I have multiple BLOBs that I want to concat to one another, in order to get one joined BLOB. In the process, the contents of the BLOBs may not be stored in memory.
My first idea was to merge the streams like that:
long size = blobs.get(0).length();
InputStream res = blobs.get(0).getBinaryStream();
for (int i = 1; i < blobs.size(); i++){
res = Stream.concat(res, blobs.get(i).getBinaryStream());
size += blobs.get(i).length();
}
Blob blob = Hibernate.getLobCreator(session).createBlob(res, size);
However, this obviously only works with Java 8 streams (not normal BinaryStreams) - and we use Java 7 anways.
My second idea then was to join the BLOBs by directly writing into its stream:
public Blob joinBlobsForHibernate(final Session session, final List<Blob> blobs) throws SQLException {
final LobCreator lc = Hibernate.getLobCreator(session);
final Blob resBlob = lc.createBlob(new byte[0]);
try {
OutputStream stream = resBlob.setBinaryStream(1);
for (final Blob blob : blobs) {
pipeInputStream(blob.getBinaryStream(), stream);
}
return resBlob;
} catch (IOException | SQLException e){
logger.error("Creating the blob threw an exception", e);
return null;
}
}
(pipeInputStream merely pipes the content of one stream into the other:
private void pipeInputStream (final InputStream is, final OutputStream os) throws IOException {
final int buffSize = 128000;
int n;
final byte[] buff = new byte[buffSize];
while ((n = is.read(buff)) >= 0){
os.write(buff, 0, n);
}
)
This however yields in the following exception:
java.lang.UnsupportedOperationException: Blob may not be manipulated from creating session
And besides, I have the suspicion that the BLOB would still temporarily store the whole content in memory.
As a third try I tried using a custom InputStream:
/**
* Combines multiple streams into one
*/
public class JoinedInputStream extends InputStream {
private List<InputStream> parts;
private List<InputStream> marked;
public JoinedInputStream(final List<InputStream> parts) {
this.parts = parts;
}
#Override
public int read() throws IOException {
int res = -1;
while (res == -1 && parts.size() > 0) {
try {
if ((res = parts.get(0).read()) == -1) {
// The stream is done, so we won't try to read from it again
parts.remove(0);
}
} catch (IOException e) {
e.printStackTrace();
throw e;
}
}
return res;
}
#Override
public synchronized void reset() throws IOException {
parts = new ArrayList<>(marked);
if (parts.size() > 0) {
parts.get(0).reset();
}
}
#Override
public synchronized void mark(final int readlimit) {
marked = new ArrayList<>(parts);
if (marked.size() > 0)
marked.get(0).mark(readlimit);
}
#Override
public boolean markSupported() {
return true;
}
#Override
public void close() throws IOException {
super.close();
for (final InputStream part : parts) {
part.close();
}
parts = new ArrayList<>();
marked = new ArrayList<>();
}
}
The BLOB could then be joined like that (don't mind the unnecessary functions, they have other uses):
#Override
public Blob createBlobForHibernate(final Session session, final InputStream stream, final long length) {
final LobCreator lc = Hibernate.getLobCreator(session);
return lc.createBlob(stream, length);
}
#Override
public Blob createBlobForHibernate(final Session session, final List<InputStream> streams, final long length) {
final InputStream joined = new JoinedInputStream(streams);
return createBlobForHibernate(session, joined, length);
}
#Override
public Blob joinBlobsForHibernate(final Session session, final List<Blob> blobs) throws SQLException {
long length = 0;
List<InputStream> streams = new ArrayList<>(blobs.size());
for (final Blob blob : blobs) {
length += blob.length();
streams.add(blob.getBinaryStream());
}
return createBlobForHibernate(session, streams, length);
}
However, this results in the following error (when persisting the newly created entity with the joined BLOB):
Caused by: java.sql.SQLException: LOB-Lese-/Schreibfunktionen aufgerufen, während ein anderer Lese-/Schreibvorgang ausgeführt wird: getBytes()
at oracle.jdbc.driver.T4CConnection.getBytes(T4CConnection.java:3200)
at oracle.sql.BLOB.getBytes(BLOB.java:391)
at oracle.jdbc.driver.OracleBlobInputStream.needBytes(OracleBlobInputStream.java:166)
... 101 more
Or in English:
Lob read/write functions called while another read/write is in progress: getBytes()
I already tried setting hibernate.temp.use_jdbc_metadata_defaults to false (as suggested in this post) - in fact, we already had this property set beforehand and it didn't help.
