Java Code Examples for org.rosuda.REngine.REXP#inherits()
The following examples show how to use
org.rosuda.REngine.REXP#inherits() .
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Example 1
| Source File: RScriptExecutor.java From Knowage-Server with GNU Affero General Public License v3.0 | 5 votes |
|
private void loadLibrariesFromRLocal(String libraryNames) throws REngineException, REXPMismatchException {
logger.debug("IN");
if (this.re != null) {
re.parseAndEval("installed_packages = rownames(installed.packages())");
REXP rHome = re.parseAndEval("try(libdir<-paste(R.home(),\"library\", sep=\"/\"))");
if (!rHome.inherits("try-error") && !rHome.isNull()) {
if (libraryNames != null && !libraryNames.isEmpty()) {
setRProxy();
String[] libs = libraryNames.split(",");
for (int i = 0; i < libs.length; i++) {
String lib = libs[i].trim();
if (!lib.isEmpty()) {
// check if the library is present in the workspace, if not try to install that package
REXP libIsPresent = re.parseAndEval("\"" + lib + "\" %in% installed_packages");
if (libIsPresent.isNull() || libIsPresent.asString().equalsIgnoreCase("false")) {
// re.parseAndEval("try(install.packages(\"" + lib + "\",destdir=libdir))");
logger.error("Libray '" + lib + "' is not present. Please, install the library in R before");
}
REXP rLibrary = re.parseAndEval("library(" + lib + ",lib.loc=libdir)");
if (rLibrary.inherits("try-error")) {
logger.error("Impossible to load library: " + lib);
}
}
}
}
}
}
logger.debug("OUT");
}
Example 2
| 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 3
| Source File: ROutputExecutor.java From Knowage-Server with GNU Affero General Public License v3.0 | 4 votes |
|
private CreateDatasetResult createAndPersistDataset(IEngUserProfile profile, String outVal, Output out, String userId, String documentLabel)
throws Exception {
logger.debug("IN");
REXP rexp = null;
CreateDatasetResult creationResult = new CreateDatasetResult();
String spagoBiDatasetname = userId + "_" + documentLabel + "_" + out.getOuputLabel();
FileDataSet dataSet = new FileDataSet();
String path = getDatasetsDirectoryPath();
String resourcePath = DAOConfig.getResourcePath();
dataSet.setResourcePath(resourcePath);
JSONObject configurationObj = new JSONObject();
configurationObj.put(DataSetConstants.FILE_TYPE, "CSV");
configurationObj.put(DataSetConstants.CSV_FILE_DELIMITER_CHARACTER, ",");
configurationObj.put(DataSetConstants.CSV_FILE_QUOTE_CHARACTER, "\"");
configurationObj.put(DataSetConstants.FILE_NAME, spagoBiDatasetname + ".csv");
configurationObj.put(DataSetConstants.CSV_FILE_ENCODING, "UTF-8");
configurationObj.put(DataSetConstants.XSL_FILE_SKIP_ROWS, DataSetConstants.XSL_FILE_SKIP_ROWS);
configurationObj.put(DataSetConstants.XSL_FILE_LIMIT_ROWS, DataSetConstants.XSL_FILE_LIMIT_ROWS);
configurationObj.put(DataSetConstants.XSL_FILE_SHEET_NUMBER, DataSetConstants.XSL_FILE_SHEET_NUMBER);
String confString = configurationObj.toString();
dataSet.setConfiguration(confString);
String rExecution = "write.csv(" + outVal + ",file='" + path + "/" + spagoBiDatasetname + ".csv',row.names=FALSE,na='')";
rexp = re.parseAndEval("try(" + rExecution + ")");
if (rexp.inherits("try-error")) {
logger.debug("Script contains error(s)");
creationResult.setRExecutionError(rexp.asString());
}
dataSet.setFileName(spagoBiDatasetname + ".csv");
dataSet.setFileType("CSV");
dataSet.setDsType(DataSetConstants.DS_FILE);
dataSet.setLabel(spagoBiDatasetname);
dataSet.setName(spagoBiDatasetname);
dataSet.setDescription("Dataset created from execution of document " + documentLabel + " by user " + userId);
dataSet.setOwner(((UserProfile) profile).getUserId().toString());
// ------------Metadata setting------------
dataSet.loadData();
IDataStore dataStore = dataSet.getDataStore();
JSONArray metadataArray = new JSONArray();
IMetaData metaData = dataStore.getMetaData();
for (int i = 0; i < metaData.getFieldCount(); i++) {
IFieldMetaData ifmd = metaData.getFieldMeta(i);
for (int j = 0; j < metadataArray.length(); j++) {
if (ifmd.getName().equals((metadataArray.getJSONObject(j)).getString("name"))) {
if ("MEASURE".equals((metadataArray.getJSONObject(j)).getString("fieldType"))) {
ifmd.setFieldType(IFieldMetaData.FieldType.MEASURE);
} else {
ifmd.setFieldType(IFieldMetaData.FieldType.ATTRIBUTE);
}
break;
}
}
}
IMetaData currentMetadata = dataStore.getMetaData();
DatasetMetadataParser dsp = new DatasetMetadataParser();
String dsMetadata = dsp.metadataToXML(currentMetadata);
dataSet.setDsMetadata(dsMetadata);
// ----------------------------------------
IDataSetDAO dataSetDAO = DAOFactory.getDataSetDAO();
