separated types for stock and fishery. The main thread will wait for the groups association thread to finish before starting the one of the files

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/grsf-publisher-ws@134895 82a268e6-3cf1-43bd-a215-b396298e98cf

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

@@ -14,7 +14,6 @@ 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.groups.Source;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Status;
-import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Type;
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
@@ -67,12 +66,6 @@ public class Common {
 	@Valid
 	private List<Resource<String>> sourceOfInformation;
 
-	@JsonProperty("type")
-	@CustomField(key="Type")
-	@Tag
-	@Group
-	private Type type;
-
 	@JsonProperty("short_title")
 	@CustomField(key="Short Title")
 	@NotNull(message="short_title cannot be null")
@@ -137,7 +130,7 @@ public class Common {
 			String maintainerContact,
 			List<Resource<Source>> databaseSources,
 			List<Resource<String>> sourceOfInformation, String dataOwner,
-			Type type, String shortTitle, String uuid,
+			String shortTitle, String uuid,
 			boolean traceabilityFlag, Map<String, List<String>> extras,
 			Status status, String productType) {
 		super();
@@ -151,7 +144,6 @@ public class Common {
 		this.databaseSources = databaseSources;
 		this.sourceOfInformation = sourceOfInformation;
 		this.dataOwner = dataOwner;
-		this.type = type;
 		this.shortTitle = shortTitle;
 		this.uuid = uuid;
 		this.traceabilityFlag = traceabilityFlag;
@@ -248,14 +240,6 @@ public class Common {
 		this.dataOwner = dataOwner;
 	}
 
-	public Type getType() {
-		return type;
-	}
-
-	public void setType(Type type) {
-		this.type = type;
-	}
-
 	public void setExtras(Map<String, List<String>> extras) {
 		this.extras = extras;
 	}
@@ -304,7 +288,7 @@ public class Common {
 				+ maintainer + ", maintainerContact=" + maintainerContact
 				+ ", dataOwner=" + dataOwner + ", databaseSources="
 				+ databaseSources + ", sourceOfInformation="
-				+ sourceOfInformation + ", type=" + type + ", shortTitle="
+				+ sourceOfInformation + ", shortTitle="
 				+ shortTitle + ", uuid=" + uuid + ", traceabilityFlag="
 				+ traceabilityFlag + ", extras=" + extras + ", status="
 				+ status + ", productType=" + productType + "]";

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

@@ -11,6 +11,7 @@ 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.groups.Production_System_Type;
+import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Type_Fishery;
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
@@ -79,6 +80,12 @@ public class FisheryRecord extends Common{
 	@Tag
 	@Valid
 	private List<TimeSeriesBean<String, String>> catchesOrLandings;
+	
+	@JsonProperty("type")
+	@CustomField(key="Type")
+	@Tag
+	@Group
+	private Type_Fishery type;
 
 	public FisheryRecord() {
 		super();
@@ -98,13 +105,15 @@ public class FisheryRecord extends Common{
 	 * @param fishingGear
 	 * @param environment
 	 * @param catchesOrLandings
+	 * @param type
 	 */
 	public FisheryRecord(String fisheryName, String fisheryId,
 			String scientificName, String fishingArea, String exploitingStocks,
 			String managementEntity, String jurisdictionArea,
 			Production_System_Type productionSystemType, String flagState,
 			String fishingGear, String environment,
-			List<TimeSeriesBean<String, String>> catchesOrLandings) {
+			List<TimeSeriesBean<String, String>> catchesOrLandings,
+			Type_Fishery type) {
 		super();
 		this.fisheryName = fisheryName;
 		this.fisheryId = fisheryId;
@@ -118,6 +127,7 @@ public class FisheryRecord extends Common{
 		this.fishingGear = fishingGear;
 		this.environment = environment;
 		this.catchesOrLandings = catchesOrLandings;
+		this.type = type;
 	}
 
 	public String getFisheryName() {
@@ -220,6 +230,14 @@ public class FisheryRecord extends Common{
 		}
 	}
 
+	public Type_Fishery getType() {
+		return type;
+	}
+
+	public void setType(Type_Fishery type) {
+		this.type = type;
+	}
+
 	@Override
 	public String toString() {
 		return "FisheryRecord [fisheryName=" + fisheryName + ", fisheryId="
@@ -230,6 +248,6 @@ public class FisheryRecord extends Common{
 				+ ", productionSystemType=" + productionSystemType
 				+ ", flagState=" + flagState + ", fishingGear=" + fishingGear
 				+ ", environment=" + environment + ", catchesOrLandings="
-				+ catchesOrLandings + "]";
+				+ catchesOrLandings + ", type=" + type + "]";
 	}
 }