Related
I have an app in which I have to read a .txt file so that I can store some values and keep them. This is working pretty well, except for the fact that I want to make those values non-readable or "non-understandable" for external users.
My idea was to convert the file content into Hex or Binary and, in the reading process, change it back to Char. The thing is that I don't have access to methods such as String.Format due to my compiler.
Here's how I'm currently reading and keeping the values:
byte[] buffer = new byte[1024];
int len = myFile.read(buffer);
String data = null;
int i=0;
data = new String(buffer,0,len);
Class to open and manipulate the file:
public class File {
private boolean debug = false;
private FileConnection fc = null;
private OutputStream os = null;
private InputStream is = null;
private String fileName = "example.txt";
private String pathName = "logs/";
final String rootName = "file:///a:/";
public File(String fileName, String pathName) {
super();
this.fileName = fileName;
this.pathName = pathName;
if (!pathName.endsWith("/")) {
this.pathName += "/"; // add a slash
}
}
public boolean isDebug() {
return debug;
}
public void setDebug(boolean debug) {
this.debug = debug;
}
public void write(String text) throws IOException {
write(text.getBytes());
}
public void write(byte[] bytes) throws IOException {
if (debug)
System.out.println(new String(bytes));
os.write(bytes);
}
private FileConnection getFileConnection() throws IOException {
// check if subfolder exists
fc = (FileConnection) Connector.open(rootName + pathName);
if (!fc.exists() || !fc.isDirectory()) {
fc.mkdir();
if (debug)
System.out.println("Dir created");
}
// open file
fc = (FileConnection) Connector.open(rootName + pathName + fileName);
if (!fc.exists())
fc.create();
return fc;
}
/**
* release resources
*/
public void close() {
if (is != null)
try {
is.close();
} catch (IOException e) {
e.printStackTrace();
}
is = null;
if (os != null)
try {
os.close();
} catch (IOException e) {
e.printStackTrace();
}
os = null;
if (fc != null)
try {
fc.close();
} catch (IOException e) {
e.printStackTrace();
}
fc = null;
}
public void open(boolean writeAppend) throws IOException {
fc = getFileConnection();
if (!writeAppend)
fc.truncate(0);
is = fc.openInputStream();
os = fc.openOutputStream(fc.fileSize());
}
public int read(byte[] buffer) throws IOException {
return is.read(buffer);
}
public void delete() throws IOException {
close();
fc = (FileConnection) Connector.open(rootName + pathName + fileName);
if (fc.exists())
fc.delete();
}
}
I would like to know a simple way on how to read this content. Binary or Hex, both would work for me.
So, with some understanding of the question, I believe you're really looking for a form of obfuscation? As mentioned in the comments, the easiest way to do this is likely a form of cipher.
Consider this example implementation of a shift cipher:
Common
int shift = 11;
Writing
// Get the data to be wrote to file.
String data = ...
// cipher the data.
char[] chars = data.toCharArray();
for (int i = 0; i < chars.length; ++i) {
chars[i] = (char)(chars[i] + shift);
}
String cipher = new String(chars);
// Write the data to the cipher file.
...
Reading
// Read the cipher file.
String data = ...
// Decipher the data.
char[] chars = data.toCharArray();
for (int i = 0; i < chars.length; ++i) {
chars[i] = (char)(chars[i] - shift);
}
String decipher = new String(chars);
// Use data as required.
...
Here's an example implementation on Ideone. The output:
Data : I can read this IP 192.168.0.1
Cipher : T+nly+}plo+st~+T[+<D=9<AC9;9<
Decipher: I can read this IP 192.168.0.1
I tried to keep this as low level as possible in order to satisfy the Java 3 requirement.
Note that this is NOT secure by any means. Shift ciphers (like most ciphers in a bubble) are trivial to break by malicious entities. Please do not use this if security is an actual concern.
Your solution is too complex. With java 8, you can try :
String fileName = "configFile.txt";
try (Stream<String> stream = Files.lines(Paths.get(fileName))) {
//TO-DO .Ex
stream.forEach(System.out::println);
} catch (IOException e) {
e.printStackTrace();
}
I use serialization to save some objects into Oracle Blob columns which I then extract and use in the same run or in other runs.
