prometheus-operator: Additional scrape configs appear to be ignored

What did you do?

Using the guide in this repository for providing additionalScrapeConfigs, I created a secret to provide additional scrape configurations per the guide in the repository.

Did you expect to see some different?

I expected the prometheus process spawned from the prometheus-operator to pick up the additional scrape configuration specified through the secret and key I created.

Environment

• Prometheus Operator version:

quay.io/coreos/prometheus-operator@sha256:ed3ec0597c2d5b7102a7f62c661a23d8e4b34d910693fc23fd40bfb1d9404dcf

• Kubernetes version information:

Client Version: version.Info{Major:"1", Minor:"16", GitVersion:"v1.16.0", GitCommit:"2bd9643cee5b3b3a5ecbd3af49d09018f0773c77", GitTreeState:"clean", BuildDate:"2019-09-18T14:36:53Z", GoVersion:"go1.12.9", Compiler:"gc", Platform:"darwin/amd64"}
Server Version: version.Info{Major:"1", Minor:"15", GitVersion:"v1.15.3", GitCommit:"2d3c76f9091b6bec110a5e63777c332469e0cba2", GitTreeState:"clean", BuildDate:"2019-08-19T11:05:50Z", GoVersion:"go1.12.9", Compiler:"gc", Platform:"linux/amd64"}

• Kubernetes cluster kind:

rke

• Manifests:

apiVersion: v1
kind: Secret
metadata:
  namespace: {{ .Release.Namespace }}
  name: prom-additional-scrape-configs
stringData:
  prometheus-additional.yaml: |
    # Scrape config for API servers.
    #
    # Kubernetes exposes API servers as endpoints to the default/kubernetes
    # service so this uses `endpoints` role and uses relabelling to only keep
    # the endpoints associated with the default/kubernetes service using the
    # default named port `https`. This works for single API server deployments as
    # well as HA API server deployments.
    - job_name: 'kubernetes-apiservers'

      kubernetes_sd_configs:
        - role: endpoints

      # Default to scraping over https. If required, just disable this or change to
      # `http`.
      scheme: https

      # This TLS & bearer token file config is used to connect to the actual scrape
      # endpoints for cluster components. This is separate to discovery auth
      # configuration because discovery & scraping are two separate concerns in
      # Prometheus. The discovery auth config is automatic if Prometheus runs inside
      # the cluster. Otherwise, more config options have to be provided within the
      # <kubernetes_sd_config>.
      tls_config:
        ca_file: /var/run/secrets/kubernetes.io/serviceaccount/ca.crt
        # If your node certificates are self-signed or use a different CA to the
        # master CA, then disable certificate verification below. Note that
        # certificate verification is an integral part of a secure infrastructure
        # so this should only be disabled in a controlled environment. You can
        # disable certificate verification by uncommenting the line below.
        #
        insecure_skip_verify: true
      bearer_token_file: /var/run/secrets/kubernetes.io/serviceaccount/token

      # Keep only the default/kubernetes service endpoints for the https port. This
      # will add targets for each API server which Kubernetes adds an endpoint to
      # the default/kubernetes service.
      relabel_configs:
        - source_labels: [__meta_kubernetes_namespace, __meta_kubernetes_service_name, __meta_kubernetes_endpoint_port_name]
          action: keep
          regex: default;kubernetes;https

    - job_name: 'kubernetes-nodes'

      # Default to scraping over https. If required, just disable this or change to
      # `http`.
      scheme: https

      # This TLS & bearer token file config is used to connect to the actual scrape
      # endpoints for cluster components. This is separate to discovery auth
      # configuration because discovery & scraping are two separate concerns in
      # Prometheus. The discovery auth config is automatic if Prometheus runs inside
      # the cluster. Otherwise, more config options have to be provided within the
      # <kubernetes_sd_config>.
      tls_config:
        ca_file: /var/run/secrets/kubernetes.io/serviceaccount/ca.crt
        # If your node certificates are self-signed or use a different CA to the
        # master CA, then disable certificate verification below. Note that
        # certificate verification is an integral part of a secure infrastructure
        # so this should only be disabled in a controlled environment. You can
        # disable certificate verification by uncommenting the line below.
        #
        insecure_skip_verify: true
      bearer_token_file: /var/run/secrets/kubernetes.io/serviceaccount/token

      kubernetes_sd_configs:
        - role: node

      relabel_configs:
        - action: labelmap
          regex: __meta_kubernetes_node_label_(.+)
        - target_label: __address__
          replacement: kubernetes.default.svc:443
        - source_labels: [__meta_kubernetes_node_name]
          regex: (.+)
          target_label: __metrics_path__
          replacement: /api/v1/nodes/$1/proxy/metrics


    - job_name: 'kubernetes-nodes-cadvisor'

      # Default to scraping over https. If required, just disable this or change to
      # `http`.
      scheme: https

      # This TLS & bearer token file config is used to connect to the actual scrape
      # endpoints for cluster components. This is separate to discovery auth
      # configuration because discovery & scraping are two separate concerns in
      # Prometheus. The discovery auth config is automatic if Prometheus runs inside
      # the cluster. Otherwise, more config options have to be provided within the
      # <kubernetes_sd_config>.
      tls_config:
        ca_file: /var/run/secrets/kubernetes.io/serviceaccount/ca.crt
        # If your node certificates are self-signed or use a different CA to the
        # master CA, then disable certificate verification below. Note that
        # certificate verification is an integral part of a secure infrastructure
        # so this should only be disabled in a controlled environment. You can
        # disable certificate verification by uncommenting the line below.
        #
        insecure_skip_verify: true
      bearer_token_file: /var/run/secrets/kubernetes.io/serviceaccount/token

      kubernetes_sd_configs:
        - role: node

      # This configuration will work only on kubelet 1.7.3+
      # As the scrape endpoints for cAdvisor have changed
      # if you are using older version you need to change the replacement to
      # replacement: /api/v1/nodes/$1:4194/proxy/metrics
      # more info here https://github.com/coreos/prometheus-operator/issues/633
      relabel_configs:
        - action: labelmap
          regex: __meta_kubernetes_node_label_(.+)
        - target_label: __address__
          replacement: kubernetes.default.svc:443
        - source_labels: [__meta_kubernetes_node_name]
          regex: (.+)
          target_label: __metrics_path__
          replacement: /api/v1/nodes/$1/proxy/metrics/cadvisor

    # Scrape config for service endpoints.
    #
    # The relabeling allows the actual service scrape endpoint to be configured
    # via the following annotations:
    #
    # * `prometheus.io/scrape`: Only scrape services that have a value of `true`
    # * `prometheus.io/scheme`: If the metrics endpoint is secured then you will need
    # to set this to `https` & most likely set the `tls_config` of the scrape config.
    # * `prometheus.io/path`: If the metrics path is not `/metrics` override this.
    # * `prometheus.io/port`: If the metrics are exposed on a different port to the
    # service then set this appropriately.
    - job_name: 'kubernetes-service-endpoints'

      kubernetes_sd_configs:
        - role: endpoints

      relabel_configs:
        - source_labels: [__meta_kubernetes_service_annotation_prometheus_io_scrape]
          action: keep
          regex: true
        - source_labels: [__meta_kubernetes_service_annotation_prometheus_io_scheme]
          action: replace
          target_label: __scheme__
          regex: (https?)
        - source_labels: [__meta_kubernetes_service_annotation_prometheus_io_path]
          action: replace
          target_label: __metrics_path__
          regex: (.+)
        - source_labels: [__address__, __meta_kubernetes_service_annotation_prometheus_io_port]
          action: replace
          target_label: __address__
          regex: ([^:]+)(?::\d+)?;(\d+)
          replacement: $1:$2
        - action: labelmap
          regex: __meta_kubernetes_service_label_(.+)
        - source_labels: [__meta_kubernetes_namespace]
          action: replace
          target_label: kubernetes_namespace
        - source_labels: [__meta_kubernetes_service_name]
          action: replace
          target_label: kubernetes_name
        - source_labels: [__meta_kubernetes_pod_node_name]
          action: replace
          target_label: kubernetes_node
    
    # Example scrape config for pods
    #
    # The relabeling allows the actual pod scrape endpoint to be configured via the
    # following annotations:
    #
    # * `prometheus.io/scrape`: Only scrape pods that have a value of `true`
    # * `prometheus.io/path`: If the metrics path is not `/metrics` override this.
    # * `prometheus.io/port`: Scrape the pod on the indicated port instead of the default of `9102`.
    - job_name: 'kubernetes-pods'

      kubernetes_sd_configs:
        - role: pod

      relabel_configs:
        - source_labels: [__meta_kubernetes_pod_annotation_prometheus_io_scrape]
          action: keep
          regex: true
        - source_labels: [__meta_kubernetes_pod_annotation_prometheus_io_path]
          action: replace
          target_label: __metrics_path__
          regex: (.+)
        - source_labels: [__address__, __meta_kubernetes_pod_annotation_prometheus_io_port]
          action: replace
          regex: ([^:]+)(?::\d+)?;(\d+)
          replacement: $1:$2
          target_label: __address__
        - action: labelmap
          regex: __meta_kubernetes_pod_label_(.+)
        - source_labels: [__meta_kubernetes_namespace]
          action: replace
          target_label: kubernetes_namespace
        - source_labels: [__meta_kubernetes_pod_name]
          action: replace
          target_label: kubernetes_pod_name
---
apiVersion: monitoring.coreos.com/v1
kind: Prometheus
metadata:
  namespace: {{ .Release.Namespace }}
  name: prometheus-main
spec:
  replicas: 1
  serviceAccountName: prometheus-k8s
  securityContext:
    runAsUser: 65534
    runAsNonRoot: true
    runAsGroup: 65534
    fsGroup: 65534
  additionalScrapeConfigs:
    key: "prometheus-additional.yaml"
    name: "prom-additional-scrape-configs"
  ruleSelector:
    matchLabels:
      role: alert-rules
  alerting:
    alertmanagers:
      - namespace: {{ .Release.Namespace }}
        name: alertmanager-main
        port: web

• Prometheus Operator Logs:

I don’t see anything useful from the operator logs.

Anything else we need to know?: