Java RConnection类代码示例

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
/**
 * Executes an R function (return: String)
 * 
 * @param function
 *        name of the R function
 * @param parameters
 *        array of parameters required by the function
 * 
 *        TODO: make more generic - not just for Strings ...
 */
public static String executeStringFunction(RConnection conn, String function, String[] parameters) {

    try {
        // create request
        String request = "try(" + function + "(";
        for (String parameter : parameters) {
            request += parameter + ",";
        }
        // remove last ","
        request = request.substring(0, request.length() - 1);
        request += "))";
        // execute function
        REXP xp = conn.parseAndEval(request);
        if (xp.inherits("try-error")) {
            close(conn);
            throw new IOException("failed to execute function '" + function + "'; \nrequest: " + request
                    + "; \nError: " + xp.asString());
        }
        String retval = xp.asString();
        return retval;
    }
    catch (Exception e) {
        return null;
    }
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
/**
 * Get an R connection
 * 
 * @param host
 * @param workspace
 * @return {@link RConnection} rConnection - a connection to RServer
 */
private static RConnection getRServeConnection(String host, String workspace) {

    try {
        // establish R connection
        RConnection conn = new RConnection(host);
        // check connection
        if (conn == null || !conn.isConnected())
            throw new IOException("Failed to establish RServe connection");

        // set workspace
        if (workspace != null) {
            REXP xp = conn.parseAndEval("try(setwd('" + workspace.replace("\\", "\\\\") + "'))");
            if (xp.inherits("try-error"))
                throw new IOException("Failed to load R workspace; \nError: " + xp.asString());
        }
        return conn;
    }
    catch (Exception e) {
        return null;
    }
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
private RConnection attemptStarts(String host, int port) throws InterruptedException, IOException, RserveException {
    startRserve();

    int attempt = 1;
    RConnection con = null;
    while (attempt <= START_ATTEMP_COUNT) {
        try {
            Thread.sleep(START_ATTEMPT_SLEEP); // wait for R to startup, then establish connection
            con = newConnection(host, port);
            break;
        }
        catch (RserveException rse) {
            if (attempt >= 5) {
                throw rse;
            }

            attempt++;
        }
    }
    return con;
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
public static void logGenericRProcess(RConnection rCon, String message) {
    String msg = prepareMessage(message);
    
    StringBuilder evalString = new StringBuilder();
    evalString.append("cat(\"[GenericRProcess @ ");
    evalString.append(format.format(new Date(System.currentTimeMillis())));
    evalString.append("] ");
    evalString.append(msg);
    evalString.append("\\n\")");
    
    try {
        rCon.eval(evalString.toString());
    }
    catch (RserveException e) {
        LOGGER.warn("Could not log message '" + msg + "'", e);
    }
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
public static void log(RConnection rCon, String message) {
    String msg = prepareMessage(message);
    
    StringBuilder evalString = new StringBuilder();
    evalString.append("cat(\"[WPS4R @ ");
    evalString.append(format.format(new Date(System.currentTimeMillis())));
    evalString.append("] ");
    evalString.append(msg);
    evalString.append("\\n\")");
    
    try {
        rCon.eval(evalString.toString());
    }
    catch (RserveException e) {
        LOGGER.warn("Could not log message '" + msg + "'", e);
    }
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
@PreDestroy
public void tearDown() {
	try {
		if(LOGGER.isInfoEnabled()) {
			LOGGER.info("Shuting down Rserve daemon....");
		}
		RConnection rConnection = rConnectionFactory.getConnection();
		rConnection.shutdown();
		rConnectionFactory.releaseConnection(rConnection);
		if(LOGGER.isInfoEnabled()) {
			LOGGER.info("Shutdown signal sent to Rserve daemon");
		}
	} catch(Exception e) {
		LOGGER.error("Unexpected error shuting down RServe", e);
	}
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
@Test
public void ksTest() throws Exception{
	
	RConnection rConnectionMock = mock(RConnection.class);
	when(rConnectionMock.parseAndEval(anyString())).thenReturn(new REXPGenericVector(new RList(new REXP[]{new REXPDouble(new double[]{0.15})})));
	when(rConnectionFactory.getConnection()).thenReturn(rConnectionMock);
	REXPDouble demoVars = getDemoContinuousVars().get(0);
	
	rServeEngineProviderService.ksTest(demoVars, demoVars);
	
	verify(rConnectionMock, times(1)).assign(eq("x"), any(REXP.class));
	verify(rConnectionMock, times(1)).assign(eq("y"), any(REXP.class));
	ArgumentCaptor<String> rCommand = ArgumentCaptor.forClass(String.class);
	verify(rConnectionMock, times(1)).parseAndEval(rCommand.capture());
	assertThat(rCommand.getValue()).isEqualTo("ks.test(x, y)['p.value']");
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
/**
 * Remove a file on the RServer.
 * @param filename File to remove
 */
public void removeFile(final String filename) throws REngineException {

  // Test if the file exists
  final RConnection c = getRConnection();

  try {

    REXP exists = c.eval("file.exists(\"" + filename + "\")");
    if (exists.asInteger() == 1) {
      c.voidEval("file.remove(\"" + filename + "\")");
    }

  } catch (RserveException | REXPMismatchException e) {
    throw new REngineException(c, "RServe exception: " + e);
  }
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
/**
 * Execute a R code.
 * @param source code to execute
 * @throws REngineException if an error while executing the code
 */
public void executeRCode(final String source) throws REngineException {

  if (source == null) {
    return;
  }

  final RConnection c = getRConnection();

  try {

    // Execute the source
    c.voidEval("source(\"" + source + "\")");

