minor changes to timeseries bean

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/grsf-publisher-ws@151416 82a268e6-3cf1-43bd-a215-b396298e98cf

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

@@ -23,7 +23,6 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 public class Common extends Base{
 
 	public static final String GRSF_DOMAIN_KEY = "GRSF Domain"; // stock, fishery
-	public static final String SOURCE_KEY = "Source"; // in case it is a RAM/FIRMS/FishSource record it is not added
 
 	// it is added in case of GRSF record
 	@JsonProperty("data_owner")
@@ -64,11 +63,6 @@ public class Common extends Base{
 	@CustomField(key=GRSF_DOMAIN_KEY)
 	private String grsfType;
 
-	// automatically compiled
-	@JsonProperty("source")
-	@CustomField(key=SOURCE_KEY)
-	private String sourceType;
-
 	@JsonProperty("catches")
 	@CustomField(key="Catches")
 	@TimeSeries
@@ -102,7 +96,6 @@ public class Common extends Base{
 	 * @param traceabilityFlag
 	 * @param status
 	 * @param grsfType
-	 * @param sourceType
 	 * @param catches
 	 * @param landings
 	 * @param species
@@ -113,7 +106,7 @@ public class Common extends Base{
 			List<Resource<String>> sourceOfInformation,
 			List<RefersToBean> refersTo, String shortTitle,
 			Boolean traceabilityFlag, Status status, String grsfType,
-			String sourceType, List<TimeSeriesBean<String, String>> catches,
+			List<TimeSeriesBean<String, String>> catches,
 			List<TimeSeriesBean<String, String>> landings,
 			List<String> species, List<SimilarRecordBean> similarRecords) {
 		super();
@@ -125,7 +118,6 @@ public class Common extends Base{
 		this.traceabilityFlag = traceabilityFlag;
 		this.status = status;
 		this.grsfType = grsfType;
-		this.sourceType = sourceType;
 		this.catches = catches;
 		this.landings = landings;
 		this.species = species;
@@ -140,14 +132,6 @@ public class Common extends Base{
 		this.grsfType = grsfType;
 	}
 
-	public String getSourceType() {
-		return sourceType;	
-	}
-
-	public void setSourceType(String sourceType) {
-		this.sourceType = sourceType;
-	}
-
 	public Boolean getTraceabilityFlag() {
 		return traceabilityFlag;
 	}
@@ -246,9 +230,9 @@ public class Common extends Base{
 				+ sourceOfInformation + ", refersTo=" + refersTo
 				+ ", shortTitle=" + shortTitle + ", traceabilityFlag="
 				+ traceabilityFlag + ", status=" + status + ", grsfType="
-				+ grsfType + ", sourceType=" + sourceType + ", catches="
-				+ catches + ", landings=" + landings + ", species=" + species
-				+ ", similarRecords=" + similarRecords + "]";
+				+ grsfType + ", catches=" + catches + ", landings=" + landings
+				+ ", species=" + species + ", similarRecords=" + similarRecords
+				+ "]";
 	}
 
 }

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

@@ -15,14 +15,14 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 @JsonIgnoreProperties(ignoreUnknown = true)
 public class TimeSeriesBean<T, T1> implements Comparable<TimeSeriesBean<T, T1>>{
 
-	public static final String YEAR_FIELD = "year";
+	public static final String YEAR_FIELD = "reference_year";
 	public static final String VALUE_FIELD = "value";
 	public static final String UNIT_FIELD = "unit";
 	public static final String SOURCE_FIELD = "source";
-	public static final String ASSESSMENT_FIELD = "assessment";
+	public static final String ASSESSMENT_FIELD = "reporting_year_or_assessment";
 
 	@JsonProperty(YEAR_FIELD)
-	@NotNull(message="year of a time series cannot be null")
+	@NotNull(message="reference_year of a time series cannot be null")
 	private Long year;
 
 	@JsonProperty(SOURCE_FIELD)
@@ -122,12 +122,13 @@ public class TimeSeriesBean<T, T1> implements Comparable<TimeSeriesBean<T, T1>>{
 	@Override
 	public String toString() {
 
-		String firstPart = "" + year;
-		String secondPart = (value != null ? " - " + value : "")
-				+ (unit != null ? " - " + unit : "") 
-				+ (source != null ? " (" + source + ")" : "")
-				+ (assessment != null ? " (Ref. year " + assessment + ")" : "");
-		return firstPart + (secondPart != null && !secondPart.isEmpty() ? secondPart : "");
+		String value = "" + this.value;
+		String unit = (this.unit != null ? " " + this.unit : "");
+		String source = (this.source != null ? " (" + this.source + ")" : "");
+		String referenceYear =  " Ref. Year " + year;
+		String reportingYearOrAssessment = (assessment != null ? " and Rep. Year or Assessment " + assessment + "" : "");
+
+		return value + unit + source + referenceYear + reportingYearOrAssessment;
 