The serialization/deserialization looks like this:
public final class BytesTransformer {
static BytesTransformer btInstance = new BytesTransformer();
private ByteArrayOutputStream bytesOutputStream = new ByteArrayOutputStream();
private ObjectOutputStream objectOutputStream;
private ByteArrayInputStream bytesInputStream;
private ObjectInputStream objectInputStream;
public static BytesTransformer getInstance() {
return btInstance;
}
private void initialiseInputStreams(byte[] bytes) throws IOException {
bytesInputStream = new ByteArrayInputStream(bytes);
objectInputStream = new ObjectInputStream(bytesInputStream);
}
private void initialiseInputStreams(InputStream bytes) throws IOException {
objectInputStream = new ObjectInputStream(bytes);
}
public byte[] getBytes(Serializable sObject) throws IOException {
bytesOutputStream.reset();
objectOutputStream = new ObjectOutputStream(bytesOutputStream);
objectOutputStream.writeObject(sObject);
objectOutputStream.close();
return bytesOutputStream.toByteArray();
}
public Object fromBytes(byte[] dataBytes) throws IOException, ClassNotFoundException {
initialiseInputStreams(dataBytes);
Object sObject = objectInputStream.readObject();
closeInputStreams();
return sObject;
}
public Object fromBytes(InputStream dataBytes) throws IOException, ClassNotFoundException {
initialiseInputStreams(dataBytes);
Object sObject = objectInputStream.readObject();
closeInputStreams();
return sObject;
}
private void closeInputStreams() {
try {
if (objectInputStream != null) {
objectInputStream.close();
}
if (bytesInputStream != null) {
bytesInputStream.close();
}
} catch (IOException ex) {
}
}
To write data to the blob column I use something like this:
PreparedStatement preparedStatement = connection.prepareStatement("UPDATE CONFIGURATION_DEFINITION SET BYTES_DATA=? WHERE NAME=?", ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_UPDATABLE);
preparedStatement.setObject(1, BytesTransformer.getInstance().getBytes(cfgDef));
preparedStatement.setString(2, cfgDef.getName());
preparedStatement.executeUpdate();
To retrieve the data:
public ConfigurationDefinition getConfigurationDefinition(String configName) {
byte[] bytes = null;
String sql = "SELECT BYTES_DATA FROM CONFIGURATION_DEFINITION WHERE NAME = '" + configName + "'";
ResultSet rs = getSQLConnector().executeQueryWithoutNoise(sql);
try {
if (rs == null || !rs.next()) {
return null;
}
Blob blob = rs.getBlob(blobColumnName);
bytes = blob.getBytes(1, (int) blob.length());
} catch (SQLException ex) {
GatewayLogger.error("Unable to extract db records for configuration: " + configName, ex);
return null;
} finally {
getSQLConnector().closeResultSet(rs);
}
ConfigurationDefinition aDefinition = (ConfigurationDefinition) BytesTransformer.getInstance().fromBytes(buffer);
return aDefinition;
}
Most of the time there is no problem, but sometimes (quite rarely) and seemingly with no discernable pattern I get either:
java.io.StreamCorruptedException: invalid type code: <first_byte>
or
java.io.StreamCorruptedException: invalid stream header: <first_four_bytes>
When I get the second error I can usually find the correct header starting a few hundred bytes into the vector.
I should mention that the Oracle schema also holds some AQ JMS Queues which I use to send similarly serialized objects through and on a couple of occasions objects of those types were retrieved from the Oracle table even though there is no way that those two could get mixed up in the code.
I've looked around at discussions about those exceptions and nothing seems to apply to my case. Everything looks to be in order as far as I can tell and the exceptions only pop up very rarely.
Any ideas?
In my servlet I am running a few command line commands in background, I've successfully printed output on console.
My doGet()
public void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException
{
String[] command =
{
"zsh"
};
Process p = Runtime.getRuntime().exec(command);
new Thread(new SyncPipe(p.getErrorStream(), response.getOutputStream())).start();
new Thread(new SyncPipe(p.getInputStream(), response.getOutputStream())).start();
PrintWriter stdin = new PrintWriter(p.getOutputStream());
stdin.println("source ./taxenv/bin/activate");
stdin.println("python runner.py");
stdin.close();
int returnCode = 0;
try {
returnCode = p.waitFor();
}
catch (InterruptedException e) {
e.printStackTrace();
} System.out.println("Return code = " + returnCode);
}
class SyncPipe implements Runnable
{
public SyncPipe(InputStream istrm, OutputStream ostrm) {
istrm_ = istrm;
ostrm_ = ostrm;
}
public void run() {
try
{
final byte[] buffer = new byte[1024];
for (#SuppressWarnings("unused")
int length = 0; (length = istrm_.read(buffer)) != -1; )
{
// ostrm_.write(buffer, 0, length);
((PrintStream) ostrm_).println();
}
}
catch (Exception e)
{
e.printStackTrace();
}
}
private final OutputStream ostrm_;
private final InputStream istrm_;
}
Now, I want to save the ostrm_ to a string or list, and use that inside doGet()
How to achieve this?
==============================EDIT============================
Based on answers below, I've edited my code as follows
int length = 0; (length = istrm_.read(buffer)) != -1; )
{
// ostrm_.write(buffer, 0, length);
String str = IOUtils.toString(istrm_, "UTF-8");
//((PrintStream) ostrm_).println();
System.out.println(str);
}
Now, How do I get the str in runnable class into my doGet()?
You can use Apache Commons IO.
Here is the documentation of IOUtils.toString() from their javadocs
Gets the contents of an InputStream as a String using the specified character encoding. This
method buffers the input internally, so there is no need to use a
BufferedInputStream.
Parameters: input - the InputStream to read from encoding - the
encoding to use, null means platform default Returns: the requested
String Throws: NullPointerException - if the input is null IOException
- if an I/O error occurs
Example Usage:
String str = IOUtils.toString(yourInputStream, "UTF-8");
You can call something like the following:
(EDIT: added also the client calls)
public void run() {
try
{
String out = getAsString(istrm_);
((PrintStream) ostrm_).println(out);
} catch (Exception e) {
e.printStackTrace();
}
}
public static String getAsString(InputStream is) throws Exception {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
int cur = -1;
while((cur = is.read()) != -1 ){
baos.write(cur);
}
return getAsString(baos.toByteArray());
}
public static String getAsString(byte[] arr) throws Exception {
String res = "";
for(byte b : arr){
res+=(char)b;
}
return res;
}
I've got following problem. I have to write small application that connects to pacs and gets images. I decided to use dcm4che toolkit. I've written following code:
public class Dcm4 {
/**
* #param args the command line arguments
*/
public static void main(String[] args) {
// TODO code application logic here
DcmQR dcmqr = new MyDcmQR("server");
dcmqr.setCalledAET("server", true);
dcmqr.setRemoteHost("213.165.94.158");
dcmqr.setRemotePort(104);
dcmqr.getKeys();
dcmqr.setDateTimeMatching(true);
dcmqr.setCFind(true);
dcmqr.setCGet(true);
dcmqr.setQueryLevel(MyDcmQR.QueryRetrieveLevel.IMAGE);
dcmqr.addMatchingKey(Tag.toTagPath("PatientID"),"2011");
dcmqr.addMatchingKey(Tag.toTagPath("StudyInstanceUID"),"1.2.276.0.7230010.3.1.2.669896852.2528.1325171276.917");
dcmqr.addMatchingKey(Tag.toTagPath("SeriesInstanceUID"),"1.2.276.0.7230010.3.1.3.669896852.2528.1325171276.916");
dcmqr.configureTransferCapability(true);
List<DicomObject> result=null;
byte[] imgTab=null;
BufferedImage bImage=null;
try {
dcmqr.start();
System.out.println("started");
dcmqr.open();
System.out.println("opened");
result = dcmqr.query();
System.out.println("queried");
dcmqr.get(result);
System.out.println("List Size = " + result.size());
for(DicomObject dco:result){
System.out.println(dco);
dcmTools.toByteArray(dco);
System.out.println("end parsing");
}
} catch (Exception e) {
System.out.println("error "+e);
}
try{
dcmqr.stop();
dcmqr.close();
}catch (Exception e) {
}
System.out.println("done");
}
}
Everything seems to be fine until I call dcmTools.toByteArray(dco).
