git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/performfish-analytics-portlet@179292 82a268e6-3cf1-43bd-a215-b396298e98cf

.settings/org.eclipse.wst.common.component

@@ -5,6 +5,6 @@
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
         <property name="context-root" value="performfish-analytics-portlet"/>
-        <property name="java-output-path" value="/performfish-analytics-portlet/target/performfish-analytics-portlet-0.0.1-SNAPSHOT/WEB-INF/classes"/>
+        <property name="java-output-path" value="/performfish-analytics-portlet/target/performfish-analytics-portlet-0.1.0-SNAPSHOT/WEB-INF/classes"/>
     </wb-module>
 </project-modules>

pom.xml

@@ -11,7 +11,7 @@
 	<groupId>org.gcube.portlets.user</groupId>
 	<artifactId>performfish-analytics-portlet</artifactId>
 	<packaging>war</packaging>
-	<version>0.1.0-SNAPSHOT</version>
+	<version>0.2.0-SNAPSHOT</version>
 	<name>Maven Archetype for GWT</name>
 
 	<scm>

src/main/java/org/gcube/portlets/user/performfishanalytics/client/PerformFishAnalyticsConstant.java

@@ -13,8 +13,8 @@ package org.gcube.portlets.user.performfishanalytics.client;
  */
 public class PerformFishAnalyticsConstant {
 
-	public static final String FARMID_PARAM = "farmid";
-	public static final String BATCHTYPE_PARAM = "batchtype";
+//	public static final String FARMID_PARAM = "farmid";
+//	public static final String BATCHTYPE_PARAM = "batchtype";
 	// PERFORM-FISH SERVICE KEYS
 	public static final String BATCHES_TABLE_INTERNAL = "BatchesTable_internal";
 	public static final String BATCHES_TABLE = "BatchesTable";

src/main/java/org/gcube/portlets/user/performfishanalytics/client/PerformFishQueryParameter.java

@@ -0,0 +1,35 @@
+package org.gcube.portlets.user.performfishanalytics.client;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Enum PerformFishQueryParameter.
+ */
+public enum PerformFishQueryParameter {
+	
+	farmid,
+	batchtype
+	
+	
+//	/** The farmid param. */
+//	FARMID_PARAM("farmid"),
+//	
+//	/** The batchtype param. */
+//	BATCHTYPE_PARAM("batchtype");
+//	
+//	/** The id. */
+//	private String id;
+//
+//	/**
+//	 * Instantiates a new perform fish query parameter.
+//	 *
+//	 * @param id the id
+//	 */
+//	PerformFishQueryParameter(String id){
+//		this.id = id;
+//	}
+//	
+//	public String getId() {
+//		return id;
+//	}
+	
+}

src/main/java/org/gcube/portlets/user/performfishanalytics/client/controllers/PerformFishAnalyticsController.java

@@ -104,22 +104,22 @@ public class PerformFishAnalyticsController {
 				
 				GWT.log("Decoded parameters: "+initParams);
 				
-				final String batchtypeParam = initParams.get(PerformFishAnalyticsConstant.BATCHTYPE_PARAM);
-				final String farmidParam = initParams.get(PerformFishAnalyticsConstant.FARMID_PARAM);
+				final String batchtypeParam = initParams.get(PerformFishAnalyticsConstant.PERFORM_FISH_BATCH_TYPE_PARAM);
+				final String farmidParam = initParams.get(PerformFishAnalyticsConstant.PERFORM_FISH_FARMID_PARAM);
 
 				if(batchtypeParam==null || batchtypeParam.isEmpty()){
-					Window.alert("Error: no '"+PerformFishAnalyticsConstant.BATCHTYPE_PARAM+"' param detected");
+					Window.alert("Error: no '"+PerformFishAnalyticsConstant.PERFORM_FISH_BATCH_TYPE_PARAM+"' param detected");
 					return;
 				}
 
 				if(farmidParam==null || farmidParam.isEmpty()){
-					Window.alert("Error: no '"+PerformFishAnalyticsConstant.FARMID_PARAM+"' param detected");
+					Window.alert("Error: no '"+PerformFishAnalyticsConstant.PERFORM_FISH_FARMID_PARAM+"' param detected");
 					return;
 				}
 
 				PerformFishInitParameter performFishInitParams = new PerformFishInitParameter();
-				performFishInitParams.addParameter(PerformFishAnalyticsConstant.BATCHTYPE_PARAM, batchtypeParam);
-				performFishInitParams.addParameter(PerformFishAnalyticsConstant.FARMID_PARAM, farmidParam);
+				performFishInitParams.addParameter(PerformFishAnalyticsConstant.PERFORM_FISH_BATCH_TYPE_PARAM, batchtypeParam);
+				performFishInitParams.addParameter(PerformFishAnalyticsConstant.PERFORM_FISH_FARMID_PARAM, farmidParam);
 
 				PerformFishAnalyticsServiceAsync.Util.getInstance().validParameters(performFishInitParams, new AsyncCallback<PerformFishInitParameter>() {
 
@@ -196,7 +196,7 @@ public class PerformFishAnalyticsController {
 				viewController.hideErrors();
 				
 				final Map<String, List<String>> mapParameters = new HashMap<String, List<String>>();
-				String farmId = decryptParameters.getParameters().get(PerformFishAnalyticsConstant.FARMID_PARAM);
+				String farmId = decryptParameters.getParameters().get(PerformFishAnalyticsConstant.PERFORM_FISH_FARMID_PARAM);
 				String batchType = viewController.getForm().getBatchType();
 				String species = viewController.getForm().getSpecies();
 				List<String> listArea = viewController.getForm().getArea();

src/main/java/org/gcube/portlets/user/performfishanalytics/client/controllers/PerformFishAnalyticsViewController.java

@@ -7,9 +7,9 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
-import org.gcube.portlets.user.performfishanalytics.client.PerformFishAnalyticsConstant;
 import org.gcube.portlets.user.performfishanalytics.client.PerformFishAnalyticsConstant.POPULATION_LEVEL;
 import org.gcube.portlets.user.performfishanalytics.client.PerformFishAnalyticsServiceAsync;
+import org.gcube.portlets.user.performfishanalytics.client.PerformFishQueryParameter;
 import org.gcube.portlets.user.performfishanalytics.client.view.BaseDockLayoutPanel;
 import org.gcube.portlets.user.performfishanalytics.client.view.BodyPanel;
 import org.gcube.portlets.user.performfishanalytics.client.view.CustomTreeModel;
@@ -189,13 +189,14 @@ public class PerformFishAnalyticsViewController {
 		return baseDockLayoutPanel;
 	}
 
+
 	/**
-	 * Load population type for population name.
+	 * Load population type for level and batch type.
 	 *
 	 * @param populationName the population name
-	 * @param decryptParameters the decrypt parameters
+	 * @param decodedParameters the decoded parameters
 	 */
-	public void loadPopulationTypeForLevelAndBatchType(final String populationName, final PerformFishInitParameter decryptParameters){
+	public void loadPopulationTypeForLevelAndBatchType(final String populationName, final PerformFishInitParameter decodedParameters){
 
 		PerformFishAnalyticsServiceAsync.Util.getInstance().getListPopulationType(populationName, new AsyncCallback<List<PopulationType>>() {
 
@@ -205,7 +206,7 @@ public class PerformFishAnalyticsViewController {
 				headerPage.showLoading(false);
 
 				if(result.size()>0){
-					String passedBatchType = decryptParameters.getParameters().get(PerformFishAnalyticsConstant.BATCHTYPE_PARAM);
+					String passedBatchType = decodedParameters.getParameters().get(PerformFishQueryParameter.batchtype.name());
 					for (PopulationType populationType : result) {
 
 						if(populationType.getName().compareToIgnoreCase(passedBatchType)==0){
@@ -268,6 +269,11 @@ public class PerformFishAnalyticsViewController {
 
