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MongoDB

What is MongoDB

MongoDB is a Kubernetes Custom Resource Definitions (CRD). It provides declarative configuration for MongoDB in a Kubernetes native way. You only need to describe the desired database configuration in a MongoDB object, and the KubeDB operator will create Kubernetes objects in the desired state for you.

MongoDB Spec

As with all other Kubernetes objects, a MongoDB needs apiVersion, kind, and metadata fields. It also needs a .spec section. Below is an example MongoDB object.

apiVersion: kubedb.com/v1alpha2
kind: MongoDB
metadata:
  name: mgo1
  namespace: demo
spec:
  autoOps:
    disabled: true
  version: "4.2.3"
  replicas: 3
  authSecret:
    name: mgo1-auth
    externallyManaged: false
  replicaSet:
    name: rs0
  shardTopology:
    configServer:
      podTemplate: {}
      replicas: 3
      storage:
        resources:
          requests:
            storage: 1Gi
        storageClassName: standard
    mongos:
      podTemplate: {}
      replicas: 2
    shard:
      podTemplate: {}
      replicas: 3
      shards: 3
      storage:
        resources:
          requests:
            storage: 1Gi
        storageClassName: standard
  sslMode: requireSSL
  tls:
    issuerRef:
      name: mongo-ca-issuer
      kind: Issuer
      apiGroup: "cert-manager.io"
    certificates:
      - alias: client
        subject:
          organizations:
            - kubedb
        emailAddresses:
          - [email protected]
      - alias: server
        subject:
          organizations:
            - kubedb
        emailAddresses:
          - [email protected]
  clusterAuthMode: x509
  storageType: "Durable"
  storageEngine: wiredTiger
  storage:
    storageClassName: "standard"
    accessModes:
      - ReadWriteOnce
    resources:
      requests:
        storage: 1Gi
  ephemeralStorage:
    medium: "Memory"
    sizeLimit: 500Mi
  init:
    script:
      configMap:
        name: mg-init-script
  monitor:
    agent: prometheus.io/operator
    prometheus:
      serviceMonitor:
        labels:
          app: kubedb
        interval: 10s
  configSecret:
    name: mg-custom-config
  podTemplate:
    metadata:      
      annotations:
        passMe: ToDatabasePod
      labels:
        thisLabel: willGoToPod
    controller:
      annotations:
        passMe: ToStatefulSet
      labels:
        thisLabel: willGoToSts
    spec:
      serviceAccountName: my-service-account
      schedulerName: my-scheduler
      nodeSelector:
        disktype: ssd
      imagePullSecrets:
        - name: myregistrykey
      args:
        - --maxConns=100
      env:
        - name: MONGO_INITDB_DATABASE
          value: myDB
      resources:
        requests:
          memory: "64Mi"
          cpu: "250m"
        limits:
          memory: "128Mi"
          cpu: "500m"
  serviceTemplates:
  - alias: primary
    spec:
      type: NodePort
      ports:
        - name: primary
          port: 27017
          nodePort: 300006
  terminationPolicy: Halt
  halted: false
  arbiter:
    podTemplate:
      spec:
        resources:
          requests:
            cpu: "200m"
            memory: "200Mi"
    configSecret:
      name: another-config
  allowedSchemas:
    namespaces:
      from: Selector
      selector:
        matchExpressions:
          - {key: kubernetes.io/metadata.name, operator: In, values: [dev]}
    selector:
      matchLabels:
        "schema.kubedb.com": "mongo"
  coordinator:
    resources:
      requests:
        cpu: "300m"
        memory: 500Mi
    securityContext:
      runAsUser: 1001
  healthChecker:
    periodSeconds: 15
    timeoutSeconds: 10
    failureThreshold: 2
    disableWriteCheck: false

spec.autoOps

AutoOps is an optional field to control the generation of versionUpdate & TLS-related recommendations.

spec.version

spec.version is a required field specifying the name of the MongoDBVersion crd where the docker images are specified. Currently, when you install KubeDB, it creates the following MongoDBVersion resources,

• 3.4.17-v1, 3.4.22-v1
• 3.6.13-v1, 3.6.8-v1,
• 4.0.3-v1, 4.0.5-v3, 4.0.11-v1,
• 4.1.4-v1, 4.1.7-v3, 4.1.13-v1
• 4.2.3, 4.4.6
• 5.0.2, 5.0.3
• percona-3.6.18
• percona-4.0.10, percona-4.2.7, percona-4.4.10

spec.replicas

spec.replicas the number of members(primary & secondary) in mongodb replicaset.

