public void doRFileEvaluate(final IScope scope, final IContainer param) {
int size = param.length(scope);
// if ( size == 0 ) { throw GamaRuntimeException.error("Missing Parameter Exception", scope); }
final String RFile = getPath();
try {
// Call R
RCaller caller = new RCaller();
String RPath = GamaPreferences.LIB_R.value(scope).getPath();
caller.setRscriptExecutable(RPath);
double[] vectorParam = new double[param.length(scope)];
int k = 0;
for (Object o : param.iterable(scope)) {
vectorParam[k++] = Cast.asFloat(scope, o);
}
RCode c = new RCode();
// Adding the parameters
c.addDoubleArray("vectorParam", vectorParam);
// Adding the codes in file
List<String> R_statements = new ArrayList<String>();
// tmthai.begin----------------------------------------------------------------------------
String fullPath = FileUtils.constructAbsoluteFilePath(scope, RFile, true);
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.RScript:" + RPath);
GuiUtils.debug("Stats.R_compute_param.Param:" + vectorParam.toString());
GuiUtils.debug("Stats.R_compute_param.RFile:" + RFile);
GuiUtils.debug("Stats.R_compute_param.fullPath:" + fullPath);
}
// FileReader fr = new FileReader(RFile);
FileReader fr = new FileReader(fullPath);
// tmthai.end----------------------------------------------------------------------------
BufferedReader br = new BufferedReader(fr);
String statement;
while ((statement = br.readLine()) != null) {
c.addRCode(statement);
R_statements.add(statement);
// java.lang.System.out.println(statement);
}
br.close();
fr.close();
caller.setRCode(c);
GamaMap<String, IList> result = GamaMapFactory.create(Types.STRING, Types.LIST);
String var = computeVariable(R_statements.get(R_statements.size() - 1).toString());
caller.runAndReturnResult(var);
// DEBUG:
// java.lang.System.out.println("Name: '" + R_statements.length(scope) + "'");
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.R_statements.length: '" + R_statements.size() + "'");
}
for (String name : caller.getParser().getNames()) {
String[] results = null;
results = caller.getParser().getAsStringArray(name);
// java.lang.System.out.println("Name: '" + name + "'");
if (DEBUG) {
GuiUtils.debug(
"Stats.R_compute_param.caller.Name: '"
+ name
+ "' length: "
+ results.length
+ " - Value: "
+ results.toString());
}
result.put(name, GamaListFactory.create(scope, Types.NO_TYPE, results));
}
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.return:" + result.serialize(false));
}
setBuffer(result);
} catch (Exception ex) {
throw GamaRuntimeException.error("RCallerExecutionException " + ex.getMessage(), scope);
}
}
private Integer seekToSubColumn(
CFMetaData metadata,
FileDataInput file,
ByteBuffer sblockId,
List<IndexHelper.IndexInfo> indexList)
throws IOException {
file.readInt(); // column count
/* get the various column ranges we have to read */
AbstractType comparator = metadata.comparator;
int index = IndexHelper.indexFor(sblockId, indexList, comparator, false);
if (index == indexList.size()) return null;
IndexHelper.IndexInfo indexInfo = indexList.get(index);
if (comparator.compare(sblockId, indexInfo.firstName) < 0) return null;
FileMark mark = file.mark();
FileUtils.skipBytesFully(file, indexInfo.offset);
while (file.bytesPastMark(mark) < indexInfo.offset + indexInfo.width) {
Integer dataLength = isSubBlockFound(metadata, file, sblockId);
if (dataLength == null) return null;
if (dataLength < 0) continue;
return dataLength;
}
return null;
}
private Class<?> findClassInComponents(final String name) throws ClassNotFoundException {
final String classFilename = this.getClassFilename(name);
final Enumeration<File> e = this.pathComponents.elements();
while (e.hasMoreElements()) {
final File pathComponent = e.nextElement();
InputStream stream = null;
try {
stream = this.getResourceStream(pathComponent, classFilename);
if (stream != null) {
this.log("Loaded from " + pathComponent + " " + classFilename, 4);
return this.getClassFromStream(stream, name, pathComponent);
}
continue;
} catch (SecurityException se) {
throw se;
} catch (IOException ioe) {
this.log(
"Exception reading component " + pathComponent + " (reason: " + ioe.getMessage() + ")",
3);
} finally {
FileUtils.close(stream);
}
}
throw new ClassNotFoundException(name);
}
/*
* Set up the platform binary download and get it ready to run the tests.
* This method is not intended to be called by clients, it will be called
* automatically when the clients use a ReconcilerTestSuite. If the executable isn't
* found on the file-system after the call, then we fail.
*/
public void initialize() throws Exception {
initialized = false;
File file = getPlatformZip();
output = getUniqueFolder();
toRemove.add(output);
// for now we will exec to un-tar archives to keep the executable bits
if (file.getName().toLowerCase().endsWith(".zip")) {
try {
FileUtils.unzipFile(file, output);
} catch (IOException e) {
fail("0.99", e);
}
} else {
untar("1.0", file);
}
File exe = new File(output, getExeFolder() + "eclipse.exe");
if (!exe.exists()) {
exe = new File(output, getExeFolder() + "eclipse");
if (!exe.exists())
fail(
"Executable file: "
+ exe.getAbsolutePath()
+ "(or .exe) not found after extracting: "
+ file.getAbsolutePath()
+ " to: "
+ output);
}
initialized = true;
}
/** Creates a .gitignore file into the working directory */
private void createGitIgnoreFile() {
/**
* create .gitignore file as in
* https://github.com/cloudspokes/jenkins-test/blob/master/.gitignore if no filenames are give,
* creates an empty one (if .gitignore file does not already exists). If .gitfile present,
* appends to the end.
*/
File gitIgnore = new File(this.workingFolderPath.concat("/.gitignore"));
FileUtils.writeToFile(gitIgnore, ignoreList, true);
}
protected ModelAndView onSubmit(
HttpServletRequest request,
HttpServletResponse response,
Object command,
BindException errors)
throws ServletException, IOException, Exception {
// cast the bean. i only care about the File property in this controller
UploadMasterBean bean = (UploadMasterBean) command;
MultipartFile multipartFile = bean.getFile();
if (multipartFile != null) {
System.out.println("name " + multipartFile.getOriginalFilename());
System.out.println("size " + multipartFile.getSize());
File fileOut = new File(FileUtils.createTempDir(), multipartFile.getOriginalFilename());
System.out.println("File written to " + fileOut.getCanonicalPath());
multipartFile.transferTo(fileOut);
String path = fileOut.getCanonicalPath();
String extension = FileUtils.getFileExtension(path);
if (("png".equals(extension))
|| ("PNG".equals(extension))
|| ("jpg".equals(extension))
|| ("JPG".equals(extension))
|| ("gif".equals(extension))
|| ("GIF".equals(extension))) {
// TODO check and warn if this isn't transparent. Alpha?
catalogManager.addWatermark(fileOut);
} else {
System.out.println(path + " not imported.");
}
}
// return new ModelAndView("uploadResults", "model", model);
return new ModelAndView("redirect:listWatermarks.html");
}
public void uploadAttachments(JiraTickets tickets)
throws ExecutionException, InterruptedException, IOException {
for (JiraTicket t : tickets) {
Promise<Issue> issuePromise = issueRestClient.getIssue(t.getId());
Issue i = issuePromise.get();
File rollback = t.getRollback();
File hotfix = t.getHotfix();
if (rollback != null && rollback.canRead()) {
issueRestClient.addAttachment(
i.getAttachmentsUri(), FileUtils.openInputStream(rollback), rollback.getName());
}
if (hotfix != null && hotfix.canRead()) {
issueRestClient.addAttachment(
i.getAttachmentsUri(), FileUtils.openInputStream(hotfix), hotfix.getName());
}
}
}
public void checkPermission(
ExtractorLayerRequest request, String secureHost, String username, String roles)
throws IOException {
URL capabilitiesURL = request.capabilitiesURL("WFS", "1.0.0");
final HttpClientBuilder httpClientBuilder = HttpClientBuilder.create();
httpClientBuilder.setUserAgent(this.userAgent);
HttpClientContext localContext = HttpClientContext.create();
final HttpHost httpHost =
new HttpHost(
capabilitiesURL.getHost(), capabilitiesURL.getPort(), capabilitiesURL.getProtocol());
HttpGet get = new HttpGet(capabilitiesURL.toExternalForm());
if (username != null
&& (secureHost.equalsIgnoreCase(request._url.getHost())
|| "127.0.0.1".equalsIgnoreCase(request._url.getHost())
|| "localhost".equalsIgnoreCase(request._url.getHost()))) {
LOG.debug(
"WfsExtractor.checkPermission - Secured Server: adding username header and role headers to request for checkPermission");
addImpersonateUserHeaders(username, roles, get);
enablePreemptiveBasicAuth(
capabilitiesURL,
httpClientBuilder,
localContext,
httpHost,
_adminUsername,
_adminPassword);
} else {
// use a user agent that does *not* trigger basic auth on remote server
httpClientBuilder.setUserAgent("Apache-HttpClient");
LOG.debug("WfsExtractor.checkPermission - Non Secured Server");
}
final CloseableHttpClient httpclient = httpClientBuilder.build();
String capabilities =
FileUtils.asString(
httpclient.execute(httpHost, get, localContext).getEntity().getContent());
Pattern regex =
Pattern.compile(
"(?m)<FeatureType[^>]*>(\\\\n|\\s)*<Name>\\s*(\\w*:)?"
+ Pattern.quote(request._layerName)
+ "\\s*</Name>");
boolean permitted = regex.matcher(capabilities).find();
if (!permitted) {
throw new SecurityException(
"User does not have sufficient privileges to access the Layer: "
+ request._layerName
+ ". \n\nCapabilities: "
+ capabilities);
}
}
static {
FILE_UTILS = FileUtils.getFileUtils();
AntClassLoader.pathMap = Collections.synchronizedMap(new HashMap<String, String>());
AntClassLoader.subClassToLoad = null;
CONSTRUCTOR_ARGS = new Class[] {ClassLoader.class, Project.class, Path.class, Boolean.TYPE};
if (JavaEnvUtils.isAtLeastJavaVersion("1.5")) {
try {
AntClassLoader.subClassToLoad =
Class.forName("org.apache.tools.ant.loader.AntClassLoader5");
} catch (ClassNotFoundException ex) {
}
}
}
/** Create the working folder (later deleted) */
private void createWorkingFolder() throws RuntimeException {
if (this.workingFolder == null
&& (this.workingFolderPath == null || this.workingFolderPath.equals("")))
throw new RuntimeException("Class needs a valid working folder!");
if (this.workingFolder == null) {
this.workingFolder = new File(this.workingFolderPath);
} else {
// sanitize working folder. If it exists and is a directory, delete
// it. If it is a file, refuse to continue.
if (this.workingFolder.exists()) {
if (this.workingFolder.isFile()) {
throw new RuntimeException("Working folder exists, and is a file!");
}
if (this.workingFolder.isDirectory()) {
Logger.log("Deleting existing working directory.");
FileUtils.deleteFolder(this.workingFolder);
}
}
}
// create temporary directory for the local repository...
