1452: Implement a GUI for StatMan Algorithms Importer

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

Updated UI behavior

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@122173 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/codeparser/CodeParser.java

@@ -4,6 +4,7 @@ import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.DataTy
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.IOType;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.SelectedRowsVariables;
 
+import com.allen_sauer.gwt.log.client.Log;
 import com.google.gwt.regexp.shared.RegExp;
 
 /**
@@ -32,24 +33,37 @@ public class CodeParser {
 
 		if (parameter.contains("<-")) {
 			String[] varDescription = parameter.split("<-");
+			String defaultValue = varDescription[1].trim();
+			if (defaultValue.startsWith("\""))
+				defaultValue = defaultValue.substring(1);
+			if (defaultValue.endsWith("\""))
+				defaultValue = defaultValue.substring(0,
+						defaultValue.length() - 1);
+
 			selectedRowsVariables = new SelectedRowsVariables(
 					varDescription[0].trim(), varDescription[0].trim(),
-					varDescription[1].trim(),
+					defaultValue, checkDataType(varDescription[1].trim()),
-					checkDataType(varDescription[1].trim()), ioType, parameter);
+					ioType, parameter);
-
 		} else {
 			if (parameter.contains("=")) {
 				String[] varDescription = parameter.split("=");
+				String defaultValue = varDescription[1].trim();
+				if (defaultValue.startsWith("\""))
+					defaultValue = defaultValue.substring(1);
+				if (defaultValue.endsWith("\""))
+					defaultValue = defaultValue.substring(0,
+							defaultValue.length() - 1);
 				selectedRowsVariables = new SelectedRowsVariables(
 						varDescription[0].trim(), varDescription[0].trim(),
-						varDescription[1].trim(),
+						defaultValue, checkDataType(varDescription[1].trim()),
-						checkDataType(varDescription[1].trim()), ioType,
+						ioType, parameter);
-						parameter);
+
 			} else {
 				return null;
 			}
 		}
 
+		Log.debug("CodeParser: " + selectedRowsVariables);
 		return selectedRowsVariables;
 	}
 

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/tools/input/EnvironmentVariablesPanel.java

@@ -106,7 +106,7 @@ public class EnvironmentVariablesPanel extends ContentPanel {
 		// nameColumn.setMenuDisabled(true);
 
 		ColumnConfig<EnvironmentVariables, String> descriptionColumn = new ColumnConfig<EnvironmentVariables, String>(
-				props.name(), 100, "Description");
+				props.description(), 100, "Description");
 		// descriptionColumn.setMenuDisabled(true);
 
 		ColumnConfig<EnvironmentVariables, DataType> inputTypeColumn = new ColumnConfig<EnvironmentVariables, DataType>(

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/tools/input/SelectedRowsPanel.java

@@ -118,7 +118,7 @@ public class SelectedRowsPanel extends ContentPanel {
 		// nameColumn.setMenuDisabled(true);
 
 		ColumnConfig<SelectedRowsVariables, String> descriptionColumn = new ColumnConfig<SelectedRowsVariables, String>(
-				props.name(), 100, "Description");
+				props.description(), 100, "Description");
 		// descriptionColumn.setMenuDisabled(true);
 
 		ColumnConfig<SelectedRowsVariables, DataType> dataTypeColumn = new ColumnConfig<SelectedRowsVariables, DataType>(

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

@@ -0,0 +1,55 @@
+package org.gcube.portlets.user.statisticalalgorithmsimporter.server.generator;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.exception.StatAlgoImporterServiceException;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.Project;
+
+/**
+ * 
+ * @author Giancarlo Panichi email: <a
+ *         href="mailto:g.panichi@isti.cnr.it">g.panichi@isti.cnr.it</a>
+ *
+ */
+public class AlgorithmGenerator {
+
+	private static final String EXTENTION_JAVA = ".java";
+	private Project project;
+
+	public AlgorithmGenerator(Project project) {
+		super();
+		this.project = project;
+	}
+
+	@Override
+	public String toString() {
+		return "AlgorithmGenerator [project=" + project + "]";
+	}
+
+	public File createAlgorithm() throws StatAlgoImporterServiceException {
+		try {
+			File fileTmp = File.createTempFile(project.getClassName(),
+					EXTENTION_JAVA);
+			fileTmp.deleteOnExit();
+			/*
+			List<String> lines = Arrays.asList("The first line", "The second line");
+			Path file = Paths.g;
+			Files.write(file, lines, Charset.forName("UTF-8"));
+			 */
+			return fileTmp;
+
+		} catch (IOException e) {
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+		}
+
+	}
+
+}

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/shared/project/Project.java

@@ -10,8 +10,12 @@ import java.io.Serializable;
  */
 public class Project implements Serializable {
 
+
 	private static final long serialVersionUID = -7906477664944910362L;
 
+	private String name;
+	private String description;
+	private String className;
 	private ProjectFolder projectFolder;
 	private MainCode mainCode;
 	private InputData inputData;
@@ -26,6 +30,30 @@ public class Project implements Serializable {
 
 	}
 
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
+	public String getClassName() {
+		return className;
+	}
+
+	public void setClassName(String className) {
+		this.className = className;
+	}
+
 	public MainCode getMainCode() {
 		return mainCode;
 	}
@@ -52,12 +80,11 @@ public class Project implements Serializable {
 
 	@Override
 	public String toString() {
-		return "Project [projectFolder=" + projectFolder + ", mainCode="
+		return "Project [name=" + name + ", description=" + description
-				+ mainCode + ", inputData=" + inputData + "]";
+				+ ", className=" + className + ", projectFolder="
+				+ projectFolder + ", mainCode=" + mainCode + ", inputData="
+				+ inputData + "]";
 	}
 
 
-
-	
-	
 }

src/main/resources/org/gcube/portlets/user/statisticalalgorithmsimporter/statalgoimporter.gwt.xml

@@ -51,17 +51,17 @@
 		name="locale" values="es" /> <set-property name="locale" value="en, it, es" 
 		/> <set-property-fallback name="locale" value="en" /> -->
 
-	<set-property name="log_ConsoleLogger" value="ENABLED" />
+	<!-- <set-property name="log_ConsoleLogger" value="ENABLED" /> <set-property 
-	<set-property name="log_DivLogger" value="ENABLED" />
+		name="log_DivLogger" value="ENABLED" /> <set-property name="log_GWTLogger" 
-	<set-property name="log_GWTLogger" value="ENABLED" />
+		value="ENABLED" /> <set-property name="log_SystemLogger" value="ENABLED" 
-	<set-property name="log_SystemLogger" value="ENABLED" />
+		/> -->
 	<!-- Not in GWT 2.6 <set-property name="log_FirebugLogger" value="ENABLED" 
 		/> -->
 
-	<!-- <set-property name="log_ConsoleLogger" value="DISABLED" /> <set-property 
+	<set-property name="log_ConsoleLogger" value="DISABLED" />
-		name="log_DivLogger" value="DISABLED" /> <set-property name="log_GWTLogger" 
+	<set-property name="log_DivLogger" value="DISABLED" />
-		value="DISABLED" /> <set-property name="log_SystemLogger" value="DISABLED" 
+	<set-property name="log_GWTLogger" value="DISABLED" />
-		/> -->
+	<set-property name="log_SystemLogger" value="DISABLED" />
 	<!-- Not in GWT 2.6 <set-property name="log_FirebugLogger" value="DISABLED" 
 		/> -->
 

src/test/resources/org/gcube/portlets/user/statisticalalgorithmsimporter/example/FileTemplate.java

@@ -0,0 +1,43 @@
+package org.gcube.dataanalysis.executor.rscripts;
+ 
+import java.io.File;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+ 
+import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
+import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
+import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
+import org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript;
+ 
+public class KnitrCompiler extends GenericRScript {
+ 
+	@Override
+	public String getDescription() {
+		return "An algorithm to compile Knitr documents. Developed by IRD (reference Julien Bard, julien.barde@ird.fr)";
+	}
+ 
+	protected void initVariables(){
+		mainScriptName="IRDTunaAtlas-master/report/knitr/compileKnitR_CNR.R";
+		packageURL="http://goo.gl/T7V8LV";
+ 
+		environmentalvariables = new ArrayList<String>();
+		inputvariables.add("zipfile");
+		inputvariables.add("file.inout");
+		outputvariables.add("pdfresult");		
+	}
+ 
+	@Override
+	protected void setInputParameters() {
+		inputs.add(new PrimitiveType(File.class.getName(), null, PrimitiveTypes.FILE, "zipfile", "The file containing R and the markdown (Rnw) files to compile","knitr_wfs.zip"));
+		inputs.add(new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "file.inout", "The name of the R file in the zip package", "main.r"));
+	}
+ 
+	@Override
+	public StatisticalType getOutput() {
+		output.put("pdfresult",new PrimitiveType(File.class.getName(), new File(outputValues.get("pdfresult")), PrimitiveTypes.FILE, "pdfresult", "The compiled PDF file"));
+		PrimitiveType o = new PrimitiveType(LinkedHashMap.class.getName(), output, PrimitiveTypes.MAP, "Output", "");
+		return o;
+	}
+ 
+}
+