Simple LocalEGA Helm setup

00_init_k3d.sh

#!/usr/bin/env bash
source _script_source.sh
set -e

has_traefik_pods() {
    L=$(kubectl get pods -n kube-system -lapp=svclb-traefik 2>/dev/null | wc -l)
    if [ $L -eq 0 ]; then
        false
    else
        true
    fi
}

has_running_traefik_pods() {
    NUM=$(kubectl get -A pods -o json \
        | jq '.items[] | .status.conditions[] | select(.type == "Ready" and .reason != "PodCompleted" and .status != "True") | .status' \
        | wc -l)
    if [ $NUM -eq 0 ]; then
        true
    else
        false
    fi
}

start_k3d() {
    if ! grep -q $K3DNAME <(k3d ls); then
        k3d create \
            --name $K3DNAME \
            --workers 4 \
            --image rancher/k3s:v0.9.1 \
            --publish 8080:80 \
            --publish 8443:443
            #--volume "$PWD/config.toml.tmpl":"/var/lib/rancher/k3s/agent/etc/containerd/config.toml.tmpl" \

        echo "Waiting for cluster to create"
        sleep 10

        export KUBECONFIG="$(k3d get-kubeconfig --name=$K3DNAME)"

        until has_traefik_pods; do
            echo "Waiting for cluster to create traefik pods"
            sleep 10
        done

        until has_running_traefik_pods; do
            echo "Waiting for cluster to have ready traefik pods"
            sleep 10
        done

        ## Fix DNS
        ## Only needed if your local network blocks the google DNS servers
        kubectl apply -f <(kubectl -n kube-system get configmap coredns -o yaml | sed 's/\/etc\/resolv.conf/130.238.4.133 130.238.7.10 130.238.164.6/')
    fi
}

start_k3d
helm init
kubectl create clusterrolebinding default-cluster-admin --clusterrole=cluster-admin --serviceaccount=kube-system:default

01_configure_localega.sh

#!/usr/bin/env bash
source _script_source.sh
set -e


pip install git+https://github.com/neicnordic/LocalEGA-deploy-init
if [ ! -d LocalEGA-helm ]; then
    git clone [email protected]:NBISweden/LocalEGA-helm.git
fi

legainit --cega \
    --config-path $CHART_PREFIX/localega/config \
    --svc-config k3d-conf.json \
    --cega-svc-config k3d-conf.json

mkdir -p $CHART_PREFIX/cega/config
cp $CHART_PREFIX/localega/config/cega.* $CHART_PREFIX/localega/config/users.* $CHART_PREFIX/cega/config/
cp -r $CHART_PREFIX/localega/config/certs $CHART_PREFIX/cega/config/

02_start_services.sh

#!/usr/bin/env bash
source _script_source.sh
set -e

echo " ========="
echo " Installing an NFS server"
helm install --namespace nfs --name nfs stable/nfs-server-provisioner

echo " ========="
echo " Installing a minio backend"
MINIO_ACCESS=$(grep s3_access_key $CHART_PREFIX/localega/config/trace.yml | awk {'print $2'} | sed --expression 's/\"//g')
MINIO_SECRET=$(grep s3_secret_key $CHART_PREFIX/localega/config/trace.yml | awk {'print $2'} | sed --expression 's/\"//g')

kubectl create ns minio || true
kubectl -n minio create secret generic minio-certs \
    --from-file=$CHART_PREFIX/localega/config/certs/s3.ca.crt \
    --from-file=$CHART_PREFIX/localega/config/certs/s3.ca.key

helm install --namespace minio --name s3 \
    --set persistence.enabled=false,accessKey=$MINIO_ACCESS,secretKey=$MINIO_SECRET,minioConfig.region=lega,tls.enabled=true,tls.publicCrt=s3.ca.crt,tls.privateKey=s3.ca.key,tls.certSecret=minio-certs \
    stable/minio --version 2.5.13

until kubectl -n minio get pods -lapp=minio -o jsonpath='{range .items[*]}{@.metadata.name}:{range @.status.conditions[*]}{@.type}={@.status}' | grep "Ready=True"; do
    echo "waiting for minio to become ready"
    sleep 10
done


echo " ========="
echo " Bringing fake central ega online"
helm install --name cega --namespace cega $CHART_PREFIX/cega \
    -f $CHART_PREFIX/localega/config/trace.yml \
    --set persistence.enabled=false

kubectl create ns lega || true
kubectl apply -f volume-claims.yaml

03_deploy_localega.sh

#!/usr/bin/env bash
source _script_source.sh
set -e

if helm status lega 1>/dev/null 2>&1; then
    helm upgrade lega $CHART_PREFIX/localega \
        -f $CHART_PREFIX/localega/config/trace.yml \
        -f extra-conf.yaml
else
    helm install --name lega --namespace lega $CHART_PREFIX/localega \
        -f $CHART_PREFIX/localega/config/trace.yml \
        -f extra-conf.yaml
fi

extra-conf.yaml

persistence:
  enabled: true

config:
  cega_mq_host: "cega-mq.cega"
  cega_users_host: "https://cega-users.cega"
  data_storage_s3_bucket: lega
  data_storage_s3_region: lega
  data_storage_url: "https://s3-minio.minio.svc.cluster.local:9000"

inbox:
  persistence:
    existingClaim: nfs-inbox-claim
  deploy: true
  repository: nbisweden/ega-mina-inbox
  imageTag: m7

# Java services

dataedge:
  deploy: true
  repository: nbisweden/ega-dataedge
  imageTag: latest

filedatabase:
  deploy: true
  repository: nbisweden/ega-filedb
  imageTag: latest

keys:
  deploy: true
  repository: nbisweden/ega-keyserver
  imageTag: latest

res:
  deploy: true
  repository: nbisweden/ega-res
  imageTag: latest

doa:
  deploy: true
  repository: nbisweden/ega-doa
  imageTag: latest

# Python services
ingest:
  deploy: true
  coLocateInbox: false
  repository: nbisweden/ega-base
  imageTag: m7
  persistence:
    existingClaim: nfs-inbox-claim

finalize:
  deploy: true
  repository: nbisweden/ega-base
  imageTag: m7

verify:
  deploy: true
  repository: nbisweden/ega-base
  imageTag: m7


# Backing services
mq:
  persistence:
    existingClaim: nfs-mq-claim

postgres:
  persistence:
    existingClaim: nfs-db-claim

tester:
  run: false
  imagePullPolicy: Always

k3d-conf.json

[
    {"name": "s3",           "dns": "s3-minio",              "ns": "minio"},
    {"name": "keys",         "dns": "localega-keys",         "ns": "lega"},
    {"name": "filedatabase", "dns": "localega-filedatabase", "ns": "lega"},
    {"name": "dataedge",     "dns": "localega-dataedge",     "ns": "lega"},
    {"name": "res",          "dns": "localega-res",          "ns": "lega"},
    {"name": "inbox",        "dns": "localega-inbox",        "ns": "lega"},
    {"name": "ingest",       "dns": "localega-ingest",       "ns": "lega"},
    {"name": "finalize",     "dns": "localega-finalize",     "ns": "lega"},
    {"name": "verify",       "dns": "localega-verify",       "ns": "lega"},
    {"name": "mq-server",    "dns": "localega-mq",           "ns": "lega"},
    {"name": "db",           "dns": "localega-db",           "ns": "lega"},
    {"name": "doa",          "dns": "localega-doa",          "ns": "lega"},
    {"name": "htsget",       "dns": "localega-htsget",       "ns": "lega"},
    {"name": "tester",       "dns": "localega-tester",       "ns": "lega"},
    {"name": "cega-users",                                   "ns": "cega"},
    {"name": "cega-mq",                                      "ns": "cega"}
]

volume-claims.yaml

kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: nfs-inbox-claim
  namespace: lega
spec:
  storageClassName: "nfs"
  accessModes:
    - ReadWriteMany
  resources:
    requests:
      storage: 1Gi
---
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: nfs-mq-claim
  namespace: lega
spec:
  storageClassName: "nfs"
  accessModes:
    - ReadWriteMany
  resources:
    requests:
      storage: 256Mi
---
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: nfs-db-claim
  namespace: lega
spec:
  storageClassName: "nfs"
  accessModes:
    - ReadWriteMany
  resources:
    requests:
      storage: 256Mi