values.yaml

ambassador:
  jupyterNamespace: jupyter-pods-qa-prometheus
arborist:
  autoscaling:
    enabled: true
    maxReplicas: 1
    minReplicas: 1
    targetCPUUtilizationPercentage: 40
  enabled: true
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist
    tag: '2025.04'
  externalSecrets:
    dbcreds: qa-prometheus-arborist-creds    
audit:
  enabled: false
  externalSecrets:
    auditG3auto: qa-prometheus-audit-g3auto
  serviceAccount:
    annotations:
      eks.amazonaws.com/role-arn: arn:aws:iam::707767160287:role/devplanetv2--qa-prometheus-helm--audit-sqs-receiver
aws-es-proxy:
  enabled: true
  esEndpoint: vpc-devplanetv2-gen3-metadata-2-xkwr2f3gbxua5mqqi7rhnat4la.us-east-1.es.amazonaws.com
  image:
    repository: quay.io/cdis/aws-es-proxy
    tag: v1.3.1
dashboard:
  dashboardConfig:
    bucket: dashboard-707767160287-qa-prometheus-gen3
    prefix: qa-prometheus.planx-pla.net
  enabled: true
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics
    tag: '2025.04'
  serviceAccount:
    annotations:
      eks.amazonaws.com/role-arn: arn:aws:iam::707767160287:role/devplanetv2--qa-prometheus-helm--dashboard-access
fence:
  autoscaling:
    enabled: true
    maxReplicas: 1
    minReplicas: 1
    targetCPUUtilizationPercentage: 40
  usersync:
    usersync: true
    userYamlS3Path: s3://cdis-gen3-users/pdp/user.yaml 
  enabled: true
  externalSecrets:
    createK8sGoogleAppSecrets: true
    fenceConfig: qa-prometheus-fence-config
    fenceJwtKeys: qa-prometheus-fence-jwt
    dbcreds: qa-prometheus-fence-creds
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence
    tag: '2025.04'
fluentd:
  enabled: true
  image:
    repository: fluent/fluentd-kubernetes-daemonset
    tag: v1.15.3-debian-cloudwatch-1.0
frontend-framework:
  enabled: true
  image:
    repository: quay.io/cdis/mc2dp-data-platform
    tag: main
gen3-user-data-library:
  enabled: true
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-user-data-library
    tag: main
  externalSecrets:
    dbcreds: qa-prometheus-gen3userdatalibrary-creds 
    gen3UserDataLibraryG3auto: qa-prometheus-gen3userdatalibrary-g3auto
global:
  crossplane:
    enabled: true
    oidcProviderUrl: "oidc.eks.us-east-1.amazonaws.com/id/F057519C0E32B7DE2580904C4007BB21"
    accountId: "707767160287"
  aws:
    account: '707767160287'
    awsEsProxyRole: devplanetv2--qa-prometheus-helm--es-access
    enabled: true
    hatchery_role: devplanetv2--qa-prometheus-helm--hatchery-sa
    secretStoreServiceAccount:
      enabled: true
      roleArn: arn:aws:iam::707767160287:role/qa-prometheus-external-secrets-sa
    wafv2:
      enabled: true
      wafAclArn: "arn:aws:wafv2:us-east-1:707767160287:regional/webacl/devplanetv2-waf/30660590-f707-4ecf-aeae-ddfbe381f388"
  dev: false
  dictionaryUrl: https://s3.amazonaws.com/dictionary-artifacts/pdp_dictionary/0.0.5/schema.json
  dispatcherJobNum: '10'
  environment: qa-prometheus
  externalSecrets:
    deploy: true
  frontendRoot: gen3ff
  hostname: qa-prometheus.planx-pla.net
  manifestGlobalExtraValues:
    ecr-access-job-role-arn: arn:aws:iam::654654631253:role/EcrRepoPolicyUpdateRole
    kube_bucket: kube_bucket.devplanetv1.gen3
    logs_bucket: logs-devplanetv1-gen3
    netpolicy: 'on'
    public_datasets: true
    sync_from_dbgap: 'False'
    useryaml_s3path: s3://cdis-gen3-users/pdp/user.yaml
  tierAccessLevel: libre
  tierAccessLimit: 50
  portalApp: gitops
  postgres:
    dbCreate: false
  revproxyArn: arn:aws:acm:us-east-1:707767160287:certificate/520ede2f-fc82-4bb9-af96-4b4af7deabbd
guppy:
  configIndex: pdp-commons-commons-config-index
  enabled: true
  esEndpoint: http://elasticsearch:9200
  image:
    repository: quay.io/cdis/guppy
    tag: '2025.04'
  indices:
  - index: pdp-commons-commons-index
    type: metadata
hatchery:
  enabled: true
  replicaCount: 2
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery
    tag: '2025.04'
  hatchery:
    json: |
        {
            "user-namespace": "jupyter-pods-qa-prometheus",
            "sub-dir": "/lw-workspace",
            "user-volume-size": "10Gi",
            "default-pay-model": {
                "workspace_type": "Trial Workspace",
                "local": true
            },
            "sidecar": {
                "cpu-limit": "1.0",
                "memory-limit": "256Mi",
                "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ecs-ws-sidecar:2025.03",
                "env": {
                    "NAMESPACE": "qa-prometheus",
                    "HOSTNAME": "qa-prometheus.planx-pla.net"
                },
                "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": "4Gi",
                    "name": "(Generic) Jupyter Lab Notebook with R Kernel",
                    "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/jupyter-prometheus:prometheus-MC2DP-362",
                    "env": {
                        "FRAME_ANCESTORS": "https://qa-prometheus.planx-pla.net"
                    },
                    "args": [
                        "--JupyterNotebookApp.base_url=/lw-workspace/proxy/",
