Merge branch 'hotfix-foreign-key' into 'dev'

Hotfix foreign key

See merge request !274

docker-compose.prod.yml → .docker/docker-compose.yml

@@ -14,7 +14,7 @@ services:
     restart: "no"
     container_name: dbrepo-metadata-db
     hostname: metadata-db
-    image: docker.io/dbrepo/metadata-db:latest
+    image: docker.io/dbrepo/metadata-db:1.4.4
     volumes:
       - metadata-db-data:/bitnami/mariadb
       - ./dist/2_setup-data.sql:/docker-entrypoint-initdb.d/2_setup-data.sql
@@ -76,7 +76,7 @@ services:
     restart: "no"
     container_name: dbrepo-auth-service
     hostname: auth-service
-    image: docker.io/dbrepo/auth-service:latest
+    image: docker.io/dbrepo/auth-service:1.4.4
     healthcheck:
       test: curl -sSL 'http://0.0.0.0:8080/realms/dbrepo' | grep "dbrepo" || exit 1
       interval: 10s
@@ -98,18 +98,19 @@ services:
     restart: "no"
     container_name: dbrepo-metadata-service
     hostname: metadata-service
-    image: docker.io/dbrepo/metadata-service:latest
+    image: docker.io/dbrepo/metadata-service:1.4.4
     volumes:
       - "${SHARED_VOLUME:-/tmp}:/tmp"
     environment:
-      ADMIN_MAIL: "${ADMIN_MAIL:-noreply@localhost}"
+      ADMIN_EMAIL: "${ADMIN_EMAIL:-noreply@localhost}"
       ADMIN_PASSWORD: "${ADMIN_PASSWORD:-admin}"
       ADMIN_USERNAME: "${ADMIN_USERNAME:-admin}"
+      ANALYSE_SERVICE_ENDPOINT: "${ANALYSE_SERVICE_ENDPOINT:-http://gateway-service}"
       AUTH_SERVICE_ADMIN: ${AUTH_SERVICE_ADMIN:-fda}
       AUTH_SERVICE_ADMIN_PASSWORD: ${AUTH_SERVICE_ADMIN_PASSWORD:-fda}
       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}
+      AUTH_SERVICE_ENDPOINT: ${AUTH_SERVICE_ENDPOINT:-http://gateway-service/api/auth}
       BASE_URL: "${BASE_URL:-http://localhost}"
       BROKER_EXCHANGE_NAME: ${BROKER_EXCHANGE_NAME:-dbrepo}
       BROKER_QUEUE_NAME: ${BROKER_QUEUE_NAME:-dbrepo}
@@ -121,10 +122,9 @@ services:
       BROKER_VIRTUALHOST: "${BROKER_VIRTUALHOST:-dbrepo}"
       DATA_SERVICE_ENDPOINT: ${DATA_SERVICE_ENDPOINT:-http://data-service:8080}
       DELETED_RECORD: "${DELETED_RECORD:-persistent}"
-      GATEWAY_SERVICE_ENDPOINT: ${GATEWAY_SERVICE_ENDPOINT:-http://gateway-service}
       GRANULARITY: "${GRANULARITY:-YYYY-MM-DDThh:mm:ssZ}"
       JWT_PUBKEY: "${JWT_PUBKEY:-MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB}"
-      LOG_LEVEL: ${LOG_LEVEL:-info}
+      LOG_LEVEL: "${LOG_LEVEL:-info}"
       METADATA_DB: "${METADATA_DB:-dbrepo}"
       METADATA_HOST: "${METADATA_HOST:-metadata-db}"
       METADATA_JDBC_EXTRA_ARGS: "${METADATA_JDBC_EXTRA_ARGS:-}"
@@ -132,9 +132,9 @@ services:
       METADATA_PASSWORD: "${METADATA_PASSWORD:-dbrepo}"
       PID_BASE: ${PID_BASE:-http://localhost/pid/}
       REPOSITORY_NAME: "${REPOSITORY_NAME:-Database Repository}"
-      SEARCH_SERVICE_ENDPOINT: "${SEARCH_SERVICE_ENDPOINT:-http://search-service:8080}"
+      SEARCH_SERVICE_ENDPOINT: "${SEARCH_SERVICE_ENDPOINT:-http://gateway-service}"
       S3_ACCESS_KEY_ID: "${S3_ACCESS_KEY_ID:-seaweedfsadmin}"
-      S3_ENDPOINT: "${S3_ENDPOINT:-http://storage-service:9000}"
+      S3_ENDPOINT: "${S3_ENDPOINT:-http://gateway-service/api/storage}"
       S3_EXPORT_BUCKET: "${S3_EXPORT_BUCKET:-dbrepo-download}"
       S3_IMPORT_BUCKET: "${S3_IMPORT_BUCKET:-dbrepo-upload}"
       S3_SECRET_ACCESS_KEY: "${S3_SECRET_ACCESS_KEY:-seaweedfsadmin}"
@@ -160,7 +160,7 @@ services:
     restart: "no"
     container_name: dbrepo-analyse-service
     hostname: analyse-service
-    image: docker.io/dbrepo/analyse-service:latest
+    image: docker.io/dbrepo/analyse-service:1.4.4
     environment:
       ADMIN_PASSWORD: "${ADMIN_PASSWORD:-admin}"
       ADMIN_USERNAME: "${ADMIN_USERNAME:-admin}"
@@ -211,7 +211,7 @@ services:
     restart: "no"
     container_name: dbrepo-search-db
     hostname: search-db
-    image: docker.io/dbrepo/search-db:latest
+    image: docker.io/dbrepo/search-db:1.4.4
     healthcheck:
       test: curl -sSL localhost:9200/_plugins/_security/health | jq .status | grep UP
       interval: 10s
@@ -235,7 +235,7 @@ services:
     restart: "no"
     container_name: dbrepo-search-service
     hostname: search-service
-    image: docker.io/dbrepo/search-service:latest
+    image: docker.io/dbrepo/search-service:1.4.4
     environment:
       ADMIN_PASSWORD: "${ADMIN_PASSWORD:-admin}"
       ADMIN_USERNAME: "${ADMIN_USERNAME:-admin}"
@@ -253,11 +253,12 @@ services:
     restart: "no"
     container_name: dbrepo-data-db-sidecar
     hostname: data-db-sidecar
-    image: docker.io/dbrepo/data-db-sidecar:latest
+    image: docker.io/dbrepo/data-db-sidecar:1.4.4
     environment:
       S3_ACCESS_KEY_ID: "${S3_ACCESS_KEY_ID:-seaweedfsadmin}"
       S3_ENDPOINT: "${S3_ENDPOINT:-http://storage-service:9000}"
       S3_EXPORT_BUCKET: "${S3_EXPORT_BUCKET:-dbrepo-download}"
+      S3_FILE_PATH: "${S3_FILE_PATH:-/tmp}"
       S3_IMPORT_BUCKET: "${S3_IMPORT_BUCKET:-dbrepo-upload}"
       S3_SECRET_ACCESS_KEY: "${S3_SECRET_ACCESS_KEY:-seaweedfsadmin}"
     volumes:
@@ -274,7 +275,7 @@ services:
     restart: "no"
     container_name: dbrepo-ui
     hostname: ui
-    image: docker.io/dbrepo/ui:latest
+    image: docker.io/dbrepo/ui:1.4.4
     depends_on:
       dbrepo-search-service:
         condition: service_started
@@ -318,7 +319,7 @@ services:
     restart: "no"
     container_name: dbrepo-search-service-init
     hostname: search-service-init
-    image: docker.io/dbrepo/search-service-init:latest
+    image: docker.io/dbrepo/search-service-init:1.4.4
     environment:
       GATEWAY_SERVICE_ENDPOINT: ${GATEWAY_SERVICE_ENDPOINT:-http://gateway-service}
       OPENSEARCH_HOST: ${OPENSEARCH_HOST:-search-db}
@@ -353,7 +354,7 @@ services:
     restart: "no"
     container_name: dbrepo-storage-service-init
     hostname: storage-service-init
-    image: docker.io/dbrepo/storage-service-init:latest
+    image: docker.io/dbrepo/storage-service-init:1.4.4
     environment:
       SEAWEEDFS_ENDPOINT: "${STORAGE_SEAWEEDFS_ENDPOINT:-storage-service:9333}"
     depends_on:
@@ -390,7 +391,7 @@ services:
     restart: "no"
     container_name: dbrepo-data-service
     hostname: data-service
-    image: docker.io/dbrepo/data-service:latest
+    image: docker.io/dbrepo/data-service:1.4.4
     volumes:
       - "${SHARED_VOLUME:-/tmp}:/tmp"
     environment:
@@ -411,7 +412,7 @@ services:
       BROKER_VIRTUALHOST: "${BROKER_VIRTUALHOST:-dbrepo}"
       CONNECTION_TIMEOUT: ${CONNECTION_TIMEOUT:-60000}
       EXCHANGE_NAME: ${EXCHANGE_NAME:-dbrepo}
-      GATEWAY_SERVICE_ENDPOINT: ${GATEWAY_SERVICE_ENDPOINT:-http://gateway-service}
+      METADATA_SERVICE_ENDPOINT: ${METADATA_SERVICE_ENDPOINT:-http://gateway-service}
       GRANT_DEFAULT_READ: "${GRANT_DEFAULT_READ:-SELECT}"
       GRANT_DEFAULT_WRITE: "${GRANT_DEFAULT_WRITE:-SELECT, CREATE, CREATE VIEW, CREATE ROUTINE, CREATE TEMPORARY TABLES, LOCK TABLES, INDEX, TRIGGER, INSERT, UPDATE, DELETE}"
       JWT_PUBKEY: "${JWT_PUBKEY:-MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB}"
@@ -421,7 +422,12 @@ services:
       QUEUE_NAME: ${QUEUE_NAME:-dbrepo}
       REQUEUE_REJECTED: ${REQUEUE_REJECTED:-false}
       ROUTING_KEY: "${ROUTING_KEY:-dbrepo.#}"
-      STORAGE_SERVICE_ENDPOINT: ${BROKER_SERVICE_ENDPOINT:-http://storage-service:9000}
+      S3_ACCESS_KEY_ID: "${S3_ACCESS_KEY_ID:-seaweedfsadmin}"
+      S3_ENDPOINT: "${S3_ENDPOINT:-http://storage-service:9000}"
+      S3_EXPORT_BUCKET: "${S3_EXPORT_BUCKET:-dbrepo-download}"
+      S3_FILE_PATH: "${S3_FILE_PATH:-/tmp}"
+      S3_IMPORT_BUCKET: "${S3_IMPORT_BUCKET:-dbrepo-upload}"
+      S3_SECRET_ACCESS_KEY: "${S3_SECRET_ACCESS_KEY:-seaweedfsadmin}"
     healthcheck:
       test: wget -qO- localhost:8080/actuator/health/readiness | grep -q "UP" || exit 1
       interval: 10s

.docs/.swagger/openapi-merge.json

+{
+  "inputs": [
+    {
+      "inputFile": "./api.base.yaml"
+    },
+    {
+      "inputFile": "./api-analyse.yaml"
+    },
+    {
+      "inputFile": "./api-data.yaml"
+    },
+    {
+      "inputFile": "./api-metadata.yaml"
+    },
+    {
+      "inputFile": "./api-search.yaml"
+    },
+    {
+      "inputFile": "./api-sidecar.yaml"
+    }
+  ],
+  "output": "./api.yaml"
+}

.docs/.swagger/swagger-ui.html

@@ -7,7 +7,7 @@
     <title>DBRepo REST API</title>
     <link rel="stylesheet" href="https://unpkg.com/swagger-ui-dist@5.17.12/swagger-ui.css"/>
     <link rel="stylesheet" href="./custom.css"/>
-    <link rel="icon" href="https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/.docs/images/signet_white.png" />
+    <link rel="icon" href="https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/.docs/images/logos/favicon.png" />
 </head>
 <body>
 <div class="swagger-ui">

.docs/api/analyse-service.md

@@ -11,19 +11,19 @@ author: Martin Weise
     * Ports: 5000/tcp
     * Prometheus: `http://<hostname>:5000/metrics`
     * Health: `http://<hostname>:5000/health`
-    * Swagger UI: `http://<hostname>:5000/swagger-ui/` <a href="../swagger/analyse" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+    * Swagger UI: `http://<hostname>:5000/swagger-ui/` <a href="./swagger/analyse" target="_blank">:fontawesome-solid-square-up-right: view online</a>
 
 ## Overview
 
-It suggests data types for the [User Interface](../system-other-ui) when creating a table from a 
+It suggests data types for the [User Interface](./system-other-ui) when creating a table from a 
 *comma separated values* (CSV) -file. It recommends enumerations for columns and returns e.g. a list of potential 
 primary key candidates. The researcher is able to confirm these suggestions manually. Moreover, the Analyse Service
 determines basic statistical properties of numerical columns.
 
 ### Analysis
 
-After [uploading](../system-services-storage/#buckets) the CSV-file into the `dbrepo-upload` bucket of 
-the [Storage Service](../system-services-storage), analysis for data types and primary keys follows the flow:
+After [uploading](./system-services-storage/#buckets) the CSV-file into the `dbrepo-upload` bucket of 
+the [Storage Service](./system-services-storage), analysis for data types and primary keys follows the flow:
  
 1. Retrieve the CSV-file from the `dbrepo-upload` bucket of the Storage Service as data stream (=nothing is stored in 
    the service) with the [`boto3`](https://boto3.amazonaws.com/v1/documentation/api/latest/index.html) client.
@@ -36,16 +36,16 @@ the [Storage Service](../system-services-storage), analysis for data types and p
 
 ### Examples
 
-See the [usage page](../usage-analyse/) for examples.
+See the [usage page](./usage-analyse/) for examples.
 
 ## Limitations
 
 !!! 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 
+    in [contact](./contact) with us, we happily answer requests for collaboration with attached CV and your programming 
     experience!
 
 ## Security
 
-1. Credentials for the [Storage Service](../system-services-storage) are stored in plaintext environment variables.
+1. Credentials for the [Storage Service](./system-services-storage) are stored in plaintext environment variables.

.docs/api/data-service.md

@@ -14,7 +14,7 @@ author: Martin Weise
         - Readiness: `http://<hostname>:9093/actuator/health/readiness`
         - Liveness: `http://<hostname>:9093/actuator/health/liveness`
     * Prometheus: `http://<hostname>:9093/actuator/prometheus`
-    * Swagger UI: `http://<hostname>:9093/swagger-ui/index.html` <a href="../swagger/data" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+    * Swagger UI: `http://<hostname>:9093/swagger-ui/index.html` <a href="./swagger/data" target="_blank">:fontawesome-solid-square-up-right: view online</a>
 
 ## Overview
 
@@ -27,7 +27,7 @@ Data Service up.
 !!! 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 
+    in [contact](./contact) with us, we happily answer requests for collaboration with attached CV and your programming 
     experience!
 
 ## Security

.docs/api/gateway-service.md

@@ -41,7 +41,7 @@ If your TLS private key as a password, you need to specify it in the `dbrepo.con
 
 ### User Interface
 
-To serve the [User Interface](../system-other-ui/) under different port than `80`, change the port mapping in 
+To serve the [User Interface](./system-other-ui/) under different port than `80`, change the port mapping in 
 the `docker-compose.yml` to e.g. port `8000`:
 
 ```yaml title="docker-compose.yml"
@@ -61,7 +61,7 @@ services:
 !!! 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 
+    in [contact](./contact) with us, we happily answer requests for collaboration with attached CV and your programming 
     experience!
 
 

.docs/api/index.md

@@ -5,7 +5,7 @@ author: Martin Weise
 # Overview
 
 We developed a Python Library for communicating with DBRepo from e.g. Jupyter Notebooks. See
-the [Python Library](../usage-python) page for more details.
+the [Python Library](./usage-python) page for more details.
 
 We give usage examples of the most important use-cases we identified.
 
@@ -30,7 +30,7 @@ A user wants to create an account in DBRepo.
     button and provide a valid work e-mail address :material-numeric-1-circle-outline: and a username (in lowercase
     alphanumeric characters) :material-numeric-2-circle-outline:. Choose a secure password in field 
     :material-numeric-3-circle-outline: and repeat it in field :material-numeric-4-circle-outline:. Click "SUBMIT" and
-    the system creates a user account in Figure 1 with the [default roles](../system-services-authentication/#roles)
+    the system creates a user account in Figure 1 with the [default roles](./system-services-authentication/#roles)
     that your administrator has assigned.
 
     <figure markdown>
@@ -425,7 +425,7 @@ A user wants to import a database dump in `.sql` (or in `.sql.gz`) format into D
     Setup a new connection in the MySQL Workbench (c.f. Figure 14) by clicking the small 
     ":material-plus-circle-outline:" button :material-numeric-1-circle-outline: to open the dialog. In the opened dialog
     fill out the connection parameters (for local deployments the hostname is `127.0.0.1` and port `3307` for the
-    [Data Database](../system-databases-data/) :material-numeric-2-circle-outline:.
+    [Data Database](./system-databases-data/) :material-numeric-2-circle-outline:.
 
     The default credentials are username `root` and password `dbrepo`, type the password in 
     :material-numeric-3-circle-outline: and click the "OK" button. Then finish the setup of the new connection by
@@ -470,8 +470,8 @@ A user wants to import a database dump in `.sql` (or in `.sql.gz`) format into D
     gunzip < dump.sql.gz | mysql -H127.0.0.1 -p3307 -uUSERNAME -pYOURPASSWORD db_name
     ```
 
-    The [Metadata Service](../system-services-metadata) periodically (by default configuration every 60 seconds) checks
-    and adds missing tables and views to the [Metadata Database](../system-databases-metadata), the database dump
+    The [Metadata Service](./system-services-metadata) periodically (by default configuration every 60 seconds) checks
+    and adds missing tables and views to the [Metadata Database](./system-databases-metadata), the database dump
     will be visible afterwards. Currently, date formats for columns with time types (e.g. `DATE`, `TIMESTAMP`) are
     assumed to match the first date format found for the database image. This may need to be manually specified by the
     administrator.
@@ -479,7 +479,7 @@ A user wants to import a database dump in `.sql` (or in `.sql.gz`) format into D
     !!! example "Specifying a custom date format"
 
         In case the pre-defined date formats are not matching the found date format in the database dump, the system
-        administrator needs to add it manually in the [Metadata Database](../system-databases-metadata).
+        administrator needs to add it manually in the [Metadata Database](./system-databases-metadata).
 
         ```sql
         INSERT INTO `mdb_images_date` (`iid`, `database_format`, `unix_format`, `example`, `has_time`)
@@ -658,7 +658,7 @@ A user wants to create a subset and export it as csv file.
     ```
 
     Afterwards, you can see the subset in the UI with subset id `@subsetId` and persist it there. Only the administrator
-    can persist the subset in the [Data Database](../system-databases-data) through JDBC by setting the `persisted`
+    can persist the subset in the [Data Database](./system-databases-data) through JDBC by setting the `persisted`
     column to `true` in the `qs_queries` table.
 
 === "Python"
@@ -732,7 +732,7 @@ A user wants to assign a persistent identifier to a database owned by them.
     <figcaption>Figure 21: Open the get persisent identifier form.</figcaption>
     </figure>
 
-    First, provide information on the dataset creator(s). Since the [Metadata Service](../system-services-metadata) 
+    First, provide information on the dataset creator(s). Since the [Metadata Service](./system-services-metadata) 
     automatically resolves external PIDs, the easiest way is to provide the correct mandatory data is by filling the
     name identifier :material-numeric-1-circle-outline:. The creator type :material-numeric-2-circle-outline:
     denotes either a natural person or organization. Optionally fill out the given 
@@ -779,7 +779,7 @@ A user wants to assign a persistent identifier to a database owned by them.
     <figcaption>Figure 25: Related identifiers, license and language of the identifier.</figcaption>
     </figure>
 
-    Optionally add funding information, again the [Metadata Service](../system-services-metadata) 
+    Optionally add funding information, again the [Metadata Service](./system-services-metadata) 
     automatically resolves external PIDs, the easiest way is to provide the correct mandatory data is by filling the
     funder identifier :material-numeric-1-circle-outline: that attempts to get the funder
     name :material-numeric-2-circle-outline:. If you provide an award number :material-numeric-3-circle-outline: and/or
@@ -817,11 +817,11 @@ A user wants to assign a persistent identifier to a database owned by them.
 
     !!! warning
 
-        Creating a PID directly in the [Metadata Database](../system-databases-metadata) is not recommended! It bypasses
+        Creating a PID directly in the [Metadata Database](./system-databases-metadata) is not recommended! It bypasses
         validation and creation of external PIDs (e.g. DOI) and may lead to inconstistent data locally compared to
         external systems (e.g. DataCite Fabrica).
 
-    Create a local PID directly in the [Metadata Database](../system-databases-metadata) by filling the tables in this
+    Create a local PID directly in the [Metadata Database](./system-databases-metadata) by filling the tables in this
     order (they have foreign key dependencies).
 
     1. `mdb_identifiers` ... identifier core information
@@ -928,7 +928,7 @@ A user wants a public database to be private and only give specific users access
 === "JDBC"
 
     To change the visibility of a database as administrator with direct JDBC access to 
-    the [Metadata Database](../system-databases-metadata), change the visibility directly by executing the SQL-query
+    the [Metadata Database](./system-databases-metadata), change the visibility directly by executing the SQL-query
     in the `fda` schema:
 
     ```sql

.docs/api/metadata-service.md

@@ -14,7 +14,7 @@ author: Martin Weise
         - Readiness: `http://<hostname>:9099/actuator/health/readiness`
         - Liveness: `http://<hostname>:9099/actuator/health/liveness`
     * Prometheus: `http://<hostname>:9099/actuator/prometheus`
-    * Swagger UI: `http://<hostname>:9099/swagger-ui/index.html` <a href="../swagger/metadata" target="_blank">:fontawesome-solid-square-up-right: view online</a>
+    * Swagger UI: `http://<hostname>:9099/swagger-ui/index.html` <a href="./swagger/metadata" target="_blank">:fontawesome-solid-square-up-right: view online</a>
 
 ## Overview
 
@@ -75,23 +75,23 @@ Executing SQL queries through the Query Endpoint must fulfill some restrictions:
 
 ### Semantics
 
-The service provides metadata to the table columns in the [Metadata Database](../system-databases-metadata) from
+The service provides metadata to the table columns in the [Metadata Database](./system-databases-metadata) from
 registered ontologies like Wikidata [`wd:`](https://wikidata.org), Ontology of Units of
 Measurement [`om2:`](https://www.ontology-of-units-of-measure.org/resource/om-2), Friend of a
 Friend [`foaf:`](http://xmlns.com/foaf/0.1/), the [`prov:`](http://www.w3.org/ns/prov#) namespace, etc.
 
 ### Tables
 
-The service manages tables in the [Data Database](../system-databases-data) and manages the metadata of these tables
-in the [Metadata Database](../system-databases-metadata). Any tables that are created outside of DBRepo (e.g. directly via the JDBC API) are
+The service manages tables in the [Data Database](./system-databases-data) and manages the metadata of these tables
+in the [Metadata Database](./system-databases-metadata). Any tables that are created outside of DBRepo (e.g. directly via the JDBC API) are
 periodically fetched by this service (based on the `OBTAIN_METADATA_RATE` environment variable, default interval is 60
 seconds).
 
 ### Users
 
-The service manages users in the [Data Database](../system-databases-data)
-and [Metadata Database](../system-databases-metadata), as well as in the [Broker Service](../system-services-broker)
-and the [Authentication Service](../system-services-authentication).
+The service manages users in the [Data Database](./system-databases-data)
+and [Metadata Database](./system-databases-metadata), as well as in the [Broker Service](./system-services-broker)
+and the [Authentication Service](./system-services-authentication).
 
 The default configuration grants the users only very basic permissions on the databases:
 
@@ -123,8 +123,8 @@ A list of all grants is available in the MariaDB documentation for [`GRANT`](htt
 
 ### Views
 
-The service manages views in the [Data Database](../system-databases-data)
-and [Metadata Database](../system-databases-metadata). Any views that are created outside of DBRepo (e.g. directly via 
+The service manages views in the [Data Database](./system-databases-data)
+and [Metadata Database](./system-databases-metadata). Any views that are created outside of DBRepo (e.g. directly via 
 the JDBC API) are periodically fetched by this service (based on the `OBTAIN_METADATA_RATE` environment variable,
 default interval is 60 seconds).
 
@@ -136,7 +136,7 @@ default interval is 60 seconds).
 !!! 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 
+    in [contact](./contact) with us, we happily answer requests for collaboration with attached CV and your programming 
     experience!
 
 ## Security

.docs/api/open-api.md

@@ -2,6 +2,12 @@
 author: Martin Weise
 ---
 
-All services are documented using the 
-[![OpenAPI 3.0](https://img.shields.io/badge/OpenAPI-3.0-leaf?logo=swagger&logoColor=white)](https://www.openapis.org/){ tabindex=-1 }
-documentation standard.
+![OpenAPI 3.1](https://img.shields.io/badge/OpenAPI-3.1-leaf)
+
+## tl;dr
+
+[:simple-swagger:  View Swagger-UI](../../swagger/){ .md-button .md-button--primary tabindex=-1 }
+
+## Overview
+
+All services are documented using the [OpenAPI 3.1](https://www.openapis.org/) documentation standard.
\ No newline at end of file

.docs/api/storage-service.md

@@ -36,7 +36,7 @@ The default configuration creates two buckets `dbrepo-upload`, `dbrepo-download`
 !!! 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 
+    in [contact](./contact) with us, we happily answer requests for collaboration with attached CV and your programming 
     experience!
 
 ## Security

.docs/deployment-docker-compose.md

@@ -53,7 +53,7 @@ technologies. The conceptualized microservices operate the basic database operat
 
 ### Notes
 
-Please note that we only save the state of the databases as well as the [Broker Service](../system-services-broker)
+Please note that we only save the state of the databases as well as the [Broker Service](./system-services-broker)
 since RabbitMQ maintains state inside the container.
 
 ## Deployment
@@ -147,8 +147,8 @@ Please be warned that the default configuration is not intended for public deplo
 running system within minutes to play around within the system and explore features. It is strongly advised to change 
 the default `.env` environment variables.
 
-Next, create a [user account](../usage-overview/#create-user-account) and 
-then [create a database](../usage-overview/#create-database) to [import a dataset](../usage-overview/#import-dataset).
+Next, create a [user account](./usage-overview/#create-user-account) and 
+then [create a database](./usage-overview/#create-database) to [import a dataset](./usage-overview/#import-dataset).
 
 ## Security
 
@@ -193,4 +193,4 @@ then [create a database](../usage-overview/#create-database) to [import a datase
 
 !!! info "Alternative Deployments"
 
-    Alternatively, you can also deploy DBRepo with [Helm](../deployment-helm/) in your virtual machine instead.
+    Alternatively, you can also deploy DBRepo with [Helm](./deployment-helm/) in your virtual machine instead.

.docs/deployment-helm.md

@@ -32,12 +32,12 @@ about values, etc.
 ## Limitations
 
 1. MariaDB Galera does not (yet) support XA-transactions required by the authentication service (=Keycloak). Therefore
-   only a single MariaDB pod can be deployed at once for the [auth database](../system-databases-authentication).
+   only a single MariaDB pod can be deployed at once for the [auth database](./system-databases-authentication).
 2. The entire Helm deployment is rootless (=`runAsNonRoot=true`) except for
-   the [Storage Service](../system-services-storage/) which still requires a root user.
+   the [Storage Service](./system-services-storage/) which still requires a root user.
 
 !!! 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 
+    in [contact](./contact) with us, we happily answer requests for collaboration with attached CV and your programming 
     experience!

.docs/docker/_header.md

@@ -10,7 +10,7 @@
 
 # Supported tags
 
-* [`1.4.x`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/blob/release-__APP_VERSION__/dbrepo-DIR/Dockerfile/)
+* [`1.4.3`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/blob/release-1.4.3/dbrepo-DIR/Dockerfile/)
 * [`latest`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/blob/release-latest/dbrepo-DIR/Dockerfile/)
 
 # Non-supported tags
@@ -29,8 +29,8 @@
 
 * **Source of this description:**
 
-  [docs repo's `.docs/docker` directory](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/tree/release-__APP_VERSION__/.docs/docker)
-  ([history](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/commits/release-__APP_VERSION__/.docs/docker))
+  [docs repo's `.docs/docker` directory](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/tree/release-1.4.3/.docs/docker)
+  ([history](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/commits/release-1.4.3/.docs/docker))
 
 # What is DBRepo?
 

.docs/publications.md

@@ -14,14 +14,14 @@ hide:
     Semantic Digital Repository for Relational Databases. *International Journal of Digital Curation*, 17(1), 11. 
     DOI: [10.2218/ijdc.v17i1.825](https://doi.org/10.2218/ijdc.v17i1.825)<br />
 
-    [[BibTeX](../papers/weise2022dbrepo.bib)] &nbsp; [[RIS](../papers/weise2022dbrepo.ris)] &nbsp; [[RDF](../papers/weise2022dbrepo.rdf)] &nbsp; [[EndNote](../papers/weise2022dbrepo.xml)]
+    [[BibTeX](./papers/weise2022dbrepo.bib)] &nbsp; [[RIS](./papers/weise2022dbrepo.ris)] &nbsp; [[RDF](./papers/weise2022dbrepo.rdf)] &nbsp; [[EndNote](./papers/weise2022dbrepo.xml)]
 
 ## Logos
 
 DBRepo logo in various formats:
 
-* PNG: [bigger](../images/logo/logo.png) ([smaller](../images/logo/favicon.png))
-* SVG: [bigger](../images/logo/logo.svg) ([smaller](../images/logo/favicon.svg))
+* PNG: [bigger](./images/logo/logo.png) ([smaller](./images/logo/favicon.png))
+* SVG: [bigger](./images/logo/logo.svg) ([smaller](./images/logo/favicon.svg))
 
 
 ## Refereed

.docs/usage-storage.md

@@ -53,7 +53,7 @@ $ aws --endpoint-url http://localhost:9000 \
 
 ## Other
 
-Alternatively, you can use the middleware of the [User Interface](../system-other-ui/) to upload files.
+Alternatively, you can use the middleware of the [User Interface](./system-other-ui/) to upload files.
 
 Alternatively, you can use a S3-compatible client:
 

.docs/usage-upload.md

@@ -11,7 +11,7 @@ We recommend using a TUS-compatible client:
 * [tus-js-client](https://github.com/tus/tus-js-client) (JavaScript/Node.js)
 * [tusd](https://github.com/tus/tusd) (Go)
 
