Add initial basic files

.gitignore

+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Pycharm project files
+.idea/**
+
+# Jobs run dir and output
+jobs_run/**
+jobs_output/**
+app/static/
+
+# Configuration
+.env
+/config.yml
+/config_playground.yml
+
+output.csv
\ No newline at end of file

.gitlab-ci.yml

+variables:
+  DOCKER_TLS_CERTDIR: ""
+  GIT_STRATEGY: clone
+  REGISTRY_USER: chembl/chembl
+  SERVER_APPLICATION: main-web-interface/es-subset-generator
+  SERVER_IMAGE_TAG: ${CI_REGISTRY}/${REGISTRY_USER}/${SERVER_APPLICATION}:${CI_COMMIT_SHORT_SHA}
+  DOCKER_DRIVER: overlay
+  CONFIGS_FOLDER: run_config
+  # Config unit tests
+  CONFIG_UNIT_TESTS_FILE_PATH: ${CONFIGS_FOLDER}/unit_tests.yml
+  # Config staging
+  CONFIG_STAGING_FILE_PATH: ${CONFIGS_FOLDER}/staging.yml
+  CONFIG_GUNICORN_STAGING_FILE_PATH: ${CONFIGS_FOLDER}/staging.gunicorn.config.py
+  INGRESS_STAGING_FILE_PATH: ${CONFIGS_FOLDER}/ingress-staging.yml
+  AUTOSCALER_STAGING_FILE_PATH: ${CONFIGS_FOLDER}/autoscaler-staging.yml
+  # Config prod_hx
+  CONFIG_PROD_HX_FILE_PATH: ${CONFIGS_FOLDER}/prod_hx.yml
+  CONFIG_GUNICORN_PROD_HX_FILE_PATH: ${CONFIGS_FOLDER}/prod_hx.gunicorn.config.py
+  INGRESS_PROD_HX_FILE_PATH: ${CONFIGS_FOLDER}/ingress-prod_hx.yml
+  AUTOSCALER_PROD_HX_FILE_PATH: ${CONFIGS_FOLDER}/autoscaler-prod_hx.yml
+  # Config prod_hh
+  CONFIG_PROD_HH_FILE_PATH: ${CONFIGS_FOLDER}/prod_hh.yml
+  CONFIG_GUNICORN_PROD_HH_FILE_PATH: ${CONFIGS_FOLDER}/prod_hh.gunicorn.config.py
+  INGRESS_PROD_HH_FILE_PATH: ${CONFIGS_FOLDER}/ingress-prod_hh.yml
+  AUTOSCALER_PROD_HH_FILE_PATH: ${CONFIGS_FOLDER}/autoscaler-prod_hh.yml
+
+image: docker:latest
+
+services:
+  - docker:dind
+
+stages:
+  - build
+#  - prepare_config_tests
+#  - test_and_qa
+#  - prepare_config_staging
+#  - deploy_to_staging
+#  - test_staging
+#  - prepare_config_hx
+#  - deploy_to_prod_hx
+#  - test_prod_hx
+#  - prepare_config_hh
+#  - deploy_to_prod_hh
+#  - test_prod_hh
+#  - functional_tests_prod_public
+#
+#
+# ----------------------------------------------------------------------------------------------------------------------
+# build
+# ----------------------------------------------------------------------------------------------------------------------
+build_docker_image:
+  image:
+    name: docker/compose:1.24.1
+    entrypoint: ["/bin/sh", "-c"]
+  except:
+    - schedules
+  stage: build
+  variables:
+    DOCKER_HOST: tcp://docker:2375
+  script:
+    - set -x
+    - docker version # verify docker cli is there. Also prints server info
+    - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
+    - echo building $SERVER_IMAGE_TAG
+    - docker-compose build elasticsearch-proxy-api-prod
+    - echo Deploying $SERVER_IMAGE_TAG
+    - docker push $SERVER_IMAGE_TAG
+#
+### ----------------------------------------------------------------------------------------------------------------------
+### QA
+### ----------------------------------------------------------------------------------------------------------------------
