15 changed files with 88 additions and 255 deletions
--- a/.gitignore
+++ b/.gitignore
@ -1,4 +1,3 @@
 target
 .classpath
 .project
-/.DS_Store
--- a/.settings/org.eclipse.core.resources.prefs
+++ b/.settings/org.eclipse.core.resources.prefs
@ -1,6 +1,4 @@
 eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
-encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
-encoding//src/test/resources=UTF-8
 encoding/<project>=UTF-8
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@ -3,24 +3,9 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

-## [v1.13.3]
-
- Adding support for "FAO SDG 14.4.1 Questionnaire" source [#23670] 
-
-
-## [v1.13.2]
-
- Migrated request to social-service-client [#23679]
- Added "Assessment Methods" as Group [#23409]
-
-
-## [v1.13.1]
+## [v1.13.1-SNAPSHOT]

 - Aligned code and wiki to the new requirements [#23167]
- Changed group assign strategy [#23211] [#23215]
- Tag are added also to legacy records [#23216]
- Fixed code which generated groups id from name [#23215]
-

 ## [v1.13.0]

--- a/pom.xml
+++ b/pom.xml
@ -11,7 +11,7 @@

 	<groupId>org.gcube.data-catalogue</groupId>
 	<artifactId>grsf-publisher-ws</artifactId>
-	<version>1.13.3</version>
+	<version>1.13.1-SNAPSHOT</version>
 	<packaging>war</packaging>
 	<name>grsf-publisher-ws</name>
 	<description>Utility library to publish GRSF products on GRSF catalogue.</description>
@ -26,7 +26,6 @@
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<jsoup.version>1.10.1</jsoup.version>
 		<serviceClass>DataPublishing</serviceClass>
-		<maven.compiler.release>8</maven.compiler.release>
 	</properties>

 	<scm>
@ -40,7 +39,7 @@
 			<dependency>
 				<groupId>org.gcube.distribution</groupId>
 				<artifactId>gcube-smartgears-bom</artifactId>
-				<version>2.2.0</version>
+				<version>2.1.1</version>
 				<type>pom</type>
 				<scope>import</scope>
 			</dependency>
@ -51,17 +50,12 @@
 		<dependency>
 			<groupId>org.gcube.data-catalogue</groupId>
 			<artifactId>grsf-common-library</artifactId>
-			<version>[2.0.0, 3.0.0-SNAPSHOT)</version>
+			<version>[1-0-0, 2.0.0-SNAPSHOT)</version>
 		</dependency>
 		<dependency>
 			<groupId>org.gcube.common</groupId>
 			<artifactId>storagehub-client-library</artifactId>
 		</dependency>
-		<dependency>
- 			<groupId>org.gcube.social-networking</groupId>
-    		<artifactId>social-service-client</artifactId>
-			<version>[1.0.0, 2.0.0-SNAPSHOT)</version>
-		</dependency>
 		<!-- jsoup HTML parser library @ http://jsoup.org/ -->
 		<dependency>
 			<groupId>org.jsoup</groupId>
@ -168,14 +162,6 @@
 			<artifactId>jersey-test-framework-provider-jetty</artifactId>
 			<scope>test</scope>
 		</dependency>
-		
-		<!-- Added to support Java 11 JDK -->
-		<dependency>
-			<groupId>org.projectlombok</groupId>
-			<artifactId>lombok</artifactId>
-			<scope>provided</scope>
-		</dependency>
-		<!-- END Added to support Java 11 JDK -->
 	</dependencies>

 	<build>
--- a/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/record/StockRecord.java
+++ b/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/record/StockRecord.java
@ -46,7 +46,6 @@ public class StockRecord extends Common{

 	@JsonProperty(Constants.ASSESSMENT_METHODS_JSON_KEY)
 	@CustomField(key=Constants.ASSESSMENT_METHODS_CUSTOM_KEY)
-	@Group(groupNameOverValue=Constants.ASSESSMENT_METHODS_CUSTOM_KEY, prependSourceToGroupName=false)
 	private List<String> assessmentMethods;

 	@JsonProperty(Constants.FIRMS_ABUNDANCE_LEVEL_JSON_KEY)
--- a/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherFisheryService.java
+++ b/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherFisheryService.java
@ -51,7 +51,7 @@ import eu.trentorise.opendata.jackan.model.CkanDataset;
 * @author Costantino Perciante (ISTI - CNR)
 * @author Luca Frosini (ISTI - CNR)
 */
-@Path("{source:firms|FIRMS|grsf|GRSF|FishSource|fishsource|sdg|SDG}/fishery/")
+@Path("{source:firms|FIRMS|grsf|GRSF|FishSource|fishsource}/fishery/")
 public class GrsfPublisherFisheryService {
 	
