From 78e32ec9471eae62bc7d9b8f133a6a31fc4efa35 Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Tue, 9 Apr 2024 07:45:44 +0200
Subject: [PATCH] Remove fluent-bit because of permission issues
---
Makefile | 2 +-
helm-charts/dbrepo/Chart.yaml | 4 -
.../dbrepo/charts/fluent-bit-0.40.0.tgz | Bin 14526 -> 0 bytes
helm-charts/dbrepo/values.dev.yaml | 485 ++++++++++++++++++
helm-charts/dbrepo/values.yaml | 49 +-
5 files changed, 494 insertions(+), 46 deletions(-)
delete mode 100644 helm-charts/dbrepo/charts/fluent-bit-0.40.0.tgz
create mode 100644 helm-charts/dbrepo/values.dev.yaml
diff --git a/Makefile b/Makefile
index 91b665427f..c9c2d4f7e6 100644
--- a/Makefile
+++ b/Makefile
@@ -273,7 +273,7 @@ cluster-image-pull:
rm -f ./ui.tar ./data-service.tar ./search-service.tar ./analyse-service.tar ./data-db-sidecar.tar ./metadata-service.tar
cluster-install: helm-build
- helm upgrade --install dbrepo -n dbrepo ./build/dbrepo-${CHART_VERSION}.tgz --create-namespace --cleanup-on-fail
+ helm upgrade --install dbrepo -n dbrepo ./build/dbrepo-${CHART_VERSION}.tgz --values ./helm-charts/dbrepo/values.dev.yaml --create-namespace --cleanup-on-fail
cluster-uninstall:
helm uninstall -n dbrepo dbrepo
diff --git a/helm-charts/dbrepo/Chart.yaml b/helm-charts/dbrepo/Chart.yaml
index 46e734f95f..3f0ac0297f 100644
--- a/helm-charts/dbrepo/Chart.yaml
+++ b/helm-charts/dbrepo/Chart.yaml
@@ -42,10 +42,6 @@ dependencies:
alias: brokerService
version: 12.5.1
repository: https://charts.bitnami.com/bitnami
- - name: fluent-bit
- alias: logservice
- version: 0.40.0
- repository: https://fluent.github.io/helm-charts
- name: seaweedfs
alias: storageservice
version: 3.59.4
diff --git a/helm-charts/dbrepo/charts/fluent-bit-0.40.0.tgz b/helm-charts/dbrepo/charts/fluent-bit-0.40.0.tgz
deleted file mode 100644
index e8057f452b586c22fa2bf9f645a74d2a64e613e2..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/helm-charts/dbrepo/values.dev.yaml b/helm-charts/dbrepo/values.dev.yaml
new file mode 100644
index 0000000000..c3d8409534
--- /dev/null
+++ b/helm-charts/dbrepo/values.dev.yaml
@@ -0,0 +1,485 @@
+namespace: dbrepo
+
+hostname: dbrepo.local
+
+strategyType: RollingUpdate
+
+clusterDomain: cluster.local
+
+metadataDb:
+ fullnameOverride: metadata-db
+ image:
+ debug: false
+ host: metadata-db
+ rootUser:
+ user: root
+ password: dbrepo
+ jdbcExtraArgs: ""
+ db:
+ name: fda
+ metrics:
+ enabled: false
+ galera:
+ mariabackup:
+ user: mariabackup
+ password: mariabackup
+ initdbScriptsConfigMap: metadata-db-setup
+ service:
+ type: ClusterIP
+ annotations: { }
+ loadBalancerIP: ""
+ loadBalancerSourceRanges: [ ]
+ persistence:
+ enabled: true
+ replicaCount: 1 # uneven 3,5,7
+
+authService:
+ fullnameOverride: auth-service
+ image:
+ debug: false
+ auth:
+ adminUser: fda
+ adminPassword: fda
+ postgresql:
+ enabled: false # not needed
+ extraStartupArgs: "--import-realm"
+ tls:
+ enabled: true
+ existingSecret: ingress-cert
+ usePem: true
+ metrics:
+ enabled: true
+ externalDatabase:
+ existingSecret: auth-service-secret
+ existingSecretDatabaseKey: db-name
+ existingSecretHostKey: db-host
+ existingSecretPortKey: db-port
+ existingSecretUserKey: db-username
