Add java 21 update fixes

buildSrc/src/main/groovy/nva.cristin.service.core.java-conventions.gradle

@@ -103,7 +103,7 @@ tasks.register('karateTest', Test) {
 }
 
 pmd {
-    toolVersion = '6.55.0'
+    toolVersion = '7.5.0'
     ruleSetConfig = rootProject.resources.text.fromFile('config/pmd/ruleset.xml')
     ruleSets = []
     ignoreFailures = false

config/pmd/ruleset.xml

@@ -10,13 +10,15 @@
   <exclude-pattern>.*/test/.*</exclude-pattern>
 
   <rule ref="category/java/errorprone.xml">
-    <exclude name="DataflowAnomalyAnalysis"/>
     <exclude name="MissingSerialVersionUID"/>
   </rule>
 
   <rule ref="category/java/multithreading.xml">
     <!-- Because it complains for the Map interface in the Resource class.-->
     <exclude name="UseConcurrentHashMap"/>
+    <!-- J2EE prohibits threads, while we don't use J2EE -->
+    <exclude name="DoNotUseThreads" />
+
   </rule>
 
   <rule ref="category/java/bestpractices.xml">
@@ -40,12 +42,6 @@
     <exclude name="TooManyStaticImports"/>
     <exclude name="ClassNamingConventions"/>
     <exclude name="UnnecessaryConstructor"/>
-    <!-- Conflicts with the rule category/java/codestyle.xml/AvoidProtectedMethodInFinalClassNotExtending -->
-    <exclude name="CommentDefaultAccessModifier"/>
-    <!-- Conflicts with the rule category/java/codestyle.xml/AvoidProtectedMethodInFinalClassNotExtending -->
-    <exclude name="DefaultPackage"/>
-
-
     <exclude name="ConfusingTernary"/>
 
     <!-- printStackTrace is used in the Default Amazon handler in a static clause
@@ -63,6 +59,8 @@
     <!-- Sometimes it is useful in debugging to assign the return value to a local variable  -->
     <exclude name="UnnecessaryLocalBeforeReturn"/>
 
+    <!-- We don't want to exclude use of "var" -->
+    <exclude name="UseExplicitTypes"/>
 
   </rule>
 

cristin-biobank/src/main/java/no/unit/nva/biobank/model/ParameterKeyBiobank.java

@@ -34,7 +34,7 @@ public enum ParameterKeyBiobank implements IParameterKey {
     public static final int IGNORE_PATH_PARAMETER_INDEX = 2;
 
     public static final Set<ParameterKeyBiobank> VALID_QUERY_PARAMETERS =
-        Arrays.stream(ParameterKeyBiobank.values())
+        Arrays.stream(values())
             .filter(ParameterKeyBiobank::ignorePathKeys)
             .collect(Collectors.toSet());
 
@@ -103,16 +103,12 @@ public String toString() {
     }
 
     public static ParameterKeyBiobank keyFromString(String paramName, String value) {
-        var result = Arrays.stream(ParameterKeyBiobank.values())
-                         .filter(ParameterKeyBiobank::ignorePathKeys)
-                         .filter(IParameterKey.equalTo(paramName))
-                         .collect(Collectors.toSet());
-        return result.size() == 1
-                   ? result.stream().findFirst().get()
-                   : result.stream()
-                         .filter(IParameterKey.hasValidValue(value))
-                         .findFirst()
-                         .orElse(INVALID);
+        return Arrays.stream(values())
+                .filter(ParameterKeyBiobank::ignorePathKeys)
+                .filter(IParameterKey.equalTo(paramName))
+                .distinct()
+                .reduce((first, second) -> IParameterKey.hasValidValue(value).test(second) ? second : first)
+                .orElse(INVALID);
     }
 
 

cristin-commons/src/main/java/no/unit/nva/cristin/common/Utils.java

@@ -29,7 +29,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class Utils {
+public final class Utils {
 
     private static final Logger logger = LoggerFactory.getLogger(Utils.class);
 
@@ -40,6 +40,9 @@ public class Utils {
     public static final String USER_IS_INTERNAL_BACKEND = "User is internal backend";
     public static final String USER_TOP_LEVEL_CRISTIN_ORGANIZATION = "User has top level cristin organization {}";
 
+    private Utils() {
+        // NO-OP
+    }
 
     /**
      * Check if a string supplied is a positive integer.
@@ -130,7 +133,7 @@ public static String getValidOrgId(RequestInfo requestInfo) throws BadRequestExc
 
 
     private static boolean isValidIdentifier(String identifier) {
-        return Utils.isPositiveInteger(identifier);
+        return isPositiveInteger(identifier);
     }
 
