Jenkinsfile-download

pipeline {
    agent none
    triggers {
        cron('H H * * 7')  //sometime on Sundays
    }
    environment {
        HOME = "${env.WORKSPACE}"
    }
    stages {
        stage('setup') {
            agent { dockerfile true }
            steps {
                // This step could (and maybe should) do a poetry install like the ingest Jenkinsfile
                // and then run downloader from within a poetry run command
                sh '''
                    python3 -mvenv venv
                    . venv/bin/activate
                    pip install click==8.0.4
                    pip install kghub-downloader
                '''
            }
        }
        stage('download') {
            agent { dockerfile true }
            steps {
                sh '''
                    . venv/bin/activate
                    downloader
                '''
            }
        }
        stage('post-process') {
            agent { dockerfile true }
            steps {
                sh '''
                    zcat data/alliance/BGI_*.gz | jq '.data[].basicGeneticEntity.primaryId' | gzip > data/alliance/alliance_gene_ids.txt.gz
                '''
            }
        }
        stage('upload') {
            agent { label 'worker' }
            steps {
                sh '''
                    gsutil -m cp -r data gs://monarch-ingest/data-cache
                '''
            }
        }
    }
}