ref 10705: Add user name to algorithms descriptions in SAI publication

https://support.d4science.org/issues/10705

Added

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@162274 82a268e6-3cf1-43bd-a215-b396298e98cf

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

@@ -32,10 +32,8 @@ import org.slf4j.LoggerFactory;
 public class AlgorithmGenerator {
 
 	private static final String EXTENTION_JAVA = ".java";
-	public static final Logger logger = LoggerFactory
+	public static final Logger logger = LoggerFactory.getLogger(AlgorithmGenerator.class);
-			.getLogger(AlgorithmGenerator.class);
 	private static final SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd HH:mm");
-	
 
 	private Project project;
 	private HashMap<String, String> enumUUID;
@@ -44,7 +42,7 @@ public class AlgorithmGenerator {
 	public AlgorithmGenerator(Project project, ServiceCredentials serviceCredentials) {
 		super();
 		this.project = project;
-		this.serviceCredentials=serviceCredentials;
+		this.serviceCredentials = serviceCredentials;
 	}
 
 	@Override
@@ -54,20 +52,17 @@ public class AlgorithmGenerator {
 
 	public Path createAlgorithm() throws StatAlgoImporterServiceException {
 		try {
-			Path tempFile = Files.createTempFile(project.getInputData()
+			Path tempFile = Files.createTempFile(project.getInputData().getProjectInfo().getAlgorithmNameToClassName(),
-					.getProjectInfo().getAlgorithmNameToClassName(),
 					EXTENTION_JAVA);
 
 			List<String> lines = createJavaCode();
-			Files.write(tempFile, lines, Charset.defaultCharset(),
+			Files.write(tempFile, lines, Charset.defaultCharset(), StandardOpenOption.WRITE);
-					StandardOpenOption.WRITE);
 			logger.debug(tempFile.toString());
 			return tempFile;
 
 		} catch (IOException e) {
-			logger.error(e.getLocalizedMessage(),e);
+			logger.error(e.getLocalizedMessage(), e);
-			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(), e);
-					e);
 		}
 
 	}
@@ -78,27 +73,19 @@ public class AlgorithmGenerator {
 		enumUUID = new HashMap<>();
 		ArrayList<String> code = new ArrayList<>();
 
-		code.addAll(Arrays
+		code.addAll(Arrays.asList("package org.gcube.dataanalysis.executor.rscripts;", "", "import java.io.File;",
-				.asList("package org.gcube.dataanalysis.executor.rscripts;",
+				"import java.util.ArrayList;", "import java.util.LinkedHashMap;",
-						"",
+				"import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;",
-						"import java.io.File;",
+				"import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;",
-						"import java.util.ArrayList;",
+				"import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;",
-						"import java.util.LinkedHashMap;",
+				"import org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript;",
-						"import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;",
+				"import org.gcube.dataanalysis.ecoengine.utils.DynamicEnum;", "import java.lang.reflect.Field;", "",
-						"import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;",
+				"public class " + project.getInputData().getProjectInfo().getAlgorithmNameToClassName()
-						"import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;",
+						+ " extends GenericRScript {"));
-						"import org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript;",
-						"import org.gcube.dataanalysis.ecoengine.utils.DynamicEnum;",
-						"import java.lang.reflect.Field;", "", "public class "
-								+ project.getInputData().getProjectInfo()
-										.getAlgorithmNameToClassName()
-								+ " extends GenericRScript {"));
 
-		for (GlobalVariables globalVariable : project.getInputData()
+		for (GlobalVariables globalVariable : project.getInputData().getListGlobalVariables()) {
-				.getListGlobalVariables()) {
 			if (globalVariable.getDataType().compareTo(DataType.ENUMERATED) == 0) {
-				if (globalVariable.getDefaultValue() == null
+				if (globalVariable.getDefaultValue() == null || globalVariable.getDefaultValue().isEmpty()) {
-						|| globalVariable.getDefaultValue().isEmpty()) {
 
 				} else {
 					String uuid = "" + UUID.randomUUID();
@@ -107,12 +94,10 @@ public class AlgorithmGenerator {
 					enumUUID.put("opGV" + globalVariable.getId(), nameEnum);
 
 					code.add("");
-					code.add("	static class " + nameEnum
+					code.add("	static class " + nameEnum + " extends DynamicEnum {");
-							+ " extends DynamicEnum {");
 					code.add("		public enum E" + nameEnum + " {};");
 					code.add("		public Field[] getFields() {");
-					code.add("			Field[] fields = E" + nameEnum
+					code.add("			Field[] fields = E" + nameEnum + ".class.getDeclaredFields();");
-							+ ".class.getDeclaredFields();");
 					code.add("			return fields;");
 					code.add("		}");
 					code.add("	}");
@@ -123,9 +108,9 @@ public class AlgorithmGenerator {
 					 * if (values.length < 1) {
 					 * 
 					 * } else { for (int i = 0; i < values.length; i++) { if (i
-					 * == values.length - 1) { code.add("		\"" + values[i] +
+					 * == values.length - 1) { code.add("		\"" + values[i]
-					 * "\""); } else { code.add("		\"" + values[i] + "\","); } }
+					 * + "\""); } else { code.add("		\"" + values[i] +
-					 * } code.add("	};");
+					 * "\","); } } } code.add("	};");
 					 */
 					/*
 					 * code.add("	public static enum opGV" +
@@ -137,32 +122,37 @@ public class AlgorithmGenerator {
 					 * identifier = values[i].trim();
 					 * identifier=identifier.replaceAll("\\s+","");
 					 * 
-					 * if (i == values.length - 1) { code.add("		" + identifier
+					 * if (i == values.length - 1) { code.add("		" +
-					 * + "(\"" + values[i] + "\");"); } else { code.add("		" +
+					 * identifier + "(\"" + values[i] + "\");"); } else {
-					 * identifier + "(\"" + values[i] + "\"),"); } } }
+					 * code.add("		" + identifier + "(\"" + values[i] +
+					 * "\"),"); } } }
 					 * 
-					 * code.add("		"); code.add("		private final String id;");
+					 * code.add("		");
+					 * code.add("		private final String id;");
 					 * code.add("		"); code.add("		private opGV" +
 					 * globalVariable.getId() + "(final String id) {");
 					 * code.add("			this.id = id;"); code.add("		}");
 					 * code.add("		"); code.add("		@Override");
 					 * code.add("		public String toString() {");
 					 * code.add("			return id;"); code.add("		}");
-					 * code.add("		"); code.add("		public String getId() {");
+					 * code.add("		");
+					 * code.add("		public String getId() {");
 					 * code.add("			return id;"); code.add("		}");
 					 * code.add("		");
 					 * 
 					 * code.add("		public opIO" + globalVariable.getId() +
-					 * " getIdentifier(String identifier){");
+					 * " getIdentifier(String identifier){"); code.
-					 * code.add("			if(identifier==null|| identifier.isEmpty()){"
+					 * add("			if(identifier==null|| identifier.isEmpty()){"
-					 * ); code.add("				return null;"); code.add("			}");
+					 * ); code.add("				return null;");
-					 * code.add("			"); code.add("			for(opIO" +
+					 * code.add("			}"); code.add("			");
-					 * globalVariable.getId() + " value:opIO" +
+					 * code.add("			for(opIO" + globalVariable.getId() +
-					 * globalVariable.getId() + ".values()){");
+					 * " value:opIO" + globalVariable.getId() + ".values()){");
-					 * code.add("				if(value.id.compareTo(identifier)==0){");
+					 * code.
-					 * code.add("					return value;"); code.add("				}");
+					 * add("				if(value.id.compareTo(identifier)==0){"
-					 * code.add("			}"); code.add("			return null;");
+					 * ); code.add("					return value;");
-					 * code.add("		}"); code.add("		"); code.add("	}");
+					 * code.add("				}"); code.add("			}");
+					 * code.add("			return null;"); code.add("		}");
+					 * code.add("		"); code.add("	}");
 					 */
 				}
 
@@ -170,41 +160,35 @@ public class AlgorithmGenerator {
 
 		}
 
-		for (InputOutputVariables inputOutputVariable : project.getInputData()
+		for (InputOutputVariables inputOutputVariable : project.getInputData().getListInputOutputVariables()) {
-				.getListInputOutputVariables()) {
+			if (inputOutputVariable.getDataType().compareTo(DataType.ENUMERATED) == 0) {
-			if (inputOutputVariable.getDataType()
+				if (inputOutputVariable.getDefaultValue() == null || inputOutputVariable.getDefaultValue().isEmpty()) {
-					.compareTo(DataType.ENUMERATED) == 0) {
-				if (inputOutputVariable.getDefaultValue() == null
-						|| inputOutputVariable.getDefaultValue().isEmpty()) {
 
 				} else {
 					String uuid = "" + UUID.randomUUID();
 					uuid = uuid.replaceAll("-", "");
-					String nameEnum = "opIO" + inputOutputVariable.getId()
+					String nameEnum = "opIO" + inputOutputVariable.getId() + uuid;
-							+ uuid;
 					enumUUID.put("opIO" + inputOutputVariable.getId(), nameEnum);
 
 					code.add("");
-					code.add("	static class " + nameEnum
+					code.add("	static class " + nameEnum + " extends DynamicEnum {");
-							+ " extends DynamicEnum {");
 					code.add("		public enum E" + nameEnum + " {};");
 					code.add("		public Field[] getFields() {");
-					code.add("			Field[] fields = E" + nameEnum
+					code.add("			Field[] fields = E" + nameEnum + ".class.getDeclaredFields();");
-							+ ".class.getDeclaredFields();");
 					code.add("			return fields;");
 					code.add("		}");
 					code.add("	}");
 
 					/*
-					 * code.add("	String[] opIO" + inputOutputVariable.getId() +
+					 * code.add("	String[] opIO" + inputOutputVariable.getId()
-					 * " = {"); String[] values =
+					 * + " = {"); String[] values =
 					 * inputOutputVariable.getDefaultValue() .split("\\|"); if
 					 * (values.length < 1) {
 					 * 
 					 * } else { for (int i = 0; i < values.length; i++) { if (i
-					 * == values.length - 1) { code.add("		\"" + values[i] +
+					 * == values.length - 1) { code.add("		\"" + values[i]
-					 * "\""); } else { code.add("		\"" + values[i] + "\","); } }
+					 * + "\""); } else { code.add("		\"" + values[i] +
-					 * } code.add("	};");
+					 * "\","); } } } code.add("	};");
 					 */
 
 					/*
@@ -217,62 +201,57 @@ public class AlgorithmGenerator {
 					 * } else { for (int i = 0; i < values.length; i++) { String
 					 * identifier = values[i].trim(); identifier =
 					 * identifier.replaceAll("\\s+", ""); if (i == values.length
-					 * - 1) { code.add("		" + identifier + "(\"" + values[i] +
+					 * - 1) { code.add("		" + identifier + "(\"" +
-					 * "\");"); } else { code.add("		" + identifier + "(\"" +
+					 * values[i] + "\");"); } else { code.add("		" +
-					 * values[i] + "\"),"); } } } code.add("		");
+					 * identifier + "(\"" + values[i] + "\"),"); } } }
-					 * code.add("		private final String id;"); code.add("		");
+					 * code.add("		");
-					 * code.add("		private opIO" + inputOutputVariable.getId() +
+					 * code.add("		private final String id;");
-					 * "(final String id) {"); code.add("			this.id = id;");
+					 * code.add("		"); code.add("		private opIO" +
-					 * code.add("		}"); code.add("		"); code.add("		@Override");
+					 * inputOutputVariable.getId() + "(final String id) {");
+					 * code.add("			this.id = id;"); code.add("		}");
+					 * code.add("		"); code.add("		@Override");
 					 * code.add("		public String toString() {");
 					 * code.add("			return id;"); code.add("		}");
-					 * code.add("		"); code.add("		public String getId() {");
+					 * code.add("		");
+					 * code.add("		public String getId() {");
 					 * code.add("			return id;"); code.add("		}");
 					 * code.add("		"); code.add("		public opIO" +
 					 * inputOutputVariable.getId() +
-					 * " getIdentifier(String identifier){");
+					 * " getIdentifier(String identifier){"); code.
-					 * code.add("			if(identifier==null|| identifier.isEmpty()){"
+					 * add("			if(identifier==null|| identifier.isEmpty()){"
-					 * ); code.add("				return null;"); code.add("			}");
+					 * ); code.add("				return null;");
-					 * code.add("			"); code.add("			for(opIO" +
+					 * code.add("			}"); code.add("			");
+					 * code.add("			for(opIO" +
 					 * inputOutputVariable.getId() + " value:opIO" +
-					 * inputOutputVariable.getId() + ".values()){");
+					 * inputOutputVariable.getId() + ".values()){"); code.
-					 * code.add("				if(value.id.compareTo(identifier)==0){");
+					 * add("				if(value.id.compareTo(identifier)==0){"
-					 * code.add("					return value;"); code.add("				}");
+					 * ); code.add("					return value;");
-					 * code.add("			}"); code.add("			return null;");
+					 * code.add("				}"); code.add("			}");
-					 * code.add("		}"); code.add("		"); code.add("	}");
+					 * code.add("			return null;"); code.add("		}");
+					 * code.add("		"); code.add("	}");
 					 */
 				}
 
 			}
 		}
 
-		
+		code.addAll(Arrays.asList("", "	@Override", "	public String getDescription() {",
-
+				"		return \"" + retrieveAlgorithmDescription() + "\";", "	}", "",
-
+				"	protected void initVariables(){", "		mainScriptName=\"" + mainScriptRelativePath + "\";",
-		code.addAll(Arrays.asList("", "	@Override",
+				"		packageURL=\"" + packageUrl + "\";",
-				"	public String getDescription() {", "		return \""
-						+ retrieveAlgorithmDescription() + "\";", "	}", "",
-				"	protected void initVariables(){", "		mainScriptName=\""
-						+ mainScriptRelativePath + "\";", "		packageURL=\""
-						+ packageUrl + "\";",
 				"		environmentalvariables = new ArrayList<String>();"));
 
-		for (GlobalVariables globalVariable : project.getInputData()
+		for (GlobalVariables globalVariable : project.getInputData().getListGlobalVariables()) {
-				.getListGlobalVariables()) {
+			code.add("		environmentalvariables.add(\"" + globalVariable.getName() + "\");");
-			code.add("		environmentalvariables.add(\""
-					+ globalVariable.getName() + "\");");
 		}
 
-		for (InputOutputVariables selVariable : project.getInputData()
+		for (InputOutputVariables selVariable : project.getInputData().getListInputOutputVariables()) {
-				.getListInputOutputVariables()) {
 			switch (selVariable.getIoType()) {
 			case INPUT:
-				code.add("		inputvariables.add(\"" + selVariable.getName()
+				code.add("		inputvariables.add(\"" + selVariable.getName() + "\");");
-						+ "\");");
 				break;
 			case OUTPUT:
-				code.add("		outputvariables.add(\"" + selVariable.getName()
+				code.add("		outputvariables.add(\"" + selVariable.getName() + "\");");
-						+ "\");");
 				break;
 			default:
 				break;
@@ -291,7 +270,8 @@ public class AlgorithmGenerator {
 		code.add("	@Override");
 		code.add("	public StatisticalType getOutput() {");
 		createOutputParameters(code);
-		code.add("		PrimitiveType o = new PrimitiveType(LinkedHashMap.class.getName(), output, PrimitiveTypes.MAP, \"Output\", \"\");");
+		code.add(
+				"		PrimitiveType o = new PrimitiveType(LinkedHashMap.class.getName(), output, PrimitiveTypes.MAP, \"Output\", \"\");");
 		code.add("		return o;");
 		code.add("	}");
 		code.add("}");
@@ -299,107 +279,91 @@ public class AlgorithmGenerator {
 	}
 
 	private String retrieveAlgorithmDescription() {
-		String algorithmDescription="";
+		String algorithmDescription = "";
-		
+
-		if (project.getInputData().getProjectInfo().getAlgorithmDescription() != null) {
+		if (project.getInputData().getProjectInfo().getAlgorithmDescription() != null
+				&& !project.getInputData().getProjectInfo().getAlgorithmDescription().isEmpty()) {
 			if (serviceCredentials.getUserName() != null && !serviceCredentials.getUserName().isEmpty()) {
 				if (serviceCredentials.getFullName() != null && !serviceCredentials.getFullName().isEmpty()) {
-					algorithmDescription="Algorithm Description: "
+					algorithmDescription = project.getInputData().getProjectInfo().getAlgorithmDescription()
-							+ project.getInputData().getProjectInfo().getAlgorithmDescription()
 							+ "[Published by " + serviceCredentials.getFullName() + "("
-							+ serviceCredentials.getUserName() + ") on "
+							+ serviceCredentials.getUserName() + ") on " + sdf.format(Calendar.getInstance().getTime())
-							+ sdf.format(Calendar.getInstance().getTime()) + "]";
+							+ "]";
 				} else {
-					algorithmDescription="Algorithm Description: "
+					algorithmDescription = project.getInputData().getProjectInfo().getAlgorithmDescription()
-							+ project.getInputData().getProjectInfo().getAlgorithmDescription()
 							+ "[Published on " + sdf.format(Calendar.getInstance().getTime()) + "]";
 				}
 			} else {
 				if (serviceCredentials.getFullName() != null && !serviceCredentials.getFullName().isEmpty()) {
-					algorithmDescription="Algorithm Description: "
+					algorithmDescription = project.getInputData().getProjectInfo().getAlgorithmDescription()
-							+ project.getInputData().getProjectInfo().getAlgorithmDescription()
 							+ "[Published by " + serviceCredentials.getFullName() + " on "
 							+ sdf.format(Calendar.getInstance().getTime()) + "]";
 				} else {
-					algorithmDescription="Algorithm Description: "
+					algorithmDescription = project.getInputData().getProjectInfo().getAlgorithmDescription()
-							+ project.getInputData().getProjectInfo().getAlgorithmDescription()
 							+ "[Published on " + sdf.format(Calendar.getInstance().getTime()) + "]";
 				}
 			}
 
 		} else {
-			
+			if (serviceCredentials.getUserName() != null && !serviceCredentials.getUserName().isEmpty()) {
+				if (serviceCredentials.getFullName() != null && !serviceCredentials.getFullName().isEmpty()) {
+					algorithmDescription = "[Published by " + serviceCredentials.getFullName() + "("
+							+ serviceCredentials.getUserName() + ") on " + sdf.format(Calendar.getInstance().getTime())
+							+ "]";
+				} else {
+					algorithmDescription = "[Published on " + sdf.format(Calendar.getInstance().getTime()) + "]";
+				}
+			} else {
+				if (serviceCredentials.getFullName() != null && !serviceCredentials.getFullName().isEmpty()) {
+					algorithmDescription = "[Published by " + serviceCredentials.getFullName() + " on "
+							+ sdf.format(Calendar.getInstance().getTime()) + "]";
+				} else {
+					algorithmDescription = "[Published on " + sdf.format(Calendar.getInstance().getTime()) + "]";
+				}
+			}
 		}
 		return algorithmDescription;
 	}
 