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

@@ -9,8 +9,9 @@ import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 /**
- * A resource object bean. The generic argument applies to the resource's name.
+ * A resource object bean. The generic argument T applies to the resource's name.
  * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
+ * @param <T> the resource's name type
  */
 @JsonIgnoreProperties(ignoreUnknown = true) // ignore in serialization/deserialization
 public class Resource<T> {

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

@@ -12,6 +12,7 @@ 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.groups.Abundance_Level;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Exploitation_Rate;
+import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Type_Stock;
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
@@ -105,6 +106,12 @@ public class StockRecord extends Common{
 	@JsonProperty("water_area")
 	@CustomField(key="Water Area")
 	private List<String> waterArea;
+	
+	@JsonProperty("type")
+	@CustomField(key="Type")
+	@Tag
+	@Group
+	private Type_Stock type;
 
 	public StockRecord() {
 		super();
@@ -130,6 +137,7 @@ public class StockRecord extends Common{
 	 * @param reportingYear
 	 * @param stockUri
 	 * @param waterArea
+	 * @param type
 	 */
 	public StockRecord(String stockName, String stockID,
 			String speciesScientificName, String area,
@@ -141,7 +149,7 @@ public class StockRecord extends Common{
 			Abundance_Level abundanceLevelForGrouping,
 			String narrativeStateAndTrend, String scientificAdvice,
 			String reportingEntity, Long reportingYear, String stockUri,
-			List<String> waterArea) {
+			List<String> waterArea, Type_Stock type) {
 		super();
 		this.stockName = stockName;
 		this.stockID = stockID;
@@ -161,8 +169,17 @@ public class StockRecord extends Common{
 		this.reportingYear = reportingYear;
 		this.stockUri = stockUri;
 		this.waterArea = waterArea;
+		this.type = type;
+	}
+	
+	public Type_Stock getType() {
+		return type;
 	}
 
+	public void setType(Type_Stock type) {
+		this.type = type;
+	}
+	
 	public Exploitation_Rate getExploitationRateForGrouping() {
 		return exploitationRateForGrouping;
 	}
@@ -319,7 +336,7 @@ public class StockRecord extends Common{
 
 	@Override
 	public String toString() {
-		return "StockRecord [" + super.toString() + "stockName=" + stockName + ", stockID=" + stockID
+		return "StockRecord [stockName=" + stockName + ", stockID=" + stockID
 				+ ", speciesScientificName=" + speciesScientificName
 				+ ", area=" + area + ", exploitingFishery=" + exploitingFishery
 				+ ", managementEntity=" + managementEntity
@@ -333,6 +350,7 @@ public class StockRecord extends Common{
 				+ narrativeStateAndTrend + ", scientificAdvice="
 				+ scientificAdvice + ", reportingEntity=" + reportingEntity
 				+ ", reportingYear=" + reportingYear + ", stockUri=" + stockUri
-				+ ", waterArea=" + waterArea + "]";
+				+ ", waterArea=" + waterArea + ", type=" + type + "]";
-	}	
+	}
+
 }

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

@@ -9,11 +9,11 @@ import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 /**
- * A time series bean that contains couple <year, value>
+ * A time series bean that contains elements &lt year, T, T1 &gt
  * Catches_and_landings contains also Unit
  * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
- * @param T the first type value of the series
+ * @param <T> the first type value of the series
- * @param T1 the second type value of the series
+ * @param <T1> the second type value of the series (optional)
  */
 @JsonIgnoreProperties(ignoreUnknown = true)
 public class TimeSeriesBean<T, T1> implements Comparable<TimeSeriesBean<T, T1>>{
@@ -72,7 +72,7 @@ public class TimeSeriesBean<T, T1> implements Comparable<TimeSeriesBean<T, T1>>{
 		// when the value belongs to these classes annotated with @Tag..
 		if(valueClass.equals(Abundance_Level.class) || valueClass.equals(Exploitation_Rate.class))
 			return year + "-" + value;
-		else if(this.unit != null && this.unit.getClass().equals(String.class)) // catches and landings
+		else if(this.unit != null && !this.unit.getClass().equals(Void.class)) // e.g., catches and landings
 			return year + "-" + value + "-" + unit;
 		else 
 			return "TimeSeriesBean [value=" + value + ", unit=" + unit + ", year="