                        "--JupyterNotebookApp.default_url=/lab",
                        "--JupyterNotebookApp.password=''",
                        "--JupyterNotebookApp.token=''",
                        "--JupyterNotebookApp.ip='*'",
                        "--JupyterNotebookApp.notebook_dir='/home/jovyan'",
                        "--JupyterNotebookApp.shutdown_no_activity_timeout=5400",
                        "--JupyterNotebookApp.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": 1010,
                    "fs-gid": 100,
                    "user-volume-location": "/home/jovyan/pd",
                    "gen3-volume-location": "/home/jovyan/.gen3"
                }
            ]
        }
indexd:
  autoscaling:
    enabled: true
    maxReplicas: 1
    minReplicas: 1
    targetCPUUtilizationPercentage: 40
  enabled: true
  externalSecrets:
    serviceCreds: qa-prometheus-indexd-service-creds
    dbcreds: qa-prometheus-indexd-creds    
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd
    tag: '2025.04'
manifestservice:
  enabled: true
  externalSecrets:
    manifestserviceG3auto: qa-prometheus-manifestservice-g3auto
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice
    tag: '2025.04'
  serviceAccount:
    annotations:
      eks.amazonaws.com/role-arn: arn:aws:iam::707767160287:role/devplanetv2--qa-prometheus-helm--manifest-service-sa
metadata:
  aggMdsConfig: |-
   {
        "configuration": {
            "schema": {
                "_subjects_count": {
                    "type": "integer"
                },
                "_manifest": {
                    "type": "array",
                    "properties": {
                        "file_name": {
                            "type": "string"
                        },
                        "file_size": {
                            "type": "integer"
                        }
                    }
                },
                "tags": {
                    "type": "array"
                },
                "advSearchFilters": {
                    "type": "array",
                "properties": {
                        "key": {
                            "type": "string"
                        },
                        "value": {
                            "type": "string"
                        }
                    }
                },
                "_unique_id": {},
                "study_description": {},
                "study_id": {},
                "study_url": {},
                "project_id": {},
                "short_name": {},
                "full_name": {},
                "commons_url": {},
                "commons": {},
                "data_source": {},
                "disease_type": {},
                "primary_site": {},
                "authz": {},
                "subject_id": {},
                "subject_id_list": {
                    "type": "array",
                    "default": []
                },
                "subject_apollo_id": {},
                "subject_race": {},
                "subject_gender": {},
                "subject_ethnicity": {},
                "subject_metastasis": {},
                "subject_cancer_type": {},
                "subject_cancer_grade": {},
                "subject_cancer_stage": {},
                "subject_year_of_birth": {},
                "subject_primary_disease": {},
                "subject_type_of_exposure": {},
                "subject_type_of_exposures": {
                    "type": "array"
                },
                "subject_chemical_agents_of_exposure": {},
                "subject_run_id": {},
                "subject_class": {},
                "subject_group": {},
                "subject_project": {},
                "subject_rundate": {},
                "subject_exp_target": {},
                "subject_ionization": {},
                "subject_chromatography": {},
                "subject_plate": {},
                "subject_injection": {},
                "subject_plate_position": {},
                "mc2dp_global_id": {},
                "data_files": {
                    "type": "array"
                },
                "filesCount": {
                    "type": "array",
                    "properties": {
                        "_typename": {
                            "type": "string"
                        },
                        "data_category": {
                            "type": "string"
                        },
                        "file_type": {
                            "type": "string"
                        },
                        "files_count": {
                            "type": "integer"
                        }
                    }
                },
                "versions": {
                    "type": "array",
                    "properties": {
                        "_typename": {
                            "type": "string"
                        },
                        "number": {
                            "type": "string"
                        }
                    }
                },