 	private void createInputParameters(ArrayList<String> code) {
 
-		for (InputOutputVariables selVariable : project.getInputData()
+		for (InputOutputVariables selVariable : project.getInputData().getListInputOutputVariables()) {
-				.getListInputOutputVariables()) {
 			if (selVariable.getIoType().compareTo(IOType.INPUT) == 0) {
 				switch (selVariable.getDataType()) {
 				case BOOLEAN:
-					code.add("		inputs.add(new PrimitiveType(Boolean.class.getName(), null,PrimitiveTypes.BOOLEAN, \""
+					code.add(
-							+ selVariable.getName()
+							"		inputs.add(new PrimitiveType(Boolean.class.getName(), null,PrimitiveTypes.BOOLEAN, \""
-							+ "\", \""
+									+ selVariable.getName() + "\", \"" + selVariable.getDescription() + "\", \""
-							+ selVariable.getDescription()
+									+ selVariable.getDefaultValue() + "\"));");
-							+ "\", \""
-							+ selVariable.getDefaultValue() + "\"));");
 					break;
 				case DOUBLE:
 					code.add("		inputs.add(new PrimitiveType(Double.class.getName(), null,PrimitiveTypes.NUMBER, \""
-							+ selVariable.getName()
+							+ selVariable.getName() + "\", \"" + selVariable.getDescription() + "\", \""
-							+ "\", \""
-							+ selVariable.getDescription()
-							+ "\", \""
 							+ selVariable.getDefaultValue() + "\"));");
 					break;
 				case ENUMERATED:
-					String[] values = selVariable.getDefaultValue()
+					String[] values = selVariable.getDefaultValue().split("\\|");
-							.split("\\|");
 					if (values.length > 0) {
 
 						// TODO
-						String nameEnum = enumUUID.get("opIO"
+						String nameEnum = enumUUID.get("opIO" + selVariable.getId());
-								+ selVariable.getId());
 
 						code.add("		if (org.gcube.dataanalysis.executor.rscripts."
-								+ project.getInputData().getProjectInfo()
+								+ project.getInputData().getProjectInfo().getAlgorithmNameToClassName() + "." + nameEnum
-										.getAlgorithmNameToClassName()
+								+ ".E" + nameEnum + ".values().length==0){");
-								+ "."
+						code.add("			" + nameEnum + " en = new " + nameEnum + "();");
-								+ nameEnum
-								+ ".E"
-								+ nameEnum
-								+ ".values().length==0){");
-						code.add("			" + nameEnum + " en = new " + nameEnum
-								+ "();");
 
 						for (String val : values) {
 							code.add("			en.addEnum(org.gcube.dataanalysis.executor.rscripts."
-									+ project.getInputData().getProjectInfo()
+									+ project.getInputData().getProjectInfo().getAlgorithmNameToClassName() + "."
-											.getAlgorithmNameToClassName()
+									+ nameEnum + ".E" + nameEnum + ".class, \"" + val + "\");");
-									+ "."
-									+ nameEnum
-									+ ".E"
-									+ nameEnum
-									+ ".class, \"" + val + "\");");
 						}
 						code.add("		}");
 						code.add("");
 						code.add("		addEnumerateInput(org.gcube.dataanalysis.executor.rscripts."
-								+ project.getInputData().getProjectInfo()
+								+ project.getInputData().getProjectInfo().getAlgorithmNameToClassName() + "." + nameEnum
-										.getAlgorithmNameToClassName()
+								+ ".E" + nameEnum + ".values(), \"" + selVariable.getName() + "\", \""
-								+ "."
+								+ selVariable.getDescription() + "\", \"" + values[0] + "\");");
-								+ nameEnum
-								+ ".E"
-								+ nameEnum
-								+ ".values(), \""
-								+ selVariable.getName()
-								+ "\", \""
-								+ selVariable.getDescription()
-								+ "\", \""
-								+ values[0] + "\");");
 						/*
 						 * code.add(
 						 * "		inputs.add(new PrimitiveType(Enum.class.getName(), opIO"
@@ -413,27 +377,19 @@ public class AlgorithmGenerator {
 					break;
 				case FILE:
 					code.add("		inputs.add(new PrimitiveType(File.class.getName(), null,PrimitiveTypes.FILE, \""
-							+ selVariable.getName()
+							+ selVariable.getName() + "\", \"" + selVariable.getDescription() + "\", \""
-							+ "\", \""
-							+ selVariable.getDescription()
-							+ "\", \""
 							+ selVariable.getDefaultValue() + "\"));");
 
 					break;
 				case INTEGER:
-					code.add("		inputs.add(new PrimitiveType(Integer.class.getName(), null,PrimitiveTypes.NUMBER, \""
+					code.add(
-							+ selVariable.getName()
+							"		inputs.add(new PrimitiveType(Integer.class.getName(), null,PrimitiveTypes.NUMBER, \""
-							+ "\", \""
+									+ selVariable.getName() + "\", \"" + selVariable.getDescription() + "\", \""
-							+ selVariable.getDescription()
+									+ selVariable.getDefaultValue() + "\"));");
-							+ "\", \""
-							+ selVariable.getDefaultValue() + "\"));");
 					break;
 				case STRING:
 					code.add("		inputs.add(new PrimitiveType(String.class.getName(), null,PrimitiveTypes.STRING, \""
-							+ selVariable.getName()
+							+ selVariable.getName() + "\", \"" + selVariable.getDescription() + "\", \""
-							+ "\", \""
-							+ selVariable.getDescription()
-							+ "\", \""
 							+ selVariable.getDefaultValue() + "\"));");
 
