com.github.rcaller.rstuff.RCaller Java Examples
The following examples show how to use
com.github.rcaller.rstuff.RCaller.
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Example #1
| Source File: RSessionWrapper.java From mzmine3 with GNU General Public License v2.0 | 5 votes |
|
private void initNewRCaller() {
this.rEngine = RCaller.create();
RCode code = RCode.create();
((RCaller) this.rEngine).setRCode(code);
this.wasRunAndReturned = false;
}
Example #2
| Source File: RSessionWrapper.java From mzmine3 with GNU General Public License v2.0 | 5 votes |
|
public void runOnlyOnline() {
if (this.rEngineType == REngineType.RCALLER) {
// Cannot 'runOnly()', all the stuff being run 'online'
((RCaller) this.rEngine).runAndReturnResultOnline("TRUE");
// ((RCaller) this.rEngine).runOnly();
}
}
Example #3
| Source File: RSessionWrapper.java From mzmine2 with GNU General Public License v2.0 | 5 votes |
|
private void initNewRCaller() {
this.rEngine = RCaller.create();
RCode code = RCode.create();
((RCaller) this.rEngine).setRCode(code);
this.wasRunAndReturned = false;
}
Example #4
| Source File: RSessionWrapper.java From mzmine2 with GNU General Public License v2.0 | 5 votes |
|
public void runOnlyOnline() {
if (this.rEngineType == REngineType.RCALLER) {
// Cannot 'runOnly()', all the stuff being run 'online'
((RCaller) this.rEngine).runAndReturnResultOnline("TRUE");
// ((RCaller) this.rEngine).runOnly();
}
}
Example #5
| Source File: RCallerMean.java From tutorials with MIT License | 5 votes |
|
/**
* Invokes the customMean R function passing the given values as arguments.
*
* @param values the input to the mean script
* @return the result of the R script
* @throws IOException if any error occurs
* @throws URISyntaxException if any error occurs
*/
public double mean(int[] values) throws IOException, URISyntaxException {
String fileContent = RUtils.getMeanScriptContent();
RCode code = RCode.create();
code.addRCode(fileContent);
code.addIntArray("input", values);
code.addRCode("result <- customMean(input)");
RCaller caller = RCaller.create(code, RCallerOptions.create());
caller.runAndReturnResult("result");
return caller.getParser()
.getAsDoubleArray("result")[0];
}
Example #6
| Source File: RSessionWrapper.java From mzmine3 with GNU General Public License v2.0 | 4 votes |
|
public void loadPackage(String packageName) throws RSessionWrapperException {
String loadCode = "library(" + packageName + ", logical.return = TRUE)";
if (TRY_MODE)
loadCode = "try(" + loadCode + ", silent=TRUE)";
String errorMsg = "The \"" + this.callerFeatureName + "\" requires " + "the \"" + packageName
+ "\" R package, which couldn't be loaded - is it installed in R?";
if (this.rEngineType == REngineType.RSERVE) {
if (this.session != null && !this.userCanceled) {
logger.log(logLvl, "Loading package '" + packageName + "'...");
int loaded = 0;
try {
REXP r = ((RConnection) this.rEngine).eval(loadCode);
if (r.inherits("try-error")) {
logger.severe("R Error [0]: " + r.asString());
logger.severe("R eval attempt [0]: " + loadCode);
}
loaded = r.asInteger();
logger.log(logLvl, "Load status: '" + (loaded != 0) + "'.");
} catch (RserveException | REXPMismatchException e) {
logger.log(logLvl, "Loaded package KO: '" + e.getMessage() + "'.");
// Remain silent if eval KO ("server down").
loaded = Integer.MIN_VALUE;
}
// Throw loading failure only if eval OK, but return FALSE
// (package not loaded).