 	// the context
@ -257,7 +257,7 @@ public class GrsfPublisherFisheryService {
 			String type = fisheryInCkan.getExtrasAsHashMap().get(Constants.DOMAIN_CUSTOM_KEY);
 			
 			if((fisheryInCkan.getOrganization().getName().equalsIgnoreCase(source)
-					|| fisheryInCkan.getOrganization().getName().toLowerCase().startsWith(source.toLowerCase()))
+					|| fisheryInCkan.getOrganization().getName().toLowerCase().contains(source))
 					&& Product_Type.FISHERY.getOrigName().equals(type)) {
 				
 				logger.debug("Ok, this is a fishery of the right source, removing it");
--- a/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherStockService.java
+++ b/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherStockService.java
@ -51,7 +51,7 @@ import eu.trentorise.opendata.jackan.model.CkanDataset;
 * @author Costantino Perciante (ISTI - CNR)
 * @author Luca Frosini (ISTI - CNR)
 */
-@Path("{source:firms|FIRMS|ram|RAM|grsf|GRSF|FishSource|fishsource|sdg|SDG}/stock/")
+@Path("{source:firms|FIRMS|ram|RAM|grsf|GRSF|FishSource|fishsource}/stock/")
 public class GrsfPublisherStockService {
 	
 	// the context
@ -260,7 +260,7 @@ public class GrsfPublisherStockService {
 			// check it is in the right source and it is a stock
 			String type = stockInCkan.getExtrasAsHashMap().get(Constants.DOMAIN_CUSTOM_KEY);
 			if((stockInCkan.getOrganization().getName().equalsIgnoreCase(source)
-					|| stockInCkan.getOrganization().getName().toLowerCase().startsWith(source.toLowerCase()))
+					|| stockInCkan.getOrganization().getName().toLowerCase().contains(source))
 					&& Product_Type.STOCK.getOrigName().equals(type)) {
 				
 				logger.debug("Ok, this is a stock of the right type, removing it");
--- a/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/CommonServiceUtils.java
+++ b/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/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;
@ -217,43 +218,6 @@ public class CommonServiceUtils {
 		}
 	}
 	
-	public static final String GROUP_SUFFIX = "-group";
-	
-	/**
-	 * Convert a group name to its id on ckan
-	 * @param origName
-	 * @return
-	 */
-	private static String getGroupIDOnCkan(String origName){
-		if(origName == null) {
-			throw new IllegalArgumentException("origName cannot be null");
-		}
-		String modified = origName.replaceAll("\\(", "");
-		modified = modified.replaceAll("\\)", "");
-		modified = modified.trim().toLowerCase().replaceAll("[^A-Za-z0-9-]", "-");
-		if(modified.startsWith("-")) {
-			modified = modified.substring(1);
-		}
-		if(modified.endsWith("-")) {
-			modified = modified.substring(0, modified.length() -1);
-		}
-		return modified;
-	}
-	
-	public static String getGroupId(String groupName) {
-		StringBuffer stringBuffer = new StringBuffer();
-		stringBuffer.append(groupName);
-		/*
-		 * The "_group" suffix is added to all groups to
-		 * avoid issues on groups and organizations having the same name
-		 * e.g. RAM organization (id=ram) and RAM group (id=ram_group)  
-		 */
-		if(!groupName.endsWith(GROUP_SUFFIX)) {
-			stringBuffer.append(GROUP_SUFFIX);
-		}
-		return getGroupIDOnCkan(stringBuffer.toString());
-	}
-	
 	private static void addGroup(Group group, Sources source, String value, Set<String> groups) {
 		String conditionToCheck = group.condition();
 		String groupNameOverValue = group.groupNameOverValue();
@ -263,44 +227,27 @@ public class CommonServiceUtils {
 				: value.matches(conditionToCheck);
 		
 		if(match) {
+		
 			StringBuffer stringBuffer = new StringBuffer();
+			
 			if(prependSource) {
-				stringBuffer.append(source.getURLPath());
+				stringBuffer.append(source.toString());
 				stringBuffer.append(" ");
 			}
+			
 			if(groupNameOverValue.isEmpty()) {
 				stringBuffer.append(value);
 			}else {
 				stringBuffer.append(groupNameOverValue);
 			}
-			String groupId = getGroupId(stringBuffer.toString());
-			groups.add(groupId);			
+			
+			String groupName = HelperMethods.getGroupNameOnCkan(stringBuffer.toString());
+							
+			groups.add(groupName);			
 		}
 		
