Fixed the id columns

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

@@ -67,10 +67,7 @@ public class TokenEndpoint {
             TokenNotEligableException {
         log.debug("endpoint create developer token, principal={}", principal);
         /* check */
-        final List<Token> tokens = tokenService.findAll(principal)
-                .stream()
-                .filter(t -> Objects.isNull(t.getDeleted()))
-                .collect(Collectors.toList());
+        final List<Token> tokens = tokenService.findAll(principal);
         log.trace("found all tokens {}", tokens);
         if (tokens.size() >= authenticationConfig.getTokenCount()) {
             log.error("Failed to create token, already exceeded maximum quota of {}", authenticationConfig.getTokenCount());

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

@@ -75,7 +75,7 @@ public class AuthenticationServiceImpl implements AuthenticationService {
 
     @Override
     @Transactional
-    public void verifyToken(String authorization) throws TokenRevokedException {
+    public void verifyToken(String authorization) {
         final String hash = authenticationMapper.authorizationToTokenHash(authorization);
         final Optional<Token> optional = tokenRepository.findByTokenHash(hash);
         if (optional.isEmpty()) {
@@ -83,10 +83,6 @@ public class AuthenticationServiceImpl implements AuthenticationService {
             return;
         }
         final Token token = optional.get();
-        if (token.getDeleted() != null) {
-            log.warn("Token with hash {} is marked as revoked", hash);
-            throw new TokenRevokedException("Token is marked as revoked");
-        }
         token.setLastUsed(Instant.now());
         tokenRepository.save(token);
         log.info("Updated token usage of token with hash {}", hash);

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

@@ -107,7 +107,6 @@ public class MariaDbServiceImpl extends HibernateConnector implements DatabaseSe
         } finally {
             dataSource.close();
         }
-        database.setDeleted(Instant.now()) /* method has void, only for debug logs */;
         /* save in metadata database */
         databaseRepository.deleteById(databaseId);
         log.info("Deleted database with id {}", databaseId);

fda-identifier-service/rest-service/src/test/java/at/tuwien/service/IdentifierServiceIntegrationTest.java

@@ -89,7 +89,6 @@ public class IdentifierServiceIntegrationTest extends BaseUnitTest {
                 .created(IDENTIFIER_2_CREATED)
                 .lastModified(IDENTIFIER_2_MODIFIED)
                 .publicationYear(IDENTIFIER_2_PUBLICATION_YEAR)
-                .deleted(Instant.now().minus(4, ChronoUnit.MINUTES))
                 .publisher(IDENTIFIER_2_PUBLISHER)
                 .type(IDENTIFIER_2_TYPE)
                 .build());

fda-metadata-db/Dockerfile

@@ -25,17 +25,13 @@ ENV METADATA_USERNAME=root
 ENV METADATA_PASSWORD=dbrepo
 ENV MARIADB_DATABASE="${METADATA_DB}"
 ENV MARIADB_ROOT_PASSWORD="${METADATA_PASSWORD}"
-ENV MARIADB_USERNAME="${METADATA_USERNAME}"
-ENV MARIADB_PASSWORD="${METADATA_PASSWORD}"
 
 # Scripts are copied to /docker-entrypoint-initdb.d/ in docker-compose from analyze service
 HEALTHCHECK --interval=10s --timeout=5s --retries=12 CMD mysqladmin ping --user="$METADATA_USERNAME" --password="$METADATA_PASSWORD" --silent
 
 WORKDIR /docker-entrypoint-initdb.d
 
-COPY ./setup-schema.sql ./1.sql
-COPY ./setup-user.sh ./2.sh
-RUN chmod +x ./2.sh
+COPY ./setup-schema.sql ./setup-schema.sql
 
 WORKDIR /app
 

fda-metadata-db/api/src/main/java/at/tuwien/api/auth/TokenBriefDto.java

@@ -40,8 +40,4 @@ public class TokenBriefDto {
     @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
     private Instant expires;
 
-    @Schema(example = "2020-08-04 11:13:00")
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
-    private Instant deleted;
-
 }

fda-metadata-db/api/src/main/java/at/tuwien/api/auth/TokenDto.java

@@ -40,10 +40,6 @@ public class TokenDto {
     @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
     private Instant expires;
 
-    @Schema(example = "2020-08-04 11:13:00")
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
-    private Instant deleted;
-
     @NotBlank
     @Schema(example = "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c")
     private String token;

fda-metadata-db/api/src/main/java/at/tuwien/api/database/DatabaseDto.java

@@ -62,8 +62,4 @@ public class DatabaseDto {
     @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
     private Instant created;
 
