CI/CD

Workflows can also be set up and run on an automation server to enable continuous integration/continuous delivery (CI/CD).

This page will guide you through the process of setting up an CI/CD automation server (Jenkins) and hosting your example workflow there.

1. Install the Jenkins-server Docker image

   In this tutorial, we will use the jenkin-server Docker image to set up our Jenkins server. The complete installation guild of the Jenkins-server image can be found in here

2. Setting up your workflow in Jenkins

   See this section in the Jenkins-server documentation to create a Jenkins pipeline for your workflow. The Setting up CI/CD pipeline sub-section is where you should provide your own Jenkins pipeline script for setting up your workflow. Below is an example of the pipeline script you can refer to.

     pipeline {
       agent any
   
       environment {
           REMOTE_URL = 'git@github.com:LIN810116/workflow-manager.git'
           CREDENTIAL_ID = 'workflow-manager-clin864'
           BRANCH = 'main'
           USER_NAME = 'lin810116'
           USER_EMAIL = 'lin810116@gmail.com'
           TEST_MODULE = 'tests/'
           SOURCE_DIR = './docs/source'
           BUILD_DIR = './docs/build'
           PYENV_VERSION = '3.6.15'
           PYTHONPATH='/var/jenkins_home/workspace/workflow-manager'
           WORKSPACE = "workspace"
       }
   
       stages {
           stage('Environment Setup') {
               steps{
                   sh 'printenv'
   
                   echo "Cloning GitHub repository..."
                   git branch: "${BRANCH}", credentialsId: "${CREDENTIAL_ID}", url: "${REMOTE_URL}"
                   echo "Creating virtual environment"
                   sh '''
                       python --version
                       python -m venv venv
                   '''
   
                   // set up mongodb
                   sh'''
                       wget -qO - https://www.mongodb.org/static/pgp/server-4.4.asc | apt-key add -
                       echo "deb http://repo.mongodb.org/apt/debian buster/mongodb-org/4.4 main" | tee /etc/apt/sources.list.d/mongodb-org-4.4.list
                       apt-get update
                       apt-get install -y mongodb-org
                   '''
                   withEnv(['JENKINS_NODE_COOKIE =dontkill']) {
                       // Run in background
                       sh '''
                           nohup mongod --port 27017 --dbpath /var/jenkins_home/workspace/workflow-manager/data/db --bind_ip 'localhost' &
                       '''
                   }
   
                   echo "Installing dependencies..."
                   sh '''
                       . venv/bin/activate
                       pip install --upgrade pip
                       pip install -r requirements.txt
                   '''
   
                   echo "Creating worspace"
                   sh '''
                   mkdir -p ${WORKSPACE}
                   '''
   
               }
           }
   
           stage ('Import Scans'){
               steps {
                   sh '''
                       . venv/bin/activate
                       python examples/scripts/pretend_import.py --workflow False --source examples/data/pretend_data.txt --dest ${WORKSPACE}
                   '''
               }
           }
   
           stage ('Segment'){
               steps {
                   sh '''
                       . venv/bin/activate
                       python examples/scripts/pretend_segment.py --workflow False --source ${WORKSPACE}/pretend_data.txt --dest ${WORKSPACE}/pointcloud.txt
                   '''
               }
           }
   
           stage ('Fit mesh'){
               steps {
                   sh '''
                       . venv/bin/activate
                       python examples/scripts/pretend_fit.py --workflow False --source ${WORKSPACE}/pointcloud.txt --dest ${WORKSPACE}/mesh.txt
                   '''
               }
           }
   
           stage ('Mechanics'){
               steps {
                   sh '''
                       . venv/bin/activate
                       python examples/scripts/pretend_mechanics1.py --workflow False --source ${WORKSPACE}/mesh.txt --dest ${WORKSPACE}/solution1.txt
                   '''
               }
           }
   
           stage ('Send results'){
               steps {
                   sh '''
                       . venv/bin/activate
                       mkdir -p results
                       python examples/scripts/pretend_send.py --workflow False --source ${WORKSPACE} --dest results
   
                   '''
               }
           }
   
           // stage ('Test'){
           //     steps {
           //         echo "Running tests"
           //         // sh '''
           //         //     . venv/bin/activate
           //         //     pytest ./tests/test_example_workflow.py
           //         //     pytest ./tests/test_functionalities.py
           //         // '''
           //         // sh '''
           //         //     . venv/bin/activate
           //         //     pytest --junit-xml=report.xml -o junit_family=xunit2 ./tests/test_example_workflow.py
           //         // '''
           //         sh '''
           //             . venv/bin/activate
           //             pytest --junit-xml=report.xml -o junit_family=xunit2 ${TEST_MODULE}
           //         '''
           //     }
           // }
   
   
   
           // stage('Build docs') {
           //     steps {
           //         echo "Building"
           //         echo "${WORKSPACE}"
           //         sh "${WORKSPACE}/venv/bin/sphinx-build -b html ${SOURCE_DIR} ${BUILD_DIR}"
           //     }
           // }
   
   
           // stage("Deploy Docs") {
           //     steps {
           //         echo "Deploying to GitHub pages"
           //         sh '''
           //             git config --global user.email ${USER_EMAIL}
           //             git config --global user.name ${USER_NAME}
           //         '''
   
           //         sh 'npm install -g --silent gh-pages@2.1.1'
           //         sh 'touch ${BUILD_DIR}/.nojekyll'
           //         sshagent(credentials: ["${CREDENTIAL_ID}"]) {
           //             sh '''
           //                 gh-pages --dotfiles --message '[skip ci] Updates' --dist ${BUILD_DIR}
           //             '''
           //         }
           //     }
           // }
   
       }
   
       // post {
       //     always {
       //         junit 'report.xml'
       //     }
       // }
   }