From 01333dfff4bdc9eb8f33bbc578d2d8e78c3e7232 Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Thu, 24 Nov 2022 21:37:14 +0100
Subject: [PATCH] Fixed the id columns
---
.../at/tuwien/endpoints/TokenEndpoint.java | 5 +-
.../impl/AuthenticationServiceImpl.java | 6 +-
.../service/impl/MariaDbServiceImpl.java | 1 -
.../IdentifierServiceIntegrationTest.java | 1 -
fda-metadata-db/Dockerfile | 6 +-
.../at/tuwien/api/auth/TokenBriefDto.java | 4 -
.../java/at/tuwien/api/auth/TokenDto.java | 4 -
.../at/tuwien/api/database/DatabaseDto.java | 4 -
.../at/tuwien/api/database/ViewBriefDto.java | 4 -
.../java/at/tuwien/api/database/ViewDto.java | 4 -
.../api/identifier/RelatedIdentifierDto.java | 3 -
.../tuwien/entities/container/Container.java | 5 -
.../container/image/ContainerImage.java | 4 +-
.../container/image/ContainerImageDate.java | 4 +-
.../image/ContainerImageEnvironmentItem.java | 4 +-
.../at/tuwien/entities/database/Database.java | 9 +-
.../at/tuwien/entities/database/View.java | 7 +-
.../tuwien/entities/database/table/Table.java | 4 +-
.../database/table/columns/TableColumn.java | 4 +-
.../table/columns/concepts/ColumnConcept.java | 4 +-
.../table/columns/concepts/Concept.java | 4 +-
.../tuwien/entities/identifier/Creator.java | 4 +-
.../entities/identifier/Identifier.java | 9 +-
.../identifier/RelatedIdentifier.java | 8 +-
.../at/tuwien/entities/user/TimeSecret.java | 4 +-
.../java/at/tuwien/entities/user/Token.java | 9 +-
.../java/at/tuwien/entities/user/User.java | 5 +-
.../main/java/at/tuwien/querystore/View.java | 3 -
fda-metadata-db/setup-schema.sql | 179 ++----------------
fda-metadata-db/setup-user.sh | 6 -
30 files changed, 53 insertions(+), 265 deletions(-)
delete mode 100644 fda-metadata-db/setup-user.sh
diff --git a/fda-authentication-service/rest-service/src/main/java/at/tuwien/endpoints/TokenEndpoint.java b/fda-authentication-service/rest-service/src/main/java/at/tuwien/endpoints/TokenEndpoint.java
index 7a7bea971b..0fed6c2a5a 100644
--- a/fda-authentication-service/rest-service/src/main/java/at/tuwien/endpoints/TokenEndpoint.java
+++ b/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());
diff --git a/fda-authentication-service/services/src/main/java/at/tuwien/service/impl/AuthenticationServiceImpl.java b/fda-authentication-service/services/src/main/java/at/tuwien/service/impl/AuthenticationServiceImpl.java
index c259757ba9..633fc469e5 100644
--- a/fda-authentication-service/services/src/main/java/at/tuwien/service/impl/AuthenticationServiceImpl.java
+++ b/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);
diff --git a/fda-database-service/services/src/main/java/at/tuwien/service/impl/MariaDbServiceImpl.java b/fda-database-service/services/src/main/java/at/tuwien/service/impl/MariaDbServiceImpl.java
index fe796dfb50..2bf9fc672e 100644
--- a/fda-database-service/services/src/main/java/at/tuwien/service/impl/MariaDbServiceImpl.java
+++ b/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);
diff --git a/fda-identifier-service/rest-service/src/test/java/at/tuwien/service/IdentifierServiceIntegrationTest.java b/fda-identifier-service/rest-service/src/test/java/at/tuwien/service/IdentifierServiceIntegrationTest.java
index 49818d1e61..1954c0579e 100644
--- a/fda-identifier-service/rest-service/src/test/java/at/tuwien/service/IdentifierServiceIntegrationTest.java
+++ b/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());
diff --git a/fda-metadata-db/Dockerfile b/fda-metadata-db/Dockerfile
index f9b7c8bece..32417ec6bf 100644
--- a/fda-metadata-db/Dockerfile
+++ b/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
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/auth/TokenBriefDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/auth/TokenBriefDto.java
index 6c22889045..cbb5060540 100644
--- a/fda-metadata-db/api/src/main/java/at/tuwien/api/auth/TokenBriefDto.java
+++ b/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;
-
}
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/auth/TokenDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/auth/TokenDto.java
index 6e3868f520..1cf442509c 100644
--- a/fda-metadata-db/api/src/main/java/at/tuwien/api/auth/TokenDto.java
+++ b/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;
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/database/DatabaseDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/DatabaseDto.java
index 9b55f61af6..5abdf33d0b 100644
--- a/fda-metadata-db/api/src/main/java/at/tuwien/api/database/DatabaseDto.java
+++ b/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;
-
}
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/database/ViewBriefDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/ViewBriefDto.java
index fa5346ca32..2b45c7b065 100644
--- a/fda-metadata-db/api/src/main/java/at/tuwien/api/database/ViewBriefDto.java
+++ b/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;
-
}
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/database/ViewDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/ViewDto.java
index 1e12924bfe..fcd6e9c00a 100644
--- a/fda-metadata-db/api/src/main/java/at/tuwien/api/database/ViewDto.java
+++ b/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;
-
}
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/RelatedIdentifierDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/RelatedIdentifierDto.java
index c6d5c13bf1..b7ffb97c90 100644
--- a/fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/RelatedIdentifierDto.java
+++ b/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;
-
}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/Container.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/Container.java
