Cray System Management Documentation > Cray System Management (CSM) Administration Guide > configuration management > Backup and Restore VCS Data

Backup and Restore VCS Data

This document describes how to perform backups and restores of the Version Control Service (VCS) data. For general information, see Version Control Service (VCS).

Overview
Backup procedure
1. Manually backup Postgres data
2. Backup PVC data
Restore procedure
1. Restore Postgres data
2. Restore PVC data
Alternative backup/restore strategy
- Alternative export method
- Alternative import method

Overview

Data for Gitea is stored in two places: Git content is stored directly in a PVC, while structural data, such as Gitea users and the list and attributes of repositories, is stored in a Postgres database. Because of this, both sources must be backed up and restored together. A full restore is not possible without backups of both the PVC and Postgres data. CSM performs automatic periodic backups of the Postgres data, but the PVC data is not automatically backed up by CSM. Administrators are recommended to take periodic backups, using one of the methods outlined on this page.

Backup procedure

Remember that backups of both the Postgres and PVC data are necessary in order to perform a complete restore of VCS data.

Manually backup Postgres data
Manually backup PVC data

1. Manually backup Postgres data

Determine which Postgres member is the leader.

ncn-mw# kubectl exec gitea-vcs-postgres-0 -n services -c postgres -it -- patronictl list

Example output:

+ Cluster: gitea-vcs-postgres (6995618180238446669) -----+----+-----------+
|        Member        |     Host     |  Role  |  State  | TL | Lag in MB |
+----------------------+--------------+--------+---------+----+-----------+
| gitea-vcs-postgres-0 |  10.45.0.21  | Leader | running |  1 |           |
| gitea-vcs-postgres-1 | 10.46.128.19 |        | running |  1 |         0 |
| gitea-vcs-postgres-2 |  10.47.0.21  |        | running |  1 |         0 |
+----------------------+--------------+--------+---------+----+-----------+

Log into the leader pod and dump the data to a local file.

ncn-mw# POSTGRES_LEADER=gitea-vcs-postgres-0
ncn-mw# kubectl exec -it ${POSTGRES_LEADER} -n services -c postgres -- pg_dumpall -c -U postgres > gitea-vcs-postgres.sql

Determine what secrets are associated with the PostgreSQL credentials:

ncn-mw# kubectl get secrets -n services | grep gitea-vcs-postgres.credentials

Example output:

postgres.gitea-vcs-postgres.credentials                   Opaque                                2      13d
service-account.gitea-vcs-postgres.credentials            Opaque                                2      13d
standby.gitea-vcs-postgres.credentials                    Opaque                                2      13d

Export each secret to a manifest file.

The creationTimestamp, resourceVersion, selfLink, and uid metadata fields are removed from each secret as they are exported.

ncn-mw# SECRETS="postgres service-account standby"
ncn-mw# tmpfile=$(mktemp)
ncn-mw# echo "---" > gitea-vcs-postgres.manifest && for secret in $SECRETS; do
            kubectl get secret "${secret}.gitea-vcs-postgres.credentials" -n services -o yaml > "${tmpfile}"
            for field in creationTimestamp resourceVersion selfLink uid; do
                yq d -i "${tmpfile}" "metadata.${field}"
            done
            cat "${tmpfile}" >> gitea-vcs-postgres.manifest
            echo "---" >> gitea-vcs-postgres.manifest
        done ; rm "${tmpfile}"

Copy all files to a safe location.

2. Backup PVC data

The VCS Postgres backups should be accompanied by backups of the VCS PVC. The export process can be run at any time while the service is running using the following commands:

ncn-mw# POD=$(kubectl -n services get pod -l app.kubernetes.io/instance=gitea -o json | jq -r '.items[] | .metadata.name')
ncn-mw# kubectl -n services exec ${POD} -- tar -cvf /tmp/vcs.tar /var/lib/gitea/ &&
        kubectl -n services cp ${POD}:/tmp/vcs.tar ./vcs.tar

Be sure to save the resulting tar file to a safe location.

Restore procedure

In order to completely restore the VCS data, first the Postgres data must be restored, then the PVC data must be restored.

