1001genomes · dependabot · Feb 19, 2020 · Feb 20, 2020
diff --git a/.dockerignore b/.dockerignore
@@ -1,3 +1,13 @@
 aragwas_ui/node_modules
 .git
 aragwas_server/static/*
+aragwas_server/GENOTYPE_DATA
+*.egg-info
+*.egg/
+*.pyc
+*.swp
+
+.tox
+.coverage
+html/*
+__pycache__
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,44 @@
+FROM python:3 as django
+RUN useradd --uid=10372 -ms /bin/bash aragwas && mkdir -p /srv/web &&  mkdir -p /srv/static && chown aragwas:aragwas /srv/static && chown aragwas:aragwas /srv/web
+COPY aragwas_server/requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt && pip install gunicorn
+# copy webservice code
+COPY --chown=aragwas:aragwas aragwas_server /srv/web
+WORKDIR /srv/web
+COPY --chown=aragwas:aragwas entrypoint.sh write_version.sh wait-for-it.sh ./
+
+RUN chmod 755 entrypoint.sh wait-for-it.sh write_version.sh
+
+ARG GIT_BRANCH
+ENV GIT_BRANCH $GIT_BRANCH
+
+ARG GIT_COMMIT
+ENV GIT_COMMIT $GIT_COMMIT
+
+ARG BUILD_NUMBER
+ENV BUILD_NUMBER $BUILD_NUMBER
+
+ARG BUILD_URL
+ENV BUILD_URL $BUILD_URL
+
+RUN /srv/web/write_version.sh /srv/web/gwasdb/__init__.py
+
+USER aragwas
+
+
+FROM django as aragwas-worker
+ENTRYPOINT ["/srv/web/entrypoint.sh", "aragwas-worker"]
+
+FROM node:11-alpine AS builder
+WORKDIR /app
+COPY aragwas_ui/package.json aragwas_ui/package-lock.json /app/
+RUN npm install
+COPY aragwas_ui /app
+RUN npm run build
+
+
+FROM django as aragwas-backend
+COPY --chown=aragwas:aragwas --from=builder /app/dist/static /srv/web/gwasdb/static
+COPY --chown=aragwas:aragwas --from=builder /app/dist/index.html /srv/web/gwasdb/templates/index.html
+ENTRYPOINT ["/srv/web/entrypoint.sh", "aragwas-backend"]
+
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -1,141 +1,19 @@
-#!/usr/bin/env groovy
-
-
-/**
-* build / test pipeline for AraGWAS
-*/
-
-pipeline {
-
-    agent any
-    stages {
-
-        // global checkout needed for Docker setup
-        stage('checkout') {
-            steps {
-                checkout scm
-            }
-        }
-
-        // prepare the dockers: testing env
-        stage('test') {
-            steps {
-                script {
-
-                    // build ui docker image to compile javascript
-                    def ui_img = docker.build("aragwas_ui","aragwas_ui")
-                    ui_img.inside('-u root') {
-                        sh """
-                        cd aragwas_ui
-                        ln -s /srv/aragwas_ui/node_modules/ || true
-                        npm run build
-                        rm node_modules
-                        """
-                    }
-                    //ui_img.run('-a -v $WORKSPACE/dist:/srv/aragwas_server/gwasdb')
-                    //sh 'cp -r dist/* $WORKSPACE/aragwas_server/gwasdb/'
-                    //FIXME this in try-catch and clean shutdown of db_cont
-                    def app_img = docker.build("aragwas","aragwas_server")
-
-                    // link app container to db container, expose platinum test config path
-                    app_img.inside() {
-                        // run the behave tests
-                        echo "running tests"
-                        sh returnStatus: true, script: "cd /srv/web/ && py.test -ra -p no:cacheprovider --junitxml ${env.WORKSPACE}/TESTS-aragwas.xml"
-                    }
-                     // collect unit test results
-                    junit "TESTS-aragwas.xml"
-                }
-            }
-        }
-
-        // not _really_ deploy, but push to local registry
-        stage('deploy') {
-            when{
-                branch 'master'
-            }
-            steps {
-                script {
-                    sh 'sh write_version.sh'
-                    //FIXME leaking local infra details
-                    docker.withRegistry('https://docker.artifactory.imp.ac.at', 'jenkins_artifactory_creds') {
-
-                        // push DB docker img to registry
-                        def server_img = docker.build("docker.artifactory.imp.ac.at/the1001genomes/aragwas", "aragwas_server")
-
-                        server_img.push('latest')
-                        sshagent(['1001genome_deploy_ssh_key']) {
-                            env.DEPLOY_HOST = 'aragwas.sci.gmi.oeaw.ac.at'
-                            sh '''
-                                scp -o StrictHostKeyChecking=no aragwas_server/docker-compose.yml root@$DEPLOY_HOST:/root/
-                                ssh -o StrictHostKeyChecking=no root@$DEPLOY_HOST "cd /root && docker-compose pull && docker-compose up -d"
-                            '''
-                        }
-                    }
-                }
-            }
-        }
-    // in the future: conditional deploy?
-    } //stages
-
-    // post block is executed after all the stages/steps in the pipeline
-    post {
-        // always {
-        //     // notify build results, see https://jenkins.io/blog/2016/07/18/pipline-notifications/
-        //     // notifyBuild(currentBuild.result)
-
-        // }
-        changed {
-            echo "build changed"
-        }
-        aborted {
-            echo "build aborted"
-        }
-        failure {
-            echo "build failed"
-        }
-        success {
-            echo "build is success"
-        }
-        unstable {
-            echo "build is unstable"
-        }
-    }
-}
-
-// send global slack notification, but fail silently if this is not possible, i.e. slack integration is not installed
-def notifyBuild(String buildStatus) {
-  // build status of null means successful
-  buildStatus = buildStatus ?: 'SUCCESS'
-
-  if (buildStatus == 'STARTED' || buildStatus == 'CHANGED' || buildStatus == 'UNSTABLE') {
-    color = 'YELLOW'
-    colorCode = '#DDDD00'
-  }
-  else if (buildStatus == 'SUCCESS') {
-    color = 'GREEN'
-    colorCode = '#00DD00'
-  }
-  else {
-    // FAILURE or UNSTABLE
-    color = 'RED'
-    colorCode = '#DD0000'
-  }
-
-  def message = "${buildStatus}: Job <${env.BUILD_URL}|${env.JOB_NAME} #${env.BUILD_NUMBER}>"
-
-  /* we could add blame to the slack message ;) but it's visible on the build details anyway
-  if (buildStatus == 'FAILURE') {
-      def changes_by = sh 'git --no-pager log -1 --format=%an'
-      message = "${buildStatus}: Job <${env.BUILD_URL}|${env.JOB_NAME} #${env.BUILD_NUMBER}> caused by ${changes_by}"
-  }
-  */
-
-  // send gracefully
-  try {
-      slackSend (color: colorCode, message: "${message}")
-  }
-  catch (e) {
-     echo "failed to send notification: ${e}"
-  }
-}
+def jobsMapping = [
+  tags: [jobName:"App AraGWAS", jobTags: "reload", extraVars: "app_generic_image_tag: latest"],
+  master: [jobName:"App AraGWAS", jobTags: "reload", extraVars: "app_generic_image_tag: master"]
+]
+
+def extraImages =
+[
+    [imageName: "aragwas-backend", dockerFile: "Dockerfile", dockerContext: ".", extraBuildArgs: '--target aragwas-backend'],
+    [imageName: "aragwas-worker", dockerFile: "Dockerfile", dockerContext: ".", extraBuildArgs: '--target aragwas-worker']
+]
+
+buildDockerImage([
+    imageName: "aragwas-backend",
+    pushRegistryNamespace: "the1001genomes",
+    pushBranches: ['develop', 'master'],
+    test: testScript('py.test -ra -p no:cacheprovider /srv/web --junitxml junit.xml', '**/junit.xml'),
+    containerImages: extraImages
+    //tower: jobsMapping
+])
diff --git a/aragwas_server/Dockerfile b/aragwas_server/Dockerfile
diff --git a/aragwas_server/aragwas/settings/defaults.py b/aragwas_server/aragwas/settings/defaults.py
@@ -23,7 +23,7 @@
 # See https://docs.djangoproject.com/en/dev/howto/deployment/checklist/
 
 # SECURITY WARNING: keep the secret key used in production secret!
-SECRET_KEY = '!x&y+0o%^+*hc5phfjh2jm+vprr=6z00*f^z03k5%e0xqrgiz0'
+SECRET_KEY = os.environ.get('SECRET_KEY','REPLACE_WITH_PROD_KEY')
 
 ALLOWED_HOSTS = os.environ.get('ALLOWED_HOSTS','127.0.0.1').split()
 
@@ -131,11 +131,14 @@
 # https://docs.djangoproject.com/en/dev/howto/static-files/
 
 STATIC_URL = '/static/'
-STATIC_ROOT = '/usr/share/nginx/html/static'
+STATIC_ROOT = '/srv/static'
+
 
 # Celery
-BROKER_HOST = os.environ.get('AMQP_HOST', 'amqp1')
-CELERY_BROKER_URL = 'amqp://%s' % (BROKER_HOST)
+BROKER_HOST = os.environ.get('RABBITMQ_HOSTNAME', 'amqp1')
+BROKER_USERNAME =  os.environ.get('RABBITMQ_DEFAULT_USER', 'guest')
+BROKER_PASSWORD =  os.environ.get('RABBITMQ_DEFAULT_PASS', 'guest')
+CELERY_BROKER_URL = 'amqp://%s:%s@%s' % (BROKER_USERNAME, BROKER_PASSWORD, BROKER_HOST)
 CELERY_ACCEPT_CONTENT = ['json']
 CELERY_TASK_SERIALIZER = 'json'
 CELERY_RESULT_SERIALIZER = 'json'
@@ -156,7 +159,10 @@
 }
 
 
-ES_HOST = os.environ.get('ES_HOST', 'http://elastic:changeme@localhost:9200')
+ES_HOSTNAME = os.environ.get('ELASTICSEARCH_HOSTNAME', 'http://elastic:changeme@localhost:9200')
+ES_USERNAME = os.environ.get('ELASTICSEARCH_USER', 'elastic')
+ES_PASSWORD = os.environ.get('ELASTICSEARCH_PASS', 'changeme')
+ES_HOST = 'http://%s:%s@%s' % (ES_USERNAME, ES_PASSWORD, ES_HOSTNAME)
 GITHUB_URL='https://github.com/1001genomes/aragwas/commit'
 HDF5_FILE_PATH = os.environ.get('ARAGWAS_HDF5_FILE_PATH','aragwas_data')
 

diff --git a/aragwas_server/web-entrypoint.sh b/aragwas_server/web-entrypoint.sh
diff --git a/aragwas_server/worker-entrypoint.sh b/aragwas_server/worker-entrypoint.sh
diff --git a/aragwas_ui/.dockerignore b/aragwas_ui/.dockerignore
diff --git a/aragwas_ui/Dockerfile b/aragwas_ui/Dockerfile
diff --git a/aragwas_ui/build/webpack.prod.conf.js b/aragwas_ui/build/webpack.prod.conf.js
@@ -8,6 +8,7 @@ var CopyWebpackPlugin = require('copy-webpack-plugin')
 var HtmlWebpackPlugin = require('html-webpack-plugin')
 var ExtractTextPlugin = require('extract-text-webpack-plugin')
 var OptimizeCSSPlugin = require('optimize-css-assets-webpack-plugin')
+const UglifyJsPlugin = require('uglifyjs-webpack-plugin')
 
 var env = process.env.NODE_ENV === 'testing'
   ? require('../config/test.env')
@@ -31,12 +32,7 @@ var webpackConfig = merge(baseWebpackConfig, {
     new webpack.DefinePlugin({
       'process.env': env
     }),
-    new webpack.optimize.UglifyJsPlugin({
-      compress: {
-        warnings: false
-      },
-      sourceMap: true
-    }),
+    new UglifyJsPlugin(),
     // extract css into its own file
     new ExtractTextPlugin({
       filename: utils.assetsPath('css/[name].[contenthash].css')

diff --git a/aragwas_ui/config/index.js b/aragwas_ui/config/index.js
@@ -4,8 +4,8 @@ var path = require('path')
 module.exports = {
   build: {
     env: require('./prod.env'),
-    index: path.resolve(__dirname, '../../aragwas_server/gwasdb/templates/index.html'),
-    assetsRoot: path.resolve(__dirname, '../../aragwas_server/gwasdb/static'),
+    index: path.resolve(__dirname, '../dist/index.html'),
+    assetsRoot: path.resolve(__dirname, '../dist/static/'),
     assetsSubDirectory: '',
     assetsPublicPath: '/static',
     productionSourceMap: true,