+ existingSecretPasswordKey: db-password
+ client:
+ id: dbrepo-client
+ secret: MUwRc7yfXSJwX8AdRMWaQC3Nep1VjwgG
+ extraEnvVarsCM: auth-service-config
+ extraVolumes:
+ - name: config-map
+ configMap:
+ name: auth-service-setup
+ extraVolumeMounts:
+ - name: config-map
+ mountPath: /opt/bitnami/keycloak/data/import
+ replicaCount: 1
+
+authDb:
+ fullnameOverride: auth-db
+ host: auth-db-pgpool
+ port: 5432
+ postgresql:
+ postgresPassword: postgres
+ username: metrics # implicit requirement for metrics container
+ password: metrics # implicit requirement for metrics container
+ repmgrPassword: repmgr # implicit requirement for rolling updates
+ database: keycloak
+ replicaCount: 1
+ pgpool:
+ adminUsername: admin
+ adminPassword: admin
+ metrics:
+ enabled: true
+ service:
+ type: ClusterIP
+ annotations: { }
+ loadBalancerIP: ""
+ loadBalancerSourceRanges: [ ]
+ persistence:
+ enabled: true
+ size: 10Gi
+
+dataDb:
+ fullnameOverride: data-db
+ image:
+ debug: false
+ extraFlags: "--character-set-server=utf8mb4 --collation-server=utf8mb4_general_ci"
+ rootUser:
+ user: root
+ password: dbrepo
+ metrics:
+ enabled: true
+ galera:
+ mariabackup:
+ user: mariabackup
+ password: mariabackup
+ sidecars:
+ - name: sidecar
+ image: dbrepo-data-db-sidecar:latest
+ imagePullPolicy: Never
+ securityContext:
+ runAsUser: 1001
+ runAsGroup: 1001
+ ports:
+ - containerPort: 3305
+ protocol: TCP
+ env:
+ - name: S3_STORAGE_ENDPOINT
+ value: http://storageservice-s3:9000
+ - name: S3_ACCESS_KEY_ID
+ value: seaweedfsadmin
+ - name: S3_SECRET_ACCESS_KEY
+ value: seaweedfsadmin
+ volumeMounts:
+ - name: tmp # share between sidecar and galera container
+ mountPath: /tmp
+ service:
+ type: ClusterIP
+ annotations: { }
+ #loadBalancerIP: 1.2.3.4
+ loadBalancerSourceRanges: [ ]
+ extraPorts:
+ - name: "sidecar"
+ port: 3305
+ targetPort: 3305
+ protocol: TCP
+ extraVolumeMounts:
+ - name: tmp # share between sidecar and galera container
+ mountPath: /tmp
+ extraVolumes:
+ # - name: tmp
+ # emptyDir: {}
+ - name: tmp
+ persistentVolumeClaim:
+ claimName: data-db-shared
+ persistence:
+ enabled: true
+ size: 10Gi
+ replicaCount: 1 # uneven
+
+searchdb:
+ fullnameOverride: search-db
+ host: search-db
+ port: 9200
+ protocol: http
+ username: admin
+ password: admin
+ clusterName: search-db
+ masterService: search-db
+ replicas: 1
+ image:
+ debug: false
+ sysctlInit:
+ enabled: true
+ persistence:
+ enabled: true
+ size: 10Gi
+ service:
+ type: ClusterIP
+ annotations: { }
+ loadBalancerSourceRanges: [ ]
+ extraEnvs:
+ - name: DISABLE_INSTALL_DEMO_CONFIG
+ value: "true"
+ extraVolumeMounts:
+ - name: node-cert
+ mountPath: /usr/share/opensearch/config/tls
+ readOnly: true
+ extraVolumes:
+ - name: node-cert
+ secret:
+ secretName: search-db-cert
+ config:
+ opensearch.yml: |
+ cluster.name: search-db
+ network.host: 0.0.0.0
+ plugins:
+ security:
+ ssl:
+ transport:
+ pemcert_filepath: tls/tls.crt
+ pemkey_filepath: tls/tls.key
+ pemtrustedcas_filepath: tls/ca.crt
+ enforce_hostname_verification: false
+ http:
+ #enabled: true # uncomment to force ssl connections
+ pemcert_filepath: tls/tls.crt
+ pemkey_filepath: tls/tls.key
+ pemtrustedcas_filepath: tls/ca.crt
