Révision 2515
| tmp/org.txm.statsengine.r.core/src/org/txm/statsengine/r/core/RWorkspace.java (revision 2515) | ||
|---|---|---|
| 108 | 108 |
*/ |
| 109 | 109 |
|
| 110 | 110 |
public final class RWorkspace {
|
| 111 |
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| 111 |
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| 112 | 112 |
/** The comm. */ |
| 113 | 113 |
private static RFileCommunication comm; |
| 114 |
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|
| 114 |
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|
| 115 | 115 |
/** The connection. */ |
| 116 | 116 |
private static RConnection connection = null; |
| 117 |
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| 117 |
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| 118 | 118 |
/** The eval logs. */ |
| 119 |
static ArrayList<String> evalLogs = new ArrayList<String>();
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| 120 |
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| 119 |
static ArrayList<String> evalLogs = new ArrayList<>(); |
|
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| 121 | 121 |
/** The filecommunication. */ |
| 122 | 122 |
private static boolean filecommunication = false; |
| 123 |
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| 123 |
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| 124 | 124 |
// -------------------------------------- |
| 125 | 125 |
/** The last safeeval expr. */ |
| 126 | 126 |
static String lastSafeevalExpr = ""; //$NON-NLS-1$ |
| 127 |
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| 127 |
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| 128 | 128 |
/** The Rserve process. */ |
| 129 | 129 |
private static Process RserveProcess = null; |
| 130 |
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| 130 |
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| 131 | 131 |
/** The workspace. */ |
| 132 | 132 |
private static RWorkspace workspace = null; |
| 133 | 133 |
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| 134 | 134 |
/** The error logger. */ |
| 135 | 135 |
private StreamHog errorLogger; |
| 136 |
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| 136 |
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| 137 | 137 |
/** The input logger. */ |
| 138 | 138 |
private StreamHog inputLogger; |
| 139 |
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| 139 |
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| 140 | 140 |
/** The loggin. */ |
| 141 | 141 |
private boolean logging; |
| 142 |
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| 142 |
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| 143 | 143 |
/** The DEFAUL t_ symbol. */ |
| 144 |
//private String DEFAULT_SYMBOL = "txmresult"; //$NON-NLS-1$ |
|
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| 144 |
// private String DEFAULT_SYMBOL = "txmresult"; //$NON-NLS-1$
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| 146 | 146 |
/** |
| 147 | 147 |
* Folder where to create the R working directory |
| 148 | 148 |
*/ |
| 149 | 149 |
protected File userdir = null; |
| 150 |
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| 151 | 150 |
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| 152 |
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| 153 | 151 |
/** |
| 154 | 152 |
* protected on purpose. See {@link #getRWorkspaceInstance()}.
|
| 155 | 153 |
* |
| 156 | 154 |
* @throws RWorkspaceException the r workspace exception |
| 157 | 155 |
*/ |
| 158 |
public RWorkspace(File userDir) throws RWorkspaceException {
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| 156 |
private RWorkspace(File userDir) throws RWorkspaceException {
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| 159 | 157 |
this.userdir = userDir; |
| 160 | 158 |
this.setLog(isLoggingEvalCommandLines()); |
| 161 | 159 |
} |
| 162 |
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| 160 |
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| 163 | 161 |
/** |
| 164 | 162 |
* Append to eval log. |
| 165 | 163 |
* |
| 166 | 164 |
* @param cmd the cmd |
| 167 | 165 |
*/ |
| 168 |
public static void appendtoEvalLog(String cmd) |
|
| 169 |
{
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|
| 166 |
public static void appendtoEvalLog(String cmd) {
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| 170 | 167 |
evalLogs.add(cmd); |
| 171 | 168 |
} |
| 172 |
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|
| 169 |
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| 173 | 170 |
/** |
| 174 | 171 |
* Close the connection. |
| 175 | 172 |
* |
| ... | ... | |
| 183 | 180 |
connection.close(); |
| 184 | 181 |
} |
| 185 | 182 |
} |
| 186 |
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|
| 183 |
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| 187 | 184 |
/** |
| 188 | 185 |
* Connect to Rserve. |
| 189 | 186 |
* |
| ... | ... | |
| 198 | 195 |
connection = new RConnection(host, port); |
| 199 | 196 |
connection.setStringEncoding("utf8"); // mandatory !
|
| 200 | 197 |
return isConnected(); |
| 201 |
} catch (RserveException x) {
|
|
| 198 |
} |
|
| 199 |
catch (RserveException x) {
|
|
| 202 | 200 |
throw new RWorkspaceException(x); |
| 203 | 201 |
} |
| 204 |
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| 202 |
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| 205 | 203 |
} |
| 206 |
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|
| 204 |
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| 207 | 205 |
/** |
| 208 | 206 |
* Connect to Rserve. |
| 209 | 207 |
* |
| ... | ... | |
| 215 | 213 |
*/ |
| 216 | 214 |
public static boolean connect(String host, int port, String user, String password) {
|
| 217 | 215 |
try {
|
| 218 |
Log.fine(TXMCoreMessages.bind(RCoreMessages.info_connectingToRAtWithUser, new Object[] {host, port, user}));
|
|
| 216 |
Log.fine(TXMCoreMessages.bind(RCoreMessages.info_connectingToRAtWithUser, new Object[] { host, port, user }));
|
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| 219 | 217 |
connection = new RConnection(host, port); |
| 220 | 218 |
connection.login(user, password); |
| 221 | 219 |
connection.setStringEncoding("utf8"); // mandatory !
|
| 222 | 220 |
return isConnected(); |
| 223 |
|
|
| 224 |
} catch (RserveException x) {
|
|
| 225 |
Log.severe(TXMCoreMessages.bind(RCoreMessages.error_failedToConnectToTheRWorkspace, host, port, user)); |
|
| 221 |
|
|
| 226 | 222 |
} |
| 223 |
catch (RserveException x) {
|
|
| 224 |
Log.severe(TXMCoreMessages.bind(RCoreMessages.error_failedToConnectToTheRWorkspace, host, port, user)); |
|
| 225 |
} |
|
| 227 | 226 |
return false; |
| 228 | 227 |
} |
| 229 |
|
|
| 228 |
|
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| 230 | 229 |
/** |
| 231 | 230 |
* Gets the last safe eval expr. |
| 232 | 231 |
* |
| ... | ... | |
| 235 | 234 |
public static String getLastSafeEvalExpr() {
|
| 236 | 235 |
return lastSafeevalExpr; |
| 237 | 236 |
} |
| 238 |
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|
| 239 |
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| 237 |
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| 238 |
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| 240 | 239 |
/** |
| 241 | 240 |
* |
| 242 | 241 |
* @return |
| 243 | 242 |
*/ |
| 244 | 243 |
public static String getRandomSymbol() {
|
| 245 |
return "Random" + UUID.randomUUID(); //$NON-NLS-1$; |
|
| 244 |
return "Random" + UUID.randomUUID(); //$NON-NLS-1$ ;
|
|
| 246 | 245 |
} |
| 247 |
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|
| 246 |
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|
| 248 | 247 |
/** |
| 249 | 248 |
* Entering the R workspace. |
| 250 | 249 |
* |
| 251 |
* @param
|
|
| 250 |
* @param |
|
| 252 | 251 |
* @return the r workspace instance |
| 253 | 252 |
* @throws RWorkspaceException the r workspace exception |
| 254 | 253 |
*/ |
| 255 | 254 |
public static final RWorkspace getRWorkspaceInstance() throws RWorkspaceException {
|
| 256 | 255 |
if (workspace == null) {
|
| 257 |
//TODO: this method uses the right directory ? |
|
| 258 |
//Bundle bundle = FrameworkUtil.getBundle(RWorkspace.class); |
|
| 259 |
//File userdir = new File(bundle.getLocation()); |
|
| 256 |
// TODO: this method uses the right directory ?
|
|
| 257 |
// Bundle bundle = FrameworkUtil.getBundle(RWorkspace.class);
|
|
| 258 |
// File userdir = new File(bundle.getLocation());
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|
| 260 | 259 |
File userDir = new File(Toolbox.getTxmHomePath(), "R"); |
| 261 |
//System.out.println("BUNDLE LOCATION OF '" + bundle.getSymbolicName() + "': " + userDir);
|
|
| 260 |
// System.out.println("BUNDLE LOCATION OF '" + bundle.getSymbolicName() + "': " + userDir);
|
|
| 262 | 261 |
workspace = new RWorkspace(userDir); |
| 263 | 262 |
} |
| 264 | 263 |
return workspace; |
| ... | ... | |
| 266 | 265 |
|
| 267 | 266 |
/** |
| 268 | 267 |
* Post initialisation of Rserve : loads libraries. |
| 269 |
* @deprecated The extensions will load themself the packages they need |
|
| 268 |
* |
|
| 269 |
* @deprecated The extensions will load themself the packages they need |
|
| 270 | 270 |
* @throws RWorkspaceException the r workspace exception |
| 271 | 271 |
*/ |
| 272 |
@Deprecated |
|
| 272 | 273 |
private static void init() throws RWorkspaceException {
|
| 273 |
String[] packagesToLoad = { }; //$NON-NLS-1$
|
|
| 274 |
String[] packagesToLoad = {};
|
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| 274 | 275 |
for (int i = 0; i < packagesToLoad.length; i++) {
|
| 275 | 276 |
String name = packagesToLoad[i]; |
| 276 | 277 |
try {
|
| 277 | 278 |
// System.out.println("load R lib : " + name);
|
| 278 | 279 |
connection.eval(("library(" + name + ")")); //$NON-NLS-1$ //$NON-NLS-2$
|
| 279 | 280 |
// System.out.println("Done : load R lib : " + name);
|
| 280 |
} catch (RserveException e) {
|
|
| 281 |
} |
|
| 282 |
catch (RserveException e) {
|
|
| 281 | 283 |
throw new RWorkspaceException(NLS.bind(RCoreMessages.error_failedToLoadLibrary, name, e)); |
| 282 |
} catch (Exception e) {
|
|
| 284 |
} |
|
| 285 |
catch (Exception e) {
|
|
| 283 | 286 |
org.txm.utils.logger.Log.printStackTrace(e); |
| 284 | 287 |
} |
| 285 | 288 |
} |
| 286 | 289 |
} |
| 287 |
|
|
| 288 |
|
|
| 290 |
|
|
| 291 |
|
|
| 289 | 292 |
// -------------------------------------- |
| 290 | 293 |
/** |
| 291 | 294 |
* check R path |
| ... | ... | |
| 293 | 296 |
* if not try to launch it. |
| 294 | 297 |
* |
| 295 | 298 |
* @param pathToRExecutable the path to r executable |
| 296 |
* @param options
|
|
| 297 |
* @param rServeArgs
|
|
| 299 |
* @param options |
|
| 300 |
* @param rServeArgs |
|
| 298 | 301 |
* @return true if Rserve is launched |
| 299 | 302 |
* @throws RWorkspaceException the r workspace exception |
| 300 | 303 |
*/ |
| ... | ... | |
| 306 | 309 |
|
| 307 | 310 |
File execFile = new File(pathToRExecutable); |
| 308 | 311 |
if (!execFile.exists() || pathToRExecutable == null || pathToRExecutable.length() == 0) {
|
| 309 |
//isRServerOk = StartRserve.checkLocalRserve(port, debug, rargs, rServeArgs); |
|
| 310 |
// if (!isRServerOk) {
|
|
| 311 |
throw new RWorkspaceException(RCoreMessages.error_rservePathNotSet); |
|
| 312 |
// } |
|
| 313 |
} else {
|
|
| 312 |
// isRServerOk = StartRserve.checkLocalRserve(port, debug, rargs, rServeArgs); |
|
| 313 |
// if (!isRServerOk) {
|
|
| 314 |
throw new RWorkspaceException(RCoreMessages.error_rservePathNotSet); |
|
| 315 |
// } |
|
| 316 |
} |
|
| 317 |
else {
|
|
| 314 | 318 |
isRServerOk = StartRserve.launchRserve(pathToRExecutable, port, debug, rargs, rServeArgs); |
| 315 | 319 |
// System.out.println("ap launchRserve");
|
| 316 | 320 |
if (!isRServerOk) {
|
| 317 | 321 |
Log.severe(NLS.bind(RCoreMessages.rserveNotStartedUsingTheP0Path, pathToRExecutable)); |
| 318 |
//isRServerOk = StartRserve.checkLocalRserve(port, debug, rargs, rServeArgs); |
|
| 322 |
// isRServerOk = StartRserve.checkLocalRserve(port, debug, rargs, rServeArgs);
|
|
| 319 | 323 |
} |
| 320 | 324 |
|
| 321 | 325 |
if (!isRServerOk) {
|
| 322 | 326 |
throw new RWorkspaceException(RCoreMessages.bind(RCoreMessages.error_cantFindRServeInPath, pathToRExecutable)); |
| 323 | 327 |
} |
| 324 | 328 |
} |
| 325 |
|
|
| 329 |
|
|
| 326 | 330 |
if (isRServerOk) {
|
| 327 | 331 |
Log.finest("RSERVE_ACTIVATED"); //$NON-NLS-1$
|
| 328 |
//System.out.println(RCoreMessages.info_connected);
|
|
| 332 |
// System.out.println(RCoreMessages.info_connected);
|
|
| 329 | 333 |
RserveProcess = StartRserve.rProcess; |
| 330 | 334 |
} |
| 331 | 335 |
return isRServerOk; |
| 332 | 336 |
} |
| 333 |
|
|
| 337 |
|
|
| 334 | 338 |
/** |
| 335 | 339 |
* Checks if is connected. |
| 336 | 340 |
* |
| ... | ... | |
| 339 | 343 |
private static boolean isConnected() {
|
| 340 | 344 |
if (!connection.isConnected()) {
|
| 341 | 345 |
return false; |
| 342 |
} else {
|
|
| 346 |
} |
|
| 347 |
else {
|
|
| 343 | 348 |
return true; |
| 344 | 349 |
} |
| 345 | 350 |
} |
| 346 |
|
|
| 351 |
|
|
| 347 | 352 |
/** |
| 348 | 353 |
* |
| 349 | 354 |
* @return The executable path set in the R Preferences |
| ... | ... | |
| 360 | 365 |
public static boolean isFileTranfert() {
|
| 361 | 366 |
return filecommunication; |
| 362 | 367 |
} |
| 363 |
|
|
| 364 | 368 |
|
| 365 | 369 |
|
| 370 |
|
|
| 366 | 371 |
/** |
| 367 | 372 |
* Load eval log. |
| 368 | 373 |
* |
| ... | ... | |
| 372 | 377 |
public static void loadEvalLog(File file) throws IOException {
|
| 373 | 378 |
BufferedReader reader = new BufferedReader(new FileReader(file)); |
| 374 | 379 |
String cmd = reader.readLine(); |
| 375 |
while(cmd != null) {
|
|
| 380 |
while (cmd != null) {
|
|
| 376 | 381 |
evalLogs.add(cmd); |
| 377 | 382 |
cmd = reader.readLine(); |
| 378 | 383 |
} |
| 379 | 384 |
reader.close(); |
| 380 | 385 |
} |
| 381 |
|
|
| 386 |
|
|
| 382 | 387 |
/** |
| 383 | 388 |
* Plot. |
| 384 | 389 |
* |
| ... | ... | |
| 390 | 395 |
public File plot(File file, String expr) throws REXPMismatchException, StatException, RserveException {
|
| 391 | 396 |
return plot(file, expr, "svg"); |
| 392 | 397 |
} |
| 398 |
|
|
| 393 | 399 |
/** |
| 394 | 400 |
* Plot. |
| 395 | 401 |
* |
| ... | ... | |
| 398 | 404 |
* @param device the device (svg, png, jpeg, ...) |
| 399 | 405 |
* @throws REXPMismatchException the rEXP mismatch exception |
| 400 | 406 |
* @throws StatException the stat exception |
| 401 |
* @throws RserveException
|
|
| 407 |
* @throws RserveException |
|
| 402 | 408 |
*/ |
| 403 |
public File plot(File file, String expr, String devicename) throws REXPMismatchException, StatException, RserveException {
|
|
| 409 |
public File plot(File file, String expr, String devicename) throws REXPMismatchException, StatException, RserveException {
|
|
| 404 | 410 |
|
| 405 | 411 |
try {
|
| 406 | 412 |
file.createNewFile(); |
| 407 |
|
|
| 413 |
|
|
| 408 | 414 |
if (!file.canWrite()) {
|
| 409 | 415 |
System.out.println(NLS.bind("{0} cannot be written.", file)); //$NON-NLS-1$
|
| 410 | 416 |
return null; |
| 411 | 417 |
} |
| 412 | 418 |
|
| 413 | 419 |
String name; |
| 414 |
if (OSDetector.isFamilyWindows()) { //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 420 |
if (OSDetector.isFamilyWindows()) {
|
|
| 415 | 421 |
name = file.getCanonicalPath().replaceAll("/", "\\");
|
| 416 | 422 |
} |
| 417 | 423 |
else {
|
| 418 | 424 |
name = file.getAbsolutePath(); |
| 419 | 425 |
} |
| 420 |
|
|
| 426 |
|
|
| 421 | 427 |
if (devicename.equals("devSVG")) safeEval("library(RSvgDevice);");
|
| 422 |
|
|
| 428 |
|
|
| 423 | 429 |
// FIXME : test for window dimensions so the large plots can be entirely displayed. Need to pass width and height to RWorkspace.plot() so |
| 424 | 430 |
// RChartsEngine will be able to dynamically compute the width from the number of bars in a barplot for example. |
| 425 |
//REXP xp = eval("try("+devicename+"(\"" + name + "\", width=20, height=10))"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 426 |
|
|
| 427 |
REXP xp = eval("try("+devicename+"(\"" + name + "\"))"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 428 |
|
|
| 431 |
// REXP xp = eval("try("+devicename+"(\"" + name + "\", width=20, height=10))"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 432 |
|
|
| 433 |
REXP xp = eval("try(" + devicename + "(\"" + name + "\"))"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 434 |
|
|
| 429 | 435 |
if (xp.isString() && xp.asString() != null) { // if there's a string
|
| 430 | 436 |
// then we have a |
| 431 | 437 |
// problem, R sent an |
| ... | ... | |
| 437 | 443 |
// if (w.asString()!=null) System.out.println(w.asString()); |
| 438 | 444 |
throw new StatException(w.asString()); |
| 439 | 445 |
} |
| 440 |
|
|
| 446 |
|
|
| 441 | 447 |
// ok, so the device should be fine - let's plot |
| 442 | 448 |
safeEval(expr); |
| 443 | 449 |
safeEval("dev.off()"); //$NON-NLS-1$
|
| ... | ... | |
| 457 | 463 |
public static void printLastSafeEvalExpr() {
|
| 458 | 464 |
Log.fine(RCoreMessages.bind(RCoreMessages.info_lastSafeEvalExpression, lastSafeevalExpr)); |
| 459 | 465 |
} |
| 460 |
|
|
| 466 |
|
|
| 461 | 467 |
/** |
| 462 | 468 |
* Save eval log. |
| 463 | 469 |
* |
| ... | ... | |
| 467 | 473 |
public static void saveEvalLog(File file) throws IOException {
|
| 468 | 474 |
FileWriter writer = new FileWriter(file); |
| 469 | 475 |
for (String cmd : evalLogs) |
| 470 |
writer.write(cmd+"\n"); //$NON-NLS-1$
|
|
| 476 |
writer.write(cmd + "\n"); //$NON-NLS-1$
|
|
| 471 | 477 |
writer.flush(); |
| 472 | 478 |
writer.close(); |
| 473 | 479 |
} |
| 474 |
|
|
| 480 |
|
|
| 475 | 481 |
/** |
| 476 | 482 |
* if state is true, the matrix will be send to R with a File. |
| 477 | 483 |
* |
| ... | ... | |
| 483 | 489 |
if (filecommunication) {
|
| 484 | 490 |
try {
|
| 485 | 491 |
comm = new RFileCommunication(); |
| 486 |
} catch (IOException e) {
|
|
| 492 |
} |
|
| 493 |
catch (IOException e) {
|
|
| 487 | 494 |
filecommunication = false; |
| 488 | 495 |
Log.severe(RCoreMessages.bind(RCoreMessages.error_failedToInitializeFileTransfert, Log.toString(e))); |
| 489 | 496 |
return false; |
| ... | ... | |
| 491 | 498 |
} |
| 492 | 499 |
return true; |
| 493 | 500 |
} |
| 494 |
|
|
| 501 |
|
|
| 495 | 502 |
/** |
| 496 | 503 |
* Close the connection and destroy the Rserve process. |
| 497 | 504 |
* |
| ... | ... | |
| 502 | 509 |
// If no R object have been created during the lif ecycle of the |
| 503 | 510 |
// application, |
| 504 | 511 |
// the connection has never been initialized. |
| 505 |
|
|
| 512 |
|
|
| 506 | 513 |
if (connection != null && connection.isConnected()) {
|
| 507 | 514 |
// connection.close(); // No: invoquing "close()" make |
| 508 | 515 |
// "shutdown()" to throw a "not connected" exception. |
| ... | ... | |
| 513 | 520 |
// ok but using it yield to a |
| 514 | 521 |
// "Broken pipe" exception. |
| 515 | 522 |
} |
| 516 |
} catch (RserveException e) {
|
|
| 523 |
} |
|
| 524 |
catch (RserveException e) {
|
|
| 517 | 525 |
throw new RWorkspaceException(e); |
| 518 | 526 |
} |
| 519 | 527 |
} |
| 520 |
|
|
| 528 |
|
|
| 521 | 529 |
/** |
| 522 | 530 |
* Start exec. |
| 523 | 531 |
* |
| 524 | 532 |
* @param pathToRExecutable the path to r executable |
| 525 |
* @param string
|
|
| 526 |
* @param string
|
|
| 533 |
* @param string |
|
| 534 |
* @param string |
|
| 527 | 535 |
* @return true, if successful |
| 528 | 536 |
*/ |
| 529 | 537 |
public static boolean startExec(String pathToRExecutable, int port, boolean debug, String rArgs, String rServeArgs) {
|
| ... | ... | |
| 531 | 539 |
try {
|
| 532 | 540 |
initRserve(pathToRExecutable, port, debug, rArgs, rServeArgs); |
| 533 | 541 |
return true; |
| 534 |
} catch (RWorkspaceException e) {
|
|
| 542 |
} |
|
| 543 |
catch (RWorkspaceException e) {
|
|
| 535 | 544 |
Log.severe(RCoreMessages.error_failedToStartRServe); |
| 536 | 545 |
org.txm.utils.logger.Log.printStackTrace(e); |
| 537 | 546 |
} |
| 538 | 547 |
return false; |
| 539 | 548 |
} |
| 540 |
|
|
| 549 |
|
|
| 541 | 550 |
/** |
| 542 | 551 |
* To double. |
| 543 | 552 |
* |
| ... | ... | |
| 548 | 557 |
public static final double[] toDouble(REXP rexp) throws RWorkspaceException {
|
| 549 | 558 |
try {
|
| 550 | 559 |
return rexp.asDoubles(); |
| 551 |
} catch (Exception e) {
|
|
| 560 |
} |
|
| 561 |
catch (Exception e) {
|
|
| 552 | 562 |
throw new RWorkspaceException(e); |
| 553 | 563 |
} |
| 554 | 564 |
} |
| 555 |
|
|
| 556 |
|
|
| 557 |
|
|
| 565 |
|
|
| 566 |
|
|
| 567 |
|
|
| 558 | 568 |
/** |
| 559 | 569 |
* Add a matrix into the workspace and link it to a name. The inner arrays |
| 560 | 570 |
* of the <code>matrix</code> parameters are the <strong>row</strong> of the |
| ... | ... | |
| 562 | 572 |
* |
| 563 | 573 |
* @param variableName the name to be used in the R workspace. |
| 564 | 574 |
* @param matrix the data to be bound to the name. In the form |
| 565 |
* <code>matrix[row][column]</code>, with exactly the same number |
|
| 566 |
* of column in every row. |
|
| 575 |
* <code>matrix[row][column]</code>, with exactly the same number
|
|
| 576 |
* of column in every row.
|
|
| 567 | 577 |
* @throws RWorkspaceException the r workspace exception |
| 568 | 578 |
*/ |
| 569 | 579 |
public void addMatrixToWorkspace(String variableName, double[][] matrix) throws RWorkspaceException {
|
| 570 |
//System.out.println("matrix len: "+matrix.length+" test="+(matrix.length == 0));
|
|
| 580 |
// System.out.println("matrix len: "+matrix.length+" test="+(matrix.length == 0));
|
|
| 571 | 581 |
if (matrix.length == 0) {
|
| 572 | 582 |
new RWorkspaceException(RCoreMessages.error_matrixIsEmpty); |
| 573 | 583 |
} |
| ... | ... | |
| 584 | 594 |
* |
| 585 | 595 |
* @param variableName the name to be used in the R workspace. |
| 586 | 596 |
* @param matrix the data to be bound to the name. In the form |
| 587 |
* <code>matrix[row][column]</code>, with exactly the same number |
|
| 588 |
* of column in every row. |
|
| 597 |
* <code>matrix[row][column]</code>, with exactly the same number
|
|
| 598 |
* of column in every row.
|
|
| 589 | 599 |
* @throws RWorkspaceException the r workspace exception |
| 590 | 600 |
*/ |
| 591 | 601 |
public void addMatrixToWorkspace(String variableName, double[][] matrix, int ncol, int nrow) |
| 592 | 602 |
throws RWorkspaceException {
|
| 593 |
|
|
| 603 |
|
|
| 594 | 604 |
double[] vector = VectorizeArray.vectorizeByInner(matrix); |
| 595 |
|
|
| 605 |
|
|
| 596 | 606 |
if (!filecommunication) {
|
| 597 | 607 |
try {
|
| 598 | 608 |
connection.assign(variableName, vector); |
| 599 |
} catch (REngineException e) {
|
|
| 609 |
} |
|
| 610 |
catch (REngineException e) {
|
|
| 600 | 611 |
throw new RWorkspaceException(e); |
| 601 | 612 |
} |
| 602 | 613 |
try {
|
| 603 |
connection .voidEval(variableName
|
|
| 614 |
connection.voidEval(variableName |
|
| 604 | 615 |
+ "<- matrix(" + variableName + ", nrow=" + nrow + ", ncol=" + ncol + ", byrow=T)"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
| 605 |
} catch (RserveException e) {
|
|
| 616 |
} |
|
| 617 |
catch (RserveException e) {
|
|
| 606 | 618 |
throw new RWorkspaceException(e); |
| 607 | 619 |
} |
| 608 |
} else {
|
|
| 620 |
} |
|
| 621 |
else {
|
|
| 609 | 622 |
comm.assign(variableName, vector, nrow, ncol); |
| 610 | 623 |
} |
| 611 | 624 |
Log.finest("MATRIX_ADDED_TO_WORKSPACE" + new Object[] { nrow, ncol, variableName }); //$NON-NLS-1$
|
| 612 | 625 |
} |
| 613 |
|
|
| 626 |
|
|
| 614 | 627 |
/** |
| 615 | 628 |
* Add a matrix into the workspace and link it to a name. Intended to be |
| 616 | 629 |
* efficient for sparse matrix. |
| ... | ... | |
| 621 | 634 |
*/ |
| 622 | 635 |
public void addMatrixToWorkspace(String variableName, DoubleMatrix2D matrix) |
| 623 | 636 |
throws RWorkspaceException {
|
| 624 |
|
|
| 637 |
|
|
| 625 | 638 |
double[][] data = RColt.doubleMatrix2D2DoubleDoubleArray(matrix); |
| 626 | 639 |
addMatrixToWorkspace(variableName, data, matrix.columns(), matrix.rows()); |
| 627 |
|
|
| 640 |
|
|
| 628 | 641 |
// // IntArrayList x = new IntArrayList(); |
| 629 | 642 |
// // IntArrayList y = new IntArrayList(); |
| 630 | 643 |
// // DoubleArrayList val = new DoubleArrayList(); |
| ... | ... | |
| 647 | 660 |
// // System.out.println(x); |
| 648 | 661 |
// // System.out.println(y); |
| 649 | 662 |
// // System.out.println(val); |
| 650 |
//
|
|
| 663 |
// |
|
| 651 | 664 |
// int nrow = matrix.rows(); |
| 652 | 665 |
// int ncol = matrix.columns(); |
| 653 | 666 |
// // System.out.println(matrix); |
| ... | ... | |
| 677 | 690 |
// y.getQuick(j) + "] <- " + val.getQuick(i * 5 + * j)); |
| 678 | 691 |
// // } |
| 679 | 692 |
// // } |
| 680 |
//
|
|
| 693 |
// |
|
| 681 | 694 |
// } catch (RserveException e) {
|
| 682 | 695 |
// throw new RWorkspaceException(e); |
| 683 | 696 |
// } |
| 684 |
//
|
|
| 697 |
// |
|
| 685 | 698 |
// removeVariableFromWorkspace(variableName + ".nonzero"); |
| 686 | 699 |
// removeVariableFromWorkspace(variableName + ".x"); |
| 687 | 700 |
// removeVariableFromWorkspace(variableName + ".y"); |
| 688 |
//
|
|
| 689 |
//
|
|
| 701 |
// |
|
| 702 |
// |
|
| 690 | 703 |
// System.out.println("--------------matrice d'origine----------");
|
| 691 | 704 |
// System.out.println(matrix); |
| 692 |
//
|
|
| 705 |
// |
|
| 693 | 706 |
// // DoubleFactory2D.dense.make(arg0) |
| 694 | 707 |
// System.out.println("--------------matrice issue de R----------");
|
| 695 | 708 |
// DenseDoubleMatrix2D m = null; |
| ... | ... | |
| 704 | 717 |
// org.txm.utils.logger.Log.printStackTrace(e); |
| 705 | 718 |
// } |
| 706 | 719 |
// System.out.println(m); |
| 707 |
|
|
| 720 |
|
|
| 708 | 721 |
} |
| 709 |
|
|
| 710 |
//TODO: is addLexiconToWorkspace used ?
|
|
| 711 |
// /**
|
|
| 712 |
// * Adds the lexicon to workspace.
|
|
| 713 |
// *
|
|
| 714 |
// * @param variableName the variable name
|
|
| 715 |
// * @param lexicon the lexicon
|
|
| 716 |
// * @throws RWorkspaceException the r workspace exception
|
|
| 717 |
// */
|
|
| 718 |
// public void addLexiconToWorkspace(String variableName, Lexicon lexicon)
|
|
| 719 |
// throws RWorkspaceException {
|
|
| 720 |
// int[] freqs = lexicon.getFreq();
|
|
| 721 |
// String[] forms = lexicon.getForms();
|
|
| 722 |
// try {
|
|
| 723 |
// addVectorToWorkspace(variableName, freqs);
|
|
| 724 |
// addVectorToWorkspace(variableName + "_names", forms); //$NON-NLS-1$
|
|
| 725 |
// connection
|
|
| 726 |
// .voidEval("names(" + variableName + ") <- " + variableName + "_names"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 727 |
// connection.voidEval("rm(" + variableName + "_names" + ")"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 728 |
// } catch (RserveException e) {
|
|
| 729 |
// throw new RWorkspaceException(e);
|
|
| 730 |
// }
|
|
| 731 |
// Log.finest("LEXICON_ADDED" + new Object[] { lexicon.nbrOfType() + variableName }); //$NON-NLS-1$
|
|
| 732 |
// }
|
|
| 733 |
|
|
| 722 |
|
|
| 723 |
// TODO: is addLexiconToWorkspace used ?
|
|
| 724 |
// /**
|
|
| 725 |
// * Adds the lexicon to workspace.
|
|
| 726 |
// *
|
|
| 727 |
// * @param variableName the variable name
|
|
| 728 |
// * @param lexicon the lexicon
|
|
| 729 |
// * @throws RWorkspaceException the r workspace exception
|
|
| 730 |
// */
|
|
| 731 |
// public void addLexiconToWorkspace(String variableName, Lexicon lexicon)
|
|
| 732 |
// throws RWorkspaceException {
|
|
| 733 |
// int[] freqs = lexicon.getFreq();
|
|
| 734 |
// String[] forms = lexicon.getForms();
|
|
| 735 |
// try {
|
|
| 736 |
// addVectorToWorkspace(variableName, freqs);
|
|
| 737 |
// addVectorToWorkspace(variableName + "_names", forms); //$NON-NLS-1$
|
|
| 738 |
// connection
|
|
| 739 |
// .voidEval("names(" + variableName + ") <- " + variableName + "_names"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 740 |
// connection.voidEval("rm(" + variableName + "_names" + ")"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 741 |
// } catch (RserveException e) {
|
|
| 742 |
// throw new RWorkspaceException(e);
|
|
| 743 |
// }
|
|
| 744 |
// Log.finest("LEXICON_ADDED" + new Object[] { lexicon.nbrOfType() + variableName }); //$NON-NLS-1$
|
|
| 745 |
// }
|
|
| 746 |
|
|
| 734 | 747 |
/** |
| 735 | 748 |
* Add a matrix into the workspace and link it to a name. The inner arrays |
| 736 | 749 |
* of the <code>matrix</code> parameters are the <strong>row</strong> of the |
| ... | ... | |
| 738 | 751 |
* |
| 739 | 752 |
* @param variableName the name to be used in the R workspace. |
| 740 | 753 |
* @param matrix the data to be bound to the name. In the form |
| 741 |
* <code>matrix[row][column]</code>, with exactly the same number |
|
| 742 |
* of column in every row. |
|
| 754 |
* <code>matrix[row][column]</code>, with exactly the same number
|
|
| 755 |
* of column in every row.
|
|
| 743 | 756 |
* @throws RWorkspaceException the r workspace exception |
| 744 | 757 |
*/ |
| 745 | 758 |
public void addMatrixToWorkspace(String variableName, int[][] matrix) throws RWorkspaceException {
|
| ... | ... | |
| 752 | 765 |
|
| 753 | 766 |
addMatrixToWorkspace(variableName, matrix, ncol, nrow); |
| 754 | 767 |
} |
| 768 |
|
|
| 755 | 769 |
/** |
| 756 | 770 |
* Add a matrix into the workspace and link it to a name. The inner arrays |
| 757 | 771 |
* of the <code>matrix</code> parameters are the <strong>row</strong> of the |
| ... | ... | |
| 759 | 773 |
* |
| 760 | 774 |
* @param variableName the name to be used in the R workspace. |
| 761 | 775 |
* @param matrix the data to be bound to the name. In the form |
| 762 |
* <code>matrix[row][column]</code>, with exactly the same number |
|
| 763 |
* of column in every row. |
|
| 776 |
* <code>matrix[row][column]</code>, with exactly the same number
|
|
| 777 |
* of column in every row.
|
|
| 764 | 778 |
* @throws RWorkspaceException the r workspace exception |
| 765 | 779 |
*/ |
| 766 | 780 |
public void addMatrixToWorkspace(String variableName, int[][] matrix, int ncol, int nrow) throws RWorkspaceException {
|
| ... | ... | |
| 769 | 783 |
if (!filecommunication) {
|
| 770 | 784 |
try {
|
| 771 | 785 |
connection.assign(variableName, vector); |
| 772 |
} catch (REngineException e) {
|
|
| 786 |
} |
|
| 787 |
catch (REngineException e) {
|
|
| 773 | 788 |
throw new RWorkspaceException(e); |
| 774 | 789 |
} |
| 775 | 790 |
try {
|
| ... | ... | |
| 777 | 792 |
|
| 778 | 793 |
Log.finest("MATRIX_ADDED_TO_WORKSPACE: " + command); //$NON-NLS-1$
|
| 779 | 794 |
|
| 780 |
connection.voidEval(command); |
|
| 781 |
} catch (RserveException e) {
|
|
| 795 |
connection.voidEval(command); |
|
| 796 |
} |
|
| 797 |
catch (RserveException e) {
|
|
| 782 | 798 |
throw new RWorkspaceException(e); |
| 783 | 799 |
} |
| 784 | 800 |
} |
| ... | ... | |
| 787 | 803 |
} |
| 788 | 804 |
Log.finest("MATRIX_ADDED_TO_WORKSPACE" + new Object[] { nrow, ncol, variableName }); //$NON-NLS-1$
|
| 789 | 805 |
} |
| 790 |
|
|
| 806 |
|
|
| 791 | 807 |
/** |
| 792 | 808 |
* Adds the vector to workspace. |
| 793 | 809 |
* |
| ... | ... | |
| 802 | 818 |
else {
|
| 803 | 819 |
try {
|
| 804 | 820 |
connection.assign(variableName, vector); |
| 805 |
} catch (REngineException e) {
|
|
| 821 |
} |
|
| 822 |
catch (REngineException e) {
|
|
| 806 | 823 |
throw new RWorkspaceException(e); |
| 807 | 824 |
} |
| 808 | 825 |
} |
| 809 |
|
|
| 826 |
|
|
| 810 | 827 |
Log.finest("DOUBLE_VECTOR_ADDED_TO_WORKSPACE" + new Object[] { vector.length, variableName }); //$NON-NLS-1$
|
| 811 | 828 |
} |
| 812 |
|
|
| 829 |
|
|
| 813 | 830 |
/** |
| 814 | 831 |
* Add a vector into the workspace and link it to a name. |
| 815 | 832 |
* |
| ... | ... | |
| 818 | 835 |
* @throws RWorkspaceException the r workspace exception |
| 819 | 836 |
*/ |
| 820 | 837 |
public void addVectorToWorkspace(String variableName, DoubleArrayList vector) throws RWorkspaceException {
|
| 821 |
|
|
| 838 |
|
|
| 822 | 839 |
vector.trimToSize(); |
| 823 | 840 |
double[] vald = vector.elements(); |
| 824 | 841 |
if (filecommunication) {
|
| ... | ... | |
| 827 | 844 |
else {
|
| 828 | 845 |
try {
|
| 829 | 846 |
connection.assign(variableName, vald); |
| 830 |
} catch (REngineException e) {
|
|
| 847 |
} |
|
| 848 |
catch (REngineException e) {
|
|
| 831 | 849 |
throw new RWorkspaceException(e); |
| 832 | 850 |
} |
| 833 | 851 |
} |
| 834 | 852 |
Log.finest("DOUBLE_VECTOR_ADDED_TO_WORKSPACE" + new Object[] { vald.length, variableName }); //$NON-NLS-1$
|
| 835 | 853 |
} |
| 836 |
|
|
| 854 |
|
|
| 837 | 855 |
/** |
| 838 | 856 |
* Adds the vector to workspace. |
| 839 | 857 |
* |
| ... | ... | |
| 842 | 860 |
* @throws RWorkspaceException the r workspace exception |
| 843 | 861 |
*/ |
| 844 | 862 |
public void addVectorToWorkspace(String variableName, int[] vector) throws RWorkspaceException {
|
| 845 |
//checkForDuplicateVariable(variableName); |
|
| 863 |
// checkForDuplicateVariable(variableName);
|
|
| 846 | 864 |
if (filecommunication) {
|
| 847 | 865 |
comm.assign(variableName, vector); |
| 848 | 866 |
} |
| 849 | 867 |
else {
|
| 850 | 868 |
try {
|
| 851 | 869 |
connection.assign(variableName, vector); |
| 852 |
} catch (REngineException e) {
|
|
| 870 |
} |
|
| 871 |
catch (REngineException e) {
|
|
| 853 | 872 |
throw new RWorkspaceException(e); |
| 854 | 873 |
} |
