Several changes to the model

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/grsf-publisher-ws@135170 82a268e6-3cf1-43bd-a215-b396298e98cf

pom.xml

@@ -135,6 +135,12 @@
 			<artifactId>jersey-bean-validation</artifactId>
 			<version>${version.jersey}</version>
 		</dependency>
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>servlet-api</artifactId>
+			<version>3.0-alpha-1</version>
+			<scope>compile</scope>
+		</dependency>
 		<dependency>
 			<groupId>org.glassfish.jersey.test-framework.providers</groupId>
 			<artifactId>jersey-test-framework-provider-jetty</artifactId>

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/custom_annotations/Group.java

@@ -13,6 +13,4 @@ import java.lang.annotation.Target;
 @Target({ElementType.FIELD, ElementType.TYPE})
 public @interface Group {
 	
-	Class parentGroup() default Class.class;
-	
 }

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/Common.java

@@ -1,5 +1,6 @@
 package org.gcube.data_catalogue.grsf_publish_ws.json.input;
 
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -12,9 +13,14 @@ import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.CkanResource;
 import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.CustomField;
 import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.Group;
 import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.Tag;
+import org.gcube.data_catalogue.grsf_publish_ws.utils.HelperMethods;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Source;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Status;
+import org.gcube.datacatalogue.ckanutillibrary.models.ResourceBean;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
+import com.fasterxml.jackson.annotation.JsonAnySetter;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
@@ -22,11 +28,12 @@ import com.fasterxml.jackson.annotation.JsonProperty;
  * Information that both Stock and Fishery must contain
  * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
  */
-@JsonIgnoreProperties(value = {"author", "author_contact", "extras", "product_type"}, ignoreUnknown = true) // ignore in serialization/deserialization
+@JsonIgnoreProperties(value = {"author", "author_contact", "product_type"}) // ignore in serialization/deserialization
 public class Common {
 
+	private static Logger logger = LoggerFactory.getLogger(Common.class);
 	public static final String PRODUCT_TYPE_KEY = "Product type";
-	
+
 	@JsonProperty("description")
 	private String description;
 
@@ -58,15 +65,11 @@ public class Common {
 	@CkanResource
 	@NotNull(message="database_source cannot be null")
 	@Size(min=1, message="database_source cannot be empty")
-	@Tag
-	@Group
 	@Valid
 	private List<Resource<Source>> databaseSources;
 
 	@JsonProperty("source_of_information")
 	@CkanResource
-	@NotNull(message="source_of_information cannot be null")
-	@Size(min=1, message="source_of_information cannot be empty")
 	@Valid
 	private List<Resource<String>> sourceOfInformation;
 
@@ -100,9 +103,16 @@ public class Common {
 	@Tag
 	@Group
 	private String productType; 
-	
+
-	@JsonProperty("extras")
+	@JsonProperty("reporting_year")
-	private Map<String, List<String>> extras = new HashMap<>();
+	@CustomField(key="Reporting year")
+	private Long reportingYear;
+
+	@JsonProperty("extras_fields")
+	private Map<String, List<String>> extrasFields = new HashMap<>();
+
+	@JsonProperty("extras_resources")
+	private List<ResourceBean> extrasResources = new ArrayList<ResourceBean>();
 
 	public Common() {
 		super();
@@ -117,26 +127,27 @@ public class Common {
 	 * @param authorContact
 	 * @param maintainer
 	 * @param maintainerContact
-	 * @param catchesOrLandings
+	 * @param dataOwner
 	 * @param databaseSources
 	 * @param sourceOfInformation
-	 * @param dataOwner
-	 * @param type
 	 * @param shortTitle
 	 * @param uuid
 	 * @param traceabilityFlag
-	 * @param extras
 	 * @param status
 	 * @param productType
+	 * @param reportingYear
+	 * @param extrasFields
+	 * @param extrasResources
 	 */
 	public Common(String description, String license, String author,
 			Long version, String authorContact, String maintainer,
-			String maintainerContact,
+			String maintainerContact, String dataOwner,
 			List<Resource<Source>> databaseSources,
-			List<Resource<String>> sourceOfInformation, String dataOwner,
+			List<Resource<String>> sourceOfInformation, String shortTitle,
-			String shortTitle, String uuid,
+			String uuid, boolean traceabilityFlag, Status status,
-			boolean traceabilityFlag, Map<String, List<String>> extras,
+			String productType, Long reportingYear,
-			Status status, String productType) {
+			Map<String, List<String>> extrasFields,
+			List<ResourceBean> extrasResources) {
 		super();
 		this.description = description;
 		this.license = license;
@@ -145,21 +156,47 @@ public class Common {
 		this.authorContact = authorContact;
 		this.maintainer = maintainer;
 		this.maintainerContact = maintainerContact;
+		this.dataOwner = dataOwner;
 		this.databaseSources = databaseSources;
 		this.sourceOfInformation = sourceOfInformation;
-		this.dataOwner = dataOwner;
 		this.shortTitle = shortTitle;
 		this.uuid = uuid;
 		this.traceabilityFlag = traceabilityFlag;
-		this.extras = extras;
 		this.status = status;
 		this.productType = productType;
+		this.reportingYear = reportingYear;
+		this.extrasFields = extrasFields;
+		this.extrasResources = extrasResources;
 	}
 
 	public String getProductType() {
 		return productType;
 	}
 
+	public Long getReportingYear() {
+		return reportingYear;
+	}
+
+	public void setReportingYear(Long reportingYear) {
+		this.reportingYear = reportingYear;
+	}
+
+	public Map<String, List<String>> getExtrasFields() {
+		return extrasFields;
+	}
+
+	public void setExtrasFields(Map<String, List<String>> extrasFields) {
+		this.extrasFields = extrasFields;
+	}
+
+	public List<ResourceBean> getExtrasResources() {
+		return extrasResources;
+	}
+
+	public void setExtrasResources(List<ResourceBean> extrasResources) {
+		this.extrasResources = extrasResources;
+	}
+
 	public void setProductType(String productType) {
 		this.productType = productType;
 	}
@@ -244,14 +281,6 @@ public class Common {
 		this.dataOwner = dataOwner;
 	}
 
-	public void setExtras(Map<String, List<String>> extras) {
-		this.extras = extras;
-	}
-
-	public Map<String, List<String>> getExtras() {
-		return extras;
-	}
-
 	public String getShortTitle() {
 		return shortTitle;
 	}
@@ -283,6 +312,28 @@ public class Common {
 	public void setStatus(Status status) {
 		this.status = status;
 	}
+	
+	@JsonAnySetter
+	/**
+	 * Use for generics object passed into the map
+	 * @param key
+	 * @param value
+	 */
+	private void genericSetter(String key, Object value){
+		
+		// found extra property
+		logger.info("Found extra property: [" + key + "," + value + "]");
+		
+		// try to convert the value to a string and put into the hashmap
+		List<String> values = new ArrayList<String>();
+		if(extrasFields.containsKey(key))
+			values = extrasFields.get(key);
+		else
+			values = new ArrayList<String>();
+			
+		values.add(HelperMethods.removeHTML(value.toString()));
+		extrasFields.put(key, values);
+	}
 
 	@Override
 	public String toString() {
@@ -292,9 +343,10 @@ public class Common {
 				+ maintainer + ", maintainerContact=" + maintainerContact
 				+ ", dataOwner=" + dataOwner + ", databaseSources="
 				+ databaseSources + ", sourceOfInformation="
-				+ sourceOfInformation + ", shortTitle="
+				+ sourceOfInformation + ", shortTitle=" + shortTitle
-				+ shortTitle + ", uuid=" + uuid + ", traceabilityFlag="
+				+ ", uuid=" + uuid + ", traceabilityFlag=" + traceabilityFlag
-				+ traceabilityFlag + ", extras=" + extras + ", status="
+				+ ", status=" + status + ", productType=" + productType
-				+ status + ", productType=" + productType + "]";
+				+ ", reportingYear=" + reportingYear + ", extrasFields="
+				+ extrasFields + ", extrasResources=" + extrasResources + "]";
 	}
 }

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/FisheryRecord.java

@@ -1,6 +1,5 @@
 package org.gcube.data_catalogue.grsf_publish_ws.json.input;
 
-import java.util.Collections;
 import java.util.List;
 
 import javax.validation.Valid;
@@ -40,11 +39,11 @@ public class FisheryRecord extends Common{
 
 	@JsonProperty("fishing_area")
 	@CustomField(key="Fishing area")
-	private String fishingArea;
+	private List<String> fishingArea;
 
 	@JsonProperty("exploited_stocks")
 	@CustomField(key="Exploited stocks")
-	private String exploitingStocks;
+	private List<String> exploitingStocks;
 
 	@JsonProperty("management_entity")
 	@Tag
@@ -53,7 +52,7 @@ public class FisheryRecord extends Common{
 
 	@JsonProperty("jurisdiction_area")
 	@CustomField(key="Jurisdiction Area")
-	private String jurisdictionArea;
+	private List<String> jurisdictionArea;
 
 	@JsonProperty("production_system_type")
 	@Group
@@ -108,8 +107,9 @@ public class FisheryRecord extends Common{
 	 * @param type
 	 */
 	public FisheryRecord(String fisheryName, String fisheryId,
-			String scientificName, String fishingArea, String exploitingStocks,
+			String scientificName, List<String> fishingArea,
-			String managementEntity, String jurisdictionArea,
+			List<String> exploitingStocks, String managementEntity,
+			List<String> jurisdictionArea,
 			Production_System_Type productionSystemType, String flagState,
 			String fishingGear, String environment,
 			List<TimeSeriesBean<String, String>> catchesOrLandings,
@@ -129,7 +129,7 @@ public class FisheryRecord extends Common{
 		this.catchesOrLandings = catchesOrLandings;
 		this.type = type;
 	}
-
+	
 	public String getFisheryName() {
 		return fisheryName;
 	}
@@ -154,22 +154,14 @@ public class FisheryRecord extends Common{
 		this.scientificName = scientificName;
 	}
 
-	public String getFishingArea() {
+	public List<String> getFishingArea() {
 		return fishingArea;
 	}
 
-	public void setFishingArea(String fishingArea) {
+	public void setFishingArea(List<String> fishingArea) {
 		this.fishingArea = fishingArea;
 	}
 
-	public String getExploitingStocks() {
-		return exploitingStocks;
-	}
-
-	public void setExploitingStocks(String exploitingStocks) {
-		this.exploitingStocks = exploitingStocks;
-	}
-
 	public String getManagementEntity() {
 		return managementEntity;
 	}
@@ -178,11 +170,11 @@ public class FisheryRecord extends Common{
 		this.managementEntity = managementEntity;
 	}
 
-	public String getJurisdictionArea() {
+	public List<String> getJurisdictionArea() {
 		return jurisdictionArea;
 	}
 
-	public void setJurisdictionArea(String jurisdictionArea) {
+	public void setJurisdictionArea(List<String> jurisdictionArea) {
 		this.jurisdictionArea = jurisdictionArea;
 	}
 
@@ -224,10 +216,6 @@ public class FisheryRecord extends Common{
 
 	public void setCatchesOrLandings(List<TimeSeriesBean<String, String>> catchesOrLandings) {
 		this.catchesOrLandings = catchesOrLandings;
-
-		if(catchesOrLandings != null){
-			Collections.sort(catchesOrLandings);
-		}
 	}
 
 	public Fishery_Type getType() {
@@ -250,4 +238,5 @@ public class FisheryRecord extends Common{
 				+ ", environment=" + environment + ", catchesOrLandings="
 				+ catchesOrLandings + ", type=" + type + "]";
 	}
+	
 }

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/Resource.java

@@ -66,7 +66,7 @@ public class Resource<T> {
 	@Override
 	public String toString() {
 
-		// in case of @Tag, we check the class of the element Name
+		// in case of @Tag/@Group, we check the class of the element Name
 		Class<? extends Object> nameClass = name.getClass();
 
 		if(nameClass.equals(Source.class))

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/StockRecord.java

@@ -1,6 +1,5 @@
 package org.gcube.data_catalogue.grsf_publish_ws.json.input;
 
-import java.util.Collections;
 import java.util.List;
 
 import javax.validation.Valid;
@@ -23,7 +22,7 @@ import com.fasterxml.jackson.annotation.JsonProperty;
  */
 @JsonIgnoreProperties(ignoreUnknown = true)
 public class StockRecord extends Common{
-	
+
 	@JsonProperty("stock_name")
 	@NotNull(message="stock_name cannot be null")
 	@Size(min=2, message="stock_name cannot be empty")
@@ -34,22 +33,20 @@ public class StockRecord extends Common{
 	@CustomField(key="Stock Id")
 	private String stockID;
 
-	@JsonProperty("species_scientific_name")
+	@JsonProperty("species")
-	@CustomField(key="Species scientific name")
+	@CustomField(key="Species")
 	@Tag
-	@NotNull(message="species_scientific_name cannot be null")
+	@Size(min=1, message="species cannot be empty")
-	@Size(min=1, message="species_scientific_name cannot be empty")
+	private List<String> species;
-	private String speciesScientificName;
 
 	@JsonProperty("assessment_distribution_area")
 	@CustomField(key="Assessment distribution area")
-	@NotNull(message="assessment distribution cannot be null")
 	@Size(min=1, message="assessment distribution area cannot be empty")
-	private String area;
+	private List<String> area;
 
 	@JsonProperty("exploiting_fishery")
 	@CustomField(key="Exploiting fishery")
-	private String exploitingFishery;
+	private List<String> exploitingFishery;
 
 	@JsonProperty("management_entity")
 	@CustomField(key="Management entity")
@@ -63,25 +60,27 @@ public class StockRecord extends Common{
 	@CustomField(key="State of marine resources")
 	private String stateOfMarineResource;
 
-	@JsonProperty("exploitation_rate")
+	@JsonProperty("standard_exploitation_rate")
-	@CustomField(key="Exploitation Rate")
+	@CustomField(key="Standard Exploitation Rate")
 	@Tag
 	@Valid
-	private List<TimeSeriesBean<Exploitation_Rate, Void>> exploitationRate;
+	private List<TimeSeriesBean<Exploitation_Rate, Void>> exploitationRateStandard;
+
+	@JsonProperty("exploitation_rate")
+	@CustomField(key="Exploitation Rate")
+	@Valid
+	private List<TimeSeriesBean<String, String>> exploitationRate;
+
+	@JsonProperty("standard_abundance_level")
+	@CustomField(key="Standard Abundance Level")
+	@Tag
+	@Valid
+	private List<TimeSeriesBean<Abundance_Level, Void>> abundanceLevelStandard;
 
 	@JsonProperty("abundance_level")
 	@CustomField(key="Abundance Level")
-	@Tag
 	@Valid
-	private List<TimeSeriesBean<Abundance_Level, Void>> abundanceLevel;
+	private List<TimeSeriesBean<String, String>> abundanceLevel;
-
-	@JsonProperty("exploitation_rate_for_grouping")
-	@Group
-	private Exploitation_Rate exploitationRateForGrouping;
-
-	@JsonProperty("abundance_level_for_grouping")
-	@Group
-	private Abundance_Level abundanceLevelForGrouping;
 
 	@JsonProperty("narrative_state_and_trend")
 	@CustomField(key="Narrative state and trend")
@@ -95,10 +94,6 @@ public class StockRecord extends Common{
 	@CustomField(key="Reporting entity")
 	private String reportingEntity;
 