+#pylint:
+#  stage: test_and_qa
+#  image:
+#    name: $SERVER_IMAGE_TAG
+#    entrypoint: [""]
+#  except:
+#    - schedules
+#  script:
+#    - set -x
+#    - find . -iname "*.py" | grep -v './app/free_text_parsing/.*' | xargs pylint
+#
+### ---------------------------------------------------------------------------------------------------------------------
+### Tests
+### ---------------------------------------------------------------------------------------------------------------------
+#prepare_config_tests:
+#  stage: prepare_config_tests
+#  image:
+#    name: alpine/git
+#    entrypoint: ["/bin/sh", "-c"]
+#  except:
+#    - schedules
+#  script:
+#    - set -x
+#    - mkdir -p ${CONFIGS_FOLDER}
+#    - git clone https://${CONFIG_DEPLOY_GITLAB_USERNAME}:${CONFIG_DEPLOY_GITLAB_TOKEN}@${CONFIGURATIONS_REPO} ${CONFIGS_FOLDER}
+#  artifacts:
+#    paths:
+#      - ${CONFIG_UNIT_TESTS_FILE_PATH}
+#
+#unit_tests:
+#  stage: test_and_qa
+#  image:
+#    name: $SERVER_IMAGE_TAG
+#    entrypoint: [""]
+#  except:
+#    - schedules
+#  script:
+#    - set -x
+#    - CONFIG_FILE_PATH=${CONFIG_UNIT_TESTS_FILE_PATH} python -m unittest
+#
+### ----------------------------------------------------------------------------------------------------------------------
+### Deployment to staging
+### ----------------------------------------------------------------------------------------------------------------------
+#prepare_config_staging:
+#  stage: prepare_config_staging
+#  image:
+#    name: alpine/git
+#    entrypoint: ["/bin/sh", "-c"]
+#  only:
+#    - staging
+#  script:
+#    - set -x
+#    - rm -rf ${CONFIGS_FOLDER} || true
+#    - mkdir -p ${CONFIGS_FOLDER}
+#    - git clone https://${CONFIG_DEPLOY_GITLAB_USERNAME}:${CONFIG_DEPLOY_GITLAB_TOKEN}@${CONFIGURATIONS_REPO} ${CONFIGS_FOLDER}
+#  artifacts:
+#    paths:
+#      - ${CONFIG_STAGING_FILE_PATH}
+#      - ${CONFIG_GUNICORN_STAGING_FILE_PATH}
+#      - ${INGRESS_STAGING_FILE_PATH}
+#      - ${AUTOSCALER_STAGING_FILE_PATH}
+#
+#deploy_to_staging:
+#  stage: deploy_to_staging
+#  image:
+#    name: lachlanevenson/k8s-kubectl:latest
+#    entrypoint: ["/bin/sh", "-c"]
+#  only:
+#    - staging
+#  except:
+#    - schedules
+#  environment:
+#    name: staging
+#    url: ${SERVER_URL_STAGING}
+#  script:
+#  - set -x
+#  - echo "$KUBE_CA_PEM_HX" > "$(pwd)/kube.ca.pem"
+#  - kubectl config set-cluster ${KUBE_CLUS_NAME_HX} --server="${KUBE_URL_HX}" --certificate-authority="$(pwd)/kube.ca.pem"
+#  - kubectl config set-credentials ${KUBE_USER_HX} --token="${KUBE_TOKEN_HX}"
+#  - kubectl config set-context ${CHEMBL_NS_STAGING} --cluster=${KUBE_CLUS_NAME_HX} --user=${KUBE_USER_HX}
+#  - kubectl config use-context ${CHEMBL_NS_STAGING}
+#  - echo ${CHEMBL_NS_STAGING} ${KUBE_URL_HX} ${KUBE_CLUS_NAME_HX} ${KUBE_USER_HX}
+#  - kubectl get pods -n ${CHEMBL_NS_STAGING}
+#  - kubectl create secret generic ${RUN_CONFIG_SECRET_NAME_STAGING} --from-file=RUN_CONFIG.yml=${CONFIG_STAGING_FILE_PATH} -o yaml -n ${CHEMBL_NS_STAGING} --dry-run=client | kubectl replace -f -
+#  - kubectl create secret generic ${GUNICORN_CONFIG_SECRET_NAME_STAGING} --from-file=GUNICORN_CONFIG.py=${CONFIG_GUNICORN_STAGING_FILE_PATH} -o yaml -n ${CHEMBL_NS_STAGING} --dry-run=client | kubectl replace -f -
+#  - cat ${CONFIG_STAGING_FILE_PATH}
+#  - cat ${CONFIG_GUNICORN_STAGING_FILE_PATH}
+#  - sed -i "s~<NAMESPACE>~${CHEMBL_NS_STAGING}~" k8s-deployment.yaml
+#  - sed -i "s~<NUM_REPLICAS>~${NUM_REPLICAS_STAGING}~" k8s-deployment.yaml
+#  - sed -i "s~<HTTP_PROXY>~${HTTP_PROXY_HX}~g" k8s-deployment.yaml
+#  - sed -i "s~<HTTPS_PROXY>~${HTTPS_PROXY_HX}~g" k8s-deployment.yaml
+#  - sed -i "s~<NO_PROXY>~${NO_PROXY_HX_DEFAULT}~g" k8s-deployment.yaml
+#  - sed -i "s~<CPU_LIMIT>~${CPU_LIMIT_STAGING}~" k8s-deployment.yaml
+#  - sed -i "s~<CPU_REQUESTED>~${CPU_REQUESTED_STAGING}~" k8s-deployment.yaml
+#  - sed -i "s~<SERVER_IMAGE_TAG>~${SERVER_IMAGE_TAG}~" k8s-deployment.yaml
+#  - sed -i "s~<RUN_CONFIG_SECRET_NAME>~${RUN_CONFIG_SECRET_NAME_STAGING}~" k8s-deployment.yaml
+#  - sed -i "s~<GUNICORN_CONFIG_SECRET_NAME>~${GUNICORN_CONFIG_SECRET_NAME_STAGING}~" k8s-deployment.yaml
+#  - cat k8s-deployment.yaml
+#  - kubectl apply -n ${CHEMBL_NS_STAGING} -f k8s-deployment.yaml
+#  - kubectl get pods -n ${CHEMBL_NS_STAGING}
+#  - cat ${INGRESS_STAGING_FILE_PATH}
+#  - kubectl apply -n ${CHEMBL_NS_STAGING} -f ${INGRESS_STAGING_FILE_PATH}
+#  - kubectl describe ingress -n ${CHEMBL_NS_STAGING}
+#  - cat ${AUTOSCALER_STAGING_FILE_PATH}
+#  - kubectl apply -n ${CHEMBL_NS_STAGING} -f ${AUTOSCALER_STAGING_FILE_PATH}
+##
+### ----------------------------------------------------------------------------------------------------------------------
+### Test staging
+### ----------------------------------------------------------------------------------------------------------------------
+#functional_tests:
+#  stage: test_staging
+#  image:
+#    name: $SERVER_IMAGE_TAG
+#    entrypoint: [""]
+#  only:
+#    - staging
+#  except:
+#    - schedules
+#  environment:
+#    name: staging
+#    url: ${SERVER_URL_STAGING}
+#  script:
+#  - set -x
+#  - functional_tests/run_functional_tests.py ${SERVER_URL_STAGING} https://wwwdev.ebi.ac.uk/chembl/interface_api/delayed_jobs
+#
+### ----------------------------------------------------------------------------------------------------------------------
+### Deployment to prod hx
+### ----------------------------------------------------------------------------------------------------------------------
+#prepare_config_prod_hx:
+#  stage: prepare_config_hx
+#  image:
+#    name: alpine/git
+#    entrypoint: ["/bin/sh", "-c"]
+#  only:
+#    - master
+#  except:
+#    - schedules
+#  script:
+#    - rm -rf ${CONFIGS_FOLDER} || true
+#    - mkdir -p ${CONFIGS_FOLDER}
+#    - git clone https://${CONFIG_DEPLOY_GITLAB_USERNAME}:${CONFIG_DEPLOY_GITLAB_TOKEN}@${CONFIGURATIONS_REPO} ${CONFIGS_FOLDER}
+#  artifacts:
+#    paths:
+#      - ${CONFIG_PROD_HX_FILE_PATH}
+#      - ${CONFIG_GUNICORN_PROD_HX_FILE_PATH}
+#      - ${INGRESS_PROD_HX_FILE_PATH}
+#      - ${AUTOSCALER_PROD_HX_FILE_PATH}
+#
+#deploy_to_prod_hx:
+#  stage: deploy_to_prod_hx
+#  image:
+#    name: lachlanevenson/k8s-kubectl:latest
+#    entrypoint: ["/bin/sh", "-c"]
+#  only:
+#    - master
+#  except:
+#    - schedules
+#  environment:
+#    name: prod_hx
+#  script:
+#    - set -x
+#    - echo "$KUBE_CA_PEM_HX" > "$(pwd)/kube.ca.pem"
+#    - kubectl config set-cluster ${KUBE_CLUS_NAME_HX} --server="${KUBE_URL_HX}" --certificate-authority="$(pwd)/kube.ca.pem"
+#    - kubectl config set-credentials ${KUBE_USER_HX} --token="${KUBE_TOKEN_HX}"
+#    - kubectl config set-context ${CHEMBL_NS_PROD} --cluster=${KUBE_CLUS_NAME_HX} --user=${KUBE_USER_HX}
+#    - kubectl config use-context ${CHEMBL_NS_PROD}
+#    - echo ${CHEMBL_NS_PROD} ${KUBE_URL_HX} ${KUBE_CLUS_NAME_HX} ${KUBE_USER_HX}
+#    - kubectl get pods -n ${CHEMBL_NS_PROD}
+#    - kubectl create secret generic ${RUN_CONFIG_SECRET_NAME_PROD_HX} --from-file=RUN_CONFIG.yml=${CONFIG_PROD_HX_FILE_PATH} -o yaml -n ${CHEMBL_NS_PROD} --dry-run=client | kubectl replace -f -
+#    - kubectl create secret generic ${GUNICORN_CONFIG_SECRET_NAME_PROD_HX} --from-file=GUNICORN_CONFIG.py=${CONFIG_GUNICORN_PROD_HX_FILE_PATH} -o yaml -n ${CHEMBL_NS_PROD} --dry-run=client | kubectl replace -f -
+#    - cat ${CONFIG_PROD_HX_FILE_PATH}
+#    - cat ${CONFIG_GUNICORN_PROD_HX_FILE_PATH}
+#    - sed -i "s~<NAMESPACE>~${CHEMBL_NS_PROD}~" k8s-deployment.yaml
+#    - sed -i "s~<NUM_REPLICAS>~${NUM_REPLICAS_PROD_HX}~" k8s-deployment.yaml
+#    - sed -i "s~<HTTP_PROXY>~${HTTP_PROXY_HX}~g" k8s-deployment.yaml
+#    - sed -i "s~<HTTPS_PROXY>~${HTTPS_PROXY_HX}~g" k8s-deployment.yaml
+#    - sed -i "s~<NO_PROXY>~${NO_PROXY_HX_DEFAULT}~g" k8s-deployment.yaml
+#    - sed -i "s~<CPU_LIMIT>~${CPU_LIMIT_PROD_HX}~" k8s-deployment.yaml
+#    - sed -i "s~<CPU_REQUESTED>~${CPU_REQUESTED_PROD_HX}~" k8s-deployment.yaml
+#    - sed -i "s~<SERVER_IMAGE_TAG>~${SERVER_IMAGE_TAG}~" k8s-deployment.yaml
+#    - sed -i "s~<RUN_CONFIG_SECRET_NAME>~${RUN_CONFIG_SECRET_NAME_PROD_HX}~" k8s-deployment.yaml
+#    - sed -i "s~<GUNICORN_CONFIG_SECRET_NAME>~${GUNICORN_CONFIG_SECRET_NAME_PROD_HX}~" k8s-deployment.yaml
+#    - cat k8s-deployment.yaml
+#    - kubectl apply -n ${CHEMBL_NS_PROD} -f k8s-deployment.yaml
+#    - kubectl get pods -n ${CHEMBL_NS_PROD}
+#    - cat ${INGRESS_PROD_HX_FILE_PATH}
+#    - kubectl apply -n ${CHEMBL_NS_PROD} -f ${INGRESS_PROD_HX_FILE_PATH}
+#    - kubectl describe ingress -n ${CHEMBL_NS_PROD}
+#    - cat ${AUTOSCALER_PROD_HX_FILE_PATH}
+#    - kubectl apply -n ${CHEMBL_NS_PROD} -f ${AUTOSCALER_PROD_HX_FILE_PATH}
+#
+#functional_tests_prod_hx:
+#  stage: test_prod_hx
+#  image:
+#    name: $SERVER_IMAGE_TAG
+#    entrypoint: [""]
+#  only:
+#    - master
+#  except:
+#    - schedules
+#  script:
+#  - set -x
+#  - sleep 30 # Give some time for the deployment to take effect.
+#  - functional_tests/run_functional_tests.py ${SERVER_URL_PROD_HX} https://wwwdev.ebi.ac.uk/chembl/interface_api/delayed_jobs
+#
+### ----------------------------------------------------------------------------------------------------------------------
+### Deployment to prod hh
+### ----------------------------------------------------------------------------------------------------------------------
+#prepare_config_prod_hh:
+#  stage: prepare_config_hh
+#  image:
+#    name: alpine/git
+#    entrypoint: ["/bin/sh", "-c"]
+#  only:
+#    - master
+#  except:
+#    - schedules
+#  script:
+#    - rm -rf ${CONFIGS_FOLDER} || true
+#    - mkdir -p ${CONFIGS_FOLDER}
+#    - git clone https://${CONFIG_DEPLOY_GITLAB_USERNAME}:${CONFIG_DEPLOY_GITLAB_TOKEN}@${CONFIGURATIONS_REPO} ${CONFIGS_FOLDER}
+#    - ls ${CONFIGS_FOLDER}
+#  artifacts:
+#    paths:
+#      - ${CONFIG_PROD_HH_FILE_PATH}
+#      - ${CONFIG_GUNICORN_PROD_HH_FILE_PATH}
+#      - ${INGRESS_PROD_HH_FILE_PATH}
+#      - ${AUTOSCALER_PROD_HH_FILE_PATH}
+#
+#deploy_to_prod_hh:
+#  stage: deploy_to_prod_hh
+#  image:
+#    name: lachlanevenson/k8s-kubectl:latest
+#    entrypoint: ["/bin/sh", "-c"]
+#  only:
+#    - master
+#  except:
+#    - schedules
+#  environment:
+#    name: prod_hh
+#  script:
+#    - set -x
+#    - echo "$KUBE_CA_PEM_HH" > "$(pwd)/kube.ca.pem"
+#    - kubectl config set-cluster ${KUBE_CLUS_NAME_HH} --server="${KUBE_URL_HH}" --certificate-authority="$(pwd)/kube.ca.pem"
+#    - kubectl config set-credentials ${KUBE_USER_HH} --token="${KUBE_TOKEN_HH}"
+#    - kubectl config set-context ${CHEMBL_NS_PROD} --cluster=${KUBE_CLUS_NAME_HH} --user=${KUBE_USER_HH}
+#    - kubectl config use-context ${CHEMBL_NS_PROD}
+#    - echo ${CHEMBL_NS_PROD} ${KUBE_URL_HH} ${KUBE_CLUS_NAME_HH} ${KUBE_USER_HH}
+#    - kubectl get pods -n ${CHEMBL_NS_PROD}
+#    - kubectl create secret generic ${RUN_CONFIG_SECRET_NAME_PROD_HH} --from-file=RUN_CONFIG.yml=${CONFIG_PROD_HH_FILE_PATH} -o yaml -n ${CHEMBL_NS_PROD} --dry-run=client | kubectl replace -f -
+#    - kubectl create secret generic ${GUNICORN_CONFIG_SECRET_NAME_PROD_HH} --from-file=GUNICORN_CONFIG.py=${CONFIG_GUNICORN_PROD_HH_FILE_PATH} -o yaml -n ${CHEMBL_NS_PROD} --dry-run=client | kubectl replace -f -
+#    - cat ${CONFIG_PROD_HH_FILE_PATH}
+#    - cat ${CONFIG_GUNICORN_PROD_HH_FILE_PATH}
+#    - sed -i "s~<NAMESPACE>~${CHEMBL_NS_PROD}~" k8s-deployment.yaml
+#    - sed -i "s~<NUM_REPLICAS>~${NUM_REPLICAS_PROD_HH}~" k8s-deployment.yaml
+#    - sed -i "s~<SERVER_IMAGE_TAG>~${SERVER_IMAGE_TAG}~" k8s-deployment.yaml
+#    - sed -i "s~<HTTP_PROXY>~${HTTP_PROXY_HH}~g" k8s-deployment.yaml
+#    - sed -i "s~<HTTPS_PROXY>~${HTTPS_PROXY_HH}~g" k8s-deployment.yaml
+#    - sed -i "s~<NO_PROXY>~${NO_PROXY_HH_DEFAULT}~g" k8s-deployment.yaml
+#    - sed -i "s~<CPU_LIMIT>~${CPU_LIMIT_PROD_HH}~" k8s-deployment.yaml
+#    - sed -i "s~<CPU_REQUESTED>~${CPU_REQUESTED_PROD_HH}~" k8s-deployment.yaml
+#    - sed -i "s~<RUN_CONFIG_SECRET_NAME>~${RUN_CONFIG_SECRET_NAME_PROD_HH}~" k8s-deployment.yaml
+#    - sed -i "s~<GUNICORN_CONFIG_SECRET_NAME>~${GUNICORN_CONFIG_SECRET_NAME_PROD_HH}~" k8s-deployment.yaml
+#    - cat k8s-deployment.yaml
+#    - kubectl apply -n ${CHEMBL_NS_PROD} -f k8s-deployment.yaml
+#    - kubectl get pods -n ${CHEMBL_NS_PROD}
+#    - cat ${INGRESS_PROD_HH_FILE_PATH}
+#    - kubectl apply -n ${CHEMBL_NS_PROD} -f ${INGRESS_PROD_HH_FILE_PATH}
+#    - kubectl describe ingress -n ${CHEMBL_NS_PROD}
+#    - cat ${AUTOSCALER_PROD_HH_FILE_PATH}
+#    - kubectl apply -n ${CHEMBL_NS_PROD} -f ${AUTOSCALER_PROD_HH_FILE_PATH}
+#
+#functional_tests_prod_hh:
+#  stage: test_prod_hh
+#  image:
+#    name: $SERVER_IMAGE_TAG
+#    entrypoint: [""]
+#  only:
+#    - master
+#  except:
+#    - schedules
+#  script:
+#  - set -x
+#  - sleep 30 # Give some time for the deployment to take effect.
