From 274b6b0e5bbdeb6e8aab8bc685de644823aee603 Mon Sep 17 00:00:00 2001 From: Aidan Hilt Date: Fri, 20 Feb 2026 17:08:33 -0500 Subject: [PATCH 1/6] Migrate healprod to local workspaces --- healprod/healdata.org/values/values.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/healprod/healdata.org/values/values.yaml b/healprod/healdata.org/values/values.yaml index 22a84aadd..ce4c4c2f4 100644 --- a/healprod/healdata.org/values/values.yaml +++ b/healprod/healdata.org/values/values.yaml @@ -177,7 +177,7 @@ hatchery: "default-pay-model": { "bmh_workspace_id": "blanket_billing_eks", "region": "us-east-1", - "account_id": "252835817747", + "local": true, "workspace_type": "healworkspaces", "hard-limit": 5, "soft-limit": 4 From b4b0a533c6fa4915ca64d763ea0ca08f033ac0ee Mon Sep 17 00:00:00 2001 From: Aidan Hilt Date: Tue, 24 Feb 2026 10:51:58 -0500 Subject: [PATCH 2/6] Bump ambassador version in healprod --- healprod/healdata.org/values/values.yaml | 2967 +++++++++-------- .../vpodc.data-commons.org/values/values.yaml | 42 +- 2 files changed, 1506 insertions(+), 1503 deletions(-) diff --git a/healprod/healdata.org/values/values.yaml b/healprod/healdata.org/values/values.yaml index ce4c4c2f4..3a9c5577e 100644 --- a/healprod/healdata.org/values/values.yaml +++ b/healprod/healdata.org/values/values.yaml @@ -1,1537 +1,1540 @@ ambassador: - jupyterNamespace: jupyter-pods + jupyterNamespace: jupyter-pods + image: + tag: "1.14.4" arborist: - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist - tag: '2026.01' + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist + tag: "2026.01" audit: - enabled: true - externalSecrets: - auditG3auto: healprod-audit-g3auto - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service - tag: '2026.01' - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-receiver + enabled: true + externalSecrets: + auditG3auto: healprod-audit-g3auto + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service + tag: "2026.01" + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-receiver aws-es-proxy: - enabled: true - esEndpoint: vpc-healprod-gen3-metadata-2-l6eifqrue4gqcmvc4u2dny3cdi.us-east-1.es.amazonaws.com - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy - tag: v1.3.1 + enabled: true + esEndpoint: vpc-healprod-gen3-metadata-2-l6eifqrue4gqcmvc4u2dny3cdi.us-east-1.es.amazonaws.com + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy + tag: v1.3.1 cedar: - enabled: true - image: - repository: quay.io/cdis/cedar-wrapper-service - tag: 0.6.0 - cedar_client_job_enabled: false - externalSecrets: - createCedarClientSecret: false - cedarG3auto: healprod-cedar-g3auto - cedarAPIKey: healprod-cedar-api-key - cedarDirectoryId: healprod-cedar-directory-id + enabled: true + image: + repository: quay.io/cdis/cedar-wrapper-service + tag: 0.6.0 + cedar_client_job_enabled: false + externalSecrets: + createCedarClientSecret: false + cedarG3auto: healprod-cedar-g3auto + cedarAPIKey: healprod-cedar-api-key + cedarDirectoryId: healprod-cedar-directory-id dashboard: - dashboardConfig: - bucket: dashboard-205252583234-healprod-gen3 - prefix: healdata.org - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics - tag: '2026.01' - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--dashboard-access + dashboardConfig: + bucket: dashboard-205252583234-healprod-gen3 + prefix: healdata.org + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics + tag: "2026.01" + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--dashboard-access etl: - enabled: false - esEndpoint: elasticsearch -fence: - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-sender - usersync: - usersync: true - userYamlS3Path: s3://cdis-gen3-users/heal/user.yaml - replicaCount: 4 - autoscaling: enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - externalSecrets: - createK8sGoogleAppSecrets: true - fenceConfig: healprod-fence-config - fenceJwtKeys: healprod-fence-jwt - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence - tag: '2026.01' - FENCE_CONFIG_PUBLIC: - S3_BUCKETS: - healprod-default-205252583234-upload: - cred: fence_bot - region: us-east-1 - heal-bucket-bacpac: - cred: fence_bot - region: us-east-1 - heal-bucket-publicaccess: - cred: fence_bot - region: us-east-1 - jcoinprod-default-258867494168-upload: - cred: fence_bot - region: us-east-1 - pennsieve-prod-discover-publish50-use1: - cred: fence_bot - requester_pays: true - region: us-east-1 - prod-rejoin-discover50-use1: - cred: fence_bot - requester_pays: true - region: us-east-1 - prd-sparc-discover50-use1: - cred: fence_bot - requester_pays: true - region: us-east-1 - sparc-prod-aod-discover-publish50-use1: - cred: fence_bot - requester_pays: true - region: us-east-1 - HIDE_IDPS: - - https://shib2.swmed.edu/idp/shibboleth + esEndpoint: elasticsearch +fence: + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-sender + usersync: + usersync: true + userYamlS3Path: s3://cdis-gen3-users/heal/user.yaml + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 + enabled: true + externalSecrets: + createK8sGoogleAppSecrets: true + fenceConfig: healprod-fence-config + fenceJwtKeys: healprod-fence-jwt + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence + tag: "2026.01" + FENCE_CONFIG_PUBLIC: + S3_BUCKETS: + healprod-default-205252583234-upload: + cred: fence_bot + region: us-east-1 + heal-bucket-bacpac: + cred: fence_bot + region: us-east-1 + heal-bucket-publicaccess: + cred: fence_bot + region: us-east-1 + jcoinprod-default-258867494168-upload: + cred: fence_bot + region: us-east-1 + pennsieve-prod-discover-publish50-use1: + cred: fence_bot + requester_pays: true + region: us-east-1 + prod-rejoin-discover50-use1: + cred: fence_bot + requester_pays: true + region: us-east-1 + prd-sparc-discover50-use1: + cred: fence_bot + requester_pays: true + region: us-east-1 + sparc-prod-aod-discover-publish50-use1: + cred: fence_bot + requester_pays: true + region: us-east-1 + HIDE_IDPS: + - https://shib2.swmed.edu/idp/shibboleth fluentd: - enabled: true - image: - repository: fluent/fluentd-kubernetes-daemonset - tag: v1.15.3-debian-cloudwatch-1.0 + enabled: true + image: + repository: fluent/fluentd-kubernetes-daemonset + tag: v1.15.3-debian-cloudwatch-1.0 frontend-framework: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/heal-data-commons - tag: 1.2.7 -global: - pdb: true - aws: - account: '205252583234' - awsEsProxyRole: healprod--healprod-helm--es-access enabled: true - hatchery_role: healprod--healprod-helm--hatchery-sa - sower_role: healprod-batch-export-sa-role - secretStoreServiceAccount: - enabled: true - roleArn: arn:aws:iam::205252583234:role/healprod-external-secrets-sa - wafv2: - enabled: true - wafAclArn: arn:aws:wafv2:us-east-1:205252583234:regional/webacl/healprod-waf/433ff65b-9bda-4850-b7b9-dd07051a11e3 - dev: false - dictionaryUrl: https://s3.amazonaws.com/dictionary-artifacts/heal_dictionary/1.1.0/schema.json - dispatcherJobNum: '10' - environment: healprod - externalSecrets: - deploy: true - createSlackWebhookSecret: true - slackWebhookSecretName: healprod-slack-webhook - frontendRoot: gen3ff - hostname: healdata.org - fenceURL: https://healdata.org/user - manifestGlobalExtraValues: - document_url: https://heal.github.io/platform-documentation - kube_bucket: kube-healprod-gen3 - logs_bucket: logs-healprod-gen3 - tierAccessLevel: libre - portalApp: gitops - dataUploadBucket: healprod-default-205252583234-upload - postgres: - dbCreate: false - revproxyArn: arn:aws:acm:us-east-1:205252583234:certificate/f87abeee-47ce-47cd-a3ca-b3f76b34c845 + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/heal-data-commons + tag: 1.2.7 +global: + pdb: true + aws: + account: "205252583234" + awsEsProxyRole: healprod--healprod-helm--es-access + enabled: true + hatchery_role: healprod--healprod-helm--hatchery-sa + sower_role: healprod-batch-export-sa-role + secretStoreServiceAccount: + enabled: true + roleArn: arn:aws:iam::205252583234:role/healprod-external-secrets-sa + wafv2: + enabled: true + wafAclArn: arn:aws:wafv2:us-east-1:205252583234:regional/webacl/healprod-waf/433ff65b-9bda-4850-b7b9-dd07051a11e3 + dev: false + dictionaryUrl: https://s3.amazonaws.com/dictionary-artifacts/heal_dictionary/1.1.0/schema.json + dispatcherJobNum: "10" + environment: healprod + externalSecrets: + deploy: true + createSlackWebhookSecret: true + slackWebhookSecretName: healprod-slack-webhook + frontendRoot: gen3ff + hostname: healdata.org + fenceURL: https://healdata.org/user + manifestGlobalExtraValues: + document_url: https://heal.github.io/platform-documentation + kube_bucket: kube-healprod-gen3 + logs_bucket: logs-healprod-gen3 + tierAccessLevel: libre + portalApp: gitops + dataUploadBucket: healprod-default-205252583234-upload + postgres: + dbCreate: false + revproxyArn: arn:aws:acm:us-east-1:205252583234:certificate/f87abeee-47ce-47cd-a3ca-b3f76b34c845 hatchery: - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - externalSecrets: - stataG3auto: stata-workspace-gen3-license-healdata - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery - tag: '2026.01' - hatchery: - json: |- - { - "pricing": { - "cpu": 0.04048, - "memory": 0.004445 - }, - "user-namespace": "jupyter-pods", - "sub-dir": "/lw-workspace", - "user-volume-size": "10Gi", - "pay-models-dynamodb-table": "bmh-admin-portal-backend-bmhworkspacetableD4D73E43-1SZM8FA8IP6F", - "default-pay-model": { - "bmh_workspace_id": "blanket_billing_eks", - "region": "us-east-1", - "local": true, - "workspace_type": "healworkspaces", - "hard-limit": 5, - "soft-limit": 4 - }, - "license-user-maps-dynamodb-table": "gen3-license-user-maps-prod-heal", - "license-user-maps-global-secondary-index": "activeUsersIndex", - "sidecar": { - "cpu-limit": "1.0", - "memory-limit": "256Mi", - "image": "quay.io/cdis/ecs-ws-sidecar:0.3.1", - "env": { - "NAMESPACE": "healprod-helm", - "GEN3_ENDPOINT": "healdata.org", - "HOSTNAME": "healdata.org", - "USER_UID": "1010" - }, - "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": "JupyterLab with Python and R Kernels", - "image": "quay.io/cdis/heal-notebooks:generic_rkernel__518649830a512a48eb4727ffa56d3a87b08d427c", - "env": { - "FRAME_ANCESTORS": "https://healdata.org" - }, - "args": [ - "--JupyterNotebookApp.base_url=/lw-workspace/proxy/", - "--JupyterNotebookApp.default_url=/lab/tree/heal-welcome.md", - "--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/$IAM/; rm /home/$IAM/pd/data; wget -O /data/external_data_download.ipynb https://raw.githubusercontent.com/uc-cdis/heal-platform-sdk/refs/heads/master/notebooks/external_data_download.ipynb; true" - ], - "user-uid": 1010, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd", - "gen3-volume-location": "/home/jovyan/.gen3" - }, - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "2Gi", - "name": "JupyterLab with User-Licensed Stata", - "image": "quay.io/cdis/jupyter-pystata-user-licensed:3.1.1", - "env": { - "FRAME_ANCESTORS": "https://healdata.org" - }, - "args": [ - "--JupyterNotebookApp.base_url=/lw-workspace/proxy/", - "--JupyterNotebookApp.default_url=/lab/tree/welcome.html", - "--JupyterNotebookApp.password=''", - "--JupyterNotebookApp.token=''", - "--JupyterNotebookApp.ip='*'", - "--JupyterNotebookApp.notebook_dir='/home/jovyan'", - "--JupyterNotebookApp.shutdown_no_activity_timeout=3600", - "--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/$IAM/; rm /home/$IAM/pd/data; true" - ], - "user-uid": 1010, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd", - "gen3-volume-location": "/home/jovyan/.gen3" - }, - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "2Gi", - "name": "JupyterLab with Shared Stata License", - "image": "quay.io/cdis/jupyter-pystata-gen3-licensed:3.1.1", - "env": { - "FRAME_ANCESTORS": "https://healdata.org" - }, - "license": { - "enabled": true, - "license-type": "STATA-HEAL", - "max-license-ids": 6, - "g3auto-name": "stata-workspace-gen3-license", - "g3auto-key": "stata-license.txt", - "file-path": "stata.lic", - "workspace-flavor": "gen3-licensed" - }, - "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=3600", - "--JupyterNotebookApp.quit_button=False" - ], - "command": [ - "/bin/bash", - "/tmp/wait_for_license.