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/output/ResponseBean.java

@@ -1,10 +1,9 @@
 package org.gcube.data_catalogue.grsf_publish_ws.json.output;
 
 /**
- * Response bean.
+ * Response bean to be used by the service.
  * @author Costantino Perciante at ISTI-CNR 
  * (costantino.perciante@isti.cnr.it)
- *
  */
 public class ResponseBean{
 

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

@@ -237,21 +237,19 @@ public class GrsfPublisherFisheryService {
 									responseBean.setProductUrl(catalogue.getPortletUrl() + "?" + URLEncoder.encode("path=/dataset/"  + futureName, "UTF-8"));
 									responseBean.setKbUuid(record.getUuid());
 									
-									// manage time series
-									logger.info("Launching thread for time series handling");
-									ManageTimeSeriesThread threadFiles = new ManageTimeSeriesThread(record, futureName, username, catalogue, ScopeProvider.instance.get());
-									
-									// wait this one to finish
-									threadFiles.start();
-									
-									logger.info("Waiting time series thread to die..");
-									threadFiles.join();
-									logger.debug("Ok, it died");
-
 									if(!groups.isEmpty()){
 										logger.info("Launching thread for association to the list of groups " + groups);
-										new AssociationToGroupThread(groups, id, organization, username, catalogue).start();
+										AssociationToGroupThread threadGroups = new AssociationToGroupThread(groups, id, organization, username, catalogue);
+										threadGroups.start();
+										logger.info("Waiting association thread to die..");
+										threadGroups.join();
+										logger.debug("Ok, it died");
 									}
+
+									// manage time series
+									logger.info("Launching thread for time series handling");
+									new ManageTimeSeriesThread(record, futureName, username, catalogue, ScopeProvider.instance.get()).start();
+
 								}
 							}
 						}

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

@@ -225,22 +225,19 @@ public class GrsfPublisherStockService {
 									status = Status.CREATED;
 									responseBean.setProductUrl(catalogue.getPortletUrl() + "?" + URLEncoder.encode("path=/dataset/"  + futureName, "UTF-8"));
 									responseBean.setKbUuid(record.getUuid());
-									
-									// manage time series
-									logger.info("Launching thread for time series handling");
-									ManageTimeSeriesThread threadFiles = new ManageTimeSeriesThread(record, futureName, username, catalogue, ScopeProvider.instance.get());
-									
-									// wait this one to finish
-									threadFiles.start();
-									
-									logger.info("Waiting time series thread to die..");
-									threadFiles.join();
-									logger.debug("Ok, it died");
 
 									if(!groups.isEmpty()){
 										logger.info("Launching thread for association to the list of groups " + groups);
-										new AssociationToGroupThread(groups, id, organization, username, catalogue).start();
+										AssociationToGroupThread threadGroups = new AssociationToGroupThread(groups, id, organization, username, catalogue);
+										threadGroups.start();
+										logger.info("Waiting association thread to die..");
+										threadGroups.join();
+										logger.debug("Ok, it died");
 									}
+
+									// manage time series
+									logger.info("Launching thread for time series handling");
+									new ManageTimeSeriesThread(record, futureName, username, catalogue, ScopeProvider.instance.get()).start();
 								}
 							}
 						}

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

@@ -25,6 +25,8 @@ public class CSVHelpers {
 	 * Write a time series to a csv file, and returns the file reference.<br>
 	 * Please give the timeSeries already sorted per year
 	 * @param timeSeries
+	 * @param <T>
+	 * @param <T1>
 	 */
 	public static <T, T1> File listToCSV(List<TimeSeriesBean<T, T1>> timeSeries){
 

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

@@ -5,19 +5,17 @@ import com.fasterxml.jackson.annotation.JsonValue;
 
 
 /**
- * Type for Stock/Fishery records
+ * Type for Fishery records
  * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
  */
-public enum Type {
+public enum Type_Fishery {
 
-	Assessment_Unit("Assessment Unit"),// for stock
-	Resource("Resource"), // for stock
 	Fishery_Activity("Fishery Activity"), // for fishery  
 	Fishing_Description("Fishing Description"); // for fishery
 
 	private String subGroupNameOrig;
 
-	private Type(String origName) {
+	private Type_Fishery(String origName) {
 		this.subGroupNameOrig = origName;
 	}
 
