Merge branch 'dev-fix-bugs' into 'dev'

Fixed the query service tests

See merge request !42

.fda-deployment/teardown

 #!/bin/bash
-docker container stop $(docker container ls -aq -f name=^/fda-.*) || true
-docker container rm $(docker container ls -aq -f name=^/fda-.*) || true
+docker container stop $(docker container ls -aq) || true
+docker container rm $(docker container ls -aq) || true
 docker volume rm $(docker volume ls -q) || true
 docker network rm fda-userdb || true
 docker network rm fda-public || true
\ No newline at end of file

docker-compose.yml

@@ -53,9 +53,6 @@ services:
     environment:
       SPRING_PROFILES_ACTIVE: docker
       TZ: Europe/Vienna
-    depends_on:
-      fda-gateway-service:
-        condition: service_healthy
     ports:
       - "9090:9090"
     logging:
@@ -73,6 +70,9 @@ services:
     environment:
       SPRING_PROFILES_ACTIVE: docker
       TZ: Europe/Vienna
+    depends_on:
+      fda-discovery-service:
+        condition: service_healthy
     ports:
       - "9095:9095"
     logging:
@@ -133,7 +133,7 @@ services:
       fda-public:
     #    ipv4_address: 172.29.0.14
     environment:
-      SPRING_PROFILES_ACTIVE: docker
+      SPRING_PROFILES_ACTIVE: docker,seeder
       TZ: Europe/Vienna
     ports:
       - "9097:9097"

fda-analyse-service/requirements.txt

@@ -6,7 +6,7 @@ psycopg2-binary==2.8.6
 py-eureka-client==0.9.1
 docker==5.0.0
 sqlalchemy==1.4.15
+gevent==21.8.0
 requests==2.26.0
 gevent==21.8.0
 markupsafe===2.0.1
-

fda-authentication-service/rest-service/src/main/java/at/tuwien/endpoints/AuthenticationEndpoint.java

@@ -11,6 +11,8 @@ import io.swagger.annotations.ApiResponses;
 import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
+import org.springframework.security.core.userdetails.UserDetails;
+import org.springframework.security.core.userdetails.UserDetailsService;
 import org.springframework.web.bind.annotation.*;
 
 import javax.validation.Valid;
@@ -24,11 +26,14 @@ import java.security.Principal;
 public class AuthenticationEndpoint {
 
     private final UserMapper userMapper;
+    private final UserDetailsService userDetailsServiceImpl;
     private final AuthenticationService authenticationService;
 
     @Autowired
-    public AuthenticationEndpoint(UserMapper userMapper, AuthenticationService authenticationService) {
+    public AuthenticationEndpoint(UserMapper userMapper, UserDetailsService userDetailsServiceImpl,
+                                  AuthenticationService authenticationService) {
         this.userMapper = userMapper;
+        this.userDetailsServiceImpl = userDetailsServiceImpl;
         this.authenticationService = authenticationService;
     }
 
@@ -49,8 +54,9 @@ public class AuthenticationEndpoint {
             @ApiResponse(code = 201, message = "Successfully authenticated a user.")
     })
     public ResponseEntity<UserDto> authenticateUser(Principal principal) {
+        final UserDetails details = userDetailsServiceImpl.loadUserByUsername(principal.getName());
         return ResponseEntity.accepted()
-                .body(userMapper.principalToUserDto(principal));
+                .body(userMapper.userDetailsToUserDto(details, principal));
     }
 
 }
\ No newline at end of file

fda-authentication-service/rest-service/src/main/java/at/tuwien/config/ReadyConfig.java → fda-authentication-service/services/src/main/java/at/tuwien/config/ReadyConfig.java

 package at.tuwien.config;
 
+import at.tuwien.seeder.Seeder;
 import com.google.common.io.Files;
 import lombok.extern.log4j.Log4j2;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.context.event.ApplicationReadyEvent;
 import org.springframework.context.annotation.Configuration;
@@ -17,8 +19,16 @@ public class ReadyConfig {
     @Value("${fda.ready.path}")
     private String readyPath;
 
+    private final Seeder seederImpl;
+
+    @Autowired
+    public ReadyConfig(Seeder seederImpl) {
+        this.seederImpl = seederImpl;
+    }
+
     @EventListener(ApplicationReadyEvent.class)
     public void init() throws IOException {
+        seederImpl.seed();
         Files.touch(new File(readyPath));
     }
 

fda-authentication-service/services/src/main/java/at/tuwien/mapper/UserMapper.java

@@ -11,6 +11,7 @@ import org.mapstruct.Mapper;
 import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
 import org.springframework.security.core.GrantedAuthority;
 import org.springframework.security.core.authority.SimpleGrantedAuthority;
+import org.springframework.security.core.userdetails.UserDetails;
 
 import java.security.Principal;
 import java.util.Objects;
@@ -68,14 +69,18 @@ public interface UserMapper {
                 .build();
     }
 
-    default UserDto principalToUserDto(Principal principal) {
+    default UserDto userDetailsToUserDto(UserDetails data, Principal principal) {
         final UsernamePasswordAuthenticationToken token = (UsernamePasswordAuthenticationToken) principal;
-        return UserDto.builder()
+        final UserDto user = UserDto.builder()
+                .username(data.getUsername())
+                .password(data.getPassword())
                 .authorities(token.getAuthorities()
                         .stream()
                         .map(this::grantedAuthorityToGrantedAuthority)
                         .collect(Collectors.toList()))
                 .build();
+        log.debug("mapped user and principal {}", user);
+        return user;
     }
 
 }

fda-authentication-service/services/src/main/java/at/tuwien/seeder/Seeder.java

+package at.tuwien.seeder;
+
+public interface Seeder {
+
+    void seed();
+}

fda-authentication-service/services/src/main/java/at/tuwien/seeder/impl/AbstractSeeder.java

+package at.tuwien.seeder.impl;
+
+import at.tuwien.entities.user.RoleType;
+import at.tuwien.entities.user.User;
+
+import java.util.List;
+
+public abstract class AbstractSeeder {
+
+    public final static Long USER_1_ID = 1L;
+    public final static String USER_1_USERNAME = "system";
+    public final static String USER_1_FIRSTNAME = "System";
+    public final static String USER_1_LASTNAME = "Default";
+    public final static String USER_1_EMAIL = "system.default@example.com";
+    public final static String USER_1_PASSWORD = "system";
+    public final static List<RoleType> USER_1_ROLES = List.of(RoleType.ROLE_RESEARCHER);
+
+    public final static User USER_1 = User.builder()
+            .id(USER_1_ID)
+            .username(USER_1_USERNAME)
+            .firstname(USER_1_FIRSTNAME)
+            .lastname(USER_1_LASTNAME)
+            .email(USER_1_EMAIL)
+            .roles(USER_1_ROLES)
+            .build();
+
+    public final static Long USER_2_ID = 2L;
+    public final static String USER_2_USERNAME = "researcher";
+    public final static String USER_2_TITLES_BEFORE = "Dr.";
+    public final static String USER_2_TITLES_AFTER = "BSc";
+    public final static String USER_2_FIRSTNAME = "Max";
+    public final static String USER_2_LASTNAME = "Mustermann";
+    public final static String USER_2_EMAIL = "max.mustermann@example.com";
+    public final static String USER_2_PASSWORD = "researcher";
+    public final static List<RoleType> USER_2_ROLES = List.of(RoleType.ROLE_RESEARCHER);
+
+    public final static User USER_2 = User.builder()
+            .id(USER_2_ID)
+            .username(USER_2_USERNAME)
+            .titlesBefore(USER_2_TITLES_BEFORE)
+            .firstname(USER_2_FIRSTNAME)
+            .lastname(USER_2_LASTNAME)
+            .titlesBefore(USER_2_TITLES_AFTER)
+            .email(USER_2_EMAIL)
+            .roles(USER_2_ROLES)
+            .build();
+
+    public final static Long USER_3_ID = 3L;
+    public final static String USER_3_USERNAME = "developer";
+    public final static String USER_3_FIRSTNAME = "Maria";
+    public final static String USER_3_LASTNAME = "Mustermann";
+    public final static String USER_3_EMAIL = "maria.mustermann@example.com";
+    public final static String USER_3_PASSWORD = "developer";
+    public final static List<RoleType> USER_3_ROLES = List.of(RoleType.ROLE_DEVELOPER);
+
+    public final static User USER_3 = User.builder()
+            .id(USER_3_ID)
+            .username(USER_3_USERNAME)
+            .firstname(USER_3_FIRSTNAME)
+            .lastname(USER_3_LASTNAME)
+            .email(USER_3_EMAIL)
+            .roles(USER_3_ROLES)
+            .build();
+
+    public final static Long USER_4_ID = 4L;
+    public final static String USER_4_USERNAME = "datasteward";
+    public final static String USER_4_FIRSTNAME = "Eva";
+    public final static String USER_4_LASTNAME = "Mustermann";
+    public final static String USER_4_EMAIL = "eva.mustermann@example.com";
+    public final static String USER_4_PASSWORD = "datasteward";
+    public final static List<RoleType> USER_4_ROLES = List.of(RoleType.ROLE_DATA_STEWARD);
+
+    public final static User USER_4 = User.builder()
+            .id(USER_4_ID)
+            .username(USER_4_USERNAME)
+            .firstname(USER_4_FIRSTNAME)
+            .lastname(USER_4_LASTNAME)
+            .email(USER_4_EMAIL)
+            .roles(USER_4_ROLES)
+            .build();
+
+}