+ allow_unsafe_democertificates: false
+ allow_default_init_securityindex: true
+ authcz:
+ admin_dn:
+ - CN=search-db
+ nodes_dn:
+ - CN=search-db
+ audit.type: internal_opensearch
+ enable_snapshot_restore_privilege: true
+ check_snapshot_restore_write_privileges: true
+ restapi:
+ roles_enabled: [ "all_access", "security_rest_api_access" ]
+ system_indices:
+ enabled: true
+ indices:
+ [
+ ".opendistro-alerting-config",
+ ".opendistro-alerting-alert*",
+ ".opendistro-anomaly-results*",
+ ".opendistro-anomaly-detector*",
+ ".opendistro-anomaly-checkpoints",
+ ".opendistro-anomaly-detection-state",
+ ".opendistro-reports-*",
+ ".opendistro-notifications-*",
+ ".opendistro-notebooks",
+ ".opendistro-asynchronous-search-response*",
+ ]
+
+searchDbDashboard:
+ fullnameOverride: search-db-dashboard
+ opensearchHosts: http://search-db:9200
+ extraInitContainers:
+ - name: init
+ image: dbrepo-search-db-init:latest
+ imagePullPolicy: Never
+ env:
+ - name: OPENSEARCH_HOST
+ value: http://search-db:9200
+ extraVolumeMounts:
+ - name: tls
+ mountPath: /usr/share/opensearch-dashboards/tls
+ readOnly: true
+ - name: config
+ mountPath: /usr/share/opensearch-dashboards/config/opensearch_dashboards.yml
+ subPath: opensearch_dashboards.yml
+ readOnly: true
+ extraVolumes:
+ - name: tls
+ secret:
+ secretName: ingress-cert
+ - name: config
+ secret:
+ secretName: search-db-dashboard-secret
+ replicaCount: 1
+
+uploadService:
+ enabled: true
+ image:
+ registry: docker.io
+ repository: tusproject/tusd
+ tag: v1.12
+ replicaCount: 1
+
+brokerService:
+ fullnameOverride: broker-service
+ image:
+ debug: true
+ url: http://broker-service:15672
+ host: broker-service
+ port: 5672
+ virtualHost: dbrepo
+ queueName: dbrepo
+ exchangeName: dbrepo
+ routingKey: dbrepo.#
+ connectionTimeout: 60000
+ auth:
+ tls:
+ enabled: false
+ sslOptionsVerify: true
+ failIfNoPeerCert: true
+ existingSecret: ingress-cert
+ username: broker
+ password: broker
+ extraConfiguration: |-
+ default_vhost = dbrepo
+ default_user_tags.administrator = true
+ default_permissions.configure = .*
+ default_permissions.read = .*
+ default_permissions.write = .*
+ load_definitions = /etc/rabbitmq/definitions.json
+ log.console = true
+ listeners.tcp.1 = 0.0.0.0:5672
+ auth_backends.1 = rabbit_auth_backend_oauth2
+ auth_backends.2 = rabbit_auth_backend_internal
+ auth_oauth2.resource_server_id = rabbitmq
+ auth_oauth2.preferred_username_claims.1 = client_id
+ auth_oauth2.default_key = t2OCeCheJ9uwoBbNQjG_nN6WKiLcceTIAZmiTbGODFM
+ auth_oauth2.signing_keys.t2OCeCheJ9uwoBbNQjG_nN6WKiLcceTIAZmiTbGODFM = /etc/rabbitmq/cert.pem
+ auth_oauth2.signing_keys.id2 = /etc/rabbitmq/pubkey.pem
+ auth_oauth2.algorithms.1 = HS256
+ auth_oauth2.algorithms.2 = RS256
+ loadDefinition:
+ enabled: true
+ file: /etc/rabbitmq/definitions.json
+ existingSecret: broker-service-secret
+ extraVolumeMounts:
+ - name: secret-map
+ mountPath: /etc/rabbitmq/definitions.json
+ subPath: definitions.json
+ readOnly: true
+ - name: secret-map
+ mountPath: /etc/rabbitmq/pubkey.pem
+ subPath: pubkey.pem
+ readOnly: true
+ - name: secret-map
+ mountPath: /etc/rabbitmq/cert.pem
+ subPath: cert.pem
+ readOnly: true
+ extraVolumes:
+ - name: secret-map
+ secret:
+ secretName: broker-service-secret
+ extraPlugins: rabbitmq_prometheus rabbitmq_auth_backend_oauth2 rabbitmq_auth_mechanism_ssl
+ persistence:
+ enabled: false
+ size: 5Gi
+ service:
+ type: ClusterIP
+ # loadBalancerIP:
+ replicaCount: 1
+
+analyseService:
+ enabled: true
+ image:
+ name: dbrepo-analyse-service:latest
+ pullPolicy: Never
+ debug: false
+ replicaCount: 1
+
+metadataService:
+ enabled: true
+ image:
+ name: dbrepo-metadata-service:latest
+ pullPolicy: Never
+ debug: false
+ adminEmail: noreply@example.com
+ authService:
+ url: http://auth-service
+ website: http://example.com
+ repositoryName: Database Repository
+ datacite:
+ enabled: false
+ url: https://api.datacite.org
+ prefix: ""
+ username: ""
+ password: ""
+ rates:
+ deleteStaleFiles: 60
+ mirror: 60
+ obtainMetadata: 60
+ deleteStaleQueries: 60
+ replicaCount: 1
+
+dataService:
+ enabled: true
+ image:
+ name: dbrepo-data-service:latest
+ pullPolicy: Never
+ debug: false
+ jwt:
+ pubkey: "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAqqnHQ2BWWW9vDNLRCcxD++xZg/16oqMo/c1l+lcFEjjAIJjJp/HqrPYU/U9GvquGE6PbVFtTzW1KcKawOW+FJNOA3CGo8Q1TFEfz43B8rZpKsFbJKvQGVv1Z4HaKPvLUm7iMm8Hv91cLduuoWx6Q3DPe2vg13GKKEZe7UFghF+0T9u8EKzA/XqQ0OiICmsmYPbwvf9N3bCKsB/Y10EYmZRb8IhCoV9mmO5TxgWgiuNeCTtNCv2ePYqL/U0WvyGFW0reasIK8eg3KrAUj8DpyOgPOVBn3lBGf+3KFSYi+0bwZbJZWqbC/Xlk20Go1YfeJPRIt7ImxD27R/lNjgDO/MwIDAQAB"
+ consumerConcurrentMin: 1
+ consumerConcurrentMax: 5
+ requeueRejected: false
+ replicaCount: 1
+
+searchService:
+ enabled: true
+ image:
+ name: dbrepo-search-service:latest
+ pullPolicy: Never
+ debug: false
+ replicaCount: 1
+
+storageservice:
+ master:
+ enabled: true
+ filer:
+ enabled: true
+ replicas: 1
+ enablePVC: false
+ storage: 25Gi
+ s3:
+ enabled: true
+ allowEmptyFolder: true
+ port: 9000
+ enableAuth: true
+ skipAuthSecretCreation: true
+ existingConfigSecret: seaweedfs-s3-secret
+ volume:
+ enabled: true
+ replicas: 1
+ s3:
+ enabled: true
+ replicas: 2
+ port: 9000
+ metricsPort: 9091
+ enableAuth: true
+ skipAuthSecretCreation: true
+ existingConfigSecret: seaweedfs-s3-secret
+ auth:
+ username: seaweedfsadmin
+ password: seaweedfsadmin
+
+ui:
+ enabled: true
+ image:
+ name: dbrepo-ui:latest
+ pullPolicy: Never
+ debug: false
+ public:
+ api:
+ client: {}
+ server: {}
+ title: "Database Repository"
+ logo: "/logo.svg"
+ icon: "/favicon.ico"
+ touch: "/apple-touch-icon.png"
+ broker:
+ host: example.com
+ port:
+ 5671: true
+ 5672: false
+ extra: "128.130.0.0/15"
+ database:
+ extra: "128.130.0.0/15"
+ pid:
+ default:
+ publisher: "Example University"
+ doi:
+ enabled: false
+ endpoint: https://doi.org
+ replicaCount: 1
+ extraVolumes: [ ]
+ # - name: images-map
+ # configMap:
+ # name: ui-config
+ extraVolumeMounts: [ ]
+ # - name: images-map
+ # mountPath: /static/logo.svg
+ # subPath: logo.svg
+
+ingress:
+ enabled: true
+ className: nginx
+ tls:
+ enabled: true
+ secretName: ingress-cert
+ annotations:
+ basic: {}
+# cert-manager.io/cluster-issuer: letsencrypt-cluster-issuer
+ secure:
+# cert-manager.io/cluster-issuer: letsencrypt-cluster-issuer
+ nginx.ingress.kubernetes.io/force-ssl-redirect: "true"
+ nginx.ingress.kubernetes.io/backend-protocol: "HTTPS"
+ upload:
+# cert-manager.io/cluster-issuer: letsencrypt-cluster-issuer
+ nginx.ingress.kubernetes.io/proxy-body-size: 2G
+ rewriteApi:
+# cert-manager.io/cluster-issuer: letsencrypt-cluster-issuer
+ nginx.ingress.kubernetes.io/use-regex: "true"
+ nginx.ingress.kubernetes.io/rewrite-target: /api/$1
+ rewriteRoot:
+# cert-manager.io/cluster-issuer: letsencrypt-cluster-issuer
+ nginx.ingress.kubernetes.io/force-ssl-redirect: "true"
+ nginx.ingress.kubernetes.io/backend-protocol: "HTTPS"
+ nginx.ingress.kubernetes.io/use-regex: "true"
+ nginx.ingress.kubernetes.io/rewrite-target: /$1
+ rewritePid:
+# cert-manager.io/cluster-issuer: letsencrypt-cluster-issuer
+ nginx.ingress.kubernetes.io/use-regex: "true"
+ nginx.ingress.kubernetes.io/rewrite-target: /api/pid/$1
diff --git a/helm-charts/dbrepo/values.yaml b/helm-charts/dbrepo/values.yaml
index b1f1d0f68e..ae50731698 100644
--- a/helm-charts/dbrepo/values.yaml
+++ b/helm-charts/dbrepo/values.yaml
@@ -1,6 +1,6 @@
namespace: dbrepo
-hostname: dbrepo.local
+hostname: example.com
strategyType: RollingUpdate
@@ -234,7 +234,7 @@ searchDbDashboard:
opensearchHosts: http://search-db:9200
extraInitContainers:
- name: init
- image: dbrepo-search-db-init:latest
+ image: s210.dl.hpc.tuwien.ac.at/dbrepo/search-db-init:1.4.2
imagePullPolicy: Never
env:
- name: OPENSEARCH_HOST
@@ -260,7 +260,7 @@ uploadService:
enabled: true
image:
registry: docker.io
- repository: tusproject/tusd
+ repository: docker.io/tusproject/tusd
tag: v1.12
replicaCount: 1
@@ -335,7 +335,7 @@ brokerService:
analyseService:
enabled: true
image:
- name: dbrepo-analyse-service:latest
+ name: s210.dl.hpc.tuwien.ac.at/dbrepo/analyse-service:1.4.2
pullPolicy: Never
debug: false
replicaCount: 1
@@ -343,7 +343,7 @@ analyseService:
metadataService:
enabled: true
image:
- name: dbrepo-metadata-service:latest
+ name: s210.dl.hpc.tuwien.ac.at/dbrepo/metadata-service:1.4.2
pullPolicy: Never
debug: false
adminEmail: noreply@example.com
@@ -367,7 +367,7 @@ metadataService:
dataService:
enabled: true
image:
- name: dbrepo-data-service:latest
+ name: s210.dl.hpc.tuwien.ac.at/dbrepo/data-service:1.4.2
pullPolicy: Never
debug: false
jwt:
@@ -380,7 +380,7 @@ dataService:
searchService:
enabled: true
image:
- name: dbrepo-search-service:latest
+ name: s210.dl.hpc.tuwien.ac.at/dbrepo/search-service:1.4.2
pullPolicy: Never
debug: false
replicaCount: 1
@@ -415,43 +415,10 @@ storageservice:
username: seaweedfsadmin
password: seaweedfsadmin
-logservice:
- fullnameOverride: log-service
- config:
- outputs: |
- [OUTPUT]
- Name opensearch
- Match kube.*
- Host search-db
- Port 9200
- HTTP_User admin
- HTTP_Passwd admin
- Logstash_Format On
- Replace_Dots On
- Type _doc
- Retry_Limit False
- Suppress_Type_Name On
-
- [OUTPUT]
- Name opensearch
- Match host.*
- Host search-db
- Port 9200
- HTTP_User admin
- HTTP_Passwd admin
- Logstash_Format On
- Logstash_Prefix node
- Replace_Dots On
- Type _doc
- Retry_Limit False
- Suppress_Type_Name On
-# Replace_Dots On
-# Suppress_Type_Name On
-
ui:
enabled: true
image:
- name: dbrepo-ui:latest
+ name: s210.dl.hpc.tuwien.ac.at/dbrepo/ui:1.4.2
pullPolicy: Never
debug: false
public:
--
GitLab