 					break;
@@ -454,57 +410,41 @@ public class AlgorithmGenerator {
 	 */
 
 	private void createOutputParameters(ArrayList<String> code) {
-		for (InputOutputVariables selVariable : project.getInputData()
+		for (InputOutputVariables selVariable : project.getInputData().getListInputOutputVariables()) {
-				.getListInputOutputVariables()) {
 			if (selVariable.getIoType().compareTo(IOType.OUTPUT) == 0) {
 				switch (selVariable.getDataType()) {
 				case BOOLEAN:
-					code.add("		output.put(\""
+					code.add("		output.put(\"" + selVariable.getName()
-							+ selVariable.getName()
 							+ "\",new PrimitiveType(Boolean.class.getName(), new File(outputValues.get(\""
-							+ selVariable.getName()
+							+ selVariable.getName() + "\")), PrimitiveTypes.BOOLEAN, \"" + selVariable.getName()
-							+ "\")), PrimitiveTypes.BOOLEAN, \""
+							+ "\", \"" + selVariable.getName() + "\"));");
-							+ selVariable.getName() + "\", \""
-							+ selVariable.getName() + "\"));");
 					break;
 				case DOUBLE:
-					code.add("		output.put(\""
+					code.add("		output.put(\"" + selVariable.getName()
-							+ selVariable.getName()
 							+ "\",new PrimitiveType(Double.class.getName(), new File(outputValues.get(\""
-							+ selVariable.getName()
+							+ selVariable.getName() + "\")), PrimitiveTypes.NUMBER, \"" + selVariable.getName()
-							+ "\")), PrimitiveTypes.NUMBER, \""
+							+ "\", \"" + selVariable.getName() + "\"));");
-							+ selVariable.getName() + "\", \""
-							+ selVariable.getName() + "\"));");
 					break;
 				case ENUMERATED:
 					break;
 				case FILE:
-					code.add("		output.put(\""
+					code.add("		output.put(\"" + selVariable.getName()
-							+ selVariable.getName()
 							+ "\",new PrimitiveType(File.class.getName(), new File(outputValues.get(\""
-							+ selVariable.getName()
+							+ selVariable.getName() + "\")), PrimitiveTypes.FILE, \"" + selVariable.getName() + "\", \""
-							+ "\")), PrimitiveTypes.FILE, \""
-							+ selVariable.getName() + "\", \""
 							+ selVariable.getName() + "\"));");
 
 					break;
 				case INTEGER:
-					code.add("		output.put(\""
+					code.add("		output.put(\"" + selVariable.getName()
-							+ selVariable.getName()
 							+ "\",new PrimitiveType(Integer.class.getName(), new File(outputValues.get(\""
-							+ selVariable.getName()
+							+ selVariable.getName() + "\")), PrimitiveTypes.NUMBER, \"" + selVariable.getName()
-							+ "\")), PrimitiveTypes.NUMBER, \""
+							+ "\", \"" + selVariable.getName() + "\"));");
-							+ selVariable.getName() + "\", \""
-							+ selVariable.getName() + "\"));");
 					break;
 				case STRING:
-					code.add("		output.put(\""
+					code.add("		output.put(\"" + selVariable.getName()
-							+ selVariable.getName()
 							+ "\",new PrimitiveType(String.class.getName(), new File(outputValues.get(\""
-							+ selVariable.getName()
+							+ selVariable.getName() + "\")), PrimitiveTypes.STRING, \"" + selVariable.getName()
-							+ "\")), PrimitiveTypes.STRING, \""
+							+ "\", \"" + selVariable.getName() + "\"));");
-							+ selVariable.getName() + "\", \""
-							+ selVariable.getName() + "\"));");
 
 					break;
 				default:
@@ -517,30 +457,25 @@ public class AlgorithmGenerator {
 	}
 
 	private String retrieveMainScriptRelativePath() {
-		logger.debug("ProjectInfo: "+project);
+		logger.debug("ProjectInfo: " + project);
 		String projectPath = project.getProjectFolder().getFolder().getPath();
-		String mainCodePath = project.getMainCode().getItemDescription()
+		String mainCodePath = project.getMainCode().getItemDescription().getPath();
-				.getPath();
+		logger.debug("ProjectPath: " + projectPath);
-		logger.debug("ProjectPath: "+projectPath);
+		logger.debug("MainCodePath: " + mainCodePath);
-		logger.debug("MainCodePath: "+mainCodePath);
+
-		
 		String relativePath = project.getProjectFolder().getFolder().getName()
 				+ mainCodePath.substring(projectPath.length());
-		logger.debug("RelativePath:"+relativePath);
+		logger.debug("RelativePath:" + relativePath);
 		return relativePath;
 
