attempt in LAZY-lize all EAGER loading references for better performance

fda-container-service/rest-service/src/main/java/at/tuwien/endpoints/ContainerEndpoint.java

@@ -13,6 +13,7 @@ import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 
 import javax.validation.Valid;
@@ -37,6 +38,7 @@ public class ContainerEndpoint {
         this.containerService = containerService;
     }
 
+    @Transactional
     @GetMapping("/")
     @ApiOperation(value = "List all containers", notes = "Lists the containers in the metadata database.")
     @ApiResponses({
@@ -51,6 +53,7 @@ public class ContainerEndpoint {
                         .collect(Collectors.toList()));
     }
 
+    @Transactional
     @PostMapping("/")
     @ApiOperation(value = "Creates a new container", notes = "Creates a new container whose image is registered in the metadata database too.")
     @ApiResponses({
@@ -67,6 +70,7 @@ public class ContainerEndpoint {
                 .body(response);
     }
 
+    @Transactional
     @GetMapping("/{id}")
     @ApiOperation(value = "Get all informations about a container", notes = "Since we follow the REST-principle, this method provides more information than the findAll method.")
     @ApiResponses({
@@ -95,6 +99,7 @@ public class ContainerEndpoint {
                 .body(containerDto);
     }
 
+    @Transactional
     @PutMapping("/{id}")
     @ApiOperation(value = "Change the state of a container", notes = "The new state can only be one of START/STOP.")
     @ApiResponses({

fda-container-service/rest-service/src/main/java/at/tuwien/endpoints/ImageEndpoint.java

@@ -16,6 +16,7 @@ import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 
 import javax.validation.Valid;
@@ -39,6 +40,7 @@ public class ImageEndpoint {
         this.imageMapper = imageMapper;
     }
 
+    @Transactional
     @GetMapping("/")
     @ApiOperation(value = "List all images", notes = "Lists the images in the metadata database.")
     @ApiResponses({
@@ -53,6 +55,7 @@ public class ImageEndpoint {
                         .collect(Collectors.toList()));
     }
 
+    @Transactional
     @PostMapping("/")
     @ApiOperation(value = "Creates a new image", notes = "Creates a new image in the metadata database.")
     @ApiResponses({
@@ -68,6 +71,7 @@ public class ImageEndpoint {
                 .body(imageMapper.containerImageToImageDto(image));
     }
 
+    @Transactional
     @GetMapping("/{id}")
     @ApiOperation(value = "Get all informations about a image", notes = "Since we follow the REST-principle, this method provides more information than the findAll method.")
     @ApiResponses({
@@ -81,6 +85,7 @@ public class ImageEndpoint {
                 .body(imageMapper.containerImageToImageDto(image));
     }
 
+    @Transactional
     @PutMapping("/{id}")
     @ApiOperation(value = "Update image information", notes = "Polls new information about an image")
     @ApiResponses({
@@ -102,7 +107,7 @@ public class ImageEndpoint {
             @ApiResponse(code = 401, message = "Not authorized to delete a image."),
             @ApiResponse(code = 404, message = "No image found with this id in metadata database."),
     })
-    public ResponseEntity delete(@NotNull @PathVariable Long id) throws ImageNotFoundException {
+    public ResponseEntity<?> delete(@NotNull @PathVariable Long id) throws ImageNotFoundException {
         imageService.delete(id);
         return ResponseEntity.status(HttpStatus.OK)
                 .build();

fda-container-service/rest-service/src/test/java/at/tuwien/service/ContainerServiceIntegrationTest.java

@@ -23,7 +23,7 @@ import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.Arrays;
 import java.util.Map;
 

fda-container-service/services/src/main/java/at/tuwien/service/ContainerService.java

@@ -24,7 +24,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.springframework.util.SocketUtils;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.time.Instant;
 import java.util.HashMap;
 import java.util.List;
@@ -109,6 +109,7 @@ public class ContainerService {
         return container.get();
     }
 
+    @Transactional
     public void remove(Long containerId) throws ContainerNotFoundException, DockerClientException,
             ContainerStillRunningException {
         final Optional<Container> container = containerRepository.findById(containerId);
@@ -128,6 +129,7 @@ public class ContainerService {
         log.debug("Removed container {}", containerId);
     }
 
