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 eaa0435b2793c187ae36d720eaaa2181a7c3cb3d..9bd14ae2ff220fbef26cfeddb6b94872d0f4a90d 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: "${METADATA_PASSWORD}" jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-authentication-service/rest-service/src/main/resources/application-local.yml b/fda-authentication-service/rest-service/src/main/resources/application-local.yml index 420671411f189b072497813b33cb16ec317bdf66..b9c10d9360e5946b84d3043dcfc20dd5c75efdae 100644 --- a/fda-authentication-service/rest-service/src/main/resources/application-local.yml +++ b/fda-authentication-service/rest-service/src/main/resources/application-local.yml @@ -4,16 +4,17 @@ spring: datasource: url: jdbc:mariadb://localhost:3306/fda driver-class-name: org.mariadb.jdbc.Driver - username: dbrepo + username: root password: dbrepo jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-authentication-service/rest-service/src/main/resources/application.yml b/fda-authentication-service/rest-service/src/main/resources/application.yml index a8fd56e659819d2904338c69d69902195d01da45..a8fb4837e380e828f1fc20ae369ea46510d30f2f 100644 --- a/fda-authentication-service/rest-service/src/main/resources/application.yml +++ b/fda-authentication-service/rest-service/src/main/resources/application.yml @@ -8,12 +8,13 @@ spring: password: "${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: "${METADATA_DB}" jdbc: time_zone: UTC application: diff --git a/fda-container-service/rest-service/src/main/resources/application-docker.yml b/fda-container-service/rest-service/src/main/resources/application-docker.yml index 24f847776bd85c40448227ab2a065067045003d9..bff6830b95cdad49e301f033e5a3515d45c540b5 100644 --- a/fda-container-service/rest-service/src/main/resources/application-docker.yml +++ b/fda-container-service/rest-service/src/main/resources/application-docker.yml @@ -8,12 +8,13 @@ spring: password: "${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 99918dae2a0975036b7fbc81dcafb918c9c24872..640df600fad225ac73cb9451f5645fd040464f5a 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 e3d7717a3ddc7019a59294b64f9759fbe3fbc878..b9605b4fdd773161b6776596887696ec4c34390e 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 576a0422f1b92925fc6d78c1286f9543144f55fc..60f5b8729a62e14c98a01fa490cc36e89d2efe3e 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: "${METADATA_PASSWORD}" jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-database-service/rest-service/src/main/resources/application-local.yml b/fda-database-service/rest-service/src/main/resources/application-local.yml index 0a7f5703599f2a16deb0a9d91ad595dc4e926ac5..76c11d7907fda8661a028f2c95f41cf65d614f90 100644 --- a/fda-database-service/rest-service/src/main/resources/application-local.yml +++ b/fda-database-service/rest-service/src/main/resources/application-local.yml @@ -8,12 +8,13 @@ spring: password: dbrepo jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-database-service/rest-service/src/main/resources/application.yml b/fda-database-service/rest-service/src/main/resources/application.yml index 2472179420fefb20335500c21f2d3ffa2d2487ad..c01a4243dff9c4df363662d2a666c8fd54714d80 100644 --- a/fda-database-service/rest-service/src/main/resources/application.yml +++ b/fda-database-service/rest-service/src/main/resources/application.yml @@ -8,12 +8,13 @@ spring: password: "${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: "${METADATA_DB}" jdbc: time_zone: UTC application: diff --git a/fda-discovery-service/discovery/src/main/resources/application-docker.yml b/fda-discovery-service/discovery/src/main/resources/application-docker.yml index 074b27b10c189f663240f6dae5261fd60f77f675..2bb1601ec6a348bf897b6a1d6ba9dfe40e88ac85 100644 --- a/fda-discovery-service/discovery/src/main/resources/application-docker.yml +++ b/fda-discovery-service/discovery/src/main/resources/application-docker.yml @@ -7,7 +7,7 @@ spring: password: postgres jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false diff --git a/fda-discovery-service/discovery/src/main/resources/application.yml b/fda-discovery-service/discovery/src/main/resources/application.yml index 6cd73409b3a6b12da0ea863868c1067dd55b4021..8b05b5cf517e6a6e73bea1aa587ff2dcc26d9088 100644 --- a/fda-discovery-service/discovery/src/main/resources/application.yml +++ b/fda-discovery-service/discovery/src/main/resources/application.yml @@ -7,7 +7,7 @@ spring: password: "${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 dfe20bf76800b010660a3171e27791ac3c503b88..5465a3c284c06ff501a08f6a4e7d018eb3f3855a 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: "${METADATA_PASSWORD}" jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-identifier-service/rest-service/src/main/resources/application-local.yml b/fda-identifier-service/rest-service/src/main/resources/application-local.yml index acb11a960690b56c300a30b9c2674f1d7211ef87..62ca8741e2e536afdef07b9aa259c085d91e291d 100644 --- a/fda-identifier-service/rest-service/src/main/resources/application-local.yml +++ b/fda-identifier-service/rest-service/src/main/resources/application-local.yml @@ -8,12 +8,13 @@ spring: password: dbrepo jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-identifier-service/rest-service/src/main/resources/application.yml b/fda-identifier-service/rest-service/src/main/resources/application.yml index 8553453894ebb1adcd0855f5f8ece52bf30b5584..f4004bb81759245e6b866e4a055c0fc1a0c814e6 100644 --- a/fda-identifier-service/rest-service/src/main/resources/application.yml +++ b/fda-identifier-service/rest-service/src/main/resources/application.yml @@ -8,12 +8,13 @@ spring: password: "${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: "${METADATA_DB}" jdbc: time_zone: UTC application: diff --git a/fda-identifier-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java b/fda-identifier-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java index 909d11f260a2c118013f88ff86a071e11a36b2b5..04e96620eff1d695426a579d63ac1e03fa54368e 100644 --- a/fda-identifier-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java +++ b/fda-identifier-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java @@ -98,7 +98,7 @@ public abstract class BaseUnitTest { public final static String IMAGE_1_TAG = "13-alpine"; public final static String IMAGE_1_HASH = "83b40f2726e5"; public final static Integer IMAGE_1_PORT = 5432; - public final static String IMAGE_1_DIALECT = "org.hibernate.dialect.PostgreSQLDialect"; + public final static String IMAGE_1_DIALECT = "org.mariadb.jdbc.Driver"; public final static String IMAGE_1_DRIVER = "org.postgresql.Driver"; public final static String IMAGE_1_JDBC = "postgresql"; public final static Long IMAGE_1_SIZE = 12000L; diff --git a/fda-metadata-db/Dockerfile b/fda-metadata-db/Dockerfile index bc6ee915761b20048b822f17b96ae98c56301a26..50141d356956c0f38a5634a269ce2eec61fc23b4 100644 --- a/fda-metadata-db/Dockerfile +++ b/fda-metadata-db/Dockerfile @@ -31,7 +31,7 @@ ENV MARIADB_PASSWORD="${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 a229dd2f1f6b6f15b87b2068f86804f149857128..2cdb741097e825472864e69595ac3ed1a6158249 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 7549845e629412779d9cd289b5d4256479402446..361736ed677b438bb99eb81d7eac50de8e280f97 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 e1f188f3212d11039e2a01ee02b7443629e713ba..baad81f5a3024ca1a98f0b8d262500c8bf0d2407 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 14466a12bd8d992f339a6367f96455fd5a67cae8..6111b151c0ade7aab3dae2379bb1a97fb94e8c10 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 c19555325c5f5baa2564deb10b048aba0f33b9d7..36e08d194f3eb81935ee3c1fa2e75f83396e6d28 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 18412a2792a1f9f9a37c560a77fc00015de5b437..a297ddc9f8d817d12f3d86fafbe2eb1d77c18f14 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 c375969f47c413cd347417e5744b4f4dc0141a28..9d38bfcef2f40f1bca8faed04ca7af3ff1d09fce 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 733b2c6b146340798d87381f979cc8e433c715b5..48dc8bcea9ba14e1e3d5274ed98ef694f6bb0970 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 2fd30300602a791c7ea64856564685e496e2a824..f5d1d3769ebc9d163b12a6eb952752bde37de206 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 fd2dd014a26803981b6dcc12f3bc7e51dcf84bf9..788aaaa7c1e557b17556820dd124bdc23cda620f 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 63c5e77afe03d5b111a836b3a3b3e71922c3e40c..724f28f273cbf917a886566a95241d462624153b 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 0d2d4dbbda2ff9d2fa7d00123c5e06d647b7188a..99da97687304696dfdbb63ef63fb5ebacb559e1c 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: "${METADATA_PASSWORD}" jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-metadata-service/rest-service/src/main/resources/application-local.yml b/fda-metadata-service/rest-service/src/main/resources/application-local.yml index 7278d3669413eaab1626315e32128c257aa7b4b1..58b27eec0a4632f96d95298137e1e4d6dad0cd87 100644 --- a/fda-metadata-service/rest-service/src/main/resources/application-local.yml +++ b/fda-metadata-service/rest-service/src/main/resources/application-local.yml @@ -8,12 +8,13 @@ spring: password: dbrepo jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-metadata-service/rest-service/src/main/resources/application.yml b/fda-metadata-service/rest-service/src/main/resources/application.yml index e10395d64fc18741d0d25038d41bd476ec735312..291622e4acb4ba6e23e3fd5865b07b42097753db 100644 --- a/fda-metadata-service/rest-service/src/main/resources/application.yml +++ b/fda-metadata-service/rest-service/src/main/resources/application.yml @@ -8,12 +8,13 @@ spring: password: "${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: "${METADATA_DB}" jdbc: time_zone: UTC application: diff --git a/fda-query-service/rest-service/src/main/resources/application-docker.yml b/fda-query-service/rest-service/src/main/resources/application-docker.yml index 19b6beb523a7650969cf5758852a66d8e9f2f83c..6ea04978aa69a337925ae034f79119f890b07644 100644 --- a/fda-query-service/rest-service/src/main/resources/application-docker.yml +++ b/fda-query-service/rest-service/src/main/resources/application-docker.yml @@ -8,12 +8,13 @@ spring: password: "${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 4e107cf208ad0f4ab51f34daa9e47e22cd595208..8f8defbb1bc7b8c7f7a719404749f21300041943 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 ee1656dd6b5c3e94eec2c9701372f29817eced34..0f84ade3e0c1c1cfe64313d30302821c174bf32b 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 32321dd3c3e5e084552997bf42b2722bd5a44ca7..51bb0170a062926431b85d1c0dfeb446a7488183 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: "${METADATA_PASSWORD}" jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-table-service/rest-service/src/main/resources/application-local.yml b/fda-table-service/rest-service/src/main/resources/application-local.yml index 3901f17037ca78736d16567c35fc400402ace4a7..843fbdebd0eee63f1dbd8dedd1b34c2ea72dda3f 100644 --- a/fda-table-service/rest-service/src/main/resources/application-local.yml +++ b/fda-table-service/rest-service/src/main/resources/application-local.yml @@ -8,12 +8,13 @@ spring: password: dbrepo jpa: show-sql: false - database-platform: org.hibernate.dialect.PostgreSQLDialect + database-platform: org.hibernate.dialect.MariaDBDialect hibernate: ddl-auto: validate open-in-view: false properties: hibernate: + default_schema: fda jdbc: time_zone: UTC application: diff --git a/fda-table-service/rest-service/src/main/resources/application.yml b/fda-table-service/rest-service/src/main/resources/application.yml index 2f82391ccc9a19e5dff9044dffa1f8b0f8aa7d6f..502aa326597a1cf1755e418b0406f55a9464aff8 100644 --- a/fda-table-service/rest-service/src/main/resources/application.yml +++ b/fda-table-service/rest-service/src/main/resources/application.yml @@ -8,12 +8,13 @@ spring: password: "${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: