fix hibernate, dependencies, empty query

apps/dnet-orgs-database-application/pom.xml

@@ -33,8 +33,7 @@
 		</dependency>
 		<dependency>
 			<groupId>org.thymeleaf.extras</groupId>
-			<artifactId>thymeleaf-extras-springsecurity4</artifactId>
-			<version>3.0.4.RELEASE</version>
+			<artifactId>thymeleaf-extras-springsecurity5</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.postgresql</groupId>
@@ -43,7 +42,7 @@
 		<dependency>
 			<groupId>com.vladmihalcea</groupId>
 			<artifactId>hibernate-types-52</artifactId>
-			<version>2.3.5</version>
+			<version>2.9.13</version>
 		</dependency>
 
 		<!-- JAXB API, java.xml.bind module -->

apps/dnet-orgs-database-application/src/main/java/eu/dnetlib/organizations/MainApplication.java

@@ -30,17 +30,19 @@ public class MainApplication {
 		log.info("Initializing SWAGGER...");
 
 		return new Docket(DocumentationType.SWAGGER_2)
-				.select()
-				.apis(RequestHandlerSelectors.any())
-				.paths(p -> p.startsWith("/api/"))
-				.build().apiInfo(new ApiInfoBuilder()
-						.title("D-Net Organizations Service APIs")
-						.description("APIs documentation")
-						.version("1.1")
-						.contact(ApiInfo.DEFAULT_CONTACT)
-						.license("Apache 2.0")
-						.licenseUrl("http://www.apache.org/licenses/LICENSE-2.0")
-						.build());
+			.select()
+			.apis(RequestHandlerSelectors.any())
+			.paths(p -> p.startsWith("/api/"))
+			.build()
+			.apiInfo(new ApiInfoBuilder()
+				.title("D-Net Organizations Service APIs")
+				.description("APIs documentation")
+				.version("1.1")
+				.contact(ApiInfo.DEFAULT_CONTACT)
+				.license("Apache 2.0")
+				.licenseUrl("http://www.apache.org/licenses/LICENSE-2.0")
+				.build());
 
 	}
+
 }

apps/dnet-orgs-database-application/src/main/java/eu/dnetlib/organizations/controller/OrganizationController.java

@@ -73,6 +73,7 @@ public class OrganizationController {
 
 	@RequestMapping(value = "/save", method = RequestMethod.POST)
 	public List<String> save(@RequestBody final OrganizationView org, final Authentication authentication) {
+
 		if (StringUtils.isBlank(org.getName())) {
 			throw new RuntimeException("Missing field: name");
 		} else if (StringUtils.isBlank(org.getCountry())) {
@@ -100,11 +101,11 @@ public class OrganizationController {
 			suggestionInfoViewByCountryRepository.findAll().forEach(info::add);
 		} else if (UserInfo.isSimpleUser(authentication) || UserInfo.isNationalAdmin(authentication)) {
 			userCountryRepository.getCountriesForUser(authentication.getName())
-					.stream()
-					.map(suggestionInfoViewByCountryRepository::findById)
-					.filter(Optional::isPresent)
-					.map(Optional::get)
-					.forEach(info::add);
+				.stream()
+				.map(suggestionInfoViewByCountryRepository::findById)
+				.filter(Optional::isPresent)
+				.map(Optional::get)
+				.forEach(info::add);
 		}
 		return info;
 	}
@@ -147,11 +148,11 @@ public class OrganizationController {
 			return groupConflicts(conflictGroupViewRepository.findByCountry1OrCountry2(country, country).stream());
 		} else if (UserInfo.isSimpleUser(authentication) || UserInfo.isNationalAdmin(authentication)) {
 			final Stream<ConflictGroupView> list = userCountryRepository.getCountriesForUser(authentication.getName())
-					.stream()
-					.filter(country::equalsIgnoreCase)
-					.map(c -> conflictGroupViewRepository.findByCountry1OrCountry2(c, c).stream())
-					.findFirst()
-					.orElse(Stream.empty());
+				.stream()
+				.filter(country::equalsIgnoreCase)
+				.map(c -> conflictGroupViewRepository.findByCountry1OrCountry2(c, c).stream())
+				.findFirst()
+				.orElse(Stream.empty());
 			return groupConflicts(list);
 		} else {
 			throw new RuntimeException("User not authorized");
@@ -166,11 +167,11 @@ public class OrganizationController {
 			return duplicateGroupViewRepository.findByCountry(country);
 		} else if (UserInfo.isSimpleUser(authentication) || UserInfo.isNationalAdmin(authentication)) {
 			return userCountryRepository.getCountriesForUser(authentication.getName())
-					.stream()
-					.filter(country::equalsIgnoreCase)
-					.map(duplicateGroupViewRepository::findByCountry)
-					.findFirst()
-					.orElse(new ArrayList<DuplicateGroupView>());
+				.stream()
+				.filter(country::equalsIgnoreCase)
+				.map(duplicateGroupViewRepository::findByCountry)
+				.findFirst()
+				.orElse(new ArrayList<DuplicateGroupView>());
 		} else {
 			throw new RuntimeException("User not authorized");
 		}
@@ -193,10 +194,10 @@ public class OrganizationController {
 	public List<OpenaireDuplicate> duplicates(@RequestBody final List<OpenaireDuplicate> simrels, final Authentication authentication) {
 