this.workingFolder = FileUtils.createFolder(this.workingFolder);
}
/*
* Copy the bundle with the given id to the specified location. (location
* is parent directory)
*/
public void copyBundle(String bundlename, File source, File destination) throws IOException {
if (destination == null) destination = output;
destination = new File(destination, "eclipse/plugins");
if (source == null) {
Bundle bundle = TestActivator.getBundle(bundlename);
if (bundle == null) {
throw new IOException("Could not find: " + bundlename);
}
String location = bundle.getLocation();
if (location.startsWith("reference:")) location = location.substring("reference:".length());
source = new File(FileLocator.toFileURL(new URL(location)).getFile());
}
destination = new File(destination, source.getName());
if (destination.exists()) return;
FileUtils.copy(source, destination, new File(""), false);
// if the target of the copy doesn't exist, then signal an error
assertTrue("Unable to copy " + source + " to " + destination, destination.exists());
}
public static void main(String[] args) {
Debug.enableAll();
String HEADER =
"<HEADER>"
+ "<REQUEST value=\"LSR_ORDER\"/>"
+ "<SUB_REQUEST value=\"loop\"/>"
+ "<SUPPLIER value=\"VZE\"/>"
+ "</HEADER>";
RequestHandlerClient sr = null;
try {
String xml = FileUtils.readFile(args[0]);
MessageProcessorContext ctx = new MessageProcessorContext();
ctx.set("NF_HEADER_LOCATION_PROP", HEADER);
sr = new RequestHandlerClient();
sr.serverName = "Nightfire.Router";
NVPair[] result = sr.process(ctx, new MessageObject((Object) xml));
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Checks if the current column is the one we are looking for
*
* @param metadata
* @param file
* @param sblockId
* @return if > 0 the length to read from current file offset. if -1 not relevent. if null out of
* bounds
*/
private Integer isSubBlockFound(CFMetaData metadata, FileDataInput file, ByteBuffer sblockId)
throws IOException {
ByteBuffer name = ByteBufferUtil.readWithShortLength(file);
// Stop if we've gone too far (return null)
if (metadata.comparator.compare(name, sblockId) > 0) return null;
// verify column type;
int b = file.readUnsignedByte();
// skip ts (since we know block ids are unique)
long ts = file.readLong();
int sblockLength = file.readInt();
if (!name.equals(sblockId)
|| (b & ColumnSerializer.DELETION_MASK) != 0
|| (b & ColumnSerializer.EXPIRATION_MASK) != 0) {
FileUtils.skipBytesFully(file, sblockLength);
return -1;
}
return sblockLength;
}
/**
* Save the document to a file.
*
* @see #write
*/
public boolean save(String filename) {
try {
setFilename(filename);
// write to tmp file
File tmpfile = File.createTempFile("gwb", null);
write(new FileOutputStream(tmpfile));
// copy to dest file and delete tmp file
FileUtils.copy(tmpfile, new File(filename));
tmpfile.delete();
//
//
fireDocumentInit();
return true;
} catch (Exception e) {
LogUtils.report(e);
return false;
}
}
public static void main(String[] args) {
Debug.enable(Debug.UNIT_TEST);
Debug.enable(Debug.BENCHMARK);
Debug.showLevels();
if (args.length != 3) {
Debug.log(
Debug.ALL_ERRORS,
"UnBatcher: USAGE: " + " jdbc:oracle:thin:@192.168.164.238:1521:e911 e911 e911 ");
return;
}
try {
DBInterface.initialize(args[0], args[1], args[2]);
} catch (DatabaseException e) {
Debug.log(
Debug.MAPPING_ERROR,
"UnBatcher: " + "Database initialization failure: " + e.getMessage());
}
Splitter spl = new Splitter();
try {
MessageProcessorContext mpx = new MessageProcessorContext();
mpx.set("FileName", "MANS9999");
String s = FileUtils.readFile("D:\\Response\\DECCCORR.txt");
System.out.println("length----------->>>>>" + s.length());
MessageObject msob = new MessageObject();
msob.set(s);
spl.initialize("E911BATCHER", "FAX_MESSAGE_SPLITTER");
spl.process(mpx, msob);
} catch (Exception ex) {
System.out.println(ex.getMessage());
}
}
/** Deletes the working folder */
private void cleanupWorkingFolder() {
// cleanup temporary folder...
FileUtils.deleteFolder(this.workingFolder);
}
private void editFile(ClientServices clientServices, File file) throws IOException {
addBaserevEntry(clientServices, file);
FileUtils.copyFile(file, EditCommand.getEditBackupFile(file));
FileUtils.setFileReadOnly(file, false);
}
/**
* Process one file.
*
* <p>\u0040param xmlFileName Input file name to check for part of speech/lemma mismatches..
*/
protected static void processOneFile(String xmlFileName) {
try {
// Report document being processed.
System.out.println(
"(" + ++currentDocNumber + "/" + docsToProcess + ") " + "processing " + xmlFileName);
// Create filter to strip <w> and <c>
// elements.
XMLFilter filter = new StripAllWordElementsFilter(XMLReaderFactory.createXMLReader());
// Strip path from input file name.
String strippedFileName = FileNameUtils.stripPathName(xmlFileName);
strippedFileName = FileNameUtils.changeFileExtension(strippedFileName, "");
// Generate output file name.
String xmlOutputFileName =
new File(outputDirectoryName, strippedFileName + ".xml").getAbsolutePath();
// Make sure output directory exists.
FileUtils.createPathForFile(xmlOutputFileName);
// Copy input xml to output xml,
// stripping <w> and <c> elements.
new FilterAdornedFile(xmlFileName, xmlOutputFileName, filter);
// Read it back and fix spacing.
String fixedXML = FileUtils.readTextFile(xmlOutputFileName, "utf-8");
fixedXML = fixedXML.replaceAll("(\\s+)", " ");
fixedXML = fixedXML.replaceAll(" ([\\.?!,;:\\)])", "\u00241");
fixedXML = fixedXML.replaceAll("\\( ", "(");
fixedXML = fixedXML.replaceAll("\u00b6 ", "\u00b6");
fixedXML = fixedXML.replaceAll("__NS1:", "");
fixedXML = fixedXML.replaceAll("__NS1", "");
/*
fixedXML =
fixedXML.replaceAll
(
"</__NS1:" ,
""
);
*/
// Emit unadorned XML.
SAXBuilder builder = new SAXBuilder();
Document document = builder.build(new StringReader(fixedXML));
new AdornedXMLWriter(document, xmlOutputFileName);
} catch (Exception e) {
System.out.println(" Error: " + e.getMessage());
e.printStackTrace();
}
}
/**
* If we know in advance that the table is numeric, can optimize a lot... For example, on 9803 x
* 294 table, TableFileLoader.readNumeric takes 6s compared to 12s for WekaMine readFromTable.
*/
public static Instances readNumeric(String fileName, String relationName, String delimiter)
throws Exception {
int numAttributes = FileUtils.fastCountLines(fileName) - 1; // -1 exclude heading.
String[] attrNames = new String[numAttributes];
// Read the col headings and figure out the number of columns in the table..
BufferedReader reader = new BufferedReader(new FileReader(fileName), 4194304);
String line = reader.readLine();
String[] instanceNames = parseColNames(line, delimiter);
int numInstances = instanceNames.length;
System.err.print("reading " + numAttributes + " x " + numInstances + " table..");
// Create an array to hold the data as we read it in...
double dataArray[][] = new double[numAttributes][numInstances];
// Populate the matrix with values...
String valToken = "";
try {
int rowIdx = 0;
while ((line = reader.readLine()) != null) {
String[] tokens = line.split(delimiter, -1);
attrNames[rowIdx] = tokens[0].trim();
for (int colIdx = 0; colIdx < (tokens.length - 1); colIdx++) {
valToken = tokens[colIdx + 1];
double value;
if (valToken.equals("null")) {
value = Instance.missingValue();
} else if (valToken.equals("?")) {
value = Instance.missingValue();
} else if (valToken.equals("NA")) {
value = Instance.missingValue();
} else if (valToken.equals("")) {
value = Instance.missingValue();
// }else value = DoubleParser.lightningParse(valToken); // faster double parser with
// MANY assumptions
} else value = Double.parseDouble(valToken);
dataArray[rowIdx][colIdx] = value;
}
rowIdx++;
}
} catch (NumberFormatException e) {
System.err.println(e.toString());
System.err.println("Parsing line: " + line);
System.err.println("Parsing token: " + valToken);
}
// Set up attributes, which for colInstances will be the rowNames...
FastVector atts = new FastVector();
for (int a = 0; a < numAttributes; a++) {
atts.addElement(new Attribute(attrNames[a]));
}
// Create Instances object..
Instances data = new Instances(relationName, atts, 0);
data.setRelationName(relationName);
System.err.print("creating instances..");
// System.err.println("DEBUG: numAttributes "+numAttributes);
/** ***** CREATE INSTANCES ************* */
// Fill the instances with data...
// For each instance...
for (int c = 0; c < numInstances; c++) {
double[] vals =
new double[data.numAttributes()]; // Even nominal values are stored as double pointers.
for (int r = 0; r < numAttributes; r++) {
double val = dataArray[r][c];
vals[r] = val;
}
// Add the a newly minted instance with those attribute values...
data.add(new Instance(1.0, vals));
}
// System.err.println("DEBUG: data.numInstances: "+data.numInstances());
// System.err.println("DEBUG: data.numAttributes: "+data.numAttributes());
// System.err.println("DEBUG: data.relationNAme"+data.relationName());
System.err.print("add feature names..");
/** ***** ADD FEATURE NAMES ************* */
// takes basically zero time... all time is in previous 2 chunks.
Instances newData = new Instances(data);
newData.insertAttributeAt(new Attribute("ID", (FastVector) null), 0);
int attrIdx = newData.attribute("ID").index(); // Paranoid... should be 0
for (int c = 0; c < numInstances; c++) {
newData.instance(c).setValue(attrIdx, instanceNames[c]);
}
data = newData;
// System.err.println("DEBUG: data.numInstances: "+data.numInstances());
// System.err.println("DEBUG: data.numAttributes: "+data.numAttributes());
return (data);
}
protected void definePackage(
final File container, final String packageName, final Manifest manifest) {
final String sectionName = packageName.replace('.', '/') + "/";
String specificationTitle = null;
String specificationVendor = null;
String specificationVersion = null;
String implementationTitle = null;
String implementationVendor = null;
String implementationVersion = null;
String sealedString = null;
URL sealBase = null;
final Attributes sectionAttributes = manifest.getAttributes(sectionName);
if (sectionAttributes != null) {
specificationTitle = sectionAttributes.getValue(Attributes.Name.SPECIFICATION_TITLE);
specificationVendor = sectionAttributes.getValue(Attributes.Name.SPECIFICATION_VENDOR);
specificationVersion = sectionAttributes.getValue(Attributes.Name.SPECIFICATION_VERSION);
implementationTitle = sectionAttributes.getValue(Attributes.Name.IMPLEMENTATION_TITLE);
implementationVendor = sectionAttributes.getValue(Attributes.Name.IMPLEMENTATION_VENDOR);
implementationVersion = sectionAttributes.getValue(Attributes.Name.IMPLEMENTATION_VERSION);
sealedString = sectionAttributes.getValue(Attributes.Name.SEALED);
}
final Attributes mainAttributes = manifest.getMainAttributes();
if (mainAttributes != null) {
if (specificationTitle == null) {
specificationTitle = mainAttributes.getValue(Attributes.Name.SPECIFICATION_TITLE);
}
if (specificationVendor == null) {
specificationVendor = mainAttributes.getValue(Attributes.Name.SPECIFICATION_VENDOR);
}
if (specificationVersion == null) {
specificationVersion = mainAttributes.getValue(Attributes.Name.SPECIFICATION_VERSION);
}
if (implementationTitle == null) {
implementationTitle = mainAttributes.getValue(Attributes.Name.IMPLEMENTATION_TITLE);
}
if (implementationVendor == null) {
implementationVendor = mainAttributes.getValue(Attributes.Name.IMPLEMENTATION_VENDOR);
}
if (implementationVersion == null) {
implementationVersion = mainAttributes.getValue(Attributes.Name.IMPLEMENTATION_VERSION);
}
if (sealedString == null) {
sealedString = mainAttributes.getValue(Attributes.Name.SEALED);
}
}
if (sealedString != null && sealedString.equalsIgnoreCase("true")) {
try {
sealBase = new URL(FileUtils.getFileUtils().toURI(container.getAbsolutePath()));
} catch (MalformedURLException ex) {
}
}
this.definePackage(
packageName,
specificationTitle,
specificationVersion,
specificationVendor,
implementationTitle,
implementationVersion,
implementationVendor,
sealBase);
}
public void doRFileEvaluate(final IScope scope) {
final String RFile = getPath();
try {
// Call R
RCaller caller = new RCaller();
String RPath = GamaPreferences.LIB_R.value(scope).getPath();
caller.setRscriptExecutable(RPath);
// caller.setRscriptExecutable("\"" + RPath + "\"");
// if(java.lang.System.getProperty("os.name").startsWith("Mac"))
// {
// caller.setRscriptExecutable(RPath);
// }
RCode c = new RCode();
List<String> R_statements = new ArrayList<String>();
// tmthai.begin----------------------------------------------------------------------------
String fullPath = FileUtils.constructAbsoluteFilePath(scope, RFile, true);
if (DEBUG) {
GuiUtils.debug("Stats.R_compute.RScript:" + RPath);
GuiUtils.debug("Stats.R_compute.RFile:" + RFile);
GuiUtils.debug("Stats.R_compute.fullPath:" + fullPath);
}
// FileReader fr = new FileReader(RFile);
FileReader fr = new FileReader(fullPath);
// tmthai.end----------------------------------------------------------------------------
BufferedReader br = new BufferedReader(fr);
String statement;
while ((statement = br.readLine()) != null) {
c.addRCode(statement);
R_statements.add(statement);
// java.lang.System.out.println(statement);
if (DEBUG) {
GuiUtils.debug("Stats.R_compute.statement:" + statement);
}
}
fr.close();
br.close();
caller.setRCode(c);
GamaMap<String, IList> result = GamaMapFactory.create(Types.STRING, Types.LIST);
String var = computeVariable(R_statements.get(R_statements.size() - 1).toString());
caller.runAndReturnResult(var);
for (String name : caller.getParser().getNames()) {
Object[] results = null;
results = caller.getParser().getAsStringArray(name);
// for (int i = 0; i < results.length; i++) {
// java.lang.System.out.println(results[i]);
// }
if (DEBUG) {
GuiUtils.debug(
"Stats.R_compute_param.caller.Name: '"
+ name
+ "' length: "
+ results.length
+ " - Value: "
+ results.toString());
}
result.put(name, GamaListFactory.createWithoutCasting(Types.NO_TYPE, results));
}
if (DEBUG) {
GuiUtils.debug("Stats.R_compute.return:" + result.serialize(false));
}
// return result;
setBuffer(result);
} catch (Exception ex) {
throw GamaRuntimeException.error("RCallerExecutionException " + ex.getMessage(), scope);
}
}
/**
* Retrieves a local subBlock