Output till calliing toByteArray() looks like this:
List Size = 1
(0008,0052) CS #6 [IMAGE] Query/Retrieve Level
(0008,0054) AE #6 [server] Retrieve AE Title
(0020,000E) UI #54 [1.2.276.0.7230010.3.1.3.669896852.2528.1325171276.916] Series Instance UID
Source of ToByteArray:
public static byte[] toByteArray(DicomObject obj) throws IOException {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
BufferedOutputStream bos = new BufferedOutputStream(baos);
DicomOutputStream dos = new DicomOutputStream(bos);
dos.writeDicomFile(obj);
dos.close();
byte[] data = baos.toByteArray();
return data;
}
After calling toByteArray I got output:
error java.lang.IllegalArgumentException: Missing (0002,0010) Transfer Syntax UID
I,ve found some informations in other forums and it seems like DcmQR.get() method doesn't send imgage data. Is it possible to force DcmQR to do it. I've written that problem is in or with DcmQR.createStorageService() method but I haven't found the solution. Please help me!!!
Hello cneller!
I've made some changes you suggested: I've add setMoveDest and setStoreDestination and DicomObject are stored in destination I've added - it looks great. Then I've tried to write response handler based on FutureDimseRSP which is used in Association.cget method:
public class MyDimseRSP extends DimseRSPHandler implements DimseRSP{
private MyEntry entry = new MyEntry(null, null);
private boolean finished;
private int autoCancel;
private IOException ex;
#Override
public synchronized void onDimseRSP(Association as, DicomObject cmd,
DicomObject data) {
super.onDimseRSP(as, cmd, data);
MyEntry last = entry;
while (last.next != null)
last = last.next;
last.next = new MyEntry(cmd, data);
if (CommandUtils.isPending(cmd)) {
if (autoCancel > 0 && --autoCancel == 0)
try {
super.cancel(as);
} catch (IOException e) {
ex = e;
}
} else {
finished = true;
}
notifyAll();
}
#Override
public synchronized void onClosed(Association as) {
if (!finished) {
// ex = as.getException();
ex = null;
if (ex == null) {
ex = new IOException("Association to " + as.getRemoteAET()
+ " closed before receive of outstanding DIMSE RSP");
}
notifyAll();
}
}
public final void setAutoCancel(int autoCancel) {
this.autoCancel = autoCancel;
}
#Override
public void cancel(Association a) throws IOException {
if (ex != null)
throw ex;
if (!finished)
super.cancel(a);
}
public DicomObject getDataset() {
return entry.command;
}
public DicomObject getCommand() {
return entry.dataset;
}
public MyEntry getEntry() {
return entry;
}
public synchronized boolean next() throws IOException, InterruptedException {
if (entry.next == null) {
if (finished)
return false;
while (entry.next == null && ex == null)
wait();
if (ex != null)
throw ex;
}
entry = entry.next;
return true;
}
}
Here is MyEntry code:
public class MyEntry {
final DicomObject command;
final DicomObject dataset;
MyEntry next;
public MyEntry(DicomObject command, DicomObject dataset) {
this.command = command;
this.dataset = dataset;
}
public DicomObject getCommand() {
return command;
}
public DicomObject getDataset() {
return dataset;
}
public MyEntry getNext() {
return next;
}
public void setNext(MyEntry next) {
this.next = next;
}
}
Then I've retyped get method from Dmcqr as follows:
public void getObject(DicomObject obj, DimseRSPHandler rspHandler)throws IOException, InterruptedException{
TransferCapability tc = selectTransferCapability(qrlevel.getGetClassUids());
MyDimseRSP myRsp=new MyDimseRSP();
if (tc == null)
throw new NoPresentationContextException(UIDDictionary
.getDictionary().prompt(qrlevel.getGetClassUids()[0])
+ " not supported by " + remoteAE.getAETitle());
String cuid = tc.getSopClass();
String tsuid = selectTransferSyntax(tc);
DicomObject key = obj.subSet(MOVE_KEYS);
assoc.cget(cuid, priority, key, tsuid, rspHandler);
assoc.waitForDimseRSP();
}
In second argument in this method I've used an instance of my response handler (MyDimseRSP). And I run my code I got null value of command and dataset of my response handler. In "next" variable only "command" is not null, and od course it's not DicomObject which I need. What I'm doing wrong!!!!
You're going to have to step through the code a bit (including the DCM4CHE toolkit code). I suspect you are using the default response handler, which just counts the number of completed operations, and doesn't actually store the image data from the get command.