If spec.shardTopology is set, then spec.replicas needs to be empty. Instead use spec.shardTopology.<shard/configServer/mongos>.replicas

If both spec.replicaset and spec.shardTopology is not set, then spec.replicas can be value 1.

KubeDB uses PodDisruptionBudget to ensure that majority of these replicas are available during voluntary disruptions so that quorum is maintained.

spec.authSecret

spec.authSecret is an optional field that points to a Secret used to hold credentials for mongodb superuser. If not set, KubeDB operator creates a new Secret {mongodb-object-name}-auth for storing the password for mongodb superuser for each MongoDB object.

We can use this field in 3 mode.

1. Using an external secret. In this case, You need to create an auth secret first with required fields, then specify the secret name when creating the MongoDB object using spec.authSecret.name & set spec.authSecret.externallyManaged to true.

authSecret:
  name: <your-created-auth-secret-name>
  externallyManaged: true

2. Specifying the secret name only. In this case, You need to specify the secret name when creating the MongoDB object using spec.authSecret.name. externallyManaged is by default false.

authSecret:
  name: <intended-auth-secret-name>

3. Let KubeDB do everything for you. In this case, no work for you.

AuthSecret contains a user key and a password key which contains the username and password respectively for mongodb superuser.

Example:

$ kubectl create secret generic mgo1-auth -n demo \
--from-literal=username=jhon-doe \
--from-literal=password=6q8u_2jMOW-OOZXk
secret "mgo1-auth" created

apiVersion: v1
data:
  password: NnE4dV8yak1PVy1PT1pYaw==
  username: amhvbi1kb2U=
kind: Secret
metadata:
  name: mgo1-auth
  namespace: demo
type: Opaque

Secrets provided by users are not managed by KubeDB, and therefore, won’t be modified or garbage collected by the KubeDB operator (version 0.13.0 and higher).

spec.replicaSet

spec.replicaSet represents the configuration for replicaset. When spec.replicaSet is set, KubeDB will deploy a mongodb replicaset where number of replicaset member is spec.replicas.

• name denotes the name of mongodb replicaset. NB. If spec.shardTopology is set, then spec.replicaset needs to be empty.

spec.keyFileSecret

keyFileSecret.name denotes the name of the secret that contains the key.txt, which provides the security between replicaset members using internal authentication. See Keyfile Authentication for more information. It will make impact only if the ClusterAuthMode is keyFile or sendKeyFile.

spec.shardTopology

spec.shardTopology represents the topology configuration for sharding.

Available configurable fields:

• shard
• configServer
• mongos

When spec.shardTopology is set, the following fields needs to be empty, otherwise validating webhook will throw error.

• spec.replicas
• spec.podTemplate
• spec.configSecret
• spec.storage
• spec.ephemeralStorage

KubeDB uses PodDisruptionBudget to ensure that majority of the replicas of these shard components are available during voluntary disruptions so that quorum and data integrity is maintained.

spec.shardTopology.shard

shard represents configuration for Shard component of mongodb.

Available configurable fields:

• shards represents number of shards for a mongodb deployment. Each shard is deployed as a replicaset.
• replicas represents number of replicas of each shard replicaset.
• prefix represents the prefix of each shard node.
• configSecret is an optional field to provide custom configuration file for shards (i.e. mongod.cnf). If specified, this file will be used as configuration file otherwise a default configuration file will be used. See below to know about spec.configSecret in details.
• podTemplate is an optional configuration for pods. See below to know about spec.podTemplate in details.
• storage to specify pvc spec for each node of sharding. You can specify any StorageClass available in your cluster with appropriate resource requests. See below to know about spec.storage in details.
• ephemeralStorage to specify the configuration of ephemeral storage type, If you want to use volatile temporary storage attached to your instances which is only present during the running lifetime of the instance.

spec.shardTopology.configServer

configServer represents configuration for ConfigServer component of mongodb.

Available configurable fields:

• replicas represents number of replicas for configServer replicaset. Here, configServer is deployed as a replicaset of mongodb.
• prefix represents the prefix of configServer nodes.
• configSecret is an optional field to provide custom configuration file for config server (i.e mongod.cnf). If specified, this file will be used as configuration file otherwise a default configuration file will be used. See below to know about spec.configSecret in details.
• podTemplate is an optional configuration for pods. See below to know about spec.podTemplate in details.
• storage to specify pvc spec for each node of configServer. You can specify any StorageClass available in your cluster with appropriate resource requests. See below to know about spec.storage in details.
• ephemeralStorage to specify the configuration of ephemeral storage type, If you want to use volatile temporary storage attached to your instances which is only present during the running lifetime of the instance.

spec.shardTopology.mongos

mongos represents configuration for Mongos component of mongodb.

Available configurable fields:

• replicas represents number of replicas of Mongos instance. Here, Mongos is deployed as stateless (deployment) instance.
• prefix represents the prefix of mongos nodes.
• configSecret is an optional field to provide custom configuration file for mongos (i.e. mongod.cnf). If specified, this file will be used as configuration file otherwise a default configuration file will be used. See below to know about spec.configSecret in details.
• podTemplate is an optional configuration for pods. See below to know about spec.podTemplate in details.

spec.sslMode

Enables TLS/SSL or mixed TLS/SSL used for all network connections. The value of sslMode field can be one of the following:

spec.tls

spec.tls specifies the TLS/SSL configurations for the MongoDB. KubeDB uses cert-manager v1 api to provision and manage TLS certificates.

The following fields are configurable in the spec.tls section:

• issuerRef is a reference to the Issuer or ClusterIssuer CR of cert-manager that will be used by KubeDB to generate necessary certificates.

  • apiGroup is the group name of the resource that is being referenced. Currently, the only supported value is cert-manager.io.
  • kind is the type of resource that is being referenced. KubeDB supports both Issuer and ClusterIssuer as values for this field.
  • name is the name of the resource (Issuer or ClusterIssuer) being referenced.

• certificates (optional) are a list of certificates used to configure the server and/or client certificate. It has the following fields:

  • alias represents the identifier of the certificate. It has the following possible value:

    • server is used for server certificate identification.
    • client is used for client certificate identification.
    • metrics-exporter is used for metrics exporter certificate identification.

  • secretName (optional) specifies the k8s secret name that holds the certificates.

    This field is optional. If the user does not specify this field, the default secret name will be created in the following format: <database-name>-<cert-alias>-cert.

  • subject (optional) specifies an X.509 distinguished name. It has the following possible field,

    • organizations (optional) are the list of different organization names to be used on the Certificate.
    • organizationalUnits (optional) are the list of different organization unit name to be used on the Certificate.
    • countries (optional) are the list of country names to be used on the Certificate.
    • localities (optional) are the list of locality names to be used on the Certificate.
    • provinces (optional) are the list of province names to be used on the Certificate.
    • streetAddresses (optional) are the list of a street address to be used on the Certificate.
    • postalCodes (optional) are the list of postal code to be used on the Certificate.
    • serialNumber (optional) is a serial number to be used on the Certificate. You can find more details from Here

  • duration (optional) is the period during which the certificate is valid.

  • renewBefore (optional) is a specifiable time before expiration duration.

  • dnsNames (optional) is a list of subject alt names to be used in the Certificate.

  • ipAddresses (optional) is a list of IP addresses to be used in the Certificate.

  • uris (optional) is a list of URI Subject Alternative Names to be set in the Certificate.

  • emailAddresses (optional) is a list of email Subject Alternative Names to be set in the Certificate.

  • privateKey (optional) specifies options to control private keys used for the Certificate.

