Update JSON schemas and use Github Actions Integration

.github/workflows/docs.yml

@@ -0,0 +1,41 @@
+name: Documentation Checks
+
+on: [push]
+
+jobs:
+  spell_check:
+    strategy:
+      max-parallel: 4
+      matrix:
+        os: [ubuntu-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Spell check install
+      run: curl -L https://git.io/misspell | bash
+    - name: Spell check docs
+      run: bin/misspell -error docs/*
+
+  code_docs:
+    strategy:
+      max-parallel: 4
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.7]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions
+    - name: Run docs tests
+      run: tox -e docs
+

.github/workflows/int.yml

@@ -0,0 +1,58 @@
+name: Integration Tests
+
+on: [pull_request]
+
+jobs:
+  build:
+    strategy:
+      max-parallel: 4
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.7]
+
+    runs-on: ${{ matrix.os }}
+
+    name: Integration Tests
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install requirements
+      run: |
+        wget https://github.com/openshift/source-to-image/releases/download/v1.2.0/source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
+        tar -xvf source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
+        sudo cp s2i /usr/local/bin
+        pip install aiohttp
+        pip install requests
+    - name: Build image
+      run:  |
+        s2i build . centos/python-36-centos7 cscfi/beacon-python
+
+    - name: Start Services
+      run: |
+        pushd deploy/test
+        docker-compose up -d
+        sleep 10
+        docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz data/example_metadata.json
+        docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_registered.json
+        docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled.json
+        docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled1.json
+
+    - name: Run Integration test
+      run: |
+        pushd deploy/test
+        python run_tests.py
+
+    - name: Collect logs from docker
+      if: ${{ failure() }}
+      run: cd deploy && docker-compose logs --no-color -t > ../tests/dockerlogs || true
+
+    - name: Persist log files
+      if: ${{ failure() }}
+      uses: actions/upload-artifact@v1
+      with:
+        name: test_debugging_help
+        path: tests

.github/workflows/publish.yml

@@ -0,0 +1,49 @@
+name: Publish Docker image
+
+on:
+  release:
+    types: [published]
+  push:
+    branches: [master]
+
+jobs:
+  push_to_registry:
+    name: Push Beacon Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - name: Login to DockerHub Registry
+        run: echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin
+      - name: Get the version
+        id: vars
+        run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
+      - name: Build the tagged Docker image
+        run: docker build . --file Dockerfile --tag cscfi/beacon-python:${{steps.vars.outputs.tag}}
+      - name: Push the tagged Docker image
+        run: docker push cscfi/beacon-python:${{steps.vars.outputs.tag}}
+      - name: Build the latest Docker image
+        run: docker build . --file Dockerfile --tag cscfi/beacon-python:latest
+      - name: Push the latest Docker image
+        run: docker push cscfi/beacon-python:latest
+  push_data_to_registry:
+    name: Push Dataloader Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - name: Login to DockerHub Registry
+        run: echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin
+      - name: Get the version
+        id: vars
+        run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
+      - name: Build the tagged Docker image
+        run: |
+          pushd deploy/test
+          docker build . --file Dockerfile --tag cscfi/beacon-dataloader:${{steps.vars.outputs.tag}}
+      - name: Push the tagged Docker image
+        run: docker push cscfi/beacon-dataloader:${{steps.vars.outputs.tag}}
+      - name: Build the latest Docker image
+        run: |
+          pushd deploy/test
+          docker build . --file Dockerfile --tag cscfi/beacon-dataloader:latest
+      - name: Push the latest Docker image
+        run: docker push cscfi/beacon-dataloader:latest

.github/workflows/style.yml

@@ -0,0 +1,28 @@
+name: Python style check
+
+on: [push]
+
+jobs:
+  style_check:
+    strategy:
+      max-parallel: 4
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.6, 3.7]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions
+    - name: Test flake8 syntax with tox
+      run: tox -e flake8
+    - name: Do bandit static check with tox
+      run: tox -e bandit

.github/workflows/unit.yml

@@ -0,0 +1,30 @@
+name: Python Unit Tests
+
+on: [push]
+
+jobs:
+  unit_test:
+    strategy:
+      max-parallel: 4
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.6, 3.7]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install libcurl-devel
+      run: sudo apt-get install libcurl4-openssl-dev
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions
+    - name: Run unit tests
+      env:
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+      run: tox -e unit_tests

README.md

@@ -1,9 +1,9 @@
 ## beacon-python - Python-based Beacon API Web Server
 
-[![Build Status](https://travis-ci.org/CSCfi/beacon-python.svg?branch=master)](https://travis-ci.org/CSCfi/beacon-python)
-[![Coverage Status](https://coveralls.io/repos/github/CSCfi/beacon-python/badge.svg?branch=master)](https://coveralls.io/github/CSCfi/beacon-python?branch=master)
+![Integration Tests](https://github.com/CSCfi/beacon-python/workflows/Integration%20Tests/badge.svg)
+![Python Unit Tests](https://github.com/CSCfi/beacon-python/workflows/Python%20Unit%20Tests/badge.svg)
+[![Coverage Status](https://coveralls.io/repos/github/CSCfi/beacon-python/badge.svg?branch=HEAD)](https://coveralls.io/github/CSCfi/beacon-python?branch=HEAD)
 [![Documentation Status](https://readthedocs.org/projects/beacon-python/badge/?version=latest)](https://beacon-python.readthedocs.io/en/latest/?badge=latest)
-[![Docker Image](https://images.microbadger.com/badges/image/cscfi/beacon-python.svg)](https://microbadger.com/images/cscfi/beacon-python)
 
 Documentation: https://beacon-python.readthedocs.io