// ("server down" case will be handled soon enough).
if (loaded == 0)
if (!this.userCanceled)
throw new RSessionWrapperException(errorMsg);
logger.log(logLvl, "Loaded package: '" + packageName + "'.");
}
} else { // RCaller
((RCaller) rEngine).getRCode().addRCode(loadCode);
// try {
//
// ((RCallerScriptEngine2) rEngine).eval(loadCode);
// } catch (ScriptException e) {
//
// if (!this.userCanceled)
// throw new RSessionWrapperException(errorMsg);
// }
}
}
Example #7
| Source File: RSessionWrapper.java From mzmine3 with GNU General Public License v2.0 | 4 votes |
|
public boolean eval(String rCode, boolean stopOnError) throws RSessionWrapperException {
// if (TRY_MODE) rCode = "try(" + rCode + ",silent=TRUE)";
if (this.rEngineType == REngineType.RSERVE) {
boolean ok = false;
if (this.session != null && !this.userCanceled) {
String msg = "Rserve error: couldn't eval R code '" + rCode + "' (instance '"
+ this.getPID() + "').";
// try {
// ////((RConnection) this.rEngine).eval(rCode);
// REXP r = ((RConnection) this.rEngine).eval(rCode);
// if (r2.inherits("try-error")) {
// logger.severe("R Error [1]: " + r.asString());
// logger.severe("R eval attempt [1]: " + rCode);
// logger.severe("Debug string" + r.toDebugString());
// }
// //else { /* success ... */ }
// logger.severe("R error [3]: " + ((RConnection)
// this.rEngine).getLastError());
// }
// catch (RserveException e) {
// logger.severe("R error [2]: " + getErrMessage());
// throw new RSessionWrapperException(msg);
// } catch (Exception e) {
// throw new RSessionWrapperException(e.getMessage());
// }
ok = this.session.voidEval(rCode, true); // TRY_MODE);
if (!ok) {
if (stopOnError)
throw new RSessionWrapperException(msg);
else
checkConnectivity();
}
}
return ok;
} else { // RCaller
try {
((RCaller) this.rEngine).getRCode().addRCode(rCode);
// ((RCallerScriptEngine2) this.rEngine).eval(rCode);
} catch (ExecutionException /* | ScriptException */ ee) { // RCaller
// exception
if (stopOnError)
throw new RSessionWrapperException(ee.getMessage());
else
return false;
}
return true;
}
}
Example #8
| Source File: RSessionWrapper.java From mzmine3 with GNU General Public License v2.0 | 4 votes |
|
public void clearCode() {
if (this.rEngineType == REngineType.RCALLER) {
((RCaller) this.rEngine).getRCode().clearOnline();
}
}
Example #9
| Source File: RSessionWrapper.java From mzmine3 with GNU General Public License v2.0 | 4 votes |
|
/**
* This can be necessary to call 'close()' from a different thread than the one which called
* 'open()', sometimes, with Rserve (if the related instance is busy).
*
* @param userCanceled Tell the application the closure came from a user action rather than from
* an unknown source error.
* @throws RSessionWrapperException
*/
public void close(boolean userCanceled) throws RSessionWrapperException {
this.userCanceled = userCanceled;
if (this.rEngineType == REngineType.RSERVE) {
if (this.session != null) {
try {
logger.log(logLvl,
"Rserve: try terminate " + ((this.rServePid == -1) ? "pending" : "") + " session"
+ ((this.rServePid == -1) ? "..."
: " (pid: '" + this.rServePid + "' | port: '" + this.session.rServeConf.port
+ "')..."));
// Avoid 'Rsession' to 'printStackTrace' while catching
// 'SocketException'
// (since we are about to brute force kill the Rserve
// instance,
// such that
// the session won't end properly).
RSessionWrapper.muteStdOutErr();
{
RSessionWrapper.killRserveInstance(this);
this.session.end();
}
RSessionWrapper.unMuteStdOutErr();
logger.log(logLvl,
"Rserve: terminated " + ((this.rServePid == -1) ? "pending" : "") + " session"
+ ((this.rServePid == -1) ? "..."
