Mongo DB Storage (#89)

* Add mongo layer

* Add mongo layer

* Update doi service

* updates

* test

* test

* Remove jsonschema2pojo

* trivy

* sonar

* sonar

* Update pidStatus to TOMBSTONED

* Update pidStatus to TOMBSTONED

* Update pidStatus to TOMBSTONED

* format

* code reivw

.github/workflows/.trivyignore

@@ -1,3 +1,3 @@
-# April 17
-# Spring boot needs to update its version of spring
-CVE-2024-22262
+# July 17
+# Spring boot needs to update its version of Apache Tomcat
+CVE-2024-34750

.gitignore

@@ -1,4 +1,4 @@
 target/
 .idea
-src/main/resources/*
+src/main/resources/application.properties
 .mvn/

pom.xml

@@ -6,7 +6,7 @@
     <artifactId>spring-boot-starter-parent</artifactId>
     <groupId>org.springframework.boot</groupId>
     <relativePath/>
-    <version>3.2.4</version> <!-- lookup parent from repository -->
+    <version>3.3.1</version> <!-- lookup parent from repository -->
   </parent>
   <artifactId>handle-manager</artifactId>
   <version>0.0.1-SNAPSHOT</version>
@@ -18,17 +18,17 @@
   <properties>
     <java.version>17</java.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <testcontainers.version>1.17.6</testcontainers.version>
+    <testcontainers.version>1.19.8</testcontainers.version>
     <apache-commons.version>4.3</apache-commons.version>
     <mockito-inline.version>5.2.0</mockito-inline.version>
+    <mongodb-driver.version>5.1.1</mongodb-driver.version>
     <okhttp3.version>4.10.0</okhttp3.version>
+    <version.victools>4.35.0</version.victools>
     <sonar.coverage.jacoco.xmlReportPaths>
       ../app-it/target/site/jacoco-aggregate/jacoco.xml
     </sonar.coverage.jacoco.xmlReportPaths>
     <sonar.host.url>https://sonarcloud.io</sonar.host.url>
     <sonar.organization>dissco</sonar.organization>
-    <spring-security.version>6.2.3</spring-security.version> <!-- 21/03/24: CVE-2024-22257-->
-    <version.victools>4.28.0</version.victools>
   </properties>
 
   <dependencyManagement>
@@ -97,21 +97,17 @@
 
     <!--Database Dependencies -->
     <dependency>
-      <groupId>org.postgresql</groupId>
-      <artifactId>postgresql</artifactId>
-      <version>${postgresql.version}</version>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-lang3</artifactId>
     </dependency>
     <dependency>
-      <groupId>org.jooq</groupId>
-      <artifactId>jooq</artifactId>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-starter-data-mongodb</artifactId>
     </dependency>
     <dependency>
-      <groupId>org.springframework</groupId>
-      <artifactId>spring-jdbc</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>org.apache.commons</groupId>
-      <artifactId>commons-lang3</artifactId>
+      <groupId>org.mongodb</groupId>
+      <artifactId>mongodb-driver-sync</artifactId>
+      <version>${mongodb-driver.version}</version>
     </dependency>
 
     <!--JsonSchema  -->
@@ -177,6 +173,11 @@
       <groupId>org.springframework.boot</groupId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>org.testcontainers</groupId>
+      <artifactId>mongodb</artifactId>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>com.squareup.okhttp3</groupId>
       <artifactId>okhttp</artifactId>

src/main/java/eu/dissco/core/handlemanager/configuration/AppConfig.java

@@ -1,6 +1,8 @@
 package eu.dissco.core.handlemanager.configuration;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.module.SimpleModule;
+import java.time.Instant;
 import java.util.Random;
 import javax.xml.XMLConstants;
 import javax.xml.parsers.DocumentBuilderFactory;
@@ -13,6 +15,8 @@
 @Configuration
 public class AppConfig {
 
+  public static final String DATE_STRING = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX";
+
   @Bean
   public DocumentBuilderFactory documentBuilderFactory() throws ParserConfigurationException {
     DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
@@ -31,7 +35,13 @@ public TransformerFactory transformerFactory() throws TransformerConfigurationEx
 
   @Bean
   public ObjectMapper objectMapper() {
-    return new ObjectMapper().findAndRegisterModules();
+    var mapper = new ObjectMapper()
+        .findAndRegisterModules();
+    SimpleModule dateModule = new SimpleModule();
+    dateModule.addSerializer(Instant.class, new InstantSerializer());
+    dateModule.addDeserializer(Instant.class, new InstantDeserializer());
+    mapper.registerModule(dateModule);
+    return mapper;
   }
 
   @Bean

src/main/java/eu/dissco/core/handlemanager/configuration/InstantDeserializer.java

@@ -0,0 +1,30 @@
+package eu.dissco.core.handlemanager.configuration;
+
+import static eu.dissco.core.handlemanager.configuration.AppConfig.DATE_STRING;
+
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
+import java.io.IOException;
+import java.time.Instant;
+import java.time.ZoneOffset;
+import java.time.format.DateTimeFormatter;
+import lombok.extern.slf4j.Slf4j;
+
+@Slf4j
+public class InstantDeserializer extends JsonDeserializer<Instant> {
+
+  private final DateTimeFormatter formatter = DateTimeFormatter.ofPattern(DATE_STRING).withZone(
+      ZoneOffset.UTC);
+
+  @Override
+  public Instant deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) {
+    try {
+      return Instant.from(formatter.parse(jsonParser.getText()));
+    } catch (IOException e) {
+      log.error("An error has occurred deserializing a date. More information: {}", e.getMessage());
+      return null;
+    }
+  }
+
+}

src/main/java/eu/dissco/core/handlemanager/configuration/InstantSerializer.java

@@ -0,0 +1,30 @@
+package eu.dissco.core.handlemanager.configuration;
+
+import static eu.dissco.core.handlemanager.configuration.AppConfig.DATE_STRING;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+import java.io.IOException;
+import java.time.Instant;
+import java.time.ZoneOffset;
+import java.time.format.DateTimeFormatter;
+import lombok.extern.slf4j.Slf4j;
+
+@Slf4j
+public class InstantSerializer extends JsonSerializer<Instant> {
+
+  private final DateTimeFormatter formatter = DateTimeFormatter.ofPattern(DATE_STRING).withZone(
+      ZoneOffset.UTC);
+
+  @Override
+  public void serialize(Instant value, JsonGenerator jsonGenerator,
+      SerializerProvider serializerProvider) {
+    try {
+      jsonGenerator.writeString(formatter.format(value));
+    } catch (IOException e) {
+      log.error("An error has occurred serializing a date. More information: {}", e.getMessage());
+    }
+  }
+
+}

src/main/java/eu/dissco/core/handlemanager/configuration/MongoConfig.java

@@ -0,0 +1,23 @@
+package eu.dissco.core.handlemanager.configuration;
+
+import com.mongodb.client.MongoClients;
+import com.mongodb.client.MongoCollection;
+import eu.dissco.core.handlemanager.properties.MongoProperties;
+import lombok.RequiredArgsConstructor;
+import org.bson.Document;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@RequiredArgsConstructor
+public class MongoConfig {
+
+  private final MongoProperties properties;
+
+  @Bean
+  public MongoCollection<Document> getHandleCollection() {
+    var client = MongoClients.create(properties.getConnectionString());
+    var database = client.getDatabase(properties.getDatabase());
+    return database.getCollection("handles");
+  }
+}

src/main/java/eu/dissco/core/handlemanager/controller/PidController.java

@@ -6,7 +6,6 @@
 
 import com.fasterxml.jackson.databind.JsonNode;
 import eu.dissco.core.handlemanager.domain.jsonapi.JsonApiWrapperRead;
-import eu.dissco.core.handlemanager.domain.jsonapi.JsonApiWrapperReadSingle;
 import eu.dissco.core.handlemanager.domain.jsonapi.JsonApiWrapperWrite;
 import eu.dissco.core.handlemanager.domain.requests.RollbackRequest;
 import eu.dissco.core.handlemanager.domain.validation.JsonSchemaValidator;
@@ -18,7 +17,6 @@
 import io.swagger.v3.oas.annotations.Operation;
 import jakarta.servlet.http.HttpServletRequest;
 import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import lombok.RequiredArgsConstructor;
@@ -54,13 +52,13 @@ public class PidController {
   // Getters
   @Operation(summary = "Resolve single PID record")
   @GetMapping("/{prefix}/{suffix}")
-  public ResponseEntity<JsonApiWrapperReadSingle> resolvePid(@PathVariable("prefix") String prefix,
+  public ResponseEntity<JsonApiWrapperRead> resolvePid(@PathVariable("prefix") String prefix,
       @PathVariable("suffix") String suffix, HttpServletRequest r) throws PidResolutionException {
-    String path = applicationProperties.getUiUrl() + r.getRequestURI();
+    String link = applicationProperties.getUiUrl() + "/" + r.getRequestURI();
     String handle = prefix + "/" + suffix;
 
     if (prefix.equals(applicationProperties.getPrefix())) {
-      var node = service.resolveSingleRecord(handle.getBytes(StandardCharsets.UTF_8), path);
+      var node = service.resolveSingleRecord(handle, link);
       return ResponseEntity.status(HttpStatus.OK).body(node);
     }
     throw new PidResolutionException(
@@ -73,17 +71,15 @@ public ResponseEntity<JsonApiWrapperReadSingle> resolvePid(@PathVariable("prefix
   public ResponseEntity<JsonApiWrapperRead> resolvePids(
       @RequestParam List<String> handles,
       HttpServletRequest r) throws InvalidRequestException {
-    String path = applicationProperties.getUiUrl() + r.getRequestURI();
+    String link = applicationProperties.getUiUrl() + "/" + r.getRequestURI();
 
     if (handles.size() > applicationProperties.getMaxHandles()) {
       throw new InvalidRequestException(
           "Attempting to resolve more than maximum permitted PIDs in a single request. Maximum handles: "
               + applicationProperties.getMaxHandles());
     }
-    List<byte[]> handleBytes = new ArrayList<>();
-    handles.forEach(h -> handleBytes.add(h.getBytes(StandardCharsets.UTF_8)));
 
-    return ResponseEntity.status(HttpStatus.OK).body(service.resolveBatchRecord(handleBytes, path));
+    return ResponseEntity.status(HttpStatus.OK).body(service.resolveBatchRecord(handles, link));
   }
 
   @Operation(summary = "Given a physical identifier (i.e. local identifier), resolve PID record")
@@ -124,18 +120,14 @@ public ResponseEntity<JsonApiWrapperWrite> updateRecord(@PathVariable("prefix")
     log.info("Received single update request for PID {}/{} from user {}", prefix, suffix,
         authentication.getName());
     schemaValidator.validatePatchRequest(request);
-
-    JsonNode data = request.get(NODE_DATA);
-    byte[] handle = (prefix + "/" + suffix).getBytes(StandardCharsets.UTF_8);
-    byte[] handleData = data.get(NODE_ID).asText().getBytes(StandardCharsets.UTF_8);
-
-    if (!Arrays.equals(handle, handleData)) {
+    var handle = (prefix + "/" + suffix);
+    var handleData = request.get(NODE_DATA).get(NODE_ID).asText();
+    if (!handle.equals(handleData)) {
       throw new InvalidRequestException(String.format(
           "Handle in request path does not match id in request body. Path: %s, Body: %s",
-          new String(handle, StandardCharsets.UTF_8),
-          new String(handleData, StandardCharsets.UTF_8)));
+          handle,
+          handleData));
     }
-
     return ResponseEntity.status(HttpStatus.OK).body(service.updateRecords(List.of(request), true));
   }
 
@@ -171,7 +163,8 @@ public ResponseEntity<JsonApiWrapperWrite> archiveRecord(@PathVariable("prefix")
               + new String(handle, StandardCharsets.UTF_8)
               + ". Body: " + new String(handleRequest, StandardCharsets.UTF_8));
     }
-    return ResponseEntity.status(HttpStatus.OK).body(service.archiveRecordBatch(List.of(request)));
+    return ResponseEntity.status(HttpStatus.OK)
+        .body(service.tombstoneRecords(List.of(request)));
   }
 
   @Operation(summary = "rollback handle creation")
@@ -227,7 +220,7 @@ public ResponseEntity<JsonApiWrapperWrite> archiveRecords(@RequestBody List<Json
       schemaValidator.validatePutRequest(request);
     }
     log.info("Received valid archive request");
-    return ResponseEntity.status(HttpStatus.OK).body(service.archiveRecordBatch(requests));
+    return ResponseEntity.status(HttpStatus.OK).body(service.tombstoneRecords(requests));
   }
 
 }