                "supplementaryFilesCount": {
                    "type": "array",
                    "properties": {
                        "_typename": {
                            "type": "string"
                        },
                        "data_category": {
                            "type": "string"
                        },
                        "file_type": {
                            "type": "string"
                        },
                        "files_count": {
                            "type": "integer"
                        }
                    }
                },
                "nonSupplementaryFilesCount": {
                    "type": "array",
                    "properties": {
                        "_typename": {
                            "type": "string"
                        },
                        "data_category": {
                            "type": "string"
                        },
                        "file_type": {
                            "type": "string"
                        },
                        "files_count": {
                            "type": "integer"
                        }
                    }
                }
            },
            "settings": {
                "cache_drs": true
            }
        },
        "adapter_commons": {
            "aggregated-subject-level-metadata": {
                "mds_url": "https://externalgen3.prometheus.data-commons.org/",
                "commons_url": "externalgen3.prometheus.data-commons.org",
                "adapter": "gen3",
                "config": {
                    "guid_type": "aggmds_metadata_entry",
                    "study_field": "gen3_discovery"
                },
                "keep_original_fields": false,
                "field_mappings": {
                    "authz": "",
                    "tags": "path:tags",
                    "_unique_id": "path:mc2dp_global_id",
                    "commons": "path:data_source",
                    "subject_id_list": "path:data_source_ids",
                    "subject_metastasis": "path:metastasis",
                    "subject_cancer_type": "path:cancer_type",
                    "subject_cancer_grade": {
                        "path": "cancer_grade",
                        "filters": [
                            "normalize_value"
                        ],
                        "filterParams": {
                            "normalize_value": {
                                "i": "I",
                                "ii": "II",
                                "iii": "III",
                                "iv": "IV"
                            }
                        },
                        "default": ""
                    },
                    "subject_primary_disease": "path:primary_disease",
                    "subject_type_of_exposures": "path:type_of_exposures",
                    "subject_ethnicity": {
                        "path": "subject_ethnicity",
                        "filters": [
                            "normalize_value"
                        ],
                        "filterParams": {
                            "normalize_value": {
                              "spanish/hispanic/latino (of any race)": "Hispanic or Latino",
                              "not hispanic or latino": "Not Hispanic or Latino",
                              "hispanic or latino": "Hispanic or Latino",
                              "unknown": "Unknown",
                              "not available": "Declined to Answer",
                              "declined to answer": "Declined to Answer",
                              "not hispanic or latino, declined to answer": "Not Hispanic or Latino / Declined to Answer",
                              "not reported / unknown": "Unknown"
                          }
                        },
                        "default": ""
                    },
                    "subject_gender": {
                        "path": "gender",
                        "filters": [
                            "normalize_value"
                        ],
                        "filterParams": {
                            "normalize_value": {
                                "male": "Male",
                                "female": "Female",
                                "female, male" : "Female, Male",
                                "male, female" : "Male, Female",
                                "not reported": "Not Reported",
                                "Not Reported": "Not Reported"
                            }
                        },
                        "default": ""
                    },
                    "subject_race": {
                        "path": "race",
                        "filters": [
                            "normalize_value"
                        ],
                        "filterParams": {
                            "normalize_value": {
                              "black or african american": "Black or African American",