: " (pid: '" + this.rServePid + "' | port: '" + this.session.rServeConf.port
+ "')..."));
// Release session (prevents from calling close again on a
// closed instance).
this.session = null;
} catch (Throwable t) {
// Adapt/refactor message accordingly to the way the
// termination
// was provoked:
// User requested or unexpectedly...
String msg;
if (userCanceled) {
msg = "Rserve error: couldn't terminate instance with pid '" + this.rServePid
+ "'. Details:\n";
} else {
msg = "Rserve error: something when wrong with instance of pid '" + this.rServePid
+ "'. Details:\n";
}
throw new RSessionWrapperException(msg + TextUtils.wrapText(t.getMessage(), 80));
} finally {
// Make sure to restore standard outputs.
System.setOut(System.out);
System.setErr(System.err);
}
}
this.unRegister();
} else { // RCaller
// if (this.wasRunAndReturned) {
// TODO: do nothing for now, see if a special treatment is required
// when 'user canceling' a task or else !!!
((RCaller) this.rEngine).StopRCallerOnline();
// } else {
// this.runOnlyOnline();
// }
// ((RCallerScriptEngine2) this.rEngine).close();
}
}
Example #10
| Source File: RSessionWrapper.java From mzmine2 with GNU General Public License v2.0 | 4 votes |
|
public void loadPackage(String packageName) throws RSessionWrapperException {
String loadCode = "library(" + packageName + ", logical.return = TRUE)";
if (TRY_MODE)
loadCode = "try(" + loadCode + ", silent=TRUE)";
String errorMsg = "The \"" + this.callerFeatureName + "\" requires " + "the \"" + packageName
+ "\" R package, which couldn't be loaded - is it installed in R?";
if (this.rEngineType == REngineType.RSERVE) {
if (this.session != null && !this.userCanceled) {
LOG.log(logLvl, "Loading package '" + packageName + "'...");
int loaded = 0;
try {
REXP r = ((RConnection) this.rEngine).eval(loadCode);
if (r.inherits("try-error")) {
LOG.severe("R Error [0]: " + r.asString());
LOG.severe("R eval attempt [0]: " + loadCode);
}
loaded = r.asInteger();
LOG.log(logLvl, "Load status: '" + (loaded != 0) + "'.");
} catch (RserveException | REXPMismatchException e) {
LOG.log(logLvl, "Loaded package KO: '" + e.getMessage() + "'.");
// Remain silent if eval KO ("server down").
loaded = Integer.MIN_VALUE;
}
// Throw loading failure only if eval OK, but return FALSE
// (package not loaded).
// ("server down" case will be handled soon enough).
if (loaded == 0)
if (!this.userCanceled)
throw new RSessionWrapperException(errorMsg);
LOG.log(logLvl, "Loaded package: '" + packageName + "'.");
}
} else { // RCaller
((RCaller) rEngine).getRCode().addRCode(loadCode);
// try {
//
// ((RCallerScriptEngine2) rEngine).eval(loadCode);
// } catch (ScriptException e) {
//
// if (!this.userCanceled)
// throw new RSessionWrapperException(errorMsg);
// }
}
}
Example #11
| Source File: RSessionWrapper.java From mzmine2 with GNU General Public License v2.0 | 4 votes |
|
public boolean eval(String rCode, boolean stopOnError) throws RSessionWrapperException {
// if (TRY_MODE) rCode = "try(" + rCode + ",silent=TRUE)";
if (this.rEngineType == REngineType.RSERVE) {
boolean ok = false;
if (this.session != null && !this.userCanceled) {
String msg = "Rserve error: couldn't eval R code '" + rCode + "' (instance '"
+ this.getPID() + "').";
// try {
// ////((RConnection) this.rEngine).eval(rCode);
// REXP r = ((RConnection) this.rEngine).eval(rCode);
// if (r2.inherits("try-error")) {
// LOG.severe("R Error [1]: " + r.asString());
// LOG.severe("R eval attempt [1]: " + rCode);