dataSetDAO.setUserProfile(profile);
logger.debug("check if dataset with label " + spagoBiDatasetname + " is already present");
// check label is already present; insert or modify dependengly
IDataSet iDataSet = dataSetDAO.loadDataSetByLabel(spagoBiDatasetname);
// loadActiveDataSetByLabel(label);
if (iDataSet != null) {
logger.debug("a dataset with label " + spagoBiDatasetname + " is already present: modify it");
dataSet.setId(iDataSet.getId());
dataSetDAO.modifyDataSet(dataSet);
} else {
logger.debug("No dataset with label " + spagoBiDatasetname + " is already present: insert it");
dataSetDAO.insertDataSet(dataSet);
}
creationResult.setDatasetlabel(spagoBiDatasetname);
return creationResult;
}
Example 4
| Source File: ROutputExecutor.java From Knowage-Server with GNU Affero General Public License v3.0 | 4 votes |
|
private CreateDatasetResult createAndPersistDatasetProductByFunction(IEngUserProfile profile, String outVal, Output out, String function, String userId,
String documentLabel) throws Exception {
logger.debug("IN");
CreateDatasetResult creationResult = new CreateDatasetResult();
REXP rexp = null;
DataMiningResult res = new DataMiningResult();
FileDataSet dataSet = new FileDataSet();
String path = getDatasetsDirectoryPath();
String resourcePath = DAOConfig.getResourcePath();
dataSet.setResourcePath(resourcePath);
String spagoBiDatasetname = userId + "_" + documentLabel + "_" + out.getOuputLabel();
JSONObject configurationObj = new JSONObject();
configurationObj.put(DataSetConstants.FILE_TYPE, "CSV");
configurationObj.put(DataSetConstants.CSV_FILE_DELIMITER_CHARACTER, ",");
configurationObj.put(DataSetConstants.CSV_FILE_QUOTE_CHARACTER, "'");
configurationObj.put(DataSetConstants.FILE_NAME, spagoBiDatasetname + ".csv");
configurationObj.put("encoding", "UTF-8");
configurationObj.put(DataSetConstants.XSL_FILE_SKIP_ROWS, DataSetConstants.XSL_FILE_SKIP_ROWS);
configurationObj.put(DataSetConstants.XSL_FILE_LIMIT_ROWS, DataSetConstants.XSL_FILE_LIMIT_ROWS);
configurationObj.put(DataSetConstants.XSL_FILE_SHEET_NUMBER, DataSetConstants.XSL_FILE_SHEET_NUMBER);
String confString = configurationObj.toString();
dataSet.setConfiguration(confString);
String rExecution = "write.csv(" + outVal + ",file=" + path + spagoBiDatasetname + ",row.names=FALSE,na='')";
rexp = re.parseAndEval("try(" + rExecution + ")");
if (rexp.inherits("try-error")) {
logger.debug("Script contains error(s)");
creationResult.setRExecutionError(rexp.asString());
}
dataSet.setFileName(spagoBiDatasetname + ".csv");
dataSet.setFileType("CSV");
dataSet.setDsType(DataSetConstants.DS_FILE);
String label = out.getOuputLabel();
dataSet.setLabel(spagoBiDatasetname);
dataSet.setName(spagoBiDatasetname);
dataSet.setDescription("Dataset created from execution of document " + documentLabel + " by user " + userId);
dataSet.setOwner(((UserProfile) profile).getUserId().toString());
// ------------Metadata setting------------
dataSet.loadData();
IDataStore dataStore = dataSet.getDataStore();
JSONArray metadataArray = new JSONArray();
IMetaData metaData = dataStore.getMetaData();
for (int i = 0; i < metaData.getFieldCount(); i++) {
IFieldMetaData ifmd = metaData.getFieldMeta(i);
for (int j = 0; j < metadataArray.length(); j++) {
if (ifmd.getName().equals((metadataArray.getJSONObject(j)).getString("name"))) {
if ("MEASURE".equals((metadataArray.getJSONObject(j)).getString("fieldType"))) {
ifmd.setFieldType(IFieldMetaData.FieldType.MEASURE);
} else {
ifmd.setFieldType(IFieldMetaData.FieldType.ATTRIBUTE);
}
break;
}
}
}
IMetaData currentMetadata = dataStore.getMetaData();
DatasetMetadataParser dsp = new DatasetMetadataParser();
String dsMetadata = dsp.metadataToXML(currentMetadata);
dataSet.setDsMetadata(dsMetadata);
// ----------------------------------------
IDataSetDAO dataSetDAO = DAOFactory.getDataSetDAO();
dataSetDAO.setUserProfile(profile);
logger.debug("check if dataset with label " + spagoBiDatasetname + " is already present");
// check label is already present; insert or modify dependengly
IDataSet iDataSet = dataSetDAO.loadDataSetByLabel(spagoBiDatasetname);
// loadActiveDataSetByLabel(label);
if (iDataSet != null) {
logger.debug("a dataset with label " + spagoBiDatasetname + " is already present: modify it");
dataSet.setId(iDataSet.getId());
dataSetDAO.modifyDataSet(dataSet);
} else {
logger.debug("No dataset with label " + spagoBiDatasetname + " is already present: insert it");
dataSetDAO.insertDataSet(dataSet);
}
creationResult.setDatasetlabel(spagoBiDatasetname);
return creationResult;
}
Example 5
| 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);
// }
}
}
