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ghga/ifrs-chart

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By German Human Genome-Phenome Archive

Updated 9 days ago

Internal File Registry Service - This service acts as a registry for the internal location and repre

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ghga/ifrs-chart repository overview

ifrs

Internal File Registry Service - This service acts as a registry for the internal location and representation of files.

Installing

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

Source

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

Service Configuration

NameDescriptionValue
config.mongo_dsnMongoDB connection string. Might include credentials. For more information see: https://naiveskill.com/mongodb-connection-string/null
config.object_storagesnull
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.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.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."ifrs"
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.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.file_upload_topicTopic containing published FileUpload outbox eventsnull
config.file_internally_registered_topicName of the topic used for events indicating that a file has been registered for download.null
config.file_internally_registered_typeThe type used for event indicating that that a file has been registered for download.null
config.file_deleted_topicName of the topic used for events indicating that a file has been deleted.null
config.file_deleted_typeThe type used for events indicating that a file has been deleted.null
config.file_staged_topicName of the topic used for events indicating that a new file has been internally registered.null
config.file_staged_typeThe type used for events indicating that a new file has been internally registered.null
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.files_to_stage_topicName of the topic used for events indicating that a download was requested for a file that is not yet available in the outbox.null
config.files_to_stage_typeThe type used for non-staged file request eventsnull
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 trying to publish an event without a valid correlation ID set for the context. If True, a new correlation ID will be generated and used in the event header.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_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.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.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

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)"ifrs"
executableArgs["consume-events"]
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/ifrs"
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:af23b62b61f86d42d2a99565a3c6866b6718fd967881173fee079f210be3cf05"
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"ifrs"
migrationInitContainer.executableArgs["migrate-db"]
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"
containerPortsContainer ports, name -> port (bare number = TCP; {port, protocol} for anything else). Also the single source the Service's and NetworkPolicy's own ports: are derived from - a Service always exposes exactly what its container listens on here, so there's one map to keep in sync, not several. A map, not a list, so an overlay can add/override one named port without repeating the rest. Empty = no ports declared anywhere.{}
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 resourcefalse
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"internal-file-registry"
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""
serviceNameLogical service name; combined with serviceNamePrefix and injected into config.yaml as service_name"ifrs"
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"ifrs"
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)[]
probe.enabledRender a Prometheus-Operator Probe CR blackbox-checking this service over HTTPfalse
probe.hostnamePublic hostname the blackbox exporter probes (combined with the API base path and healthEndpoint below to build the target URL)"default.ghga.dev"
healthEndpointPath appended to the probe target URL (after the API base path)"/health"
destinationRule.enabledRender an Istio DestinationRule for this servicefalse
networkPolicy.enabledRender a NetworkPolicy restricting ingress traffic to the podfalse
networkPolicy.ingressOnly allow traffic from namespaces labeled ghga-ingress: allow, on the Service's own ports[{"from": [{"namespaceSelector": {"matchLabels": {"ghga-ingress": "allow"}}}]}]
strimziApiVersionapiVersion used for the rendered Strimzi KafkaUser resource"kafka.strimzi.io/v1"

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/ifrs/README.md

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9 days ago

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

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