// LOG.severe("Debug string" + r.toDebugString());
// }
// //else { /* success ... */ }
// LOG.severe("R error [3]: " + ((RConnection)
// this.rEngine).getLastError());
// }
// catch (RserveException e) {
// LOG.severe("R error [2]: " + getErrMessage());
// throw new RSessionWrapperException(msg);
// } catch (Exception e) {
// throw new RSessionWrapperException(e.getMessage());
// }
ok = this.session.voidEval(rCode, true); // TRY_MODE);
if (!ok) {
if (stopOnError)
throw new RSessionWrapperException(msg);
else
checkConnectivity();
}
}
return ok;
} else { // RCaller
try {
((RCaller) this.rEngine).getRCode().addRCode(rCode);
// ((RCallerScriptEngine2) this.rEngine).eval(rCode);
} catch (ExecutionException /* | ScriptException */ ee) { // RCaller exception
if (stopOnError)
throw new RSessionWrapperException(ee.getMessage());
else
return false;
}
return true;
}
}
Example #12
| Source File: RSessionWrapper.java From mzmine2 with GNU General Public License v2.0 | 4 votes |
|
public void clearCode() {
if (this.rEngineType == REngineType.RCALLER) {
((RCaller) this.rEngine).getRCode().clearOnline();
}
}
Example #13
| Source File: RSessionWrapper.java From mzmine2 with GNU General Public License v2.0 | 4 votes |
|
/**
* This can be necessary to call 'close()' from a different thread than the one which called
* 'open()', sometimes, with Rserve (if the related instance is busy).
*
* @param userCanceled Tell the application the closure came from a user action rather than from
* an unknown source error.
* @throws RSessionWrapperException
*/
public void close(boolean userCanceled) throws RSessionWrapperException {
this.userCanceled = userCanceled;
if (this.rEngineType == REngineType.RSERVE) {
if (this.session != null) {
try {
LOG.log(logLvl,
"Rserve: try terminate " + ((this.rServePid == -1) ? "pending" : "") + " session"
+ ((this.rServePid == -1) ? "..."
: " (pid: '" + this.rServePid + "' | port: '" + this.session.rServeConf.port
+ "')..."));
// Avoid 'Rsession' to 'printStackTrace' while catching
// 'SocketException'
// (since we are about to brute force kill the Rserve instance,
// such that
// the session won't end properly).
RSessionWrapper.muteStdOutErr();
{
RSessionWrapper.killRserveInstance(this);
this.session.end();
}
RSessionWrapper.unMuteStdOutErr();
LOG.log(logLvl,
"Rserve: terminated " + ((this.rServePid == -1) ? "pending" : "") + " session"
+ ((this.rServePid == -1) ? "..."
: " (pid: '" + this.rServePid + "' | port: '" + this.session.rServeConf.port
+ "')..."));
// Release session (prevents from calling close again on a
// closed instance).
this.session = null;
} catch (Throwable t) {
// Adapt/refactor message accordingly to the way the termination
// was provoked:
// User requested or unexpectedly...
String msg;
if (userCanceled) {
msg = "Rserve error: couldn't terminate instance with pid '" + this.rServePid
+ "'. Details:\n";
} else {
msg = "Rserve error: something when wrong with instance of pid '" + this.rServePid
+ "'. Details:\n";
}
throw new RSessionWrapperException(msg + TextUtils.wrapText(t.getMessage(), 80));
} finally {
// Make sure to restore standard outputs.
System.setOut(System.out);
System.setErr(System.err);
}
}
this.unRegister();
} else { // RCaller
// if (this.wasRunAndReturned) {
// TODO: do nothing for now, see if a special treatment is required
// when 'user canceling' a task or else !!!
((RCaller) this.rEngine).StopRCallerOnline();
// } else {
// this.runOnlyOnline();
// }
// ((RCallerScriptEngine2) this.rEngine).close();
}
}