-	@JsonProperty("reporting_year")
-	@CustomField(key="Reporting year")
-	private Long reportingYear;
-
 	@JsonProperty("stock_uri")
 	@CustomField(key="Stock Uri")
 	private String stockUri;
@@ -106,7 +101,7 @@ public class StockRecord extends Common{
 	@JsonProperty("water_area")
 	@CustomField(key="Water Area")
 	private List<String> waterArea;
-	
+
 	@JsonProperty("type")
 	@CustomField(key="Type")
 	@Tag
@@ -121,16 +116,16 @@ public class StockRecord extends Common{
 	 * Create a Stock element.
 	 * @param stockName
 	 * @param stockID
-	 * @param speciesScientificName
+	 * @param species
 	 * @param area
 	 * @param exploitingFishery
 	 * @param managementEntity
 	 * @param assessmentMethods
 	 * @param stateOfMarineResource
+	 * @param exploitationRateStandard
 	 * @param exploitationRate
+	 * @param abundanceLevelStandard
 	 * @param abundanceLevel
-	 * @param exploitationRateForGrouping
-	 * @param abundanceLevelForGrouping
 	 * @param narrativeStateAndTrend
 	 * @param scientificAdvice
 	 * @param reportingEntity
@@ -139,39 +134,43 @@ public class StockRecord extends Common{
 	 * @param waterArea
 	 * @param type
 	 */
-	public StockRecord(String stockName, String stockID,
+	public StockRecord(
-			String speciesScientificName, String area,
+			String stockName,
-			String exploitingFishery, String managementEntity,
+			String stockID,
-			String assessmentMethods, String stateOfMarineResource,
+			List<String> species,
-			List<TimeSeriesBean<Exploitation_Rate, Void>> exploitationRate,
+			List<String> area,
-			List<TimeSeriesBean<Abundance_Level, Void>> abundanceLevel,
+			List<String> exploitingFishery,
-			Exploitation_Rate exploitationRateForGrouping,
+			String managementEntity,
-			Abundance_Level abundanceLevelForGrouping,
+			String assessmentMethods,
+			String stateOfMarineResource,
+			List<TimeSeriesBean<Exploitation_Rate, Void>> exploitationRateStandard,
+			List<TimeSeriesBean<String, String>> exploitationRate,
+			List<TimeSeriesBean<Abundance_Level, Void>> abundanceLevelStandard,
+			List<TimeSeriesBean<String, String>> abundanceLevel,
 			String narrativeStateAndTrend, String scientificAdvice,
 			String reportingEntity, Long reportingYear, String stockUri,
 			List<String> waterArea, Stock_Type type) {
 		super();
 		this.stockName = stockName;
 		this.stockID = stockID;
-		this.speciesScientificName = speciesScientificName;
+		this.species = species;
 		this.area = area;
 		this.exploitingFishery = exploitingFishery;
 		this.managementEntity = managementEntity;
 		this.assessmentMethods = assessmentMethods;
 		this.stateOfMarineResource = stateOfMarineResource;
+		this.exploitationRateStandard = exploitationRateStandard;
 		this.exploitationRate = exploitationRate;
+		this.abundanceLevelStandard = abundanceLevelStandard;
 		this.abundanceLevel = abundanceLevel;
-		this.exploitationRateForGrouping = exploitationRateForGrouping;
-		this.abundanceLevelForGrouping = abundanceLevelForGrouping;
 		this.narrativeStateAndTrend = narrativeStateAndTrend;
 		this.scientificAdvice = scientificAdvice;
 		this.reportingEntity = reportingEntity;
-		this.reportingYear = reportingYear;
 		this.stockUri = stockUri;
 		this.waterArea = waterArea;
 		this.type = type;
 	}
-	
+
 	public Stock_Type getType() {
 		return type;
 	}
@@ -179,24 +178,6 @@ public class StockRecord extends Common{
 	public void setType(Stock_Type type) {
 		this.type = type;
 	}
-	
-	public Exploitation_Rate getExploitationRateForGrouping() {
-		return exploitationRateForGrouping;
-	}
-
-	public void setExploitationRateForGrouping(
-			Exploitation_Rate exploitationRateForGrouping) {
-		this.exploitationRateForGrouping = exploitationRateForGrouping;
-	}
-
-	public Abundance_Level getAbundanceLevelForGrouping() {
-		return abundanceLevelForGrouping;
-	}
-
-	public void setAbundanceLevelForGrouping(
-			Abundance_Level abundanceLevelForGrouping) {
-		this.abundanceLevelForGrouping = abundanceLevelForGrouping;
-	}
 
 	public String getStockUri() {
 		return stockUri;
@@ -230,27 +211,27 @@ public class StockRecord extends Common{
 		this.stockID = stockID;
 	}
 
-	public String getSpeciesScientificName() {
+	public List<String> getSpecies() {
-		return speciesScientificName;
+		return species;
 	}
 
-	public void setSpeciesScientificName(String speciesScientificName) {
+	public void setSpecies(List<String> species) {
-		this.speciesScientificName = speciesScientificName;
+		this.species = species;
 	}
 
-	public String getArea() {
+	public List<String> getArea() {
 		return area;
 	}
 
-	public void setArea(String area) {
+	public void setArea(List<String> area) {
 		this.area = area;
 	}
 
-	public String getExploitingFishery() {
+	public List<String> getExploitingFishery() {
 		return exploitingFishery;
 	}
 