     /**
@@ -169,7 +172,7 @@ public static String extractCristinInstitutionIdentifier(RequestInfo requestInfo
 
     private static String extractInstitution(URI organization) {
         var organizationIdentifier = UriUtils.extractLastPathElement(organization);
-        return Utils.removeUnitPartFromIdentifierIfPresent(organizationIdentifier);
+        return removeUnitPartFromIdentifierIfPresent(organizationIdentifier);
     }
 
     private static BadRequestException failedToRetrieveTopLevelOrgCristinId() {

cristin-commons/src/main/java/no/unit/nva/cristin/common/client/ApiClient.java

@@ -240,9 +240,11 @@ private List<HttpResponse<String>> collectSuccessfulResponses(
                    .filter(Try::isSuccess)
                    .map(Try::get)
                    .filter(this::isSuccessfulRequest)
-                   .collect(Collectors.toList());
+                   .toList();
     }
 
+    // This is reported as unused, but it is…
+    @SuppressWarnings("PMD.UnusedPrivateMethod")
     private boolean isSuccessfulRequest(HttpResponse<String> response) {
         try {
             checkHttpStatusCode(response.uri(), response.statusCode(), response.body());

cristin-commons/src/main/java/no/unit/nva/utils/AccessUtils.java

@@ -12,14 +12,14 @@
 import java.net.URI;
 import java.net.http.HttpClient;
 import java.net.http.HttpRequest;
-import java.net.http.HttpResponse;
 import java.nio.charset.StandardCharsets;
 import java.time.Duration;
 import java.util.Base64;
 
 import static com.google.common.net.HttpHeaders.AUTHORIZATION;
 import static com.google.common.net.HttpHeaders.CONTENT_TYPE;
 import static java.net.http.HttpRequest.newBuilder;
+import static java.net.http.HttpResponse.BodyHandlers.ofString;
 import static nva.commons.apigateway.AccessRight.MANAGE_CUSTOMERS;
 import static nva.commons.apigateway.AccessRight.MANAGE_OWN_AFFILIATION;
 import static nva.commons.core.attempt.Try.attempt;
@@ -80,23 +80,27 @@ public static boolean clientIsCustomerAdministrator(RequestInfo requestInfo) {
      * Fetches an internal backend token from Cognito.
      */
     public static String getBackendAccessToken() throws IOException, InterruptedException {
-        var cognitoTokenUrl = getCognitoTokenUrl();
-        var payload = GRANT_TYPE_PAYLOAD;
 
-        var request = newBuilder(cognitoTokenUrl)
-                .POST(HttpRequest.BodyPublishers.ofString(payload))
-                .header(CONTENT_TYPE, APPLICATION_X_WWW_FORM_URLENCODED)
-                .header(AUTHORIZATION, basicAuthHeader())
-                .build();
-        HttpClient client = HttpClient.newBuilder()
+        try (var client = createHttpClient()) {
+            var response = client.send(createTokenRequest(), ofString(StandardCharsets.UTF_8));
+            var jsonTree = JsonUtils.dtoObjectMapper.readTree(response.body());
+            return jsonTree.get(ACCESS_TOKEN).textValue();
+        }
+    }
+
+    private static HttpClient createHttpClient() {
+        return HttpClient.newBuilder()
                 .followRedirects(HttpClient.Redirect.ALWAYS)
                 .connectTimeout(Duration.ofSeconds(30))
                 .build();
+    }
 
-        HttpResponse<String> response = client.send(request,
-                                                    HttpResponse.BodyHandlers.ofString(StandardCharsets.UTF_8));
-        var jsonTree = JsonUtils.dtoObjectMapper.readTree(response.body());
-        return jsonTree.get(ACCESS_TOKEN).textValue();
+    private static HttpRequest createTokenRequest() {
+        return newBuilder(getCognitoTokenUrl())
+                .POST(HttpRequest.BodyPublishers.ofString(GRANT_TYPE_PAYLOAD))
+                .header(CONTENT_TYPE, APPLICATION_X_WWW_FORM_URLENCODED)
+                .header(AUTHORIZATION, basicAuthHeader())
+                .build();
     }
 
     private static URI getCognitoTokenUrl() {

cristin-commons/src/main/java/no/unit/nva/utils/UriUtils.java

@@ -15,13 +15,17 @@
 import java.util.regex.Pattern;
 import nva.commons.core.paths.UriWrapper;
 
-public class UriUtils {
+public final class UriUtils {
 
     public static final String POSITION = "position";
     public static final String PROJECT = "project";
     public static final String PERSON = "person";
     private static final String NATIONAL_IDENTITY_PATTERN = "national_id=(\\d+)(\\d{2})";
 
+    private UriUtils() {
+        // NO-OP
+    }
+
     /**
      * Create URI identifying NVA resource from path and identifier.
      *
@@ -85,7 +89,7 @@ public static URI getNvaApiUri(String path) {
 
     public static URI createNvaProjectId(String identifier) {
         return new UriWrapper(HTTPS, DOMAIN_NAME)
-            .addChild(BASE_PATH).addChild(UriUtils.PROJECT).addChild(identifier).getUri();
+            .addChild(BASE_PATH).addChild(PROJECT).addChild(identifier).getUri();
     }
 
     public static String extractLastPathElement(URI uri) {

cristin-commons/src/main/java/no/unit/nva/utils/UserUtils.java

@@ -1,7 +1,6 @@
 package no.unit.nva.utils;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
-import java.net.http.HttpResponse;
 import no.unit.nva.cognito.CognitoUtil;
 import no.unit.nva.commons.json.JsonUtils;
 import nva.commons.core.paths.UriWrapper;
@@ -19,16 +18,20 @@
 
 import static com.google.common.net.HttpHeaders.AUTHORIZATION;
 import static java.net.http.HttpRequest.newBuilder;
+import static java.net.http.HttpResponse.BodyHandlers.ofString;
 import static no.unit.nva.cristin.model.Constants.DOMAIN_NAME;
 import static no.unit.nva.cristin.model.Constants.HTTPS;
 import static no.unit.nva.utils.AccessUtils.BASIC;
 
-public class UserUtils {
+public final class UserUtils {
 
     private static final Logger logger = LoggerFactory.getLogger(UserUtils.class);
     public static final String RESPONSE_FROM_USER_CREATE = "Response from user create={}";
     public static final String USER_CREATED_WITH_ROLES = "User {} created with role(s) '{}'";
 
+    private UserUtils() {
+        // NO-OP
+    }
 
     /**
      * Creates user in Cognito used for Karate tests.
@@ -50,20 +53,29 @@ public static void createUserWithRoles(String username, String password, String
 
     private static void createNvaUserWithRoles(String nationalIdentityNumber, URI customerId, Set<String> roles)
         throws IOException, InterruptedException {
+        try (var client = createHttpClient()) {
+            final var response = client.send(createHttpRequest(nationalIdentityNumber, customerId, roles),
+                    ofString(StandardCharsets.UTF_8));
+            logger.info(RESPONSE_FROM_USER_CREATE, response);
+        }
+    }
+
+    private static HttpClient createHttpClient() {
+        return HttpClient.newBuilder()
+                .followRedirects(HttpClient.Redirect.ALWAYS)
+                .connectTimeout(Duration.ofSeconds(30))
+                .build();
+    }
+
+    private static HttpRequest createHttpRequest(String nationalIdentityNumber,
+                                                 URI customerId,
+                                                 Set<String> roles) throws IOException, InterruptedException {
         final var userRoles = new UserRoles(nationalIdentityNumber, customerId, roles);
         final var body = JsonUtils.dtoObjectMapper.writeValueAsString(userRoles);
-        final var request = newBuilder(createUserServiceUri())
+        return newBuilder(createUserServiceUri())
                 .header(AUTHORIZATION, BASIC + AccessUtils.getBackendAccessToken())
                 .POST(HttpRequest.BodyPublishers.ofString(body))
                 .build();
-        final var client = HttpClient.newBuilder()
-                .followRedirects(HttpClient.Redirect.ALWAYS)
-                .connectTimeout(Duration.ofSeconds(30))
-                .build();
-
-        final var response =
-            client.send(request, HttpResponse.BodyHandlers.ofString(StandardCharsets.UTF_8));
-        logger.info(RESPONSE_FROM_USER_CREATE, response);
     }
 
 

cristin-funding/src/main/java/no/unit/nva/cristin/funding/sources/model/cristin/CristinFundingSource.java

@@ -4,6 +4,8 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import java.util.Map;
 
+// The private fields in the record are viewed as unused, this is a bug
+@SuppressWarnings("PMD.UnusedPrivateField")
 public record CristinFundingSource(@JsonProperty(CODE_FIELD) String code,
                                    @JsonProperty(NAME_FIELD) Map<String, String> name) {
 
@@ -14,5 +16,4 @@ public record CristinFundingSource(@JsonProperty(CODE_FIELD) String code,
     public Map<String, String> name() {
         return nonEmptyOrDefault(name);
     }
-
 }

cristin-keyword/src/main/java/no/unit/nva/cristin/keyword/query/QueryKeywordsHandler.java