index b8f9ecabe1..25d86eee19 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/Container.java
+++ b/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;
-
}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java
index 07c389d693..f6fd50d0fd 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImage.java
+++ b/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)
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageDate.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageDate.java
index 26adee0347..e5624a464a 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageDate.java
+++ b/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")
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageEnvironmentItem.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageEnvironmentItem.java
index 121933d4c3..a1abe5acad 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/container/image/ContainerImageEnvironmentItem.java
+++ b/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
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/Database.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/Database.java
index 190d971539..41fe84a528 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/Database.java
+++ b/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;
-
}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/View.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/View.java
index 0a60f175b5..ab289dd9d2 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/View.java
+++ b/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;
-
}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/Table.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/Table.java
index 77e548c47d..eff1bce677 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/Table.java
+++ b/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
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumn.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumn.java
index eb13193b15..f74fb634a5 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/TableColumn.java
+++ b/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
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java
index a2ed5eb24a..1afdedcd0f 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/ColumnConcept.java
+++ b/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
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Concept.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Concept.java
index 6def65fe55..00c984934c 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Concept.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/table/columns/concepts/Concept.java
@@ -23,8 +23,8 @@ public class Concept {
@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 = "URI", nullable = false, columnDefinition = "TEXT")
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Creator.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Creator.java
index 1681f68d4a..b1bd315be0 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Creator.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Creator.java
@@ -23,8 +23,8 @@ public class Creator {
@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
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java
index 950e54da3a..44c3a096e4 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java
@@ -23,9 +23,7 @@ import java.util.List;
@ToString
@AllArgsConstructor
@NoArgsConstructor
-@Where(clause = "deleted is null")
@EntityListeners(AuditingEntityListener.class)
-@SQLDelete(sql = "update mdb_identifiers set deleted = NOW() where id = ?")
@javax.persistence.Table(name = "mdb_identifiers", uniqueConstraints = {
@UniqueConstraint(columnNames = {"qid", "cid", "dbid"})
})
@@ -33,8 +31,8 @@ public class Identifier {
@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 = "cid", nullable = false)
@@ -133,9 +131,6 @@ public class Identifier {
@LastModifiedDate
private Instant lastModified;
- @Column
- private Instant deleted;
-
}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/RelatedIdentifier.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/RelatedIdentifier.java
index ad318c4a22..280715c956 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/RelatedIdentifier.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/RelatedIdentifier.java
@@ -19,7 +19,6 @@ import java.time.Instant;
@AllArgsConstructor
@NoArgsConstructor
@IdClass(RelatedIdentifierKey.class)
-@Where(clause = "deleted is null")
@EqualsAndHashCode(onlyExplicitlyIncluded = true)
@EntityListeners(AuditingEntityListener.class)
@Table(name = "mdb_related_identifiers", uniqueConstraints = {
@@ -29,8 +28,8 @@ public class RelatedIdentifier {
@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
@@ -62,9 +61,6 @@ public class RelatedIdentifier {
@LastModifiedDate
private Instant lastModified;
- @Column
- private Instant deleted;
-
}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/TimeSecret.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/TimeSecret.java
index c6922b8541..53d71c8cc7 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/TimeSecret.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/TimeSecret.java
@@ -23,8 +23,8 @@ public class TimeSecret {
@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(nullable = false)
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/Token.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/Token.java
index bacb80fc34..241f16e777 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/Token.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/Token.java
@@ -16,7 +16,6 @@ import java.time.Instant;
@AllArgsConstructor
@NoArgsConstructor
@ToString
-@SQLDelete(sql = "update mdb_tokens set deleted = NOW() where id = ?")
