chore: test python with connexion

.dockerignore

@@ -2,8 +2,9 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
-*
 !target/*-runner
 !target/*-runner.jar
 !target/lib/*
-!target/quarkus-app/*
+!target/quarkus-app/*
+venv
+__pycache__/

.github/workflows/test.yml

@@ -7,18 +7,6 @@ name: Run Tests
 on: push
 
 jobs:
-  test:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up GraalVM JDK 21
-        uses: graalvm/setup-graalvm@v1
-        with:
-          java-version: '21'
-      - name: Run the Maven
-        run: mvn --batch-mode --update-snapshots verify checkstyle:check
   reuse:
     runs-on: ubuntu-latest
     permissions:

.gitignore

@@ -42,6 +42,9 @@ nb-configuration.xml
 
 # Local environment
 .env
+venv
 
 # Plugin directory
 /.quarkus/cli/plugins/
+
+__pycache__/

Dockerfile

@@ -1,33 +1,14 @@
 # SPDX-FileCopyrightText: 2024 PNED G.I.E.
 #
 # SPDX-License-Identifier: Apache-2.0
-####
-# This Dockerfile is used in order to build a container that runs the Quarkus application in native (no JVM) mode.
-# It uses a micro base image, tuned for Quarkus native executables.
-# It reduces the size of the resulting container image.
-# Check https://quarkus.io/guides/quarkus-runtime-base-image for further information about this image.
-#
-# Before building the container image run:
-#
-# mvn package -Dnative
-#
-# Then, build the image with:
-#
-# docker build -f src/main/docker/Dockerfile.native-micro -t quarkus/code-with-quarkus .
-#
-# Then run the container using:
-#
-# docker run -i --rm -p 8080:8080 quarkus/code-with-quarkus
-#
-###
-FROM quay.io/quarkus/quarkus-micro-image:2.0
-WORKDIR /work/
-RUN chown 1001 /work \
-    && chmod "g+rwX" /work \
-    && chown 1001:root /work
-COPY --chown=1001:root target/*-runner /work/application
+FROM python:3.10-slim-bookworm
+
+WORKDIR /code
+
+COPY ./requirements.txt /code/requirements.txt
+COPY ./run.py /code/run.py
+COPY ./openapi.yaml /code/openapi.yaml
 
-EXPOSE 8080
-USER 1001
+RUN pip install --no-cache-dir --upgrade -r /code/requirements.txt
 
-ENTRYPOINT ["./application", "-Dquarkus.http.host=0.0.0.0"]
+CMD ["uvicorn", "run:app", "--host", "0.0.0.0", "--port", "8080"]

openapi.yaml

@@ -0,0 +1,79 @@
+# SPDX-FileCopyrightText: 2024 PNED G.I.E.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+openapi: 3.0.3
+info:
+  title: Access Request Management Service - OpenAPI 3.0
+  description: |-
+    This is the OpenAPI 3.0 specification for the Access Request Management Service.
+    This service is responsible for managing access requests to the Genomic Data Infrastructure (GDI).
+    The service provides endpoints for creating, updating, and retrieving access requests, as well as managing the datasets and members associated with each request.
+    The service also provides endpoints for managing baskets of access requests.
+
+  #termsOfService: http://TODO/terms/
+  contact:
+    email: [email protected]
+  license:
+    name: Apache 2.0
+    url: https://spdx.org/licenses/Apache-2.0.html
+  version: 0.0.0
+externalDocs:
+  description: Find out more about GDI
+  url: https://genomicdatainfrastructure.github.io/gdi-userportal-docs/
+servers:
+  - url: https://localhost:8080
+    description: Development server
+tags:
+  - name: applications
+    description: All endpoints related to access request management
+  - name: baskets
+    description: All endpoints related to baskets
+  - name: attachments
+    description: All endpoints related to attachments
+  - name: members
+    description: All endpoints related to members
+  - name: terms
+    description: All endpoints related to terms
+  - name: datasets
+    description: All endpoints related to datasets
+  - name: forms
+    description: All endpoints related to forms
+  - name: actions
+    description: All endpoints related to user actions
+  - name: events
+    description: All endpoints related to events
+paths:
+  /api/v1/applications:
+    get:
+      summary: List applications
+      operationId: run.list_applications_v1
+      tags:
+        - "applications"
+      responses:
+        "200":
+          description: Successful Response
+          content:
+            application/json:
+              schema:
+                type: array
+                title: collection of applications
+                items:
+                  $ref: "#/components/schemas/ListedApplication"
+components:
+  schemas:
+    ListedApplication:
+      properties:
+        id:
+          type: string
+          title: Application id
+        title:
+          type: string
+          title: Application title
+        currentState:
+          type: string
+          title: Application state
+        stateChangedAt:
+          type: string
+          format: date-time
+          title: Status changed at

requirements.txt

@@ -0,0 +1,2 @@
+connexion==3.0.5
+uvicorn==0.27.1

requirements.txt.license

@@ -0,0 +1,3 @@
+SPDX-FileCopyrightText: Genomic Data Infrastructure
+
+SPDX-License-Identifier: Apache-2.0