@@ -59,7 +59,7 @@ protected Integer getSuccessStatusCode(Void input, SearchResponse<Keyword> outpu
         return HTTP_OK;
     }
 
-    private ConcurrentHashMap<String, String> parseQueryParams(RequestInfo requestInfo) throws BadRequestException {
+    private Map<String, String> parseQueryParams(RequestInfo requestInfo) throws BadRequestException {
         validateQueryParameterKeys(requestInfo);
 
         var queryParams = new ConcurrentHashMap<String, String>();

cristin-organization/src/main/java/no/unit/nva/cristin/organization/common/client/CristinOrganizationApiClient.java

@@ -62,7 +62,6 @@ public class CristinOrganizationApiClient
     public static final String NULL_HTTP_RESPONSE_ERROR_MESSAGE = "No HttpResponse found";
     public static final int SINGLE_HIT = 1;
     public static final String UNIQUELY_IDENTIFY_ORGANIZATION = "Identifier does not uniquely identify organization";
-    public static final int FIRST_AND_ONLY_UNIT = 0;
     private static final int NO_HITS = 0;
 
     /**
@@ -120,12 +119,11 @@ public Organization executeFetch(Map<String, String> params) throws ApiGatewayEx
 
     private Organization extractOrganization(String identifier, HttpResponse<String> response)
             throws ApiGatewayException {
-        List<SubUnitDto> units = attempt(() ->
-                OBJECT_MAPPER.readValue(response.body(), new TypeReference<List<SubUnitDto>>() {
-                }))
+        var type = new TypeReference<List<SubUnitDto>>() {};
+        List<SubUnitDto> units = attempt(() -> OBJECT_MAPPER.readValue(response.body(), type))
                 .orElseThrow(fail -> new FailedHttpRequestException(fail.getException()));
         if (SINGLE_HIT == units.size()) {
-            return toOrganization(identifier, units.get(FIRST_AND_ONLY_UNIT));
+            return toOrganization(identifier, units.getFirst());
         } else {
             throw new BadRequestException(UNIQUELY_IDENTIFY_ORGANIZATION);
         }

cristin-organization/src/main/java/no/unit/nva/cristin/organization/query/QueryCristinOrganizationHandler.java

@@ -78,7 +78,7 @@ protected Integer getSuccessStatusCode(Void input, SearchResponse<Organization>
         return HttpURLConnection.HTTP_OK;
     }
 
-    private ConcurrentHashMap<String, String> extractQueryParameters(RequestInfo requestInfo)
+    private Map<String, String> extractQueryParameters(RequestInfo requestInfo)
         throws BadRequestException {
 
         var requestQueryParams = new ConcurrentHashMap<String, String>();

cristin-person/src/main/java/no/unit/nva/cristin/person/client/CristinPersonApiClient.java

@@ -41,6 +41,7 @@
 import static no.unit.nva.utils.UriUtils.getNvaApiId;
 import static nva.commons.core.attempt.Try.attempt;
 
+@SuppressWarnings("PMD.CouplingBetweenObjects")
 public class CristinPersonApiClient extends ApiClient
     implements ClientVersion,
                CristinAuthorizedQueryClient<Map<String, String>, Person> {

cristin-person/src/main/java/no/unit/nva/cristin/person/model/cristin/CristinPerson.java

@@ -39,7 +39,8 @@
 import static no.unit.nva.cristin.model.Constants.PERSON_PATH_NVA;
 import static no.unit.nva.cristin.person.model.nva.JsonPropertyNames.NATIONAL_IDENTITY_NUMBER;
 
-@SuppressWarnings({"unused", "PMD.GodClass", "PMD.TooManyFields", "PMD.ExcessivePublicCount"})
+@SuppressWarnings({"unused", "PMD.GodClass", "PMD.TooManyFields", "PMD.ExcessivePublicCount",
+        "PMD.CouplingBetweenObjects"})
 @JacocoGenerated
 @JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
 public class CristinPerson implements JsonSerializable {
@@ -394,11 +395,8 @@ private Set<Employment> extractEmployments() {
     private Boolean extractVerified() {
         if (nonNull(getIdentifiedCristinPerson()) && getIdentifiedCristinPerson()) {
             return true;
-        } else if (isNviVerified()) {
-            return true;
-        } else {
-            return getIdentifiedCristinPerson();
         }
+        return isNviVerified() || Boolean.TRUE.equals(getIdentifiedCristinPerson());
     }
 
     private boolean isNviVerified() {