some model changes

fao_state added (it's a new time series)
catches/landings separated
reference_year added
reporting_year is now a list
narrative_state_and_trend changed (is a time series)

species is a series with code, system and name (no longer species code and name separated)
assessment_distribution_area is now a list with objects having code, system, name 
assessment_methods  changed as list having name, reference_year and reporting_year_or_assessment

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/grsf-publisher-ws@150670 82a268e6-3cf1-43bd-a215-b396298e98cf

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

@@ -61,7 +61,11 @@ public class Common extends Base{
 
 	@JsonProperty("reporting_year")
 	@CustomField(key="Reporting year")
-	private Long reportingYear;
+	private List<Long> reportingYear;
+
+	@JsonProperty("reference_year")
+	@CustomField(key="Reference year")
+	private List<Long> referenceYear;
 
 	// automatically compiled
 	@JsonProperty("grsf_type")
@@ -75,21 +79,27 @@ public class Common extends Base{
 	@CustomField(key=SOURCE_KEY)
 	private String sourceType;
 
-	@JsonProperty("catches_or_landings")
-	@CustomField(key="Catches or landings")
+	@JsonProperty("catches")
+	@CustomField(key="Catches")
 	@TimeSeries
 	@Valid
-	private List<TimeSeriesBean<String, String>> catchesOrLandings;
+	private List<TimeSeriesBean<String, String>> catches;
 
-	@JsonProperty("species_name")
-	@CustomField(key="Species Scientific Name")
-	@Tag
-	private List<String> speciesName;
+	@JsonProperty("landings")
+	@CustomField(key="Landings")
+	@TimeSeries
+	@Valid
+	private List<TimeSeriesBean<String, String>> landings;
 
-	@JsonProperty("species_code")
-	@CustomField(key="Species code")
-	@Tag
-	private List<String> speciesCode;
+	@JsonProperty("species")
+	@CustomField(key="species")
+	private List<String> species;
+
+	@JsonProperty("fao_state")
+	@CustomField(key="Fao State")
+	@TimeSeries
+	@Valid
+	private List<TimeSeriesBean<String, Void>> faoState;
 
 	public Common() {
 		super();
@@ -104,19 +114,22 @@ public class Common extends Base{
 	 * @param traceabilityFlag
 	 * @param status
 	 * @param reportingYear
+	 * @param referenceYear
 	 * @param grsfType
 	 * @param sourceType
-	 * @param catchesOrLandings
-	 * @param speciesName
-	 * @param speciesCode
+	 * @param catches
+	 * @param landings
+	 * @param species
+	 * @param faoState
 	 */
 	public Common(String dataOwner, List<Resource<Sources>> databaseSources,
 			List<Resource<String>> sourceOfInformation,
 			List<RefersToBean> refersTo, String shortTitle,
-			Boolean traceabilityFlag, Status status, Long reportingYear,
-			String grsfType, String sourceType,
-			List<TimeSeriesBean<String, String>> catchesOrLandings,
-			List<String> speciesName, List<String> speciesCode) {
+			Boolean traceabilityFlag, Status status, List<Long> reportingYear,
+			List<Long> referenceYear, String grsfType, String sourceType,
+			List<TimeSeriesBean<String, String>> catches,
+			List<TimeSeriesBean<String, String>> landings,
+			List<String> species, List<TimeSeriesBean<String, Void>> faoState) {
 		super();
 		this.dataOwner = dataOwner;
 		this.databaseSources = databaseSources;
@@ -126,11 +139,13 @@ public class Common extends Base{
 		this.traceabilityFlag = traceabilityFlag;
 		this.status = status;
 		this.reportingYear = reportingYear;
+		this.referenceYear = referenceYear;
 		this.grsfType = grsfType;
 		this.sourceType = sourceType;
-		this.catchesOrLandings = catchesOrLandings;
-		this.speciesName = speciesName;
-		this.speciesCode = speciesCode;
+		this.catches = catches;
+		this.landings = landings;
+		this.species = species;
+		this.faoState = faoState;
 	}
 
 	public String getGrsfType() {
@@ -165,11 +180,11 @@ public class Common extends Base{
 		this.refersTo = refersTo;
 	}
 
-	public Long getReportingYear() {
+	public List<Long> getReportingYear() {
 		return reportingYear;
 	}
 
-	public void setReportingYear(Long reportingYear) {
+	public void setReportingYear(List<Long> reportingYear) {
 		this.reportingYear = reportingYear;
 	}
 
@@ -221,30 +236,44 @@ public class Common extends Base{
 		this.status = status;
 	}
 
-
-	public List<TimeSeriesBean<String, String>> getCatchesOrLandings() {
-		return catchesOrLandings;
+	public List<String> getSpecies() {
+		return species;
 	}
 
-	public void setCatchesOrLandings(
-			List<TimeSeriesBean<String, String>> catchesOrLandings) {
-		this.catchesOrLandings = catchesOrLandings;
+	public void setSpecies(List<String> species) {
+		this.species = species;
 	}
 
-	public List<String> getSpeciesName() {
-		return speciesName;
+	public List<TimeSeriesBean<String, String>> getCatches() {
+		return catches;
 	}
 
-	public void setSpeciesName(List<String> speciesName) {
-		this.speciesName = speciesName;
+	public void setCatches(List<TimeSeriesBean<String, String>> catches) {
+		this.catches = catches;
 	}
 
-	public List<String> getSpeciesCode() {
-		return speciesCode;
+	public List<TimeSeriesBean<String, String>> getLandings() {
+		return landings;
 	}
 
-	public void setSpeciesCode(List<String> speciesCode) {
-		this.speciesCode = speciesCode;
+	public void setLandings(List<TimeSeriesBean<String, String>> landings) {
+		this.landings = landings;
+	}
+
+	public List<Long> getReferenceYear() {
+		return referenceYear;
+	}
+
+	public void setReferenceYear(List<Long> referenceYear) {
+		this.referenceYear = referenceYear;
+	}
+
+	public List<TimeSeriesBean<String, Void>> getFaoState() {
+		return faoState;
+	}
+
+	public void setFaoState(List<TimeSeriesBean<String, Void>> faoState) {
+		this.faoState = faoState;
 	}
 
 	@Override
@@ -254,10 +283,10 @@ public class Common extends Base{
 				+ sourceOfInformation + ", refersTo=" + refersTo
 				+ ", shortTitle=" + shortTitle + ", traceabilityFlag="
 				+ traceabilityFlag + ", status=" + status + ", reportingYear="
-				+ reportingYear + ", grsfType=" + grsfType + ", sourceType="
-				+ sourceType + ", catchesOrLandings=" + catchesOrLandings
-				+ ", speciesName=" + speciesName + ", speciesCode="
-				+ speciesCode + "]";
+				+ reportingYear + ", referenceYear=" + referenceYear
+				+ ", grsfType=" + grsfType + ", sourceType=" + sourceType
+				+ ", catches=" + catches + ", landings=" + landings
+				+ ", species=" + species + ", faoState=" + faoState + "]";
 	}
 
 }

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

@@ -34,14 +34,8 @@ public class StockRecord extends Common{
 	@CustomField(key="Stock id")
 	private String stockId;
 
-	//	@JsonProperty("species")
-	//	@CustomField(key="Species")
-	//	@Tag
-	//	private List<String> species;
-
 	@JsonProperty("assessment_distribution_area")
 	@CustomField(key="Assessment distribution area")
-	@Tag
 	private List<String> area;
 
 	@JsonProperty("exploiting_fishery")
@@ -55,7 +49,7 @@ public class StockRecord extends Common{
 
 	@JsonProperty("assessment_methods")
 	@CustomField(key="Assessment methods")
-	private String assessmentMethods;
+	private List<String> assessmentMethods;
 
 	@JsonProperty("state_of_marine_resource")
 	@CustomField(key="State of marine resources")
@@ -99,9 +93,9 @@ public class StockRecord extends Common{
 	@Valid
 	private List<TimeSeriesBean<String, String>> fishingPressure;
 