Clearly, your for loop, below, is looping over the results of the find operation, not the get (which needs to be handled in the response handler).
for(DicomObject dco:result)
I expect you will have to override the response handler to write your DICOM files appropriately. See also the DcmRcv class for writing DICOM files from the DicomObject you'll receive.
:
From your edits above, I assume you are just trying to get the raw DICOM instance data (not the command that stored it). What about a response handler roughly like:
List<DicomObject> dataList = new ArrayList<DicomObject>();
#Override
public void onDimseRSP(Association as, DicomObject cmd, DicomObject data) {
if( shouldAdd(as, cmd) ) {
dataList.add( data )
}
}
Watch out for large lists, but it should get you the data in memory.
Does anyone know where to find a little how to on using dbpedia spotlight in java or scala? Or could anyone explain how it's done? I can't find any information on this...
The DBpedia Spotlight wiki pages would be a good place to start.
And I believe the installation page has listed the most popular ways (using a jar, or set up a web service) to use the application.
It includes instructions on using the Java/Scala API with your own installation, or calling the Web Service.
There are some additional data needed to be downloaded to run your own server for full service, good time to make a coffee for yourself.
you need download dbpedia spotlight (jar file) after that u can use next two classes ( author pablomendes ) i only make some change .
public class db extends AnnotationClient {
//private final static String API_URL = "http://jodaiber.dyndns.org:2222/";
private static String API_URL = "http://spotlight.dbpedia.org:80/";
private static double CONFIDENCE = 0.0;
private static int SUPPORT = 0;
private static String powered_by ="non";
private static String spotter ="CoOccurrenceBasedSelector";//"LingPipeSpotter"=Annotate all spots
//AtLeastOneNounSelector"=No verbs and adjs.
//"CoOccurrenceBasedSelector" =No 'common words'
//"NESpotter"=Only Per.,Org.,Loc.
private static String disambiguator ="Default";//Default ;Occurrences=Occurrence-centric;Document=Document-centric
private static String showScores ="yes";
#SuppressWarnings("static-access")
public void configiration(double CONFIDENCE,int SUPPORT,
String powered_by,String spotter,String disambiguator,String showScores){
this.CONFIDENCE=CONFIDENCE;
this.SUPPORT=SUPPORT;
this.powered_by=powered_by;
this.spotter=spotter;
this.disambiguator=disambiguator;
this.showScores=showScores;
}
public List<DBpediaResource> extract(Text text) throws AnnotationException {
LOG.info("Querying API.");
String spotlightResponse;
try {
String Query=API_URL + "rest/annotate/?" +
"confidence=" + CONFIDENCE
+ "&support=" + SUPPORT
+ "&spotter=" + spotter
+ "&disambiguator=" + disambiguator
+ "&showScores=" + showScores
+ "&powered_by=" + powered_by
+ "&text=" + URLEncoder.encode(text.text(), "utf-8");
LOG.info(Query);
GetMethod getMethod = new GetMethod(Query);
getMethod.addRequestHeader(new Header("Accept", "application/json"));
spotlightResponse = request(getMethod);
} catch (UnsupportedEncodingException e) {
throw new AnnotationException("Could not encode text.", e);
}
assert spotlightResponse != null;
JSONObject resultJSON = null;
JSONArray entities = null;
try {
resultJSON = new JSONObject(spotlightResponse);
entities = resultJSON.getJSONArray("Resources");
} catch (JSONException e) {
//throw new AnnotationException("Received invalid response from DBpedia Spotlight API.");
}
LinkedList<DBpediaResource> resources = new LinkedList<DBpediaResource>();
if(entities!=null)
for(int i = 0; i < entities.length(); i++) {
try {
JSONObject entity = entities.getJSONObject(i);
resources.add(
new DBpediaResource(entity.getString("#URI"),
Integer.parseInt(entity.getString("#support"))));
} catch (JSONException e) {
LOG.error("JSON exception "+e);
}
}
return resources;
}
}
second class
/**
* #author pablomendes
*/
public abstract class AnnotationClient {
public Logger LOG = Logger.getLogger(this.getClass());
private List<String> RES = new ArrayList<String>();
// Create an instance of HttpClient.
private static HttpClient client = new HttpClient();
public List<String> getResu(){
return RES;
}
public String request(HttpMethod method) throws AnnotationException {
String response = null;
// Provide custom retry handler is necessary
method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
new DefaultHttpMethodRetryHandler(3, false));
try {
// Execute the method.
int statusCode = client.executeMethod(method);
if (statusCode != HttpStatus.SC_OK) {
LOG.error("Method failed: " + method.getStatusLine());
}
// Read the response body.
byte[] responseBody = method.getResponseBody(); //TODO Going to buffer response body of large or unknown size. Using getResponseBodyAsStream instead is recommended.