-    @Schema(example = "2020-08-04 11:13:00")
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
-    private Instant deleted;
-
 }

fda-metadata-db/api/src/main/java/at/tuwien/api/database/ViewBriefDto.java

@@ -53,8 +53,4 @@ public class ViewBriefDto {
     @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
     private Instant lastModified;
 
-    @Schema(example = "2020-08-04 11:13:00")
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
-    private Instant deleted;
-
 }

fda-metadata-db/api/src/main/java/at/tuwien/api/database/ViewDto.java

@@ -56,8 +56,4 @@ public class ViewDto {
     @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
     private Instant lastModified;
 
-    @Schema(example = "2020-08-04 11:13:00")
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
-    private Instant deleted;
-
 }

fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/RelatedIdentifierDto.java

@@ -47,9 +47,6 @@ public class RelatedIdentifierDto {
     @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
     private Instant lastModified;
 
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX", timezone = "UTC")
-    private Instant deleted;
-
 }
 
 

fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/Container.java

@@ -22,10 +22,8 @@ import java.util.List;
 @ToString
 @AllArgsConstructor
 @NoArgsConstructor
-@Where(clause = "deleted is null")
 @EntityListeners(AuditingEntityListener.class)
 @EqualsAndHashCode(onlyExplicitlyIncluded = true)
-@SQLDelete(sql = "update mdb_containers set deleted = NOW() where id = ?")
 @Table(name = "mdb_containers")
 public class Container {
 
@@ -75,7 +73,4 @@ public class Container {
     @LastModifiedDate
     private Instant lastModified;
 
-    @Column
-    private Instant deleted;
-
 }

fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java

@@ -26,8 +26,8 @@ public class ContainerImage {
 
     @Id
     @EqualsAndHashCode.Include
-    @GenericGenerator(name = "native", strategy = "native")
-    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(updatable = false, nullable = false)
     public Long id;
 
     @Column(nullable = false)

fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageDate.java

@@ -23,8 +23,8 @@ public class ContainerImageDate {
 
     @Id
     @EqualsAndHashCode.Include
-    @GenericGenerator(name = "native", strategy = "native")
-    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(updatable = false, nullable = false)
     private Long id;
 
     @Column(name = "iid")

fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageEnvironmentItem.java

@@ -23,8 +23,8 @@ public class ContainerImageEnvironmentItem {
 
     @Id
     @EqualsAndHashCode.Include
-    @GenericGenerator(name = "native", strategy = "native")
-    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(updatable = false, nullable = false)
     public Long id;
 
     @Id

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

@@ -24,9 +24,7 @@ import java.util.List;
 @AllArgsConstructor
 @NoArgsConstructor
 @Document(indexName = "databaseindex", createIndex = false)
-@Where(clause = "deleted is null")
 @EntityListeners(AuditingEntityListener.class)
-@SQLDelete(sql = "update mdb_databases set deleted = NOW() where id = ?")
 @javax.persistence.Table(name = "mdb_databases", uniqueConstraints = {
         @UniqueConstraint(columnNames = {"id", "internalName"})
 })
@@ -34,8 +32,8 @@ public class Database {
 
     @Id
     @EqualsAndHashCode.Include
-    @GenericGenerator(name = "native", strategy = "native")
-    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(updatable = false, nullable = false)
     private Long id;
 
     @ManyToOne(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
@@ -87,7 +85,4 @@ public class Database {
     @LastModifiedDate
     private Instant lastModified;
 
-    @Column
-    private Instant deleted;
-
 }

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

@@ -23,8 +23,8 @@ public class View {
 
     @Id
     @EqualsAndHashCode.Include
-    @GenericGenerator(name = "native", strategy = "native")
-    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(updatable = false, nullable = false)
     private Long id;
 
     @Id
@@ -69,7 +69,4 @@ public class View {
     @LastModifiedDate
     private Instant lastModified;
 
-    @Column
-    private Instant deleted;
-
 }

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

@@ -31,8 +31,8 @@ public class Table {
 
     @Id
     @EqualsAndHashCode.Include
-    @GenericGenerator(name = "native", strategy = "native")
-    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(updatable = false, nullable = false)
     private Long id;
 
     @Id

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

@@ -32,8 +32,8 @@ public class TableColumn implements Comparable<TableColumn> {
 
     @Id
     @EqualsAndHashCode.Include
-    @GenericGenerator(name = "native", strategy = "native")
-    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(updatable = false, nullable = false)
     private Long id;
 
     @Id

fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java

@@ -24,8 +24,8 @@ public class ColumnConcept implements Serializable {
 
     @Id
     @EqualsAndHashCode.Include
-    @GenericGenerator(name = "native", strategy = "native")
-    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(updatable = false, nullable = false)
     private Long cid;
 
     @Id