From d6d05b5ba5a970fef29e901af23a22500d313a7b Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Wed, 23 Nov 2022 09:38:35 +0100
Subject: [PATCH] Further progress
---
.../src/main/resources/application-docker.yml | 3 +-
.../src/main/resources/application-local.yml | 5 +--
.../src/main/resources/application.yml | 3 +-
.../src/main/resources/application-docker.yml | 3 +-
.../src/main/resources/application-local.yml | 3 +-
.../src/main/resources/application.yml | 3 +-
.../src/main/resources/application-docker.yml | 3 +-
.../src/main/resources/application-local.yml | 3 +-
.../src/main/resources/application.yml | 3 +-
.../src/main/resources/application-docker.yml | 2 +-
.../src/main/resources/application.yml | 2 +-
.../src/main/resources/application-docker.yml | 3 +-
.../src/main/resources/application-local.yml | 3 +-
.../src/main/resources/application.yml | 3 +-
.../src/test/java/at/tuwien/BaseUnitTest.java | 2 +-
fda-metadata-db/Dockerfile | 4 +--
.../table/columns/concepts/ConceptDto.java | 3 ++
.../at/tuwien/entities/database/Database.java | 2 +-
.../at/tuwien/entities/database/License.java | 2 +-
.../at/tuwien/entities/database/View.java | 2 +-
.../tuwien/entities/database/table/Table.java | 2 +-
.../database/table/columns/TableColumn.java | 2 +-
.../table/columns/concepts/ColumnConcept.java | 6 ++--
.../table/columns/concepts/Concept.java | 14 ++++++--
.../entities/identifier/Identifier.java | 6 ++--
fda-metadata-db/setup-schema.sql | 36 +++++++++----------
fda-metadata-db/setup-user.sh | 3 +-
.../src/main/resources/application-docker.yml | 3 +-
.../src/main/resources/application-local.yml | 3 +-
.../src/main/resources/application.yml | 3 +-
.../src/main/resources/application-docker.yml | 3 +-
.../src/main/resources/application-local.yml | 3 +-
.../src/main/resources/application.yml | 3 +-
.../src/main/resources/application-docker.yml | 3 +-
.../src/main/resources/application-local.yml | 3 +-
.../src/main/resources/application.yml | 3 +-
36 files changed, 94 insertions(+), 59 deletions(-)
diff --git a/fda-authentication-service/rest-service/src/main/resources/application-docker.yml b/fda-authentication-service/rest-service/src/main/resources/application-docker.yml
index eaa0435b27..9bd14ae2ff 100644
--- a/fda-authentication-service/rest-service/src/main/resources/application-docker.yml
+++ b/fda-authentication-service/rest-service/src/main/resources/application-docker.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-authentication-service/rest-service/src/main/resources/application-local.yml b/fda-authentication-service/rest-service/src/main/resources/application-local.yml
index 420671411f..b9c10d9360 100644
--- a/fda-authentication-service/rest-service/src/main/resources/application-local.yml
+++ b/fda-authentication-service/rest-service/src/main/resources/application-local.yml
@@ -4,16 +4,17 @@ spring:
datasource:
url: jdbc:mariadb://localhost:3306/fda
driver-class-name: org.mariadb.jdbc.Driver
- username: dbrepo
+ username: root
password: dbrepo
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-authentication-service/rest-service/src/main/resources/application.yml b/fda-authentication-service/rest-service/src/main/resources/application.yml
index a8fd56e659..a8fb4837e3 100644
--- a/fda-authentication-service/rest-service/src/main/resources/application.yml
+++ b/fda-authentication-service/rest-service/src/main/resources/application.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: "${METADATA_DB}"
jdbc:
time_zone: UTC
application:
diff --git a/fda-container-service/rest-service/src/main/resources/application-docker.yml b/fda-container-service/rest-service/src/main/resources/application-docker.yml
index 24f847776b..bff6830b95 100644
--- a/fda-container-service/rest-service/src/main/resources/application-docker.yml
+++ b/fda-container-service/rest-service/src/main/resources/application-docker.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-container-service/rest-service/src/main/resources/application-local.yml b/fda-container-service/rest-service/src/main/resources/application-local.yml
