215 lines
7.4 KiB
Java
215 lines
7.4 KiB
Java
package org.gcube.portlets.user.statisticalalgorithmsimporter.server.annotation;
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import java.io.IOException;
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import java.io.InputStream;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.StandardCopyOption;
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import java.nio.file.StandardOpenOption;
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import java.util.ArrayList;
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import java.util.List;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.server.storage.FilesStorage;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.server.util.ServiceCredentials;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.exception.StatAlgoImporterServiceException;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.DataType;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.IOType;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.InputOutputVariables;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.ProjectInfo;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.InputData;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.Project;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.workspace.ItemDescription;
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import org.n52.wps.server.r.R_Config;
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import org.n52.wps.server.r.metadata.RAnnotationParser;
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import org.n52.wps.server.r.syntax.RAnnotation;
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import org.n52.wps.server.r.syntax.RAnnotationException;
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import org.n52.wps.server.r.syntax.RAnnotationType;
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import org.n52.wps.server.r.syntax.RAttribute;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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/**
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*
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* @author Giancarlo Panichi email: <a
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* href="mailto:g.panichi@isti.cnr.it">g.panichi@isti.cnr.it</a>
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*
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*/
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public class WPS4RParser {
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public static final Logger logger = LoggerFactory
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.getLogger(WPS4RParser.class);
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private Project project;
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private ServiceCredentials serviceCredentials;
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public WPS4RParser(Project project, ServiceCredentials serviceCredentials) {
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this.project = project;
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this.serviceCredentials = serviceCredentials;
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}
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public Project parse() throws StatAlgoImporterServiceException {
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logger.debug("MainCode: " + project.getMainCode());
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ItemDescription mainCode = project.getMainCode().getItemDescription();
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FilesStorage fileStorage = new FilesStorage();
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InputStream is = fileStorage.retrieveItemOnWorkspace(
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serviceCredentials.getUserName(), mainCode.getId());
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logger.debug("MainCode InputStream: " + is);
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Path tempFile = null;
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try {
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tempFile = Files.createTempFile("RCodeToParse", ".R");
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Files.copy(is, tempFile, StandardCopyOption.REPLACE_EXISTING);
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} catch (IOException e) {
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e.printStackTrace();
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throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
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} finally {
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try {
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is.close();
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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logger.debug("" + tempFile);
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R_Config config = R_Config.getInstance();
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logger.debug("R_Config: " + config);
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List<RAnnotation> annotations;
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try {
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RAnnotationParser parser = new RAnnotationParser(config);
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logger.debug("RAnnotations Parser:" + parser);
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annotations = parser.parseAnnotationsfromScript(Files
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.newInputStream(tempFile, StandardOpenOption.READ));
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} catch (RAnnotationException e) {
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e.printStackTrace();
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throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
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} catch (Throwable e) {
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e.printStackTrace();
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throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
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}
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try {
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Files.delete(tempFile);
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} catch (IOException e) {
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e.printStackTrace();
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}
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logger.debug("RAnnotations: " + annotations);
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WPSAlgorithmInfo wpsAlgorithmInfo = mapAnnotations(annotations);
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logger.debug("wpsAlgorithmInfo: " + wpsAlgorithmInfo);
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if (wpsAlgorithmInfo == null
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|| wpsAlgorithmInfo.getAlgorithmName() == null)
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return project;
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else
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return mapToProject(wpsAlgorithmInfo);
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}
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private Project mapToProject(WPSAlgorithmInfo wpsAlgorithmInfo)
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throws StatAlgoImporterServiceException {
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if (project == null) {
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throw new StatAlgoImporterServiceException("Open project before!");
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}
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if (project.getInputData() == null) {
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ProjectInfo projectInfo = new ProjectInfo(
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wpsAlgorithmInfo.getAlgorithmName(),
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wpsAlgorithmInfo.getDescription(), null);
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InputData inputData = new InputData(projectInfo, null, null,
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wpsAlgorithmInfo.getInputOutputVariables());
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project.setInputData(inputData);
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} else {
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InputData inputData = project.getInputData();
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ProjectInfo projectInfo = new ProjectInfo(
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wpsAlgorithmInfo.getAlgorithmName(),
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wpsAlgorithmInfo.getDescription(), null);
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inputData.setProjectInfo(projectInfo);
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inputData.setListInputOutputVariables(wpsAlgorithmInfo
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.getInputOutputVariables());
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inputData.setListGlobalVariables(null);
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}
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return project;
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}
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private WPSAlgorithmInfo mapAnnotations(List<RAnnotation> annotations)
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throws StatAlgoImporterServiceException {
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try {
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WPSAlgorithmInfo wpsAlgorithmInfo = new WPSAlgorithmInfo();
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ArrayList<InputOutputVariables> inputOutputVariables = new ArrayList<>();
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int index = 1;
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for (RAnnotation rAnnotation : annotations) {
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logger.debug("RAnnotation: " + rAnnotation);
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if (rAnnotation.getType().equals(RAnnotationType.DESCRIPTION)) {
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wpsAlgorithmInfo.setVersion(rAnnotation
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.getStringValue(RAttribute.VERSION));
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wpsAlgorithmInfo.setDescription(rAnnotation
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.getStringValue(RAttribute.ABSTRACT));
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String algorithmName = rAnnotation
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.getStringValue(RAttribute.TITLE);
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algorithmName = algorithmName.replaceAll("[^A-Za-z0-9]",
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"_");
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wpsAlgorithmInfo.setAlgorithmName(algorithmName);
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wpsAlgorithmInfo.setVersion(rAnnotation
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.getStringValue(RAttribute.VERSION));
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} else if (rAnnotation.getType().equals(RAnnotationType.OUTPUT)
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|| rAnnotation.getType().equals(RAnnotationType.INPUT)) {
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// output, text, Random number list,
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String type = rAnnotation.getStringValue(RAttribute.TYPE);
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String name = rAnnotation
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.getStringValue(RAttribute.IDENTIFIER);
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String description = rAnnotation
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.getStringValue(RAttribute.TITLE);
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String defaultValue = rAnnotation
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.getStringValue(RAttribute.DEFAULT_VALUE);
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if (type == null)
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type = "string";
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if (name == null)
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name = "";
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if (description == null)
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description = "";
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if (defaultValue == null)
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defaultValue = "";
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IOType ioType = IOType.INPUT;
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if (rAnnotation.getType().equals(RAnnotationType.OUTPUT))
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ioType = IOType.OUTPUT;
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DataType dataType = WPStype2DataType(type);
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if (defaultValue != null && defaultValue.contains("|")
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&& dataType == DataType.STRING)
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dataType = DataType.ENUMERATED;
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InputOutputVariables ioVariable = new InputOutputVariables(
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index, name, description, defaultValue, dataType,
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ioType, "");
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inputOutputVariables.add(ioVariable);
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index++;
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}
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}
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wpsAlgorithmInfo.setInputOutputVariables(inputOutputVariables);
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return wpsAlgorithmInfo;
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} catch (Throwable e) {
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e.printStackTrace();
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throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
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}
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}
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private static DataType WPStype2DataType(String type) {
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if (type.equalsIgnoreCase("double"))
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return DataType.DOUBLE;
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else if (type.equalsIgnoreCase("integer"))
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return DataType.INTEGER;
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else if (type.equalsIgnoreCase("string"))
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return DataType.STRING;
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else if (type.equalsIgnoreCase("boolean"))
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return DataType.BOOLEAN;
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else
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return DataType.FILE;
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}
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}
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