WIP: Migrate to PostgreSQL

FAIRDataTeam · Mar 17, 2024 · 0772681 · 0772681
1 parent b62a88d
commit 0772681
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -8,13 +8,29 @@ jobs:
   test:
     name: Test
     strategy:
+      fail-fast: false
       matrix:
         os:
-          - ubuntu-20.04
-          # - windows-2022 (MongoDB issues in CI)
-          - macos-12
+          - ubuntu-22.04
+          # - windows-2022 (cannot use Docker for postgres)
+          # - macos-12 (cannot use Docker for postgres)
     runs-on: ${{ matrix.os }}
 
+    services:
+      postgres:
+        image: postgres:16
+        env:
+          POSTGRES_DB: fdp_test
+          POSTGRES_USER: fdp
+          POSTGRES_PASSWORD: fdp
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 54321:5432
+
     env:
       JAVA_DISTRIBUTION: temurin
       JAVA_VERSION: 21
@@ -25,15 +41,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Set up MongoDB
-        uses: ankane/setup-mongodb@v1
-        with:
-          mongodb-version: '5.0'
-
-      - name: Check MongoDB
-        run: |
-          mongo --eval "db.version()"
-
       - name: Setup Java
         uses: actions/setup-java@v3
         with:
@@ -48,6 +55,12 @@ jobs:
       - name: Test
         run: |
           mvn -q -U -B test
+        env:
+          FDP_POSTGRES_HOST: localhost
+          FDP_POSTGRES_PORT: 54321
+          FDP_POSTGRES_DB: fdp_test
+          FDP_POSTGRES_USERNAME: fdp
+          FDP_POSTGRES_PASSWORD: fdp
 
       - name: Package
         run: |

diff --git a/.gitignore b/.gitignore
@@ -3,4 +3,5 @@ target/
 
 # Netbeans
 nb-configuration\.xml
-/nbproject/
+/nbproject/
+*.iml
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>3.1.5</version>
+        <version>3.2.3</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
     <groupId>nl.dtls</groupId>
@@ -52,16 +52,15 @@
 
         <!-- Project related -->
         <spring.rdf.migration.version>1.2.0.RELEASE</spring.rdf.migration.version>
-        <spring.security.acl.mongo.version>5.2.4.RELEASE</spring.security.acl.mongo.version>
 
         <!-- Core -->
         <springdoc.version>2.2.0</springdoc.version>
-        <mongock.version>5.3.5</mongock.version>
-        <mongodb.spring-data.version>4.1.5</mongodb.spring-data.version>
+        <postgresql.version>42.7.2</postgresql.version>
         <rdf4j.version>4.3.8</rdf4j.version>
         <jwt.version>0.12.3</jwt.version>
         <lombok.version>1.18.30</lombok.version>
         <rdf-resolver.version>0.1.2-SNAPSHOT</rdf-resolver.version>
+        <hypersistence.version>3.7.3</hypersistence.version>
 
         <!-- Test -->
         <httpclient5.version>5.2.2</httpclient5.version>
@@ -104,18 +103,6 @@
         </repository>
     </repositories>
 
-    <dependencyManagement>
-        <dependencies>
-            <dependency>
-                <groupId>io.mongock</groupId>
-                <artifactId>mongock-bom</artifactId>
-                <version>${mongock.version}</version>
-                <type>pom</type>
-                <scope>import</scope>
-            </dependency>
-        </dependencies>
-    </dependencyManagement>
-
     <dependencies>
 
         <!-- ////////////////// -->
@@ -154,7 +141,7 @@
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-data-mongodb</artifactId>
+            <artifactId>spring-boot-starter-data-jpa</artifactId>
         </dependency>
         <dependency>
             <groupId>org.springframework.security</groupId>
@@ -172,28 +159,6 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-validation</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.springframework.security</groupId>
-            <artifactId>spring-security-acl-mongodb</artifactId>
-            <version>${spring.security.acl.mongo.version}</version>
-        </dependency>
-
-        <!-- ////////////////// -->
-        <!--   Mongock          -->
-        <!-- ////////////////// -->
-        <dependency>
-            <groupId>io.mongock</groupId>
-            <artifactId>mongock-springboot</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.mongock</groupId>
-            <artifactId>mongodb-springdata-v4-driver</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.springframework.data</groupId>
-            <artifactId>spring-data-mongodb</artifactId>
-            <version>${mongodb.spring-data.version}</version>
-        </dependency>
 
         <!-- ////////////////// -->
         <!--   Core             -->
@@ -257,6 +222,22 @@
             <artifactId>rdf-resource-resolver-api</artifactId>
             <version>${rdf-resolver.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.flywaydb</groupId>
+            <artifactId>flyway-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>io.hypersistence</groupId>
+            <artifactId>hypersistence-utils-hibernate-63</artifactId>
+            <version>${hypersistence.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.postgresql</groupId>
+            <artifactId>postgresql</artifactId>
+            <version>${postgresql.version}</version>
+            <scope>runtime</scope>
+        </dependency>
 
         <!-- ////////////////// -->
         <!--   Test             -->

diff --git a/src/main/java/nl/dtls/fairdatapoint/api/controller/apikey/ApiKeyController.java b/src/main/java/nl/dtls/fairdatapoint/api/controller/apikey/ApiKeyController.java
@@ -23,26 +23,27 @@
 package nl.dtls.fairdatapoint.api.controller.apikey;
 
 import io.swagger.v3.oas.annotations.tags.Tag;
+import lombok.RequiredArgsConstructor;
 import nl.dtls.fairdatapoint.api.dto.apikey.ApiKeyDTO;
 import nl.dtls.fairdatapoint.entity.exception.ResourceNotFoundException;
 import nl.dtls.fairdatapoint.service.apikey.ApiKeyService;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
 
 import java.util.List;
+import java.util.UUID;
 
 import static java.lang.String.format;
 
 @Tag(name = "Authentication and Authorization")
 @RestController
 @RequestMapping("/api-keys")
+@RequiredArgsConstructor
 public class ApiKeyController {
 
-    @Autowired
-    private ApiKeyService apiKeyService;
+    private final ApiKeyService apiKeyService;
 
     @GetMapping(produces = MediaType.APPLICATION_JSON_VALUE)
     public ResponseEntity<List<ApiKeyDTO>> getApiKeys() {
@@ -59,7 +60,7 @@ public ResponseEntity<ApiKeyDTO> createApiKey() {
     @DeleteMapping("/{uuid}")
     @ResponseStatus(HttpStatus.NO_CONTENT)
     public ResponseEntity<Void> deleteApiKey(
-            @PathVariable final String uuid
+            @PathVariable final UUID uuid
     ) throws ResourceNotFoundException {
         final boolean result = apiKeyService.delete(uuid);
         if (result) {

diff --git a/src/main/java/nl/dtls/fairdatapoint/api/controller/config/ConfigController.java b/src/main/java/nl/dtls/fairdatapoint/api/controller/config/ConfigController.java
@@ -23,9 +23,9 @@
 package nl.dtls.fairdatapoint.api.controller.config;
 
 import io.swagger.v3.oas.annotations.tags.Tag;
+import lombok.RequiredArgsConstructor;
 import nl.dtls.fairdatapoint.api.dto.config.BootstrapConfigDTO;
 import nl.dtls.fairdatapoint.service.config.ConfigService;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -36,10 +36,10 @@
 @Tag(name = "Client")
 @RestController
 @RequestMapping("/configs")
+@RequiredArgsConstructor
 public class ConfigController {
 
-    @Autowired
-    private ConfigService configService;
+    private final ConfigService configService;
 
     @GetMapping(path = "/bootstrap", produces = MediaType.APPLICATION_JSON_VALUE)
     public ResponseEntity<BootstrapConfigDTO> getBootstrapConfig() {

diff --git a/src/main/java/nl/dtls/fairdatapoint/api/controller/dashboard/DashboardController.java b/src/main/java/nl/dtls/fairdatapoint/api/controller/dashboard/DashboardController.java
@@ -24,12 +24,11 @@
 
 import io.swagger.v3.oas.annotations.tags.Tag;
 import jakarta.servlet.http.HttpServletRequest;
+import lombok.RequiredArgsConstructor;
 import nl.dtls.fairdatapoint.api.dto.dashboard.DashboardItemDTO;
 import nl.dtls.fairdatapoint.service.dashboard.DashboardService;
 import nl.dtls.fairdatapoint.service.metadata.exception.MetadataServiceException;
 import org.eclipse.rdf4j.model.IRI;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -46,14 +45,12 @@
 @Tag(name = "Client")
 @RestController
 @RequestMapping("/dashboard")
+@RequiredArgsConstructor
 public class DashboardController {
 
-    @Autowired
-    @Qualifier("persistentUrl")
-    private String persistentUrl;
+    private final String persistentUrl;
 
-    @Autowired
-    private DashboardService dashboardService;
+    private final DashboardService dashboardService;
 
     @GetMapping(produces = MediaType.APPLICATION_JSON_VALUE)
     public ResponseEntity<List<DashboardItemDTO>> getDashboard(

diff --git a/src/main/java/nl/dtls/fairdatapoint/api/controller/exception/ExceptionControllerAdvice.java b/src/main/java/nl/dtls/fairdatapoint/api/controller/exception/ExceptionControllerAdvice.java
@@ -78,6 +78,7 @@ public class ExceptionControllerAdvice {
     public ErrorDTO handleConstraintViolation(Exception exception) {
         log.warn(exception.getMessage());
         log.debug("Handling bad request (ConstraintViolation)", exception);
+        exception.printStackTrace();
         return new ErrorDTO(HttpStatus.BAD_REQUEST, exception.getMessage());
     }
 
@@ -95,6 +96,7 @@ public ErrorDTO handleConstraintViolation(Exception exception) {
     public ErrorDTO handleValidationException(Exception exception) {
         log.warn(exception.getMessage());
         log.debug("Handling bad request (ValidationException)", exception);
+        exception.printStackTrace();
         return new ErrorDTO(HttpStatus.BAD_REQUEST, exception.getMessage());
     }
 
@@ -112,6 +114,7 @@ public ErrorDTO handleValidationException(Exception exception) {
     public Model handleRdfValidationException(RdfValidationException exception) {
         final Model validationReportModel = exception.getModel();
         log.debug("Handling bad request (RdfValidationException)", exception);
+        exception.printStackTrace();
 
         // Log number of errors
         final IRI validationResultIri = i("http://www.w3.org/ns/shacl#ValidationResult");
@@ -140,6 +143,7 @@ public Model handleRdfValidationException(RdfValidationException exception) {
             )
     )
     public ErrorDTO handleInvalidQuery(MalformedQueryException exception) {
+        exception.printStackTrace();
         return handleInvalidSparqlQuery(exception);
     }
 
@@ -155,6 +159,7 @@ public ErrorDTO handleInvalidQuery(MalformedQueryException exception) {
             )
     )
     public ErrorDTO handleInvalidQuery(QueryEvaluationException exception) {
+        exception.printStackTrace();
         return handleInvalidSparqlQuery(exception);
     }
 
@@ -172,6 +177,7 @@ public ErrorDTO handleInvalidQuery(QueryEvaluationException exception) {
     public ErrorDTO handleUnauthorized(Exception exception) {
         log.error(exception.getMessage());
         log.debug("Handling unauthorized", exception);
+        exception.printStackTrace();
         return new ErrorDTO(HttpStatus.UNAUTHORIZED, exception.getMessage());
     }
 
@@ -189,6 +195,7 @@ public ErrorDTO handleUnauthorized(Exception exception) {
     public ErrorDTO handleForbidden(Exception exception) {
         log.error(exception.getMessage());
         log.debug("Handling forbidden", exception);
+        exception.printStackTrace();
         return new ErrorDTO(HttpStatus.FORBIDDEN, exception.getMessage());
     }
 
@@ -206,6 +213,7 @@ public ErrorDTO handleForbidden(Exception exception) {
     public ErrorDTO handleResourceNotFound(ResourceNotFoundException exception) {
         log.error(exception.getMessage());
         log.debug("Handling resource not found", exception);
+        exception.printStackTrace();
         return new ErrorDTO(HttpStatus.NOT_FOUND, exception.getMessage());
     }
 
@@ -223,12 +231,14 @@ public ErrorDTO handleResourceNotFound(ResourceNotFoundException exception) {
     public ErrorDTO handleInternalServerError(Exception exception) {
         log.error(exception.getMessage());
         log.debug("Handling internal server error (MetadataServiceException)", exception);
+        exception.printStackTrace();
         return new ErrorDTO(HttpStatus.INTERNAL_SERVER_ERROR, exception.getMessage());
     }
 
     @ExceptionHandler(AbstractIndexException.class)
     public ResponseEntity<ErrorDTO> handleIndexException(AbstractIndexException exception) {
         log.debug("Handling index exception", exception);
+        exception.printStackTrace();
         return new ResponseEntity<>(exception.getErrorDTO(), exception.getStatus());
     }
 

diff --git a/src/main/java/nl/dtls/fairdatapoint/api/controller/form/FormAutocompleteController.java b/src/main/java/nl/dtls/fairdatapoint/api/controller/form/FormAutocompleteController.java
@@ -24,10 +24,10 @@
 
 import io.swagger.v3.oas.annotations.tags.Tag;
 import jakarta.validation.Valid;
+import lombok.RequiredArgsConstructor;
 import nl.dtls.fairdatapoint.api.dto.form.FormAutocompleteItemDTO;
 import nl.dtls.fairdatapoint.api.dto.form.FormAutocompleteRequestDTO;
 import nl.dtls.fairdatapoint.service.form.autocomplete.FormsAutocompleteService;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -41,10 +41,10 @@
 @Tag(name = "Client")
 @RestController
 @RequestMapping("/forms")
+@RequiredArgsConstructor
 public class FormAutocompleteController {
 
-    @Autowired
-    private FormsAutocompleteService autocompleteService;
+    private final FormsAutocompleteService autocompleteService;
 
     @PostMapping(
             path = "/autocomplete",