-	@JsonProperty("narrative_state_and_trend")
-	@CustomField(key="Narrative state and trend")
-	private String narrativeStateAndTrend;
+	@JsonProperty("narrative_state")
+	@CustomField(key="Narrative state")
+	private List<TimeSeriesBean<String, Void>> narrativeState;
 
 	@JsonProperty("scientific_advice")
 	@CustomField(key="Scientific advice")
@@ -123,7 +117,6 @@ public class StockRecord extends Common{
 
 	@JsonProperty("type")
 	@CustomField(key="Type")
-	//@Tag
 	@Group
 	private Stock_Type type;
 
@@ -132,10 +125,8 @@ public class StockRecord extends Common{
 	}
 
 	/**
-	 * Create a Stock element.
 	 * @param stockName
-	 * @param stockID
-	 * @param species
+	 * @param stockId
 	 * @param area
 	 * @param exploitingFishery
 	 * @param managementEntity
@@ -145,10 +136,11 @@ public class StockRecord extends Common{
 	 * @param exploitationRate
 	 * @param abundanceLevelStandard
 	 * @param abundanceLevel
-	 * @param narrativeStateAndTrend
+	 * @param fishingPressureStandard
+	 * @param fishingPressure
+	 * @param narrativeState
 	 * @param scientificAdvice
-	 * @param reportingEntity
-	 * @param reportingYear
+	 * @param assessor
 	 * @param stockUri
 	 * @param waterArea
 	 * @param type
@@ -156,23 +148,23 @@ public class StockRecord extends Common{
 	public StockRecord(
 			String stockName,
 			String stockId,
-			//List<String> species,
 			List<String> area,
 			List<String> exploitingFishery,
 			String managementEntity,
-			String assessmentMethods,
+			List<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 assessor, Long reportingYear, String stockUri,
+			List<TimeSeriesBean<String, Void>> fishingPressureStandard,
+			List<TimeSeriesBean<String, String>> fishingPressure,
+			List<TimeSeriesBean<String, Void>> narrativeState,
+			String scientificAdvice, String assessor, String stockUri,
 			List<String> waterArea, Stock_Type type) {
 		super();
 		this.stockName = stockName;
 		this.stockId = stockId;
-		//this.species = species;
 		this.area = area;
 		this.exploitingFishery = exploitingFishery;
 		this.managementEntity = managementEntity;
@@ -182,7 +174,9 @@ public class StockRecord extends Common{
 		this.exploitationRate = exploitationRate;
 		this.abundanceLevelStandard = abundanceLevelStandard;
 		this.abundanceLevel = abundanceLevel;
-		this.narrativeStateAndTrend = narrativeStateAndTrend;
+		this.fishingPressureStandard = fishingPressureStandard;
+		this.fishingPressure = fishingPressure;
+		this.narrativeState = narrativeState;
 		this.scientificAdvice = scientificAdvice;
 		this.assessor = assessor;
 		this.stockUri = stockUri;
@@ -190,6 +184,10 @@ public class StockRecord extends Common{
 		this.type = type;
 	}
 
+	public void setAssessmentMethods(List<String> assessmentMethods) {
+		this.assessmentMethods = assessmentMethods;
+	}
+
 	public Stock_Type getType() {
 		return type;
 	}
@@ -230,14 +228,6 @@ public class StockRecord extends Common{
 		this.stockId = stockId;
 	}
 
-	//	public List<String> getSpecies() {
-	//		return species;
-	//	}
-	//
-	//	public void setSpecies(List<String> species) {
-	//		this.species = species;
-	//	}
-
 	public List<String> getArea() {
 		return area;
 	}
@@ -280,14 +270,6 @@ public class StockRecord extends Common{
 		this.managementEntity = managementEntity;
 	}
 
-	public String getAssessmentMethods() {
-		return assessmentMethods;
-	}
-
-	public void setAssessmentMethods(String assessmentMethods) {
-		this.assessmentMethods = assessmentMethods;
-	}
-
 	public String getStateOfMarineResource() {
 		return stateOfMarineResource;
 	}
@@ -323,12 +305,12 @@ public class StockRecord extends Common{
 		this.abundanceLevel = abundanceLevel;
 	}
 