fda-authentication-service/services/src/main/java/at/tuwien/seeder/impl/SeederImpl.java

+package at.tuwien.seeder.impl;
+
+import at.tuwien.seeder.Seeder;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.stereotype.Service;
+
+
+@Slf4j
+@Service
+public class SeederImpl implements Seeder {
+
+    private final Seeder userSeederImpl;
+
+    public SeederImpl(Seeder userSeederImpl) {
+        this.userSeederImpl = userSeederImpl;
+    }
+
+    @Override
+    public void seed() {
+        userSeederImpl.seed();
+    }
+}

fda-authentication-service/services/src/main/java/at/tuwien/seeder/impl/UserSeederImpl.java

+package at.tuwien.seeder.impl;
+
+import at.tuwien.entities.user.User;
+import at.tuwien.repositories.UserRepository;
+import at.tuwien.seeder.Seeder;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.env.Environment;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.stereotype.Service;
+
+import java.util.Arrays;
+
+
+@Slf4j
+@Service
+public class UserSeederImpl extends AbstractSeeder implements Seeder {
+
+    private final Environment environment;
+    private final UserRepository userRepository;
+    private final PasswordEncoder passwordEncoder;
+
+    @Autowired
+    public UserSeederImpl(Environment environment, PasswordEncoder passwordEncoder, UserRepository userRepository) {
+        this.environment = environment;
+        this.passwordEncoder = passwordEncoder;
+        this.userRepository = userRepository;
+    }
+
+    @Override
+    public void seed() {
+        if (userRepository.findAll().size() > 0) {
+            log.warn("Already seeded. Skip.");
+            return;
+        }
+        USER_1.setPassword(passwordEncoder.encode(USER_1_PASSWORD));
+        final User user1 = userRepository.save(USER_1);
+        log.info("Created user with id {}", user1);
+        if (Arrays.asList(environment.getActiveProfiles()).contains("seeder")) {
+            USER_2.setPassword(passwordEncoder.encode(USER_2_PASSWORD));
+            final User user2 = userRepository.save(USER_2);
+            log.info("Created user with id {}", user2);
+            USER_3.setPassword(passwordEncoder.encode(USER_3_PASSWORD));
+            final User user3 = userRepository.save(USER_3);
+            log.info("Created user with id {}", user3);
+            USER_4.setPassword(passwordEncoder.encode(USER_4_PASSWORD));
+            final User user4 = userRepository.save(USER_4);
+            log.info("Created user with id {}", user4);
+        }
+    }
+}

fda-authentication-service/services/src/main/java/at/tuwien/service/impl/UserDetailsServiceImpl.java

@@ -36,14 +36,14 @@ public class UserDetailsServiceImpl implements UserDetailsService {
             log.error("Failed to load user by username {}", username);
             throw new UsernameNotFoundException("Failed to load user by username");
         }
-        log.debug("loaded user {}", user);
+        log.trace("loaded user {}", user);
         final UserDetailsDto details = userMapper.userToUserDetailsDto(user.get());
         details.setAuthorities(user.get()
                 .getRoles()
                 .stream()
                 .map(userMapper::roleTypeToGrantedAuthority)
                 .collect(Collectors.toList()));
-        log.debug("mapped user {}", details);
+        log.trace("mapped user {}", details);
         return details;
     }
 

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

@@ -18,6 +18,7 @@ import org.springframework.web.bind.annotation.*;
 
 import javax.validation.Valid;
 import javax.validation.constraints.NotNull;
+import java.security.Principal;
 import java.util.List;
 import java.util.stream.Collectors;
 
@@ -61,10 +62,10 @@ public class ContainerEndpoint {
             @ApiResponse(code = 201, message = "Successfully created a new container."),
             @ApiResponse(code = 400, message = "Malformed payload."),
             @ApiResponse(code = 401, message = "Not authorized to create a container."),
-            @ApiResponse(code = 404, message = "The container was not found after creation."),
+            @ApiResponse(code = 404, message = "The container was not found after creation or the user was not found."),
     })
     public ResponseEntity<ContainerBriefDto> create(@Valid @RequestBody ContainerCreateRequestDto data)
-            throws ImageNotFoundException, DockerClientException, ContainerAlreadyExistsException {
+            throws ImageNotFoundException, DockerClientException, UserNotFoundException {
         final Container container = containerService.create(data);
         final ContainerBriefDto response = containerMapper.containerToDatabaseContainerBriefDto(container);
         return ResponseEntity.status(HttpStatus.CREATED)

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

@@ -25,5 +25,6 @@ eureka:
   instance.hostname: fda-container-service
   client.serviceUrl.defaultZone: http://fda-discovery-service:9090/eureka/
 fda:
+  mount.path: /tmp
   ready.path: /ready
   gateway.endpoint: http://fda-gateway-service:9095
\ No newline at end of file

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

@@ -25,5 +25,6 @@ eureka:
   instance.hostname: fda-container-service
   client.serviceUrl.defaultZone: http://localhost:9090/eureka/
 fda:
+  mount.path: /tmp
   ready.path: ./ready
   gateway.endpoint: http://localhost:9095
\ No newline at end of file

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

@@ -15,8 +15,11 @@ import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.mock.mockito.MockBean;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
+import org.springframework.security.test.context.support.WithMockUser;
+import org.springframework.security.test.context.support.WithUserDetails;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
+import java.security.Principal;
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
@@ -54,7 +57,7 @@ public class ContainerEndpointUnitTest extends BaseUnitTest {
     }
 
     @Test
-    public void create_succeeds() throws ImageNotFoundException, DockerClientException, ContainerAlreadyExistsException {
+    public void create_succeeds() throws ImageNotFoundException, DockerClientException, UserNotFoundException {
         final ContainerCreateRequestDto request = ContainerCreateRequestDto.builder()
                 .name(CONTAINER_1_NAME)
                 .repository(IMAGE_1.getRepository())
@@ -72,7 +75,7 @@ public class ContainerEndpointUnitTest extends BaseUnitTest {
 
