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ghga/pcs-chart

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By German Human Genome-Phenome Archive

Updated 8 days ago

Purge Controller Service - a service to commission file deletions

Helm
0

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ghga/pcs-chart repository overview

pcs

Purge Controller Service - a service to commission file deletions

Installing

helm install pcs oci://registry-1.docker.io/ghga/pcs-chart

Source

Part of the GHGA monorepo. See values.yaml for the full set of configurable values.

Service Configuration

NameDescriptionValue
config.hostIP of the host."127.0.0.1"
config.mongo_dsnMongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/null
config.db_nameName of the database located on the MongoDB server. NOTE: this chart's configmap.tpl always overwrites config.db_name with the value computed from mongodb.dbName - a value set directly under config.db_name is silently discarded. Set mongodb.dbName instead.null
config.service_instance_idA string that uniquely identifies this instance across all instances of this service. A globally unique Kafka client ID will be created by concatenating the service_name and the service_instance_id.null
config.token_hashesList of token hashes corresponding to the tokens that can be used to authenticate calls to this service.null
config.enable_opentelemetryIf set to true, this will run necessary setup code.If set to false, no setup code is run, which leaves tracing disabled.false
config.db_version_collectionThe name of the collection containing DB version information for this servicenull
config.migration_wait_secThe number of seconds to wait before checking the DB version againnull
config.otel_trace_sampling_rateDetermines which proportion of spans should be sampled. A value of 1.0 means all and is equivalent to the previous behaviour. Setting this to 0 will result in no spans being sampled, but this does not automatically set enable_opentelemetry to False.1.0
config.file_deletion_request_topicThe name of the topic to receive events informing about files to delete.null
config.file_deletion_request_typeThe type used for events indicating that a request to delete a file has been received.null
config.log_levelThe minimum log level to capture."INFO"
config.service_nameNOTE: this chart's configmap.tpl always overwrites config.service_name with the value computed from serviceName - a value set directly under config.service_name is silently discarded. Set serviceName instead."pcs"
config.log_formatIf set, will replace JSON formatting with the specified string format. If not set, has no effect. In addition to the standard attributes, the following can also be specified: timestamp, service, instance, level, correlation_id, and detailsnull
config.log_tracebackWhether to include exception tracebacks in log messages.true
config.kafka_serversA list of connection strings to connect to Kafka bootstrap servers.null
config.kafka_security_protocolProtocol used to communicate with brokers. Valid values are: PLAINTEXT, SSL."PLAINTEXT"
config.kafka_ssl_cafileCertificate Authority file path containing certificates used to sign broker certificates. If a CA is not specified, the default system CA will be used if found by OpenSSL.""
config.kafka_ssl_certfileOptional filename of client certificate, as well as any CA certificates needed to establish the certificate's authenticity.""
config.kafka_ssl_keyfileOptional filename containing the client private key.""
config.kafka_ssl_passwordOptional password to be used for the client private key.""
config.generate_correlation_idA flag, which, if False, will result in an error when inbound requests don't possess a correlation ID. If True, requests without a correlation ID will be assigned a newly generated ID in the correlation ID middleware function.true
config.kafka_max_message_sizeThe largest message size that can be transmitted, in bytes, before compression. Only services that have a need to send/receive larger messages should set this. When used alongside compression, this value can be set to something greater than the broker's message.max.bytes field, which effectively concerns the compressed message size.1048576
config.kafka_compression_typeThe compression type used for messages. Valid values are: None, gzip, snappy, lz4, and zstd. If None, no compression is applied. This setting is only relevant for the producer and has no effect on the consumer. If set to a value, the producer will compress messages before sending them to the Kafka broker. If unsure, zstd provides a good balance between speed and compression ratio.null
config.kafka_max_retriesThe maximum number of times to immediately retry consuming an event upon failure. Works independently of the dead letter queue.0
config.kafka_enable_dlqA flag to toggle the dead letter queue. If set to False, the service will crash upon exhausting retries instead of publishing events to the DLQ. If set to True, the service will publish events to the DLQ topic after exhausting all retriesfalse
config.kafka_dlq_topicThe name of the topic used to resolve error-causing events."dlq"
config.kafka_retry_backoffThe number of seconds to wait before retrying a failed event. The backoff time is doubled for each retry attempt.0
config.mongo_timeoutTimeout in seconds for API calls to MongoDB. The timeout applies to all steps needed to complete the operation, including server selection, connection checkout, serialization, and server-side execution. When the timeout expires, PyMongo raises a timeout exception. If set to None, the operation will not time out (default MongoDB behavior).null
config.migration_max_wait_secThe maximum number of seconds to wait for migrations to complete before raising an error.null
config.portPort to expose the server on the specified host8080
config.auto_reloadA development feature. Set to True to automatically reload the server upon code changesfalse
config.workersNumber of workers processes to run.1
config.timeout_keep_aliveThe time in seconds to keep an idle connection open for subsequent requests before closing it. This value should be higher than the timeout used by any client or reverse proxy to avoid premature connection closures.90
config.api_root_pathRoot path at which the API is reachable. This is relative to the specified host and port. NOTE: this chart's configmap.tpl always overwrites config.api_root_path with the value computed from apiBasePath - a value set directly under config.api_root_path is silently discarded. Set apiBasePath instead.""
config.openapi_urlPath to get the openapi specification in JSON format. This is relative to the specified host and port."/openapi.json"
config.docs_urlPath to host the swagger documentation. This is relative to the specified host and port."/docs"
config.cors_allowed_originsA list of origins that should be permitted to make cross-origin requests. By default, cross-origin requests are not allowed. You can use ['*'] to allow any origin.null
config.cors_allow_credentialsIndicate that cookies should be supported for cross-origin requests. Defaults to False. Also, cors_allowed_origins cannot be set to ['*'] for credentials to be allowed. The origins must be explicitly specified.null
config.cors_allowed_methodsA list of HTTP methods that should be allowed for cross-origin requests. Defaults to ['GET']. You can use ['*'] to allow all standard methods.null
config.cors_allowed_headersA list of HTTP request headers that should be supported for cross-origin requests. Defaults to []. You can use ['*'] to allow all request headers. The Accept, Accept-Language, Content-Language, Content-Type and some are always allowed for CORS requests.null
config.cors_exposed_headersA list of HTTP response headers that should be exposed for cross-origin responses. Defaults to []. Note that you can NOT use ['*'] to expose all response headers. The Cache-Control, Content-Language, Content-Length, Content-Type, Expires, Last-Modified and Pragma headers are always exposed for CORS responses.null

Parameters

NameDescriptionValue
global.imageRegistryRegistry override applied to every image reference in the umbrella (read by the vendored common library chart's common.images.image helper)""
global.imagePullSecretsPull secrets applied to every workload in the umbrella, combined with each image's own pullSecrets below (read by the vendored common library chart's common.images.renderPullSecrets helper)[]
commandPrefixPath prefix prepended to executable before it's rendered into command/args""
commandStyle"shell": wrap executable+args in command via a shell string (needs a shell in the image). "exec": render command=[prefixed executable], args as a real argv list - for shell-less hardened runtime images."exec"
executableExecutable name and arguments (will be combined into a shell command)"pcs"
executableArgs["run-rest"]
deployment.enabledRender the Deployment resource; disable for Job/CronJob-only chartstrue
job.enabledRender a one-off Job resource alongside (or instead of) the Deploymentfalse
cronjobs.default.enabledfalse
nameOverrideOverride just the chart-name portion of generated resource names (the vendored common library chart's common.names.name convention)""
fullnameOverrideOverride the entire generated resource name, bypassing the <release>-<chart> convention (the vendored common library chart's common.names.fullname)""
namespaceOverrideOverride the namespace resources render into instead of .Release.Namespace (the vendored common library chart's common.names.namespace)""
commonLabelsLabels merged onto every rendered resource's metadata - Deployment, CronJob, Job, Service, HPA, DestinationRule, HTTPRoute, Probe, ConfigMap, ServiceAccount, NetworkPolicy, KafkaUser. No separate, narrower per-workload-only value: use service.labels below for Service/DestinationRule-only labels{}
commonAnnotationsAnnotations merged onto the same set of resources as commonLabels (see there); use service.annotations below for Service/DestinationRule-only annotations{}
image.registryDefault image registry; overridden by global.imageRegistry when set"docker.io"
image.repositoryImage repository path (create_charts.py fills this in per member)"ghga/pcs"
image.tagImage tag; left empty so it falls back to the chart's appVersion == the platform version (ADR-0004)""
image.digestPin the image by digest instead of tag, when set (takes precedence in the vendored common library chart's common.images.image helper)"sha256:4aebbed13dcd02a4be6b16e93a48866edbe05d6c91368ff61b87da6709084be7"
image.pullPolicyimagePullPolicy override; null defaults to Always for a latest tag, IfNotPresent otherwisenull
image.pullSecretsExtra pull secrets for just this image reference[]
replicaCountDeployment replica count; ignored when autoscaling.enabled1
revisionHistoryLimitNumber of old ReplicaSets Kubernetes keeps around for rollback1
shareProcessNamespaceShare the pod's process namespace across containers; forced true whenever vaultAgent.enabled (the agent sends signals to the app's PID)false
podSecurityContext.fsGroupGroup ID Kubernetes chowns mounted volumes to1000
initContainersExtra init containers to run before the main container (the migration init container below is prepended to this list when enabled)[]
migrationInitContainer.enabledRun a dedicated init container for DB migrations before the main container startsfalse
migrationInitContainer.imageImage for the migration init container; defaults to the main container's image when empty""
migrationInitContainer.imagePullPolicyimagePullPolicy for just the migration init container; defaults to the main container's own imagePullPolicy when unsetnull
migrationInitContainer.executableExecutable name and arguments run inside the migration init container""
migrationInitContainer.executableArgs[]
migrationInitContainer.envExtra env vars for just the migration init container[]
migrationInitContainer.resources{}
migrationInitContainer.volumeMountsExtra volume mounts for just the migration init container (on top of the shared volumeMounts every container gets)[]
hostAliasesExtra /etc/hosts entries for the pod[]
podLabelsLabels applied only to the Pod template (Deployment/CronJob/Job pod spec), distinct from labels/commonLabels on the parent resource{}
podAnnotationsAnnotations applied only to the Pod template; combined with any Vault Agent annotations when vaultAgent.enabled{}
podAffinityPresetPod-affinity preset name (e.g. "soft"/"hard"), from the vendored common library chart; empty disables it""
podAntiAffinityPresetPod-anti-affinity preset name (vendored common library chart convention); "soft" spreads replicas across nodes when possible"soft"
nodeAffinityPreset.typeNode-affinity preset type ("soft"/"hard"), from the vendored common library chart; empty disables it""
nodeAffinityPreset.keyNode label key to match""
nodeAffinityPreset.valuesNode label values to match[]
affinityRaw Kubernetes affinity spec; overrides all three presets above when set{}
nodeSelectorPlain node-selector labels for pod scheduling{}
tolerationsTaints the pod tolerates[]
topologySpreadConstraintsKubernetes pod topology spread constraints[]
priorityClassNamePriorityClass to schedule the pod with""
schedulerNameAlternate Kubernetes scheduler to use""
terminationGracePeriodSecondsGrace period before SIGKILL on pod termination""
updateStrategy.typeDeployment rollout strategy (e.g. RollingUpdate/Recreate)"RollingUpdate"
podRestartPolicyPod-level restart policy for the Deployment (Jobs/CronJobs set their own, ignoring this)"Always"
containerPorts.http8080
livenessProbe.enabledRender a container livenessProbe from this block (minus enabled)false
livenessProbe.tcpSocket.port8080
livenessProbe.initialDelaySeconds30
livenessProbe.periodSeconds15
readinessProbe.enabledRender a container readinessProbe from this block (minus enabled)false
readinessProbe.tcpSocket.port8080
readinessProbe.initialDelaySeconds30
readinessProbe.periodSeconds15
startupProbe.enabledRender a container startupProbe from this block (minus enabled)false
startupProbe.tcpSocket.port8080
startupProbe.periodSeconds10
startupProbe.failureThreshold30
containerSecurityContext.enabledRender the container securityContext from this block (minus enabled)true
containerSecurityContext.runAsUser1000
containerSecurityContext.capabilities.drop["ALL"]
containerSecurityContext.seccompProfile.type"RuntimeDefault"
containerSecurityContext.readOnlyRootFilesystemtrue
containerSecurityContext.runAsNonRoottrue
containerSecurityContext.allowPrivilegeEscalationfalse
lifecycleHooksContainer lifecycle hooks (postStart/preStop){}
resources.limits.cpu"1500m"
resources.limits.memory"2048M"
resources.requests.cpu"1000m"
resources.requests.memory"1024M"
extraVolumesExtra volumes for the pod (on top of the config/kafka-secret volumes this chart already renders)[]
extraVolumeMountsExtra volume mounts for the main container (on top of the shared ones every container gets)[]
sidecarsExtra full container specs appended alongside the main container[]
envVarsExtra literal env vars for the main container (the generated CONFIG_YAML env var is appended to this list when configMap.envVar.enabled)[]
envVarsConfigMapName of a ConfigMap to load as bulk env vars via envFrom""
envVarsSecretName of a Secret to load as bulk env vars via envFrom""
service.enabledRender the Service resourcetrue
service.type"ClusterIP"
service.labelsExtra labels on just the Service (and DestinationRule, which shares its address){}
service.annotationsExtra annotations on just the Service (and DestinationRule, which shares its address) - e.g. cloud load-balancer or ingress-controller annotations{}
serviceAccount.createCreate a dedicated ServiceAccount for this releasetrue
autoscaling.enabledRender a HorizontalPodAutoscaler targeting the Deploymentfalse
autoscaling.minReplicas3
autoscaling.maxReplicas5
autoscaling.targetCPUTarget average CPU utilization percentage; omit/empty to skip this metric80
