Merge pull request #458 from NUM-Forschungsdatenplattform/feature/NUM…

…-2160-upgrade-to-spring-boot-3-2

NUM-2160 upgrade to spring boot 3.2.2 and some cleanup

pom.xml

@@ -12,7 +12,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.1.8</version>
+    <version>3.2.2</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
 
@@ -21,16 +21,16 @@
     <commons-io.version>2.15.1</commons-io.version>
     <ehr-sdk.version>2.6.0</ehr-sdk.version>
     <!-- aql-editor-backend-starter repo was archived on August 2023 -->
-    <num-aql-editor-backend-starter.version>1.0.4</num-aql-editor-backend-starter.version>
+    <num-aql-editor-backend-starter.version>1.0.5</num-aql-editor-backend-starter.version>
     <logstash-logback-encoder.version>7.4</logstash-logback-encoder.version>
     <modelmapper.version>3.2.0</modelmapper.version>
     <springdoc.version>2.3.0</springdoc.version>
     <java.version>17</java.version>
     <commons-csv.version>1.10.0</commons-csv.version>
     <jacoco.version>0.8.11</jacoco.version>
     <dependency-check.version>9.0.8</dependency-check.version>
-    <failsafe.version>3.2.2</failsafe.version>
-    <surefire.version>3.2.2</surefire.version>
+    <failsafe.version>3.2.5</failsafe.version>
+    <surefire.version>3.2.5</surefire.version>
     <ehcache.version>3.10.8</ehcache.version>
     <git-commit-id-plugin.version>4.9.10</git-commit-id-plugin.version>
     <skip.integration.tests>false</skip.integration.tests>
@@ -41,7 +41,7 @@
     <wiremock-standalone.version>3.2.0</wiremock-standalone.version>
     <testcontainers.version>1.19.3</testcontainers.version>
     <ossindexAnalyzerEnabled>false</ossindexAnalyzerEnabled>
-    <spring.cloud-version>2022.0.3</spring.cloud-version>
+    <spring.cloud-version>2023.0.0</spring.cloud-version>
   </properties>
 
   <repositories>

src/main/java/de/vitagroup/num/domain/dto/AqlDto.java

@@ -18,7 +18,7 @@
 @NoArgsConstructor
 public class AqlDto {
 
-  @Schema(description = "The unique identifier", example = "1")
+  @Schema(description = "The unique identifier", example = "1", accessMode = Schema.AccessMode.READ_ONLY)
   private Long id;
 
   @Schema(requiredMode = Schema.RequiredMode.REQUIRED, description = "The name of the aql")
@@ -56,6 +56,7 @@ public class AqlDto {
   private String query;
 
   @Schema(description = "Flag marking aql as being public")
+  @Builder.Default
   private boolean publicAql = true;
 
   @Schema(description = "The owner of the aql", hidden = true)
@@ -67,9 +68,9 @@ public class AqlDto {
   @Schema(description = "to for category data", hidden = true)
   private AqlCategoryDto category;
 
-  @Schema
+  @Schema(accessMode = Schema.AccessMode.READ_ONLY)
   private OffsetDateTime createDate;
 
-  @Schema
+  @Schema(accessMode = Schema.AccessMode.READ_ONLY)
   private OffsetDateTime modifiedDate;
 }

src/main/java/de/vitagroup/num/domain/dto/ParameterOptionsDto.java

@@ -16,6 +16,7 @@
 @AllArgsConstructor
 public class ParameterOptionsDto {
 
+  @Builder.Default
   private Map<String, Object> options = new LinkedHashMap<>();
   private String aqlPath;
   private String archetypeId;

src/main/java/de/vitagroup/num/domain/dto/ProjectDto.java

@@ -27,6 +27,7 @@
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public class ProjectDto {
 
+  @Schema(accessMode = Schema.AccessMode.READ_ONLY)
   private Long id;
 
   @NotNull(message = "Project name cannot be null")

src/main/java/de/vitagroup/num/domain/model/Organization.java

@@ -34,5 +34,6 @@ public class Organization implements Serializable {
   private Set<MailDomain> domains = new HashSet<>();
 
   @Column(nullable = false, columnDefinition = "BOOLEAN DEFAULT TRUE")
+  @Builder.Default
   private Boolean active = Boolean.TRUE;
 }

src/main/java/de/vitagroup/num/domain/model/admin/User.java

@@ -49,7 +49,6 @@ public class User {
   private String email;
 
   @NotNull
-  @NotEmpty
   @Schema(description = "The timestamp of user registration")
   private Long createdTimestamp;
 

src/main/java/de/vitagroup/num/domain/model/admin/UserDetails.java

@@ -26,6 +26,7 @@ public class UserDetails implements Serializable {
   @JoinColumn(name = "organization_id")
   private Organization organization;
 
+  @Builder.Default
   private boolean approved = false;
 
   private LocalDateTime createdDate;

src/main/java/de/vitagroup/num/service/AqlService.java

@@ -2,14 +2,14 @@
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import de.vitagroup.num.domain.dto.Language;
+import de.vitagroup.num.domain.dto.SearchCriteria;
+import de.vitagroup.num.domain.dto.SlimAqlDto;
 import de.vitagroup.num.domain.model.Aql;
 import de.vitagroup.num.domain.model.AqlCategory;
 import de.vitagroup.num.domain.model.Roles;
 import de.vitagroup.num.domain.model.admin.User;
 import de.vitagroup.num.domain.model.admin.UserDetails;
-import de.vitagroup.num.domain.dto.Language;
-import de.vitagroup.num.domain.dto.SearchCriteria;
-import de.vitagroup.num.domain.dto.SlimAqlDto;
 import de.vitagroup.num.domain.repository.AqlCategoryRepository;
 import de.vitagroup.num.domain.repository.AqlRepository;
 import de.vitagroup.num.domain.specification.AqlSpecification;
@@ -26,7 +26,6 @@
 import org.ehrbase.aqleditor.dto.aql.Result;
 import org.ehrbase.aqleditor.service.AqlEditorAqlService;
 import org.ehrbase.openehr.sdk.aql.parser.AqlParseException;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.dao.EmptyResultDataAccessException;
 import org.springframework.data.domain.*;
 import org.springframework.data.jpa.domain.JpaSort;

src/main/java/de/vitagroup/num/service/SetupHealthiness.java

@@ -11,22 +11,16 @@
 import org.springframework.stereotype.Service;
 
 import java.io.IOException;
-import java.net.*;
-import java.net.http.HttpClient;
-import java.net.http.HttpRequest;
+import java.net.HttpURLConnection;
+import java.net.URISyntaxException;
+import java.net.URL;
 import java.nio.charset.StandardCharsets;
-import java.time.Duration;
-import java.time.temporal.ChronoUnit;
-import java.time.temporal.TemporalAmount;
-import java.time.temporal.TemporalUnit;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import static de.vitagroup.num.domain.templates.ExceptionsTemplate.ANNOUNCEMENT_IN_PLACE;
-import static de.vitagroup.num.domain.templates.ExceptionsTemplate.EXCEPTION_HAPPENED_IN_CLASS_FOR_ENVIRONMENT;
-import static de.vitagroup.num.domain.templates.ExceptionsTemplate.EXCEPTION_IN_PARSING_PAGE;
+import static de.vitagroup.num.domain.templates.ExceptionsTemplate.*;
 
 @Slf4j
 @Service

src/main/java/de/vitagroup/num/service/exception/CustomizedExceptionHandler.java

@@ -8,10 +8,11 @@
 import org.springframework.http.HttpStatusCode;
 import org.springframework.http.ResponseEntity;
 import org.springframework.security.access.AccessDeniedException;
-import org.springframework.validation.BindException;
+import org.springframework.validation.method.ParameterErrors;
 import org.springframework.web.bind.MethodArgumentNotValidException;
 import org.springframework.web.bind.annotation.ExceptionHandler;
 import org.springframework.web.context.request.WebRequest;
+import org.springframework.web.method.annotation.HandlerMethodValidationException;
 import org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler;
 
 import java.util.*;
@@ -314,4 +315,27 @@ protected ResponseEntity<Object> handleMethodArgumentNotValid(MethodArgumentNotV
                 .build();
         return ResponseEntity.status( HttpStatus.BAD_REQUEST ).body( errorDetails );
     }
+
+    @Override
+    protected ResponseEntity<Object> handleHandlerMethodValidationException(HandlerMethodValidationException ex, HttpHeaders headers, HttpStatusCode status, WebRequest request) {
+        Map<String, String> errors = new HashMap<>();
+        for (final var validation : ex.getAllValidationResults()) {
+            if (validation instanceof ParameterErrors) {
+                ParameterErrors parameterErrors = (ParameterErrors) validation;
+                parameterErrors.getFieldErrors().forEach(fieldError -> errors.put(fieldError.getField(), fieldError.getDefaultMessage()));
+            } else {
+                final String parameterName = validation.getMethodParameter().getParameterName();
+                validation
+                        .getResolvableErrors()
+                        .forEach(
+                                error -> errors.put(parameterName, error.getDefaultMessage()));
+            }
+        }
+        ErrorDetails errorDetails = ErrorDetails
+                .builder()
+                .message("Validation failed")
+                .details(errors)
+                .build();
+        return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(errorDetails);
+    }
 }

src/main/java/de/vitagroup/num/service/policy/EhrPolicy.java

@@ -1,11 +1,6 @@
 package de.vitagroup.num.service.policy;
 
 import de.vitagroup.num.service.exception.SystemException;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-
 import de.vitagroup.num.service.util.AqlQueryConstants;
 import lombok.Builder;
 import lombok.extern.slf4j.Slf4j;
@@ -15,7 +10,10 @@
 import org.ehrbase.openehr.sdk.aql.dto.operand.IdentifiedPath;
 import org.ehrbase.openehr.sdk.aql.dto.path.AqlObjectPath;
 import org.ehrbase.openehr.sdk.aql.dto.select.SelectExpression;
-import org.ehrbase.openehr.sdk.aql.render.AqlRenderer;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
 
 import static de.vitagroup.num.domain.templates.ExceptionsTemplate.COHORT_SIZE_CANNOT_BE_0;
 import static de.vitagroup.num.domain.templates.ExceptionsTemplate.INVALID_AQL;

src/main/java/de/vitagroup/num/service/policy/EuropeanConsentPolicy.java

@@ -5,7 +5,6 @@
 import lombok.extern.slf4j.Slf4j;
 import org.ehrbase.openehr.sdk.aql.dto.AqlQuery;
 import org.ehrbase.openehr.sdk.aql.dto.operand.Primitive;
-import org.ehrbase.openehr.sdk.aql.render.AqlRenderer;
 
 import java.util.List;
 

src/main/java/de/vitagroup/num/service/policy/TemplatesPolicy.java

@@ -6,7 +6,6 @@
 import org.apache.commons.collections.MapUtils;
 import org.ehrbase.openehr.sdk.aql.dto.AqlQuery;
 import org.ehrbase.openehr.sdk.aql.dto.operand.Primitive;
-import org.ehrbase.openehr.sdk.aql.render.AqlRenderer;
 
 import java.util.List;
 import java.util.Map;

src/main/java/de/vitagroup/num/web/controller/AqlController.java

@@ -46,7 +46,7 @@ public class AqlController extends CustomizedExceptionHandler {
   @Operation(description = "Retrieves public or owned aql query by id.")
   @PreAuthorize(Role.MANAGER_OR_STUDY_COORDINATOR_OR_RESEARCHER_OR_CRITERIA_EDITOR)
   public ResponseEntity<AqlDto> getAqlById(
-      @AuthenticationPrincipal @NotNull Jwt principal, @NotNull @NotEmpty @PathVariable Long id) {
+      @AuthenticationPrincipal @NotNull Jwt principal, @NotNull @PathVariable Long id) {
     return ResponseEntity.ok(
         mapper.convertToDto(aqlService.getAqlById(id, principal.getSubject())));
   }
@@ -68,7 +68,7 @@ public ResponseEntity<AqlDto> createAql(
   @PreAuthorize(Role.CRITERIA_EDITOR)
   public ResponseEntity<AqlDto> updateAql(
       @AuthenticationPrincipal @NotNull Jwt principal,
-      @PathVariable("id") Long aqlId,
+      @NotNull @PathVariable("id") Long aqlId,
       @Valid @NotNull @RequestBody AqlDto aqlDto) {
     var aql = aqlService.updateAql(mapper.convertToEntity(aqlDto), aqlId, principal.getSubject(), aqlDto.getCategoryId());
 
@@ -79,7 +79,7 @@ public ResponseEntity<AqlDto> updateAql(
   @DeleteMapping("/{id}")
   @Operation(description = "Delete AQL criteria")
   @PreAuthorize(Role.CRITERIA_EDITOR_OR_SUPER_ADMIN)
-  public void deleteAql(@AuthenticationPrincipal @NotNull Jwt principal, @PathVariable Long id) {
+  public void deleteAql(@AuthenticationPrincipal @NotNull Jwt principal, @NotNull @PathVariable Long id) {
     aqlService.deleteById(id, principal.getSubject(), Roles.extractRoles(principal));
   }
 

src/main/java/de/vitagroup/num/web/controller/CohortController.java

@@ -1,11 +1,11 @@
 package de.vitagroup.num.web.controller;
 
-import de.vitagroup.num.domain.model.Cohort;
-import de.vitagroup.num.domain.model.Roles;
 import de.vitagroup.num.domain.dto.CohortDto;
 import de.vitagroup.num.domain.dto.CohortGroupDto;
 import de.vitagroup.num.domain.dto.CohortSizeDto;
 import de.vitagroup.num.domain.dto.TemplateSizeRequestDto;
+import de.vitagroup.num.domain.model.Cohort;
+import de.vitagroup.num.domain.model.Roles;
 import de.vitagroup.num.mapper.CohortMapper;
 import de.vitagroup.num.service.CohortService;
 import de.vitagroup.num.service.exception.CustomizedExceptionHandler;
@@ -14,10 +14,11 @@
 import de.vitagroup.num.web.config.Role;
 import io.swagger.v3.oas.annotations.Operation;
 import io.swagger.v3.oas.annotations.security.SecurityRequirement;
+import jakarta.validation.Valid;
+import jakarta.validation.constraints.NotNull;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.http.HttpHeaders;
-import org.springframework.http.HttpStatus;
 import org.springframework.http.HttpStatusCode;
 import org.springframework.http.ResponseEntity;
 import org.springframework.http.converter.HttpMessageNotReadableException;
@@ -27,8 +28,6 @@
 import org.springframework.web.bind.annotation.*;
 import org.springframework.web.context.request.WebRequest;
 
-import jakarta.validation.Valid;
-import jakarta.validation.constraints.NotNull;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.stream.Collectors;

src/main/java/de/vitagroup/num/web/controller/NumAttachmentController.java

@@ -21,7 +21,6 @@
 import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
 
 import jakarta.validation.Valid;
-import jakarta.validation.constraints.NotEmpty;
 import jakarta.validation.constraints.NotNull;
 import java.io.IOException;
 import java.util.List;
@@ -52,7 +51,7 @@ public ResponseEntity<String> createAttachment(@AuthenticationPrincipal @NotNull
     @PreAuthorize(Role.STUDY_COORDINATOR)
     @PostMapping(path = "/{projectId}", consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
     public ResponseEntity<String> createMultipleAttachments(@AuthenticationPrincipal @NotNull Jwt principal,
-                                                            @NotNull @NotEmpty @PathVariable Long projectId,
+                                                            @NotNull @PathVariable Long projectId,
                                                             @ModelAttribute @Valid LightAttachmentDto lightDto) throws IOException {
         attachmentService.saveAttachments(projectId, principal.getSubject(), lightDto, false);
         return ResponseEntity.ok("ok");
@@ -61,7 +60,7 @@ public ResponseEntity<String> createMultipleAttachments(@AuthenticationPrincipal
     @AuditLog(description = "Get a list of all attachments for one project (by projectId)")
     @Operation(description = "Get a list of all attachments for one project (by projectId)")
     @GetMapping("/project/{projectId}")
-    public ResponseEntity<List<AttachmentDto>> listAllAttachments(@NotNull @NotEmpty @PathVariable Long projectId) {
+    public ResponseEntity<List<AttachmentDto>> listAllAttachments(@NotNull @PathVariable Long projectId) {
         return ResponseEntity.ok(attachmentService.getAttachmentsBy(projectId).stream()
                 .map(attachment -> modelMapper.map(attachment, AttachmentDto.class))
                 .collect(Collectors.toList()));
@@ -89,7 +88,7 @@ public void deleteAql(@AuthenticationPrincipal @NotNull Jwt principal, @PathVari
     @AuditLog(description = "Download attachment")
     @Operation(description = "Download attachment with given id")
     @GetMapping("/{attachmentId}")
-    public ResponseEntity<StreamingResponseBody> downloadAttachment(@NotNull @NotEmpty @PathVariable Long attachmentId) {
+    public ResponseEntity<StreamingResponseBody> downloadAttachment(@NotNull @PathVariable Long attachmentId) {
         Attachment attachment = attachmentService.getAttachmentById(attachmentId);
         HttpHeaders header = new HttpHeaders();
         header.setContentDisposition(ContentDisposition.builder("attachment").filename(attachment.getName()).build());

src/main/java/de/vitagroup/num/web/controller/OrganizationController.java

@@ -23,7 +23,6 @@
 import org.springframework.web.bind.annotation.*;
 
 import jakarta.validation.Valid;
-import jakarta.validation.constraints.NotEmpty;
 import jakarta.validation.constraints.NotNull;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -47,8 +46,7 @@ public ResponseEntity<List<String>> getAllMailDomainsForActiveOrganizations() {
   @AuditLog
   @GetMapping("/{id}")
   @Operation(description = "Retrieves an organization by external id")
-  public ResponseEntity<OrganizationDto> getOrganizationById(
-      @NotNull @NotEmpty @PathVariable Long id) {
+  public ResponseEntity<OrganizationDto> getOrganizationById(@NotNull @PathVariable Long id) {
     return ResponseEntity.ok(mapper.convertToDto(organizationService.getOrganizationById(id)));
   }
 
@@ -102,9 +100,8 @@ public ResponseEntity<OrganizationDto> createOrganization(
   @PutMapping(value = "/{id}")
   @Operation(description = "Updates an organization")
   @PreAuthorize(Role.SUPER_ADMIN_OR_ORGANIZATION_ADMIN)
-  public ResponseEntity<OrganizationDto> updateOrganization(
-      @AuthenticationPrincipal @NotNull Jwt principal,
-      @PathVariable("id") Long organizationId,
+  public ResponseEntity<OrganizationDto> updateOrganization(@AuthenticationPrincipal @NotNull Jwt principal,
+      @NotNull @PathVariable("id") Long organizationId,
       @Valid @NotNull @RequestBody OrganizationDto organizationDto) {
     return ResponseEntity.ok(
         mapper.convertToDto(
@@ -120,7 +117,7 @@ public ResponseEntity<OrganizationDto> updateOrganization(
   @DeleteMapping(value = "/{id}")
   @PreAuthorize(Role.SUPER_ADMIN)
   public void deleteOrganization(@AuthenticationPrincipal @NotNull Jwt principal,
-                                 @PathVariable("id") Long organizationId) {
+                                 @NotNull @PathVariable("id") Long organizationId) {
     organizationService.deleteOrganization(organizationId, principal.getSubject());
   }
 }