@@ -44,9 +42,9 @@ public enum Type {
 	 * @return
 	 */
 	@JsonCreator
-	public static Type onDeserialize(String typeString) {
+	public static Type_Fishery onDeserialize(String typeString) {
 		if(typeString != null) {
-			for(Type type : Type.values()) {
+			for(Type_Fishery type : Type_Fishery.values()) {
 				if(type.getOrigName().equalsIgnoreCase(typeString.trim()))
 					return type;
 			}

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

@@ -0,0 +1,63 @@
+package org.gcube.data_catalogue.grsf_publish_ws.utils.groups;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonValue;
+
+/**
+ * Stock types
+ * @author Costantino Perciante at ISTI-CNR 
+ * (costantino.perciante@isti.cnr.it)
+ */
+public enum Type_Stock {
+	
+	Assessment_Unit("Assessment Unit"),// for stock
+	Resource("Resource"); // for stock
+	
+	private String subGroupNameOrig;
+
+	private Type_Stock(String origName) {
+		this.subGroupNameOrig = origName;
+	}
+
+	/**
+	 * Return the original name
+	 * @return
+	 */
+	public String getOrigName(){
+		return subGroupNameOrig;
+	}
+
+	/**
+	 * Get the json value
+	 * @return
+	 */
+	@JsonValue
+	public String onSerialize(){
+		return subGroupNameOrig.toLowerCase();
+	}
+
+	/**
+	 * Get back an enum from json string
+	 * @param typeString
+	 * @return
+	 */
+	@JsonCreator
+	public static Type_Stock onDeserialize(String typeString) {
+		if(typeString != null) {
+			for(Type_Stock type : Type_Stock.values()) {
+				if(type.getOrigName().equalsIgnoreCase(typeString.trim()))
+					return type;
+			}
+		}
+		return null;
+	}
+	
+	/**
+	 * Used by reflection
+	 */
+	@Override
+	public String toString() {
+		return getOrigName();
+	}
+
+}

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

@@ -14,7 +14,8 @@ import org.gcube.data_catalogue.grsf_publish_ws.services.GrsfPublisherFisherySer
 import org.gcube.data_catalogue.grsf_publish_ws.services.GrsfPublisherStockService;
 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.groups.Type;
+import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Type_Fishery;
+import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Type_Stock;
 import org.glassfish.jersey.server.ResourceConfig;
 import org.glassfish.jersey.test.JerseyTest;
 import org.glassfish.jersey.test.TestProperties;
@@ -34,7 +35,7 @@ public class JJerseyTest extends JerseyTest{
 		recordFishery.setAuthorContact("costantino.perciante@isti.cnr.it");
 		recordFishery.setLicense("a caso una lincense");
 		recordFishery.setDataOwner("data owner");
-		recordFishery.setType(Type.Fishing_Description);
+		recordFishery.setType(Type_Fishery.Fishing_Description);
 		recordFishery.setDatabaseSources(new ArrayList<Resource<Source>>(1));
 		recordFishery.setSourceOfInformation(new ArrayList<Resource<String>>(1));
 		recordFishery.setStatus(Status.Pending);
@@ -47,7 +48,7 @@ public class JJerseyTest extends JerseyTest{
 		StockRecord stock = new StockRecord();
 		stock.setAuthor("Costantino Perciante");
 		stock.setAuthorContact("costantino.perciante@isti.cnr.it");
-		stock.setType(Type.Fishing_Description);
+		stock.setType(Type_Stock.Assessment_Unit);
 		stock.setDatabaseSources(null);
 		stock.setStatus(Status.Pending);
 

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

@@ -28,7 +28,7 @@ import org.gcube.data_catalogue.grsf_publish_ws.utils.HelperMethods;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Abundance_Level;
 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.groups.Type;
+import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Type_Fishery;
 import org.gcube.datacatalogue.ckanutillibrary.DataCatalogue;
 import org.gcube.datacatalogue.ckanutillibrary.DataCatalogueFactory;
 import org.junit.Test;
@@ -51,7 +51,7 @@ public class JTests {
 	public void test() throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, IntrospectionException {
 
 		FisheryRecord recordFishery = new FisheryRecord();
-		recordFishery.setType(Type.Fishing_Description);
+		recordFishery.setType(Type_Fishery.Fishing_Description);
 		recordFishery.setDatabaseSources(new ArrayList<Resource<Source>>());
 		recordFishery.setStatus(Status.Pending);