-	public String getNarrativeStateAndTrend() {
-		return narrativeStateAndTrend;
+	public List<TimeSeriesBean<String, Void>> getNarrativeState() {
+		return narrativeState;
 	}
 
-	public void setNarrativeStateAndTrend(String narrativeStateAndTrend) {
-		this.narrativeStateAndTrend = narrativeStateAndTrend;
+	public void setNarrativeState(List<TimeSeriesBean<String, Void>> narrativeState) {
+		this.narrativeState = narrativeState;
 	}
 
 	public String getScientificAdvice() {
@@ -368,11 +350,10 @@ public class StockRecord extends Common{
 				+ ", abundanceLevelStandard=" + abundanceLevelStandard
 				+ ", abundanceLevel=" + abundanceLevel
 				+ ", fishingPressureStandard=" + fishingPressureStandard
-				+ ", fishingPressure=" + fishingPressure
-				+ ", narrativeStateAndTrend=" + narrativeStateAndTrend
-				+ ", scientificAdvice=" + scientificAdvice + ", assessor="
-				+ assessor + ", stockUri=" + stockUri + ", waterArea="
-				+ waterArea + ", type=" + type + "]";
+				+ ", fishingPressure=" + fishingPressure + ", narrativeState="
+				+ narrativeState + ", scientificAdvice=" + scientificAdvice
+				+ ", assessor=" + assessor + ", stockUri=" + stockUri
+				+ ", waterArea=" + waterArea + ", type=" + type + "]";
 	}
 
 }

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

@@ -87,10 +87,9 @@ public class CommonServiceUtils {
 		if(record.getClass().equals(StockRecord.class)){
 
 			StockRecord stock = (StockRecord) record;
-			List<String> speciesNames = stock.getSpeciesName();
-			List<String> speciesCodes = stock.getSpeciesCode();
-			if(speciesNames == null || speciesNames.isEmpty() || speciesCodes == null || speciesCodes.isEmpty())
-				throw new Exception("species name/code cannot be null/empty in a GRSF record");
+			List<String> species = stock.getSpecies();
+			if(species == null || species.isEmpty())
+				throw new Exception("species cannot be null/empty in a GRSF record");
 		}
 
 		// check if it is a stock and perform related checks

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

@@ -291,14 +291,14 @@ public class GrsfPublisherFisheryService {
 
 								// write a post if the product has been published in grsf context
 								if(context.equals((String)contextServlet.getInitParameter(HelperMethods.PUBLIC_CONTEX_KEY))){
-									new WritePostCatalogueManagerThread(
+									/*new WritePostCatalogueManagerThread(
 											context, 
 											token, 
 											futureTitle, 
 											itemUrl, 
 											false, 
 											new ArrayList<String>(),  
-											authorFullname).start();
+											authorFullname).start();*/
 
 									logger.info("Thread to write a post about the new product has been launched");
 								}

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

@@ -288,7 +288,7 @@ public class GrsfPublisherStockService {
 
 								// write a post if the product has been published in grsf context
 								if(context.equals((String)contextServlet.getInitParameter(HelperMethods.PUBLIC_CONTEX_KEY))){
-									new WritePostCatalogueManagerThread(
+									/*new WritePostCatalogueManagerThread(
 											context, 
 											token, 
 											futureTitle, 
@@ -296,7 +296,7 @@ public class GrsfPublisherStockService {
 											false, 
 											new ArrayList<String>(), 
 											authorFullname).start();
-									logger.info("Thread to write a post about the new product has been launched");
+									logger.info("Thread to write a post about the new product has been launched");*/
 								}
 
 							}else

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/cache/CacheImpl.java

@@ -17,7 +17,7 @@ public class  CacheImpl <K, V> implements CacheInterface<K, V> {
 	/**
 	 * The hashmap
 	 */
-	private Map<K, CacheValueBean<V>> userSpaceMap;
+	private Map<K, CacheValueBean<V>> cache;
 
