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README.md
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# Code Infrastructure Lab
This module defines configurations for creating a Kubernetes cluster for generating the OpenAIRE Research Graph.
## Cluster definition
The Kubernetes cluster will include some essential services for testing OpenAIRE Graph generation:
- Storage: Minio will be used as storage.
- Workflow Orchestrator: Airflow will be used as the workflow orchestrator.
- Processing Framework: Spark-Operator will be used as the processing framework.
### Storage
[Minio](https://min.io/)": is an open-source object storage service that will be used to store the data that is used to generate the intermediate version of the OpenAIRE Research Graph.
### Workflow Orchestrator
[Airflow](https://airflow.apache.org/) is an open-source workflow management platform that will be used to orchestrate the generation of the OpenAIRE Research Graph. Airflow is a powerful and flexible workflow orchestration tool that can be used to automate complex workflows.
### Processing Framework
[Spark-Operator](https://github.com/kubeflow/spark-operator) The Kubernetes Operator for Apache Spark aims to make specifying and running Spark applications as easy and idiomatic as running other workloads on Kubernetes. It uses Kubernetes custom resources for specifying, running, and surfacing status of Spark applications. For a complete reference of the custom resource definitions, please refer to the API Definition. For details on its design, please refer to the design doc.
## How to use in local
### Prerequisite
This section outlines the prerequisites for setting up a developer cluster on your local machine using Docker and Kind. A developer cluster is a small-scale Kubernetes cluster that can be used for developing and testing applications. Docker and Kind are two tools that can be used to create and manage Kubernetes clusters locally.
Before you begin, you will need to install the following software on your local machine:
1. Docker: Docker is a containerization platform that allows you to run applications in isolated environments. You can download Docker from https://docs.docker.com/get-docker/.
2. Kind: Kind is a tool for creating local Kubernetes clusters using Docker container "nodes". You can download Kind from https://kind.sigs.k8s.io/docs/user/quick-start/.
### Create Kubernetes cluster
For creating kubernetes cluster run the following command
```console
kind create cluster --config clusters/local/kind-cluster-config.yaml
```
this command will generate a cluster named `openaire-data-platform`
Then we create Ingress that is a Kubernetes resource that allows you to manage external access to services running on a cluster (like minio console or sparkUI).
To enable ingress run the command:
```console
kubectl apply --context kind-openaire-data-platform -f ./clusters/local/nginx-kind-deploy.yaml
```

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clusters/local/kind-cluster-config.yaml Normal file
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kind: Cluster
apiVersion: kind.x-k8s.io/v1alpha4
name: openaire-data-platform
nodes:
- role: control-plane
image: kindest/node:v1.28.6@sha256:e9e59d321795595d0eed0de48ef9fbda50388dc8bd4a9b23fb9bd869f370ec7e
kubeadmConfigPatches:
- |
kind: InitConfiguration
nodeRegistration:
kubeletExtraArgs:
node-labels: "ingress-ready=true"
authorization-mode: "AlwaysAllow"
extraPortMappings:
- containerPort: 80
hostPort: 80
protocol: TCP
- containerPort: 443
hostPort: 443
protocol: TCP
containerdConfigPatches:
- |-
[plugins."io.containerd.grpc.v1.cri".registry]
config_path = "/etc/containerd/certs.d"

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clusters/local/kind-with-registry.sh Executable file