// Deal with the response.
// Use caution: ensure correct character encoding and is not binary data
response = new String(responseBody);
} catch (HttpException e) {
LOG.error("Fatal protocol violation: " + e.getMessage());
throw new AnnotationException("Protocol error executing HTTP request.",e);
} catch (IOException e) {
LOG.error("Fatal transport error: " + e.getMessage());
LOG.error(method.getQueryString());
throw new AnnotationException("Transport error executing HTTP request.",e);
} finally {
// Release the connection.
method.releaseConnection();
}
return response;
}
protected static String readFileAsString(String filePath) throws java.io.IOException{
return readFileAsString(new File(filePath));
}
protected static String readFileAsString(File file) throws IOException {
byte[] buffer = new byte[(int) file.length()];
#SuppressWarnings("resource")
BufferedInputStream f = new BufferedInputStream(new FileInputStream(file));
f.read(buffer);
return new String(buffer);
}
static abstract class LineParser {
public abstract String parse(String s) throws ParseException;
static class ManualDatasetLineParser extends LineParser {
public String parse(String s) throws ParseException {
return s.trim();
}
}
static class OccTSVLineParser extends LineParser {
public String parse(String s) throws ParseException {
String result = s;
try {
result = s.trim().split("\t")[3];
} catch (ArrayIndexOutOfBoundsException e) {
throw new ParseException(e.getMessage(), 3);
}
return result;
}
}
}
public void saveExtractedEntitiesSet(String Question, LineParser parser, int restartFrom) throws Exception {
String text = Question;
int i=0;
//int correct =0 ; int error = 0;int sum = 0;
for (String snippet: text.split("\n")) {
String s = parser.parse(snippet);
if (s!= null && !s.equals("")) {
i++;
if (i<restartFrom) continue;
List<DBpediaResource> entities = new ArrayList<DBpediaResource>();
try {
entities = extract(new Text(snippet.replaceAll("\\s+"," ")));
System.out.println(entities.get(0).getFullUri());
} catch (AnnotationException e) {
// error++;
LOG.error(e);
e.printStackTrace();
}
for (DBpediaResource e: entities) {
RES.add(e.uri());
}
}
}
}
public abstract List<DBpediaResource> extract(Text text) throws AnnotationException;
public void evaluate(String Question) throws Exception {
evaluateManual(Question,0);
}
public void evaluateManual(String Question, int restartFrom) throws Exception {
saveExtractedEntitiesSet(Question,new LineParser.ManualDatasetLineParser(), restartFrom);
}
}
main()
public static void main(String[] args) throws Exception {
String Question ="Is the Amazon river longer than the Nile River?";
db c = new db ();
c.configiration(0.0, 0, "non", "CoOccurrenceBasedSelector", "Default", "yes");
System.out.println("resource : "+c.getResu());
}
I just add one little fix for your answer.
Your code is running, if you add the evaluate method call:
public static void main(String[] args) throws Exception {
String question = "Is the Amazon river longer than the Nile River?";
db c = new db ();
c.configiration(0.0, 0, "non", "CoOccurrenceBasedSelector", "Default", "yes");
c.evaluate(question);
System.out.println("resource : "+c.getResu());
}
Lamine
In the request method of the second class (AnnotationClient) in Adel's answer, the author Pablo Mendes hasn't finished
TODO Going to buffer response body of large or unknown size. Using getResponseBodyAsStream instead is recommended.
which is an annoying warning that needs to be removed by replacing
byte[] responseBody = method.getResponseBody(); //TODO Going to buffer response body of large or unknown size. Using getResponseBodyAsStream instead is recommended.
// Deal with the response.
// Use caution: ensure correct character encoding and is not binary data
response = new String(responseBody);
with
Reader in = new InputStreamReader(method.getResponseBodyAsStream(), "UTF-8");
StringWriter writer = new StringWriter();
org.apache.commons.io.IOUtils.copy(in, writer);
response = writer.toString();