1452: Implement a GUI for StatMan Algorithms Importer

Task-Url: https://support.d4science.org/issues/1452

Fixed InputStream on Annotations

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@122714 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/annotation/WPS4RParser.java

@@ -2,6 +2,10 @@ package org.gcube.portlets.user.statisticalalgorithmsimporter.server.annotation;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import java.nio.file.StandardOpenOption;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -18,6 +22,7 @@ import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.workspace.It
 import org.n52.wps.server.r.R_Config;
 import org.n52.wps.server.r.metadata.RAnnotationParser;
 import org.n52.wps.server.r.syntax.RAnnotation;
+import org.n52.wps.server.r.syntax.RAnnotationException;
 import org.n52.wps.server.r.syntax.RAnnotationType;
 import org.n52.wps.server.r.syntax.RAttribute;
 import org.slf4j.Logger;
@@ -30,11 +35,10 @@ import org.slf4j.LoggerFactory;
  *
  */
 public class WPS4RParser {
-	
+
 	public static final Logger logger = LoggerFactory
 			.getLogger(WPS4RParser.class);
 
-	
 	private Project project;
 	private ASLSession aslSession;
 
@@ -44,56 +48,88 @@ public class WPS4RParser {
 	}
 
 	public Project parse() throws StatAlgoImporterServiceException {
+		logger.debug("MainCode: " + project.getMainCode());
 		ItemDescription mainCode = project.getMainCode().getItemDescription();
 		FilesStorage fileStorage = new FilesStorage();
 		InputStream is = fileStorage.retrieveItemOnWorkspace(
 				aslSession.getUsername(), mainCode.getId());
-
+		logger.debug("MainCode InputStream: " + is);
-		R_Config config = R_Config.getInstance();
+		
-
+		Path tempFile=null;
-		List<RAnnotation> annotations;
 		try {
-			RAnnotationParser parser = new RAnnotationParser(config);
+			tempFile = Files.createTempFile("RCodeToParse", ".R");
-			annotations = parser.parseAnnotationsfromScript(is);
+			Files.copy(is, tempFile, StandardCopyOption.REPLACE_EXISTING);
-		} catch (Throwable e) {
+		} catch (IOException e) {
 			e.printStackTrace();
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
 		} finally {
 			try {
 				is.close();
 			} catch (IOException e) {
-				// TODO Auto-generated catch block
 				e.printStackTrace();
 			}
 		}
+		logger.debug("" + tempFile);
 
+		
+		R_Config config = R_Config.getInstance();
+		logger.debug("R_Config: " + config);
+		List<RAnnotation> annotations;
+		try {
+			RAnnotationParser parser = new RAnnotationParser(config);
+			logger.debug("RAnnotations Parser:" + parser);
+			annotations = parser.parseAnnotationsfromScript(Files.newInputStream(tempFile, StandardOpenOption.READ));
+		} catch (RAnnotationException e) {
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+		} catch (Throwable e) {
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+		} 
+		
+		try {
+			Files.delete(tempFile);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		
+		logger.debug("RAnnotations: " + annotations);
+		
 		WPSAlgorithmInfo wpsAlgorithmInfo = mapAnnotations(annotations);
-		logger.debug("wpsAlgorithmInfo: "+wpsAlgorithmInfo);
+		logger.debug("wpsAlgorithmInfo: " + wpsAlgorithmInfo);
-		if (wpsAlgorithmInfo.getAlgorithmName() == null)
+		if (wpsAlgorithmInfo==null || wpsAlgorithmInfo.getAlgorithmName() == null)
 			return project;
 		else
 			return mapToProject(wpsAlgorithmInfo);
 
 	}
 
-	private Project mapToProject(WPSAlgorithmInfo wpsAlgorithmInfo) throws StatAlgoImporterServiceException {
+	private Project mapToProject(WPSAlgorithmInfo wpsAlgorithmInfo)
-		if(project==null){
+			throws StatAlgoImporterServiceException {
+		if (project == null) {
 			throw new StatAlgoImporterServiceException("Open project before!");
 		}
 		
-		if(project.getInputData()==null){
+		
-			ProjectInfo projectInfo=new ProjectInfo(wpsAlgorithmInfo.getAlgorithmName(), wpsAlgorithmInfo.getDescription(), null);
+		if (project.getInputData() == null) {
-			InputData inputData=new InputData(projectInfo, null, null, wpsAlgorithmInfo.getInputOutputVariables());
+			ProjectInfo projectInfo = new ProjectInfo(
+					wpsAlgorithmInfo.getAlgorithmName(),
+					wpsAlgorithmInfo.getDescription(), null);
+			InputData inputData = new InputData(projectInfo, null, null,
+					wpsAlgorithmInfo.getInputOutputVariables());
 			project.setInputData(inputData);
 		} else {
-			InputData inputData=project.getInputData();
+			InputData inputData = project.getInputData();
-			ProjectInfo projectInfo=new ProjectInfo(wpsAlgorithmInfo.getAlgorithmName(), wpsAlgorithmInfo.getDescription(), null);
+			ProjectInfo projectInfo = new ProjectInfo(
+					wpsAlgorithmInfo.getAlgorithmName(),
+					wpsAlgorithmInfo.getDescription(), null);
 			inputData.setProjectInfo(projectInfo);
-			inputData.setListInputOutputVariables(wpsAlgorithmInfo.getInputOutputVariables());	
+			inputData.setListInputOutputVariables(wpsAlgorithmInfo
+					.getInputOutputVariables());
 			inputData.setListGlobalVariables(null);
 		}
 		return project;
-		
+
 	}
 
 	private WPSAlgorithmInfo mapAnnotations(List<RAnnotation> annotations)
@@ -102,15 +138,18 @@ public class WPS4RParser {
 
 			WPSAlgorithmInfo wpsAlgorithmInfo = new WPSAlgorithmInfo();
 			ArrayList<InputOutputVariables> inputOutputVariables = new ArrayList<>();
-			int index=1;
+			int index = 1;
 			for (RAnnotation rAnnotation : annotations) {
+				logger.debug("RAnnotation: " + rAnnotation);
 				if (rAnnotation.getType().equals(RAnnotationType.DESCRIPTION)) {
 					wpsAlgorithmInfo.setVersion(rAnnotation
 							.getStringValue(RAttribute.VERSION));
 					wpsAlgorithmInfo.setDescription(rAnnotation
 							.getStringValue(RAttribute.ABSTRACT));
-					wpsAlgorithmInfo.setAlgorithmName(rAnnotation
+					String algorithmName=rAnnotation
-							.getStringValue(RAttribute.TITLE));
+					.getStringValue(RAttribute.TITLE);
+					algorithmName=algorithmName.replaceAll("[^A-Za-z0-9]", "_");
+					wpsAlgorithmInfo.setAlgorithmName(algorithmName);
 					wpsAlgorithmInfo.setVersion(rAnnotation
 							.getStringValue(RAttribute.VERSION));
 				} else if (rAnnotation.getType().equals(RAnnotationType.OUTPUT)
@@ -144,8 +183,8 @@ public class WPS4RParser {
 						dataType = DataType.ENUMERATED;
 
 					InputOutputVariables ioVariable = new InputOutputVariables(
-							index, name, description, defaultValue, dataType, ioType,
+							index, name, description, defaultValue, dataType,
-							"");
+							ioType, "");
 					inputOutputVariables.add(ioVariable);
 					index++;
 				}

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/generator/ProjectBuilder.java

@@ -84,6 +84,19 @@ public class ProjectBuilder {
 		createAlgorithm();
 		createIntegrationInfo();
 		createProjectJarFile();
+		try {
+			if (algorithmJava != null)
+				Files.delete(algorithmJava);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		try {
+			if (infoTXT != null)
+				Files.delete(infoTXT);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
 
 		return project;
 
@@ -128,24 +141,23 @@ public class ProjectBuilder {
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
 		}
 
-		
+		filesStorage.saveInputStreamInItem(aslSession.getUsername(), project
-		filesStorage.saveInputStreamInItem(
+				.getProjectTarget().getProjectDeploy().getPackageProject()
-				aslSession.getUsername(), project.getProjectTarget()
+				.getId(), inputStream);
-						.getProjectDeploy().getPackageProject().getId(),
+
-				inputStream);
+		WorkspaceItem packageProject = filesStorage
-		
+				.retrieveItemInfoOnWorkspace(aslSession.getUsername(), project
-		
+						.getProjectTarget().getProjectDeploy()
-		WorkspaceItem packageProject=filesStorage.retrieveItemInfoOnWorkspace(aslSession.getUsername(), project.getProjectTarget()
+						.getPackageProject().getId());
-						.getProjectDeploy().getPackageProject().getId());
+
-		
 		ItemDescription packageProjectItemDescription;
 		try {
-			packageProjectItemDescription = new ItemDescription(packageProject.getId(),
+			packageProjectItemDescription = new ItemDescription(
-					packageProject.getName(), packageProject
+					packageProject.getId(), packageProject.getName(),
-							.getOwner().getPortalLogin(),
+					packageProject.getOwner().getPortalLogin(),
-					packageProject.getPath(), packageProject
+					packageProject.getPath(), packageProject.getType().name());
-							.getType().name());
+			packageProjectItemDescription.setPublicLink(packageProject
-			packageProjectItemDescription.setPublicLink(packageProject.getPublicLink(true));
+					.getPublicLink(true));
 		} catch (InternalErrorException e) {
 			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();
@@ -153,11 +165,11 @@ public class ProjectBuilder {
 
 		}
 
-		project.getProjectTarget().getProjectDeploy().setPackageProject(packageProjectItemDescription);
+		project.getProjectTarget().getProjectDeploy()
+				.setPackageProject(packageProjectItemDescription);
 		logger.debug("ProjectDeploy: "
 				+ project.getProjectTarget().getProjectDeploy());
-		
+
-		
 	}
 
 	private void copyJarInDeploy() throws StatAlgoImporterServiceException {
@@ -447,7 +459,8 @@ public class ProjectBuilder {
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
 
 		}
-		project.getProjectTarget().getProjectDeploy().setPackageProject(packageUrl);
+		project.getProjectTarget().getProjectDeploy()
+				.setPackageProject(packageUrl);
 	}
 
 	private void createTargetFolder() throws StatAlgoImporterServiceException {