 	}
 

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

@@ -4,6 +4,7 @@ import java.beans.PropertyDescriptor;
 import java.lang.reflect.Field;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -113,8 +114,6 @@ public class CommonServiceUtils {
 			if((fishingArea == null || fishingArea.isEmpty()) && (jurisdictionArea == null || jurisdictionArea.isEmpty()))
 				throw new Exception("fishing_area and jurisdiction_area cannot be null/empty at the same time!");
 		}
-
-
 	}
 
 	/**
@@ -261,9 +260,7 @@ public class CommonServiceUtils {
 				logger.error("Failed to read value for field " + field.getName() + " skipping", e);
 			}
 		}
-
-		// add the record among the source group (check for grsf-group)
-		//groups.add(source.equals(Sources.GRSF) ? CommonServiceUtils.GRSF_GROUP_NAME : source.getOrigName().toLowerCase());
+		
 	}
 
 	/**
@@ -363,14 +360,6 @@ public class CommonServiceUtils {
 	public static void hasAdminRole(String username, DataCatalogue catalogue, String apiKey, String organization) throws Exception{
 
 		String role = catalogue.getRoleOfUserInOrganization(username, organization, apiKey);
-		//		Iterator<Entry<CkanOrganization, RolesCkanGroupOrOrg>> roles = catalogue.getUserRoleByOrganization(username, apiKey).get(organization).entrySet().iterator();
-		//
-		//		while (roles.hasNext()) {
-		//			Map.Entry<CkanOrganization, RolesCkanGroupOrOrg> entry = (Map.Entry<CkanOrganization, RolesCkanGroupOrOrg>) roles
-		//					.next();
-		//			role = RolesCkanGroupOrOrg.convertToCkanCapacity(entry.getValue());
-		//		}
-
 		logger.info("Role of the user " + username + " is " + role + " in " + organization);
 
 		if(role == null || role.isEmpty() || !role.equalsIgnoreCase(RolesCkanGroupOrOrg.ADMIN.toString()))
@@ -403,7 +392,6 @@ public class CommonServiceUtils {
 
 	/**
 	 * Validate and check sources
-	 * @author Costantino Perciante at ISTI-CNR (costantino.perciante@isti.cnr.it)
 	 * @param apiKey
 	 * @param context
 	 * @param contextServlet
@@ -425,19 +413,28 @@ public class CommonServiceUtils {
 		// Status field is needed only in the Manage context for GRSF records
 		if(context.equals((String)contextServlet.getInitParameter(HelperMethods.MANAGE_CONTEX_KEY))){
 			if(sourceInPath.equals(Sources.GRSF)){
-				//Evaluate the sources
-				List<Resource<Sources>> recordSources = record.getDatabaseSources();
-				String sources = "";
-				for (Resource<Sources> resource : recordSources) {
-					sources += resource.getName() + ", ";
+
+				List<RefersToBean> refersTo = record.getRefersTo();
+				if(refersTo == null || refersTo.isEmpty())
+					throw new Exception("refers_to is empty for a GRSF record");
+
+				List<String> sourcesList = new ArrayList<String>();
+
+				// we have the id within the catalog of this record. This means that we can retrieve the record and its system:type
+				for (RefersToBean refersToBean : refersTo) {
+					String sourceSysType = getSystemTypeValue(refersToBean.getId(), apiKey, context);
+					resources.add(new ResourceBean(refersToBean.getUrl(), sourceSysType , "The source record has id " + refersToBean.getId() + " in the catalog", null, username, null, null));
+					sourcesList.add(sourceSysType.toLowerCase());
 				}
-				sources = sources.endsWith(", ") ? sources.substring(0, sources.length() -2) : sources;
-				record.setSourceType(sources);
+
+				// append to groups: we need to add this record to the correspondent group of the sources
+				addRecordToGroupSources(groups, sourcesList, productType, sourceInPath);
+
+				// validate
 				CommonServiceUtils.validateAggregatedRecord(record);
 			}
 		}
 
-
 		// set the grsf type: fishery or stock
 		record.setGrsfType(productType.getOrigName());
 
@@ -446,22 +443,29 @@ public class CommonServiceUtils {
 		boolean skipTags = !sourceInPath.equals(Sources.GRSF); // no tags for the Original records
 		CommonServiceUtils.getTagsGroupsResourcesExtrasByRecord(tags, skipTags, groups, false, resources, false, customFields, record, username, sourceInPath);
 
-		// manage the refers to
-		if(sourceInPath.equals(Sources.GRSF)){
-			List<RefersToBean> refersTo = record.getRefersTo();
-			if(refersTo == null || refersTo.isEmpty())
-				throw new Exception("refers_to is empty for a GRSF record");
-
-			// we have the id within the catalog of this record. This means that we can retrieve the record and its system:type
-			for (RefersToBean refersToBean : refersTo) {
-				resources.add(new ResourceBean(refersToBean.getUrl(), getSystemTypeValue(refersToBean.getId(), apiKey, context) , "The source record has id " + refersToBean.getId() + " in the catalog", null, username, null, null));
-			}
-		}
-
 		// add the SYSTEM_TYPE
 		customFields.put(CommonServiceUtils.SYSTEM_TYPE, Arrays.asList(sourceInPath.getOrigName()));
 	}
 
+	/**
+	 * Add the record to the group of sources
+	 * @param groups
+	 * @param sourcesList
+	 * @param productType
+	 * @param sourceInPath 
+	 */
+	private static void addRecordToGroupSources(Set<String> groups,
+			List<String> sourcesList, Product_Type productType, Sources sourceInPath) {
+
+		Collections.sort(sourcesList); // be sure the name are sorted because the groups have been generated this way
+		String groupName = sourceInPath.getOrigName().toLowerCase() + "-" + productType.getOrigName().toLowerCase();
+		for (String source : sourcesList) {
+			groupName += "-" + source;
+		}
+
+		groups.add(groupName);
+	}
+
 	/**
 	 * Fetch the system:type property from a record
 	 * @param itemIdOrName

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

@@ -14,7 +14,8 @@ public enum Abundance_Level {
 	Uncertain_Not_Assessed("Uncertain/Not assessed"),
 	Not_applicable("Not applicable"),
 	Pre_exploitation_Or_High_Abundance("Pre-exploitation biomass or high abundance"),
-	Depleted("Depleted");
+	Depleted("Depleted"),
+	Virgin_Or_High_Abundance("Virgin or High abundance");
 
 	private String subGroupNameOrig;
 
@@ -39,7 +40,7 @@ public enum Abundance_Level {
 	public static Abundance_Level onDeserialize(String abundanceString) {
 		if(abundanceString != null) {
 			for (Abundance_Level abundanceValue : Abundance_Level.values()) {
-				if(abundanceValue.getOrigName().replaceAll("[^A-Za-z]", " ").equalsIgnoreCase(abundanceString.replaceAll("[^A-Za-z]", " ")))
+				if(abundanceValue.getOrigName().replaceAll("[^A-Za-z]", " ").equalsIgnoreCase(abundanceString.trim().replaceAll("[^A-Za-z]", " ")))
 					return abundanceValue;
 			}
 		}

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

@@ -32,7 +32,7 @@ public enum Exploitation_Rate {
 	public static Exploitation_Rate onDeserialize(String exploitationString) {
 		if(exploitationString != null) {
 			for (Exploitation_Rate exploitationValue : Exploitation_Rate.values()) {
-				if(exploitationValue.getOrigName().replaceAll("[^A-Za-z]", " ").equalsIgnoreCase(exploitationString.replaceAll("[^A-Za-z]", " ")))
+				if(exploitationValue.getOrigName().replaceAll("[^A-Za-z]", " ").equalsIgnoreCase(exploitationString.trim().replaceAll("[^A-Za-z]", " ")))
 					return exploitationValue;
 			}
 		}

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

@@ -33,7 +33,7 @@ public enum Fishing_Pressure {
 	public static Fishing_Pressure onDeserialize(String fishing_Pressure) {
 		if(fishing_Pressure != null) {
 			for (Fishing_Pressure fishingPressure : Fishing_Pressure.values()) {
-				if(fishingPressure.getOrigName().replaceAll("[^A-Za-z]", " ").equalsIgnoreCase(fishing_Pressure.replaceAll("[^A-Za-z]", " ")))
+				if(fishingPressure.getOrigName().replaceAll("[^A-Za-z]", " ").equalsIgnoreCase(fishing_Pressure.trim().replaceAll("[^A-Za-z]", " ")))
 					return fishingPressure;
 			}
 		}

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

@@ -41,7 +41,7 @@ public enum Production_System_Type {
 	public static Production_System_Type onDeserialize(String productionString) {
 		if(productionString != null) {
 			for (Production_System_Type productionValue : Production_System_Type.values()) {
-				if(productionValue.getOrigName().replaceAll("[^A-Za-z]", " ").equalsIgnoreCase(productionString.replaceAll("[^A-Za-z]", " ")))
+				if(productionValue.getOrigName().replaceAll("[^A-Za-z]", " ").equalsIgnoreCase(productionString.trim().replaceAll("[^A-Za-z]", " ")))
 					return productionValue;
 			}
 		}