Merge NSQA into main

.github/workflows/Quality_Assessment_&_Awarding_v1.yml

@@ -0,0 +1,99 @@
+name: Quality_Assessment_&_Awarding_v1
+
+on:
+  workflow_dispatch
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Create Docker volumes
+        run: |
+          docker volume create neo4j_data
+          docker volume create neo4j_logs
+          docker volume create yprov_data
+
+      - name: Create Docker network
+        run: docker network create yprov_net
+
+      - name: Start Neo4j service
+        run: |
+          docker run \
+            --name db \
+            --network=yprov_net \
+            -p 7474:7474 -p 7687:7687 \
+            -d \
+            -v neo4j_data:/data \
+            -v neo4j_logs:/logs \
+            -v $HOME/neo4j/import:/var/lib/neo4j/import \
+            -v $HOME/neo4j/plugins:/plugins \
+            --env NEO4J_AUTH=neo4j/password \
+            --env NEO4J_ACCEPT_LICENSE_AGREEMENT=eval \
+            -e NEO4J_apoc_export_file_enabled=true \
+            -e NEO4J_apoc_import_file_enabled=true \
+            -e NEO4J_apoc_import_file_use__neo4j__config=true \
+            -e NEO4J_PLUGINS='["apoc"]' \
+            neo4j:enterprise
+
+      - name: Start API service
+        run: |
+          docker run \
+            --restart on-failure \
+            --name web \
+            --network=yprov_net \
+            -p 3000:3000 \
+            -d \
+            -v yprov_data:/app/conf \
+            --env USER=neo4j \
+            --env PASSWORD=password \
+            hpci/yprov:latest
+
+      - name: Wait for API to be ready
+        run: |
+          echo "Waiting for API to be ready..."
+          max_attempts=30
+          attempt=0
+          until [ $attempt -ge $max_attempts ]
+          do
+            if curl -s -o /dev/null -w "%{http_code}" http://localhost:3000/api/v0/documents | grep -q "200"; then
+              echo "API is ready!"
+              break
+            fi
+            attempt=$((attempt+1))
+            echo "Attempt $attempt/$max_attempts: API is not ready yet. Waiting..."
+            sleep 10
+          done
+
+      - name: Set up Python environment
+        run: |
+          python3 -m pip install --upgrade pip
+          pip install pytest
+
+      - name: Run tests
+        run: |
+          python3 -m pytest -v
+
+      - name: Quality Tests
+        uses: eosc-synergy/sqaaas-assessment-action@v2
+        with:
+          repo: 'https://github.com/HPCI-Lab/yProv.git'
+          branch: 'main'    
+
+      - name: Clean up
+        run: |
+          docker stop web
+          docker rm web
+          docker stop db
+          docker rm db
+          docker network rm yprov_net
+          docker volume rm neo4j_data
+          docker volume rm neo4j_logs
+          docker volume rm yprov_data