 	}
 	
+	/**
+	 * Expand all tree node.
+	 *
+	 * @param rootNode the root node
+	 */
 	private void expandAllTreeNode(TreeNode rootNode) {
 		
 		if(rootNode==null || rootNode.getChildCount()==0)

src/main/java/org/gcube/portlets/user/performfishanalytics/server/util/UrlEncoderUtil.java

@@ -5,11 +5,14 @@ package org.gcube.portlets.user.performfishanalytics.server.util;
 
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
+import java.util.Base64;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.log4j.Logger;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
+// TODO: Auto-generated Javadoc
 /**
  * The Class UrlEncoderUtil.
  *
@@ -18,32 +21,11 @@ import org.apache.log4j.Logger;
  */
 public class UrlEncoderUtil {
 
+	/** The charset. */
 	public static String charset = "UTF-8";
 
-	public static Logger logger = Logger.getLogger(UrlEncoderUtil.class);
-
-//	/**
-//	 * Encode query.
-//	 *
-//	 * @param parameters the parameters
-//	 * @return the string
-//	 */
-//	public static String encodeQuery(String... parameters){
-//
-//		String query = "";
-//		for (String string : parameters) {
-//
-//			try {
-//				query+=URLEncoder.encode(string, charset)+"&";
-//			} catch (UnsupportedEncodingException e) {
-//				logger.error(e);
-//				return query;
-//			}
-//
-//		}
-//		return removeLastChar(query);
-//	}
-
+	/** The logger. */
+	public static final Logger logger = LoggerFactory.getLogger(UrlEncoderUtil.class);
 
 	/**
 	 * Encode query.
@@ -65,7 +47,7 @@ public class UrlEncoderUtil {
 					query+=String.format(key+"=%s", URLEncoder.encode(value, charset))+"&";
 				}
 			} catch (UnsupportedEncodingException e) {
-				logger.error(e);
+				logger.error("Error:", e);
 				return query;
 			}
 
@@ -91,5 +73,20 @@ public class UrlEncoderUtil {
 
 		return string;
 	}
+	
+
+	/**
+	 * Base 64 decode.
+	 *
+	 * @param valueToDecode the value to decode
+	 * @return the long
+	 */
+	public static String base64Decode(String valueToDecode) throws Exception{
+		try {
+			return new String(Base64.getDecoder().decode(valueToDecode));
+		}catch (Exception e) {
+			throw new Exception("Error on decoding the parameter: "+ valueToDecode, e);
+		}
+	}
 
 }

src/main/java/org/gcube/portlets/user/performfishanalytics/server/util/csv/CSVReader.java

@@ -100,7 +100,7 @@ public class CSVReader {
 
 		List<String> result = new ArrayList<>();
 		// if empty, return!
-		if (cvsLine == null && cvsLine.isEmpty()) {
+		if (cvsLine == null || cvsLine.isEmpty()) {
 			return result;
 		}
 		if (customQuote == ' ') {

src/main/java/org/gcube/portlets/user/performfishanalytics/server/util/database/FillDatabasePerBatchType.java

@@ -18,6 +18,7 @@ import org.gcube.portlets.user.performfishanalytics.server.util.database.data.KP
 import org.gcube.portlets.user.performfishanalytics.server.util.database.data.PeriodData;
 import org.gcube.portlets.user.performfishanalytics.server.util.database.data.QuarterData;
 import org.gcube.portlets.user.performfishanalytics.server.util.database.data.SpeciesData;
+import org.gcube.portlets.user.performfishanalytics.server.util.database.data.YearData;
 import org.gcube.portlets.user.performfishanalytics.shared.Area;
 import org.gcube.portlets.user.performfishanalytics.shared.KPI;
 import org.gcube.portlets.user.performfishanalytics.shared.Period;
@@ -61,7 +62,7 @@ public class FillDatabasePerBatchType {
 		GROW_OUT_INDIVIDUAL_CLOSED_BATCHES,
 		GROW_OUT_AGGREGATED,
 		GROW_OUT_AGGREGATED_CLOSED_BATCHES
-		}
+	}
 
 	/**
 	 * Prints the database data.
@@ -197,7 +198,8 @@ public class FillDatabasePerBatchType {
 				batchType.setListQuarter(QuarterData.getListQuarter(batchType));
 				//Areas
 				batchType.setListArea(AreaData.getListArea(batchType));
-
+				//Years
+				batchType.setListYears(YearData.getListYears(batchType));
 			}
 
 		}

src/main/java/org/gcube/portlets/user/performfishanalytics/server/util/database/data/YearData.java

@@ -0,0 +1,35 @@
+package org.gcube.portlets.user.performfishanalytics.server.util.database.data;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.gcube.portlets.user.performfishanalytics.shared.PopulationType;
+import org.gcube.portlets.user.performfishanalytics.shared.Year;
+
+/**
+ * The Class YearData.
+ *
+ * @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
+ * 
+ * May 6, 2019
+ */
+public class YearData {
+	
+
+	/**
+	 * Gets the list years.
+	 *
+	 * @param batchType the batch type
+	 * @return the list years
+	 */
+	public static ArrayList<Year> getListYears(PopulationType batchType){
+
+		List<Year> listSpecies = new ArrayList<Year>();
+		listSpecies.add(new Year(java.util.UUID.randomUUID().toString(), "2016", batchType));
+		listSpecies.add(new Year(java.util.UUID.randomUUID().toString(), "2017", batchType));
+		listSpecies.add(new Year(java.util.UUID.randomUUID().toString(), "2018", batchType));
+
+		return (ArrayList<Year>) listSpecies;
+	}
+
+}

src/main/java/org/gcube/portlets/user/performfishanalytics/server/util/xml/NamespaceContextMap.java

@@ -83,7 +83,9 @@ public final class NamespaceContextMap implements NamespaceContext {
 				XMLConstants.XML_NS_URI);
 		addConstant(prefixMap, XMLConstants.XMLNS_ATTRIBUTE,
 				XMLConstants.XMLNS_ATTRIBUTE_NS_URI);
-		return Collections.unmodifiableMap(prefixMap);
+		//return Collections.unmodifiableMap(prefixMap);
+		
+		return prefixMap;
 	}
 
 	/**

src/main/java/org/gcube/portlets/user/performfishanalytics/shared/PopulationType.java

@@ -28,7 +28,7 @@ import org.eclipse.persistence.annotations.CascadeOnDelete;
 @Entity
 @CascadeOnDelete
 public class PopulationType implements GenericDao, Serializable {
-
+	
 	/**
 	 *
 	 */
@@ -68,6 +68,12 @@ public class PopulationType implements GenericDao, Serializable {
 	@CascadeOnDelete
 	@OrderColumn
 	private List<KPI> listKPI = new ArrayList<KPI>();
+	
+	
+	@OneToMany(mappedBy = "populationType", orphanRemoval = true, cascade = CascadeType.PERSIST, fetch = FetchType.EAGER)
+	@CascadeOnDelete
+	@OrderColumn
+	private List<Year> listYears = new ArrayList<Year>();
 
 	/**
 	 * Instantiates a new population type.
@@ -362,6 +368,25 @@ public class PopulationType implements GenericDao, Serializable {
 
 		this.listSpecies = listSpecies;
 	}
+	
+
+	/**
+	 * Gets the list years.
+	 *
+	 * @return the list years
+	 */
+	public List<Year> getListYears() {
+		return listYears;
+	}
+
+	/**
+	 * Sets the list years.
+	 *
+	 * @param listYears the new list years
+	 */
+	public void setListYears(List<Year> listYears) {
+		this.listYears = listYears;
+	}
 
 	/*
 	 * (non-Javadoc)

src/main/java/org/gcube/portlets/user/performfishanalytics/shared/Year.java

@@ -0,0 +1,129 @@
+package org.gcube.portlets.user.performfishanalytics.shared;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+import org.eclipse.persistence.annotations.CascadeOnDelete;
+
+/**
+ * The Class Year.
+ *
+ * @author Francesco Mangiacrapa at ISTI-CNR (francesco.mangiacrapa@isti.cnr.it)
+ * 
+ * May 6, 2019
+ */
+@Entity
+@CascadeOnDelete
+public class Year implements GenericDao, ReferencePopulationType, Serializable{
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 1L;
+	@Id
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
+	private int internalId; // PRIMARY KEY
+	private String id;
+	private String value;
+	
+	@CascadeOnDelete
+	private PopulationType populationType;
+	
+	
+	/**
+	 * Instantiates a new year.
+	 */
+	public Year() {
+	}
+
+
+	/**
+	 * Instantiates a new year.
+	 *
+	 * @param id the id
+	 * @param value the value
+	 * @param populationType the population type
+	 */
+	public Year(String id, String value, PopulationType populationType) {
+		super();
+		this.id = id;
+		this.value = value;
+		this.populationType = populationType;
+	}
+
+
+	/* (non-Javadoc)
+	 * @see org.gcube.portles.user.performfishannual.shared.GenericDao#getId()
+	 */
+	public String getId() {
+		return id;
+	}
+
+
+	/**
+	 * Sets the id.
+	 *
+	 * @param id the new id
+	 */
+	public void setId(String id) {
+		this.id = id;
+	}
+
+
+	/**
+	 * Gets the value.
+	 *
+	 * @return the value
+	 */
+	public String getValue() {
+		return value;
+	}
+
+
+	/**
+	 * Sets the value.
+	 *
+	 * @param value the new value
+	 */
+	public void setValue(String value) {
+		this.value = value;
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.gcube.portlets.user.performfishanalytics.shared.ReferencePopulationType#getPopulationType()
+	 */
+	public PopulationType getPopulationType() {
+		return populationType;
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.gcube.portlets.user.performfishanalytics.shared.ReferencePopulationType#setPopulationType(org.gcube.portlets.user.performfishanalytics.shared.PopulationType)
+	 */
+	@Override
+	public void setPopulationType(PopulationType populationType) {
+		this.populationType = populationType;
+	}
+
+
+	/* (non-Javadoc)
+	 * @see java.lang.Object#toString()
+	 */
+	@Override
+	public String toString() {
+		StringBuilder builder = new StringBuilder();
+		builder.append("Year [internalId=");
+		builder.append(internalId);
+		builder.append(", id=");
+		builder.append(id);
+		builder.append(", value=");
+		builder.append(value);
+		builder.append("]");
+		return builder.toString();
+	}
+
+
+}

src/main/resources/BATCH/KPI/GROW_OUT_AGGREGATED_CLOSED_BATCHES.csv

@@ -0,0 +1,21 @@
+KPI CODE,KPI NAME - LEVEL 1,KPI NAME – LEVEL 2,KPI NAME - LEVEL 3
+,Dependency on treatments KPIs,,
+,,Number of therapeutic treatments,
+G9,,,Total number of antiparasitic treatments - at harvest 
+G10,,,Total number of antibiotic treatments - at harvest 
+,Productivity KPIs,,
+G20,,Biomass produced per number of FTE employees ,
+G21,,Biomass produced per volumes of sea water used ,
+,Environmental KPIs,,
+,,Preservation of biodiversity and habitats KPIs,
+G22,,,Oxygen depletion persistence days
+G23,,,Escapes - Number of episodes
+G24,,,Escapes - Estimated number of escaped fish
+,,Use of resources,
+G28,,,Marine space use for farming
+G29,,,Land use 
+G30,,,Freshwater use 
+G31,,,Energy use
+G32,,,Fuel (Diesel) for transport
+G33,,,Fuel (Diesel) for other uses
+G35,,,Use of renewable energy

src/main/resources/META-INF/persistence.xml

@@ -11,6 +11,7 @@
 		<class>org.gcube.portlets.user.performfishanalytics.shared.Area</class>
 		<class>org.gcube.portlets.user.performfishanalytics.shared.Period</class>
 		<class>org.gcube.portlets.user.performfishanalytics.shared.KPI</class>
+		<class>org.gcube.portlets.user.performfishanalytics.shared.Year</class>
 		<properties>
 			<property name="javax.persistence.jdbc.driver" value="org.h2.Driver" />
 			<!-- <property name="eclipselink.ddl-generation" value="create-tables"