-	public void setExploitingFishery(String exploitingFishery) {
+	public void setExploitingFishery(List<String> exploitingFishery) {
 		this.exploitingFishery = exploitingFishery;
 	}
 
@@ -278,28 +259,31 @@ public class StockRecord extends Common{
 		this.stateOfMarineResource = stateOfMarineResource;
 	}
 
-	public List<TimeSeriesBean<Exploitation_Rate, Void>> getExploitationRate() {
+	public List<TimeSeriesBean<Exploitation_Rate, Void>> getExploitationRateStandard() {
-		return exploitationRate;
+		return exploitationRateStandard;
 	}
 
-	public void setExploitationRate(List<TimeSeriesBean<Exploitation_Rate, Void>> exploitationRate) {
+	public void setExploitationRateStandard(
-		this.exploitationRate = exploitationRate;
+			List<TimeSeriesBean<Exploitation_Rate, Void>> exploitationRateStandard) {
-		
+		this.exploitationRateStandard = exploitationRateStandard;
-		if(exploitationRate != null){
-			Collections.sort(exploitationRate);
-		}
 	}
 
-	public List<TimeSeriesBean<Abundance_Level, Void>> getAbundanceLevel() {
+	public List<TimeSeriesBean<Abundance_Level, Void>> getAbundanceLevelStandard() {
+		return abundanceLevelStandard;
+	}
+
+	public void setAbundanceLevelStandard(
+			List<TimeSeriesBean<Abundance_Level, Void>> abundanceLevelStandard) {
+		this.abundanceLevelStandard = abundanceLevelStandard;
+	}
+
+	public List<TimeSeriesBean<String, String>> getAbundanceLevel() {
 		return abundanceLevel;
 	}
 
-	public void setAbundanceLevel(List<TimeSeriesBean<Abundance_Level, Void>> abundanceLevel) {
+	public void setAbundanceLevel(
+			List<TimeSeriesBean<String, String>> abundanceLevel) {
 		this.abundanceLevel = abundanceLevel;
-		
-		if(abundanceLevel != null){
-			Collections.sort(abundanceLevel);
-		}
 	}
 
 	public String getNarrativeStateAndTrend() {
@@ -325,32 +309,33 @@ public class StockRecord extends Common{
 	public void setReportingEntity(String reportingEntity) {
 		this.reportingEntity = reportingEntity;
 	}
-
+	
-	public Long getReportingYear() {
+	public List<TimeSeriesBean<String, String>> getExploitationRate() {
-		return reportingYear;
+		return exploitationRate;
 	}
 
-	public void setReportingYear(Long reportingYear) {
+	public void setExploitationRate(
-		this.reportingYear = reportingYear;
+			List<TimeSeriesBean<String, String>> exploitationRate) {
+		this.exploitationRate = exploitationRate;
 	}
 
 	@Override
 	public String toString() {
 		return "StockRecord [stockName=" + stockName + ", stockID=" + stockID
-				+ ", speciesScientificName=" + speciesScientificName
+				+ ", species=" + species + ", area=" + area
-				+ ", area=" + area + ", exploitingFishery=" + exploitingFishery
+				+ ", exploitingFishery=" + exploitingFishery
 				+ ", managementEntity=" + managementEntity
 				+ ", assessmentMethods=" + assessmentMethods
 				+ ", stateOfMarineResource=" + stateOfMarineResource
+				+ ", exploitationRateStandard=" + exploitationRateStandard
 				+ ", exploitationRate=" + exploitationRate
+				+ ", abundanceLevelStandard=" + abundanceLevelStandard
 				+ ", abundanceLevel=" + abundanceLevel
-				+ ", exploitationRateForGrouping="
+				+ ", narrativeStateAndTrend=" + narrativeStateAndTrend
-				+ exploitationRateForGrouping + ", abundanceLevelForGrouping="
+				+ ", scientificAdvice=" + scientificAdvice
-				+ abundanceLevelForGrouping + ", narrativeStateAndTrend="
+				+ ", reportingEntity=" + reportingEntity + ", stockUri="
-				+ narrativeStateAndTrend + ", scientificAdvice="
+				+ stockUri + ", waterArea=" + waterArea + ", type=" + type
-				+ scientificAdvice + ", reportingEntity=" + reportingEntity
+				+ "]";
-				+ ", reportingYear=" + reportingYear + ", stockUri=" + stockUri
-				+ ", waterArea=" + waterArea + ", type=" + type + "]";
 	}
 
 }

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherFisheryService.java

@@ -149,8 +149,8 @@ public class GrsfPublisherFisheryService {
 					// fishing area and jurisdiction area cannot be empty at the same time
 					String futureName = record.getUuid();
 					String futureTitle = record.getFisheryName();
-					String fishingArea = record.getFishingArea();
+					List<String> fishingArea = record.getFishingArea();
-					String jurisdictionArea = record.getJurisdictionArea();
+					List<String> jurisdictionArea = record.getJurisdictionArea();
 					if(!HelperMethods.isNameValid(futureName)){
 
 						status = Status.BAD_REQUEST;
@@ -186,10 +186,7 @@ public class GrsfPublisherFisheryService {
 							HelperMethods.getGroups(groups, record);
 
 							// evaluate the custom fields
-							Map<String, List<String>> customFields = new HashMap<String, List<String>>();
+							Map<String, List<String>> customFields = record.getExtrasFields();
-
-							if(record.getExtras() != null)
-								customFields = record.getExtras();
 
