.Result result = new SaxonXQueryExpression.Result();
try {
try {
for (Map.Entry<String, Object> entry : parameterValues.entrySet()) {
Object value = entry.getValue();
if (value instanceof SQLXML) {
value = XMLSystemFunctions.convertToSource(value);
result.sources.add((Source) value);
value = wrapStax((Source) value, xquery.getConfig());
} else if (value instanceof java.util.Date) {
value = XMLSystemFunctions.convertToAtomicValue(value);
} else if (value instanceof BinaryType) {
value = new HexBinaryValue(((BinaryType) value).getBytesDirect());
}
dynamicContext.setParameter(entry.getKey(), value);
}
} catch (TransformerException e) {
throw new TeiidProcessingException(QueryPlugin.Event.TEIID30148, e);
}
if (context != null) {
Source source = XMLSystemFunctions.convertToSource(context);
result.sources.add(source);
source = wrapStax(source, xquery.getConfig());
if (xquery.contextRoot != null) {
// create our own filter as this logic is not provided in the free saxon
ProxyReceiver filter = new PathMapFilter(xquery.contextRoot);
AugmentedSource sourceInput = AugmentedSource.makeAugmentedSource(source);
sourceInput.addFilter(filter);
source = sourceInput;
// use streamable processing instead
if (xquery.streamingPath != null && processor != null) {
if (LogManager.isMessageToBeRecorded(LogConstants.CTX_DQP, MessageLevel.DETAIL)) {
LogManager.logDetail(
LogConstants.CTX_DQP,
"Using stream processing for evaluation of",
xquery.xQueryString); // $NON-NLS-1$
}
// set to non-blocking in case default expression evaluation blocks
boolean isNonBlocking = commandContext.isNonBlocking();
commandContext.setNonBlocking(true);
final StreamingTransform myTransform =
new StreamingTransform() {
public Nodes transform(Element elem) {
processor.processRow(XQueryEvaluator.wrap(elem, xquery.config));
return NONE;
}
};
Builder builder =
new Builder(
new SaxonReader(xquery.config, sourceInput),
false,
new StreamingPathFilter(xquery.streamingPath, xquery.namespaceMap)
.createNodeFactory(null, myTransform));
try {
// the builder is hard wired to parse the source, but the api will throw an exception
// if the stream is null
builder.build(FAKE_IS);
return result;
} catch (ParsingException e) {
if (e.getCause() instanceof TeiidRuntimeException) {
RelationalNode.unwrapException((TeiidRuntimeException) e.getCause());
}
throw new TeiidProcessingException(
QueryPlugin.Event.TEIID30151,
e,
QueryPlugin.Util.gs(QueryPlugin.Event.TEIID30151));
} catch (IOException e) {
throw new TeiidProcessingException(
QueryPlugin.Event.TEIID30151,
e,
QueryPlugin.Util.gs(QueryPlugin.Event.TEIID30151));
} finally {
if (!isNonBlocking) {
commandContext.setNonBlocking(false);
}
}
}
}
DocumentInfo doc;
try {
doc = xquery.config.buildDocument(source);
} catch (XPathException e) {
throw new TeiidProcessingException(
QueryPlugin.Event.TEIID30151, e, QueryPlugin.Util.gs(QueryPlugin.Event.TEIID30151));
}
dynamicContext.setContextItem(doc);
}
try {
result.iter = xquery.xQuery.iterator(dynamicContext);
return result;
} catch (TransformerException e) {
throw new TeiidProcessingException(
QueryPlugin.Event.TEIID30152, e, QueryPlugin.Util.gs(QueryPlugin.Event.TEIID30152));
}
} finally {
if (result.iter == null) {
result.close();
}
}
}
/**
* Removes a model. Removes extension and any files.
*
* @param model
*/
public void removeModel(IDSTest model, String pluginID) {
// Remove from DSBusinessModel
dsBusinessModel.getTests().remove(model);
for (Endpoint ep : dsBusinessModel.getEndpoints()) {
if (ep.getTests() != null) {
ep.getTests().remove(model);
logger.debug("Removed model " + model.getName() + " from EP " + ep.getName());
}
}
// Remove extensions in models.container plugin
// =============================================
File pluginXMLfile;
try {
pluginXMLfile = new File(FileUtil.getFilePath("plugin.xml", pluginID));
Builder parser = new Builder();
Document doc = parser.build(pluginXMLfile);
Element root = doc.getRootElement();
Element extension = null;
// Find extension in plugin.xml, if exists
Elements existingExtensions = root.getChildElements("extension");
if (existingExtensions != null && existingExtensions.size() > 0) {
for (int i = 0; i < existingExtensions.size(); i++) {
extension = existingExtensions.get(i);
// If exists a model with same name, remove it
Elements existingTests = extension.getChildElements("test");
if (existingTests != null && existingTests.size() > 0) {
for (int j = 0; j < existingTests.size(); j++) {
Element test = existingTests.get(j);
String testName = test.getAttribute("name").getValue();
// Remove spaces included by XML serialization
while (testName.contains(" ")) testName = testName.replace(" ", " ");
if (model.getName().equals(testName)) {
test.getParent().removeChild(test);
logger.debug("Removing existing model extension: " + model.getName());
// Also remove the files
Elements resources = test.getChildElements("resource");
for (int rescnt = 0; rescnt < resources.size(); rescnt++) {
Element resource = resources.get(rescnt);
String path = resource.getAttribute("path").getValue();
try {
File reFile = new File(FileUtil.getFilePath(path, pluginID));
if (reFile.exists()) {
logger.debug("Removing file: " + reFile);
reFile.delete();
} else logger.debug("Unable to locate file to remove: " + path);
} catch (Exception e) {
logger.error("Problems removing file: " + path);
}
}
}
}
}
}
}
// Serialize the updated plugin.xml to file
Serializer serializer = new Serializer(new FileOutputStream(pluginXMLfile));
serializer.setIndent(4);
serializer.setMaxLength(64);
serializer.write(doc);
} catch (IllegalArgumentException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} catch (ValidityException e) {
e.printStackTrace();
} catch (ParsingException e) {
e.printStackTrace();
}
}