index 99918dae2a..640df600fa 100644
--- a/fda-container-service/rest-service/src/main/resources/application-local.yml
+++ b/fda-container-service/rest-service/src/main/resources/application-local.yml
@@ -8,12 +8,13 @@ spring:
password: dbrepo
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-container-service/rest-service/src/main/resources/application.yml b/fda-container-service/rest-service/src/main/resources/application.yml
index e3d7717a3d..b9605b4fdd 100644
--- a/fda-container-service/rest-service/src/main/resources/application.yml
+++ b/fda-container-service/rest-service/src/main/resources/application.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: "${METADATA_DB}"
jdbc:
time_zone: UTC
application:
diff --git a/fda-database-service/rest-service/src/main/resources/application-docker.yml b/fda-database-service/rest-service/src/main/resources/application-docker.yml
index 576a0422f1..60f5b8729a 100644
--- a/fda-database-service/rest-service/src/main/resources/application-docker.yml
+++ b/fda-database-service/rest-service/src/main/resources/application-docker.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-database-service/rest-service/src/main/resources/application-local.yml b/fda-database-service/rest-service/src/main/resources/application-local.yml
index 0a7f570359..76c11d7907 100644
--- a/fda-database-service/rest-service/src/main/resources/application-local.yml
+++ b/fda-database-service/rest-service/src/main/resources/application-local.yml
@@ -8,12 +8,13 @@ spring:
password: dbrepo
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-database-service/rest-service/src/main/resources/application.yml b/fda-database-service/rest-service/src/main/resources/application.yml
index 2472179420..c01a4243df 100644
--- a/fda-database-service/rest-service/src/main/resources/application.yml
+++ b/fda-database-service/rest-service/src/main/resources/application.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: "${METADATA_DB}"
jdbc:
time_zone: UTC
application:
diff --git a/fda-discovery-service/discovery/src/main/resources/application-docker.yml b/fda-discovery-service/discovery/src/main/resources/application-docker.yml
index 074b27b10c..2bb1601ec6 100644
--- a/fda-discovery-service/discovery/src/main/resources/application-docker.yml
+++ b/fda-discovery-service/discovery/src/main/resources/application-docker.yml
@@ -7,7 +7,7 @@ spring:
password: postgres
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
diff --git a/fda-discovery-service/discovery/src/main/resources/application.yml b/fda-discovery-service/discovery/src/main/resources/application.yml
index 6cd73409b3..8b05b5cf51 100644
--- a/fda-discovery-service/discovery/src/main/resources/application.yml
+++ b/fda-discovery-service/discovery/src/main/resources/application.yml
@@ -7,7 +7,7 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
diff --git a/fda-identifier-service/rest-service/src/main/resources/application-docker.yml b/fda-identifier-service/rest-service/src/main/resources/application-docker.yml
index dfe20bf768..5465a3c284 100644
--- a/fda-identifier-service/rest-service/src/main/resources/application-docker.yml
+++ b/fda-identifier-service/rest-service/src/main/resources/application-docker.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-identifier-service/rest-service/src/main/resources/application-local.yml b/fda-identifier-service/rest-service/src/main/resources/application-local.yml
index acb11a9606..62ca8741e2 100644
--- a/fda-identifier-service/rest-service/src/main/resources/application-local.yml
+++ b/fda-identifier-service/rest-service/src/main/resources/application-local.yml
@@ -8,12 +8,13 @@ spring:
password: dbrepo
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-identifier-service/rest-service/src/main/resources/application.yml b/fda-identifier-service/rest-service/src/main/resources/application.yml
index 8553453894..f4004bb817 100644
--- a/fda-identifier-service/rest-service/src/main/resources/application.yml
+++ b/fda-identifier-service/rest-service/src/main/resources/application.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: "${METADATA_DB}"
jdbc:
time_zone: UTC
application:
diff --git a/fda-identifier-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java b/fda-identifier-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
index 909d11f260..04e96620ef 100644
--- a/fda-identifier-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
+++ b/fda-identifier-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java
@@ -98,7 +98,7 @@ public abstract class BaseUnitTest {
public final static String IMAGE_1_TAG = "13-alpine";
public final static String IMAGE_1_HASH = "83b40f2726e5";
public final static Integer IMAGE_1_PORT = 5432;
- public final static String IMAGE_1_DIALECT = "org.hibernate.dialect.PostgreSQLDialect";
+ public final static String IMAGE_1_DIALECT = "org.mariadb.jdbc.Driver";
public final static String IMAGE_1_DRIVER = "org.postgresql.Driver";
public final static String IMAGE_1_JDBC = "postgresql";
public final static Long IMAGE_1_SIZE = 12000L;
diff --git a/fda-metadata-db/Dockerfile b/fda-metadata-db/Dockerfile
index bc6ee91576..50141d3569 100644
--- a/fda-metadata-db/Dockerfile
+++ b/fda-metadata-db/Dockerfile
@@ -31,7 +31,7 @@ ENV MARIADB_PASSWORD="${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
-COPY ./setup-schema.sql /docker-entrypoint-initdb.d/1.sql
-COPY ./setup-user.sh /docker-entrypoint-initdb.d/2.sh
+COPY ./setup-user.sh /docker-entrypoint-initdb.d/1.sh
+COPY ./setup-schema.sql /docker-entrypoint-initdb.d/2.sql
COPY --from=build /root/.m2/repository/at/tuwien /root/.m2/repository/at/tuwien
\ No newline at end of file
diff --git a/fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptDto.java b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptDto.java
index a229dd2f1f..2cdb741097 100644
--- a/fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptDto.java
+++ b/fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/concepts/ConceptDto.java
@@ -16,6 +16,9 @@ import java.time.Instant;
@NoArgsConstructor
public class ConceptDto {
+ @NotNull
+ private String id;
+
@NotNull
private String uri;
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 7549845e62..361736ed67 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
@@ -65,7 +65,7 @@ public class Database {
@Column(nullable = false)
private String exchange;
- @Column
+ @Column(columnDefinition = "TEXT")
private String description;
@ManyToOne(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
diff --git a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/License.java b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/License.java
index e1f188f321..baad81f5a3 100644
--- a/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/License.java
+++ b/fda-metadata-db/entities/src/main/java/at/tuwien/entities/database/License.java
@@ -21,7 +21,7 @@ public class License {
@Column(nullable = false)
private String identifier;
- @Column(nullable = false)
+ @Column(nullable = false, columnDefinition = "TEXT")
private String uri;
}
\ No newline at end of file
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 14466a12bd..6111b151c0 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
@@ -62,7 +62,7 @@ public class View {
@Column(name = "initialview", nullable = false)
private Boolean isInitialView;
- @Column(nullable = false)
+ @Column(nullable = false, columnDefinition = "TEXT")
private String query;
@Column(nullable = false, updatable = false)
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 c19555325c..36e08d194f 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
@@ -58,7 +58,7 @@ public class Table {
@Column(nullable = false, updatable = false)
private String topic;
- @Column(name = "tdescription")
+ @Column(name = "tdescription", columnDefinition = "TEXT")
private String description;
@org.springframework.data.annotation.Transient
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 18412a2792..a297ddc9f8 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
@@ -124,7 +124,7 @@ public class TableColumn implements Comparable<TableColumn> {
@JoinColumn(name = "tid", referencedColumnName = "tid", insertable = false, updatable = false),
@JoinColumn(name = "cdbid", referencedColumnName = "cdbid", insertable = false, updatable = false)
},
- inverseJoinColumns = @JoinColumn(name = "uri"))
+ inverseJoinColumns = @JoinColumn(name = "concept_id", referencedColumnName = "id"))
private Concept concept;
@Column
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 c375969f47..9d38bfcef2 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
@@ -6,6 +6,9 @@ import org.springframework.data.jpa.domain.support.AuditingEntityListener;
import javax.persistence.*;
import java.io.Serializable;
+/**
+ * Join Table
+ */
@Data
@Entity
@Builder
@@ -30,7 +33,4 @@ public class ColumnConcept implements Serializable {
@Id
@EqualsAndHashCode.Include
private Long cdbid;
-
- @Column(nullable = false)
- private String uri;
}
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 733b2c6b14..48dc8bcea9 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
@@ -2,6 +2,7 @@ package at.tuwien.entities.database.table.columns.concepts;
import at.tuwien.entities.database.table.columns.TableColumn;
import lombok.*;
+import org.hibernate.annotations.GenericGenerator;
import org.springframework.data.annotation.CreatedDate;
import org.springframework.data.jpa.domain.support.AuditingEntityListener;
@@ -21,7 +22,16 @@ import java.util.List;
public class Concept {
@Id
- @Column(name = "URI", nullable = false)
+ @EqualsAndHashCode.Include
+ @GeneratedValue(generator = "concept-sequence")
+ @GenericGenerator(
+ name = "concept-sequence",
+ strategy = "enhanced-sequence",
+ parameters = @org.hibernate.annotations.Parameter(name = "sequence_name", value = "mdb_concepts_seq")
+ )
+ private Long id;
+
+ @Column(name = "URI", nullable = false, columnDefinition = "TEXT")
private String uri;
@Column(name = "name", nullable = false)
@@ -31,7 +41,7 @@ public class Concept {
@ToString.Exclude
@OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.MERGE)
@JoinTable(name = "mdb_columns_concepts",
- joinColumns = @JoinColumn(name = "uri"),
+ joinColumns = @JoinColumn(name = "concept_id", referencedColumnName = "id", insertable = false, updatable = false),
inverseJoinColumns = {
@JoinColumn(name = "cid", referencedColumnName = "id", insertable = false, updatable = false),
@JoinColumn(name = "tid", referencedColumnName = "tid", insertable = false, updatable = false),
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 2fd3030060..f5d1d3769e 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
@@ -60,7 +60,7 @@ public class Identifier {
@Column(nullable = false)
private String title;
- @Column
+ @Column(columnDefinition = "TEXT")
private String description;
@NotBlank
@@ -81,10 +81,10 @@ public class Identifier {
@Enumerated(EnumType.STRING)
private IdentifierType type;
- @Column
+ @Column(columnDefinition = "TEXT")
private String query;
- @Column
+ @Column(columnDefinition = "TEXT")
private String queryNormalized;
@Column
diff --git a/fda-metadata-db/setup-schema.sql b/fda-metadata-db/setup-schema.sql
index fd2dd014a2..788aaaa7c1 100644
--- a/fda-metadata-db/setup-schema.sql
+++ b/fda-metadata-db/setup-schema.sql
@@ -212,7 +212,7 @@ CREATE TABLE mdb_images_date
created_at timestamp NOT NULL DEFAULT NOW(),
PRIMARY KEY (id),
FOREIGN KEY (iid) REFERENCES mdb_images (id),
- UNIQUE (database_format)
+ UNIQUE (database_format, unix_format, example)
);
CREATE TABLE IF NOT EXISTS mdb_containers
@@ -328,7 +328,7 @@ CREATE TABLE IF NOT EXISTS mdb_tables
FOREIGN KEY (tDBID) REFERENCES mdb_databases (id)
);
-CREATE TABLE IF NOT EXISTS mdb_COLUMNS
+CREATE TABLE IF NOT EXISTS mdb_columns
(
ID bigint NOT NULL DEFAULT nextval(mdb_columns_seq),
cDBID bigint NOT NULL,
@@ -353,7 +353,7 @@ CREATE TABLE IF NOT EXISTS mdb_COLUMNS
PRIMARY KEY (cDBID, tID, ID)
);
-CREATE TABLE IF NOT EXISTS mdb_COLUMNS_ENUMS
+CREATE TABLE IF NOT EXISTS mdb_columns_enums
(
ID bigint NOT NULL DEFAULT nextval(mdb_columns_enum_seq),
eDBID bigint NOT NULL,
@@ -362,11 +362,11 @@ CREATE TABLE IF NOT EXISTS mdb_COLUMNS_ENUMS
enum_values CHARACTER VARYING(255) NOT NULL,
created timestamp NOT NULL DEFAULT NOW(),
last_modified timestamp,
- FOREIGN KEY (eDBID, tID, cID) REFERENCES mdb_COLUMNS (cDBID, tID, ID),
+ FOREIGN KEY (eDBID, tID, cID) REFERENCES mdb_columns (cDBID, tID, ID),
PRIMARY KEY (ID, eDBID, tID, cID)
);
-CREATE TABLE IF NOT EXISTS mdb_COLUMNS_nom
+CREATE TABLE IF NOT EXISTS mdb_columns_nom
(
cDBID bigint,
tID bigint,
@@ -374,11 +374,11 @@ CREATE TABLE IF NOT EXISTS mdb_COLUMNS_nom
maxlength INTEGER,
last_modified timestamp,
created timestamp NOT NULL DEFAULT NOW(),
- FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_COLUMNS (cDBID, tID, ID),
+ FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_columns (cDBID, tID, ID),
PRIMARY KEY (cDBID, tID, cID)
);
-CREATE TABLE IF NOT EXISTS mdb_COLUMNS_num
+CREATE TABLE IF NOT EXISTS mdb_columns_num
(
cDBID bigint,
tID bigint,
@@ -392,11 +392,11 @@ CREATE TABLE IF NOT EXISTS mdb_COLUMNS_num
-- Histogram INTEGER[],
last_modified timestamp,
created timestamp NOT NULL DEFAULT NOW(),
- FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_COLUMNS (cDBID, tID, ID),
+ FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_columns (cDBID, tID, ID),
PRIMARY KEY (cDBID, tID, cID)
);
-CREATE TABLE IF NOT EXISTS mdb_COLUMNS_cat
+CREATE TABLE IF NOT EXISTS mdb_columns_cat
(
cDBID bigint,
tID bigint,
@@ -405,7 +405,7 @@ CREATE TABLE IF NOT EXISTS mdb_COLUMNS_cat
-- cat_array TEXT[],
last_modified timestamp,
created timestamp NOT NULL DEFAULT NOW(),
- FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_COLUMNS (cDBID, tID, ID),
+ FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_columns (cDBID, tID, ID),
PRIMARY KEY (cDBID, tID, cID)
);
@@ -413,7 +413,7 @@ CREATE TABLE IF NOT EXISTS mdb_concepts
(
id bigint not null default nextval(mdb_concepts_seq),
URI TEXT,
- name TEXT,
+ name VARCHAR(255),
created timestamp NOT NULL DEFAULT NOW(),
created_by bigint,
FOREIGN KEY (created_by) REFERENCES mdb_users (UserID),
@@ -427,11 +427,11 @@ CREATE TABLE IF NOT EXISTS mdb_columns_concepts
cID bigint NOT NULL,
concept_id bigint REFERENCES mdb_concepts (id), /* mysql does not allow text primary keys */
created timestamp NOT NULL DEFAULT NOW(),
- FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_COLUMNS (cDBID, tID, ID),
+ FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_columns (cDBID, tID, ID),
PRIMARY KEY (cDBID, tID, cID)
);
-CREATE TABLE IF NOT EXISTS mdb_VIEW
+CREATE TABLE IF NOT EXISTS mdb_view
(
id bigint NOT NULL DEFAULT nextval(mdb_view_seq),
vcid bigint NOT NULL,
@@ -488,13 +488,13 @@ CREATE TABLE IF NOT EXISTS mdb_identifiers
CREATE TABLE IF NOT EXISTS mdb_related_identifiers
(
- id bigint DEFAULT nextval(mdb_related_identifiers_seq),
- iid bigint NOT NULL,
- value text NOT NULL,
+ id bigint DEFAULT nextval(mdb_related_identifiers_seq),
+ iid bigint NOT NULL,
+ value varchar(255) NOT NULL,
type varchar(255),
relation varchar(255),
- created timestamp NOT NULL DEFAULT NOW(),
- created_by bigint NOT NULL,
+ 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 */
diff --git a/fda-metadata-db/setup-user.sh b/fda-metadata-db/setup-user.sh
index 63c5e77afe..724f28f273 100644
--- a/fda-metadata-db/setup-user.sh
+++ b/fda-metadata-db/setup-user.sh
@@ -1,5 +1,6 @@
#!/bin/sh
mysql --user="root" --password="${METADATA_PASSWORD}" --database="${METADATA_DB}" << EOF
CREATE USER '${MARIADB_USERNAME}' IDENTIFIED BY '${MARIADB_PASSWORD}';
-GRANT ALL PRIVILEGES ON '${METADATA_DB}' TO '${MARIADB_USERNAME}';
+GRANT SELECT ON ${METADATA_DB}.* TO '${MARIADB_USERNAME}';
+FLUSH PRIVILEGES;
EOF
\ No newline at end of file
diff --git a/fda-metadata-service/rest-service/src/main/resources/application-docker.yml b/fda-metadata-service/rest-service/src/main/resources/application-docker.yml
index 0d2d4dbbda..99da976873 100644
--- a/fda-metadata-service/rest-service/src/main/resources/application-docker.yml
+++ b/fda-metadata-service/rest-service/src/main/resources/application-docker.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-metadata-service/rest-service/src/main/resources/application-local.yml b/fda-metadata-service/rest-service/src/main/resources/application-local.yml
index 7278d36694..58b27eec0a 100644
--- a/fda-metadata-service/rest-service/src/main/resources/application-local.yml
+++ b/fda-metadata-service/rest-service/src/main/resources/application-local.yml
@@ -8,12 +8,13 @@ spring:
password: dbrepo
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-metadata-service/rest-service/src/main/resources/application.yml b/fda-metadata-service/rest-service/src/main/resources/application.yml
index e10395d64f..291622e4ac 100644
--- a/fda-metadata-service/rest-service/src/main/resources/application.yml
+++ b/fda-metadata-service/rest-service/src/main/resources/application.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: "${METADATA_DB}"
jdbc:
time_zone: UTC
application:
diff --git a/fda-query-service/rest-service/src/main/resources/application-docker.yml b/fda-query-service/rest-service/src/main/resources/application-docker.yml
index 19b6beb523..6ea04978aa 100644
--- a/fda-query-service/rest-service/src/main/resources/application-docker.yml
+++ b/fda-query-service/rest-service/src/main/resources/application-docker.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-query-service/rest-service/src/main/resources/application-local.yml b/fda-query-service/rest-service/src/main/resources/application-local.yml
index 4e107cf208..8f8defbb1b 100644
--- a/fda-query-service/rest-service/src/main/resources/application-local.yml
+++ b/fda-query-service/rest-service/src/main/resources/application-local.yml
@@ -8,12 +8,13 @@ spring:
password: dbrepo
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-query-service/rest-service/src/main/resources/application.yml b/fda-query-service/rest-service/src/main/resources/application.yml
index ee1656dd6b..0f84ade3e0 100644
--- a/fda-query-service/rest-service/src/main/resources/application.yml
+++ b/fda-query-service/rest-service/src/main/resources/application.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: "${METADATA_DB}"
jdbc:
time_zone: UTC
application:
diff --git a/fda-table-service/rest-service/src/main/resources/application-docker.yml b/fda-table-service/rest-service/src/main/resources/application-docker.yml
index 32321dd3c3..51bb0170a0 100644
--- a/fda-table-service/rest-service/src/main/resources/application-docker.yml
+++ b/fda-table-service/rest-service/src/main/resources/application-docker.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-table-service/rest-service/src/main/resources/application-local.yml b/fda-table-service/rest-service/src/main/resources/application-local.yml
index 3901f17037..843fbdebd0 100644
--- a/fda-table-service/rest-service/src/main/resources/application-local.yml
+++ b/fda-table-service/rest-service/src/main/resources/application-local.yml
@@ -8,12 +8,13 @@ spring:
password: dbrepo
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: fda
jdbc:
time_zone: UTC
application:
diff --git a/fda-table-service/rest-service/src/main/resources/application.yml b/fda-table-service/rest-service/src/main/resources/application.yml
index 2f82391ccc..502aa32659 100644
--- a/fda-table-service/rest-service/src/main/resources/application.yml
+++ b/fda-table-service/rest-service/src/main/resources/application.yml
@@ -8,12 +8,13 @@ spring:
password: "${METADATA_PASSWORD}"
jpa:
show-sql: false
- database-platform: org.hibernate.dialect.PostgreSQLDialect
+ database-platform: org.hibernate.dialect.MariaDBDialect
hibernate:
ddl-auto: validate
open-in-view: false
properties:
hibernate:
+ default_schema: "${METADATA_DB}"
jdbc:
time_zone: UTC
application:
--
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