Updated stuff

Signed-off-by: Martin Weise <martin.weise@tuwien.ac.at>

.docker/docker-compose.yml

@@ -13,9 +13,9 @@ services:
     restart: "no"
     container_name: dbrepo-metadata-db
     hostname: metadata-db
-    image: docker.io/bitnami/mariadb-galera:11.3.2-debian-12-r9
+    image: docker.io/mariadb:11.3.2
     volumes:
-      - metadata-db-data:/bitnami/mariadb
+      - metadata-db-data:/var/lib/mysql
       - ./config/1_setup-schema.sql:/docker-entrypoint-initdb.d/1_setup-schema.sql
       - ./config/2_setup-data.sql:/docker-entrypoint-initdb.d/2_setup-data.sql
     ports:
@@ -23,9 +23,8 @@ services:
     environment:
       MARIADB_DATABASE: "${METADATA_DB:-dbrepo}"
       MARIADB_ROOT_PASSWORD: "${METADATA_DB_PASSWORD:-dbrepo}"
-      MARIADB_GALERA_MARIABACKUP_PASSWORD: "${METADATA_DB_BACKUP_PASSWORD:-dbrepobackup}"
     healthcheck:
-      test: mysqladmin ping --user=root --password="${METADATA_DB_PASSWORD:-dbrepo}" --silent
+      test: ./usr/local/bin/healthcheck.sh --connect --innodb_initialized
       interval: 10s
       timeout: 5s
       retries: 12
@@ -36,18 +35,18 @@ services:
     restart: "no"
     container_name: dbrepo-data-db
     hostname: data-db
-    image: docker.io/bitnami/mariadb-galera:11.3.2-debian-12-r9
+    image: docker.io/mariadb:11.3.2
     volumes:
-      - data-db-data:/bitnami/mariadb
+      - data-db-data:/var/lib/mysql
+      - ./config/1_grant-user.sql:/docker-entrypoint-initdb.d/1_grant-user.sql
     ports:
       - "3307:3306"
     environment:
-      MARIADB_GALERA_MARIABACKUP_PASSWORD: "${DATA_DB_BACKUP_PASSWORD:-dbrepobackup}"
       MARIADB_PASSWORD: "${READONLY_PASSWORD:-user}"
       MARIADB_ROOT_PASSWORD: "${DATA_DB_PASSWORD:-dbrepo}"
       MARIADB_USER: "${READONLY_USERNAME:-user}"
     healthcheck:
-      test: mysqladmin ping --user=root --password="${DATA_DB_PASSWORD:-dbrepo}" --silent
+      test: ./usr/local/bin/healthcheck.sh --connect --innodb_initialized
       interval: 10s
       timeout: 5s
       retries: 12
@@ -119,14 +118,13 @@ services:
     container_name: dbrepo-auth-service-init
     image: registry.datalab.tuwien.ac.at/dbrepo/auth-service-init:1.8.0
     environment:
-      AUTH_SERVICE_ADMIN: ${AUTH_SERVICE_ADMIN:-admin}
-      AUTH_SERVICE_ADMIN_PASSWORD: ${AUTH_SERVICE_ADMIN_PASSWORD:-admin}
       AUTH_SERVICE_ENDPOINT: ${AUTH_SERVICE_ENDPOINT:-http://auth-service:8080}
       METADATA_DB: "${METADATA_DB:-dbrepo}"
       METADATA_DB_PASSWORD: "${METADATA_DB_PASSWORD:-dbrepo}"
       METADATA_USERNAME: "root"
       READONLY_USERNAME: "${READONLY_USERNAME:-user}"
       SYSTEM_USERNAME: "${SYSTEM_USERNAME:-admin}"
+      SYSTEM_PASSWORD: ${SYSTEM_PASSWORD:-admin}
     depends_on:
       dbrepo-auth-service:
         condition: service_healthy
@@ -145,8 +143,6 @@ services:
     environment:
       ADMIN_EMAIL: "${ADMIN_EMAIL:-noreply@localhost}"
       ANALYSE_SERVICE_ENDPOINT: "${ANALYSE_SERVICE_ENDPOINT:-http://analyse-service:8080}"
-      AUTH_SERVICE_ADMIN: ${AUTH_SERVICE_ADMIN:-admin}
-      AUTH_SERVICE_ADMIN_PASSWORD: ${AUTH_SERVICE_ADMIN_PASSWORD:-admin}
       AUTH_SERVICE_CLIENT: ${AUTH_SERVICE_CLIENT:-dbrepo-client}
       AUTH_SERVICE_CLIENT_SECRET: ${AUTH_SERVICE_CLIENT_SECRET:-MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG}
       AUTH_SERVICE_ENDPOINT: ${AUTH_SERVICE_ENDPOINT:-http://auth-service:8080}
@@ -477,8 +473,6 @@ services:
     hostname: data-service
     image: registry.datalab.tuwien.ac.at/dbrepo/data-service:1.8.0
     environment:
-      AUTH_SERVICE_ADMIN: "${AUTH_SERVICE_ADMIN:-admin}"
-      AUTH_SERVICE_ADMIN_PASSWORD: "${AUTH_SERVICE_ADMIN_PASSWORD:-admin}"
       AUTH_SERVICE_CLIENT: "${AUTH_SERVICE_CLIENT:-dbrepo-client}"
       AUTH_SERVICE_CLIENT_SECRET: "${AUTH_SERVICE_CLIENT:-MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG}"
       AUTH_SERVICE_ENDPOINT: "${AUTH_SERVICE_ENDPOINT:-http://auth-service:8080}"
@@ -558,8 +552,6 @@ services:
     ports:
       - "4070:8080"
     environment:
-      AUTH_SERVICE_ADMIN: ${AUTH_SERVICE_ADMIN:-admin}
-      AUTH_SERVICE_ADMIN_PASSWORD: ${AUTH_SERVICE_ADMIN_PASSWORD:-admin}
       AUTH_SERVICE_ENDPOINT: ${AUTH_SERVICE_ENDPOINT:-http://auth-service:8080}
       BASE_URL: "${BASE_URL:-http://localhost}"
       DASHBOARD_UI_ENDPOINT: "${DASHBOARD_UI_ENDPOINT:-http://dashboard-ui:3000}"

.docs/api/metadata-db.md

@@ -53,3 +53,14 @@ the `setup-schema.sql` into the container. This can be done more transparently t
 
     Beware that the init script provided by Bitnami executes files in alphabetic order! For example: the file 
     `setup-schema.sql` is executed **after** the file `setup-data.sql`! Thefore a sorting prefix 1-9 is recommended!
+
+
+## Limitations
+
+(none)
+
+!!! question "Do you miss functionality? Do these limitations affect you?"
+
+    We strongly encourage you to help us implement it as we are welcoming contributors to open-source software and get
+    in [contact](../contact) with us, we happily answer requests for collaboration with attached CV and your programming 
+    experience!
\ No newline at end of file

.docs/api/search-db.md

+---
+author: Martin Weise
+---
+
+!!! debug "Debug Information"
+
+    Image: [`docker.io/bitnami/opensearch:2.10.0`](https://hub.docker.com/r/bitnami/opensearch)
+
+    * Ports: 9200/tcp
+
+    To directly access in Kubernetes (for e.g. debugging), forward the svc port to your local machine:
+
+    ```shell
+    kubectl [-n namespace] port-forward svc/search-db 9200:9200
+    ```
+
+## Overview
+
+The Search Database contains duplicate metadata from the Metadata Database for fast and efficient search.
+
+## Configuration
+
+This section will be expanded soon.
+
+## Limitations
+
+(none)
+
+!!! question "Do you miss functionality? Do these limitations affect you?"
+
+    We strongly encourage you to help us implement it as we are welcoming contributors to open-source software and get
+    in [contact](../contact) with us, we happily answer requests for collaboration with attached CV and your programming 
+    experience!
+
+## Security
+
+* By default, the security plugin is not used in the [Docker](../../installation) installation. This allows anyone to
+  read/write and is considered not secure.

dbrepo-auth-service/init/app.py

@@ -3,19 +3,16 @@ import os
 import mariadb
 from requests import post, get
 
-endpoint = os.getenv('AUTH_SERVICE_ENDPOINT', 'http://localhost:8080')
-system_username = os.getenv('SYSTEM_USERNAME', 'admin')
-readonly_username = os.getenv('READONLY_USERNAME', 'user')
-
 
 def fetch_keycloak_master_access_token() -> str:
     """
     Fetch admin access token from the master realm.
     :return: The access token.
     """
+    endpoint = os.getenv('AUTH_SERVICE_ENDPOINT', 'http://localhost:8080')
     response = post(url=f'{endpoint}/realms/master/protocol/openid-connect/token', data=dict({
-        'username': os.getenv('AUTH_SERVICE_ADMIN', 'admin'),
-        'password': os.getenv('AUTH_SERVICE_ADMIN_PASSWORD', 'admin'),
+        'username': os.getenv('SYSTEM_USERNAME', 'admin'),
+        'password': os.getenv('SYSTEM_PASSWORD', 'admin'),
         'grant_type': 'password',
         'client_id': 'admin-cli'
     }))
@@ -26,7 +23,7 @@ def fetch_keycloak_master_access_token() -> str:
 
 def fetch(username) -> (str, str):
     print(f'Fetching user id of internal user with username: {username}')
-
+    endpoint = os.getenv('AUTH_SERVICE_ENDPOINT', 'http://localhost:8080')
     response = get(url=f'{endpoint}/admin/realms/dbrepo/users/?username={username}', headers=dict({
         'Authorization': f'Bearer {fetch_keycloak_master_access_token()}'
     }))
@@ -63,6 +60,8 @@ def save(user_id: str, keycloak_id: str, username: str) -> None:
 
 
 if __name__ == '__main__':
+    system_username = os.getenv('SYSTEM_USERNAME', 'admin')
+    readonly_username = os.getenv('READONLY_USERNAME', 'user')
     user_id, keycloak_id = fetch(system_username)
     save(user_id, keycloak_id, system_username)
     user_id, keycloak_id = fetch(readonly_username)

dbrepo-data-db/1_grant-user.sql

+GRANT SELECT ON *.* TO `user`@`%`;
\ No newline at end of file

dbrepo-data-service/pom.xml

@@ -13,7 +13,7 @@
         <url>https://www.tuwien.ac.at</url>
     </organization>
 
-    <groupId>at.tuwien</groupId>
+    <groupId>at.ac.tuwien.ac.at.ifs.dbrepo</groupId>
     <artifactId>dbrepo-data-service</artifactId>
     <name>dbrepo-data-service</name>
     <version>1.8.0</version>
@@ -53,7 +53,7 @@
         <hsqldb.version>2.7.2</hsqldb.version>
         <testcontainers.version>1.19.1</testcontainers.version>
         <jackson.version>2.15.2</jackson.version>
-        <c3p0.version>0.9.5.5</c3p0.version>
+        <c3p0.version>0.10.2</c3p0.version>
         <c3p0-hibernate.version>6.2.2.Final</c3p0-hibernate.version>
         <aws-s3.version>2.25.23</aws-s3.version>
         <minio.version>8.5.7</minio.version>
@@ -160,6 +160,12 @@
             <artifactId>hibernate-c3p0</artifactId>
             <version>${c3p0-hibernate.version}</version>
         </dependency>
+        <!-- Storage -->
+        <dependency>
+            <groupId>software.amazon.awssdk</groupId>
+            <artifactId>s3</artifactId>
+            <version>${aws-s3.version}</version>
+        </dependency>
         <!-- Monitoring -->
         <dependency>
             <groupId>org.springframework.boot</groupId>
@@ -230,18 +236,21 @@
             <artifactId>amqp-client</artifactId>
             <version>${rabbitmq.version}</version>
         </dependency>
-        <!-- Storage -->
+        <!-- Testing -->
         <dependency>
-            <groupId>software.amazon.awssdk</groupId>
-            <artifactId>s3</artifactId>
-            <version>${aws-s3.version}</version>
+            <groupId>org.springframework</groupId>
+            <artifactId>spring-test</artifactId>
         </dependency>
-        <!-- Testing -->
         <dependency>
             <groupId>org.springframework.security</groupId>
             <artifactId>spring-security-test</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-test</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>rabbitmq</artifactId>

dbrepo-data-service/querystore/pom.xml

@@ -4,7 +4,7 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
-        <groupId>at.tuwien</groupId>
+        <groupId>at.ac.tuwien.ac.at.ifs.dbrepo</groupId>
         <artifactId>dbrepo-data-service</artifactId>
         <version>1.8.0</version>
     </parent>

dbrepo-data-service/querystore/src/main/java/at/tuwien/querystore/Query.java → dbrepo-data-service/querystore/src/main/java/at/ac/tuwien/ac/at/ifs/dbrepo/querystore/Query.java

-package at.tuwien.querystore;
+package at.ac.tuwien.ac.at.ifs.dbrepo.querystore;
 
 import io.swagger.v3.oas.annotations.media.Schema;
 import lombok.*;

dbrepo-data-service/report/pom.xml

@@ -4,7 +4,7 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
-        <groupId>at.tuwien</groupId>
+        <groupId>at.ac.tuwien.ac.at.ifs.dbrepo</groupId>
         <artifactId>dbrepo-data-service</artifactId>
         <version>1.8.0</version>
     </parent>
@@ -19,12 +19,12 @@
 
     <dependencies>
         <dependency>
-            <groupId>at.tuwien</groupId>
+            <groupId>at.ac.tuwien.ac.at.ifs.dbrepo</groupId>
             <artifactId>rest-service</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
-            <groupId>at.tuwien</groupId>
+            <groupId>at.ac.tuwien.ac.at.ifs.dbrepo</groupId>
             <artifactId>services</artifactId>
             <version>${project.version}</version>
         </dependency>

dbrepo-data-service/rest-service/pom.xml

@@ -4,7 +4,7 @@
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
-        <groupId>at.tuwien</groupId>
+        <groupId>at.ac.tuwien.ac.at.ifs.dbrepo</groupId>
         <artifactId>dbrepo-data-service</artifactId>
         <version>1.8.0</version>
     </parent>
@@ -15,7 +15,7 @@
 
     <dependencies>
         <dependency>
-            <groupId>at.tuwien</groupId>
+            <groupId>at.ac.tuwien.ac.at.ifs.dbrepo</groupId>
             <artifactId>services</artifactId>
             <version>1.8.0</version>
         </dependency>