                              "american indian / alaskan native": "American Indian / Alaskan Native",
                              "black or african american; white": "Black or African American / White",
                              "black or african american; white; other(mixed)": "Black or African American / White / Other",
                              "not available": "Not Reported",
                              "native hawaiian or other pacific islander": "Native Hawaiian or Other Pacific Islander",
                              "asian": "Asian",
                              "not reported, white": "Declined to Answer, White",
                              "declined to answer": "Declined to Answer",
                              "asian; black or african american": "Asian / Black or African American",
                              "white": "White"
                          }
                        },
                        "default": ""
                    },
                    "data_source": "aggregated data",
                    "commons_url": "externalgen3.prometheus.data-commons.org",
                    "mc2dp_global_id": "path:mc2dp_global_id",
                    "is_synthetic": "No",
                    "data_files": "path:data_type"
                }
            },
            "PNNL-subject-level-metadata": {
                "mds_url": "https://externalgen3.prometheus.data-commons.org/",
                "commons_url": "externalgen3.prometheus.data-commons.org",
                "adapter": "gen3",
                "config": {
                    "guid_type": "PNNL_subject_metadata",
                    "study_field": "gen3_discovery"
                },
                "keep_original_fields": false,
                "field_mappings": {
                    "authz": "",
                    "tags": "path:tags",
                    "_unique_id": "path:_unique_id",
                    "commons": "path:commons",
                    "subject_id": "path:sample_id",
                    "subject_run_id": "path:replicate_info.run_id",
                    "subject_class": "path:class",
                    "subject_group": "path:group",
                    "subject_project": "path:project",
                    "subject_rundate": "path:rundate",
                    "subject_exp_target": "path:exp_target",
                    "subject_ionization": "path:ionization",
                    "subject_chromatography": "path:chromatography",
                    "subject_plate": "path:replicate_info.plate",
                    "subject_injection": "path:replicate_info.injection",
                    "subject_plate_position": "path:replicate_info.plate_position",
                    "data_source": "path:data_source",
                    "mc2dp_global_id": "",
                    "is_synthetic": "Yes",
                    "commons_url": "externalgen3.prometheus.data-commons.org"
                }
            }
        }
    }
  aggMdsNamespace: pdp-commons
  autoscaling:
    enabled: true
    maxReplicas: 1
    minReplicas: 1
    targetCPUUtilizationPercentage: 40
  enabled: true
  esEndpoint: http://elasticsearch:9200
  externalSecrets:
    metadataG3auto: qa-prometheus-metadata-g3auto
    dbcreds: qa-prometheus-metadata-creds
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service
    tag: master
  useAggMds: true
mutatingWebhook:
  enabled: true
peregrine:
  enabled: true
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine
    tag: '2025.04'
portal:
  enabled: false
requestor:
  enabled: true
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor
    tag: '2025.04'
  externalSecrets:
    dbcreds: qa-prometheus-requestor-creds 
revproxy:
  autoscaling:
    enabled: true
    maxReplicas: 1
    minReplicas: 1
    targetCPUUtilizationPercentage: 40
  enabled: true
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx
    tag: '2025.04'
  ingress:
    aws:
      group: qa-prometheus-helm
sheepdog:
  enabled: true
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog
    tag: '2025.04'
  externalSecrets:
    dbcreds: qa-prometheus-sheepdog-creds    
ssjdispatcher:
  enabled: false
  externalSecrets:
    credsFile: qa-prometheus-ssjdispatcher-creds
    dbcreds: qa-prometheus-ssjdispatcher-creds
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher
    tag: '2025.04'
  indexing: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2025.04
wts:
  enabled: true
  externalSecrets:
    createWtsOidcClientSecret: false
    wtsG3auto: qa-prometheus-wts-g3auto
    wtsOidcClient: qa-prometheus-wts-client-secret
    dbcreds: qa-prometheus-wts-creds
  image:
    repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service
    tag: 0.4.4

# AuroraRDSCopy Job configuration
auroraRdsCopyJob:
  enabled: true
  auroraMasterSecret: aurora-creds
  sourceNamespace: qa-mc2dp-helm
  targetNamespace: qa-mc2dp-helm
  writeToK8sSecret: true
  pushToAwsSecret: true
  services:
    - serviceName: indexd
      sourceSecret: indexd-dbcreds
      targetSecret: indexd-dbcreds
    - serviceName: metadata
      sourceSecret: metadata-dbcreds
      targetSecret: metadata-dbcreds