 							// automatically retrieve the other ones
 							HelperMethods.getExtras(customFields, record);
@@ -207,7 +204,8 @@ public class GrsfPublisherFisheryService {
 							}else{
 
 								// evaluate the resources
-								List<ResourceBean> resources = HelperMethods.getResourcesFromBean(record, username, tags, groups);
+								List<ResourceBean> resources = record.getExtrasResources();
+								HelperMethods.getResourcesFromBean(record, username, tags, groups, resources);
 
 								// check the license id
 								String license = null;
@@ -225,7 +223,7 @@ public class GrsfPublisherFisheryService {
 										catalogue.getApiKeyFromUsername(username), 
 										futureTitle, 
 										futureName,
-										organization, 
+										organization,//"grsf", //TO DELETE TODO 
 										authorFullname, 
 										authorMail, 
 										record.getMaintainer(), 

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherStockService.java

@@ -175,10 +175,7 @@ public class GrsfPublisherStockService {
 							HelperMethods.getGroups(groups, record);
 
 							// evaluate the custom fields
-							Map<String, List<String>> customFields = new HashMap<String, List<String>>();
+							Map<String, List<String>> customFields = record.getExtrasFields();
-
-							if(record.getExtras() != null)
-								customFields = record.getExtras();
 
 							// automatically retrieve the other ones
 							HelperMethods.getExtras(customFields, record);
@@ -197,7 +194,8 @@ public class GrsfPublisherStockService {
 							}else{
 
 								// evaluate the resources
-								List<ResourceBean> resources = HelperMethods.getResourcesFromBean(record, username, tags, groups);
+								List<ResourceBean> resources = record.getExtrasResources();
+								HelperMethods.getResourcesFromBean(record, username, tags, groups, resources);
 
 								// check the license id
 								String license = null;
@@ -215,7 +213,7 @@ public class GrsfPublisherStockService {
 										catalogue.getApiKeyFromUsername(username), 
 										futureTitle, 
 										futureName,
-										organization, 
+										organization,//"grsf", //TO DELETE TODO 
 										authorFullname, 
 										authorMail, 
 										record.getMaintainer(), 

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/HelperMethods.java

@@ -74,7 +74,7 @@ public abstract class HelperMethods {
 			modified = modified.substring(1);
 		if(modified.endsWith("-"))
 			modified = modified.substring(0, modified.length() -1);
-		
+
 		logger.info("Group name generated is " + modified);
 
 		return modified;
@@ -169,34 +169,43 @@ public abstract class HelperMethods {
 						Object f = new PropertyDescriptor(field.getName(), current).getReadMethod().invoke(record);
 						if(f != null){
 
-							// also convert to the group name that should be on ckan
+							if(f instanceof List<?>){
-							String groupName = getGroupNameOnCkan(f.toString().trim());
+								List asList = ((List) f);
-							if(!groups.contains(groupName))
+								if(!asList.isEmpty()){
-								groups.add(groupName);
 
+									logger.debug("The object annotated with @Tag/@Group is a list. Adding ... ");
+
+									// else add all the available elements
+									for (int i = 0; i < asList.size(); i++) {
+										String groupName = getGroupNameOnCkan(asList.get(i).toString().trim());
+										logger.debug(groupName);
+										if(!groups.contains(groupName))
+											groups.add(groupName);	
+									}
+
+								}
+							}else{
+
+								// also convert to the group name that should be on ckan
+								String groupName = getGroupNameOnCkan(f.toString().trim());
+								if(!groups.contains(groupName))
+									groups.add(groupName);
+							}
 						}
-						
+
 						// check if the field is an enumerator, and the enum class is also annotated with @Group
 						if(field.getType().isEnum() && field.getType().isAnnotationPresent(Group.class)){
-							
+
 							logger.info("Class " + field.getClass().getSimpleName() + " has annotation @Group");
-							
+
 							// extract the name from the enum class and add it to the groups
 							// also convert to the group name that should be on ckan
 							String groupName = getGroupNameOnCkan(field.getType().getSimpleName());
 							if(!groups.contains(groupName))
 								groups.add(groupName);
-							
+
-							// check if this class has a father too (@Group annotation allows it)
-							Group groupAnnotationOnEnum = field.getType().getAnnotation(Group.class);
-							if(!groupAnnotationOnEnum.parentGroup().equals(Class.class)){
-								String groupNameFather = getGroupNameOnCkan(groupAnnotationOnEnum.parentGroup().getSimpleName());
-								if(!groups.contains(groupNameFather))
-									groups.add(groupNameFather);
-							}
-							
 						}
-						
+
 					}catch(Exception e){
 						logger.error("Failed ot read value for field " + field.getName() + " skipping", e);
 					}
@@ -427,11 +436,11 @@ public abstract class HelperMethods {
 	 * @param username
 	 * @param tags 
 	 * @param groups 
+	 * @param resources 
 	 * @return 
 	 */
-	public static List<ResourceBean> getResourcesFromBean(Common record, String username, List<String> tags, List<String> groups){
+	public static void getResourcesFromBean(Common record, String username, List<String> tags, List<String> groups, List<ResourceBean> resources){
 