@EntityListeners(AuditingEntityListener.class)
@EqualsAndHashCode(onlyExplicitlyIncluded = true)
@Table(name = "mdb_tokens")
@@ -24,9 +23,8 @@ public class Token {
@Id
@EqualsAndHashCode.Include
- @Column(name = "id")
- @GenericGenerator(name = "native", strategy = "native")
- @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(updatable = false, nullable = false)
private Long id;
@Column(nullable = false, updatable = false)
@@ -50,7 +48,4 @@ public class Token {
@Column(nullable = false, updatable = false)
private Instant lastUsed;
- @Column(nullable = false, updatable = false)
- private Instant deleted;
-
}
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/User.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/User.java
index 691bc2af6d..eb1f77d74a 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/User.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/user/User.java
@@ -25,9 +25,8 @@ public class User {
@Id
@EqualsAndHashCode.Include
- @Column(name = "userid")
- @GenericGenerator(name = "native", strategy = "native")
- @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "userid", updatable = false, nullable = false)
private Long id;
@Column(unique = true, nullable = false)
diff --git a/fda-metadata-db/querystore/src/main/java/at/tuwien/querystore/View.java b/fda-metadata-db/querystore/src/main/java/at/tuwien/querystore/View.java
index 6a45ec9d0e..79419fca6e 100644
--- a/fda-metadata-db/querystore/src/main/java/at/tuwien/querystore/View.java
+++ b/fda-metadata-db/querystore/src/main/java/at/tuwien/querystore/View.java
@@ -55,9 +55,6 @@ public class View implements Serializable {
@Column(nullable = false)
private String query;
- @Column
- private Instant deleted;
-
@Column(nullable = false, updatable = false)
@CreatedDate
private Instant created;
diff --git a/fda-metadata-db/setup-schema.sql b/fda-metadata-db/setup-schema.sql
index b8e6d24fe5..944a6b9e07 100644
--- a/fda-metadata-db/setup-schema.sql
+++ b/fda-metadata-db/setup-schema.sql
@@ -1,141 +1,8 @@
BEGIN;
-CREATE SEQUENCE mdb_images_environment_item_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_images_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_images_date_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_containers_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_user_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_user_role_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_data_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_databases_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_tables_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_columns_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_columns_enum_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_view_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_columns_concepts_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_identifiers_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_related_identifiers_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_creators_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_time_secrets_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_tokens_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
-CREATE SEQUENCE mdb_concepts_seq
- START WITH 1
- INCREMENT BY 1
- NO MINVALUE
- NO MAXVALUE
- CACHE 1;
-
CREATE TABLE IF NOT EXISTS mdb_users
(
- UserID bigint not null DEFAULT nextval(mdb_user_seq),
+ UserID bigint not null AUTO_INCREMENT,
external_id VARCHAR(255) UNIQUE,
OID bigint,
username VARCHAR(255) not null,
@@ -160,7 +27,7 @@ CREATE TABLE IF NOT EXISTS mdb_users
CREATE TABLE mdb_images
(