 	}
 
 	private String retrievePackageUrl() {
 		String packageUrl = "";
-		if (project.getProjectTarget() != null
+		if (project.getProjectTarget() != null && project.getProjectTarget().getProjectDeploy() != null
-				&& project.getProjectTarget().getProjectDeploy() != null
+				&& project.getProjectTarget().getProjectDeploy().getPackageProject() != null) {
-				&& project.getProjectTarget().getProjectDeploy()
+			if (project.getProjectTarget().getProjectDeploy().getPackageProject().getPublicLink() != null) {
-						.getPackageProject() != null) {
+				packageUrl = project.getProjectTarget().getProjectDeploy().getPackageProject().getPublicLink();
-			if (project.getProjectTarget().getProjectDeploy()
-					.getPackageProject().getPublicLink() != null) {
-				packageUrl = project.getProjectTarget().getProjectDeploy()
-						.getPackageProject().getPublicLink();
 			}
 		}
 		return packageUrl;

test.log

@@ -910,3 +910,44 @@ return $entry0ValueAuth/..
 2017-10-10 10:49:57 DEBUG InformationSystemUtils:118 - Resources: [GCoreEndpoint [id=a13cd300-a66e-4f9d-b2cc-a4229b148d8a, scopes=[/gcube/devNext, /gcube/devsec, /gcube], type=RunningInstance, version=0.4.x, profile=[description=, version=0.0.1, ghn=[id=96550b2e-09e9-4c4e-9bac-2f59ecaff1e7], service=[id=dataminer-pool-managerDataAnalysis0.0.1], serviceName=dataminer-pool-manager, serviceClass=DataAnalysis, runningInstanceInterfaces=[], platform=null, deploymentData=[instanceName=null, localPath=null, activationTime=10/9/17 5:55 PM, terminationTime=, status=ready, messageState=null, plugins=[]], functions=[], endpoints=[Endpoint [name=REST-API, uri=http://dm-pool-manager-dev.d4science.org:80/dataminer-pool-manager/api], Endpoint [name=dataminer-pool-manager-remote-management, uri=http://dm-pool-manager-dev.d4science.org:80/dataminer-pool-manager/gcube/resource]], specificData=[doc: null], accountings=[]]]]
 2017-10-10 10:49:57 DEBUG InformationSystemUtils:162 - DataMiner PoolManager URI: null
 2017-10-10 10:49:57 INFO  ISResourceTest:109 - DataMinerPoolManager: null
+2018-01-17 12:59:38 DEBUG InformationSystemUtils:101 - Retrieve dataminer-pool-manager
+2018-01-17 12:59:38 INFO  ScopeProviderScanner:50 - using scope provider org.gcube.common.scope.impl.DefaultScopeProvider@71c7db30
+2018-01-17 12:59:38 DEBUG DefaultScopeProvider:38 - setting scope /d4science.research-infrastructures.eu/ParthenosVO/PARTHENOS_LAB in thread 1
+2018-01-17 12:59:38 DEBUG InformationSystemUtils:106 - Retrieve DataMiner Pool Manager resource in scope: /d4science.research-infrastructures.eu/ParthenosVO/PARTHENOS_LAB
+2018-01-17 12:59:39 INFO  DefaultScanner:63 - matched 16 resources from 170 urls in 236 ms
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/socialisti.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/devsec.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/farm.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/edison.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/sobigdata.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/gcube.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/openaire.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/smartarea.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/d4science.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/gcubeapps.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/isti.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/devnext.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/parthenosvo.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/cnr.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/d4research.servicemap 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:62 - overwriting older map (v.1.0.7-SNAPSHOT) with newer map (v.1.0.7-SNAPSHOT) for /d4science.research-infrastructures.eu/D4Research 
+2018-01-17 12:59:39 INFO  ServiceMapScanner:52 - loading jar:file:/home/giancarlo/.m2/repository/org/gcube/core/common-scope-maps/1.0.7-SNAPSHOT/common-scope-maps-1.0.7-SNAPSHOT.jar!/preprod.servicemap 
+2018-01-17 12:59:39 INFO  ICClient:75 - connectinfg to http://collector-parthenosvo.d4science.org:8080/wsrf/services/gcube/informationsystem/collector/XQueryAccess
+2018-01-17 12:59:39 INFO  StubFactory:147 - fetching wsdl for XQueryAccessService at http://collector-parthenosvo.d4science.org:8080/wsrf/services/gcube/informationsystem/collector/XQueryAccess?wsdl
+2018-01-17 12:59:39 INFO  StubCache:63 - caching stub for interface org.gcube.resources.discovery.icclient.stubs.CollectorStub
+2018-01-17 12:59:40 DEBUG MethodRetriever:18 - for interface org.gcube.resources.discovery.icclient.stubs.CollectorStub the proxy class is com.sun.proxy.$Proxy36