+    @Transactional
     public Container getById(Long containerId) throws ContainerNotFoundException {
         final Optional<Container> container = containerRepository.findById(containerId);
         if (container.isEmpty()) {
@@ -137,6 +139,7 @@ public class ContainerService {
         return container.get();
     }
 
+    @Transactional
     public List<Container> getAll() {
         return containerRepository.findAll();
     }
@@ -147,6 +150,7 @@ public class ContainerService {
      * @param containerId The container ID
      * @return The container
      */
+    @Transactional
     public Container start(Long containerId) throws ContainerNotFoundException, DockerClientException {
         Container container = getById(containerId);
         try {

fda-container-service/services/src/main/java/at/tuwien/service/ImageService.java

@@ -17,6 +17,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.dao.EmptyResultDataAccessException;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
 
 import javax.persistence.EntityNotFoundException;
 import javax.validation.ConstraintViolationException;
@@ -40,10 +41,12 @@ public class ImageService {
         this.imageMapper = imageMapper;
     }
 
+    @Transactional
     public List<ContainerImage> getAll() {
         return imageRepository.findAll();
     }
 
+    @Transactional
     public ContainerImage getById(Long imageId) throws ImageNotFoundException {
         final Optional<ContainerImage> image = imageRepository.findById(imageId);
         if (image.isEmpty()) {
@@ -53,6 +56,7 @@ public class ImageService {
         return image.get();
     }
 
+    @Transactional
     public ContainerImage create(ImageCreateDto createDto) throws ImageNotFoundException, ImageAlreadyExistsException {
         pull(createDto.getRepository(), createDto.getTag());
         final ContainerImage image = inspect(createDto.getRepository(), createDto.getTag());
@@ -70,6 +74,7 @@ public class ImageService {
         return out;
     }
 
+    @Transactional
     public ContainerImage update(Long imageId, ImageChangeDto changeDto) throws ImageNotFoundException {
         final ContainerImage image = getById(imageId);
         /* pull changes */

fda-database-service/rest-service/src/main/java/at/tuwien/endpoints/DatabaseEndpoint.java

@@ -14,6 +14,7 @@ import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 
 import javax.validation.Valid;
@@ -36,6 +37,7 @@ public class DatabaseEndpoint {
         this.databaseService = databaseService;
     }
 
+    @Transactional
     @GetMapping("/")
     @ApiOperation(value = "List all databases", notes = "Currently a container supports only databases of the same image, e.g. there is one PostgreSQL engine running with multiple databases inside a container.")
     @ApiResponses({
@@ -50,6 +52,7 @@ public class DatabaseEndpoint {
         return ResponseEntity.ok(databases);
     }
 
+    @Transactional
     @PostMapping("/")
     @ApiOperation(value = "Creates a new database in a container", notes = "Creates a new database in a container. Note that the backend distincts between numerical (req: categories), nominal (req: max_length) and categorical (req: max_length, siUnit, min, max, mean, median, standard_deviation, histogram) column types.")
     @ApiResponses({
@@ -66,6 +69,7 @@ public class DatabaseEndpoint {
                 .body(databaseMapper.databaseToDatabaseBriefDto(database));
     }
 
+    @Transactional
     @GetMapping("/{id}")
     @ApiOperation(value = "Get all informations about a database")
     @ApiResponses({

fda-database-service/rest-service/src/test/java/at/tuwien/service/PostgresIntegrationTest.java

@@ -18,7 +18,7 @@ import org.springframework.boot.test.mock.mockito.MockBean;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.sql.Connection;
 import java.sql.DriverManager;
 import java.sql.SQLException;

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

@@ -11,7 +11,7 @@ import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import javax.transaction.Transactional;
+import org.springframework.transaction.annotation.Transactional;
 import java.util.List;
 import java.util.Optional;
 
@@ -39,6 +39,7 @@ public class DatabaseService {
      *
      * @return A list of databases
      */
+    @Transactional
     public List<Database> findAll() {
         return databaseRepository.findAll();
     }
@@ -50,6 +51,7 @@ public class DatabaseService {
      * @return The database
      * @throws DatabaseNotFoundException In case the database was not found
      */
+    @Transactional
     public Database findById(Long databaseId) throws DatabaseNotFoundException {
         final Optional<Database> opt = databaseRepository.findById(databaseId);
         if (opt.isEmpty()) {

fda-query-service/rest-service/src/main/java/at/tuwien/endpoint/QueryEndpoint.java