- id bigint NOT NULL DEFAULT nextval(mdb_images_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
repository character varying(255) NOT NULL,
tag character varying(255) NOT NULL,
default_port integer NOT NULL,
@@ -178,7 +45,7 @@ CREATE TABLE mdb_images
CREATE TABLE mdb_time_secrets
(
- id bigint not null default nextval(mdb_time_secrets_seq),
+ id bigint not null AUTO_INCREMENT,
uid bigint not null,
token character varying(255) NOT NULL,
processed boolean NOT NULL default false,
@@ -190,20 +57,19 @@ CREATE TABLE mdb_time_secrets
CREATE TABLE mdb_tokens
(
- id bigint not null default nextval(mdb_tokens_seq),
+ id bigint not null AUTO_INCREMENT,
token_hash varchar(255) NOT NULL,
creator bigint not null,
created timestamp NOT NULL DEFAULT NOW(),
expires timestamp NOT NULL,
last_used timestamp,
- deleted timestamp,
PRIMARY KEY (id),
FOREIGN KEY (creator) REFERENCES mdb_users (UserID)
);
CREATE TABLE mdb_images_date
(
- id bigint NOT NULL DEFAULT nextval(mdb_images_date_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
iid bigint NOT NULL,
database_format character varying(255) NOT NULL,
unix_format character varying(255) NOT NULL,
@@ -217,7 +83,7 @@ CREATE TABLE mdb_images_date
CREATE TABLE IF NOT EXISTS mdb_containers
(
- id bigint NOT NULL DEFAULT nextval(mdb_containers_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
HASH character varying(255) NOT NULL,
INTERNAL_NAME character varying(255) NOT NULL,
NAME character varying(255) NOT NULL,
@@ -227,7 +93,6 @@ CREATE TABLE IF NOT EXISTS mdb_containers
created timestamp NOT NULL DEFAULT NOW(),
created_by bigint NOT NULL,
LAST_MODIFIED timestamp,
- deleted timestamp,
PRIMARY KEY (id),
FOREIGN KEY (created_by) REFERENCES mdb_users (UserID),
FOREIGN KEY (image_id) REFERENCES mdb_images (id)
@@ -235,7 +100,7 @@ CREATE TABLE IF NOT EXISTS mdb_containers
CREATE TABLE mdb_images_environment_item
(
- id bigint NOT NULL DEFAULT nextval(mdb_images_environment_item_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
`key` character varying(255) NOT NULL,
value character varying(255) NOT NULL,
etype ENUM ('PRIVILEGED_USERNAME', 'PRIVILEGED_PASSWORD', 'USERNAME', 'PASSWORD') NOT NULL,
@@ -248,7 +113,7 @@ CREATE TABLE mdb_images_environment_item
CREATE TABLE IF NOT EXISTS mdb_data
(
- ID bigint DEFAULT nextval(mdb_data_seq),
+ ID bigint NOT NULL AUTO_INCREMENT,
PROVENANCE TEXT,
FileEncoding TEXT,
FileType VARCHAR(100),
@@ -278,7 +143,7 @@ CREATE TABLE IF NOT EXISTS mdb_licenses
CREATE TABLE IF NOT EXISTS mdb_databases
(
- id bigint NOT NULL DEFAULT nextval(mdb_databases_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
name character varying(255) NOT NULL,
internal_name character varying(255) NOT NULL,
exchange character varying(255) NOT NULL,
@@ -289,7 +154,6 @@ CREATE TABLE IF NOT EXISTS mdb_databases
Contactperson BIGINT,
created timestamp NOT NULL DEFAULT NOW(),
last_modified timestamp,
- deleted timestamp NULL,
PRIMARY KEY (id),
FOREIGN KEY (Creator) REFERENCES mdb_users (UserID),
FOREIGN KEY (Contactperson) REFERENCES mdb_users (UserID),
@@ -305,7 +169,7 @@ CREATE TABLE IF NOT EXISTS mdb_databases_subjects
CREATE TABLE IF NOT EXISTS mdb_tables
(
- ID bigint NOT NULL DEFAULT nextval(mdb_tables_seq),
+ ID bigint NOT NULL AUTO_INCREMENT,
tDBID bigint NOT NULL,
internal_name character varying(255) NOT NULL,
topic character varying(255) NOT NULL,
@@ -323,14 +187,14 @@ CREATE TABLE IF NOT EXISTS mdb_tables
created timestamp NOT NULL DEFAULT NOW(),
created_by bigint NOT NULL,
last_modified timestamp,
- PRIMARY KEY (tDBID, ID),
+ PRIMARY KEY (ID, tDBID),
FOREIGN KEY (created_by) REFERENCES mdb_users (UserID),
FOREIGN KEY (tDBID) REFERENCES mdb_databases (id)
);
CREATE TABLE IF NOT EXISTS mdb_columns
(
- ID bigint NOT NULL DEFAULT nextval(mdb_columns_seq),
+ ID bigint NOT NULL AUTO_INCREMENT,
cDBID bigint NOT NULL,
tID bigint NOT NULL,
dfID bigint,
@@ -350,12 +214,12 @@ CREATE TABLE IF NOT EXISTS mdb_columns
last_modified timestamp,
FOREIGN KEY (cDBID, tID) REFERENCES mdb_tables (tDBID, ID),
FOREIGN KEY (created_by) REFERENCES mdb_users (UserID),
- PRIMARY KEY (cDBID, tID, ID)
+ PRIMARY KEY (ID, cDBID, tID)
);
CREATE TABLE IF NOT EXISTS mdb_columns_enums
(
- ID bigint NOT NULL DEFAULT nextval(mdb_columns_enum_seq),
+ ID bigint NOT NULL AUTO_INCREMENT,
eDBID bigint NOT NULL,
tID bigint NOT NULL,
cID bigint NOT NULL,
@@ -411,7 +275,7 @@ CREATE TABLE IF NOT EXISTS mdb_columns_cat
CREATE TABLE IF NOT EXISTS mdb_concepts
(
- id bigint not null default nextval(mdb_concepts_seq),
+ id bigint not null AUTO_INCREMENT,
URI TEXT,
name VARCHAR(255),
created timestamp NOT NULL DEFAULT NOW(),
@@ -435,7 +299,7 @@ CREATE TABLE IF NOT EXISTS mdb_columns_concepts
CREATE TABLE IF NOT EXISTS mdb_view
(
- id bigint NOT NULL DEFAULT nextval(mdb_view_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
vcid bigint NOT NULL,
vdbid bigint NOT NULL,
vName VARCHAR(255) NOT NULL,
@@ -447,16 +311,15 @@ CREATE TABLE IF NOT EXISTS mdb_view
InitialView BOOLEAN NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
last_modified timestamp,
- deleted timestamp,
created_by bigint NOT NULL,
FOREIGN KEY (created_by) REFERENCES mdb_users (UserID),
FOREIGN KEY (vdbid) REFERENCES mdb_databases (id),
- PRIMARY KEY (vdbid, id)
+ PRIMARY KEY (id, vdbid)
);
CREATE TABLE IF NOT EXISTS mdb_identifiers
(
- id bigint DEFAULT nextval(mdb_identifiers_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
cid bigint NOT NULL,
dbid bigint NOT NULL,
qid bigint,
@@ -480,7 +343,6 @@ CREATE TABLE IF NOT EXISTS mdb_identifiers
created timestamp NOT NULL DEFAULT NOW(),
created_by bigint NOT NULL,
last_modified timestamp,
- deleted timestamp,
PRIMARY KEY (id), /* must be a single id from persistent identifier concept */
FOREIGN KEY (cid) REFERENCES mdb_containers (id),
FOREIGN KEY (dbid) REFERENCES mdb_databases (id),
@@ -490,7 +352,7 @@ CREATE TABLE IF NOT EXISTS mdb_identifiers
CREATE TABLE IF NOT EXISTS mdb_related_identifiers
(
- id bigint DEFAULT nextval(mdb_related_identifiers_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
iid bigint NOT NULL,
value varchar(255) NOT NULL,
type varchar(255),
@@ -498,7 +360,6 @@ CREATE TABLE IF NOT EXISTS mdb_related_identifiers
created timestamp NOT NULL DEFAULT NOW(),
created_by bigint NOT NULL,
last_modified timestamp,
- deleted timestamp,
PRIMARY KEY (id, iid), /* must be a single id from persistent identifier concept */
FOREIGN KEY (iid) REFERENCES mdb_identifiers (id),
FOREIGN KEY (created_by) REFERENCES mdb_users (UserID)
@@ -506,7 +367,7 @@ CREATE TABLE IF NOT EXISTS mdb_related_identifiers
CREATE TABLE IF NOT EXISTS mdb_creators
(
- id bigint DEFAULT nextval(mdb_creators_seq),
+ id bigint NOT NULL AUTO_INCREMENT,
pid bigint NOT NULL,
name VARCHAR(255) NOT NULL,
affiliation VARCHAR(255),
diff --git a/fda-metadata-db/setup-user.sh b/fda-metadata-db/setup-user.sh
deleted file mode 100644
index 724f28f273..0000000000
--- a/fda-metadata-db/setup-user.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-mysql --user="root" --password="${METADATA_PASSWORD}" --database="${METADATA_DB}" << EOF
-CREATE USER '${MARIADB_USERNAME}' IDENTIFIED BY '${MARIADB_PASSWORD}';
-GRANT SELECT ON ${METADATA_DB}.* TO '${MARIADB_USERNAME}';
-FLUSH PRIVILEGES;
-EOF
\ No newline at end of file
--
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