-Upload a file to the `dbrepo-upload` bucket in the [Storage Service](../system-services-storage/) using the Node.js
+Upload a file to the `dbrepo-upload` bucket in the [Storage Service](./system-services-storage/) using the Node.js
 middleware.
 
 === "Terminal"

.gitlab-ci.yml

@@ -5,8 +5,8 @@ variables:
   DOCKER_HOST: "unix:///var/run/dind/docker.sock"
   TESTCONTAINERS_RYUK_DISABLED: "false"
   DOC_VERSIONS: "latest,1.4.3,1.4.2,1.4.1,1.4.0"
-  APP_VERSION: "1.4.3"
-  CHART_VERSION: "1.4.3"
+  APP_VERSION: "1.4.4"
+  CHART_VERSION: "1.4.4"
 
 image: debian:12-slim
 
@@ -569,7 +569,6 @@ docs-registry:
     - "apt-get update && apt-get install -y sed"
   script:
     - pip install -r ./requirements.txt
-    - find .docs -type f -exec sed -i -e "s/__APP_VERSION__/${APP_VERSION}/g" {} \;
     - python3 .docs/docker/release.py
 
 release-images:
@@ -588,7 +587,7 @@ release-images:
     - "ifconfig eth0 mtu 1450 up"
     - "apk add make bash"
   script:
-    - "make release"
+    - "make release-images"
 
 release-chart:
   stage: release
@@ -596,13 +595,14 @@ release-chart:
   only:
     refs:
       - /^release-.*/
+  except:
+    refs:
+      - release-latest
   before_script:
     - "echo ${CI_REGISTRY2_PASSWORD} | docker login --username ${CI_REGISTRY2_USER} --password-stdin $CI_REGISTRY2_URL"
-    - "echo ${CI_GPG_KEYRING} | base64 -d > ~/keyring.gpg"
     - "apk add sed helm curl"
     - "helm plugin install https://github.com/sigstore/helm-sigstore"
   script:
-    - "helm package --sign --key 'Martin Weise' ./helm/dbrepo --keyring ~/keyring.gpg --destination ./build"
     - "helm push ./build/dbrepo-${CHART_VERSION}.tgz oci://${CI_REGISTRY2_URL}/helm"
     - "helm sigstore upload ./build/dbrepo-${CHART_VERSION}.tgz"
 
@@ -617,26 +617,29 @@ release-docs:
   before_script:
     - "wget https://github.com/mikefarah/yq/releases/download/v4.2.0/yq_linux_amd64 -O /usr/bin/yq"
     - "chmod +x /usr/bin/yq"
-    - "apt-get update && apt-get install -y git make sed wget ssh"
+    - "apk add --update alpine-sdk bash sed wget openssh"
+    - "pip install -r ./requirements.txt"
     - "mkdir -p ./final/${VERSION}/swagger"
   script:
-    - "make gen-swagger-doc gen-lib-doc gen-docs-doc"
+    - "make gen-lib-doc gen-docs-doc"
     - "cp -r ./lib/python/docs/build/html ./final/${VERSION}/sphinx" # sphinx
     - "cp .docs/.swagger/api.yaml ./final/${VERSION}/swagger/api.yaml" # swagger
     - "cp .docs/.swagger/swagger-ui.html ./final/${VERSION}/swagger/index.html" # swagger
     - "cp .docs/.swagger/custom.css ./final/${VERSION}/swagger/custom.css" # swagger
-    - "cp -r ./site ./final/${VERSION}" # mkdocs
+    - "cp -r ./site/* ./final/${VERSION}" # mkdocs
     - eval $(ssh-agent -s)
+    - "mkdir -p /root/.ssh"
     - echo "$CI_KEY_PRIVATE" > /root/.ssh/id_rsa && chmod 0600 /root/.ssh/id_rsa
     - echo "$CI_KEY_PUBLIC" > /root/.ssh/id_rsa.pub
     - echo "$CI_DOC_ID" > ~/.ssh/known_hosts
     - tar czf ./final.tar.gz ./final
     - "scp -oHostKeyAlgorithms=+ssh-rsa -oPubkeyAcceptedAlgorithms=+ssh-rsa final.tar.gz $CI_DOC_USER@$CI_DOC_IP:final.tar.gz"
-    - "ssh -oHostKeyAlgorithms=+ssh-rsa -oPubkeyAcceptedAlgorithms=+ssh-rsa $CI_DOC_USER@$CI_DOC_IP 'rm -rf /system/user/ifs/infrastructures/public_html/dbrepo/*; tar xzf ./final.tar.gz; rm -f ./final.tar.gz; cp -r ./final/* /system/user/ifs/infrastructures/public_html/dbrepo; rm -rf ./final'"
+    - "ssh -oHostKeyAlgorithms=+ssh-rsa -oPubkeyAcceptedAlgorithms=+ssh-rsa $CI_DOC_USER@$CI_DOC_IP 'rm -rf /system/user/ifs/infrastructures/public_html/dbrepo/*; tar xzf ./final.tar.gz; rm -f ./final.tar.gz; cp -r ./final/* /system/user/ifs/infrastructures/public_html/dbrepo/${VERSION}; rm -rf ./final'"
 
 release-libs:
   stage: release
   image: docker.io/python:3.11-alpine
+  when: manual
   only:
     refs:
       - /^release-.*/

Makefile

@@ -2,8 +2,7 @@
 
 APP_VERSION ?= 1.4.3
 CHART_VERSION ?= 1.4.3
-REPOSITORY_1_URL ?= docker.io/dbrepo
-REPOSITORY_2_URL ?= s210.dl.hpc.tuwien.ac.at/dbrepo
+REPOSITORY_URL ?= docker.io/dbrepo
 
 .PHONY: all
 all: help

build-docs.sh

@@ -88,6 +88,7 @@ done
 
 # finalization
 echo "==================================================="
-echo "Moving default version $APP_VERSION docs to /"
-cp -r ./final/${APP_VERSION}/* ./final/
+echo "Moving HTML redirect and JSON versions to /"
+cp ./final/${APP_VERSION}/redirect.html ./final/index.html
+cp ./final/${APP_VERSION}/versions.json ./final/versions.json
 echo "==================================================="