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#!/bin/sh
set -o errexit
# Script Origin: https://kind.sigs.k8s.io/docs/user/local-registry/
# create registry container unless it already exists
reg_name='kind-registry'
reg_port='5001'
if [ "$(docker inspect -f '{{.State.Running}}' "${reg_name}" 2>/dev/null || true)" != 'true' ]; then
docker run \
-d --restart=always -p "127.0.0.1:${reg_port}:5000" --name "${reg_name}" \
registry:2
fi
# connect the registry to the cluster network if not already connected
if [ "$(docker inspect -f='{{json .NetworkSettings.Networks.kind}}' "${reg_name}")" = 'null' ]; then
docker network connect "kind" "${reg_name}"
fi
# Document the local registry
# https://github.com/kubernetes/enhancements/tree/master/keps/sig-cluster-lifecycle/generic/1755-communicating-a-local-registry
cat <<EOF | kubectl apply --context $1 -f -
apiVersion: v1
kind: ConfigMap
metadata:
name: local-registry-hosting
namespace: kube-public
data:
localRegistryHosting.v1: |
host: "localhost:${reg_port}"
help: "https://kind.sigs.k8s.io/docs/user/local-registry/"
EOF

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clusters/local/nginx-kind-deploy.yaml Normal file
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apiVersion: v1
kind: Namespace
metadata:
labels:
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
name: ingress-nginx
---
apiVersion: v1
automountServiceAccountToken: true
kind: ServiceAccount
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx
namespace: ingress-nginx
---
apiVersion: v1
kind: ServiceAccount
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission
namespace: ingress-nginx
---
apiVersion: rbac.authorization.k8s.io/v1
kind: Role
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx
namespace: ingress-nginx
rules:
- apiGroups:
- ""
resources:
- namespaces
verbs:
- get
- apiGroups:
- ""
resources:
- configmaps
- pods
- secrets
- endpoints
verbs:
- get
- list
- watch
- apiGroups:
- ""
resources:
- services
verbs:
- get
- list
- watch
- apiGroups:
- networking.k8s.io
resources:
- ingresses
verbs:
- get
- list
- watch
- apiGroups:
- networking.k8s.io
resources:
- ingresses/status
verbs:
- update
- apiGroups:
- networking.k8s.io
resources:
- ingressclasses
verbs:
- get
- list
- watch
- apiGroups:
- coordination.k8s.io
resourceNames:
- ingress-nginx-leader
resources:
- leases
verbs:
- get
- update
- apiGroups:
- coordination.k8s.io
resources:
- leases
verbs:
- create
- apiGroups:
- ""
resources:
- events
verbs:
- create
- patch
- apiGroups:
- discovery.k8s.io
resources:
- endpointslices
verbs:
- list
- watch
- get
---
apiVersion: rbac.authorization.k8s.io/v1
kind: Role
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission
namespace: ingress-nginx
rules:
- apiGroups:
- ""
resources:
- secrets
verbs:
- get
- create
---
apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRole
metadata:
labels:
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx
rules:
- apiGroups:
- ""
resources:
- configmaps
- endpoints
- nodes
- pods
- secrets
- namespaces
verbs:
- list
- watch
- apiGroups:
- coordination.k8s.io
resources:
- leases
verbs:
- list
- watch
- apiGroups:
- ""
resources:
- nodes
verbs:
- get
- apiGroups:
- ""
resources:
- services
verbs:
- get
- list
- watch
- apiGroups:
- networking.k8s.io
resources:
- ingresses
verbs:
- get
- list
- watch
- apiGroups:
- ""
resources:
- events
verbs:
- create
- patch
- apiGroups:
- networking.k8s.io
resources:
- ingresses/status
verbs:
- update
- apiGroups:
- networking.k8s.io
resources:
- ingressclasses
verbs:
- get
- list
- watch
- apiGroups:
- discovery.k8s.io
resources:
- endpointslices
verbs:
- list
- watch
- get
---
apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRole
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission
rules:
- apiGroups:
- admissionregistration.k8s.io
resources:
- validatingwebhookconfigurations
verbs:
- get
- update
---
apiVersion: rbac.authorization.k8s.io/v1
kind: RoleBinding
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx
namespace: ingress-nginx
roleRef:
apiGroup: rbac.authorization.k8s.io
kind: Role
name: ingress-nginx
subjects:
- kind: ServiceAccount
name: ingress-nginx
namespace: ingress-nginx
---
apiVersion: rbac.authorization.k8s.io/v1
kind: RoleBinding
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission
namespace: ingress-nginx
roleRef:
apiGroup: rbac.authorization.k8s.io
kind: Role
name: ingress-nginx-admission
subjects:
- kind: ServiceAccount
name: ingress-nginx-admission
namespace: ingress-nginx
---
apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRoleBinding
metadata:
labels:
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx
roleRef:
apiGroup: rbac.authorization.k8s.io
kind: ClusterRole
name: ingress-nginx
subjects:
- kind: ServiceAccount
name: ingress-nginx
namespace: ingress-nginx
---
apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRoleBinding
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission
roleRef:
apiGroup: rbac.authorization.k8s.io
kind: ClusterRole
name: ingress-nginx-admission
subjects:
- kind: ServiceAccount
name: ingress-nginx-admission
namespace: ingress-nginx
---
apiVersion: v1
data:
allow-snippet-annotations: "false"
kind: ConfigMap
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-controller
namespace: ingress-nginx
---
apiVersion: v1
kind: Service
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-controller
namespace: ingress-nginx
spec:
ipFamilies:
- IPv4
ipFamilyPolicy: SingleStack
ports:
- appProtocol: http
name: http
port: 80
protocol: TCP
targetPort: http
- appProtocol: https
name: https
port: 443
protocol: TCP
targetPort: https
selector:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
type: NodePort
---
apiVersion: v1
kind: Service
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-controller-admission
namespace: ingress-nginx
spec:
ports:
- appProtocol: https
name: https-webhook
port: 443
targetPort: webhook
selector:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
type: ClusterIP
---
apiVersion: apps/v1
kind: Deployment
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-controller
namespace: ingress-nginx
spec:
minReadySeconds: 0
revisionHistoryLimit: 10
selector:
matchLabels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
strategy:
rollingUpdate:
maxUnavailable: 1
type: RollingUpdate
template:
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
spec:
containers:
- args:
- /nginx-ingress-controller
- --election-id=ingress-nginx-leader
- --controller-class=k8s.io/ingress-nginx
- --ingress-class=nginx
- --configmap=$(POD_NAMESPACE)/ingress-nginx-controller
- --validating-webhook=:8443
- --validating-webhook-certificate=/usr/local/certificates/cert
- --validating-webhook-key=/usr/local/certificates/key
- --watch-ingress-without-class=true
- --publish-status-address=localhost
env:
- name: POD_NAME
valueFrom:
fieldRef:
fieldPath: metadata.name
- name: POD_NAMESPACE
valueFrom:
fieldRef:
fieldPath: metadata.namespace
- name: LD_PRELOAD
value: /usr/local/lib/libmimalloc.so
image: registry.k8s.io/ingress-nginx/controller:v1.9.6@sha256:1405cc613bd95b2c6edd8b2a152510ae91c7e62aea4698500d23b2145960ab9c
imagePullPolicy: IfNotPresent
lifecycle:
preStop:
exec:
command:
- /wait-shutdown
livenessProbe:
failureThreshold: 5
httpGet:
path: /healthz
port: 10254
scheme: HTTP
initialDelaySeconds: 10
periodSeconds: 10
successThreshold: 1
timeoutSeconds: 1
name: controller
ports:
- containerPort: 80
hostPort: 80
name: http
protocol: TCP
- containerPort: 443
hostPort: 443
name: https
protocol: TCP
- containerPort: 8443
name: webhook
protocol: TCP
readinessProbe:
failureThreshold: 3
httpGet:
path: /healthz
port: 10254
scheme: HTTP
initialDelaySeconds: 10
periodSeconds: 10
successThreshold: 1
timeoutSeconds: 1
resources:
requests:
cpu: 100m
memory: 90Mi
securityContext:
allowPrivilegeEscalation: false
capabilities:
add:
- NET_BIND_SERVICE
drop:
- ALL
readOnlyRootFilesystem: false
runAsNonRoot: true
runAsUser: 101
seccompProfile:
type: RuntimeDefault
volumeMounts:
- mountPath: /usr/local/certificates/
name: webhook-cert
readOnly: true
dnsPolicy: ClusterFirst
nodeSelector:
ingress-ready: "true"
kubernetes.io/os: linux
serviceAccountName: ingress-nginx
terminationGracePeriodSeconds: 0
tolerations:
- effect: NoSchedule
key: node-role.kubernetes.io/master
operator: Equal
- effect: NoSchedule
key: node-role.kubernetes.io/control-plane
operator: Equal
volumes:
- name: webhook-cert
secret:
secretName: ingress-nginx-admission
---
apiVersion: batch/v1
kind: Job
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission-create
namespace: ingress-nginx
spec:
template:
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission-create
spec:
containers:
- args:
- create
- --host=ingress-nginx-controller-admission,ingress-nginx-controller-admission.$(POD_NAMESPACE).svc
- --namespace=$(POD_NAMESPACE)
- --secret-name=ingress-nginx-admission
env:
- name: POD_NAMESPACE
valueFrom:
fieldRef:
fieldPath: metadata.namespace
image: registry.k8s.io/ingress-nginx/kube-webhook-certgen:v20231226-1a7112e06@sha256:25d6a5f11211cc5c3f9f2bf552b585374af287b4debf693cacbe2da47daa5084
imagePullPolicy: IfNotPresent
name: create
securityContext:
allowPrivilegeEscalation: false
capabilities:
drop:
- ALL
readOnlyRootFilesystem: true
runAsNonRoot: true
runAsUser: 65532
seccompProfile:
type: RuntimeDefault
nodeSelector:
kubernetes.io/os: linux
restartPolicy: OnFailure
serviceAccountName: ingress-nginx-admission
---
apiVersion: batch/v1
kind: Job
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission-patch
namespace: ingress-nginx
spec:
template:
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission-patch
spec:
containers:
- args:
- patch
- --webhook-name=ingress-nginx-admission
- --namespace=$(POD_NAMESPACE)
- --patch-mutating=false
- --secret-name=ingress-nginx-admission
- --patch-failure-policy=Fail
env:
- name: POD_NAMESPACE
valueFrom:
fieldRef:
fieldPath: metadata.namespace
image: registry.k8s.io/ingress-nginx/kube-webhook-certgen:v20231226-1a7112e06@sha256:25d6a5f11211cc5c3f9f2bf552b585374af287b4debf693cacbe2da47daa5084
imagePullPolicy: IfNotPresent
name: patch
securityContext:
allowPrivilegeEscalation: false
capabilities:
drop:
- ALL
readOnlyRootFilesystem: true
runAsNonRoot: true
runAsUser: 65532
seccompProfile:
type: RuntimeDefault
nodeSelector:
kubernetes.io/os: linux
restartPolicy: OnFailure
serviceAccountName: ingress-nginx-admission
---
apiVersion: networking.k8s.io/v1
kind: IngressClass
metadata:
labels:
app.kubernetes.io/component: controller
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: nginx
spec:
controller: k8s.io/ingress-nginx
---
apiVersion: admissionregistration.k8s.io/v1
kind: ValidatingWebhookConfiguration
metadata:
labels:
app.kubernetes.io/component: admission-webhook
app.kubernetes.io/instance: ingress-nginx
app.kubernetes.io/name: ingress-nginx
app.kubernetes.io/part-of: ingress-nginx
app.kubernetes.io/version: 1.9.6
name: ingress-nginx-admission
webhooks:
- admissionReviewVersions:
- v1
clientConfig:
service:
name: ingress-nginx-controller-admission
namespace: ingress-nginx
path: /networking/v1/ingresses
failurePolicy: Fail
matchPolicy: Equivalent
name: validate.nginx.ingress.kubernetes.io
rules:
- apiGroups:
- networking.k8s.io
apiVersions:
- v1
operations:
- CREATE
- UPDATE
resources:
- ingresses
sideEffects: None