diff --git a/unfunded/vpodcstaging.data-commons.org/Chart.yaml b/unfunded/vpodcstaging.data-commons.org/Chart.yaml new file mode 100644 index 000000000..15161fd2e --- /dev/null +++ b/unfunded/vpodcstaging.data-commons.org/Chart.yaml @@ -0,0 +1,23 @@ +apiVersion: v2 +name: vpodcstaging.data-commons.org +description: vpodcstaging.data-commons.org argo application + +# A chart can be either an 'application' or a 'library' chart. +# +# Application charts are a collection of templates that can be packaged into versioned archives +# to be deployed. +# +# Library charts provide useful utilities or functions for the chart developer. They're included as +# a dependency of application charts to inject those utilities and functions into the rendering +# pipeline. Library charts do not define any templates and therefore cannot be deployed. +type: application + +# This is the chart version. This version number should be incremented each time you make changes +# to the chart and its templates, including the app version. +# Versions are expected to follow Semantic Versioning (https://semver.org/) +version: 0.1.0 + +# This is the version number of the application being deployed. This version number should be +# incremented each time you make changes to the application. Versions are not expected to +# follow Semantic Versioning. They should reflect the version the application is using. +appVersion: "1.0" diff --git a/unfunded/vpodcstaging.data-commons.org/templates/app.yaml b/unfunded/vpodcstaging.data-commons.org/templates/app.yaml new file mode 100644 index 000000000..8104d62ed --- /dev/null +++ b/unfunded/vpodcstaging.data-commons.org/templates/app.yaml @@ -0,0 +1,31 @@ +apiVersion: argoproj.io/v1alpha1 +kind: Application +metadata: + name: gen3-vpodcstaging + namespace: argocd + finalizers: + - resources-finalizer.argocd.argoproj.io +spec: + project: default + sources: + - path: helm/gen3 + repoURL: https://github.com/uc-cdis/gen3-helm + targetRevision: master + helm: + releaseName: gen3-vpodcstaging + valueFiles: + - $values/unfunded/vpodcstaging.data-commons.org/values/values.yaml + - repoURL: 'https://github.com/uc-cdis/gen3-gitops.git' + targetRevision: feat/vpodcstaging + ref: values + destination: + server: "https://kubernetes.default.svc" + namespace: vpodc-staging + syncPolicy: + managedNamespaceMetadata: + labels: + role: gen3 + syncOptions: + - CreateNamespace=true + automated: + selfHeal: true diff --git a/unfunded/vpodcstaging.data-commons.org/values.yaml b/unfunded/vpodcstaging.data-commons.org/values.yaml new file mode 100644 index 000000000..e69de29bb diff --git a/unfunded/vpodcstaging.data-commons.org/values/values.yaml b/unfunded/vpodcstaging.data-commons.org/values/values.yaml new file mode 100644 index 000000000..db99e68d4 --- /dev/null +++ b/unfunded/vpodcstaging.data-commons.org/values/values.yaml @@ -0,0 +1,321 @@ +# Updated staging values.yaml +# Base: user-provided staging values +# Applied: prod service enablement and image/version pins from user-provided prod values +# Review inferred staging resources before deploy: argo-wrapper buckets, dashboard bucket/IRSA, +# cohort-middleware secret, ohdsi-webapi secret, ssjdispatcher secret, and sower/pelican secret. + +global: + aws: + enabled: true + account: '662843554732' + hatchery_role: arn:aws:iam::662843554732:role/gen3-service/unfunded-vpodc-staging-hatchery-sa + secretStoreServiceAccount: + enabled: true + name: external-secrets + roleArn: arn:aws:iam::662843554732:role/gen3_service/unfunded-vpodc-staging-external-secrets-sa + wafv2: + enabled: true + wafAclArn: '' + dev: false + externalSecrets: + deploy: true + postgres: + dbCreate: true + externalSecret: unfunded-aurora-master-password + environment: unfunded + hostname: vpodc-staging.data-commons.org + revproxyArn: arn:aws:acm:us-east-1:662843554732:certificate/12c79298-0ff5-4c52-b63b-3302b7119e12 + dictionaryUrl: https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json + portalApp: gitops + publicDataSets: false + tierAccessLevel: private + tierAccessLimit: '100' + netPolicy: + enabled: false + dispatcherJobNum: '10' + frontendRoot: gen3ff + ddEnabled: false + +ambassador: + replicaCount: 2 + enabled: true + +arborist: + replicaCount: 2 + enabled: true + externalSecrets: + dbcreds: unfunded-vpodc-staging-arborist-creds + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist + tag: '2025.12' + +argo-wrapper: + enabled: true + replicaCount: 2 + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/argo-wrapper + tag: VA-2025.10.28 + scalingGroups: + default: '{{workflow.name}}' + s3Bucket: unfunded-vpodc-staging-argo-user-artifacts-downloadable + internalS3Bucket: unfunded-vpodc-staging-argo-bucket + environment: unfunded-vpodc-staging +audit: + enabled: true + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::662843554732:role/gen3_service/unfunded-vpodc-staging-audit-sa + externalSecrets: + dbcreds: unfunded-vpodc-staging-audit-creds + createK8sAuditSecret: true + image: + tag: '2025.12' +aws-es-proxy: + enabled: true + esEndpoint: vpc-unfunded-gen3-metadata-2-tf3gyjftzrgm5asaxuvqxxwv2m.us-east-1.es.amazonaws.com + externalSecrets: + awsCreds: unfunded-vpodc-staging-aws-es-proxy-creds + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy + tag: v1.3.1 +dicom-server: + enabled: false + externalSecrets: + dbcreds: unfunded-vpodc-staging-dicom-server-creds +dicom-viewer: + enabled: false + externalSecrets: + dbcreds: unfunded-vpodc-staging-dicom-viewer-creds +fence: + enabled: true + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::662843554732:role/gen3_service/unfunded-vpodc-staging-fence-sa + externalSecrets: + fenceJwtKeys: unfunded-vpodc-staging-fence-jwt-keys + fenceConfig: unfunded-vpodc-staging-fence-config + fenceGoogleAppCredsSecret: '' + fenceGoogleStorageCredsSecret: '' + createK8sGoogleAppSecrets: true + dbcreds: unfunded-vpodc-staging-fence-creds + usersync: + usersync: true + schedule: '*/30 * * * *' + syncFromDbgap: false + userYamlS3Path: s3://cdis-gen3-users/vadcprod/user.yaml + slack_webhook: '' + slack_send_dbgap: false + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence + tag: '2025.12' +frontend-framework: + enabled: true + image: + repository: quay.io/cdis/vpodc-data-commons + tag: 0.15 + replicaCount: 2 +grafana: + enabled: false +guppy: + enabled: true + authFilterField: auth_resource_path + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 1 + minReplicas: 1 + targetCPUUtilizationPercentage: 40 + configIndex: etl_mickey_array-config + esEndpoint: http://elasticsearch:9200 + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy + tag: '2026.02' + indices: + - index: etl_mickey + type: patients + - index: file_etl_mickey + type: file + - index: omop_etl_index_cohortb_20251119 + type: cohort_b_patients + - index: omop_etl_index_cohorta_20260311 + type: cohort_a_patients + - index: omop_etl_index_cohortf_20260408 + type: cohort_f_patients + - index: vpodc_patients + type: vpodc_patients +hatchery: + enabled: true + hatchery: + sidecarContainer: + cpu-limit: '0.1' + memory-limit: 256Mi + image: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ecs-ws-sidecar:2026.02 + env: + NAMESPACE: '{{ .Release.Namespace }}' + HOSTNAME: '{{ .Values.global.hostname }}' + args: [] + command: + - /bin/bash + - ./sidecar.sh + lifecycle-pre-stop: + - su + - -c + - echo test + - -s + - /bin/sh + - root + containers: + - target-port: 8888 + cpu-limit: '1.0' + memory-limit: 2Gi + name: (Tutorials) Example Analysis Jupyter Lab Notebooks + image: quay.io/cdis/heal-notebooks:combined_tutorials__latest + env: + FRAME_ANCESTORS: https://{{ .Values.global.hostname }} + args: + - --NotebookApp.base_url=/lw-workspace/proxy/ + - --NotebookApp.default_url=/lab + - --NotebookApp.password='' + - --NotebookApp.token='' + - --NotebookApp.shutdown_no_activity_timeout=5400 + - --NotebookApp.quit_button=False + command: + - start-notebook.sh + path-rewrite: /lw-workspace/proxy/ + use-tls: 'false' + ready-probe: /lw-workspace/proxy/ + lifecycle-post-start: + - /bin/sh + - -c + - export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true + user-uid: 1000 + fs-gid: 100 + user-volume-location: /home/jovyan/pd + gen3-volume-location: /home/jovyan/.gen3 + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery + tag: 2.7.2 +indexd: + enabled: true + defaultPrefix: dg.XXXX/ + externalSecrets: + dbcreds: unfunded-vpodc-staging-indexd-creds + createK8sServiceCredsSecret: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd + tag: '2025.12' +manifestservice: + enabled: true + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::662843554732:role/gen3_service/unfunded-vpodc-staging-manifestservice-sa + externalSecrets: + createK8sManifestServiceSecret: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice + tag: '2025.12' +metadata: + enabled: true + externalSecrets: + dbcreds: unfunded-vpodc-staging-metadata-creds + createK8sMetadataSecret: true + esEndpoint: http://elasticsearch:9200 + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service + tag: '2025.12' +peregrine: + enabled: true + externalSecrets: + dbcreds: unfunded-vpodc-staging-sheepdog-creds + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine + tag: '2025.12' +pidgin: + enabled: false +portal: + enabled: false +requestor: + enabled: false + externalSecrets: + dbcreds: unfunded-vpodc-staging-requestor-creds +revproxy: + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx + tag: '2025.12' + ingress: + aws: + group: unfunded-vpodc-staging + sslPolicy: ELBSecurityPolicy-TLS13-1-2-Res-FIPS-2023-04 +sheepdog: + enabled: true + externalSecrets: + dbcreds: unfunded-vpodc-staging-sheepdog-creds + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog + tag: '2025.12' +ssjdispatcher: + enabled: true + externalSecrets: + credsFile: unfunded-vpodc-staging-ssjdispatcher-creds + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher + tag: '2025.12' + indexing: quay.io/cdis/indexs3client:2025.12 +sower: + enabled: true + externalSecrets: + pelicanserviceG3auto: unfunded-vpodc-staging-pelicanservice-g3auto + createK8sSowerJobsSecret: false + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower + tag: '2025.12' + sowerConfig: [] +wts: + enabled: true + externalSecrets: + dbcreds: unfunded-vpodc-staging-wts-creds + createK8sWtsSecret: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service + tag: '2025.12' +cohort-middleware: + enabled: true + replicaCount: 2 + externalSecrets: + cohortMiddlewareG3Auto: unfunded-vpodc-staging-cohort-middleware-g3auto + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cohort-middleware + tag: VA-2026.03.18 +dashboard: + enabled: true + replicaCount: 4 + dashboardConfig: + bucket: dashboard-662843554732-unfunded-gen3 + prefix: vpodc-staging.data-commons.org + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics + tag: '2025.12' + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::662843554732:role/gen3_service/unfunded-vpodc-staging-dashboard-access +etl: + esEndpoint: elasticsearch + image: + tube: + tag: '2025.12' + spark: + tag: '2025.12' +ohdsi-atlas: + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-atlas + tag: VA-2026.02.24 +ohdsi-webapi: + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-webapi + tag: VA-2025.10.24 + externalSecrets: + dbcreds: unfunded-vpodc-staging-ohdsi-creds + createK8sOhdsiWebApiConfigSecret: true diff --git a/vadcprod/vpodc.data-commons.org/values/values.yaml b/vadcprod/vpodc.data-commons.org/values/values.yaml index 9e1959b85..8389f10e5 100644 --- a/vadcprod/vpodc.data-commons.org/values/values.yaml +++ b/vadcprod/vpodc.data-commons.org/values/values.yaml @@ -441,6 +441,8 @@ ohdsi-webapi: tag: VA-2025.10.24 externalSecrets: dbcreds: vadcprod-ohdsi-webapi-creds + createK8sOhdsiWebApiConfigSecret: true + pushSecret: true peregrine: replicaCount: 4 autoscaling: