Progress on fixing int to bigint and references

fda-authentication-service/Dockerfile

@@ -22,8 +22,8 @@ RUN mvn -q clean package -DskipTests
 FROM openjdk:11-jre-slim as runtime
 
 ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
 ENV BROKER_USERNAME=fda
 ENV BROKER_PASSWORD=fda
 ENV WEBSITE=http://example.com

fda-authentication-service/pom.xml

@@ -117,6 +117,11 @@
             <artifactId>h2</artifactId>
             <scope>runtime</scope>
         </dependency>
+        <dependency>
+            <groupId>org.mariadb.jdbc</groupId>
+            <artifactId>mariadb-java-client</artifactId>
+            <version>${mariadb.version}</version>
+        </dependency>
         <!-- IDE -->
         <dependency>
             <groupId>org.projectlombok</groupId>

fda-container-service/Dockerfile

@@ -22,8 +22,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
 FROM openjdk:11-jre-slim as runtime
 
 ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
 ENV BROKER_USERNAME=fda
 ENV BROKER_PASSWORD=fda
 ENV SHARED_FILESYSTEM=/tmp

fda-database-service/Dockerfile

@@ -22,8 +22,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
 FROM openjdk:11-jre-slim as runtime
 
 ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
 ENV BROKER_USERNAME=fda
 ENV BROKER_PASSWORD=fda
 ENV SEARCH_ENDPOINT=search-service

fda-identifier-service/Dockerfile

@@ -23,8 +23,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
 FROM openjdk:11-jre-slim as runtime
 
 ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
 ENV GATEWAY_ENDPOINT=http://gateway-service:9095
 ENV WEBSITE=http://localhost:3000
 ENV LOG_LEVEL=debug

fda-metadata-db/Dockerfile

@@ -18,14 +18,20 @@ RUN mvn -q clean package -DskipTests > /dev/null
 RUN mvn -q clean install > /dev/null
 
 ###### SECOND STAGE ######
-FROM postgres:14-alpine as runtime
+FROM mariadb:10.5 as runtime
 
+ENV METADATA_DB=fda
 ENV METADATA_USERNAME=dbrepo
 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 pg_isready
+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/
+COPY ./setup-schema.sql /docker-entrypoint-initdb.d/1.sql
+COPY ./setup-user.sh /docker-entrypoint-initdb.d/2.sh
 
 COPY --from=build /root/.m2/repository/at/tuwien /root/.m2/repository/at/tuwien
\ No newline at end of file

fda-metadata-db/setup-schema.sql

@@ -126,6 +126,13 @@ CREATE SEQUENCE mdb_tokens_seq
     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),
@@ -306,7 +313,7 @@ CREATE TABLE IF NOT EXISTS mdb_tables
     tDescription  TEXT,
     NumCols       INTEGER,
     NumRows       INTEGER,
-    separator     CHAR(1),
+    `separator`   CHAR(1),
     quote         CHAR(1),
     element_null  VARCHAR(50),
     skip_lines    BIGINT,
@@ -404,12 +411,13 @@ CREATE TABLE IF NOT EXISTS mdb_COLUMNS_cat
 
 CREATE TABLE IF NOT EXISTS mdb_concepts
 (
+    id         bigint    not null default nextval(mdb_concepts_seq),
     URI        TEXT,
     name       TEXT,
     created    timestamp NOT NULL DEFAULT NOW(),
     created_by bigint,
     FOREIGN KEY (created_by) REFERENCES mdb_users (UserID),
-    PRIMARY KEY (URI)
+    PRIMARY KEY (id)
 );
 
 CREATE TABLE IF NOT EXISTS mdb_columns_concepts
@@ -417,7 +425,7 @@ CREATE TABLE IF NOT EXISTS mdb_columns_concepts
     cDBID      bigint    NOT NULL,
     tID        bigint    NOT NULL,
     cID        bigint    NOT NULL,
-    URI     TEXT REFERENCES mdb_concepts (URI),
+    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),
     PRIMARY KEY (cDBID, tID, cID)
@@ -509,21 +517,12 @@ CREATE TABLE IF NOT EXISTS mdb_creators
     FOREIGN KEY (pid) REFERENCES mdb_identifiers (id)
 );
 
-CREATE TABLE IF NOT EXISTS mdb_views_databases
-(
-    mdb_view_id  bigint,
-    databases_id bigint REFERENCES mdb_databases (id),
-    created      timestamp NOT NULL DEFAULT NOW(),
-    FOREIGN KEY (mdb_view_id, databases_id) REFERENCES mdb_VIEW (id, vdbid),
-    PRIMARY KEY (mdb_view_id, databases_id)
-);
-
 CREATE TABLE IF NOT EXISTS mdb_feed
 (
     fDBID   bigint,
     fID     bigint,
-    fUserId INTEGER REFERENCES mdb_users (UserID),
-    fDataID INTEGER REFERENCES mdb_data (ID),
+    fUserId bigint REFERENCES mdb_users (UserID),
+    fDataID bigint REFERENCES mdb_data (ID),
     created timestamp NOT NULL DEFAULT NOW(),
     FOREIGN KEY (fDBID, fID) REFERENCES mdb_tables (tDBID, ID),
     PRIMARY KEY (fDBID, fID, fUserId, fDataID)
@@ -531,7 +530,7 @@ CREATE TABLE IF NOT EXISTS mdb_feed
 
 CREATE TABLE IF NOT EXISTS mdb_update
 (
-    uUserID INTEGER REFERENCES mdb_users (UserID),
+    uUserID bigint REFERENCES mdb_users (UserID),
     uDBID   bigint REFERENCES mdb_databases (id),
     created timestamp NOT NULL DEFAULT NOW(),
     PRIMARY KEY (uUserID, uDBID)
@@ -539,7 +538,7 @@ CREATE TABLE IF NOT EXISTS mdb_update
 
 CREATE TABLE IF NOT EXISTS mdb_access
 (
-    aUserID  INTEGER REFERENCES mdb_users (UserID),
+    aUserID  bigint REFERENCES mdb_users (UserID),
     aDBID    bigint REFERENCES mdb_databases (id),
     attime   TIMESTAMP,
     download BOOLEAN,
@@ -558,7 +557,7 @@ CREATE TABLE IF NOT EXISTS mdb_have_access
 
 CREATE TABLE IF NOT EXISTS mdb_owns
 (
-    oUserID INTEGER REFERENCES mdb_users (UserID),
+    oUserID bigint REFERENCES mdb_users (UserID),
     oDBID   bigint REFERENCES mdb_databases (ID),
     created timestamp NOT NULL DEFAULT NOW(),
     PRIMARY KEY (oUserID, oDBID)

fda-metadata-db/setup-user.sh

+#!/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}';
+EOF
\ No newline at end of file

fda-metadata-service/Dockerfile

@@ -22,8 +22,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
 FROM openjdk:11-jre-slim as runtime
 
 ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
 ENV GATEWAY_ENDPOINT=http://gateway-service:9095
 ENV PID_BASE="https://example.com/pid/"
 ENV REPOSITORY_NAME="Example Repository"

fda-metadata-service/pom.xml

@@ -60,6 +60,12 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-actuator</artifactId>
         </dependency>
+        <!-- Datasource -->
+        <dependency>
+            <groupId>org.mariadb.jdbc</groupId>
+            <artifactId>mariadb-java-client</artifactId>
+            <version>${mariadb.version}</version>
+        </dependency>
         <!-- Monitoring -->
         <dependency>
             <groupId>io.micrometer</groupId>

fda-query-service/Dockerfile

@@ -23,8 +23,8 @@ RUN mvn -q clean package -DskipTests > /dev/null
 FROM openjdk:11-jre-slim as runtime
 
 ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
 ENV BROKER_USERNAME=fda
 ENV BROKER_PASSWORD=fda
 ENV GATEWAY_ENDPOINT=http://gateway-service:9095

fda-table-service/Dockerfile

@@ -24,8 +24,8 @@ FROM openjdk:11-jre-slim as runtime
 
 ENV multipart.location=/tmp
 ENV METADATA_DB=fda
-ENV METADATA_USERNAME=postgres
-ENV METADATA_PASSWORD=postgres
+ENV METADATA_USERNAME=dbrepo
+ENV METADATA_PASSWORD=dbrepo
 ENV BROKER_USERNAME=fda
 ENV BROKER_PASSWORD=fda
 ENV SEARCH_ENDPOINT=search-service