    • encoding (optional) is the private key cryptography standards (PKCS) encoding for this certificate’s private key to be encoded in. If provided, allowed values are “pkcs1” and “pkcs8” standing for PKCS#1 and PKCS#8, respectively. It defaults to PKCS#1 if not specified.

spec.clusterAuthMode

The authentication mode used for cluster authentication. This option can have one of the following values:

spec.storageType

spec.storageType is an optional field that specifies the type of storage to use for database. It can be either Durable or Ephemeral. The default value of this field is Durable. If Ephemeral is used then KubeDB will create MongoDB database using emptyDir volume. In this case, you don’t have to specify spec.storage field. Specify spec.ephemeralStorage spec instead.

spec.storageEngine

spec.storageEngine is an optional field that specifies the type of storage engine is going to be used by mongodb. There are two types of storage engine, wiredTiger and inMemory. Default value of storage engine is wiredTiger. inMemory storage engine is only supported by the percona variant of mongodb, i.e. the version that has the percona- prefix in the mongodb-version name.

spec.storage

Since 0.9.0-rc.0, If you set spec.storageType: to Durable, then spec.storage is a required field that specifies the StorageClass of PVCs dynamically allocated to store data for the database. This storage spec will be passed to the StatefulSet created by KubeDB operator to run database pods. You can specify any StorageClass available in your cluster with appropriate resource requests.

• spec.storage.storageClassName is the name of the StorageClass used to provision PVCs. PVCs don’t necessarily have to request a class. A PVC with its storageClassName set equal to "" is always interpreted to be requesting a PV with no class, so it can only be bound to PVs with no class (no annotation or one set equal to “”). A PVC with no storageClassName is not quite the same and is treated differently by the cluster depending on whether the DefaultStorageClass admission plugin is turned on.
• spec.storage.accessModes uses the same conventions as Kubernetes PVCs when requesting storage with specific access modes.
• spec.storage.resources can be used to request specific quantities of storage. This follows the same resource model used by PVCs.

To learn how to configure spec.storage, please visit the links below:

• https://kubernetes.io/docs/concepts/storage/persistent-volumes/#persistentvolumeclaims

NB. If spec.shardTopology is set, then spec.storage needs to be empty. Instead use spec.shardTopology.<shard/configServer>.storage

spec.ephemeralStorage

Use this field to specify the configuration of ephemeral storage type, If you want to use volatile temporary storage attached to your instances which is only present during the running lifetime of the instance.

• spec.ephemeralStorage.medium refers to the name of the storage medium.
• spec.ephemeralStorage.sizeLimit to specify the sizeLimit of the emptyDir volume.

For more details of these two fields, see EmptyDir struct

spec.init

spec.init is an optional section that can be used to initialize a newly created MongoDB database. MongoDB databases can be initialized by Script.

Initialize from Snapshot is still not supported.

Initialize via Script

To initialize a MongoDB database using a script (shell script, js script), set the spec.init.script section when creating a MongoDB object. It will execute files alphabetically with extensions .sh and .js that are found in the repository. script must have the following information:

• VolumeSource: Where your script is loaded from.

Below is an example showing how a script from a configMap can be used to initialize a MongoDB database.

apiVersion: kubedb.com/v1alpha2
kind: MongoDB
metadata:
  name: mgo1
  namespace: demo
spec:
  version: 4.2.3
  init:
    script:
      configMap:
        name: mongodb-init-script

In the above example, KubeDB operator will launch a Job to execute all js script of mongodb-init-script in alphabetical order once StatefulSet pods are running. For more details tutorial on how to initialize from script, please visit here.

These are the fields of spec.init which you can make use of :

• spec.init.initialized indicating that this database has been initialized or not. false by default.
• spec.init.script.scriptPath to specify where all the init scripts should be mounted.
• spec.init.script.<volumeSource> as described in the above example. To see all the volumeSource options go to VolumeSource.
• spec.init.waitForInitialRestore to tell the operator if it should wait for the initial restore process or not.

spec.monitor

MongoDB managed by KubeDB can be monitored with builtin-Prometheus and Prometheus operator out-of-the-box. To learn more,

• Monitor MongoDB with builtin Prometheus
• Monitor MongoDB with Prometheus operator

spec.configSecret

spec.configSecret is an optional field that allows users to provide custom configuration for MongoDB. You can provide the custom configuration in a secret, then you can specify the secret name spec.configSecret.name.