-		List<ResourceBean> toReturn = new ArrayList<ResourceBean>();
 		Class<?> current = record.getClass();
 		do{
 			Field[] fields = current.getDeclaredFields();
@@ -446,13 +455,13 @@ public abstract class HelperMethods {
 								List<Resource> listOfResources = (List<Resource>)f;
 
 								for (Resource resource : listOfResources) {
-									toReturn.add(new ResourceBean(resource.getUrl(), resource.getName().toString(), resource.getDescription(), null, username, null, null));
+									resources.add(new ResourceBean(resource.getUrl(), resource.getName().toString(), resource.getDescription(), null, username, null, null));
 								}
 
 							}else{
 
 								Resource res = (Resource)f;
-								toReturn.add(new ResourceBean(res.getUrl(), res.getName().toString(), res.getDescription(), null, username, null, null));
+								resources.add(new ResourceBean(res.getUrl(), res.getName().toString(), res.getDescription(), null, username, null, null));
 
 							}
 						}
@@ -464,8 +473,7 @@ public abstract class HelperMethods {
 		}
 		while((current = current.getSuperclass())!=null); // iterate from the inherited class up to the Object.class
 
-		logger.info("Returning resources " + toReturn);
+		logger.info("Returning resources " + resources);
-		return toReturn;
 	}
 
 	/**
@@ -563,29 +571,12 @@ public abstract class HelperMethods {
 		if(html == null || html.isEmpty())
 			return html;
 
-		logger.info("Incoming text is " + html);
-
 		// remove html and clean
 		String withoutHTML = Jsoup.parse(html).text();
 		withoutHTML = Jsoup.clean(withoutHTML, Whitelist.basic());
 
-		// TODO ...
-		// could contain non ascii chars ... try to convert them to question marks and then remove them
-		//		try{
-		//			String strippedWithQuestionMarks = Normalizer.normalize(withoutHTML, Normalizer.Form.NFD);
-		//			String regex = "[\\p{InCombiningDiacriticalMarks}\\p{IsLm}\\p{IsSk}]+";
-		//			strippedWithQuestionMarks = new String(strippedWithQuestionMarks.replaceAll(regex, "").getBytes("ascii"), "ascii");
-		//			strippedWithQuestionMarks = strippedWithQuestionMarks.replaceAll("[?]+", " ");
-		//			withoutHTML = strippedWithQuestionMarks;
-		//		}catch(UnsupportedEncodingException e){
-		//			logger.warn("Unable to convert to question marks non ascii chars..", e);
-		//			// remove non ascii directly
-		//			withoutHTML = withoutHTML.replaceAll("[^\\x00-\\x7F]", " "); 
-		//		}
-
 		// remove non ascii chars ...
 		withoutHTML = withoutHTML.replaceAll("[^\\p{ASCII}]", " ");
-		logger.info("Without html is " + withoutHTML);
 		return withoutHTML;
 	}
 }

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/groups/Abundance_Level.java

@@ -9,7 +9,7 @@ import com.fasterxml.jackson.annotation.JsonValue;
  * Abundance_Level for Stock records
  * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
  */
-@Group(parentGroup=Indicator.class)
+@Group
 public enum Abundance_Level {
 
 	Intermediate_Abundance("Intermediate abundance"),

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/groups/Exploitation_Rate.java

@@ -8,7 +8,7 @@ import com.fasterxml.jackson.annotation.JsonCreator;
  * Exploitation_Rate for Stock records
  * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
  */
-@Group(parentGroup=Indicator.class)
+@Group
 public enum Exploitation_Rate {
 
 	Moderate_Fishing_Mortality("Moderate fishing mortality"),

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/groups/Indicator.java

@@ -1,12 +0,0 @@
-package org.gcube.data_catalogue.grsf_publish_ws.utils.groups;
-
-import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.Group;
-
-/**
- * Indicator group: father of Abundance level and Exploitation Rate
- * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
- */
-@Group
-public enum Indicator {
-
-}

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/threads/AssociationToGroupThread.java

@@ -1,12 +1,19 @@
 package org.gcube.data_catalogue.grsf_publish_ws.utils.threads;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
 import java.util.List;
+import java.util.ListIterator;
+import java.util.Set;
 
 import org.gcube.datacatalogue.ckanutillibrary.DataCatalogue;
 import org.gcube.datacatalogue.ckanutillibrary.models.RolesCkanGroupOrOrg;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import eu.trentorise.opendata.jackan.model.CkanGroup;
+
 /**
  * Associate the dataset to a group.
  * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
@@ -40,31 +47,76 @@ public class AssociationToGroupThread extends Thread {
 	@Override
 	public void run() {
 
-		logger.info("Association thread started to put the dataset with id="+ datasetId + " into group with title(s) " + groupsTitles + " for user " + username);
+		try{
 
-		String userApiKey = catalogue.getApiKeyFromUsername(username);
+			logger.info("Association thread started to put the dataset with id="+ datasetId + " into group with title(s) " + groupsTitles + " for user " + username);
 
-		// retrieve the role to be assigned according the one the user has into the organization of the dataset
+			// find parents' groups
-		RolesCkanGroupOrOrg role = RolesCkanGroupOrOrg.valueOf(catalogue.getRoleOfUserInOrganization(username, organizationId, catalogue.getApiKeyFromUsername(username)).toUpperCase());
+			String userApiKey = catalogue.getApiKeyFromUsername(username);
-		
+			findHierarchy(groupsTitles, catalogue, userApiKey);
-		if(!role.equals(RolesCkanGroupOrOrg.ADMIN))
-			role = RolesCkanGroupOrOrg.MEMBER; // decrease the role to member if it is not an admin
 
-		for (String groupTitle : groupsTitles) {
+			Set<String> uniqueGroups = new HashSet<String>(groupsTitles);
+			
+			logger.info("Full set of groups is " + groupsTitles);
+			
 
-			logger.debug("Setting role " + role + " into group " + groupTitle + " to user " + username);
+			// retrieve the role to be assigned according the one the user has into the organization of the dataset
-			boolean assigned = catalogue.checkRoleIntoGroup(username, groupTitle, role);
+			RolesCkanGroupOrOrg role = RolesCkanGroupOrOrg.valueOf(catalogue.getRoleOfUserInOrganization(username, organizationId, userApiKey).toUpperCase());
 
-			if(!assigned){
+			if(!role.equals(RolesCkanGroupOrOrg.ADMIN))
-				logger.warn("The user " + username + " has not enough privileges to associate the dataset into group OR the group doesn't exist" + groupTitle);
+				role = RolesCkanGroupOrOrg.MEMBER; // decrease the role to member if it is not an admin
-				continue;
+
+			for (String groupTitle : uniqueGroups) {
+
+				logger.debug("Setting role " + role + " into group " + groupTitle + " to user " + username);
+				boolean assigned = catalogue.checkRoleIntoGroup(username, groupTitle, role);
+
+				if(!assigned){
+					logger.warn("The user " + username + " has not enough privileges to associate the dataset into group OR the group doesn't exist" + groupTitle);
+					continue;
+				}
+				else{
+					boolean putIntoGroup = catalogue.assignDatasetToGroup(groupTitle, datasetId, userApiKey);
+					logger.info("Was product put into group " + groupTitle + "? " + putIntoGroup);
+				}
 			}
-			else{
+			logger.info("The Association Group thread ended correctly");
-				boolean putIntoGroup = catalogue.assignDatasetToGroup(groupTitle, datasetId, userApiKey);
+		}catch(Exception e){
-				logger.info("Was product put into group " + groupTitle + "? " + putIntoGroup);
+			logger.error("Exception follows ", e);
+		}
+	}
+
+	/**
+	 * Find the hierarchy of trees
+	 * @param uniqueGroups
+	 * @param catalogue
+	 * @param user's api key
+	 */
+	public static void findHierarchy(
+			List<String> groupsTitles,
+			DataCatalogue catalogue, 
+			String apiKey) {
+
+		ListIterator<String> iterator = groupsTitles.listIterator();
+		
+		while (iterator.hasNext()) {
+			String group = (String) iterator.next();
+			
+			List<CkanGroup> parents = catalogue.getParentGroups(group, apiKey);
+
+			if(parents == null || parents.isEmpty())
+				return;
+
+			for (CkanGroup ckanGroup : parents) {
+				List<String> parentsList = new ArrayList<String>(Arrays.asList(ckanGroup.getName()));
+				findHierarchy(parentsList, catalogue, apiKey);
+				
+				for (String parent : parentsList) {
+					iterator.add(parent);	
+				}
 			}
 		}
-		logger.info("The Association Group thread ended correctly");
+	
 	}
 
 }

src/test/java/org/gcube/data_catalogue/grsf_publish_ws/JTests.java

@@ -13,8 +13,10 @@ import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
 import org.gcube.common.homelibrary.home.HomeLibrary;
@@ -41,9 +43,9 @@ import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Abundance_Level;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Fishery_Type;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Source;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Status;
+import org.gcube.data_catalogue.grsf_publish_ws.utils.threads.AssociationToGroupThread;
 import org.gcube.datacatalogue.ckanutillibrary.DataCatalogue;
 import org.gcube.datacatalogue.ckanutillibrary.DataCatalogueFactory;
-import org.junit.Test;
 import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
@@ -547,7 +549,7 @@ public class JTests {
 						logger.debug("Name is " +groupName );
 
 					}
-					
+
 				}
 			}
 		}
@@ -555,4 +557,27 @@ public class JTests {
 
 	}
 
+	//@Test
+	public void testHierarchy(){
+		String name = "low-abundance";
+		DataCatalogue catalogue = HelperMethods.getDataCatalogueRunningInstance("/gcube/devNext/NextNext");
+		List<String> uniqueGroups = new ArrayList<String>();
+		uniqueGroups.add(name);
+		uniqueGroups.add(name);
+		AssociationToGroupThread.findHierarchy(uniqueGroups, catalogue, catalogue.getApiKeyFromUsername("costantino_perciante"));
+		logger.debug("Hierarchy is " + uniqueGroups);
+	}
+	
+	//@Test
+	public void testAssociationThread() throws InterruptedException{
+		String name = "low-abundance";
+		DataCatalogue catalogue = HelperMethods.getDataCatalogueRunningInstance("/gcube/devNext/NextNext");
+		AssociationToGroupThread threadGroups = new AssociationToGroupThread(Arrays.asList(name), "another-test-test-please-ignore", "grsf", "costantino_perciante", catalogue);
+		threadGroups.start();
+		threadGroups.join();
+		logger.info("Thread stopped!");
+
+		
+	}
+
 }