.github/workflows/Quality_Assessment_&_Awarding_v2.yml

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+name: Quality_Assessment_&_Awarding_v2
+
+on:
+  push:
+    branches:
+      - '**'
+
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Create Docker volumes
+        run: |
+          docker volume create neo4j_data
+          docker volume create neo4j_logs
+          docker volume create yprov_data
+
+      - name: Create Docker network
+        run: docker network create yprov_net
+
+      - name: Start Neo4j service
+        run: |
+          docker run \
+            --name db \
+            --network=yprov_net \
+            -p 7474:7474 -p 7687:7687 \
+            -d \
+            -v neo4j_data:/data \
+            -v neo4j_logs:/logs \
+            -v $HOME/neo4j/import:/var/lib/neo4j/import \
+            -v $HOME/neo4j/plugins:/plugins \
+            --env NEO4J_AUTH=neo4j/password \
+            --env NEO4J_ACCEPT_LICENSE_AGREEMENT=eval \
+            -e NEO4J_apoc_export_file_enabled=true \
+            -e NEO4J_apoc_import_file_enabled=true \
+            -e NEO4J_apoc_import_file_use__neo4j__config=true \
+            -e NEO4J_PLUGINS='["apoc"]' \
+            neo4j:enterprise
+
+      - name: Start API service
+        run: |
+          docker run \
+            --restart on-failure \
+            --name web \
+            --network=yprov_net \
+            -p 3000:3000 \
+            -d \
+            -v yprov_data:/app/conf \
+            --env USER=neo4j \
+            --env PASSWORD=password \
+            hpci/yprov:latest
+
+      - name: Wait for API to be ready
+        run: |
+          echo "Waiting for API to be ready..."
+          max_attempts=30
+          attempt=0
+          until [ $attempt -ge $max_attempts ]
+          do
+            if curl -s -o /dev/null -w "%{http_code}" http://localhost:3000/api/v0/documents | grep -q "200"; then
+              echo "API is ready!"
+              break
+            fi
+            attempt=$((attempt+1))
+            echo "Attempt $attempt/$max_attempts: API is not ready yet. Waiting..."
+            sleep 10
+          done
+
+      - name: Set up Python environment
+        run: |
+          python3 -m pip install --upgrade pip
+          pip install pytest
+
+      - name: Run tests
+        run: |
+          python3 -m pytest -v SQA/tests/test_auth.py SQA/tests/test_documents.py
+
+      - name: Step definition for validating the workflow
+        uses: eosc-synergy/sqaaas-step-action@v1
+        with:
+          name: pytest-test
+          tool: commands
+          commands: pytest /app/tests/test_mock_auth.py /app/tests/test_mock_documents.py
+          container: hpci/yprov-sqa:mocktest
+
+      - name: SQAaaS assessment with unit testing (QC.Uni) step
+        uses: eosc-synergy/sqaaas-assessment-action@v2
+        with:
+          qc_uni_steps: pytest-test
+          repo: https://github.com/HPCI-Lab/yProv.git
+          branch: main
+
+      - name: Clean up
+        run: |
+            docker stop web
+            docker rm web
+            docker stop db
+            docker rm db
+            docker network rm yprov_net
+            docker volume rm neo4j_data
+            docker volume rm neo4j_logs
+            docker volume rm yprov_data
+
+
+

CITATION.cff

@@ -0,0 +1,26 @@
+cff-version: 1.2.0
+message: 'If you use yProv, please cite it as below'
+title: yProv
+type: software
+authors:
+  - family-names: Fiore
+    given-names: Sandro
+    email: [email protected]
+    affiliation: University of Trento
+  - family-names: Antonio
+    given-names: Fabrizio
+    email: [email protected]
+    affiliation: CMCC
+date-released: 2025-01-14  
+repository-code: 'https://github.com/HPCI-Lab/yProv'
+license: MIT
+version: 1.1
+keywords:
+  - provenance
+  - W3C Provenance
+  - multi-level provenance
+  - yProv
+abstract: >-
+  yProv is a provenance service aimed at addressing multi-level provenance as well as reproducibility challenges in climate analytics experiments. 
+  It  allows scientists to manage provenance information compliant with the W3C PROV standard in a more structured way and navigate and explore the provenance space 
+  across multiple dimensions, thus enabling the possibility to get coarse- or fine-grained information according to the level requested.

CODE_OF_CONDUCT.md

@@ -0,0 +1 @@
+# Code of Conduct

CONTRIBUTING.md

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+# Contributing to yProv
+
+Thank you for your interest in contributing to yProv!  
+To contribute, please follow these steps:
+
+1. Fork the repository.
+2. Make your changes in a new branch.
+3. Test your changes locally.
+4. Submit a pull request describing your changes.
+
+For any questions, feel free to open an issue or contact us.
+
+We appreciate your contributions!