autoscaling.targetMemoryTarget average memory utilization percentage; omit/empty to skip this metric80
autoscaling.metricsExtra raw HPA metric entries appended after CPU/memory[]
topicPrefixPrefix prepended to every Kafka topic name this chart renders/references""
kafkaTopicsParametersFold _topics/_consumerGroup into the rendered config.yaml as service config parameters (topic name/type env vars); set false to render topics for KafkaUser ACLs only, without also injecting them as configtrue
kafkaUser.enabledRender a Strimzi KafkaUser (TLS cert + ACLs from _topics/_consumerGroup)false
kafkaUser.clusterName"kafka"
kafkaUser.clusterNamespace"strimzi"
kafkaUser.caCertSecretNameSecret holding the Kafka cluster's CA cert, mounted alongside the user's own TLS secret"kafka-cluster-ca-cert"
mongodb.dbNameDatabase name; combined with dbNamePrefix and injected into config.yaml as db_name. NOTE: mongodb.dbName is the fallback used when the top-level dbName (set per-member, not defaulted here) is empty"purge-controller"
mongodb.service.namespaceTogether with mongodb.service.name and cluster.name, forms the Vault KV path this chart reads a dynamic MongoDB credential from"mongodb"
mongodb.service.name"mongodb"
apiBasePathPublic API path prefix; combined with apiBasePathPrefix (set by an aliasing umbrella) and injected into config.yaml as api_root_path"/pcs/"
serviceNameLogical service name; combined with serviceNamePrefix and injected into config.yaml as service_name"pcs-rest"
serviceInstanceId.fromPodNameInject a <CONFIG_PREFIX>_SERVICE_INSTANCE_ID env var sourced from the Kubernetes Downward API (metadata.name), overriding config.service_instance_id per-pod. Env vars beat the YAML config file in hexkit config_from_yaml priority order, so this makes the value genuinely unique per replica instead of the static per-member string every service currently hardcodes in its own chart-values.yaml config block (which collides across replicas once replicaCount > 1, contradicting hexkit KafkaConfig.service_instance_id's own "uniquely identifies this instance" contract).false
configMap.enabledRender the ConfigMap holding config.yaml and mount it into the containertrue
configMap.mountPath"/etc/config.yaml"
configMap.subPath"config.yaml"
configMap.envVar.enabledAlso add a <CONFIG_PREFIX>_CONFIG_YAML env var pointing at mountPathtrue
configPrefixPrefix for the generated CONFIG_YAML env var and every Vault Agent-injected env var; create_charts.py derives this automatically from the package name"pcs"
enableServiceLinksStandard Kubernetes field: whether to inject <SVC>_SERVICE_HOST-style env vars for every Service in the namespacetrue
successfulJobsHistoryLimitFallback successfulJobsHistoryLimit for any cronjobs entry that doesn't set its own5
environment.nameIdentifies which environment this release belongs to; part of the Vault secret path for the "service" secrets bundle"default"
cluster.nameIdentifies which cluster this release belongs to; part of the Vault secret path for MongoDB credentials"default"
httpRoute.enabledRender an HTTPRoute (Gateway API, ADR-0012) routing to this servicefalse
httpRoute.port8080
httpRoute.rewritePathstrip the base path before forwarding. Services that reconstruct their own public URLs (an OIDC discovery document, for example) need the full path instead and rely on api_root_path to route - set this to false for them.true
httpRoute.rulesExtra HTTPRoute rules rendered before the generated default rule (deduplicated)[]

This README is longer than Docker Hub's 25000-character overview limit, so it has been cut short here. Read the rest on GitHub: https://github.com/ghga-de/ghga/blob/main/deploy/charts/pcs/README.md

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Helm

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sha256:d47585c60

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Last updated

8 days ago

helm pull oci://registry-1.docker.io/ghga/pcs-chart --version 15.3.1-rc.5

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