@@ -17,6 +17,7 @@ import net.sf.jsqlparser.JSQLParserException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PostMapping;
@@ -42,6 +43,7 @@ public class QueryEndpoint {
         this.queryMapper = queryMapper;
     }
 
+    @Transactional
     @GetMapping("/query")
     @ApiOperation(value = "List all queries", notes = "Lists all already executed queries")
     @ApiResponses({
@@ -71,6 +73,7 @@ public class QueryEndpoint {
                 .build();
     }
 
+    @Transactional
     @PutMapping("/query")
     @ApiOperation(value = "executes a query")
     @ApiResponses(value = {
@@ -85,7 +88,7 @@ public class QueryEndpoint {
         return ResponseEntity.ok(response);
     }
 
-
+    @Transactional
     @PutMapping("/query/version/{timestamp}")
     @ApiOperation(value = "executes a query with a given timestamp")
     @ApiResponses(value = {@ApiResponse(code = 201, message = "result of Query with Timestamp")})

fda-query-service/services/src/main/java/at/tuwien/service/QueryService.java

@@ -18,6 +18,7 @@ import net.sf.jsqlparser.statement.select.Select;
 import net.sf.jsqlparser.statement.select.SelectItem;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
 
 import javax.persistence.EntityNotFoundException;
 import java.io.StringReader;
@@ -42,13 +43,7 @@ public class QueryService {
         this.postgresService = postgresService;
     }
 
-
-    public QueryResultDto executeQuery(String id, ExecuteQueryDto dto) {
-        System.out.println("test");
-
-        return null;
-    }
-
+    @Transactional
     public List<Query> findAll(Long id) throws ImageNotSupportedException, DatabaseNotFoundException, DatabaseConnectionException, QueryMalformedException {
         return postgresService.getQueries(findDatabase(id));
     }
@@ -74,7 +69,6 @@ public class QueryService {
         return null;
     }
     
-
     public void create(Long id) throws DatabaseConnectionException, ImageNotSupportedException, DatabaseNotFoundException {
         postgresService.createQuerystore(findDatabase(id));
     }

fda-table-service/rest-service/src/main/java/at/tuwien/endpoints/TableEndpoint.java

@@ -17,6 +17,7 @@ import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 import org.springframework.web.multipart.MultipartFile;
 
@@ -42,6 +43,7 @@ public class TableEndpoint {
         this.queryResultMapper = queryResultMapper;
     }
 
+    @Transactional
     @GetMapping("/table")
     @ApiOperation(value = "List all tables", notes = "Lists the tables in the metadata database for this database.")
     @ApiResponses({
@@ -57,6 +59,7 @@ public class TableEndpoint {
                 .collect(Collectors.toList()));
     }
 
+    @Transactional
     @PostMapping("/table")
     @ApiOperation(value = "Create a table", notes = "Creates a new table for a database, requires a running container.")
     @ApiResponses({
@@ -77,6 +80,7 @@ public class TableEndpoint {
                 .body(tableMapper.tableToTableBriefDto(table));
     }
 
+    @Transactional
     @PostMapping("/table/csv")
     @ApiOperation(value = "Create a table", notes = "Creates a file, which is given as a multipart file.")
     @ApiResponses({
@@ -93,6 +97,7 @@ public class TableEndpoint {
                 .body(tableMapper.tableToTableDto(table));
     }
 
+    @Transactional
     @PostMapping("/table/csv/local")
     @ApiOperation(value = "Create a table", notes = "This is done by saving a file on the shared docker filesystem and then sending the link to the file.")
     @ApiResponses({
@@ -110,6 +115,7 @@ public class TableEndpoint {
     }
 
 
+    @Transactional
     @GetMapping("/table/{tableId}")
     @ApiOperation(value = "List all tables", notes = "Lists the tables in the metadata database for this database.")
     @ApiResponses({
@@ -118,7 +124,7 @@ public class TableEndpoint {
             @ApiResponse(code = 404, message = "Table not found in metadata database."),
     })
     public ResponseEntity<TableDto> findById(@PathVariable("id") Long databaseId, @PathVariable("tableId") Long tableId)
-            throws TableNotFoundException {
+            throws TableNotFoundException, DatabaseNotFoundException, ImageNotSupportedException {
         final Table table = tableService.findById(databaseId, tableId);
         return ResponseEntity.ok(tableMapper.tableToTableDto(table));
     }
@@ -147,10 +153,11 @@ public class TableEndpoint {
     @ResponseStatus(HttpStatus.OK)
     public void delete(@PathVariable("id") Long databaseId, @PathVariable("tableId") Long tableId)
             throws TableNotFoundException, DatabaseConnectionException, TableMalformedException,
-            DataProcessingException {
+            DataProcessingException, DatabaseNotFoundException, ImageNotSupportedException {
         tableService.delete(databaseId, tableId);
     }
 
+    @Transactional
     @PostMapping("/table/{tableId}")
     @ApiOperation(value = "Insert values", notes = "Insert Data into a Table in the database.")
     @ApiResponses({
@@ -168,6 +175,7 @@ public class TableEndpoint {
         return ResponseEntity.ok(queryResultMapper.queryResultToQueryResultDto(queryResult));
     }
 
+    @Transactional
     @GetMapping("/table/{tableId}/data")
     @ApiOperation(value = "show data", notes = "Show all the data for a table")
     @ApiResponses({

fda-table-service/rest-service/src/test/java/at/tuwien/endpoint/TableEndpointUnitTest.java

@@ -137,7 +137,7 @@ public class TableEndpointUnitTest extends BaseUnitTest {
 
     @Disabled("not throwing")
     @Test
-    public void create_notSql_fails() throws TableNotFoundException, SQLException {
+    public void create_notSql_fails() throws TableNotFoundException, SQLException, DatabaseNotFoundException, ImageNotSupportedException {
         final TableCreateDto request = TableCreateDto.builder()
                 .name(TABLE_1_NAME)
                 .description(TABLE_1_DESCRIPTION)
@@ -153,7 +153,7 @@ public class TableEndpointUnitTest extends BaseUnitTest {
     }
 
     @Test
-    public void findById_succeeds() throws TableNotFoundException {
+    public void findById_succeeds() throws TableNotFoundException, DatabaseNotFoundException, ImageNotSupportedException {
         when(tableService.findById(DATABASE_1_ID, TABLE_1_ID))
                 .thenReturn(TABLE_1);
 
@@ -184,7 +184,7 @@ public class TableEndpointUnitTest extends BaseUnitTest {
 
     @Test
     public void delete_notFound_fails() throws TableNotFoundException, DatabaseConnectionException,
-            TableMalformedException, DataProcessingException {
+            TableMalformedException, DataProcessingException, DatabaseNotFoundException, ImageNotSupportedException {
         doThrow(TableNotFoundException.class)
                 .when(tableService)
                 .delete(DATABASE_1_ID, TABLE_1_ID);
@@ -197,7 +197,7 @@ public class TableEndpointUnitTest extends BaseUnitTest {
 
     @Test
     public void delete_succeeds() throws TableNotFoundException, DatabaseConnectionException, TableMalformedException,
-            DataProcessingException {
+            DataProcessingException, DatabaseNotFoundException, ImageNotSupportedException {
         /* test */
         tableEndpoint.delete(DATABASE_1_ID, TABLE_1_ID);
     }

fda-table-service/rest-service/src/test/java/at/tuwien/service/TableServiceUnitTest.java

@@ -76,7 +76,7 @@ public class TableServiceUnitTest extends BaseUnitTest {
     @Disabled("invalid mock")
     @Test
     public void delete_succeeds() throws TableNotFoundException, DatabaseConnectionException, TableMalformedException,
-            DataProcessingException {
+            DataProcessingException, DatabaseNotFoundException, ImageNotSupportedException {
         when(tableRepository.findById(TABLE_1_ID))
                 .thenReturn(Optional.of(TABLE_1));
         doNothing()
@@ -92,11 +92,11 @@ public class TableServiceUnitTest extends BaseUnitTest {
 
     @Test
     public void delete_notFound_fails() {
-        when(tableRepository.findByDatabaseAndId(DATABASE_1, TABLE_1_ID))
+        when(databaseRepository.findById(DATABASE_1_ID))
                 .thenReturn(Optional.empty());
 
         /* test */
-        assertThrows(TableNotFoundException.class, () -> {
+        assertThrows(DatabaseNotFoundException.class, () -> {
             tableService.delete(DATABASE_1_ID, TABLE_1_ID);
         });
     }
@@ -104,8 +104,8 @@ public class TableServiceUnitTest extends BaseUnitTest {
     @Test
     public void delete_noConnection_fails() throws DatabaseConnectionException, TableMalformedException,
             DataProcessingException {
-        when(tableRepository.findByDatabaseAndId(DATABASE_1, TABLE_1_ID))
-                .thenReturn(Optional.empty());
+        when(databaseRepository.findById(DATABASE_1_ID))
+                .thenReturn(Optional.of(DATABASE_1));
         doAnswer(invocation -> new TableMalformedException("no connection"))
                 .when(postgresService)
                 .deleteTable(TABLE_1);
@@ -118,6 +118,8 @@ public class TableServiceUnitTest extends BaseUnitTest {
 
     @Test
     public void delete_noSql_fails() throws DataProcessingException {
+        when(databaseRepository.findById(DATABASE_1_ID))
+                .thenReturn(Optional.of(DATABASE_1));
         when(tableRepository.findByDatabaseAndId(DATABASE_1, TABLE_1_ID))
                 .thenReturn(Optional.empty());
 
@@ -128,7 +130,9 @@ public class TableServiceUnitTest extends BaseUnitTest {
     }
 
     @Test
-    public void findById_succeeds() throws TableNotFoundException {
+    public void findById_succeeds() throws TableNotFoundException, DatabaseNotFoundException, ImageNotSupportedException {
+        when(databaseRepository.findById(DATABASE_1_ID))
+                .thenReturn(Optional.of(DATABASE_1));
         when(tableRepository.findByDatabaseAndId(DATABASE_1, TABLE_1_ID))
                 .thenReturn(Optional.of(TABLE_1));
 
@@ -140,6 +144,8 @@ public class TableServiceUnitTest extends BaseUnitTest {
 
     @Test
     public void findById_noTable_fails() {
+        when(databaseRepository.findById(DATABASE_1_ID))
+                .thenReturn(Optional.of(DATABASE_1));
         when(tableRepository.findByDatabaseAndId(DATABASE_1, 9999L))
                 .thenReturn(Optional.empty());
 

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

@@ -15,6 +15,7 @@ import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.mock.web.MockMultipartFile;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.multipart.MultipartFile;
 import org.supercsv.cellprocessor.constraint.NotNull;
 import org.supercsv.cellprocessor.ift.CellProcessor;
@@ -23,7 +24,6 @@ import org.supercsv.io.ICsvMapReader;
 import org.supercsv.prefs.CsvPreference;
 
 import javax.persistence.EntityNotFoundException;
-import javax.transaction.Transactional;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.Reader;
@@ -70,18 +70,15 @@ public class TableService {
     }
 
     @Transactional
-    public void delete(Long databaseId, Long tableId) throws TableNotFoundException, DatabaseConnectionException, TableMalformedException, DataProcessingException {
+    public void delete(Long databaseId, Long tableId) throws TableNotFoundException, DatabaseConnectionException, TableMalformedException, DataProcessingException, DatabaseNotFoundException, ImageNotSupportedException {
         final Table table = findById(databaseId, tableId);
         postgresService.deleteTable(table);
         tableRepository.deleteById(tableId);
     }
 
     @Transactional
-    public Table findById(Long databaseId, Long tableId) throws TableNotFoundException {
-        final Database database = Database.builder()
-                .id(databaseId)
-                .build();
-        final Optional<Table> table = tableRepository.findByDatabaseAndId(database, tableId);
+    public Table findById(Long databaseId, Long tableId) throws TableNotFoundException, DatabaseNotFoundException, ImageNotSupportedException {
+        final Optional<Table> table = tableRepository.findByDatabaseAndId(findDatabase(databaseId), tableId);
         if (table.isEmpty()) {
             log.error("table {} not found in database {}", tableId, databaseId);
             throw new TableNotFoundException("table not found in database");