SQA/Dockerfile

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+# Usa l'immagine ufficiale di Python come base
+FROM python:3.9-slim
+
+# Imposta la directory di lavoro nel container
+WORKDIR /app
+
+# Installa curl
+RUN apt-get update && apt-get install -y curl
+
+# Copia l'intero contenuto della directory del progetto nella directory di lavoro del container
+COPY . .
+
+# Assegna i permessi di esecuzione allo script 'tests.sh'
+RUN chmod +x /app/tests/tests.sh
+
+# Installa le dipendenze del progetto, se necessario
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Comando di default: esegue lo script 'tests.sh'
+CMD ["/app/tests/tests.sh"]

SQA/README.md

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+# Test Suite and SQAaaS
+
+The unit and mock tests are split into two files, auth and documents, respectively, to respect the division of the swagger documentation files. 
+To run the tests you need to start Docker Desktop locally and run the command in any folder of the project:
+```
+pytest
+```
+or if you want a more detailed output:
+```
+pytest -v
+```
+
+### SQAaaS
+
+Every time a push is made to the SQA branch, the Github Action QAA file is invoked. It automatically starts the SQAaaS platform pipeline and runs mock tests inside it. Unit tests are instead run locally, so it is always necessary to start docker desktop. The file automatically generates the volumes, containers and docker network and removes them once the files have finished running. The file uses the hpci-yprov:mocktest image to run mock tests inside the SQAaaS platform, the dockerfile code is in the hpci-yprov:mocktest folder.
+
+### Future works
+
+The SQAaaS platform is not yet able to handle multi-container architectures like yProv, however it is working on a solution that can include a docker-compose file. This approach has already been implemented and the code is contained in the docker-compose and dockerfile files in the root folder. To run it use the commands:
+```
+docker-compose build --no-cache
+docker-compose up
+```
+There is also an image that allows you to run both unit tests and mock tests inside a single container and this is contained in the hpci-yprov:1.3 folder.   

SQA/docker-compose.yaml

@@ -0,0 +1,49 @@
+version: "3"
+services:
+  web:
+    image: hpci/yprov:latest
+    restart: on-failure
+    depends_on:
+      - db
+    links: 
+      - db
+    networks:
+      - yprov_net
+    ports:
+      - "3000:3000"
+    environment:
+      USER: neo4j
+      PASSWORD: password
+      ADDRESS: db:7687
+    volumes:
+      - yprov_data:/app/conf
+
+  db:
+    image: "neo4j:enterprise"
+    ports:
+      - "7474:7474"
+      - "7687:7687"
+    environment:
+      NEO4J_AUTH: neo4j/password
+      NEO4J_ACCEPT_LICENSE_AGREEMENT: eval 
+      NEO4J_PLUGINS: '["graph-data-science"]'
+    volumes:
+      - neo4j_data:/data
+      - neo4j_logs:/logs
+    networks:
+      - yprov_net
+
+  test:
+    image: hpci/yprov-sqa:1.4 
+    depends_on:
+      - web
+    networks:
+      - yprov_net
+
+volumes:
+  neo4j_data:
+  neo4j_logs:
+  yprov_data:
+
+networks:
+  yprov_net:

SQA/hpci-yprov:1.3/Dockerfile

@@ -0,0 +1,26 @@
+FROM python:3.9-slim
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+    curl \
+    git \
+    docker.io \
+    docker-compose
+
+# Work Directory
+WORKDIR /app
+
+# Clean and clone updated GitHub repo
+RUN rm -rf /app/* && \
+    git clone --branch sqa https://github.com/HPCI-Lab/yProv.git .
+
+# Install requirements
+COPY requirements.txt /app/requirements.txt
+RUN pip install -r requirements.txt
+
+# Make the script_dockerfile.sh script executable and run it
+COPY tests.sh /app/tests.sh 
+RUN chmod +x /app/tests.sh
+
+# Default command to keep the container running
+CMD ["/app/tests.sh"]