config.yml

# This is a CircleCI configuration that you can add to your Github repository,
# and connect to CircleCI to generate your bioschema files! If you don't
# define any custom variables, your files will be generated and available
# as artifacts. If you define the GITHUB variables for a bot, we can put
# them back to Github Pages for more programmatic use (and version control
# archive)

# Variables you can customize
# OPENBASES_CONTAINER: is the container that will be used, see default section

# The following variables are optional and will give you
# additional deployments / functionality.

# GITHUB_USER
# GITHUB_EMAIL if defined, you can deploy your archive and site back to Github pages.
# REPO_VERSION: derived from the sha, for naming the archive

################################################################################
# Functions
################################################################################

# Defaults
defaults: &defaults
  docker:
    - image: docker:18.01.0-ce-git
  working_directory: /tmp/src

# Installation
install: &install
    name: Install parallel gzip, gettext, python3, openbases, and jq
    command: |
        apk add --no-cache pigz python3 gettext jq

# Environment
sourceenv: &sourceenv
    name: Source environment variables from the BASH_ENV
    command: source $BASH_ENV 

schemaenv: &schemaenv
    name: Define container and open bases names
    command: |
        # If not set, define OPENBASES_CONTAINER
        if [ ! -n "${OPENBASES_CONTAINER:-}" ]; then
            OPENBASES_CONTAINER="openschemas/schema-builder"
        fi
        # If not set, define REPO_VERSION
        if [ ! -n "${REPO_VERSION:-}" ]; then
            REPO_VERSION=$(echo "${CIRCLE_SHA1}" | cut -c1-10)
        fi
        echo "Open Bases OpenSchema builder is ${OPENBASES_CONTAINER}"
        # export to bash environment
        echo "export OPENBASES_CONTAINER=${OPENBASES_CONTAINER}" >> ${BASH_ENV}
        echo "export REPO_VERSION=${REPO_VERSION}" >> ${BASH_ENV}
        cat ${BASH_ENV}

githubsetup: &githubsetup
    name: Prepare Github account credentials
    command: |
        # Only proceed if we minimally have a Github email
        if [[ -n "${GITHUB_EMAIL:-}" ]];
            then
                echo "Preparing Github account credentials"
                git config --global user.email $GITHUB_EMAIL
                # If username is defined, use it (otherwuse use circle project)
                if [[ -n "${GITHUB_USER:-}" ]];
                    then
                    git config --global user.name $GITHUB_USER
                else
                    git config --global user.name $CIRCLE_PROJECT_USERNAME
                fi
        fi


schema: &schema
    name: use openschema/schema-builder docker container to generate specifications
    command: |
        source ${BASH_ENV}
        cd /tmp/src
        echo "0. Pulling latest OpenBases Schema Builder!"
        echo "docker pull ${OPENBASES_CONTAINER}"
        docker pull ${OPENBASES_CONTAINER}
        echo "docker run --name schema  --entrypoint bash -dt ${OPENBASES_CONTAINER}"
        docker run --name schema  --entrypoint bash -dt "${OPENBASES_CONTAINER}"
        docker exec schema rm -rf /data/*
        docker exec schema mkdir --p /data/specifications
        echo "2. Copying specification files for Open Bases schema..."
        echo "docker cp ./specifications/. schema:/data/specifications"
        docker cp ./specifications/. schema:/data/specifications
        echo "docker cp ./specifications/configuration.yml schema:/data/configuration.yml"
        docker cp ./specifications/configuration.yml schema:/data/configuration.yml
        echo "3. Generating specification files!"
        echo "Files in /data"
        docker exec schema ls /data
        echo "docker exec schema map2model --config /data/configuration.yml --folder /data/specifications --output /data/output"
        docker exec schema map2model --config /data/configuration.yml --folder /data/specifications --output /data/output
        echo "4. Obtaining finished files"
        mkdir -p /tmp/specifications
        echo "docker cp schema:/data/output/. /tmp/specifications"
        docker cp schema:/data/output/. /tmp/specifications/
        echo "5. Creating archive."
        echo "tar czf specs.tar.gz /tmp/specifications"
        tar czf "specs-${REPO_VERSION}.tar.gz" /tmp/specifications
        mv "specs-${REPO_VERSION}.tar.gz" /tmp/specifications
        echo "6. Stopping schema container..."
        docker stop schema
        echo "Contents of /tmp"
        ls /tmp
        echo "Contents of /tmp/specifications"
        ls /tmp/specifications

