Merge branch 'dev' into 393-frontend-needs-yaml-configuration-for-cloud-environments

.docs/deployment-docker-compose.md

@@ -58,6 +58,41 @@ since RabbitMQ maintains state inside the container.
 We maintain a rapid prototype deployment option through Docker Compose (v2.17.0 and newer). This deployment creates the
 core infrastructure and a single Docker container for all user-generated databases.
 
+=== ":simple-linux: Linux"
+
+    Download and install [Docker Engine](https://docs.docker.com/desktop/install/linux-install/) for your Linux
+    distribution. Although the installation might work, we *do not* recommend Docker Desktop.
+    
+    Ensure the Docker daemon is running at all times:
+
+        systemctl enable docker --now
+
+    Install DBRepo with the default configuration:
+
+        curl -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/install.sh | bash
+
+=== ":simple-windows: Windows"
+
+    Open `cmd.exe` as administrator and install WSL2 and the Debian subsystem:
+
+        wsl --install Debian
+
+    Open `optionalfeatures` by typing into the open terminal window or searching for it and enable "Windows Subsystem 
+    for Linux":
+
+    <figure markdown>
+    ![Data ingest](images/optionalfeatures.png){ .img-border }
+       <figcaption>Enable Subsystem for Linux in Windows Features</figcaption>
+    </figure>
+
+    Install [Docker Desktop](https://docs.docker.com/desktop/install/windows-install/) on the Windows host machine.
+    Open Docker Desktop and go to settings (:fontawesome-solid-gear:) > General > Tick "Use WSL2 based engine" if not
+    already ticked.
+
+    Open the Debian container by typing "Debian" into the search, you should see a terminal window.
+
+    Install DBRepo with the default configuration from the Debian container:
+
         curl -sSL https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/install.sh | bash
 
 View the logs:

.docs/deployment-helm.md

@@ -31,7 +31,7 @@ The helm chart depends on four components:
 ## Configuration before the installation
 
 Define an admin user that the services can use to communicate with 
-the [authentication service](../system-services-authentication). You will need to manually create this user later after
+the [Authentication Service](../system-services-authentication). You will need to manually create this user later after
 the installation.
 
 ## Configuration after the installation
@@ -55,6 +55,10 @@ the [authentication service](../system-services-authentication) as `admin` and:
 3. Assign this user the role `admin`.
 4. Delete the user `admin`.
 
+Then import the DBRepo realm by clicking the dropdown "master" > Create Realm and import 
+the [`dbrepo-realm.json`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-authentication-service/dbrepo-realm.json)
+by uploading the file *or* copying the contents and click "Create".
+
 ### Backup
 
 tbd

dbrepo-metadata-db/setup-schema.sql

@@ -282,10 +282,8 @@ CREATE TABLE IF NOT EXISTS `mdb_concepts`
     name        VARCHAR(255)          null,
     description TEXT                  null,
     created     timestamp             NOT NULL DEFAULT NOW(),
-    created_by  character varying(36) NOT NULL,
     PRIMARY KEY (id),
-    UNIQUE (uri(200)),
-    FOREIGN KEY (created_by) REFERENCES mdb_users (id)
+    UNIQUE (uri(200))
 ) WITH SYSTEM VERSIONING;
 
 CREATE TABLE IF NOT EXISTS `mdb_units`
@@ -295,10 +293,8 @@ CREATE TABLE IF NOT EXISTS `mdb_units`
     name        VARCHAR(255)          null,
     description TEXT                  null,
     created     timestamp             NOT NULL DEFAULT NOW(),
-    created_by  character varying(36) NOT NULL,
     PRIMARY KEY (id),
-    UNIQUE (uri(200)),
-    FOREIGN KEY (created_by) REFERENCES mdb_users (id)
+    UNIQUE (uri(200))
 ) WITH SYSTEM VERSIONING;
 
 CREATE TABLE IF NOT EXISTS `mdb_columns_concepts`

dbrepo-search-service/Dockerfile

 FROM python:3.10-alpine
 
-RUN adduser -D alpine
+RUN apk add bash curl && adduser -D alpine
 
 WORKDIR /home/alpine
 
@@ -12,6 +12,7 @@ RUN pip install pipenv && \
 
 COPY ./app ./app
 COPY ./scripts ./scripts
+COPY ./us-yml ./us-yml
 COPY config.py wsgi.py ./
 
 ENV FLASK_APP=wsgi.py

dbrepo-search-service/app/__init__.py

@@ -2,7 +2,7 @@
 
 import os
 import logging
-from flasgger import LazyJSONEncoder
+from flasgger import LazyJSONEncoder, Swagger
 from flask import Flask
 from opensearchpy import OpenSearch
 from config import Config
@@ -41,7 +41,55 @@ def create_app(config_class=Config):
 
     metrics = PrometheusMetrics(app)
     metrics.info("app_info", "Application info", version="0.0.1")
-    app.config["SWAGGER"] = {"openapi": "3.0.0", "title": "Swagger UI", "uiversion": 3}
+    app.config["SWAGGER"] = {"openapi": "3.0.1", "title": "Swagger UI", "uiversion": 3}
+
+    swagger_config = {
+        "headers": [],
+        "specs": [
+            {
+                "endpoint": "api-search",
+                "route": "/api-search.json",
+                "rule_filter": lambda rule: rule.endpoint.startswith('actuator'),
+                "model_filter": lambda tag: True,  # all in
+            }
+        ],
+        "static_url_path": "/flasgger_static",
+        "swagger_ui": True,
+        "specs_route": "/swagger-ui/",
+    }
+
+    template = {
+        "openapi": "3.0.0",
+        "info": {
+            "title": "Database Repository Search Service API",
+            "description": "Service that searches the search database",
+            "version": "1.3.0",
+            "contact": {
+                "name": "Prof. Andreas Rauber",
+                "email": "andreas.rauber@tuwien.ac.at"
+            },
+            "license": {
+                "name": "Apache 2.0",
+                "url": "https://www.apache.org/licenses/LICENSE-2.0"
+            },
+        },
+        "externalDocs": {
+            "description": "Sourcecode Documentation",
+            "url": "https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services"
+        },
+        "servers": [
+            {
+                "url": "http://localhost:4000",
+                "description": "Generated server url"
+            },
+            {
+                "url": "https://test.dbrepo.tuwien.ac.at",
+                "description": "Sandbox"
+            }
+        ]
+    }
+
+    swagger = Swagger(app, config=swagger_config, template=template)
     # https://flask-jwt-extended.readthedocs.io/en/stable/options/
     app.config["JWT_ALGORITHM"] = "HS256"
     app.config["JWT_DECODE_ISSUER"] = os.getenv("JWT_ISSUER")

dbrepo-search-service/app/api/__init__.py

 from flask import Blueprint
 
-api_bp = Blueprint("api", __name__, url_prefix="/api/search")
+api_bp = Blueprint("api", __name__)
 
 from app.api import routes

dbrepo-search-service/app/api/routes.py

@@ -56,7 +56,13 @@ def general_filter(index, results):
     return results
 
 
-@api_bp.route("<string:index>", methods=["GET"], endpoint="endpoint")
+@api_bp.route("/health", methods=["GET"], endpoint="actuator_health")
+@swag_from("us-yml/get_health")  # ToDo: get the SWAG right
+def health():
+    return {"status": "UP"}
+
+
+@api_bp.route("/api/search/<string:index>", methods=["GET"], endpoint="search_get_index")
 @swag_from("us-yml")  # ToDo: get the SWAG right
 def get_index(index):
     """
@@ -91,7 +97,7 @@ def get_index(index):
     return {"results": results, "total": total_number_of_results, "status": 200}
 
 
-@api_bp.route("<string:index>/fields", methods=["GET"], endpoint="blabla")
+@api_bp.route("/api/search/<string:index>/fields", methods=["GET"], endpoint="search_get_index_fields")
 def get_fields(index):
     """
     returns a list of attributes of the data for a specific index.
@@ -120,7 +126,7 @@ def get_fields(index):
     return {"fields": fields, "status": 200}
 
 
-@api_bp.route("", methods=["POST"], endpoint="endpoint2")
+@api_bp.route("/api/search", methods=["POST"], endpoint="search_fuzzy_search")
 def search():
     """
     Main endpoint for general searching.

dbrepo-search-service/us-yml/get_health.yml

+summary: Return a healthcheck
+description: |
+    Return UP if the instance is ready to serve connections.
+consumes:
+  - application/json
+produces:
+  - application/json
+parameters: []
+definitions:
+  Health:
+    type: object
+    properties:
+      status:
+        type: string
+        description: UP
+responses:
+  200:
+    description: OK, service is up and running
+    schema:
+      $ref: "#/definitions/Column"
+  404:
+    description: Service is not yet ready
+tags:
+  - actuator
\ No newline at end of file