Please note that, the secret key needs to be mongod.conf.

To learn more about how to use a custom configuration file see here.

NB. If spec.shardTopology is set, then spec.configSecret needs to be empty. Instead use spec.shardTopology.<shard/configServer/mongos>.configSecret

spec.podTemplate

KubeDB allows providing a template for database pod through spec.podTemplate. KubeDB operator will pass the information provided in spec.podTemplate to the StatefulSet created for MongoDB database.

KubeDB accept following fields to set in spec.podTemplate:

• metadata:
  • annotations (pod’s annotation)
  • labels (pod’s labels)
• controller:
  • annotations (statefulset’s annotation)
  • labels (statefulset’s labels)
• spec:
  • args
  • env
  • resources
  • initContainers
  • imagePullSecrets
  • nodeSelector
  • affinity
  • serviceAccountName
  • schedulerName
  • tolerations
  • priorityClassName
  • priority
  • securityContext
  • livenessProbe
  • readinessProbe
  • lifecycle

You can checkout the full list here. Uses of some field of spec.podTemplate is described below,

NB. If spec.shardTopology is set, then spec.podTemplate needs to be empty. Instead use spec.shardTopology.<shard/configServer/mongos>.podTemplate

spec.podTemplate.spec.args

spec.podTemplate.spec.args is an optional field. This can be used to provide additional arguments to database installation. To learn about available args of mongod, visit here.

spec.podTemplate.spec.env

spec.podTemplate.spec.env is an optional field that specifies the environment variables to pass to the MongoDB docker image. To know about supported environment variables, please visit here.

Note that, KubeDB does not allow MONGO_INITDB_ROOT_USERNAME and MONGO_INITDB_ROOT_PASSWORD environment variables to set in spec.podTemplate.spec.env. If you want to use custom superuser and password, please use spec.authSecret instead described earlier.

If you try to set MONGO_INITDB_ROOT_USERNAME or MONGO_INITDB_ROOT_PASSWORD environment variable in MongoDB crd, Kubedb operator will reject the request with following error,

Error from server (Forbidden): error when creating "./mongodb.yaml": admission webhook "mongodb.validators.kubedb.com" denied the request: environment variable MONGO_INITDB_ROOT_USERNAME is forbidden to use in MongoDB spec

Also, note that KubeDB does not allow updating the environment variables as updating them does not have any effect once the database is created. If you try to update environment variables, KubeDB operator will reject the request with following error,

Error from server (BadRequest): error when applying patch:
...
for: "./mongodb.yaml": admission webhook "mongodb.validators.kubedb.com" denied the request: precondition failed for:
...At least one of the following was changed:
    apiVersion
    kind
    name
    namespace
    spec.ReplicaSet
    spec.authSecret
    spec.init
    spec.storageType
    spec.storage
    spec.podTemplate.spec.nodeSelector
    spec.podTemplate.spec.env

spec.podTemplate.spec.imagePullSecret

KubeDB provides the flexibility of deploying MongoDB database from a private Docker registry. spec.podTemplate.spec.imagePullSecrets is an optional field that points to secrets to be used for pulling docker image if you are using a private docker registry. To learn how to deploy MongoDB from a private registry, please visit here.

spec.podTemplate.spec.nodeSelector

spec.podTemplate.spec.nodeSelector is an optional field that specifies a map of key-value pairs. For the pod to be eligible to run on a node, the node must have each of the indicated key-value pairs as labels (it can have additional labels as well). To learn more, see here .

spec.podTemplate.spec.serviceAccountName

serviceAccountName is an optional field supported by KubeDB Operator (version 0.13.0 and higher) that can be used to specify a custom service account to fine tune role based access control.

If this field is left empty, the KubeDB operator will create a service account name matching MongoDB crd name. Role and RoleBinding that provide necessary access permissions will also be generated automatically for this service account.

If a service account name is given, but there’s no existing service account by that name, the KubeDB operator will create one, and Role and RoleBinding that provide necessary access permissions will also be generated for this service account.

If a service account name is given, and there’s an existing service account by that name, the KubeDB operator will use that existing service account. Since this service account is not managed by KubeDB, users are responsible for providing necessary access permissions manually. Follow the guide here to grant necessary permissions in this scenario.

spec.podTemplate.spec.resources

spec.podTemplate.spec.resources is an optional field. This can be used to request compute resources required by the database pods. To learn more, visit here.

spec.serviceTemplates

You can also provide template for the services created by KubeDB operator for MongoDB database through spec.serviceTemplates. This will allow you to set the type and other properties of the services.

KubeDB allows following fields to set in spec.serviceTemplates:

• alias represents the identifier of the service. It has the following possible value:
  • primary is used for the primary service identification.
  • standby is used for the secondary service identification.
  • stats is used for the exporter service identification.
• metadata:
  • labels
  • annotations
• spec:
  • type
  • ports
  • clusterIP
  • externalIPs
  • loadBalancerIP
  • loadBalancerSourceRanges
  • externalTrafficPolicy
  • healthCheckNodePort
  • sessionAffinityConfig

See here to understand these fields in detail.

spec.terminationPolicy

terminationPolicy gives flexibility whether to nullify(reject) the delete operation of MongoDB crd or which resources KubeDB should keep or delete when you delete MongoDB crd. KubeDB provides following four termination policies:

• DoNotTerminate
• Halt
• Delete (Default)
• WipeOut

When terminationPolicy is DoNotTerminate, KubeDB takes advantage of ValidationWebhook feature in Kubernetes 1.9.0 or later clusters to implement DoNotTerminate feature. If admission webhook is enabled, DoNotTerminate prevents users from deleting the database as long as the spec.terminationPolicy is set to DoNotTerminate.

Following table show what KubeDB does when you delete MongoDB crd for different termination policies,

If you don’t specify spec.terminationPolicy KubeDB uses Delete termination policy by default.

spec.halted

Indicates that the database is halted and all offshoot Kubernetes resources except PVCs are deleted.

spec.arbiter

If spec.arbiter is not null, there will be one arbiter pod on each of the replicaset structure, including shards. It has two fields.

• spec.arbiter.podTemplate defines the arbiter-pod’s template. See spec.podTemplate part for more details of this.
• spec.arbiter.configSecret is an optional field that allows users to provide custom configurations for MongoDB arbiter. You just need to refer the configuration secret in spec.arbiter.configSecret.name field.

Please note that, the secret key needs to be mongod.conf.

N.B. If spec.replicaset & spec.shardTopology both is empty, spec.arbiter has to be empty too.

spec.allowedSchemas

It defines which consumers may refer to a database instance. We implemented double-optIn feature between database instance and schema-manager using this field.

• spec.allowedSchemas.namespace.from indicates how you want to filter the namespaces, from which a schema-manager will be able to communicate with this db instance. Possible values are : i) All to allow all namespaces, ii) Same to allow only if schema-manager & MongoDB is deployed in same namespace & iii) Selector to select some namespaces through labels.
• spec.allowedSchemas.namespace.selector. You need to set this field only if spec.allowedSchemas.namespace.from is set to selector. Here you will give the labels of the namespaces to allow.
• spec.allowedSchemas.selctor denotes the labels of the schema-manager instances, which you want to give allowance to use this database.

spec.coordinator

We use a dedicated container, named replication-mode-detector, to continuously select primary pod and add label as primary. By specifying spec.coordinator.resources & spec.coordinator.securityContext, you can set the resources and securityContext of that mode-detector container.

spec.healthChecker

It defines the attributes for the health checker.

• spec.healthChecker.periodSeconds specifies how often to perform the health check.
• spec.healthChecker.timeoutSeconds specifies the number of seconds after which the probe times out.
• spec.healthChecker.failureThreshold specifies minimum consecutive failures for the healthChecker to be considered failed.
• spec.healthChecker.disableWriteCheck specifies whether to disable the writeCheck or not.

Know details about KubeDB Health checking from this blog post.

Next Steps

• Learn how to use KubeDB to run a MongoDB database here.
• Want to hack on KubeDB? Check our contribution guidelines.