Merge branch '84-search-service' into dev

# Conflicts:
#	fda-database-service/services/src/main/java/at/tuwien/service/DatabaseService.java
#	fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/Database.java
#	fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/Table.java
#	fda-table-service/rest-service/src/main/resources/application-docker.yml
#	fda-table-service/rest-service/src/main/resources/application.yml
#	fda-table-service/services/src/main/java/at/tuwien/service/TableService.java


Former-commit-id: 0f9801f0

docker-compose.yml

@@ -230,6 +230,7 @@ services:
     container_name: fda-search-service
     hostname: fda-search-service
     image: elasticsearch:7.13.4
+    command: ["elasticsearch", "-Elogger.level=WARN"]
     networks:
       - fda-public
     environment:
@@ -239,6 +240,8 @@ services:
     ports:
       - 9200:9200
       - 9600:9600
+    logging:
+      driver: json-file
 
   fda-ui:
     restart: on-failure
@@ -269,4 +272,4 @@ services:
       API_IMAGE: http://fda-container-service:9091
       API_DATABASE: http://fda-database-service:9092
       API_TABLES: http://fda-table-service:9094
-      API_ANALYSE: http://fda-analyse-service:5000
+      API_ANALYSE: http://fda-analyse-service:5000
\ No newline at end of file

fda-database-service/services/src/main/java/at/tuwien/config/IndexInitializer.java

+package at.tuwien.config;
+
+import at.tuwien.entities.database.Database;
+import com.google.common.collect.ImmutableMap;
+import lombok.extern.log4j.Log4j2;
+import org.springframework.boot.context.event.ApplicationReadyEvent;
+import org.springframework.context.event.EventListener;
+import org.springframework.data.elasticsearch.core.ElasticsearchOperations;
+import org.springframework.data.elasticsearch.core.mapping.IndexCoordinates;
+import org.springframework.stereotype.Component;
+
+import java.util.HashMap;
+
+@Component
+@Log4j2
+public class IndexInitializer {
+
+    private final ElasticsearchOperations elasticsearchOperations;
+
+    public IndexInitializer(ElasticsearchOperations elasticsearchOperations) {
+        this.elasticsearchOperations = elasticsearchOperations;
+    }
+
+    @EventListener(ApplicationReadyEvent.class)
+    public void initIndex() {
+        log.debug("creating index");
+        IndexCoordinates indexCoordinates = IndexCoordinates.of("databaseindex");
+        if (!elasticsearchOperations.indexOps(indexCoordinates).exists()) {
+            elasticsearchOperations.indexOps(indexCoordinates).create();
+            elasticsearchOperations.indexOps(indexCoordinates).createMapping(Database.class);
+        }
+    }
+}

fda-database-service/services/src/main/java/at/tuwien/repository/elastic/DatabaseRepository.java → fda-database-service/services/src/main/java/at/tuwien/repository/elastic/DatabaseidxRepository.java

@@ -5,5 +5,5 @@ import org.springframework.data.elasticsearch.repository.ElasticsearchRepository
 import org.springframework.stereotype.Repository;
 
 @Repository(value = "ElasticDatabaseRepository")
-public interface DatabaseRepository extends ElasticsearchRepository<Database, Long> {
+public interface DatabaseidxRepository extends ElasticsearchRepository<Database, Long> {
 }

fda-database-service/services/src/main/java/at/tuwien/service/DatabaseService.java

@@ -11,6 +11,7 @@ import at.tuwien.mapper.DatabaseMapper;
 import at.tuwien.mapper.ImageMapper;
 import at.tuwien.repository.jpa.ContainerRepository;
 import at.tuwien.repository.jpa.DatabaseRepository;
+import at.tuwien.repository.elastic.DatabaseidxRepository;
 import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
@@ -31,18 +32,21 @@ public class DatabaseService extends JdbcConnector {
 
     private final ContainerRepository containerRepository;
     private final DatabaseRepository databaseRepository;
+    private final DatabaseidxRepository databaseidxRepository;
     private final DatabaseMapper databaseMapper;
     private final AmqpService amqpService;
     private final AmqpMapper amqpMapper;
 
     @Autowired
     public DatabaseService(ContainerRepository containerRepository, DatabaseRepository databaseRepository,
-                           ImageMapper imageMapper, DatabaseMapper databaseMapper,
+                           DatabaseidxRepository databaseidxRepository, ImageMapper imageMapper,
+                           DatabaseMapper databaseMapper,
                            AmqpService amqpService, AmqpMapper amqpMapper) {
         super(imageMapper, databaseMapper);
         this.containerRepository = containerRepository;
         this.databaseRepository = databaseRepository;
         this.databaseMapper = databaseMapper;
+        this.databaseidxRepository = databaseidxRepository;
         this.amqpService = amqpService;
         this.amqpMapper = amqpMapper;
     }
@@ -125,6 +129,8 @@ public class DatabaseService extends JdbcConnector {
         final Database out = databaseRepository.save(database);
         log.info("Created database {}", out.getId());
         log.debug("created database {}", out);
+        // save in database_index - elastic search
+        databaseidxRepository.save(database);
         return out;
     }
 
@@ -148,6 +154,8 @@ public class DatabaseService extends JdbcConnector {
         final Database out = databaseRepository.save(database);
         log.info("Updated database {}", out.getId());
         log.debug("updated database {}", out);
+        // save in database_index - elastic search
+        databaseidxRepository.save(database);
         return out;
     }
 

fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/Database.java

@@ -21,8 +21,8 @@ import java.util.List;
 @Builder
 @AllArgsConstructor
 @NoArgsConstructor
+@Document(indexName = "databaseindex", createIndex = false)
 @Where(clause = "deleted is null")
-@Document(indexName = "databaseindex")
 @ToString(onlyExplicitlyIncluded = true)
 @EntityListeners(AuditingEntityListener.class)
 @EqualsAndHashCode(onlyExplicitlyIncluded = true)

fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/Table.java

@@ -6,6 +6,9 @@ import lombok.*;
 import org.hibernate.annotations.GenericGenerator;
 import org.springframework.data.annotation.CreatedDate;
 import org.springframework.data.annotation.LastModifiedDate;
+import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
 import javax.persistence.*;
@@ -17,6 +20,7 @@ import java.util.List;
 @Builder
 @AllArgsConstructor
 @NoArgsConstructor
+@Document(indexName = "tblindex", createIndex = false)
 @IdClass(TableKey.class)
 @ToString(onlyExplicitlyIncluded = true)
 @EntityListeners(AuditingEntityListener.class)
@@ -67,6 +71,7 @@ public class Table {
 
     @ToString.Include
     @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.ALL, mappedBy = "table")
+    @Field(type = FieldType.Nested)
     private List<TableColumn> columns;
 
     @Column(nullable = false, updatable = false)

fda-table-service/rest-service/src/main/resources/application-docker.yml

@@ -31,6 +31,7 @@ eureka:
 fda:
   mapping.path: /root
   table.path: /root
+  elastic.endpoint: fda-search-service:9200
 zenodo:
   endpoint: https://sandbox.zenodo.org/
   api_key: "${ZENODO_API_KEY}"
\ No newline at end of file

fda-table-service/rest-service/src/main/resources/application.yml

@@ -32,6 +32,7 @@ eureka:
 fda:
   mapping.path: rest-service/src/main/resources
   table.path: rest-service/src/main/java/at/tuwien/userdb
+  elastic.endpoint: fda-search-service:9200
 zenodo:
   endpoint: https://sandbox.zenodo.org/
   api_key: "${ZENODO_API_KEY}"
\ No newline at end of file

fda-table-service/services/src/main/java/at/tuwien/config/ElasticsearchConfig.java

+package at.tuwien.config;
+
+import org.elasticsearch.client.RestHighLevelClient;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.data.elasticsearch.client.ClientConfiguration;
+import org.springframework.data.elasticsearch.client.RestClients;
+import org.springframework.data.elasticsearch.core.ElasticsearchOperations;
+import org.springframework.data.elasticsearch.core.ElasticsearchRestTemplate;
+import org.springframework.data.elasticsearch.repository.config.EnableElasticsearchRepositories;
+
+import java.util.Properties;
+
+@Configuration
+public class ElasticsearchConfig {
+
+    @Value("${fda.elastic.endpoint}")
+    private String elasticEndpoint;
+
+    @Bean
+    public RestHighLevelClient client() {
+        ClientConfiguration clientConfiguration = ClientConfiguration.builder()
+                .connectedTo(elasticEndpoint)
+                .build();
+
+        return RestClients.create(clientConfiguration).rest();
+    }
+
+    @Bean
+    public ElasticsearchOperations elasticsearchTemplate() {
+        return new ElasticsearchRestTemplate(client());
+    }
+}
\ No newline at end of file

fda-table-service/services/src/main/java/at/tuwien/config/IndexInitializer.java

+package at.tuwien.config;
+
+import at.tuwien.entities.database.Database;
+import com.google.common.collect.ImmutableMap;
+import lombok.extern.log4j.Log4j2;
+import org.springframework.boot.context.event.ApplicationReadyEvent;
+import org.springframework.context.event.EventListener;
+import org.springframework.data.elasticsearch.core.ElasticsearchOperations;
+import org.springframework.data.elasticsearch.core.mapping.IndexCoordinates;
+import org.springframework.stereotype.Component;
+
+import java.util.HashMap;
+
+@Component
+@Log4j2
+public class IndexInitializer {
+
+    private final ElasticsearchOperations elasticsearchOperations;
+
+    public IndexInitializer(ElasticsearchOperations elasticsearchOperations) {
+        this.elasticsearchOperations = elasticsearchOperations;
+    }
+
+    @EventListener(ApplicationReadyEvent.class)
+    public void initIndex() {
+        log.debug("creating index");
+        IndexCoordinates indexCoordinates = IndexCoordinates.of("tblindex");
+        if (!elasticsearchOperations.indexOps(indexCoordinates).exists()) {
+            elasticsearchOperations.indexOps(indexCoordinates).create();
+            elasticsearchOperations.indexOps(indexCoordinates).createMapping(Database.class);
+        }
+    }
+}

fda-table-service/services/src/main/java/at/tuwien/repository/elastic/DatabaseidxRepository.java

+package at.tuwien.repository.elastic;
+
+import at.tuwien.entities.database.Database;
+import org.springframework.data.elasticsearch.repository.ElasticsearchRepository;
+import org.springframework.stereotype.Repository;
+
+@Repository(value = "ElasticDatabaseRepository")
+public interface DatabaseidxRepository extends ElasticsearchRepository<Database, Long> {
+}

fda-table-service/services/src/main/java/at/tuwien/repository/elastic/DatabaseRepository.java → fda-table-service/services/src/main/java/at/tuwien/repository/elastic/TableidxRepository.java

 package at.tuwien.repository.elastic;
 
-import at.tuwien.entities.database.Database;
+import at.tuwien.entities.database.table.Table;
 import org.springframework.data.elasticsearch.repository.ElasticsearchRepository;
 import org.springframework.stereotype.Repository;
 
 @Repository(value = "ElasticDatabaseService")
-public interface DatabaseRepository extends ElasticsearchRepository<Database, Long> {
+public interface TableidxRepository extends ElasticsearchRepository<Table, Long> {
 }
\ No newline at end of file