 	}
 	
-	/**
-	 * Add the record to the group of sources
-	 * @param groups
-	 * @param sourcesList
-	 * @param productType
-	 * @param sourceInPath 
-	 */
-	private static void addRecordToGroups(Set<String> groups, Set<String> sourcesList,  Product_Type productType, Sources sourceInPath) {
-		if(sourceInPath == Sources.GRSF) {
-			groups.add(getGroupId(Sources.GRSF.getURLPath())); // i.e. grsf_group
-		}else {
-			groups.add(getGroupId(Constants.SYSTEM_TYPE_LEGACY_RECORD)); // i.e. legacy_group
-		}
-		
-		// evaluate the custom fields/tags, resources and groups
-		groups.add(getGroupId(productType.getOrigName())); //i.e. stock_group or fishery_group
-		
-		for(String source : sourcesList) {
-			groups.add(getGroupId(source)); // i.e. firms_group, fishsource_group, ram_group
-		}
-	}
-	
 	/**
 	 * Retrieve the list of groups' names for this object
 	 */
@ -542,7 +489,7 @@ public class CommonServiceUtils {
 			if(databaseSources!=null) {
 				for(Resource<Sources> source : databaseSources) {
 					Sources sourceName = source.getName();
-					sourcesList.add(sourceName.getURLPath());
+					sourcesList.add(sourceName.getOrigName().toLowerCase());
 				}
 			}
 		}
@ -575,6 +522,28 @@ public class CommonServiceUtils {
 		
 	}
 	
+	/**
+	 * Add the record to the group of sources
+	 * @param groups
+	 * @param sourcesList
+	 * @param productType
+	 * @param sourceInPath 
+	 */
+	private static void addRecordToGroups(Set<String> groups, Set<String> sourcesList,  Product_Type productType, Sources sourceInPath) {
+		if(sourceInPath == Sources.GRSF) {
+			groups.add(HelperMethods.getGroupNameOnCkan(Sources.GRSF.getOrigName())); // i.e. grsf
+		}else {
+			groups.add(HelperMethods.getGroupNameOnCkan(Constants.SYSTEM_TYPE_LEGACY_RECORD)); // i.e. legacy
+		}
+		
+		// evaluate the custom fields/tags, resources and groups
+		groups.add(HelperMethods.getGroupNameOnCkan(productType.getOrigName())); //i.e. stock or fishery
+		
+		for(String source : sourcesList) {
+			groups.add(HelperMethods.getGroupNameOnCkan(source)); // i.e. FIRMS, FishSource, RAM
+		}
+	}
+	
 //	/**
 //	 * Fetch the system:type property from a record
 //	 * @param itemIdOrName
@ -718,6 +687,6 @@ public class CommonServiceUtils {
 				return Constants.GRSF_PRE_ORGANIZATION_NAME;
 			}
 		}else
-			return sourceInPath.getURLPath();
+			return sourceInPath.getOrigName().toLowerCase();
 	}
 }
--- a/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/HelperMethods.java
+++ b/src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/HelperMethods.java
@ -31,7 +31,6 @@ import org.gcube.datacatalogue.common.caches.CacheInterface;
 import org.gcube.resources.discovery.client.api.DiscoveryClient;
 import org.gcube.resources.discovery.client.queries.api.Query;
 import org.gcube.resources.discovery.client.queries.impl.QueryBox;
-import org.gcube.social_networking.social_networking_client_library.UserClient;
 import org.jsoup.Jsoup;
 import org.jsoup.safety.Whitelist;
 import org.slf4j.LoggerFactory;
@ -81,6 +80,29 @@ public abstract class HelperMethods {
 	private static CacheInterface<String, Map<String, String>> namespacesCache = new CacheImpl<String, Map<String, String>>(1000 * 60 * 60 * 24);
 	private static CacheInterface<String, DataCatalogue> catalogueCache = new CacheImpl<String, DataCatalogue>(1000 * 60 * 60 * 24);

+	/**
+	 * Convert a group name to its id on ckan
+	 * @param origName
+	 * @return
+	 */
+	public static String getGroupNameOnCkan(String origName){
+
+		if(origName == null)
+			throw new IllegalArgumentException("origName cannot be null");
+
+		String modified = origName.replaceAll("\\(", "");
+		modified = origName.replaceAll("\\)", "");
+		modified = origName.trim().toLowerCase().replaceAll("[^A-Za-z0-9-]", "-");
+		if(modified.startsWith("-"))
+			modified = modified.substring(1);
+		if(modified.endsWith("-"))
+			modified = modified.substring(0, modified.length() -1);
+
+		logger.info("Group name generated is " + modified);
+
+		return modified;
+	}
+
 	/**
 	 * Retrieve the running instance of the data catalogue for this scope
 	 * @return
@ -135,18 +157,21 @@ public abstract class HelperMethods {
 	 * @return
 	 * @throws Exception 
 	 */
-	public static String getUserEmail(String context, String token) throws Exception{
+	public static String getUserEmail(String context, String token){