1. Restore Postgres data

Copy the database dump to an accessible location.
- If a manual dump of the database was taken, then check that the dump file exists in a location off the Postgres cluster. It will be needed in the steps below.
- If the database is being automatically backed up, then the most recent version of the dump and the secrets should exist in the postgres-backup S3 bucket. These will be needed in the steps below. List the files in the postgres-backup S3 bucket and if the files exist, download the dump and secrets out of the S3 bucket. The cray artifacts CLI can be used list and download the files. Note that the .psql file contains the database dump and the .manifest file contains the secrets. The CLI must be configured and authenticated in order to do this. See Configure the Cray CLI.
1. List the available backups.
```
ncn-mw# cray artifacts list postgres-backup --format json | jq -r '.artifacts[].Key | select(contains("vcs"))'
```
  Example output:
```
gitea-vcs-postgres-2022-09-14T01:10:04.manifest
gitea-vcs-postgres-2022-09-14T01:10:04.psql
```
2. Set the environment variables to the name of the backup files.
  
  In order to avoid a kubectl cp bug, the dump file will be downloaded with a slightly altered name (: characters replaced with - characters).
```
ncn-mw# MANIFEST=gitea-vcs-postgres-2022-09-14T01:10:04.manifest
ncn-mw# DUMPFILE_SRC=gitea-vcs-postgres-2022-09-14T01:10:04.psql
ncn-mw# DUMPFILE=${DUMPFILE_SRC//:/-}
```
3. Download the backup files.
```
ncn-mw# cray artifacts get postgres-backup "${DUMPFILE_SRC}" "${DUMPFILE}"
ncn-mw# cray artifacts get postgres-backup "${MANIFEST}" "${MANIFEST}"
```

Set helper variables.

ncn-mw# SERVICE=gitea-vcs
ncn-mw# SERVICELABEL=vcs
ncn-mw# NAMESPACE=services
ncn-mw# POSTGRESQL=gitea-vcs-postgres

Scale the VCS service to 0.

ncn-mw# kubectl scale deployment ${SERVICE} -n "${NAMESPACE}" --replicas=0

Wait for the pods to terminate.

ncn-mw# while kubectl get pods -n "${NAMESPACE}" -l app.kubernetes.io/name="${SERVICELABEL}" | grep -qv NAME ; do
            echo "  waiting for pods to terminate"; sleep 2
        done

Delete the VCS Postgres cluster.

ncn-mw# kubectl get postgresql "${POSTGRESQL}" -n "${NAMESPACE}" -o json | jq 'del(.spec.selector)' |
            jq 'del(.spec.template.metadata.labels."controller-uid")' | jq 'del(.status)' > postgres-cr.json
ncn-mw# kubectl delete -f postgres-cr.json

Wait for the pods to terminate.

ncn-mw# while kubectl get pods -l "application=spilo,cluster-name=${POSTGRESQL}" -n "${NAMESPACE}" | grep -qv NAME ; do
            echo "  waiting for pods to terminate"; sleep 2
        done

Create a new single instance VCS Postgres cluster.

ncn-mw# cp postgres-cr.json postgres-orig-cr.json
ncn-mw# jq '.spec.numberOfInstances = 1' postgres-orig-cr.json > postgres-cr.json
ncn-mw# kubectl create -f postgres-cr.json

Wait for the pod to start.

ncn-mw# while ! kubectl get pods -l "application=spilo,cluster-name=${POSTGRESQL}" -n "${NAMESPACE}" | grep -qv NAME ; do
            echo "  waiting for pod to start"; sleep 2
        done

Wait for the Postgres cluster to start running.

ncn-mw# while [ $(kubectl get postgresql "${POSTGRESQL}" -n "${NAMESPACE}" -o json | jq -r '.status.PostgresClusterStatus') != "Running" ]
        do
            echo "  waiting for postgresql to start running"; sleep 2
        done

Copy the database dump file to the Postgres member.

ncn-mw# kubectl cp "./${DUMPFILE}" "${POSTGRESQL}-0:/home/postgres/${DUMPFILE}" -c postgres -n services

Restore the data.
```
ncn-mw# kubectl exec "${POSTGRESQL}-0" -c postgres -n services -it -- psql -U postgres < "${DUMPFILE}"
```
Errors such as ... already exists can be ignored; the restore can be considered successful when it completes.

Either update or re-create the gitea-vcs-postgres secrets.