 		final boolean b = UserInfo.isSuperAdmin(authentication)
-				|| simrels.stream()
-						.map(OpenaireDuplicate::getLocalId)
-						.distinct()
-						.allMatch(id -> userCountryRepository.verifyAuthorizationForId(id, authentication.getName()));
+			|| simrels.stream()
+				.map(OpenaireDuplicate::getLocalId)
+				.distinct()
+				.allMatch(id -> userCountryRepository.verifyAuthorizationForId(id, authentication.getName()));
 
 		if (b) {
 			return openaireDuplicateRepository.saveAll(simrels);
@@ -207,19 +208,19 @@ public class OrganizationController {
 
 	@RequestMapping(value = "/search/{page}/{size}", method = RequestMethod.GET)
 	public Page<OrganizationSimpleView> search(@PathVariable final int page,
-			@PathVariable final int size,
-			@RequestParam final String q,
-			final Authentication authentication) {
+		@PathVariable final int size,
+		@RequestParam final String q,
+		final Authentication authentication) {
 		return UserInfo.isSuperAdmin(authentication)
-				? organizationSimpleViewRepository.findByNameContainingIgnoreCase(q, PageRequest.of(page, size))
-				: organizationSimpleViewRepository.findByNameForUser(q, authentication.getName(), PageRequest.of(page, size));
+			? organizationSimpleViewRepository.findByNameContainingIgnoreCase(q, PageRequest.of(page, size))
+			: organizationSimpleViewRepository.findByNameForUser(q, authentication.getName(), PageRequest.of(page, size));
 	}
 
 	@RequestMapping(value = "/byCountry/{code}/{page}/{size}", method = RequestMethod.GET)
 	public Page<OrganizationSimpleView> findByCountry(@PathVariable final String code,
-			@PathVariable final int page,
-			@PathVariable final int size,
-			final Authentication authentication) {
+		@PathVariable final int page,
+		@PathVariable final int size,
+		final Authentication authentication) {
 		if (UserInfo.isSuperAdmin(authentication) || userCountryRepository.verifyAuthorizationForCountry(code, authentication.getName())) {
 			return organizationSimpleViewRepository.findByCountry(code, PageRequest.of(page, size));
 		} else {
@@ -229,26 +230,26 @@ public class OrganizationController {
 
 	@RequestMapping(value = "/byType/{type}/{page}/{size}", method = RequestMethod.GET)
 	public Page<OrganizationSimpleView> findByType(@PathVariable final String type,
-			@PathVariable final int page,
-			@PathVariable final int size,
-			final Authentication authentication) {
+		@PathVariable final int page,
+		@PathVariable final int size,
+		final Authentication authentication) {
 		return UserInfo.isSuperAdmin(authentication)
-				? organizationSimpleViewRepository.findByType(type, PageRequest.of(page, size))
-				: organizationSimpleViewRepository.findByTypeForUser(type, authentication.getName(), PageRequest.of(page, size));
+			? organizationSimpleViewRepository.findByType(type, PageRequest.of(page, size))
+			: organizationSimpleViewRepository.findByTypeForUser(type, authentication.getName(), PageRequest.of(page, size));
 	}
 
 	@RequestMapping(value = "/browse/countries", method = RequestMethod.GET)
 	public List<BrowseEntry> browseCountries(final Authentication authentication) {
 		return UserInfo.isSuperAdmin(authentication)
-				? organizationSimpleViewRepository.browseCountries()
-				: organizationSimpleViewRepository.browseCountriesForUser(authentication.getName());
+			? databaseUtils.browseCountries()
+			: databaseUtils.browseCountriesForUser(authentication.getName());
 	}
 
 	@RequestMapping(value = "/browse/types", method = RequestMethod.GET)
 	public List<BrowseEntry> browseOrganizationTypes(final Authentication authentication) {
 		return UserInfo.isSuperAdmin(authentication)
-				? organizationSimpleViewRepository.browseTypes()
-				: organizationSimpleViewRepository.browseTypesForUser(authentication.getName());
+			? databaseUtils.browseTypes()
+			: databaseUtils.browseTypesForUser(authentication.getName());
 	}
 
 	@RequestMapping(value = "/conflicts/fix/{masterId}", method = RequestMethod.POST)
@@ -256,10 +257,10 @@ public class OrganizationController {
 		if (UserInfo.isSuperAdmin(authentication) || userCountryRepository.verifyAuthorizationForId(masterId, authentication.getName())) {
 
 			return otherIds.stream()
-					.filter(id -> UserInfo.isSuperAdmin(authentication) || userCountryRepository.verifyAuthorizationForId(id, authentication.getName()))
-					.map(id -> databaseUtils.makeRelation(masterId, id, RelationType.Merges))
-					.flatMap(List::stream)
-					.collect(Collectors.toList());
+				.filter(id -> UserInfo.isSuperAdmin(authentication) || userCountryRepository.verifyAuthorizationForId(id, authentication.getName()))
+				.map(id -> databaseUtils.makeRelation(masterId, id, RelationType.Merges))
+				.flatMap(List::stream)
+				.collect(Collectors.toList());
 
 		} else {
 			return new ArrayList<>();

apps/dnet-orgs-database-application/src/main/java/eu/dnetlib/organizations/model/utils/BrowseEntry.java

@@ -1,9 +1,31 @@
 package eu.dnetlib.organizations.model.utils;
 
-public interface BrowseEntry {
+import java.io.Serializable;
 
-	String getValue();
+public class BrowseEntry implements Serializable {
 
-	int getCount();
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 8854955977257064470L;
+
+	private String value;
+	private int count;
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(final String value) {
+		this.value = value;
+	}
+
+	public int getCount() {
+		return count;
+	}
+
+	public void setCount(final int count) {
+		this.count = count;
+	}
 
 }

apps/dnet-orgs-database-application/src/main/java/eu/dnetlib/organizations/repository/readonly/OrganizationSimpleViewRepository.java

@@ -1,13 +1,10 @@
 package eu.dnetlib.organizations.repository.readonly;
 
-import java.util.List;
-
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.stereotype.Repository;
 
-import eu.dnetlib.organizations.model.utils.BrowseEntry;
 import eu.dnetlib.organizations.model.view.OrganizationSimpleView;
 
 @Repository
@@ -20,29 +17,8 @@ public interface OrganizationSimpleViewRepository extends ReadOnlyRepository<Org
 	@Query(value = "select o.* from organizations_simple_view o left outer join user_countries uc on (uc.country = o.country) where o.name ilike %:text% and uc.email = :email", nativeQuery = true)
 	Page<OrganizationSimpleView> findByNameForUser(String text, String email, Pageable pageable);
 
-	// BROWSE BY COUNTRY
-	@Query(value = "select country as value, count(*) as count from organizations group by country order by count desc", nativeQuery = true)
-	List<BrowseEntry> browseCountries();
-
-	// BROWSE BY COUNTRY FOR USER
-	@Query(value = "select o.country as value, count(o.country) as count from user_countries uc left outer join organizations o on (uc.country = o.country) where uc.email=?1 group by o.country order by count desc", nativeQuery = true)
-	List<BrowseEntry> browseCountriesForUser(String email);
-
 	Page<OrganizationSimpleView> findByCountry(String country, Pageable pageable);
 
-	// BROWSE BY ORG TYPE
-	@Query(value = "select type as value, count(*) as count from organizations group by type order by count desc", nativeQuery = true)
-	List<BrowseEntry> browseTypes();
-
-	// BROWSE BY ORG TYPE FOR USER
-	@Query(value = "select o.type as value, count(o.type) as count "
-			+ "from organizations o "
-			+ "left outer join user_countries uc on (uc.country = o.country) "
-			+ "where uc.email=?1 "
-			+ "group by o.type "
-			+ "order by count desc;", nativeQuery = true)
-	List<BrowseEntry> browseTypesForUser(String email);
-
 	Page<OrganizationSimpleView> findByType(String type, Pageable pageable);
 
 	@Query(value = "select o.* from organizations_simple_view o left outer join user_countries uc on (uc.country = o.country) where uc.email = ?2 and o.type = ?1", nativeQuery = true)

apps/dnet-orgs-database-application/src/main/java/eu/dnetlib/organizations/utils/DatabaseUtils.java

@@ -16,6 +16,7 @@ import javax.transaction.Transactional;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.annotation.Cacheable;
+import org.springframework.jdbc.core.BeanPropertyRowMapper;
 import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.stereotype.Component;
 import org.springframework.web.bind.annotation.RequestBody;
@@ -31,6 +32,7 @@ import eu.dnetlib.organizations.model.Relationship;
 import eu.dnetlib.organizations.model.Url;
 import eu.dnetlib.organizations.model.User;
 import eu.dnetlib.organizations.model.UserCountry;
+import eu.dnetlib.organizations.model.utils.BrowseEntry;
 import eu.dnetlib.organizations.model.view.OrganizationView;
 import eu.dnetlib.organizations.model.view.UserView;
 import eu.dnetlib.organizations.repository.AcronymRepository;
@@ -68,7 +70,12 @@ public class DatabaseUtils {
 	private JdbcTemplate jdbcTemplate;
 
 	public enum VocabularyTable {
-		languages, countries, org_types, id_types, rel_types, simrel_types
+		languages,
+		countries,
+		org_types,
+		id_types,
+		rel_types,
+		simrel_types
 	}
 
 	@Transactional
@@ -79,10 +86,10 @@ public class DatabaseUtils {
 		}
 
 		final Organization org = new Organization(update ? orgView.getId() : null,
-				orgView.getName(),
-				orgView.getType(),
-				orgView.getLat(), orgView.getLng(),
-				orgView.getCity(), orgView.getCountry());
+			orgView.getName(),
+			orgView.getType(),
+			orgView.getLat(), orgView.getLng(),
+			orgView.getCity(), orgView.getCountry());
 
 		final String orgId = organizationRepository.save(org).getId();
 
@@ -139,7 +146,7 @@ public class DatabaseUtils {
 		userCountryRepository.deleteByEmail(userView.getEmail());
 		if (userView.getCountries() != null) {
 			userCountryRepository
-					.saveAll(Arrays.stream(userView.getCountries()).map(c -> new UserCountry(userView.getEmail(), c)).collect(Collectors.toList()));
+				.saveAll(Arrays.stream(userView.getCountries()).map(c -> new UserCountry(userView.getEmail(), c)).collect(Collectors.toList()));
 		}
 	}
 
@@ -208,13 +215,13 @@ public class DatabaseUtils {
 
 	private List<String> findExistingGroupsForRel(final OpenaireConflict w, final Map<String, Set<String>> groups) {
 		return groups.entrySet()
-				.stream()
-				.filter(e -> {
-					return e.getValue().contains(w.getId1()) || e.getValue().contains(w.getId2());
-				})
-				.map(e -> e.getKey())
-				.distinct()
-				.collect(Collectors.toList());
+			.stream()
+			.filter(e -> {
+				return e.getValue().contains(w.getId1()) || e.getValue().contains(w.getId2());
+			})
+			.map(e -> e.getKey())
+			.distinct()
+			.collect(Collectors.toList());
 	}
 
 	private void addToGroup(final Map<String, Set<String>> groups, final String gid, final OpenaireConflict w) {
@@ -236,4 +243,36 @@ public class DatabaseUtils {
 
 		return Arrays.asList(r1, r2);
 	}
+
+	// BROWSE BY COUNTRY
+	public List<BrowseEntry> browseCountries() {
+		final String sql = "select country as value, count(*) as count from organizations group by country order by count desc";
+		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class));
+	}
+
+	// BROWSE BY COUNTRY FOR USER
+	public List<BrowseEntry> browseCountriesForUser(final String email) {
+		final String sql =
+			"select o.country as value, count(o.country) as count from user_countries uc left outer join organizations o on (uc.country = o.country) where uc.email=? group by o.country order by count desc";
+		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class), email);
+	}
+
+	// BROWSE BY ORG TYPE
+	public List<BrowseEntry> browseTypes() {
+		final String sql = "select type as value, count(*) as count from organizations group by type order by count desc";
+		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class));
+	}
+
+	// BROWSE BY ORG TYPE FOR USER
+	public List<BrowseEntry> browseTypesForUser(final String email) {
+		final String sql = "select o.type as value, count(o.type) as count "
+			+ "from organizations o "
+			+ "left outer join user_countries uc on (uc.country = o.country) "
+			+ "where uc.email=? "
+			+ "group by o.type "
+			+ "order by count desc;";
+		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class), email);
+
+	}
+
 }

apps/dnet-orgs-database-application/src/main/resources/static/resources/js/organizations.js

@@ -31,6 +31,7 @@ orgsModule.directive('selectOrgModal', function($http) {
 			
 			scope.search = function(text, page, size) {
 				scope.searchOrgs = {};
+								
 				$http.get('api/organizations/search/' + page + '/' + size + '?q=' + text).then(function successCallback(res) {
 					if((typeof res.data) == 'string') { alert("Session expired !"); location.reload(true); }
 					scope.searchValue = text;
@@ -438,14 +439,21 @@ orgsModule.controller('newOrgCtrl', function ($scope, $http, $routeParams, $loca
 orgsModule.controller('searchCtrl', function ($scope, $location) {
 	$scope.searchText = '';
 	$scope.search = function() {
-		$location.url('/searchResults/0/50/' + encodeURIComponent(encodeURIComponent($scope.searchText)));
+		if ($scope.searchText) {
+			$location.url('/searchResults/0/50/' + encodeURIComponent(encodeURIComponent($scope.searchText)));
+		} else {
+			$location.url('/searchResults/0/50/_');
+		}
 	}
 });
 
 orgsModule.controller('searchResultsCtrl', function ($scope, $http, $routeParams, $location) {
-	$scope.searchText = decodeURIComponent($routeParams.text);
+	$scope.searchText = '';	
+	if ($routeParams.text != '_') {
+		$scope.searchText = decodeURIComponent($routeParams.text);
+	}
 	$scope.orgs = {};
-	
+
 	$http.get('api/organizations/search/' + $routeParams.page + '/' + $routeParams.size + '?q=' + $scope.searchText).then(function successCallback(res) {
 		if((typeof res.data) == 'string') { alert("Session expired !"); location.reload(true); }
 		$scope.orgs = res.data;
@@ -454,11 +462,19 @@ orgsModule.controller('searchResultsCtrl', function ($scope, $http, $routeParams
 	});
 	
 	$scope.prev = function() {
-		$location.url('/searchResults/' + ($scope.orgs.number - 1) + '/' + $scope.orgs.size + '/' + encodeURIComponent($scope.searchText));
+		if ($scope.searchText) {
+			$location.url('/searchResults/' + ($scope.orgs.number - 1) + '/' + $scope.orgs.size + '/' + encodeURIComponent($scope.searchText));
+		} else {
+			$location.url('/searchResults/' + ($scope.orgs.number - 1) + '/' + $scope.orgs.size + '/_');
+		}
 	}
 	
 	$scope.next = function() {
-		$location.url('/searchResults/' + ($scope.orgs.number + 1) + '/' + $scope.orgs.size + '/' + encodeURIComponent($scope.searchText));
+		if ($scope.searchText) {
+			$location.url('/searchResults/' + ($scope.orgs.number + 1) + '/' + $scope.orgs.size + '/' + encodeURIComponent($scope.searchText));
+		} else {
+			$location.url('/searchResults/' + ($scope.orgs.number + 1) + '/' + $scope.orgs.size + '/_');
+		}
 	}
 });
 

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
-		<version>2.3.1.RELEASE</version>
+		<version>2.3.2.RELEASE</version>
 		<relativePath />
 	</parent>