Exception when importing devfile with kubernetes component including a Deployment with environment variables referencing secrets #18508

rromannissen · 2020-12-02T10:05:34Z

Describe the bug

An exception occurs when trying to import a devfile that references a kubernets component file including a Deployment that defines environment variables on the container template that reference a Secret. The following error is displayed on the factory UI:

And after clicking OK:

As a workaround, removing the reference to the Secret and setting the environment variable value directly solves the problem.

Che version

latest
nightly
other: please specify

Eclipse Che 7.22.0 and CodeReady Workspaces 2.5.0.GA :: crw_2.5/20 :: che-dev @ 9348 (19) :: che-parent @ a6dd7f (7.15.0) :: che @ 7a66a (7.20.2-SNAPSHOT) :: codeready-workspaces @ a1180 (2.5.0.GA)

Steps to reproduce

Use the following devfile contents:

apiVersion: 1.0.0
metadata:
  name: order-management
projects:
- name: gateway
  source:
    type: git
    location: https://github.com/rromannissen/gateway-crw.git
    branch: master
- name: orders
  source:
    type: git
    location: https://github.com/rromannissen/orders-crw.git
    branch: master
- name: inventory
  source:
    type: git
    location: https://github.com/rromannissen/inventory-crw.git
    branch: master
- name: customers
  source:
    type: git
    location: https://github.com/rromannissen/customers-crw.git
    branch: master
components:
- alias: postgresql-customers
  type: kubernetes
  reference: ./postgresql-customers.yaml

The referenced file postgrestql-customers.yaml would have the following contents:

apiVersion: v1
kind: List
items:
- apiVersion: v1
  kind: Secret
  metadata:
    annotations:
      template.openshift.io/expose-database_name: '{.data[''database-name'']}'
      template.openshift.io/expose-password: '{.data[''database-password'']}'
      template.openshift.io/expose-username: '{.data[''database-user'']}'
    labels:
      template: postgresql-ephemeral-template
    name: postgresql-customers
  stringData:
    database-name: customers
    database-password: customers
    database-user: customers
- apiVersion: v1
  kind: Service
  metadata:
    annotations:
      template.openshift.io/expose-uri: postgres://{.spec.clusterIP}:{.spec.ports[?(.name=="postgresql")].port}
    labels:
      template: postgresql-ephemeral-template
    name: postgresql-customers
  spec:
    ports:
    - name: postgresql
      nodePort: 0
      port: 5432
      protocol: TCP
      targetPort: 5432
    selector:
      name: postgresql-customers
    sessionAffinity: None
    type: ClusterIP
  status:
    loadBalancer: {}
- apiVersion: apps/v1
  kind: Deployment
  metadata:
    annotations:
      template.alpha.openshift.io/wait-for-ready: "true"
    labels:
      template: postgresql-ephemeral-template
    name: postgresql-customers
  spec:
    replicas: 1
    selector:
      matchLabels:
        name: postgresql-customers
    strategy:
      type: Recreate
    template:
      metadata:
        labels:
          name: postgresql-customers
      spec:
        containers:
        - capabilities: {}
          env:
          - name: POSTGRESQL_USER
            valueFrom:
              secretKeyRef:
                key: database-user
                name: postgresql-customers
          - name: POSTGRESQL_PASSWORD
            valueFrom:
              secretKeyRef:
                key: database-password
                name: postgresql-customers
          - name: POSTGRESQL_DATABASE
            valueFrom:
              secretKeyRef:
                key: database-name
                name: postgresql-customers
          image: registry.redhat.io/rhel8/postgresql-10
          imagePullPolicy: IfNotPresent
          livenessProbe:
            exec:
              command:
              - /usr/libexec/check-container
              - --live
            initialDelaySeconds: 120
            timeoutSeconds: 10
          name: postgresql
          ports:
          - containerPort: 5432
            protocol: TCP
          readinessProbe:
            exec:
              command:
              - /usr/libexec/check-container
            initialDelaySeconds: 5
            timeoutSeconds: 1
          resources:
            limits:
              memory: 512Mi
          securityContext:
            capabilities: {}
            privileged: false
          terminationMessagePath: /dev/termination-log
          volumeMounts:
          - mountPath: /var/lib/pgsql/data
            name: postgresql-customers-data
        dnsPolicy: ClusterFirst
        restartPolicy: Always
        volumes:
        - emptyDir:
            medium: ""
          name: postgresql-customers-data
  status: {}

This file is an instantiation of the postgresql-ephemeral template from OCP, changing the DeploymentConfig into a Deployment object for CodeReady Workspaces to accept it.

Expected behavior

The objects defined in the postgresql-customers.yaml file for the postgresql-customers kubernetes component get created correctly.

Runtime

kubernetes (include output of kubectl version)
Openshift (include output of oc version)
minikube (include output of minikube version and kubectl version)
minishift (include output of minishift version and oc version)
docker-desktop + K8S (include output of docker version and kubectl version)
other: (please specify)

Reproduced in https://che.openshift.io and CodeReady Workspaces 2.5.0 in OCP 4.6.4.

Screenshots

Installation method

chectl
- provide a full command that was used to deploy Eclipse Che (including the output)
- provide an output of chectl version command
OperatorHub
I don't know

OperatorHub for CodeReady Workspaces 2.5.0 in OCP 4.6.4

Environment

Reproduced in https://che.openshift.io and CodeReady Workspaces 2.5.0 in OCP 4.6.4.

Eclipse Che Logs

Obtained from CodeReady Workspaces 2.5.0 in OCP 4.6.4.

2020-12-02 10:02:11,147[nio-8080-exec-8]  [INFO ] [o.e.c.a.w.s.WorkspaceRuntimes 480]   - Starting workspace 'dev1/order-managementu8pos' with id 'workspacewvk46diujcocsbo2' by user 'dev1'
2020-12-02 10:02:40,158[aceSharedPool-9]  [WARN ] [.i.k.KubernetesInternalRuntime 255]  - Failed to start Kubernetes runtime of workspace workspacewvk46diujcocsbo2.
java.lang.NullPointerException: null
	at java.base/java.util.regex.Matcher.getTextLength(Matcher.java:1770)
	at java.base/java.util.regex.Matcher.reset(Matcher.java:416)
	at java.base/java.util.regex.Matcher.<init>(Matcher.java:253)
	at java.base/java.util.regex.Pattern.matcher(Pattern.java:1133)
	at org.eclipse.che.workspace.infrastructure.kubernetes.util.EnvVars.extractReferencedVariables(EnvVars.java:96)
	at org.eclipse.che.commons.lang.TopologicalSort.sort(TopologicalSort.java:96)
	at org.eclipse.che.workspace.infrastructure.kubernetes.provision.env.EnvVarsConverter.provision(EnvVarsConverter.java:77)
	at org.eclipse.che.workspace.infrastructure.openshift.OpenShiftEnvironmentProvisioner.provision(OpenShiftEnvironmentProvisioner.java:151)
	at org.eclipse.che.workspace.infrastructure.openshift.OpenShiftEnvironmentProvisioner.provision(OpenShiftEnvironmentProvisioner.java:57)
	at org.eclipse.che.workspace.infrastructure.kubernetes.KubernetesInternalRuntime.provisionWorkspace(KubernetesInternalRuntime.java:303)
	at org.eclipse.che.workspace.infrastructure.openshift.OpenShiftInternalRuntime.provisionWorkspace(OpenShiftInternalRuntime.java:131)
	at org.eclipse.che.workspace.infrastructure.kubernetes.KubernetesInternalRuntime.internalStart(KubernetesInternalRuntime.java:202)
	at org.eclipse.che.api.workspace.server.spi.InternalRuntime.start(InternalRuntime.java:141)
	at org.eclipse.che.api.workspace.server.WorkspaceRuntimes$StartRuntimeTask.run(WorkspaceRuntimes.java:960)
	at org.eclipse.che.commons.lang.concurrent.CopyThreadLocalRunnable.run(CopyThreadLocalRunnable.java:38)
	at java.base/java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1736)
	at io.micrometer.core.instrument.internal.TimedRunnable.run(TimedRunnable.java:44)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at org.eclipse.che.commons.observability.CountedThreadFactory.lambda$newThread$0(CountedThreadFactory.java:75)
	at java.base/java.lang.Thread.run(Thread.java:834)
2020-12-02 10:02:40,364[aceSharedPool-9]  [INFO ] [o.e.c.a.w.s.WorkspaceRuntimes 984]   - Workspace 'dev1:order-managementu8pos' with id 'workspacewvk46diujcocsbo2' start failed
2020-12-02 10:02:40,364[aceSharedPool-9]  [ERROR] [o.e.c.a.w.s.WorkspaceRuntimes 994]   - An exception occurred.
org.eclipse.che.api.workspace.server.spi.InternalInfrastructureException: An exception occurred.
	at org.eclipse.che.workspace.infrastructure.kubernetes.KubernetesInternalRuntime.wrapAndRethrow(KubernetesInternalRuntime.java:963)
	at org.eclipse.che.workspace.infrastructure.kubernetes.KubernetesInternalRuntime.internalStart(KubernetesInternalRuntime.java:275)
	at org.eclipse.che.api.workspace.server.spi.InternalRuntime.start(InternalRuntime.java:141)
	at org.eclipse.che.api.workspace.server.WorkspaceRuntimes$StartRuntimeTask.run(WorkspaceRuntimes.java:960)
	at org.eclipse.che.commons.lang.concurrent.CopyThreadLocalRunnable.run(CopyThreadLocalRunnable.java:38)
	at java.base/java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1736)
	at io.micrometer.core.instrument.internal.TimedRunnable.run(TimedRunnable.java:44)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at org.eclipse.che.commons.observability.CountedThreadFactory.lambda$newThread$0(CountedThreadFactory.java:75)
	at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.NullPointerException: null
	at java.base/java.util.regex.Matcher.getTextLength(Matcher.java:1770)
	at java.base/java.util.regex.Matcher.reset(Matcher.java:416)
	at java.base/java.util.regex.Matcher.<init>(Matcher.java:253)
	at java.base/java.util.regex.Pattern.matcher(Pattern.java:1133)
	at org.eclipse.che.workspace.infrastructure.kubernetes.util.EnvVars.extractReferencedVariables(EnvVars.java:96)
	at org.eclipse.che.commons.lang.TopologicalSort.sort(TopologicalSort.java:96)
	at org.eclipse.che.workspace.infrastructure.kubernetes.provision.env.EnvVarsConverter.provision(EnvVarsConverter.java:77)
	at org.eclipse.che.workspace.infrastructure.openshift.OpenShiftEnvironmentProvisioner.provision(OpenShiftEnvironmentProvisioner.java:151)
	at org.eclipse.che.workspace.infrastructure.openshift.OpenShiftEnvironmentProvisioner.provision(OpenShiftEnvironmentProvisioner.java:57)
	at org.eclipse.che.workspace.infrastructure.kubernetes.KubernetesInternalRuntime.provisionWorkspace(KubernetesInternalRuntime.java:303)
	at org.eclipse.che.workspace.infrastructure.openshift.OpenShiftInternalRuntime.provisionWorkspace(OpenShiftInternalRuntime.java:131)
	at org.eclipse.che.workspace.infrastructure.kubernetes.KubernetesInternalRuntime.internalStart(KubernetesInternalRuntime.java:202)
	... 9 common frames omitted

The text was updated successfully, but these errors were encountered:

l0rd · 2020-12-02T22:10:34Z

Thank you @rromannissen for reporting this bug. We do declare that we support secrets indeed.

FYI we have a mechanism to automatically mount secrets in the containers of a workspace. But I am not sure if it's applicable in your use case.

mshaposhnik · 2021-01-18T10:41:31Z

Fixed in master;

rromannissen added the kind/bug Outline of a bug - must adhere to the bug report template. label Dec 2, 2020

che-bot added the status/need-triage An issue that needs to be prioritized by the curator responsible for the triage. See https://github. label Dec 2, 2020

l0rd added area/che-server severity/P1 Has a major impact to usage or development of the system. and removed status/need-triage An issue that needs to be prioritized by the curator responsible for the triage. See https://github. labels Dec 2, 2020

skabashnyuk mentioned this issue Dec 30, 2020

Che Platform Sprint 195 #18712

Closed

6 tasks

skabashnyuk added this to the 7.25 milestone Dec 30, 2020

skabashnyuk added the team/platform label Dec 30, 2020

mshaposhnik mentioned this issue Jan 18, 2021

Fix NPE for ENV-s that not contain value, but only valueFrom. #18816

Merged

9 tasks

mshaposhnik closed this as completed Jan 18, 2021

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Exception when importing devfile with kubernetes component including a Deployment with environment variables referencing secrets #18508

Exception when importing devfile with kubernetes component including a Deployment with environment variables referencing secrets #18508

rromannissen commented Dec 2, 2020

l0rd commented Dec 2, 2020

mshaposhnik commented Jan 18, 2021

Exception when importing devfile with kubernetes component including a Deployment with environment variables referencing secrets #18508

Exception when importing devfile with kubernetes component including a Deployment with environment variables referencing secrets #18508

Comments

rromannissen commented Dec 2, 2020

Describe the bug

Che version

Steps to reproduce

Expected behavior

Runtime

Screenshots

Installation method

Environment

Eclipse Che Logs

l0rd commented Dec 2, 2020

mshaposhnik commented Jan 18, 2021