 	/**
 	 * Cache entry expires after EXPIRED_AFTER ms
@@ -26,16 +26,16 @@ public class  CacheImpl <K, V> implements CacheInterface<K, V> {
 
 	public CacheImpl(long timeout){
 		ttl = timeout;
-		userSpaceMap = new ConcurrentHashMap<>();
+		cache = new ConcurrentHashMap<>();
 	}
 
 	@Override
 	public V get(K key) {
 
-		if(userSpaceMap.containsKey(key)){
-			CacheValueBean<V> bean = userSpaceMap.get(key);
+		if(cache.containsKey(key)){
+			CacheValueBean<V> bean = cache.get(key);
 			if(CacheUtilities.expired(bean.getTTL(), ttl)){
-				userSpaceMap.remove(key);
+				cache.remove(key);
 				logger.debug("Amount of space in the infrastructure used expired for key " + key + ", returning null");
 			}
 			else 
@@ -47,7 +47,7 @@ public class  CacheImpl <K, V> implements CacheInterface<K, V> {
 	@Override
 	public boolean insert(K key, V obj) {
 		CacheValueBean<V> newBean = new CacheValueBean<V>(obj, System.currentTimeMillis());
-		userSpaceMap.put(key, newBean);
+		cache.put(key, newBean);
 		return true;
 	}
 }

src/main/webapp/WEB-INF/web.xml

@@ -27,16 +27,16 @@
 	<context-param>
 		<description>Context of pending products under manage activities</description>
 		<param-name>ManageVRE</param-name>
-		<param-value>/d4science.research-infrastructures.eu/FARM/GRSF_Admin</param-value>
-		<!-- <param-value>/gcube/devNext/NextNext</param-value> -->
+		<!-- <param-value>/d4science.research-infrastructures.eu/FARM/GRSF_Admin</param-value> -->
+		<param-value>/gcube/devNext/NextNext</param-value>
 		<!-- <param-value>/gcube/preprod/Dorne</param-value> -->
 	</context-param>
 
 	<context-param>
 		<description>Context of products no longer under manage activities</description>
 		<param-name>PublicVRE</param-name>
-		<param-value>/d4science.research-infrastructures.eu/FARM/GRSF</param-value>
-		<!-- <param-value>/gcube/devNext/NextNext</param-value> -->
+		<!-- <param-value>/d4science.research-infrastructures.eu/FARM/GRSF</param-value> -->
+		<param-value>/gcube/devNext/NextNext</param-value>
 		<!-- <param-value>/gcube/preprod/preVRE</param-value> -->
 	</context-param>
 

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

@@ -8,7 +8,6 @@ import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -289,39 +288,6 @@ public class JTests {
 		instance.uploadResourceFile(csvFile, datasetName, instance.getApiKeyFromUsername("costantino.perciante"), "random_name.csv", null);
 	}
 
-	//@Test
-	public void testlist() throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, IntrospectionException{
-
-		FisheryRecord record = new FisheryRecord();
-		ArrayList<TimeSeriesBean<String, String>> list = new ArrayList<TimeSeriesBean<String,String>>();
-		list.add(new TimeSeriesBean<String, String>("as", 65445L, "asd"));
-		record.setCatchesOrLandings(list);
-		Class<?> current = record.getClass();
-		do{
-			Field[] fields = current.getDeclaredFields();
-			for (Field field : fields) {
-				if (Collection.class.isAssignableFrom(field.getType())) {
-					// if the list is not null, get an element
-					Object f = new PropertyDescriptor(field.getName(), current).getReadMethod().invoke(record);
-					if(f != null){
-						List asList = (List)f;
-						if(!asList.isEmpty())
-							if(asList.get(0).getClass().equals(TimeSeriesBean.class)){
-								logger.debug("Name is " + field.getName());
-								CustomField customAnnotation = field.getAnnotation(CustomField.class);
-								if(customAnnotation != null)
-									logger.debug("Name is " + customAnnotation.key());
-
-							}
-					}
-				}
-
-			}
-		}
-		while((current = current.getSuperclass())!=null); // iterate from the inherited class up to the Object.class
-
-	}
-
 	//	@Test
 	public void sharedVREFolderWriteTest() throws Exception{