refs 4823: DataMiner - Preserve the order of the output (Example Bionym Local)

Task-Url: https://support.d4science.org/issues/4823

In the case of Check The Computation, now the interaface shows the input parameters in the order requested by the algorithm and the output parameters sorted by name

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/data-miner-manager@130969 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/portlets/user/dataminermanager/client/computations/ComputationsPanel.java

@@ -32,6 +32,7 @@ public class ComputationsPanel extends SimpleContainer {
 
 	public ComputationsPanel() {
 		super();
+		Log.debug("ComputationsPanel");
 		init();
 		create();
 		bind();

src/main/java/org/gcube/portlets/user/dataminermanager/client/computations/ComputationsViewerPanel.java

@@ -37,8 +37,9 @@ public class ComputationsViewerPanel extends FramedPanel {
 
 	public ComputationsViewerPanel(ComputationData computationData) {
 		super();
-		Log.debug("ComputationsPanel");
+		Log.debug("ComputationsViewerPanel");
 		this.computationData = computationData;
+		Log.debug("ComputationData: " + computationData);
 		init();
 		create();
 
@@ -58,15 +59,21 @@ public class ComputationsViewerPanel extends FramedPanel {
 	}
 
 	private void create() {
+		try {
 			v = new VerticalLayoutContainer();
 			v.setScrollMode(ScrollMode.AUTO);
 			add(v);
 			createView();
 			forceLayout();
+		} catch (Throwable e) {
+			Log.error("Error creating ComputationsViewerPanel: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+		}
 	}
 
-
 	private void createView() {
+
 		if (computationData == null) {
 			Log.error("ComputationData is null!");
 			UtilsGXT3.alert("Error",
@@ -74,6 +81,15 @@ public class ComputationsViewerPanel extends FramedPanel {
 			return;
 		}
 
+		if (computationData.getComputationId() == null
+				|| computationData.getComputationId().getId() == null
+				|| computationData.getComputationId().getId().isEmpty()) {
+			Log.error("Error in computationId: " + computationData);
+			UtilsGXT3.alert("Error",
+					"No information on computation id is retrieved!");
+			return;
+		}
+
 		SimpleContainer sectionTitle = new SimpleContainer();
 		// title
 		HtmlLayoutContainer title = new HtmlLayoutContainer(
@@ -82,7 +98,8 @@ public class ComputationsViewerPanel extends FramedPanel {
 						+ "</b></center>");
 		sectionTitle.add(title, new MarginData());
 		sectionTitle.getElement().getStyle().setMarginRight(20, Unit.PX);
-		// v.add(sectionTitle, new VerticalLayoutData(1, -1, new Margins(0)));
+		// v.add(sectionTitle, new VerticalLayoutData(1, -1, new
+		// Margins(0)));
 		v.add(sectionTitle, new VerticalLayoutData(-1, -1, new Margins(10)));
 
 		if (computationData.getOutputParameters() != null
@@ -105,11 +122,11 @@ public class ComputationsViewerPanel extends FramedPanel {
 		FieldSet operatorFieldSet = operatorView();
 		v.add(operatorFieldSet, new VerticalLayoutData(-1, -1, new Margins(10)));
 
-	
-
 	}
 
 	private FieldSet operatorView() {
+		try {
+
 			VerticalLayoutContainer operatorVBox = new VerticalLayoutContainer();
 			TextField operatorNameField = new TextField();
 			operatorNameField.setValue(computationData.getComputationId()
@@ -132,25 +149,35 @@ public class ComputationsViewerPanel extends FramedPanel {
 			operatorDescriptionLabel.setLabelWidth(200);
 			operatorDescriptionLabel.setLabelWordWrap(true);
 			operatorDescriptionLabel.setHeight(65);
-		operatorVBox.add(operatorDescriptionLabel, new VerticalLayoutData(1,
-				-1, new Margins(0,5,0,5)));
+			operatorVBox.add(operatorDescriptionLabel, new VerticalLayoutData(
+					1, -1, new Margins(0, 5, 0, 5)));
 