################################################################################
# Jobs
################################################################################


version: 2
jobs:
  setup:
    <<: *defaults
    steps:
      - run: *schemaenv
      - run: *install
      - run: *githubsetup

  build:
    <<: *defaults
    steps:
      - run: *install
      - setup_remote_docker
      - checkout
      - run: *schemaenv
      - run: *schema
      - store_artifacts:
          path: /tmp/specifications
          destination: specs
      - persist_to_workspace:
          root: /tmp
          paths:
            - src
            - specifications

  manifest:
    <<: *defaults
    steps:
      - attach_workspace:
          at: /tmp
      - run: *schemaenv
      - run: *githubsetup
      - run: *install
      - run:
          name: Generate Archive of Specs, and Deploy to gh-pages
          no_output_timeout: 40m
          command: |
            source ${BASH_ENV}
            ls /tmp
            ls /tmp/specifications
            mkdir -p ${HOME}/.ssh
            if [[ -n "${GITHUB_EMAIL:-}" ]];
                then
                    echo "=== Deploying site to Github Pages ==="
                    echo "1. Checking out Github pages branch"
                    ssh-keyscan -H github.com >> ~/.ssh/known_hosts
                    git clone "git@github.com:${CIRCLE_PROJECT_USERNAME}/${CIRCLE_PROJECT_REPONAME}.git" out
                    cd out
                    # either checkout github pages, or create orphan
                    git checkout gh-pages || git checkout --orphan gh-pages
                    mkdir -p ../out-old/archive
                    mkdir -p archive
                    mkdir -p _specifications
                    cp -R _specifications ../out-old/
                    # Keep archive contents
                    for ext in tar.gz html
                        do
                        if /bin/bash -c "ls archive/*.${ext}" 1> /dev/null 2>&1; then
                                /bin/bash -c "cp archive/*.${ext} ../out-old/archive" 
                        fi
                        if /bin/bash -c "ls _specifications/*.${ext}" 1> /dev/null 2>&1; then
                                /bin/bash -c "cp _specifications/*.${ext} ../out-old/_specifications/" 
                        fi
                    done                    
                    git rm -rf .
                    # ensure that github pages are ignored
                    mkdir -p .circleci && cp -a ../.circleci/. .circleci/.
                    # Copy back previous files to archive
                    mv ../out-old/archive ${PWD}
                    mv ../out-old/_specifications ${PWD}
                    mkdir -p _yaml
                    echo "2. Preparing template..."
                    # Add latest to archive
                    mv /tmp/specifications/specs-${REPO_VERSION}.tar.gz archive/
                    cp archive/specs-${REPO_VERSION}.tar.gz archive/specs-latest.tar.gz
                    # Add build folders
                    for folder in `ls /tmp/specifications`
                        do
                            if [[ -f "_specifications/${folder}.html" ]];
                                then
                                    rm _specifications/${folder}.html
                                    rm -rf "_specifications/${folder}"
                            fi
                            echo "Moving /tmp/specifications/${folder} to _specifications"
                            mv "/tmp/specifications/${folder}/${folder}.html" "_specifications/"
                            mv "/tmp/specifications/${folder}/${folder}.yml" _yaml/
                    done
                    # Copy jekyll templates to static
                    cp -R /tmp/src/.circleci/_includes _includes
                    cp -R /tmp/src/.circleci/_layouts _layouts
                    cp /tmp/src/.circleci/_config.yml _config.yml
                    cp /tmp/src/.circleci/specifications.md specifications.md
                    git add -A;
                    git commit -m "Automated deployment to GitHub Pages ${CIRCLE_SHA1}" --allow-empty
                    git push origin gh-pages
            else
                echo "GITHUB_EMAIL not set, skipping manifest deploy to Github pages"
            fi


################################################################################
# Workflows
################################################################################


workflows:
  version: 2
  build_deploy:
    jobs:
      - build:
          filters:
            branches:
              ignore: gh-pages
            tags:
              only: /.*/

      # Push the manifest back to Github pages
      - manifest:
          requires:
            - build
          filters:
            branches:
              only: master
            tags:
              only: /.*/