  } catch (RserveException e) {
    throw new REngineException(c, "RServe exception: " + e);
  }
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
public CellHTS2(ScreenResult screenResult, 
                String title,
                String reportsPath,
                String saveRObjectsPath) throws RserveException, REngineException,
REXPMismatchException {
  this.screenResult = screenResult;
  this.rConnection = new RConnection();
  this.arrayDimensions = calculateArrayDimensions(screenResult);
  this.title = title;
  this.reportsPath = reportsPath;
  if (!StringUtils.isEmpty(saveRObjectsPath)) {
    this.saveRObjectsPath = saveRObjectsPath;
    File file = new File(saveRObjectsPath);
    if (file.exists()) {
      this.saveRObjects = true;
    }
    else {
      log.error(saveRObjectsPath +
        "does not exist (cellHTS2.saveRObjects.directory system property); R objects will not be saved");
    }
  }
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
@Test
@Ignore
public void tt () throws Exception {
  SimpleDatasetBuilder s = new SimpleDatasetBuilder ();
  s.setParserFactories (asList (new SuperCsvParserFactory ()));
  s.setValueStoreBuilder (new MapBackedValueStoreBuilder ());

  RConnection c = new RConnection ();
  c.assign ("ds", new REXPString (mapper.writeValueAsString (s.build (new MockTsvInput ("mock", "id\tsa\tsb\tsc\n" +
                                                                                                "g1\t.1\t.2\t.3\n" +
                                                                                                "g2\t.4\t.5\t.6")))));
  System.out.println (mapper.readValue (c.eval ("m <- NMF::nmf (jsonlite::fromJSON (ds), rank = 3);"
                                                +
                                                "w <- NMF::basis (m);"
                                                +
                                                "h <- NMF::coef (m);"
                                                +
                                                "jsonlite::toJSON (list (w = w, h = list (matrix = h)), auto_unbox = TRUE)")
                                         .asString (),
                                        Nmf.class));
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
/**
 * <p>
 * The RContainer constructor opens a connection (an RConnection) to either
 * local or remote RServe, and combines the object with the current Vaadin
 * main window. Thus, the main window must have been set earlier with
 * {@link com.vaadin.Application#setMainWindow(Window)} for the grahics to
 * work. See {@link RContainer#RContainer(Application, String, int)} for
 * accessing remote R Servers.
 * </p>
 * 
 * <p>
 * Example:<br>
 * {@code Window main = new Window("My Fabulous Analysis App");}<br>
 * {@code setMainWindow(main);}<br>
 * {@code RContainer R = new RContainer(main.getApplication());}
 * </p>
 * 
 * @param app
 *            Vaadin Application reference. Needed in the construction of
 *            StreamResource objects for R graphics.
 */
public RContainer() {

	try {
		rc = new RConnection();
		rc.parseAndEval("library('Cairo')");

	} catch (Exception e) {
		if (verboseErrors) {
			Notification.show("RVaadin: Could not connect to R.",
					Notification.Type.ERROR_MESSAGE);
		}
		e.printStackTrace();
	}

	/*
	 * Random session identifier for this particular R connection (used to
	 * e.g. tell the browser not to cache the images)
	 */
	rand = new Random((new GregorianCalendar()).getTimeInMillis());
	String chars = "abcdefghijklmnopqrstuvwxyz";
	sessionID = getRandomString(rand, chars, 10);

}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
/** sends a request with one string parameter attached
@param cmd command
@param par parameter - length and DT_STRING will be prepended
@return returned packet or <code>null</code> if something went wrong */
   public RPacket request(int cmd, String par) {
try {
           byte[] b=par.getBytes(RConnection.transferCharset);
           int sl=b.length+1;
           if ((sl&3)>0) sl=(sl&0xfffffc)+4; // make sure the length is divisible by 4
    byte[] rq=new byte[sl+5];
           int i;
    for(i=0;i<b.length;i++)
               rq[i+4]=b[i];
           while (i<sl) { // pad with 0
               rq[i+4]=0; i++;
           };
    setHdr(DT_STRING,sl,rq,0);
    return request(cmd,rq);
} catch (Exception e) {
    e.printStackTrace();
}
return null;
   }
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
public void stop() {
    println("stopping R daemon... " + conf, Level.INFO);
    if (!conf.isLocal()) {
        throw new UnsupportedOperationException(
                "Not authorized to stop a remote R daemon: "
                        + conf.toString());
    }

    try {
        RConnection s = conf.connect();
        if (s == null || !s.isConnected()) {
            println("R daemon already stoped.", Level.INFO);
            return;
        }
        s.shutdown();

    } catch (Exception ex) {
        // ex.printStackTrace();
        println(ex.getMessage(), Level.ERROR);
    }

    /*
     * if (br != null) { try { br.close(); } catch (IOException ex) {
     * ex.printStackTrace(); println(ex.getMessage()); } }
     */

    // if (pw != null) {
    // pw.close();
    // }

    // process.destroy();

    println("R daemon stoped.", Level.INFO);

    log = null;
}
 

import org.rosuda.REngine.Rserve.RConnection; //导入依赖的package包/类
/** check whether Rserve is currently running (on local machine and default port).
@return <code>true</code> if local Rserve instance is running, <code>false</code> otherwise
 */
public static boolean isRserveRunning() {
    try {
        RConnection c = new RConnection();
        System.err.println("Rserve is running.");
        c.close();
        return true;
    } catch (Exception e) {
        System.err.println("First connect try failed with: " + e.getMessage());
    }
    return false;
}