*
* @param blockId row key
* @param sblockId SubBlock column name
* @param offset inside the sblock
* @return a local sublock
* @throws TException
*/
private LocalBlock getLocalSubBlock(
String subBlockCFName, ByteBuffer blockId, ByteBuffer sblockId, int offset)
throws TException {
DecoratedKey<Token<?>> decoratedKey =
new DecoratedKey<Token<?>>(StorageService.getPartitioner().getToken(blockId), blockId);
Table table = Table.open(cfsKeyspace);
ColumnFamilyStore sblockStore = table.getColumnFamilyStore(subBlockCFName);
Collection<SSTableReader> sstables = sblockStore.getSSTables();
for (SSTableReader sstable : sstables) {
long position = sstable.getPosition(decoratedKey, Operator.EQ);
if (position == -1) continue;
String filename = sstable.descriptor.filenameFor(Component.DATA);
RandomAccessFile raf = null;
int mappedLength = -1;
MappedByteBuffer mappedData = null;
MappedFileDataInput file = null;
try {
raf = new RandomAccessFile(filename, "r");
assert position < raf.length();
mappedLength =
(raf.length() - position) < Integer.MAX_VALUE
? (int) (raf.length() - position)
: Integer.MAX_VALUE;
mappedData = raf.getChannel().map(FileChannel.MapMode.READ_ONLY, position, mappedLength);
file = new MappedFileDataInput(mappedData, filename, 0);
if (file == null) continue;
// Verify key was found in data file
DecoratedKey keyInDisk =
SSTableReader.decodeKey(
sstable.partitioner, sstable.descriptor, ByteBufferUtil.readWithShortLength(file));
assert keyInDisk.equals(decoratedKey)
: String.format("%s != %s in %s", keyInDisk, decoratedKey, file.getPath());
long rowSize = SSTableReader.readRowSize(file, sstable.descriptor);
assert rowSize > 0;
assert rowSize < mappedLength;
Filter bf = IndexHelper.defreezeBloomFilter(file, sstable.descriptor.usesOldBloomFilter);
// verify this column in in this version of the row.
if (!bf.isPresent(sblockId)) continue;
List<IndexHelper.IndexInfo> indexList = IndexHelper.deserializeIndex(file);
// we can stop early if bloom filter says none of the
// columns actually exist -- but,
// we can't stop before initializing the cf above, in
// case there's a relevant tombstone
ColumnFamilySerializer serializer = ColumnFamily.serializer();
try {
ColumnFamily cf =
serializer.deserializeFromSSTableNoColumns(
ColumnFamily.create(sstable.metadata), file);
if (cf.isMarkedForDelete()) continue;
} catch (Exception e) {
e.printStackTrace();
throw new IOException(
serializer
+ " failed to deserialize "
+ sstable.getColumnFamilyName()
+ " with "
+ sstable.metadata
+ " from "
+ file,
e);
}
Integer sblockLength = null;
if (indexList == null) sblockLength = seekToSubColumn(sstable.metadata, file, sblockId);
else sblockLength = seekToSubColumn(sstable.metadata, file, sblockId, indexList);
if (sblockLength == null || sblockLength < 0) continue;
int bytesReadFromStart = mappedLength - (int) file.bytesRemaining();
if (logger.isDebugEnabled())
logger.debug("BlockLength = " + sblockLength + " Availible " + file.bytesRemaining());
assert offset <= sblockLength : String.format("%d > %d", offset, sblockLength);
long dataOffset = position + bytesReadFromStart;
if (file.bytesRemaining() == 0 || sblockLength == 0) continue;
return new LocalBlock(file.getPath(), dataOffset + offset, sblockLength - offset);
} catch (IOException e) {
throw new TException(e);
} finally {
FileUtils.closeQuietly(raf);
}
}
return null;
}
/**
* Check if the Tangara application is executed from a jar file.
*
* @return <code>true</code> if the application is executed from a jar file, <code>false</code>
* otherwise.
*/
public boolean isExecutedFromJAR() {
return FileUtils.isExtension(getTangaraPath(), JAR_FILE_EXT);
}
