Pre-commit hook installation:

ln -s $(pwd)/.githooks/pre-commit $(pwd)/.git/hooks/pre-commit

TL;DR

Centrally manage and log configuration including which versions of which services get deployed where. Ex:

$ cat dev.planx-pla.net/manifest.json 
{
  "notes": [
    "This is the dev environment manifest",
    "That's all I have to say"
  ],
  "jenkins": {
    "autodeploy": "yes"
  },
  "versions": {
    "fence": "quay.io/cdis/fence:2.4.0",
    "peregrine": "quay.io/cdis/peregrine:1.0.2",
    "sheepdog": "quay.io/cdis/sheepdog:1.1.2",
    "portal": "quay.io/cdis/data-portal:2.0.1",
    "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
    "jupyterhub": "quay.io/occ_data/jupyterhub:master"
  }
  "jupyterhub": {
    "enabled": "yes"
  }
}

Policies

• Never release :master or :latest docker tags to production.
• {DOMAIN}/manifest.json is the manifest for a particular commons - ex: manifest_dev.planx-pla.net_.json
• default/manifest.json is the fall-through default manifest if {DOMAIN}/manifest.json does not exist

Deployment workflow

We run a dev kubernetes cluster and a qa cluster. The dev cluster allows each developer to run her own gen3 stack in its own namespace. A developer can manipulate the cluster directly (with kubectl) from the cluster's admin vm:

$ ssh [email protected]
$ kubectl get pods

The qa cluster is administered by a Jenkins server at https://jenkins.planx-pla.net/, and is not directly accessible by kubectl. Jenkins jobs monitor the QA branch of the cdis-manifest github repository, and auto-updates the gen3 qa environments running on the cluster. Jenkins also periodically runs gen3's system level integration tests against each QA environment. We run one QA environment per production commons (https://kidsfirstqa.planx-pla.net, https://bloodpacqa.planx-pla.net, ...). Each QA environment is configured (via its manifest) to run the latest :master Docker image of each gen3 service.

We also run one QA environment per developer (https://reubenqa.planx-pla.net, https://phillisqa.planx-pla.net, ...), so a developer can test new code in the QA environment before merging the code into the master branch.

To update a QA environment such as reubenqa.planx-pla.net

• checkout the QA branch
• update reubenqa.planx-pla.net/manifest.json and push to github
• the Jenkins server running in the QA k8s cluster auto-deploys the new manifest - the QA environment's Jenkins server pulls manifests from the QA git branch

To update a production environment such as data.bloodpac.org

• first - tag each service with a semver version - we only deploy version-tagged images to production (not :latest or :master)
• checkout the QA branch of the cdis-manifest repo
• update data.bloodpac.org/manifest.json and push to github
• submit a pull request (PR)
• after the PR is approved and merged, then kickoff a deployment script (details TBD) - production deployment automation pulls manifests from the master git branch
• run gen3's integration test suite against the new production deployment (this happens automatically)

Note that the Google Data Access integration tests are NOT ran when changes are made to environments that do not use Google Data Access features. The list of environments that do run these tests can be updated in this file.

Automation

We implement manifest based versioning of our services in kubernetes via the gen3 helper scripts in cloud-automation. The -deployment.yaml template defining each service's k8s deployment includes GEN3 variables that gen3 roll replaces. For example:

$ cat cloud-automation/kube/services/peregrine/peregrine-deploy.yaml 
apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: peregrine-deployment
spec:
  revisionHistoryLimit: 2
  strategy:
    type: RollingUpdate
    rollingUpdate:
      maxSurge: 1
      maxUnavailable: 0
  template:
    metadata:
      labels:
        app: peregrine
        GEN3_DATE_LABEL
    spec:
      automountServiceAccountToken: false
      ...
      containers:
        - name: peregrine
          GEN3_PEREGRINE_IMAGE
          livenessProbe:
            httpGet:

$ gen3 roll peregrine
...

Release notes

• fence
• peregrine
• portal
• sheepdog