+2018-01-17 12:59:40 INFO  ICClient:57 - executing query declare namespace ic = 'http://gcube-system.org/namespaces/informationsystem/registry'; for $resource in collection('/db/Profiles/RunningInstance')//Document/Data/ic:Profile/Resource where ($resource/Profile/ServiceClass/text() eq 'DataAnalysis') and ($resource/Profile/ServiceName/text() eq 'dataminer-pool-manager') return $resource
+2018-01-17 12:59:40 INFO  Helper:200 - submitting filtered query: declare namespace ic = 'http://gcube-system.org/namespaces/informationsystem/registry'; declare namespace functx = "http://www.functx.com"; declare function functx:is-value-in-sequence   ( $value as xs:anyAtomicType? , $seq as xs:anyAtomicType* )  as xs:boolean { $value = $seq } ; 
+ for  $entry0ValueAuth in  collection('/db/Profiles/RunningInstance')//Document/Data/ic:Profile/Resource/Scopes 
+ 
+where  (functx:is-value-in-sequence('/d4science.research-infrastructures.eu/ParthenosVO/PARTHENOS_LAB',$entry0ValueAuth/child::*[local-name()='Scope']/text()) or functx:is-value-in-sequence('/d4science.research-infrastructures.eu/ParthenosVO',$entry0ValueAuth/child::*[local-name()='Scope']/text()))  and ( ($entry0ValueAuth/../Profile/ServiceClass/text() eq 'DataAnalysis') and ($entry0ValueAuth/../Profile/ServiceName/text() eq 'dataminer-pool-manager')  ) 
+return $entry0ValueAuth/..
+2018-01-17 12:59:40 INFO  HandlerRegistry:30 - loaded call handler org.gcube.common.clients.stubs.jaxws.handlers.ScopeHandler@140c9f39
+2018-01-17 12:59:40 INFO  HandlerRegistry:30 - loaded call handler org.gcube.common.clients.stubs.jaxws.handlers.AuthorizationHandler@7690781
+2018-01-17 12:59:40 INFO  HandlerRegistry:30 - loaded call handler org.gcube.common.clients.stubs.jaxws.handlers.TargetServiceHandler@2e222612
+2018-01-17 12:59:40 INFO  HandlerRegistry:30 - loaded call handler org.gcube.common.clients.stubs.jaxws.handlers.ClientInfoHandler@7671cb68
+2018-01-17 12:59:40 INFO  HandlerRegistry:30 - loaded call handler org.gcube.common.clients.stubs.jaxws.handlers.LegacyWSAddressingHandler@68c72235
+2018-01-17 12:59:40 INFO  ICClient:65 - executed query declare namespace ic = 'http://gcube-system.org/namespaces/informationsystem/registry'; for $resource in collection('/db/Profiles/RunningInstance')//Document/Data/ic:Profile/Resource where ($resource/Profile/ServiceClass/text() eq 'DataAnalysis') and ($resource/Profile/ServiceName/text() eq 'dataminer-pool-manager') return $resource in 251 ms
+2018-01-17 12:59:40 DEBUG InformationSystemUtils:118 - Resources: [GCoreEndpoint [id=86981339-1a07-4eb3-9919-c42344e6dfc8, scopes=[/d4science.research-infrastructures.eu/ParthenosVO/ParthenosLab, /d4science.research-infrastructures.eu/SoBigData/SoBigDataLab, /d4science.research-infrastructures.eu/D4Research, /d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab, /d4science.research-infrastructures.eu/SoBigData, /d4science.research-infrastructures.eu/gCubeApps/ICCAT_BFT-E, /d4science.research-infrastructures.eu/D4Research/FoodborneOutbreak, /d4science.research-infrastructures.eu/D4Research/AgroClimaticModelling, /d4science.research-infrastructures.eu/gCubeApps/ScalableDataMining, /d4science.research-infrastructures.eu/D4Research/RAKIP_portal, /d4science.research-infrastructures.eu/gCubeApps/FAO_TunaAtlas, /d4science.research-infrastructures.eu/ParthenosVO, /d4science.research-infrastructures.eu/gCubeApps/StockAssessment, /d4science.research-infrastructures.eu/gCubeApps, /d4science.research-infrastructures.eu/D4Research/Sinay, /d4science.research-infrastructures.eu/D4Research/StatnMap, /d4science.research-infrastructures.eu/D4Research/IOTC_SS3, /d4science.research-infrastructures.eu/D4Research/FoodSecurity, /d4science.research-infrastructures.eu/D4Research/TextCrowd], type=RunningInstance, version=0.4.x, profile=[description=, version=0.0.1, ghn=[id=5ddf1091-87d2-4c38-b288-7ac3ed19cdc3], service=[id=dataminer-pool-managerDataAnalysis0.0.1], serviceName=dataminer-pool-manager, serviceClass=DataAnalysis, runningInstanceInterfaces=[], platform=null, deploymentData=[instanceName=null, localPath=null, activationTime=12/19/17 3:08 PM, terminationTime=, status=ready, messageState=null, plugins=[]], functions=[], endpoints=[Endpoint [name=REST-API, uri=http://dm-pool-manager-proto.d4science.org:80/dataminer-pool-manager/api], Endpoint [name=dataminer-pool-manager-remote-management, uri=http://dm-pool-manager-proto.d4science.org:80/dataminer-pool-manager/gcube/resource]], specificData=[doc: null], accountings=[]]]]
+2018-01-17 12:59:40 DEBUG InformationSystemUtils:162 - DataMiner PoolManager URI: null
+2018-01-17 12:59:40 INFO  ISResourceTest:109 - DataMinerPoolManager: null