 			FieldSet operatorFieldSet = new FieldSet();
 			operatorFieldSet.setHeadingText("Operator Details");
 			operatorFieldSet.setCollapsible(true);
 			operatorFieldSet.setHeight(130);
 			operatorFieldSet.add(operatorVBox);
-		operatorFieldSet.getElement().getStyle().setMarginBottom(120, Unit.PX);
-		operatorFieldSet.getElement().getStyle().setMarginRight(20, Unit.PX);
+			operatorFieldSet.getElement().getStyle()
+					.setMarginBottom(120, Unit.PX);
+			operatorFieldSet.getElement().getStyle()
+					.setMarginRight(20, Unit.PX);
 			return operatorFieldSet;
+		} catch (Throwable e) {
+			Log.error("Error in ComputationsViewerPanel in operator: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw e;
+		}
 	}
 
 	private FieldSet detailsView() {
+		try {
 			VerticalLayoutContainer detailsVBox = new VerticalLayoutContainer();
 			TextField startDateField = new TextField();
 			startDateField.setValue(computationData.getStartDate());
 			startDateField.setReadOnly(true);
-		FieldLabel startDateLabel = new FieldLabel(startDateField, "Start Date");
+			FieldLabel startDateLabel = new FieldLabel(startDateField,
+					"Start Date");
 			startDateLabel.setLabelWidth(200);
 			startDateLabel.setLabelWordWrap(true);
 			detailsVBox.add(startDateLabel, new VerticalLayoutData(1, -1,
@@ -171,8 +198,8 @@ public class ComputationsViewerPanel extends FramedPanel {
 			FieldLabel statusLabel = new FieldLabel(statusField, "Status");
 			statusLabel.setLabelWidth(200);
 			statusLabel.setLabelWordWrap(true);
-		detailsVBox.add(statusLabel, new VerticalLayoutData(1, -1, new Margins(
-				0,4,0,4)));
+			detailsVBox.add(statusLabel, new VerticalLayoutData(1, -1,
+					new Margins(0, 4, 0, 4)));
 
 			TextField vreField = new TextField();
 			vreField.setValue(computationData.getVre());
@@ -180,8 +207,8 @@ public class ComputationsViewerPanel extends FramedPanel {
 			FieldLabel vreLabel = new FieldLabel(vreField, "VRE");
 			vreLabel.setLabelWidth(200);
 			vreLabel.setLabelWordWrap(true);
-		detailsVBox
-				.add(vreLabel, new VerticalLayoutData(1, -1, new Margins(0,4,0,4)));
+			detailsVBox.add(vreLabel, new VerticalLayoutData(1, -1,
+					new Margins(0, 4, 0, 4)));
 
 			FieldSet detailsFieldSet = new FieldSet();
 			detailsFieldSet.setHeadingText("Computation Details");
@@ -189,34 +216,58 @@ public class ComputationsViewerPanel extends FramedPanel {
 			detailsFieldSet.add(detailsVBox);
 			detailsFieldSet.getElement().getStyle().setMarginRight(20, Unit.PX);
 			return detailsFieldSet;
+		} catch (Throwable e) {
+			Log.error("Error in ComputationsViewerPanel in details: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw e;
+		}
 	}
 
 	private FieldSet inputView() {
+		try {
 			VerticalLayoutContainer inputVBox = new VerticalLayoutContainer();
 			LinkedHashMap<String, ComputationValue> input = computationData
 					.getInputParameters();
 			for (String key : input.keySet()) {
 				ComputationValue computationValue = input.get(key);
+				Log.debug("Input: [key=" + key + ", ComputationValue="
+						+ computationValue + "]");
 				FieldLabel fieldLabel = null;
 				SimpleContainer simpleContainer;
+				if(computationValue==null){
+					TextField textField = new TextField();
+					textField.setReadOnly(true);
+					fieldLabel = new FieldLabel(textField, key);
+					fieldLabel.setLabelWidth(200);
+					fieldLabel.setLabelWordWrap(true);
+					inputVBox.add(fieldLabel, new VerticalLayoutData(1, -1,
+							new Margins(0, 4, 0, 4)));
+					continue;
+				}
+				
+				
 				switch (computationValue.getType()) {
 				case File:
 					ComputationValueFile computationValueFile = (ComputationValueFile) computationValue;
-				simpleContainer=new ComputationValueFilePanel(computationValueFile);
+					simpleContainer = new ComputationValueFilePanel(
+							computationValueFile);
 					fieldLabel = new FieldLabel(simpleContainer, key);
 					fieldLabel.setLabelWidth(200);
 					fieldLabel.setLabelWordWrap(true);
 					break;
 				case Image:
 					ComputationValueImage computationValueImage = (ComputationValueImage) computationValue;
-				simpleContainer=new ComputationValueImagePanel(computationValueImage);
+					simpleContainer = new ComputationValueImagePanel(
+							computationValueImage);
 					fieldLabel = new FieldLabel(simpleContainer, key);
 					fieldLabel.setLabelWidth(200);
 					fieldLabel.setLabelWordWrap(true);
 					break;
 				case FileList:
 					ComputationValueFileList computationValueFileList = (ComputationValueFileList) computationValue;
-				simpleContainer=new ComputationValueFileListPanel(computationValueFileList);
+					simpleContainer = new ComputationValueFileListPanel(
+							computationValueFileList);
 					fieldLabel = new FieldLabel(simpleContainer, key);
 					fieldLabel.setLabelWidth(200);
 					fieldLabel.setLabelWordWrap(true);
@@ -242,34 +293,57 @@ public class ComputationsViewerPanel extends FramedPanel {
 			inputFieldSet.add(inputVBox);
 			inputFieldSet.getElement().getStyle().setMarginRight(20, Unit.PX);
 			return inputFieldSet;
+		} catch (Throwable e) {
+			Log.error("Error in ComputationsViewerPanel creating input view: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw e;
+		}
 	}
 
 	private FieldSet outputView() {
+		try {
 			VerticalLayoutContainer outputVBox = new VerticalLayoutContainer();
 			LinkedHashMap<String, ComputationValue> output = computationData
 					.getOutputParameters();
 			for (String key : output.keySet()) {
 				ComputationValue computationValue = output.get(key);
+				Log.debug("Output: [key=" + key + ", ComputationValue="
+						+ computationValue + "]");
 				FieldLabel fieldLabel = null;
 				SimpleContainer simpleContainer;
+				if(computationValue==null){
+					TextField textField = new TextField();
+					textField.setReadOnly(true);
+					fieldLabel = new FieldLabel(textField, key);
+					fieldLabel.setLabelWidth(200);
+					fieldLabel.setLabelWordWrap(true);
+					outputVBox.add(fieldLabel, new VerticalLayoutData(1, -1,
+							new Margins(0, 4, 0, 4)));
+					continue;
+				}
+				
 				switch (computationValue.getType()) {
 				case File:
 					ComputationValueFile computationValueFile = (ComputationValueFile) computationValue;
-				simpleContainer=new ComputationValueFilePanel(computationValueFile);
+					simpleContainer = new ComputationValueFilePanel(
+							computationValueFile);
 					fieldLabel = new FieldLabel(simpleContainer, key);
 					fieldLabel.setLabelWidth(200);
 					fieldLabel.setLabelWordWrap(true);
 					break;
 				case Image:
 					ComputationValueImage computationValueImage = (ComputationValueImage) computationValue;
-				simpleContainer=new ComputationValueImagePanel(computationValueImage);
+					simpleContainer = new ComputationValueImagePanel(
+							computationValueImage);
 					fieldLabel = new FieldLabel(simpleContainer, key);
 					fieldLabel.setLabelWidth(200);
 					fieldLabel.setLabelWordWrap(true);
 					break;
 				case FileList:
 					ComputationValueFileList computationValueFileList = (ComputationValueFileList) computationValue;
-				simpleContainer=new ComputationValueFileListPanel(computationValueFileList);
+					simpleContainer = new ComputationValueFileListPanel(
+							computationValueFileList);
 					fieldLabel = new FieldLabel(simpleContainer, key);
 					fieldLabel.setLabelWidth(200);
 					fieldLabel.setLabelWordWrap(true);
@@ -294,6 +368,12 @@ public class ComputationsViewerPanel extends FramedPanel {
 			outputFieldSet.add(outputVBox);
 			outputFieldSet.getElement().getStyle().setMarginRight(20, Unit.PX);
 			return outputFieldSet;
+		} catch (Throwable e) {
+			Log.error("Error in ComputationsViewerPanel creating output view: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw e;
+		}
 	}
 
 }

src/main/java/org/gcube/portlets/user/dataminermanager/server/DataMinerManagerServiceImpl.java

@@ -1,5 +1,6 @@
 package org.gcube.portlets.user.dataminermanager.server;
 
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -343,6 +344,8 @@ public class DataMinerManagerServiceImpl extends RemoteServiceServlet implements
 			logger.debug("OutputDataByComputationItemt(): " + itemDescription);
 			Map<String, String> properties = StorageUtil.getProperties(
 					aslSession.getUsername(), itemDescription.getId());
+			
+			
 			logger.debug("Properties: " + properties);
 			SClient smClient = SessionUtil.getSClient(aslSession, session);
 			ComputationData computationData = smClient

src/main/java/org/gcube/portlets/user/dataminermanager/server/smservice/SClient4WPS.java

@@ -989,7 +989,7 @@ public class SClient4WPS extends SClient {
 	@Override
 	public OutputData getOutputDataByComputationId(ComputationId computationId)
 			throws Exception {
-		Map<String, Resource> resources = retrieveOutput(computationId);
+		LinkedHashMap<String, Resource> resources = retrieveOutput(computationId);
 		MapResource mapResource = new MapResource("mapResource", "Resources",
 				"Resources", resources);
 		OutputData outputData = new OutputData(computationId, mapResource);
@@ -997,10 +997,10 @@ public class SClient4WPS extends SClient {
 		return outputData;
 	}
 
-	private Map<String, Resource> retrieveOutput(ComputationId computationId)
-			throws Exception {
-		Map<String, Resource> outputResource = new LinkedHashMap<>();
-		Map<String, Parameter> outputParameters = new LinkedHashMap<>();
+	private LinkedHashMap<String, Resource> retrieveOutput(
+			ComputationId computationId) throws Exception {
+		LinkedHashMap<String, Resource> outputResource = new LinkedHashMap<>();
+		LinkedHashMap<String, Parameter> outputParameters = new LinkedHashMap<>();
 		ProcessInformations processInformations = runningProcess
 				.get(computationId);
 
@@ -1289,7 +1289,9 @@ public class SClient4WPS extends SClient {
 	@Override
 	public ComputationData getComputationDataByComputationProperties(
 			Map<String, String> computationProperties) throws Exception {
-		if (computationProperties == null || computationProperties.isEmpty()) {
+		try {
+			if (computationProperties == null
+					|| computationProperties.isEmpty()) {
 				throw new Exception("Invalid computation properties: "
 						+ computationProperties);
 			}
@@ -1318,7 +1320,8 @@ public class SClient4WPS extends SClient {
 				if (key != null) {
 					if (key.startsWith("input")) {
 						int inputSeparatorIndex = key.indexOf("_");
-					String inputKey = key.substring(inputSeparatorIndex + 1);
+						String inputKey = key
+								.substring(inputSeparatorIndex + 1);
 						if (inputKey.compareToIgnoreCase("user.name") != 0
 								&& inputKey.compareToIgnoreCase("scope") != 0) {
 							inputValueParameters.put(inputKey,
@@ -1350,12 +1353,95 @@ public class SClient4WPS extends SClient {
 			LinkedHashMap<String, ComputationValue> outputParameters = computationValueBuilder
 					.create();
 
-		ComputationData computationData = new ComputationData(computationId,
-				inputParameters, outputParameters, operatorDescritpion,
-				startDate, endDate, status, executionType, vre);
+			logger.debug("inputParameters: " + inputParameters);
+			logger.debug("outputParameters: " + outputParameters);
+
+			LinkedHashMap<String, ComputationValue> inputParametersSorted = new LinkedHashMap<>();
+			LinkedHashMap<String, ComputationValue> outputParametersSorted = new LinkedHashMap<>();
+
+			ProcessInformations processInfos = describeProcess(operatorId);
+			if (processInfos != null) {
+				for (InputDescriptionType inputDesc : processInfos.getInputs()) {
+					if (inputDesc != null
+							&& inputDesc.getIdentifier() != null
+							&& inputDesc.getIdentifier().getStringValue() != null) {
+						logger.debug("InputParametr Match: "
+								+ inputDesc.getIdentifier().getStringValue());
+						ComputationValue inputComputationValue = inputParameters
+								.get(inputDesc.getIdentifier().getStringValue());
+						inputParametersSorted.put(inputDesc.getIdentifier()
+								.getStringValue(), inputComputationValue);
+					}
+
+				}
+
+			} else {
+				inputParametersSorted.putAll(inputParameters);
+			}
+
+			ArrayList<String> keys=new ArrayList<>(outputParameters.keySet());
+			Comparator<String> comparator = new Comparator<String>() {
+			    public int compare(String c1, String c2) {
+			    	Integer c1Int=null;
+			    	
+			    	try {
+			        	c1Int=Integer.valueOf(c1);
+			        } catch(NumberFormatException e){
+			        	
+			        }
+			    	
+			    	Integer c2Int=null;
+			    	
+			    	try {
+			        	c2Int=Integer.valueOf(c2);
+			        } catch(NumberFormatException e){
+			        	
+			        }
+			    	
+			    	if(c1Int!=null && c2Int!=null){
+			    		return c1Int.compareTo(c2Int);
+			    	} else {
+			    		if(c1Int==null && c2Int==null){
+			    			return c1.compareTo(c2);
+			    		} else {
+			    			if(c1Int==null){
+			    				return -1; 
+			    			} else {
+			    				return 1;
+			    				
+			    			}
+			    		}
+			    	}  
+			    }
+			};
+
+			Collections.sort(keys, comparator);
+			for(String key:keys){
+				ComputationValue outputComputationValue = outputParameters
+						.get(key);
+				outputParametersSorted.put(key, outputComputationValue);
+			}
+			
+			ComputationData computationData = new ComputationData(
+					computationId, inputParametersSorted,
+					outputParametersSorted, operatorDescritpion, startDate,
+					endDate, status, executionType, vre);
 
 			logger.debug("ComputationData: " + computationData);
 			return computationData;
 
+		} catch (DataMinerServiceException e) {
+			logger.error("Error in getComutationDataByComputationProperties: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw e;
+		} catch (Throwable e) {
+			logger.error("Error in getComutationDataByComputationProperties: "
+					+ e.getLocalizedMessage());
+			e.printStackTrace();
+			throw new Exception(e.getLocalizedMessage(), e);
+
+		}
+
 	}
 }

src/main/java/org/gcube/portlets/user/dataminermanager/shared/Constants.java

@@ -19,9 +19,9 @@ public class Constants {
 	
 	public static final String DEFAULT_USER = "giancarlo.panichi";
 	public static final String DEFAULT_ROLE = "OrganizationMember";
-	//public static final String DEFAULT_SCOPE = "/gcube/devsec/devVRE";
+	public static final String DEFAULT_SCOPE = "/gcube/devsec/devVRE";
 	// public final static String DEFAULT_SCOPE = "/gcube/devNext";
-	public final static String DEFAULT_SCOPE = "/gcube/devNext/NextNext";
+	//public final static String DEFAULT_SCOPE = "/gcube/devNext/NextNext";
 	
 
 

src/main/java/org/gcube/portlets/user/dataminermanager/shared/data/computations/ComputationValue.java

@@ -16,6 +16,7 @@ public class ComputationValue implements Serializable {
 
 	public ComputationValue() {
 		super();
+		this.type = ComputationValueType.String;
 	}
 
 	public ComputationValue(ComputationValueType type) {

src/main/java/org/gcube/portlets/user/dataminermanager/shared/data/computations/ComputationValueFile.java

@@ -13,7 +13,7 @@ public class ComputationValueFile extends ComputationValue {
 	private String mimeType;
 
 	public ComputationValueFile() {
-		super();
+		super(ComputationValueType.File);
 	}
 
 	public ComputationValueFile(String url, String fileName, String mimeType) {

src/main/java/org/gcube/portlets/user/dataminermanager/shared/data/computations/ComputationValueFileList.java

@@ -15,7 +15,7 @@ public class ComputationValueFileList extends ComputationValue {
 	private String separator;
 
 	public ComputationValueFileList() {
-		super();
+		super(ComputationValueType.FileList);
 	}
 
 	public ComputationValueFileList(ArrayList<ComputationValue> fileList,

src/main/java/org/gcube/portlets/user/dataminermanager/shared/data/computations/ComputationValueImage.java

@@ -13,7 +13,7 @@ public class ComputationValueImage extends ComputationValue {
 	private String mimeType;
 
 	public ComputationValueImage(){
-		super();
+		super(ComputationValueType.Image);
 	}
 	
 	public ComputationValueImage(String url, String fileName, String mimeType) {

src/main/java/org/gcube/portlets/user/dataminermanager/shared/data/output/MapResource.java

@@ -4,6 +4,7 @@
 package org.gcube.portlets.user.dataminermanager.shared.data.output;
 
 import java.io.Serializable;
+import java.util.LinkedHashMap;
 import java.util.Map;
 
 /**
@@ -18,7 +19,7 @@ public class MapResource extends Resource implements Serializable {
 	 * 
 	 */
 	private static final long serialVersionUID = 8772836076910728324L;
-	private Map<String, Resource> map;
+	private LinkedHashMap<String, Resource> map;
 
 	/**
 	 * 
@@ -29,7 +30,7 @@ public class MapResource extends Resource implements Serializable {
 	}
 
 	public MapResource(String resourceId, String name, String description,
-			Map<String, Resource> map) {
+			LinkedHashMap<String, Resource> map) {
 		super(resourceId, name, description, ResourceType.MAP);
 		this.map = map;
 	}
@@ -38,7 +39,7 @@ public class MapResource extends Resource implements Serializable {
 		return map;
 	}
 
-	public void setMap(Map<String, Resource> map) {
+	public void setMap(LinkedHashMap<String, Resource> map) {
 		this.map = map;
 	}
 

src/main/resources/org/gcube/portlets/user/dataminermanager/dataminermanager.gwt.xml

@@ -36,14 +36,12 @@
 		value="ENABLED" /> <set-property name="log_SystemLogger" value="ENABLED" 
 		/> -->
 
-
 	<set-property name="log_ConsoleLogger" value="DISABLED" />
 	<set-property name="log_DivLogger" value="DISABLED" />
 	<set-property name="log_GWTLogger" value="DISABLED" />
 	<set-property name="log_SystemLogger" value="DISABLED" />
 
 
-
 	<source path='client' />
 	<source path='shared' />