| 855 | 874 |
} |
| 856 |
|
|
| 875 |
|
|
| 857 | 876 |
Log.finest("INT_VECTOR_ADDED_TO_WORKSPACE" + new Object[] { vector.length, variableName }); //$NON-NLS-1$
|
| 858 | 877 |
} |
| 859 |
|
|
| 878 |
|
|
| 860 | 879 |
/** |
| 861 | 880 |
* Adds the vector to workspace. |
| 862 | 881 |
* |
| ... | ... | |
| 869 | 888 |
int[] vald = vector.elements(); |
| 870 | 889 |
if (filecommunication) {
|
| 871 | 890 |
comm.assign(variableName, vald); |
| 872 |
} else {
|
|
| 891 |
} |
|
| 892 |
else {
|
|
| 873 | 893 |
try {
|
| 874 | 894 |
connection.assign(variableName, vald); |
| 875 |
} catch (REngineException e) {
|
|
| 895 |
} |
|
| 896 |
catch (REngineException e) {
|
|
| 876 | 897 |
throw new RWorkspaceException(e); |
| 877 | 898 |
} |
| 878 | 899 |
} |
| 879 |
|
|
| 900 |
|
|
| 880 | 901 |
Log.finest("INT_VECTOR_ADDED_TO_WORKSPACE" + new Object[] { vald.length, variableName }); //$NON-NLS-1$
|
| 881 | 902 |
} |
| 882 |
|
|
| 903 |
|
|
| 883 | 904 |
// -------------------------------------- |
| 884 |
|
|
| 905 |
|
|
| 885 | 906 |
/** |
| 886 | 907 |
* Adds the vector to workspace. |
| 887 | 908 |
* |
| ... | ... | |
| 890 | 911 |
* @throws RWorkspaceException the r workspace exception |
| 891 | 912 |
*/ |
| 892 | 913 |
public void addVectorToWorkspace(String variableName, String[] vector) throws RWorkspaceException {
|
| 893 |
|
|
| 914 |
|
|
| 894 | 915 |
try {
|
| 895 | 916 |
connection.assign(variableName, vector); |
| 896 |
} catch (REngineException e) {
|
|
| 917 |
} |
|
| 918 |
catch (REngineException e) {
|
|
| 897 | 919 |
throw new RWorkspaceException(e); |
| 898 | 920 |
} |
| 899 |
|
|
| 921 |
|
|
| 900 | 922 |
Log.finest("CHAR_VECTOR_ADDED_TO_WORKSPACE" + new Object[] { vector.length, variableName }); //$NON-NLS-1$
|
| 901 | 923 |
} |
| 902 |
|
|
| 924 |
|
|
| 903 | 925 |
/** |
| 904 | 926 |
* Assign col names to matrix. |
| 905 | 927 |
* |
| ... | ... | |
| 910 | 932 |
public void assignColNamesToMatrix(String matrix, String colNames) throws RWorkspaceException {
|
| 911 | 933 |
voidEval("colnames(" + matrix + ") <- " + colNames); //$NON-NLS-1$ //$NON-NLS-2$
|
| 912 | 934 |
} |
| 913 |
|
|
| 935 |
|
|
| 914 | 936 |
/** |
| 915 | 937 |
* Assign row names to matrix. |
| 916 | 938 |
* |
| ... | ... | |
| 922 | 944 |
throws RWorkspaceException {
|
| 923 | 945 |
voidEval("rownames(" + matrix + ") <- " + rowNames); //$NON-NLS-1$ //$NON-NLS-2$
|
| 924 | 946 |
} |
| 925 |
|
|
| 947 |
|
|
| 926 | 948 |
/** |
| 927 | 949 |
* Builds the string args. |
| 928 | 950 |
* |
| ... | ... | |
| 936 | 958 |
if (arguments[i] == null) { // null may be used for specif ying
|
| 937 | 959 |
// "NULL" R object. |
| 938 | 960 |
arguments_as_string[i] = "NULL"; //$NON-NLS-1$ |
| 939 |
} else {
|
|
| 961 |
} |
|
| 962 |
else {
|
|
| 940 | 963 |
if (!containsVariable(arguments[i].getSymbol())) {
|
| 941 |
throw new RWorkspaceException(NLS.bind(RCoreMessages.error_requestedObjectNotFoundInR, arguments[i].getSymbol()));
|
|
| 964 |
throw new RWorkspaceException(NLS.bind(RCoreMessages.error_requestedObjectNotFoundInR, arguments[i].getSymbol())); |
|
| 942 | 965 |
} |
| 943 | 966 |
arguments_as_string[i] = arguments[i].getSymbol(); |
| 944 | 967 |
} |
| 945 | 968 |
} |
| 946 | 969 |
return arguments_as_string; |
| 947 | 970 |
} |
| 948 |
|
|
| 971 |
|
|
| 949 | 972 |
/** |
| 950 | 973 |
* Call a function, with an array of {@link QuantitativeDataStructure}.
|
| 951 | 974 |
* |
| ... | ... | |
| 965 | 988 |
String[] arguments_as_string = buildStringArgs(arguments); |
| 966 | 989 |
return callFunction(functionName, arguments_as_string); |
| 967 | 990 |
} |
| 968 |
|
|
| 991 |
|
|
| 969 | 992 |
/** |
| 970 | 993 |
* Call a function, with an array of {@link QuantitativeDataStructure}.
|
| 971 | 994 |
* |
| ... | ... | |
| 986 | 1009 |
String[] arguments_as_string = buildStringArgs(arguments); |
| 987 | 1010 |
return callFunctionAndAffect(functionName, arguments_as_string, symbol); |
| 988 | 1011 |
} |
| 989 |
|
|
| 1012 |
|
|
| 990 | 1013 |
/** |
| 991 | 1014 |
* See {@link #callFunction(String, String[])}.
|
| 992 | 1015 |
* |
| ... | ... | |
| 998 | 1021 |
public REXP callFunction(String functionName, String argument) throws RWorkspaceException {
|
| 999 | 1022 |
return callFunction(functionName, new String[] { argument });
|
| 1000 | 1023 |
} |
| 1001 |
|
|
| 1024 |
|
|
| 1002 | 1025 |
/** |
| 1003 | 1026 |
* Call a function, with a list of non-named parameters, and return the |
| 1004 | 1027 |
* result as a <code>REXP</code> object. |
| ... | ... | |
| 1010 | 1033 |
*/ |
| 1011 | 1034 |
public REXP callFunction(String functionName, String[] arguments) |
| 1012 | 1035 |
throws RWorkspaceException {
|
| 1013 |
//return eval(makeFunctionCall(functionName, arguments)); |
|
| 1036 |
// return eval(makeFunctionCall(functionName, arguments));
|
|
| 1014 | 1037 |
return callFunctionAndAffect(functionName, arguments, "txmresult"); //$NON-NLS-1$ |
| 1015 | 1038 |
} |
| 1016 |
|
|
| 1039 |
|
|
| 1017 | 1040 |
/** |
| 1018 | 1041 |
* Same as {@link #callFunction(String, String[])}, but affect the result to
|
| 1019 | 1042 |
* a R name in the R workspace. |
| ... | ... | |
| 1025 | 1048 |
* @throws RWorkspaceException the r workspace exception |
| 1026 | 1049 |
*/ |
| 1027 | 1050 |
public REXP callFunctionAndAffect(String functionName, String[] arguments, String symbol) throws RWorkspaceException {
|
| 1028 |
//symbol must be well formed |
|
| 1051 |
// symbol must be well formed
|
|
| 1029 | 1052 |
if (symbol.length() == 0) {
|
| 1030 | 1053 |
symbol = "txmresult"; //$NON-NLS-1$ |
| 1031 | 1054 |
} |
| ... | ... | |
| 1035 | 1058 |
sb.append(makeFunctionCall(functionName, arguments)); |
| 1036 | 1059 |
return eval(sb.toString()); |
| 1037 | 1060 |
} |
| 1038 |
|
|
| 1061 |
|
|
| 1039 | 1062 |
/** |
| 1040 | 1063 |
* Check for duplicate variable. |
| 1041 | 1064 |
* |
| ... | ... | |
| 1048 | 1071 |
throw new RObjectAlreadyExist("Duplicate variable name: " + variableName + ". Existing variables: " + Arrays.toString(this.getExistingVariableName())); //$NON-NLS-1$ //$NON-NLS-2$
|
| 1049 | 1072 |
} |
| 1050 | 1073 |
} |
| 1051 |
|
|
| 1052 |
|
|
| 1074 |
|
|
| 1075 |
|
|
| 1053 | 1076 |
/** |
| 1054 | 1077 |
* Remove all variables from workspace. |
| 1055 | 1078 |
* |
| ... | ... | |
| 1058 | 1081 |
public void clearWorkspace() throws RWorkspaceException {
|
| 1059 | 1082 |
try {
|
| 1060 | 1083 |
connection.voidEval("rm(list=ls(), inherits=FALSE)"); //$NON-NLS-1$
|
| 1061 |
} catch (RserveException e) {
|
|
| 1084 |
} |
|
| 1085 |
catch (RserveException e) {
|
|
| 1062 | 1086 |
throw new RWorkspaceException(e); |
| 1063 | 1087 |
} |
| 1064 | 1088 |
Log.finest("R WORKSPACE_PURGED"); //$NON-NLS-1$
|
| 1065 | 1089 |
} |
| 1066 |
|
|
| 1090 |
|
|
| 1067 | 1091 |
/** |
| 1068 | 1092 |
* connect to Rserve using the defaults address and port 127.0.0.1:6311 |
| 1069 | 1093 |
* |
| ... | ... | |
| 1073 | 1097 |
private boolean connect() throws RWorkspaceException {
|
| 1074 | 1098 |
return connect("127.0.0.1", 6311); //$NON-NLS-1$
|
| 1075 | 1099 |
} |
| 1076 |
|
|
| 1100 |
|
|
| 1077 | 1101 |
/** |
| 1078 | 1102 |
* Test if a variable exists in the R workspace. A variable exists in the R |
| 1079 | 1103 |
* workspace if the R function <code>exists</code> return true on that |
| ... | ... | |
| 1081 | 1105 |
* |
| 1082 | 1106 |
* @param variableName the variable supposed to exists in the R workspace. |
| 1083 | 1107 |
* @return <code>true</code> if the variable exist, <code>false</code> |
| 1084 |
* otherwise. |
|
| 1108 |
* otherwise.
|
|
| 1085 | 1109 |
* @throws RWorkspaceException the r workspace exception |
| 1086 | 1110 |
*/ |
| 1087 | 1111 |
public boolean containsVariable(String variableName) |
| ... | ... | |
| 1089 | 1113 |
REXP res = null; |
| 1090 | 1114 |
try {
|
| 1091 | 1115 |
res = connection.eval("exists(\"" + variableName + "\")"); //$NON-NLS-1$ //$NON-NLS-2$
|
| 1092 |
} catch (RserveException e) {
|
|
| 1116 |
} |
|
| 1117 |
catch (RserveException e) {
|
|
| 1093 | 1118 |
throw new RWorkspaceException(e); |
| 1094 | 1119 |
} |
| 1095 | 1120 |
if (res.isLogical() && ((REXPLogical) res).isTRUE()[0]) {
|
| ... | ... | |
| 1097 | 1122 |
} |
| 1098 | 1123 |
return false; |
| 1099 | 1124 |
} |
| 1100 |
|
|
| 1125 |
|
|
| 1101 | 1126 |
/** |
| 1102 | 1127 |
* Bar delegate call to {@link Rengine#eval(String)}.
|
| 1103 | 1128 |
* |
| ... | ... | |
| 1112 | 1137 |
REXP res = null; |
| 1113 | 1138 |
try {
|
| 1114 | 1139 |
res = safeEval(exp); |
| 1115 |
} catch (RserveException e) {
|
|
| 1140 |
} |
|
| 1141 |
catch (RserveException e) {
|
|
| 1116 | 1142 |
RWorkspace.printLastSafeEvalExpr(); |
| 1117 | 1143 |
throw new RWorkspaceException(e); |
| 1118 |
} catch (Exception e) {
|
|
| 1144 |
} |
|
| 1145 |
catch (Exception e) {
|
|
| 1119 | 1146 |
throw new RException(exp + "; " + e.getMessage(), e); //$NON-NLS-1$ |
| 1120 | 1147 |
} |
| 1121 |
|
|
| 1148 |
|
|
| 1122 | 1149 |
return res; |
| 1123 | 1150 |
} |
| 1124 |
|
|
| 1151 |
|
|
| 1125 | 1152 |
/** |
| 1126 | 1153 |
* Eval to double. |
| 1127 | 1154 |
* |
| ... | ... | |
| 1133 | 1160 |
double[] res = null; |
| 1134 | 1161 |
try {
|
| 1135 | 1162 |
res = eval(exp).asDoubles(); |
| 1136 |
} catch (Exception e) {
|
|
| 1163 |
} |
|
| 1164 |
catch (Exception e) {
|
|
| 1137 | 1165 |
throw new RWorkspaceException(e); |
| 1138 | 1166 |
} |
| 1139 | 1167 |
return res; |
| 1140 | 1168 |
} |
| 1141 |
|
|
| 1169 |
|
|
| 1142 | 1170 |
// public REXP safeVoidEval(String s) throws RserveException, RException, |
| 1143 | 1171 |
// REXPMismatchException {
|
| 1144 | 1172 |
// REXP r = connection.voidEval("try({" + s + "}, silent=TRUE)");
|
| 1145 | 1173 |
// if (r.inherits("try-error")) throw new RException(r.asString());
|
| 1146 | 1174 |
// return r; |
| 1147 | 1175 |
// } |
| 1148 |
|
|
| 1176 |
|
|
| 1149 | 1177 |
/** |
| 1150 | 1178 |
* Eval to double2 d. |
| 1151 | 1179 |
* |
| ... | ... | |
| 1157 | 1185 |
double[][] res = null; |
| 1158 | 1186 |
try {
|
| 1159 | 1187 |
res = eval(exp).asDoubleMatrix(); |
| 1160 |
} catch (Exception e) {
|
|
| 1188 |
} |
|
| 1189 |
catch (Exception e) {
|
|
| 1161 | 1190 |
throw new RWorkspaceException(e); |
| 1162 | 1191 |
} |
| 1163 | 1192 |
return res; |
| 1164 | 1193 |
} |
| 1165 |
|
|
| 1194 |
|
|
| 1166 | 1195 |
/* |
| 1167 | 1196 |
* Eval to int 2d. |
| 1168 |
* |
|
| 1169 | 1197 |
* @param exp the exp |
| 1170 | 1198 |
* @return the double[][] |
| 1171 | 1199 |
* @throws RWorkspaceException the r workspace exception |
| ... | ... | |
| 1176 | 1204 |
int[] dims = eval("dim(" + exp + ")").asIntegers(); //$NON-NLS-1$ //$NON-NLS-2$
|
| 1177 | 1205 |
int ncol = dims[1]; |
| 1178 | 1206 |
int nrow = dims[0]; |
| 1179 |
int[] tmp = eval("c("+exp+")").asIntegers(); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 1180 |
|
|
| 1207 |
int[] tmp = eval("c(" + exp + ")").asIntegers(); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 1208 |
|
|
| 1181 | 1209 |
int c = 0; |
| 1182 | 1210 |
res = new int[nrow][ncol]; |
| 1183 |
for (int i = 0 ; i < ncol ; i++) {
|
|
| 1184 |
for (int j = 0 ; j < nrow ; j++) {
|
|
| 1211 |
for (int i = 0; i < ncol; i++) {
|
|
| 1212 |
for (int j = 0; j < nrow; j++) {
|
|
| 1185 | 1213 |
res[j][i] = tmp[c++]; |
| 1186 | 1214 |
} |
| 1187 | 1215 |
} |
| 1188 |
} catch (Exception e) {
|
|
| 1216 |
} |
|
| 1217 |
catch (Exception e) {
|
|
| 1189 | 1218 |
throw new RWorkspaceException(e); |
| 1190 | 1219 |
} |
| 1191 | 1220 |
return res; |
| 1192 | 1221 |
} |
| 1193 |
|
|
| 1222 |
|
|
| 1194 | 1223 |
/** |
| 1195 | 1224 |
* Eval to string. |
| 1196 | 1225 |
* |
| ... | ... | |
| 1202 | 1231 |
String[] res = null; |
| 1203 | 1232 |
try {
|
| 1204 | 1233 |
res = eval(exp).asStrings(); |
| 1205 |
} catch (Exception e) {
|
|
| 1234 |
} |
|
| 1235 |
catch (Exception e) {
|
|
| 1206 | 1236 |
throw new RWorkspaceException(e); |
| 1207 | 1237 |
} |
| 1208 | 1238 |
return res; |
| 1209 | 1239 |
} |
| 1210 |
|
|
| 1240 |
|
|
| 1211 | 1241 |
/** |
| 1212 | 1242 |
* Extract item from list by name. |
| 1213 | 1243 |
* |
| ... | ... | |
| 1219 | 1249 |
public REXP extractItemFromListByName(REXP list, String item_name) throws RWorkspaceException {
|
| 1220 | 1250 |
try {
|
| 1221 | 1251 |
return list.asList().at(item_name); |
| 1222 |
} catch (Exception e) {
|
|
| 1252 |
} |
|
| 1253 |
catch (Exception e) {
|
|
| 1223 | 1254 |
throw new RWorkspaceException(RCoreMessages.error_errorDuringItemsListExtraction |
| 1224 |
+ e.getMessage());
|
|
| 1255 |
+ e.getMessage()); |
|
| 1225 | 1256 |
} |
| 1226 | 1257 |
} |
| 1227 |
|
|
| 1258 |
|
|
| 1228 | 1259 |
/** |
| 1229 | 1260 |
* Extract item from list by name. |
| 1230 | 1261 |
* |
| ... | ... | |
| 1236 | 1267 |
public REXP extractItemFromListByName(String list_symbol, String item_name) throws RWorkspaceException {
|
| 1237 | 1268 |
return eval(list_symbol + RConstant.LIST_EXTRACTOR + item_name); |
| 1238 | 1269 |
} |
| 1239 |
|
|
| 1270 |
|
|
| 1240 | 1271 |
/** |
| 1241 | 1272 |
* Gets the connection. |
| 1242 | 1273 |
* |
| ... | ... | |
| 1245 | 1276 |
public RConnection getConnection() {
|
| 1246 | 1277 |
return connection; |
| 1247 | 1278 |
} |
| 1248 |
|
|
| 1279 |
|
|
| 1249 | 1280 |
public StreamHog getErrorLogger() {
|
| 1250 | 1281 |
return errorLogger; |
| 1251 | 1282 |
} |
| 1252 |
|
|
| 1283 |
|
|
| 1253 | 1284 |
// -------------------------------------- |
| 1254 |
|
|
| 1285 |
|
|
| 1255 | 1286 |
/** |
| 1256 | 1287 |
* Gets the existing variable name. |
| 1257 | 1288 |
* |
| ... | ... | |
| 1262 | 1293 |
REXP res; |
| 1263 | 1294 |
try {
|
| 1264 | 1295 |
res = connection.eval("ls()"); //$NON-NLS-1$
|
| 1265 |
} catch (RserveException e) {
|
|
| 1296 |
} |
|
| 1297 |
catch (RserveException e) {
|
|
| 1266 | 1298 |
throw new RWorkspaceException(e); |
| 1267 | 1299 |
} |
| 1268 | 1300 |
try {
|
| 1269 | 1301 |
return res.asStrings(); |
| 1270 |
} catch (Exception e) {
|
|
| 1302 |
} |
|
| 1303 |
catch (Exception e) {
|
|
| 1271 | 1304 |
throw new RWorkspaceException(e); |
| 1272 | 1305 |
} |
| 1273 | 1306 |
} |
| 1274 |
|
|
| 1307 |
|
|
| 1275 | 1308 |
// -------------------------------------- |
| 1276 |
|
|
| 1309 |
|
|
| 1277 | 1310 |
public StreamHog getInputLogger() {
|
| 1278 | 1311 |
return inputLogger; |
| 1279 | 1312 |
} |
| 1280 |
|
|
| 1313 |
|
|
| 1281 | 1314 |
/** |
| 1282 | 1315 |
* Gets the last error line. |
| 1283 | 1316 |
* |
| ... | ... | |
| 1286 | 1319 |
public String getLastErrorLine() {
|
| 1287 | 1320 |
return this.errorLogger.lastline; |
| 1288 | 1321 |
} |
| 1289 |
|
|
| 1322 |
|
|
| 1290 | 1323 |
/** |
| 1291 | 1324 |
* Gets the last log line. |
| 1292 | 1325 |
* |
| ... | ... | |
| 1295 | 1328 |
public String getLastLogLine() {
|
| 1296 | 1329 |
return this.inputLogger.lastline; |
| 1297 | 1330 |
} |
| 1298 |
|
|
| 1331 |
|
|
| 1299 | 1332 |
/** |
| 1300 |
* Initializes the R connection configuration (time out and proxy configuration, if needed). |
|
| 1333 |
* Initializes the R connection configuration (time out and proxy configuration, if needed). |
|
| 1334 |
* |
|
| 1301 | 1335 |
* @param conf |
| 1302 | 1336 |
* @throws RserveException |
| 1303 | 1337 |
*/ |
| ... | ... | |
| 1314 | 1348 |
this.getConnection().eval("Sys.setenv(http_proxy=\"" + proxyUrl + "\")"); //$NON-NLS-1$ //$NON-NLS-2$
|
| 1315 | 1349 |
} |
| 1316 | 1350 |
} |
| 1317 |
|
|
| 1351 |
|
|
| 1318 | 1352 |
/** |
| 1319 | 1353 |
* Checks if is logging. |
| 1320 | 1354 |
* |
| ... | ... | |
| 1324 | 1358 |
// TODO Auto-generated method stub |
| 1325 | 1359 |
return logging; |
| 1326 | 1360 |
} |
| 1327 |
|
|
| 1361 |
|
|
| 1328 | 1362 |
// -------------------------------------- |
| 1329 |
|
|
| 1363 |
|
|
| 1330 | 1364 |
/** |
| 1331 | 1365 |
* Make function call. |
| 1332 | 1366 |
* |
| ... | ... | |
| 1347 | 1381 |
sb.append(RConstant.CLOSE_PAREN); |
| 1348 | 1382 |
return sb.toString(); |
| 1349 | 1383 |
} |
| 1350 |
|
|
| 1384 |
|
|
| 1351 | 1385 |
@SuppressWarnings("rawtypes")
|
| 1352 | 1386 |
/** |
| 1353 | 1387 |
* Post configuration. |
| ... | ... | |
| 1360 | 1394 |
try {
|
| 1361 | 1395 |
// more logs |
| 1362 | 1396 |
connection.eval("try(options(max.print=5000))"); //$NON-NLS-1$
|
| 1363 |
|
|
| 1397 |
|
|
| 1364 | 1398 |
// set TXM R workspace directory |
| 1365 |
File RWorkspaceDirectory = new File(userdir, "R"); //$NON-NLS-1$ |
|
| 1366 |
RWorkspaceDirectory.mkdir(); |
|
| 1367 |
if (!RWorkspaceDirectory.exists()) {
|
|
| 1368 |
System.out.println("TXM R workspace directory not found: "+RWorkspaceDirectory);
|
|
| 1369 |
} else {
|
|
| 1370 |
Log.fine("Setting TXM R workspace directory: "+RWorkspaceDirectory.getAbsolutePath());
|
|
| 1371 |
connection.eval("setwd(\""+RWorkspaceDirectory.getAbsolutePath().replace("\\", "/")+"\")"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 1399 |
userdir.mkdirs(); |
|
| 1400 |
if (!userdir.exists()) {
|
|
| 1401 |
System.out.println("TXM R workspace directory not found: " + userdir);
|
|
| 1372 | 1402 |
} |
| 1373 |
|
|
| 1374 |
File RLibrariesWorkspaceDirectory = new File(RWorkspaceDirectory, "libraries"); |
|
| 1403 |
else {
|
|
| 1404 |
Log.fine("Setting TXM R workspace directory: " + userdir.getAbsolutePath());
|
|
| 1405 |
connection.eval("setwd(\"" + userdir.getAbsolutePath().replace("\\", "/") + "\")"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 1406 |
} |
|
| 1407 |
|
|
| 1408 |
File RLibrariesWorkspaceDirectory = new File(userdir, "libraries"); |
|
| 1375 | 1409 |
RLibrariesWorkspaceDirectory.mkdir(); |
| 1376 | 1410 |
if (!RLibrariesWorkspaceDirectory.exists()) {
|
| 1377 |
System.out.println("TXM R libraries workspace directory not found: "+RLibrariesWorkspaceDirectory);
|
|
| 1378 |
} else {
|
|
| 1379 |
Log.fine("Setting TXM R libraries workspace directory: "+RLibrariesWorkspaceDirectory.getAbsolutePath());
|
|
| 1380 |
connection.eval(".libPaths(c(\""+RLibrariesWorkspaceDirectory.getAbsolutePath().replace("\\", "/")+"\",.libPaths()))");//$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 1411 |
System.out.println("TXM R libraries workspace directory not found: " + RLibrariesWorkspaceDirectory);
|
|
| 1381 | 1412 |
} |
| 1382 |
|
|
| 1383 |
if (OSDetector.isFamilyWindows()) {
|
|
| 1413 |
else {
|
|
| 1414 |
Log.fine("Setting TXM R libraries workspace directory: " + RLibrariesWorkspaceDirectory.getAbsolutePath());
|
|
| 1415 |
connection.eval(".libPaths(c(\"" + RLibrariesWorkspaceDirectory.getAbsolutePath().replace("\\", "/") + "\",.libPaths()))");//$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 1416 |
} |
|
| 1417 |
|
|
| 1418 |
if (OSDetector.isFamilyWindows()) {
|
|
| 1384 | 1419 |
rPackagesPath = rPackagesPath.replace("\\", "/"); //$NON-NLS-1$ //$NON-NLS-2$
|
| 1385 | 1420 |
} |
| 1386 |
|
|
| 1421 |
|
|
| 1387 | 1422 |
// set proxy configuration using detected system proxy if exists |
| 1388 | 1423 |
SystemProxyDetector conf = new SystemProxyDetector(); |
| 1389 | 1424 |
this.initializeRWorkspaceConnectionConfiguration(conf); |
| 1390 |
|
|
| 1425 |
|
|
| 1391 | 1426 |
// load R libraries: this is now done by extensions/commands themself |
| 1392 | 1427 |
try {
|
| 1393 | 1428 |
init(); // load libs |
| 1394 |
} catch (RWorkspaceException e) {
|
|
| 1429 |
} |
|
| 1430 |
catch (RWorkspaceException e) {
|
|
| 1395 | 1431 |
org.txm.utils.logger.Log.printStackTrace(e); |
| 1396 | 1432 |
return false; |
| 1397 | 1433 |
} |
| 1398 |
|
|
| 1399 |
//connection.eval("try(.libPaths(\"" + rPackagesPath + "\"))"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 1400 |
|
|
| 1434 |
|
|
| 1435 |
// connection.eval("try(.libPaths(\"" + rPackagesPath + "\"))"); //$NON-NLS-1$ //$NON-NLS-2$
|
|
| 1436 |
|
|
| 1401 | 1437 |
return true; |
| 1402 |
} catch (RserveException e) {
|
|
| 1438 |
} |
|
| 1439 |
catch (RserveException e) {
|
|
| 1403 | 1440 |
org.txm.utils.logger.Log.printStackTrace(e); |
| 1404 | 1441 |
} |
| 1405 | 1442 |
return false; |
| 1406 | 1443 |
} |
| 1407 |
|
|
| 1444 |
|
|
| 1408 | 1445 |
/** |
| 1409 | 1446 |
* Start logger. |
| 1410 | 1447 |
* |
| ... | ... | |
| 1417 | 1454 |
this.inputLogger = streamHog2; |
| 1418 | 1455 |
return null; |
| 1419 | 1456 |
} |
| 1420 |
|
|
| 1457 |
|
|
| 1421 | 1458 |
/** |
| 1422 | 1459 |
* Remove a variable from the workspace. The content is lost, and the name |
| 1423 | 1460 |
* refers to nothing. |
| ... | ... | |
| 1431 | 1468 |
|
| 1432 | 1469 |
try {
|
| 1433 | 1470 |
connection.voidEval("rm(" + variableName + ")"); //$NON-NLS-1$ //$NON-NLS-2$
|
| 1434 |
} catch (RserveException e) {
|
|
| 1471 |
} |
|
| 1472 |
catch (RserveException e) {
|
|
| 1435 | 1473 |
throw new RWorkspaceException(e); |
| 1436 | 1474 |
} |
| 1437 | 1475 |
Log.finest("R VARIABLE_REMOVED: " + new Object[] { variableName }); //$NON-NLS-1$
|
| 1438 | 1476 |
} |
| 1439 |
|
|
| 1477 |
|
|
| 1440 | 1478 |
/** |
| 1441 | 1479 |
* Casts the specified REXP to a displayable object. |
| 1442 | 1480 |
* |
| 1443 | 1481 |
* @param rexp |
| 1444 | 1482 |
* @return the casted object : String, int, etc. |
| 1445 | 1483 |
*/ |
| 1446 |
public Object getCastedREXP(REXP rexp) {
|
|
| 1484 |
public Object getCastedREXP(REXP rexp) {
|
|
| 1447 | 1485 |
try {
|
| 1448 | 1486 |
if (rexp instanceof org.rosuda.REngine.REXPString) {
|
| 1449 | 1487 |
if (rexp.isVector()) {
|
| ... | ... | |
| 1451 | 1489 |
} |
| 1452 | 1490 |
else {
|
| 1453 | 1491 |
return rexp.asString(); |
| 1454 |
}
|
|
| 1455 |
}
|
|
| 1492 |
} |
|
| 1493 |
} |
|
| 1456 | 1494 |
else if (rexp instanceof org.rosuda.REngine.REXPDouble) {
|
| 1457 | 1495 |
if (rexp.isVector()) {
|
| 1458 | 1496 |
return Arrays.toString(rexp.asDoubles()); |
| ... | ... | |
| 1490 | 1528 |
* @throws REXPMismatchException the rEXP mismatch exception |
| 1491 | 1529 |
*/ |
| 1492 | 1530 |
public REXP safeEval(String expr) throws RserveException, RException, REXPMismatchException {
|
| 1493 |
if (logging && inputLogger != null ) {
|
|
| 1531 |
if (logging && inputLogger != null) {
|
|
| 1494 | 1532 |
inputLogger.printMessage(expr); |
| 1495 | 1533 |
} |
| 1496 | 1534 |
lastSafeevalExpr = expr; |
| 1497 | 1535 |
|
| 1498 | 1536 |
expr = "try({" + expr + "}, silent=FALSE)";
|
| 1499 | 1537 |
|
| 1500 |
if(isLoggingEvalCommandLines()) {
|
|
| 1501 |
//TODO SJ: for debuggin puprose |
|
| 1502 |
//Log.info("R safeEval: " + expr, 8); //$NON-NLS-1$
|
|
| 1538 |
if (isLoggingEvalCommandLines()) {
|
|
| 1539 |
// TODO SJ: for debuggin puprose
|
|
| 1540 |
// Log.info("R safeEval: " + expr, 8); //$NON-NLS-1$
|
|
| 1503 | 1541 |
Log.info("R safeEval: " + expr); //$NON-NLS-1$
|
| 1504 | 1542 |
} |
| 1505 | 1543 |
|
| 1506 | 1544 |
REXP r = null; |
| 1507 | 1545 |
try {
|
| 1508 | 1546 |
r = connection.eval(expr); |
| 1509 |
if(isLoggingEvalCommandLines()) {
|
|
| 1547 |
if (isLoggingEvalCommandLines()) {
|
|
| 1510 | 1548 |
Log.info(" return: " + this.getCastedREXP(r)); //$NON-NLS-1$
|
| 1511 | 1549 |
} |
| 1512 | 1550 |
} |
| ... | ... | |
| 1514 | 1552 |
// TODO Auto-generated catch block |
| 1515 | 1553 |
e.printStackTrace(); |
| 1516 | 1554 |
} |
| 1517 |
finally {
|
|
| 1518 |
if (r !=null && r.inherits("try-error")) {
|
|
| 1519 |
throw new RException(expr, r.asString()); //$NON-NLS-1$
|
|
| 1555 |
finally {
|
|
| 1556 |
if (r != null && r.inherits("try-error")) {
|
|
| 1557 |
throw new RException(expr, r.asString()); |
|
| 1520 | 1558 |
} |
| 1521 | 1559 |
} |
| 1522 | 1560 |
return r; |
| 1523 | 1561 |
} |
| 1524 |
|
|
| 1525 | 1562 |
|
| 1563 |
|
|
| 1526 | 1564 |
/** |
| 1527 |
|
|
| 1565 |
* |
|
| 1528 | 1566 |
* Bar delegate call to {@link Connection#voidEval(String)}.
|
| 1529 | 1567 |
* |
| 1530 | 1568 |
* It is up to the caller to check if everything goes well (testing if the |
| ... | ... | |
| 1537 | 1575 |
public String userEval(String exp) throws RWorkspaceException {
|
| 1538 | 1576 |
if (exp.trim().length() == 0) |
| 1539 | 1577 |
return ""; //$NON-NLS-1$ |
| 1540 |
//if (loggin) |
|
| 1541 |
//System.out.println("R>"+exp); //$NON-NLS-1$
|
|
| 1542 |
|
|
| 1578 |
// if (loggin)
|
|
| 1579 |
// System.out.println("R>"+exp); //$NON-NLS-1$
|
|
| 1580 |
|
|
| 1543 | 1581 |
if (exp.endsWith(";")) //$NON-NLS-1$
|
| 1544 |
exp = exp.substring(0, exp.length()-1);
|
|
| 1545 |
|
|
| 1546 |
// String trybegin = "try("; //$NON-NLS-1$
|
|
| 1547 |
// String tryend = ")"; //$NON-NLS-1$
|
|
| 1548 |
|
|
| 1582 |
exp = exp.substring(0, exp.length() - 1);
|
|
| 1583 |
|
|
| 1584 |
// String trybegin = "try("; //$NON-NLS-1$
|
|
| 1585 |
// String tryend = ")"; //$NON-NLS-1$
|
|
| 1586 |
|
|
| 1549 | 1587 |
String out = null; |
| 1550 | 1588 |
try {
|
| 1551 |
if (isLoggingEvalCommandLines()) {
|
|
| 1552 |
Log.info("R userEval: " + exp ); //$NON-NLS-1$
|
|
| 1589 |
if (isLoggingEvalCommandLines()) {
|
|
| 1590 |
Log.info("R userEval: " + exp); //$NON-NLS-1$
|
|
| 1553 | 1591 |
} |
| 1554 |
//out = connection.eval("paste(capture.output(print(" + trybegin + trybegin +"("+ exp+")" + tryend + tryend + ")),collapse=\"\\n\")").asString(); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 1555 |
//String cmd = "paste(capture.output(print(" + trybegin + "("+ exp+")" + tryend + ")),collapse=\"\\n\")"; //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 1556 |
REXP ret = connection.eval(exp); |
|
| 1557 |
//REXP ret = connection.eval(exp); |
|
| 1558 |
|
|
| 1592 |
// out = connection.eval("paste(capture.output(print(" + trybegin + trybegin +"("+ exp+")" + tryend + tryend + ")),collapse=\"\\n\")").asString(); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
|
|
| 1593 |
// //$NON-NLS-4$ |
|
| 1594 |
// String cmd = "paste(capture.output(print(" + trybegin + "("+ exp+")" + tryend + ")),collapse=\"\\n\")"; //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
|
|
| 1595 |
REXP ret = connection.eval(exp); |
|
| 1596 |
// REXP ret = connection.eval(exp); |
|
| 1597 |
|
|
| 1559 | 1598 |
if (ret instanceof org.rosuda.REngine.REXPString) {
|
| 1560 | 1599 |
if (ret.isVector()) {
|
| 1561 |
out = "result: "+StringUtils.join(ret.asStrings(), ", "); |
|
| 1562 |
} else {
|
|
| 1563 |
out = "result: "+ret.asString(); |
|
| 1564 |
} |
|
| 1565 |
} else if (ret instanceof org.rosuda.REngine.REXPDouble) {
|
|
| 1600 |
out = "result: " + StringUtils.join(ret.asStrings(), ", "); |
|
| 1601 |
} |
|
| 1602 |
else {
|
|
| 1603 |
out = "result: " + ret.asString(); |
|
| 1604 |
} |
|
| 1605 |
} |
|
| 1606 |
else if (ret instanceof org.rosuda.REngine.REXPDouble) {
|
|
| 1566 | 1607 |
if (ret.isVector()) {
|
| 1567 |
out = "result: "+ret.asDouble(); |
|
| 1568 |
} else {
|
|
| 1569 |
out = "result: "+Arrays.toString(ret.asDoubles()); |
|
| 1608 |
out = "result: " + ret.asDouble(); |
|
| 1570 | 1609 |
} |
| 1571 |
} else if (ret instanceof org.rosuda.REngine.REXPInteger) {
|
|
| 1610 |
else {
|
|
| 1611 |
out = "result: " + Arrays.toString(ret.asDoubles()); |
|
| 1612 |
} |
|
| 1613 |
} |
|
| 1614 |
else if (ret instanceof org.rosuda.REngine.REXPInteger) {
|
|
| 1572 | 1615 |
if (ret.isVector()) {
|
| 1573 |
out = "result: "+ret.asInteger(); |
|
| 1574 |
} else {
|
|
| 1575 |
out = "result: "+Arrays.toString(ret.asIntegers()); |
|
| 1616 |
out = "result: " + ret.asInteger(); |
|
| 1576 | 1617 |
} |
| 1577 |
} else if (ret instanceof org.rosuda.REngine.REXPNull) {
|
|
| 1578 |
out = "NULL"; |
|
| 1579 |
} else {
|
|
| 1580 |
out = "result: "+ret; |
|
| 1618 |
else {
|
|
| 1619 |
out = "result: " + Arrays.toString(ret.asIntegers()); |
|
| 1620 |
} |
|
| 1581 | 1621 |
} |
| 1622 |
else if (ret instanceof org.rosuda.REngine.REXPNull) {
|
|
| 1623 |
out = "NULL"; |
|
| 1624 |
} |
|
| 1625 |
else {
|
|
| 1626 |
out = "result: " + ret; |
|
| 1627 |
} |
|
| 1582 | 1628 |
|
| 1583 |
} catch (RserveException e) {
|
|
| 1629 |
} |
|
| 1630 |
catch (RserveException e) {
|
|
| 1584 | 1631 |
System.out.println(NLS.bind(RCoreMessages.error_evaluationError, e.getMessage(), exp)); |
| 1585 | 1632 |
Log.printStackTrace(e); |
| 1586 |
} catch (Exception e) {
|
|
| 1587 |
System.out.println("REXPMismatchException: "+e);
|
|
Formats disponibles : Unified diff