Update the secrets in Postgres.

If a manual dump was done, and the secrets were not saved, then the secrets in the newly created Postgres cluster will need to be updated.

From the three gitea-vcs-postgres secrets, collect the password for each Postgres username: postgres, service_account, and standby.

ncn-mw# for secret in postgres.gitea-vcs-postgres.credentials service-account.gitea-vcs-postgres.credentials \
            standby.gitea-vcs-postgres.credentials
        do
            echo -n "secret ${secret} username & password: "
            echo -n "`kubectl get secret "${secret}" -n "${NAMESPACE}" -ojsonpath='{.data.username}' | base64 -d` "
            echo `kubectl get secret "${secret}" -n "${NAMESPACE}" -ojsonpath='{.data.password}'| base64 -d`
        done

Example output:

secret postgres.gitea-vcs-postgres.credentials username & password: postgres ABCXYZ
secret service-account.gitea-vcs-postgres.credentials username & password: service_account ABC123
secret standby.gitea-vcs-postgres.credentials username & password: standby 123456

kubectl exec into the Postgres pod.

ncn-mw# kubectl exec "${POSTGRESQL}-0" -n "${NAMESPACE}" -c postgres -it -- bash

Open a Postgres console.
```
pod# /usr/bin/psql postgres postgres
```
Update the password for each user to match the values found in the secrets.
1. Update the password for the postgres user.
```
postgres# ALTER USER postgres WITH PASSWORD 'ABCXYZ';
```
  Example of successful output:
```
ALTER ROLE
```
2. Update the password for the service_account user.
```
postgres# ALTER USER service_account WITH PASSWORD 'ABC123';
```
  Example of successful output:
```
ALTER ROLE
```
3. Update the password for the standby user.
```
postgres# ALTER USER standby WITH PASSWORD '123456';
```
  Example of successful output:
```
ALTER ROLE
```
Exit the Postgres console with the \q command.
Exit the Postgres pod with the exit command.

Re-create secrets in Kubernetes.

If the Postgres secrets were auto-backed up, then re-create the secrets in Kubernetes.

Delete and re-create the three gitea-vcs-postgres secrets using the manifest that was copied from S3 earlier.

ncn-mw# kubectl delete secret postgres.gitea-vcs-postgres.credentials \
            service-account.gitea-vcs-postgres.credentials standby.gitea-vcs-postgres.credentials -n services
ncn-mw# kubectl apply -f "${MANIFEST}"

Restart the Postgres cluster.

ncn-mw# kubectl delete pod -n "${NAMESPACE}" "${POSTGRESQL}-0"

Wait for the postgresql pod to start.

ncn-mw# while ! kubectl get pods -l "application=spilo,cluster-name=${POSTGRESQL}" -n "${NAMESPACE}" | grep -qv NAME ; do
            echo "  waiting for pods to start"; sleep 2
        done

Scale the Postgres cluster back to 3 instances.

ncn-mw# kubectl patch postgresql "${POSTGRESQL}" -n "${NAMESPACE}" --type='json' \
            -p='[{"op" : "replace", "path":"/spec/numberOfInstances", "value" : 3}]'

Wait for the postgresql cluster to start running.

ncn-mw# while [ $(kubectl get postgresql "${POSTGRESQL}" -n "${NAMESPACE}" -o json | jq -r '.status.PostgresClusterStatus') != "Running" ]
        do
            echo "  waiting for postgresql to start running"; sleep 2
        done

Scale the Gitea service back up.

ncn-mw# kubectl scale deployment ${SERVICE} -n "${NAMESPACE}" --replicas=1

Wait for the Gitea pods to start.

ncn-mw# while ! kubectl get pods -n "${NAMESPACE}" -l app.kubernetes.io/name="${SERVICELABEL}" | grep -qv NAME ; do
            echo "  waiting for pods to start"; sleep 2
        done

2. Restore PVC data

When restoring the VCS Postgres database, the PVC should also be restored to the same point in time. The restore process can be run at any time while the service is running using the following commands:

ncn-mw# POD=$(kubectl -n services get pod -l app.kubernetes.io/instance=gitea -o json | jq -r '.items[] | .metadata.name')
ncn-mw# kubectl -n services cp ./vcs.tar ${POD}:/tmp/vcs.tar &&
        kubectl -n services exec ${POD} -- tar -C / -xvf /tmp/vcs.tar &&
        kubectl -n services rollout restart deployment gitea-vcs

Alternative backup/restore strategy

An alternative to the separate backups of the Postgres and PVC data is to backup the Git data. This has the advantage that only one backup is needed and that the Git backups can be imported into any Git server, not just Gitea. This has the disadvantage that some information about the Gitea deployment is lost (such as user and organization information) and may need to be recreated manually if the VCS deployment is lost.

The following scripts create and use a vcs-content directory that contains all Git data. This should be copied to a safe location after export, and moved back to the system before import.

Alternative export method

WARNING: The following example uses the VCS admin username and password in plaintext on the command line, meaning it will be stored in the shell history as well as be visible to all users on the system in the process table. These dangers can be avoided by modifying or replacing the curl command (such as supplying the credentials to curl using the --netrc-file argument instead of the --user argument, or replacing it with a simple Python script).

Use the following commands to do the export:

ncn-mw# RESULTS=vcs-content
ncn-mw# mkdir $RESULTS
ncn-mw# VCS_USER=$(kubectl get secret -n services vcs-user-credentials --template={{.data.vcs_username}} | base64 --decode)
ncn-mw# VCS_PASSWORD=$(kubectl get secret -n services vcs-user-credentials --template={{.data.vcs_password}} | base64 --decode)
ncn-mw# git config --global credential.helper store
ncn-mw# echo "https://${VCS_USER}:${VCS_PASSWORD}@api-gw-service-nmn.local" > ~/.git-credentials
ncn-mw# for repo in $(curl -s https://api-gw-service-nmn.local/vcs/api/v1/orgs/cray/repos --user ${VCS_USER}:${VCS_PASSWORD}| jq -r '.[] | .name') ; do
            git clone --mirror https://api-gw-service-nmn.local/vcs/cray/${repo}.git
            cd ${repo}.git
            git bundle create ${repo}.bundle --all
            cp ${repo}.bundle ../$RESULTS
            cd ..
            rm -r $repo.git
        done

Alternative import method

Use the following commands to do the import:

ncn-mw# SOURCE=vcs-content
ncn-mw# VCS_USER=$(kubectl get secret -n services vcs-user-credentials --template={{.data.vcs_username}} | base64 --decode)
ncn-mw# VCS_PASSWORD=$(kubectl get secret -n services vcs-user-credentials --template={{.data.vcs_password}} | base64 --decode)
ncn-mw# git config --global credential.helper store
ncn-mw# echo "https://${VCS_USER}:${VCS_PASSWORD}@api-gw-service-nmn.local" > ~/.git-credentials
ncn-mw# for file in $(ls $SOURCE); do
            repo=$(echo $file | sed 's/.bundle$//')
            git clone --mirror ${SOURCE}/${repo}.bundle
            cd ${repo}.git
            git remote set-url origin https://api-gw-service-nmn.local/vcs/cray/${repo}.git
            git push
            cd ..
            rm -r ${repo}.git
        done

Prior to import, the repository structure may need to be recreated if it has not already been by an install.

Adjust the repository list as necessary, if any additional repositories are present. Repository settings such as public or private will also need to be manually set, if applicable.

For example:

WARNING: The following example uses the VCS admin username and password in plaintext on the command line, meaning it will be stored in the shell history as well as be visible to all users on the system in the process table. These dangers can be avoided by modifying or replacing the curl command (such as supplying the credentials to curl using the --netrc-file argument instead of the --user argument, or replacing it with a simple Python script).

ncn-mw# VCS_USER=$(kubectl get secret -n services vcs-user-credentials --template={{.data.vcs_username}} | base64 --decode)
ncn-mw# VCS_PASSWORD=$(kubectl get secret -n services vcs-user-credentials --template={{.data.vcs_password}} | base64 --decode)
ncn-mw# REPOS="analytics-config-management cos-config-management cpe-config-management slurm-config-management sma-config-management uan-config-management csm-config-management"
ncn-mw# for repo in $REPOS ; do
            curl -X POST https://api-gw-service-nmn.local/vcs/api/v1/orgs/cray/repos -u ${VCS_USER}:${VCS_PASSWORD} -d name=${repo}
        done