 		// check in cache
-		String email = null;
-		if((email = (String) userEmailCache.get(token)) != null){
-			return email;
+		String result = null;
+		if((result = (String) userEmailCache.get(token)) != null){
+			return result;
 		}else{
-			UserClient userClient = new UserClient();
-			email = userClient.getEmail();
-			userEmailCache.insert(token, email);
+			String baseUrl = new GcoreEndPointReaderSocial(context).getBasePath();
+			String url = baseUrl.endsWith("/") ?  baseUrl + "users/getUserEmail?gcube-token=" + token :
+				baseUrl + "/users/getUserEmail?gcube-token=" + token;
+			logger.debug("Request url is " + url);
+			result = executGETHttpRequest(url, 200);
+			userEmailCache.insert(token, result);
 		}
-		return email;
+		return result;
 	}

 	/**
@ -156,18 +181,21 @@ public abstract class HelperMethods {
 	 * @return
 	 * @throws Exception 
 	 */
-	public static String getUserFullname(String context, String token) throws Exception{
+	public static String getUserFullname(String context, String token){

 		// check in cache
-		String fullName = null;
-		if((fullName = (String) userFullnameCache.get(token)) != null){
-			return fullName;
+		String result = null;
+		if((result = (String) userFullnameCache.get(token)) != null){
+			return result;
 		}else{
-			UserClient userClient = new UserClient();
-			fullName = userClient.getFullName();
-			userFullnameCache.insert(token, fullName);
+			String baseUrl = new GcoreEndPointReaderSocial(context).getBasePath();
+			String url = baseUrl.endsWith("/") ?  baseUrl + "users/getUserFullname?gcube-token=" + token :
+				baseUrl + "/users/getUserFullname?gcube-token=" + token;
+			logger.debug("Request url is " + url);
+			result = executGETHttpRequest(url, 200);
+			userFullnameCache.insert(token, result);
 		}
-		return fullName;
+		return result;
 	}

 	/**
--- a/src/main/resources/GRSF
+++ b/src/main/resources/GRSF
@ -70,7 +70,7 @@
 				</field>				
 				<field>
 					<originalKey>Assessment Method</originalKey>
-					<modifiedKey>none:none</modifiedKey>
+					<modifiedKey>stock_data:Assessment Method</modifiedKey>
 				</field>
 				<field>
 					<originalKey>Abundance Level (FIRMS Standard)</originalKey>
--- a/src/main/resources/GRSFManageEntries.xml
+++ b/src/main/resources/GRSFManageEntries.xml
@ -1,40 +0,0 @@
-<Resource version="0.4.x">
-    
-   <ID>7ee9c6e9-ff73-4428-88e4-185aeb4b3742</ID>
-    
-   <Type>GenericResource</Type>
-    
-   <Scopes>
-        
-      <Scope>/d4science.research-infrastructures.eu/FARM/GRSF_Pre</Scope>
-        
-      <Scope>/d4science.research-infrastructures.eu/FARM/GRSF_Admin</Scope>
-    
-   </Scopes>
-    
-   <Profile>
-        
-      <SecondaryType>ApplicationProfile</SecondaryType>
-        
-      <Name>GRSFManageEntries</Name>
-        
-      <Description>A list of extras metadata to be looked up and prompted by the GRSF Manage widget. The body reports the key values.</Description>
-        
-      <Body>
-      	fishery_identity:GRSF Type, 
-      	fishery_identity:Short Name, 
-      	fishery_identity:Database Source, 
-      	fishery_identity:GRSF Semantic Identifier, 
-      	fishery_data:Catch,
-      	fishery_data:Landing,
-      	stock_identity:GRSF Type,
-      	stock_identity:Short Name,
-      	stock_identity:Database Source,
-      	stock_identity:GRSF Semantic Identifier,
-      	stock_data:Catch,
-      	stock_data:Landing
-      </Body>
-      
-   </Profile>
-
-</Resource>
--- a/src/test/java/org/gcube/data_catalogue/grsf_publish_ws/JTests.java
+++ b/src/test/java/org/gcube/data_catalogue/grsf_publish_ws/JTests.java
@ -270,7 +270,7 @@ public class JTests {
 	}
 	
 	//@Test
-	public void testCaches() throws Exception{
+	public void testCaches(){
 		
 		String context = "/gcube/devNext/NextNext";
 		String token = "";
--- a/src/test/java/org/gcube/data_catalogue/grsf_publish_ws/TestJson.java
+++ b/src/test/java/org/gcube/data_catalogue/grsf_publish_ws/TestJson.java
@ -1,38 +0,0 @@
-package org.gcube.data_catalogue.grsf_publish_ws;
-
-import java.io.File;
-import java.net.URL;
-
-import org.gcube.data_catalogue.grsf_publish_ws.json.input.record.StockRecord;
-import org.junit.Test;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-/**
- * @author Luca Frosini (ISTI - CNR)
- */
-public class TestJson {
-	
-	private static final Logger logger = LoggerFactory.getLogger(Test.class);
-	
-	public File getResourcesDirectory() throws Exception {
-		URL logbackFileURL = TestJson.class.getClassLoader().getResource("logback-test.xml");
-		File logbackFile = new File(logbackFileURL.toURI());
-		File resourcesDirectory = logbackFile.getParentFile();
-		return resourcesDirectory;
-	}
-	
-	@Test
-	public void testJsonDeserialization() throws Exception {
-		File jsonQueryFile = new File(getResourcesDirectory(), "70ae6895-7d3d-4f4a-86f9-bcb17d41bff6.json");
-		ObjectMapper objectMapper = new ObjectMapper();
-		JsonNode jsonNode = objectMapper.readTree(jsonQueryFile);
-		logger.debug("{}", jsonNode);
-		StockRecord sr = objectMapper.readValue(jsonQueryFile, StockRecord.class);
-		logger.debug("{}", sr);
-	}
-	
-}
--- a/src/test/resources/70ae6895-7d3d-4f4a-86f9-bcb17d41bff6.json
+++ b/src/test/resources/70ae6895-7d3d-4f4a-86f9-bcb17d41bff6.json
@ -1,34 +0,0 @@
-{
-  "stock_name" : "European hake - Southern Adriatic",
-  "license_id" : "CC-BY-SA-4.0",
-  "version" : 1.0,
-  "database_sources" : [ {
-    "name" : "FAO SDG 14.4.1 questionnaire",
-    "description" : "FAO SDG 14.4.1 questionnaire",
-    "url" : "https://www.fao.org/sustainable-development-goals/indicators/14.4.1/en/"
-  } ],
-  "stock_uri" : "https://github.com/grsf/resource/sdg_14_4_1/stock/70ae6895-7d3d-4f4a-86f9-bcb17d41bff6",
-  "grsf_uuid" : "70ae6895-7d3d-4f4a-86f9-bcb17d41bff6",
-  "short_name" : "European hake - Southern Adriatic",
-  "description" : "European hake - Southern Adriatic",
-  "grsf_type" : "assessment unit",
-  "species" : [ "Code: HKE, Classification System: ASFIS, Scientific Name: Merluccius merluccius" ],
-  "assessment_area" : [ "Code: 18, System: gfcm, Name: Southern Adriatic " ],
-  "source_of_information" : [ {
-    "name" : "https://www.fao.org/sustainable-development-goals/indicators/14.4.1/en/sdg-alb-1",
-    "description" : "",
-    "url" : "https://www.fao.org/sustainable-development-goals/indicators/14.4.1/en/sdg-alb-1"
-  } ],
-  "data_owner" : [ "Albania" ],
-  "assessment_methods" : [ "The official stock assessment concludes 'Overfished' with respect to abundance reference points. [Rep. Year or Assessment ID: 2019, Ref. Year: 2018]" ],
-  "connections_indicator" : "not connected",
-  "similarities_indicator" : "without similar records",
-  "landings" : [ {
-    "value" : "872",
-    "unit" : "Tonnes",
-    "reference_year" : 2018,
-    "reporting_year_or_assessment_id" : "2020",
-    "data_owner" : "Albania"
-  } ],
-  "citation" : "citation TBD"
-}
--- a/src/test/resources/logback-test.xml
+++ b/src/test/resources/logback-test.xml
@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE xml>
-<configuration>
-
-  <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-   <encoder>
-      <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{0}: %msg%n</pattern>
-    </encoder>
-  </appender>
-  
-  
-  <logger name="org.gcube" level="INFO" />
-  <logger name="org.gcube.data_catalogue.grsf_publish_ws" level="TRACE" />
-
-  <root level="WARN">
-    <appender-ref ref="STDOUT" />
-  </root>
-  
-</configuration>