     @Disabled
     @Test
-    public void create_noImage_fails() throws DockerClientException, ImageNotFoundException, ContainerAlreadyExistsException {
+    public void create_noImage_fails() throws DockerClientException, ImageNotFoundException, UserNotFoundException {
         final ContainerCreateRequestDto request = ContainerCreateRequestDto.builder()
                 .name(CONTAINER_1_NAME)
                 .repository("image")
@@ -88,8 +91,9 @@ public class ContainerEndpointUnitTest extends BaseUnitTest {
     }
 
     @Disabled
+    @WithMockUser(username = "not3x1st1ng", roles = {"ROLE_RESEARCHER"})
     @Test
-    public void create_docker_fails() throws DockerClientException, ImageNotFoundException, ContainerAlreadyExistsException {
+    public void create_docker_fails() throws DockerClientException, ImageNotFoundException, UserNotFoundException {
         final ContainerCreateRequestDto request = ContainerCreateRequestDto.builder()
                 .name(CONTAINER_1_NAME)
                 .repository(IMAGE_1.getRepository())

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

@@ -27,6 +27,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import org.springframework.transaction.annotation.Transactional;
 
+import java.security.Principal;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -146,7 +147,7 @@ public class ContainerServiceIntegrationTest extends BaseUnitTest {
     }
 
     @Test
-    public void create_succeeds() throws DockerClientException, ImageNotFoundException, ContainerAlreadyExistsException {
+    public void create_succeeds() throws DockerClientException, ImageNotFoundException, UserNotFoundException {
         final ContainerCreateRequestDto request = ContainerCreateRequestDto.builder()
                 .repository(IMAGE_1_REPOSITORY)
                 .tag(IMAGE_1_TAG)
@@ -159,7 +160,7 @@ public class ContainerServiceIntegrationTest extends BaseUnitTest {
     }
 
     @Test
-    public void create_conflictingNames_fails() throws DockerClientException, ImageNotFoundException, ContainerAlreadyExistsException {
+    public void create_conflictingNames_fails() throws DockerClientException, ImageNotFoundException, UserNotFoundException {
         final ContainerCreateRequestDto request = ContainerCreateRequestDto.builder()
                 .repository(IMAGE_1_REPOSITORY)
                 .tag(IMAGE_1_TAG)

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

+package at.tuwien.config;
+
+import lombok.Getter;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Configuration;
+
+@Getter
+@Configuration
+public class MountProperties {
+
+    @Value("${fda.mount.path}")
+    private String mountPath;
+
+}

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

+package at.tuwien.exception;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(code = HttpStatus.NOT_FOUND, reason = "User not found")
+public class UserNotFoundException extends Exception {
+
+    public UserNotFoundException(String message) {
+        super(message);
+    }
+
+    public UserNotFoundException(String message, Throwable thr) {
+        super(message, thr);
+    }
+
+    public UserNotFoundException(Throwable thr) {
+        super(thr);
+    }
+
+}

fda-container-service/services/src/main/java/at/tuwien/gateway/impl/AuthenticationServiceGatewayImpl.java

@@ -3,6 +3,7 @@ package at.tuwien.gateway.impl;
 import at.tuwien.api.user.UserDto;
 import at.tuwien.gateway.AuthenticationServiceGateway;
 import at.tuwien.mapper.UserMapper;
+import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;
@@ -12,6 +13,7 @@ import org.springframework.security.core.userdetails.UserDetails;
 import org.springframework.stereotype.Service;
 import org.springframework.web.client.RestTemplate;
 
+@Log4j2
 @Service
 public class AuthenticationServiceGatewayImpl implements AuthenticationServiceGateway {
 

fda-container-service/services/src/main/java/at/tuwien/repository/jpa/UserRepository.java

+
+package at.tuwien.repository.jpa;
+
+import at.tuwien.entities.user.User;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+
+import java.util.Optional;
+
+@Repository
+public interface UserRepository extends JpaRepository<User, Long> {
+
+    Optional<User> findByUsername(String username);
+
+}