+#  - functional_tests/run_functional_tests.py ${SERVER_URL_PROD_HH} https://www.ebi.ac.uk/chembl/interface_api/delayed_jobs
+#
+## ----------------------------------------------------------------------------------------------------------------------
+## Test prod public url
+## ----------------------------------------------------------------------------------------------------------------------
+#functional_tests_prod_public:
+#  stage: functional_tests_prod_public
+#  image:
+#    name: $SERVER_IMAGE_TAG
+#    entrypoint: [""]
+#  only:
+#  - master
+#  script:
+#  - set -x
+#  - sleep 30 # Give some time for the deployment to take effect.
+#  - functional_tests/run_functional_tests.py ${SERVER_URL_PROD_PUBLIC} https://www.ebi.ac.uk/chembl/interface_api/delayed_jobs

Dockerfile

+# ==================================== BASE ====================================
+ARG INSTALL_PYTHON_VERSION=${INSTALL_PYTHON_VERSION:-3.8}
+FROM python:${INSTALL_PYTHON_VERSION}-slim-buster AS base
+ENV CONFIG_FILE_PATH=${CONFIG_FILE_PATH:-'/etc/run_config/RUN_CONFIG.yml'}
+ENV GUNICORN_CONFIG_FILE_PATH=${GUNICORN_CONFIG_FILE_PATH:-'/etc/gunicorn_config/GUNICORN_CONFIG.py'}
+
+RUN apt-get update
+RUN apt-get install -y \
+    curl \
+    netcat \
+    iputils-ping \
+    ssh
+
+WORKDIR /app
+COPY requirements.txt .
+
+RUN useradd -m glados -u 4321
+RUN chown -R glados:glados /app
+USER glados
+ENV PATH="/home/glados/.local/bin:${PATH}"
+
+RUN pip install --user -r requirements.txt
+COPY . .
+
+FROM base AS development-server
+ENTRYPOINT FLASK_APP=app flask run --host=0.0.0.0
+
+FROM base AS production-server
+ENTRYPOINT gunicorn wsgi:FLASK_APP -c ${GUNICORN_CONFIG_FILE_PATH}

docker-compose.yml

+version: '3.8'
+
+x-build-args: &build_args
+  INSTALL_PYTHON_VERSION: 3.8
+
+services:
+  es-subset-generator-dev:
+    build:
+      context: .
+      target: development-server
+      args:
+        <<: *build_args
+    image: chembl/es-subset-generator:dev
+    environment:
+      - CONFIG_FILE_PATH=/app/config.yml
+    ports:
+      - "5000:5000"
+  es-subset-generator-prod:
+    build:
+      context: .
+      target: production-server
+      args:
+        <<: *build_args
+    image: "${SERVER_IMAGE_TAG:-chembl/es-subset-generator:prod}"
+    ports:
+      - "5000:5000"
\ No newline at end of file

requirements.txt

+Flask==1.1.1
+pylint==2.4.2
+flask-sqlalchemy==2.4.1
+pyyaml==5.1.2
+elasticsearch>=7.0.0,<8.0.0 # Recommended by the official documentation
+gunicorn==20.0.4
+marshmallow==3.5.0