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/$IAM/; rm /home/$IAM/pd/data; true" - ], - "user-uid": 1010, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd", - "gen3-volume-location": "/home/jovyan/.gen3" - }, - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "2Gi", - "name": "Use JupyterLab with Example Analysis Notebooks", - "image": "quay.io/cdis/heal-notebooks:combined_tutorials__efec6b81db6f08d1c94f610463951610410a96ce", - "env": { - "FRAME_ANCESTORS": "https://healdata.org" - }, - "args": [ - "--JupyterNotebookApp.base_url=/lw-workspace/proxy/", - "--JupyterNotebookApp.default_url=/lab/tree/tutorial-welcome.md", - "--JupyterNotebookApp.password=''", - "--JupyterNotebookApp.token=''", - "--JupyterNotebookApp.ip='*'", - "--JupyterNotebookApp.notebook_dir='/home/jovyan'", - "--JupyterNotebookApp.shutdown_no_activity_timeout=3600", - "--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/$IAM/; rm /home/$IAM/pd/data; true" - ], - "user-uid": 1010, - "fs-gid": 100, - "user-volume-location": "/home/jovyan/pd", - "gen3-volume-location": "/home/jovyan/.gen3" - } - ] - } - workspaceLaunchTest: + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 enabled: true - schedule: 0 */4 * * * - workspaceImages: (Generic) Jupyter Lab Notebook with R Kernel+(Tutorials) Example - Analysis Jupyter Lab Notebooks - operatorName: planxdemo@gmail.com - hostname: https://healdata.org -indexd: - defaultPrefix: dg.H34L/ - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - externalSecrets: - serviceCreds: healprod-indexd-service-creds - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd - tag: '2026.01' -manifestservice: - enabled: true - externalSecrets: - manifestserviceG3auto: healprod-manifestservice-g3auto - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice - tag: '2026.01' - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--manifest-service-sa -metadata: - aggMdsConfig: |- - { - "configuration": { - "schema": { - "__manifest": { - "type": "array", - "default": [], - "properties": { - "file_name": { - "type": "string" - }, - "file_size": { - "type": "integer" - } - } - }, - "commons_url": {}, - "appl_id": { - "type": "string" + externalSecrets: + stataG3auto: stata-workspace-gen3-license-healdata + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery + tag: "2026.01" + hatchery: + json: |- + { + "pricing": { + "cpu": 0.04048, + "memory": 0.004445 + }, + "user-namespace": "jupyter-pods", + "sub-dir": "/lw-workspace", + "user-volume-size": "10Gi", + "pay-models-dynamodb-table": "bmh-admin-portal-backend-bmhworkspacetableD4D73E43-1SZM8FA8IP6F", + "default-pay-model": { + "bmh_workspace_id": "blanket_billing_eks", + "region": "us-east-1", + "local": true, + "workspace_type": "healworkspaces", + "hard-limit": 5, + "soft-limit": 4 + }, + "license-user-maps-dynamodb-table": "gen3-license-user-maps-prod-heal", + "license-user-maps-global-secondary-index": "activeUsersIndex", + "sidecar": { + "cpu-limit": "1.0", + "memory-limit": "256Mi", + "image": "quay.io/cdis/ecs-ws-sidecar:0.3.1", + "env": { + "NAMESPACE": "healprod-helm", + "GEN3_ENDPOINT": "healdata.org", + "HOSTNAME": "healdata.org", + "USER_UID": "1010" }, - "investigators_name": { - "type": "array", - "items": { - "type": "string" - }, - "default": [] + "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": "JupyterLab with Python and R Kernels", + "image": "quay.io/cdis/heal-notebooks:generic_rkernel__518649830a512a48eb4727ffa56d3a87b08d427c", + "env": { + "FRAME_ANCESTORS": "https://healdata.org" + }, + "args": [ + "--JupyterNotebookApp.base_url=/lw-workspace/proxy/", + "--JupyterNotebookApp.default_url=/lab/tree/heal-welcome.md", + "--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/$IAM/; rm /home/$IAM/pd/data; wget -O /data/external_data_download.ipynb https://raw.githubusercontent.com/uc-cdis/heal-platform-sdk/refs/heads/master/notebooks/external_data_download.ipynb; true" + ], + "user-uid": 1010, + "fs-gid": 100, + "user-volume-location": "/home/jovyan/pd", + "gen3-volume-location": "/home/jovyan/.gen3" }, - "_hdp_uid": { - "type": "string" + { + "target-port": 8888, + "cpu-limit": "1.0", + "memory-limit": "2Gi", + "name": "JupyterLab with User-Licensed Stata", + "image": "quay.io/cdis/jupyter-pystata-user-licensed:3.1.1", + "env": { + "FRAME_ANCESTORS": "https://healdata.org" + }, + "args": [ + 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707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal - tag: '2026.01' + customConfig: + enabled: true + dir: healprod/healdata.org/values/portal/ + repo: https://github.com/uc-cdis/gen3-gitops.git + branch: master + gitops: + gen3Bundle: heal + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal + tag: "2026.01" requestor: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor - tag: '2026.01' + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor + tag: "2026.01" revproxy: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx - tag: '2026.01' - ingress: - aws: - group: healprod - replicaCount: 4 + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx + tag: "2026.01" + ingress: + aws: + group: healprod + replicaCount: 4 sheepdog: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog - tag: '2026.01' - replicaCount: 4 + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog + tag: "2026.01" + replicaCount: 4 sower: - serviceAccount: - create: true - name: sower-service-account - enabled: true - externalSecrets: - createK8sPelicanServiceSecret: true - createK8sSowerJobsSecret: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower - tag: '2026.01' - sowerConfig: - - action: batch-export - activeDeadlineSeconds: 600 - container: - cpu-limit: '1' - env: - - name: GEN3_HOSTNAME - valueFrom: - configMapKeyRef: - key: hostname - name: manifest-global - - name: BUCKET - value: healdata-org-batch-export-bucket - image: quay.io/cdis/batch-export:2026.01 - labels: - internet: 'yes' - memory-limit: 1Gi - name: job-task - pull_policy: Always - name: batch-export - restart_policy: Never - serviceAccountName: sower-service-account + serviceAccount: + create: true + name: sower-service-account + enabled: true + externalSecrets: + createK8sPelicanServiceSecret: true + createK8sSowerJobsSecret: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower + tag: "2026.01" + sowerConfig: + - action: batch-export + activeDeadlineSeconds: 600 + container: + cpu-limit: "1" + env: + - name: GEN3_HOSTNAME + valueFrom: + configMapKeyRef: + key: hostname + name: manifest-global + - name: BUCKET + value: healdata-org-batch-export-bucket + image: quay.io/cdis/batch-export:2026.01 + labels: + internet: "yes" + memory-limit: 1Gi + name: job-task + pull_policy: Always + name: batch-export + restart_policy: Never + serviceAccountName: sower-service-account ssjdispatcher: - gen3Namespace: healprod-helm - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/gen3_service/healprod--default--ssj - jobServiceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/gen3_service/healprod--default--ssj-job - enabled: true - externalSecrets: - credsFile: healprod-ssjdispatcher-creds - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher - tag: '2026.01' - indexing: quay.io/cdis/indexs3client:2026.01 + gen3Namespace: healprod-helm + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/gen3_service/healprod--default--ssj + jobServiceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/gen3_service/healprod--default--ssj-job + enabled: true + externalSecrets: + credsFile: healprod-ssjdispatcher-creds + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher + tag: "2026.01" + indexing: quay.io/cdis/indexs3client:2026.01 wts: - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - externalSecrets: - createWtsOidcClientSecret: false - wtsG3auto: healprod-wts-g3auto - wtsOidcClient: healprod-wts-client-secret - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service - tag: '2026.01' + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 + enabled: true + externalSecrets: + createWtsOidcClientSecret: false + wtsG3auto: healprod-wts-g3auto + wtsOidcClient: healprod-wts-client-secret + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service + tag: "2026.01" diff --git a/vadcprod/vpodc.data-commons.org/values/values.yaml b/vadcprod/vpodc.data-commons.org/values/values.yaml index 8fecb7a11..02d95822f 100644 --- a/vadcprod/vpodc.data-commons.org/values/values.yaml +++ b/vadcprod/vpodc.data-commons.org/values/values.yaml @@ -10,7 +10,7 @@ arborist: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist - tag: '2025.12' + tag: "2025.12" audit: externalSecrets: auditG3auto: vadcprod-audit-g3auto @@ -18,7 +18,7 @@ audit: annotations: eks.amazonaws.com/role-arn: arn:aws:iam::663707118480:role/vadcprod--vadcprod-helm--audit-sqs-receiver image: - tag: '2025.12' + tag: "2025.12" aws-es-proxy: enabled: true esEndpoint: vpc-vadcprod-gen3-metadata-2-vqrbyt4omluv7b2uqw5idjdwua.us-east-1.es.amazonaws.com @@ -32,7 +32,7 @@ argo-wrapper: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/argo-wrapper tag: VA-2025.10.28 scalingGroups: - default: '{{workflow.name}}' + default: "{{workflow.name}}" s3Bucket: vadcprod-argo-user-artifacts-downloadable internalS3Bucket: vadcprod-argo-bucket environment: vadcprod-helm @@ -57,7 +57,7 @@ dashboard: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics - tag: '2025.12' + tag: "2025.12" serviceAccount: annotations: eks.amazonaws.com/role-arn: arn:aws:iam::663707118480:role/vadcprod--vadcprod-helm--dashboard-access @@ -85,9 +85,9 @@ etl: type: collector image: tube: - tag: '2025.12' + tag: "2025.12" spark: - tag: '2025.12' + tag: "2025.12" fence: usersync: usersync: true @@ -108,7 +108,7 @@ fence: fenceJwtKeys: vadcprod-fence-jwt image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence - tag: '2025.12' + tag: "2025.12" portal: enabled: false frontend-framework: @@ -120,7 +120,7 @@ frontend-framework: global: pdb: true aws: - account: '663707118480' + account: "663707118480" awsEsProxyRole: vadcprod--vadcprod-helm--es-access enabled: true hatchery_role: vadcprod--vadcprod-helm--hatchery-sa @@ -132,7 +132,7 @@ global: wafAclArn: arn:aws:wafv2:us-east-1:663707118480:regional/webacl/vadcprod-waf/144cec8b-dab0-4bec-809f-79b787add403 dev: false dictionaryUrl: https://s3.amazonaws.com/dictionary-artifacts/vadictionary/0.5.4/schema.json - dispatcherJobNum: '10' + dispatcherJobNum: "10" environment: vadcprod frontendRoot: gen3ff externalSecrets: @@ -144,7 +144,7 @@ global: manifestGlobalExtraValues: kube_bucket: kube-vadcprod-gen3 logs_bucket: logs-vadcprod-gen3 - maintenanceMode: 'off' + maintenanceMode: "off" portalApp: gitops postgres: dbCreate: false @@ -162,7 +162,7 @@ guppy: esEndpoint: http://elasticsearch:9200 image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy - tag: '2026.02' + tag: "2026.02" indices: - index: etl_mickey type: patients @@ -174,7 +174,7 @@ hatchery: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery - tag: '2025.12' + tag: "2025.12" hatchery: json: |- { @@ -437,14 +437,14 @@ indexd: serviceCreds: vadcprod-indexd-service-creds image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd - tag: '2025.12' + tag: "2025.12" manifestservice: enabled: true externalSecrets: manifestserviceG3auto: vadcprod-manifestservice-g3auto image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice - tag: '2025.12' + tag: "2025.12" serviceAccount: annotations: eks.amazonaws.com/role-arn: arn:aws:iam::663707118480:role/vadcprod--vadcprod-helm--manifest-service-sa @@ -461,7 +461,7 @@ metadata: metadataG3auto: vadcprod-metadata-g3auto image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service - tag: '2025.12' + tag: "2025.12" ohdsi-atlas: enabled: true image: @@ -482,7 +482,7 @@ peregrine: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine - tag: '2025.12' + tag: "2025.12" revproxy: replicaCount: 4 autoscaling: @@ -493,7 +493,7 @@ revproxy: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx - tag: '2025.12' + tag: "2025.12" ingress: aws: group: vadcprod @@ -508,7 +508,7 @@ sheepdog: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog - tag: '2025.12' + tag: "2025.12" sower: enabled: true externalSecrets: @@ -516,7 +516,7 @@ sower: createK8sSowerJobsSecret: false image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower - tag: '2025.12' + tag: "2025.12" sowerConfig: [] ssjdispatcher: enabled: true @@ -524,7 +524,7 @@ ssjdispatcher: credsFile: vadcprod-ssjdispatcher-creds image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher - tag: '2025.12' + tag: "2025.12" indexing: quay.io/cdis/indexs3client:2025.12 wts: replicaCount: 4 @@ -540,4 +540,4 @@ wts: wtsOidcClient: vadcprod-wts-client-secret image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service - tag: '2025.12' + tag: "2025.12" From eb10f487885f571e168b86c069d21de1c1382790 Mon Sep 17 00:00:00 2001 From: Aidan Hilt Date: Tue, 24 Feb 2026 12:55:44 -0500 Subject: [PATCH 3/6] Enable hot nodes for healprod as well --- .secrets.baseline | 590 +++- healprod/healdata.org/values/values.yaml | 3117 ++++++++++------------ 2 files changed, 2040 insertions(+), 1667 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 4aed60145..06680929a 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -90,10 +90,6 @@ { "path": "detect_secrets.filters.allowlist.is_line_allowlisted" }, - { - "path": "detect_secrets.filters.common.is_baseline_file", - "filename": ".secrets.baseline" - }, { "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies", "min_level": 2 @@ -155,7 +151,7 @@ "filename": "brhprod/brhstaging.data-commons.org/values/values.yaml", "hashed_secret": "4c7e5a7eedc322089e3a64d1911d6f823431162a", "is_verified": false, - "line_number": 1087 + "line_number": 1089 } ], "chordsprod/chordshealth.org/values/portal.yaml": [ @@ -176,6 +172,584 @@ "line_number": 1305 } ], + "healprod/healdata.org/values/values.yaml": [ + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "a63133a51a782d2fc02b5453d9e4b8d97311edf9", + "is_verified": false, + "line_number": 710 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "e268aefcb792ce6a57d1133c8fa48095525ea529", + "is_verified": false, + "line_number": 713 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "c8c6d6c462b1cf551b73730c34d1e023575a88dc", + "is_verified": false, + "line_number": 720 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "42702f9e49552d91607038925ad0fca153756cc9", + "is_verified": false, + "line_number": 727 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "1daece92f86cbaa6e9e0a1279a125a393576fd40", + "is_verified": false, + "line_number": 734 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "49c19ac2e140df87e67f22f362ba39f783e093b8", + "is_verified": false, + "line_number": 753 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "39ef2666d50ef83983d1c4196c6e0fa086cd9144", + "is_verified": false, + "line_number": 756 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "17fc3763345b8c2780d429de102fb0e411c9711b", + "is_verified": false, + "line_number": 763 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "12cd3610b2685ccc60c2c32b2f198201ce63204b", + "is_verified": false, + "line_number": 770 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "d64e3cc4e2e87a699af44fcff567bdff597c0376", + "is_verified": false, + "line_number": 777 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "32e35d2f2f45a586529f521d6219eb538d5a0288", + "is_verified": false, + "line_number": 796 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "172998ec3620b09f4990636c07537dda11c20676", + "is_verified": false, + "line_number": 799 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "30363496823494a724a496240bc3db15f75d2b5e", + "is_verified": false, + "line_number": 806 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "5e37fb59991835cc65717844a7435ad64f568b15", + "is_verified": false, + "line_number": 813 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "6c3d4066f2f89edd496d51c4b49f515d93b29cda", + "is_verified": false, + "line_number": 820 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "de02bb6ecb18736657eb6eb6e0470ba7c485ad78", + "is_verified": false, + "line_number": 839 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "a733cb129be3fbe2fe5a5ddd01c19f0234c27342", + "is_verified": false, + "line_number": 842 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "b21bd94145db03c88dc273c428415e6369d66feb", + "is_verified": false, + "line_number": 849 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "8b54b2b9700f6124004fa67adaaa7d99e3483dd8", + "is_verified": false, + "line_number": 856 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "8f2621649c866378946c5fcbc76f6e0369106ed4", + "is_verified": false, + "line_number": 863 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "d1737fc3b7ab355408b23e8760c9f1265b65c0eb", + "is_verified": false, + "line_number": 882 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "ca9950ca9fcdf27eda36b24eac22213fa474d647", + "is_verified": false, + "line_number": 885 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "6b4ceca80e2339590dea5e0287e50a0e29616711", + "is_verified": false, + "line_number": 892 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "4a00438621ce6d6b5fe3749b5fe62bada1b7e436", + "is_verified": false, + "line_number": 899 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "fa04a9a10bc5915ae04eca4db2b9292d898b37f2", + "is_verified": false, + "line_number": 906 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "82e7adbf4e6ca8d24f89e7b6c03727130e2b0cbd", + "is_verified": false, + "line_number": 913 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "8b4ed6e209e3dff1fdd4a01c273cfd8607d70c40", + "is_verified": false, + "line_number": 934 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "e0de54968873cbcba524cba465b3b9f5463dd41a", + "is_verified": false, + "line_number": 937 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "d391fd6e2d79791bcdbfa9df308cc9cf5b551af6", + "is_verified": false, + "line_number": 944 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "a6171f48ad9bfbf08ec950fe7b08f15e58ca7fde", + "is_verified": false, + "line_number": 951 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "9b68777479917d27b0ed60ef5a881524dd32d76e", + "is_verified": false, + "line_number": 958 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "d13a1bd4cc93d48d365bebe3a945d45b2a90c5a9", + "is_verified": false, + "line_number": 977 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "3111c9596494082a282733deec5cd35972541343", + "is_verified": false, + "line_number": 980 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "c13240f56f84c4a68a9f0765020df1b7dc57b3b4", + "is_verified": false, + "line_number": 987 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "f1565b2bf1a1d9a827d196c42b86808d43fd3c5c", + "is_verified": false, + "line_number": 994 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "2e3c3459ae07130e7bd32755740431d73dee1bf5", + "is_verified": false, + "line_number": 1001 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "d856b7d922db2a8f3b995509b18b1df9731a1b01", + "is_verified": false, + "line_number": 1008 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "68f3e1f89974ee0a254ba5ad8e21f3875507de6f", + "is_verified": false, + "line_number": 1029 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "a70714f6811ca1984285a274d803d397a854f437", + "is_verified": false, + "line_number": 1032 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "6fc3b39e677ed0674bb766d511036cb644061b25", + "is_verified": false, + "line_number": 1039 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "59fd8c3f61f33197f02003e856946037d304692d", + "is_verified": false, + "line_number": 1046 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "cfc071d4b772406b421d6c11107af0452c7791a3", + "is_verified": false, + "line_number": 1053 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "6497035d007fbb86db29830a98375a2d07441e26", + "is_verified": false, + "line_number": 1072 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "60d65b9cd0ae04bf2d25698255f9fe9c97b5a9b3", + "is_verified": false, + "line_number": 1075 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "36690c5f0476bf03772314800d25b8439bf0bc27", + "is_verified": false, + "line_number": 1082 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "e6792e08a82410fff9037572786261320ce41799", + "is_verified": false, + "line_number": 1089 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "4b3732ebb3fde431f4f3754c3e37cfbfd39ebc75", + "is_verified": false, + "line_number": 1096 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "e301ed844716902def444c1ce6224999da4b5443", + "is_verified": false, + "line_number": 1115 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "1677089ffb27fe27f8eb47b005d595adb249eaba", + "is_verified": false, + "line_number": 1118 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "5c4e740e6edcce4b32ba215f376c46ff685f84ba", + "is_verified": false, + "line_number": 1125 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "e42f676bca01cfa08a9dd66221ba4c1c965f8d4a", + "is_verified": false, + "line_number": 1132 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "f2b5ccaff2ce715767e90ba4ee942cb49c269e04", + "is_verified": false, + "line_number": 1139 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "4829156f57536223a66876c11203f0232f16b0ba", + "is_verified": false, + "line_number": 1158 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "f6f71352db31c6a057b4f37e9dda102366e5e2ff", + "is_verified": false, + "line_number": 1161 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "df8364d52aabf1d380a99bfb0ef6d6a34de461a6", + "is_verified": false, + "line_number": 1168 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "632db2776362cbd194bcecda2f3a011ef09f0e5d", + "is_verified": false, + "line_number": 1175 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "2bfc4e00f3a391f240d8cb6702b2daba2ef5fb26", + "is_verified": false, + "line_number": 1182 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "93ef759d083104f19ae77c221f76a7d8a679a710", + "is_verified": false, + "line_number": 1204 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "25988519ec331829f445662006767e0dd0abc130", + "is_verified": false, + "line_number": 1211 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "43b25a71a5cf1293710ba14ba6ab577a1ae35563", + "is_verified": false, + "line_number": 1218 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "f7fddcb97ba38b1ca1979eb1de3088b812bdd834", + "is_verified": false, + "line_number": 1225 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "b11396ee35dd076a7f08a2d02bfcdb9fd2c0b3ee", + "is_verified": false, + "line_number": 1244 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "b364e8eafbf161dc1789e1e099be2c07f7690ecb", + "is_verified": false, + "line_number": 1247 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "0b2a961e1f852d93ee413d2dbcfe2e09637ae92a", + "is_verified": false, + "line_number": 1254 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "9860b5f9b5478bdb72cfeb2a6f40c7eb7106755e", + "is_verified": false, + "line_number": 1261 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "a709cddb975dedf3c0a6931a710937206f734758", + "is_verified": false, + "line_number": 1268 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "f720282990073f87db353f82c9fe11bb5fd17330", + "is_verified": false, + "line_number": 1287 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "cfe6faa430f539de6a804046e9f92f97c5573431", + "is_verified": false, + "line_number": 1290 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "5c0e0176bf11adac3253cca8c4c2fe350f59eb73", + "is_verified": false, + "line_number": 1297 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "79cde8590d0dedc41f2c0f1fdca767f0f5f6b2aa", + "is_verified": false, + "line_number": 1304 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "35358c7055a2a6a8997239918588e01ed6ae1392", + "is_verified": false, + "line_number": 1311 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "5a2cf84d549c25cf8c117adc380e8d501b6c3c82", + "is_verified": false, + "line_number": 1330 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "2ab98077a4a68016d72b75f4d22fef06db6fd605", + "is_verified": false, + "line_number": 1333 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "68463d5b987ed3868e08bd30c3ec5be831b952b7", + "is_verified": false, + "line_number": 1340 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "ef62359609ac68617f0a01a4419a3dbd9af64f5c", + "is_verified": false, + "line_number": 1347 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "963db3117b5c98e3645a9cdd9d77df9e5feb1302", + "is_verified": false, + "line_number": 1354 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "8ed37aa21f5c9f21ade6e4dd2527bfde5c71ff87", + "is_verified": false, + "line_number": 1373 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "e128ecc842f57ce57e883cc0ab67eaac557c520e", + "is_verified": false, + "line_number": 1376 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "3bcefddae71fd94340005f4b81c06ff1644a9643", + "is_verified": false, + "line_number": 1383 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "d4f7da97231deec20a5de30a8f9ec36cda85cf9c", + "is_verified": false, + "line_number": 1390 + }, + { + "type": "Hex High Entropy String", + "filename": "healprod/healdata.org/values/values.yaml", + "hashed_secret": "499dd9a0da3623a288ad3c2bb6c08c787a4750f5", + "is_verified": false, + "line_number": 1397 + } + ], + "icgc/icgc.bionimbus.org/values/values.yaml": [ + { + "type": "Secret Keyword", + "filename": "icgc/icgc.bionimbus.org/values/values.yaml", + "hashed_secret": "a1faaa633be4dbecf49dc41a2f93b81684665fbe", + "is_verified": false, + "line_number": 153 + } + ], "jcoinprod/jcoin.datacommons.io/values/values.yaml": [ { "type": "Base64 High Entropy String", @@ -191,7 +765,7 @@ "filename": "kidsfirst-kfqa2/gen3qa.kidsfirstdrc.org/values/values.yaml", "hashed_secret": "cf17f42c0c730b5582614d768b907020ceedbfe2", "is_verified": false, - "line_number": 240 + "line_number": 237 } ], "kidsfirst-prodv1/data.kidsfirstdrc.org/values/values.yaml": [ @@ -218,7 +792,7 @@ "filename": "kidsfirst-skfqa/gen3staging.kidsfirstdrc.org/values/values.yaml", "hashed_secret": "cf17f42c0c730b5582614d768b907020ceedbfe2", "is_verified": false, - "line_number": 231 + "line_number": 228 } ], "vhdcprod/va.data-commons.org/values/values.yaml": [ @@ -231,5 +805,5 @@ } ] }, - "generated_at": "2026-02-12T21:47:17Z" + "generated_at": "2026-02-24T17:55:37Z" } diff --git a/healprod/healdata.org/values/values.yaml b/healprod/healdata.org/values/values.yaml index 46e2d0255..a9588564c 100644 --- a/healprod/healdata.org/values/values.yaml +++ b/healprod/healdata.org/values/values.yaml @@ -4,156 +4,160 @@ ambassador: tag: "1.14.4" replicaCount: 4 arborist: - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist - tag: "2026.01" + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist + tag: "2026.01" audit: - enabled: true - externalSecrets: - auditG3auto: healprod-audit-g3auto - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service - tag: "2026.01" - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-receiver + enabled: true + externalSecrets: + auditG3auto: healprod-audit-g3auto + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service + tag: "2026.01" + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-receiver aws-es-proxy: - enabled: true - esEndpoint: vpc-healprod-gen3-metadata-2-l6eifqrue4gqcmvc4u2dny3cdi.us-east-1.es.amazonaws.com - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy - tag: v1.3.1 + enabled: true + esEndpoint: vpc-healprod-gen3-metadata-2-l6eifqrue4gqcmvc4u2dny3cdi.us-east-1.es.amazonaws.com + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy + tag: v1.3.1 cedar: - enabled: true - image: - repository: quay.io/cdis/cedar-wrapper-service - tag: 0.6.0 - cedar_client_job_enabled: false - externalSecrets: - createCedarClientSecret: false - cedarG3auto: healprod-cedar-g3auto - cedarAPIKey: healprod-cedar-api-key - cedarDirectoryId: healprod-cedar-directory-id + enabled: true + image: + repository: quay.io/cdis/cedar-wrapper-service + tag: 0.6.0 + cedar_client_job_enabled: false + externalSecrets: + createCedarClientSecret: false + cedarG3auto: healprod-cedar-g3auto + cedarAPIKey: healprod-cedar-api-key + cedarDirectoryId: healprod-cedar-directory-id dashboard: - dashboardConfig: - bucket: dashboard-205252583234-healprod-gen3 - prefix: healdata.org - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics - tag: "2026.01" - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--dashboard-access + dashboardConfig: + bucket: dashboard-205252583234-healprod-gen3 + prefix: healdata.org + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics + tag: "2026.01" + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--dashboard-access etl: - enabled: false - esEndpoint: elasticsearch + enabled: false + esEndpoint: elasticsearch fence: - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-sender - usersync: - usersync: true - userYamlS3Path: s3://cdis-gen3-users/heal/user.yaml - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - externalSecrets: - createK8sGoogleAppSecrets: true - fenceConfig: healprod-fence-config - fenceJwtKeys: healprod-fence-jwt - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence - tag: "2026.01" - FENCE_CONFIG_PUBLIC: - S3_BUCKETS: - healprod-default-205252583234-upload: - cred: fence_bot - region: us-east-1 - heal-bucket-bacpac: - cred: fence_bot - region: us-east-1 - heal-bucket-publicaccess: - cred: fence_bot - region: us-east-1 - jcoinprod-default-258867494168-upload: - cred: fence_bot - region: us-east-1 - pennsieve-prod-discover-publish50-use1: - cred: fence_bot - requester_pays: true - region: us-east-1 - prod-rejoin-discover50-use1: - cred: fence_bot - requester_pays: true - region: us-east-1 - prd-sparc-discover50-use1: - cred: fence_bot - requester_pays: true - region: us-east-1 - sparc-prod-aod-discover-publish50-use1: - cred: fence_bot - requester_pays: true - region: us-east-1 - HIDE_IDPS: - - https://shib2.swmed.edu/idp/shibboleth + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-sender + usersync: + usersync: true + userYamlS3Path: s3://cdis-gen3-users/heal/user.yaml + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 + enabled: true + externalSecrets: + createK8sGoogleAppSecrets: true + fenceConfig: healprod-fence-config + fenceJwtKeys: healprod-fence-jwt + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence + tag: "2026.01" + FENCE_CONFIG_PUBLIC: + S3_BUCKETS: + healprod-default-205252583234-upload: + cred: fence_bot + region: us-east-1 + heal-bucket-bacpac: + cred: fence_bot + region: us-east-1 + heal-bucket-publicaccess: + cred: fence_bot + region: us-east-1 + jcoinprod-default-258867494168-upload: + cred: fence_bot + region: us-east-1 + pennsieve-prod-discover-publish50-use1: + cred: fence_bot + requester_pays: true + region: us-east-1 + prod-rejoin-discover50-use1: + cred: fence_bot + requester_pays: true + region: us-east-1 + prd-sparc-discover50-use1: + cred: fence_bot + requester_pays: true + region: us-east-1 + sparc-prod-aod-discover-publish50-use1: + cred: fence_bot + requester_pays: true + region: us-east-1 + HIDE_IDPS: + - https://shib2.swmed.edu/idp/shibboleth fluentd: - enabled: true - image: - repository: fluent/fluentd-kubernetes-daemonset - tag: v1.15.3-debian-cloudwatch-1.0 + enabled: true + image: + repository: fluent/fluentd-kubernetes-daemonset + tag: v1.15.3-debian-cloudwatch-1.0 frontend-framework: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/heal-data-commons - tag: 1.2.7 + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/heal-data-commons + tag: 1.2.7 global: - pdb: true - aws: - account: "205252583234" - awsEsProxyRole: healprod--healprod-helm--es-access - enabled: true - hatchery_role: healprod--healprod-helm--hatchery-sa - sower_role: healprod-batch-export-sa-role - secretStoreServiceAccount: - enabled: true - roleArn: arn:aws:iam::205252583234:role/healprod-external-secrets-sa - wafv2: - enabled: true - wafAclArn: arn:aws:wafv2:us-east-1:205252583234:regional/webacl/healprod-waf/433ff65b-9bda-4850-b7b9-dd07051a11e3 - dev: false - dictionaryUrl: https://s3.amazonaws.com/dictionary-artifacts/heal_dictionary/1.1.0/schema.json - dispatcherJobNum: "10" - environment: healprod - externalSecrets: - deploy: true - createSlackWebhookSecret: true - slackWebhookSecretName: healprod-slack-webhook - frontendRoot: gen3ff - hostname: healdata.org - fenceURL: https://healdata.org/user - manifestGlobalExtraValues: - document_url: https://heal.github.io/platform-documentation - kube_bucket: kube-healprod-gen3 - logs_bucket: logs-healprod-gen3 - tierAccessLevel: libre - portalApp: gitops - dataUploadBucket: healprod-default-205252583234-upload - postgres: - dbCreate: false - revproxyArn: arn:aws:acm:us-east-1:205252583234:certificate/f87abeee-47ce-47cd-a3ca-b3f76b34c845 + pdb: true + aws: + account: "205252583234" + awsEsProxyRole: healprod--healprod-helm--es-access + enabled: true + hatchery_role: healprod--healprod-helm--hatchery-sa + sower_role: healprod-batch-export-sa-role + secretStoreServiceAccount: + enabled: true + roleArn: arn:aws:iam::205252583234:role/healprod-external-secrets-sa + wafv2: + enabled: true + wafAclArn: arn:aws:wafv2:us-east-1:205252583234:regional/webacl/healprod-waf/433ff65b-9bda-4850-b7b9-dd07051a11e3 + dev: false + dictionaryUrl: https://s3.amazonaws.com/dictionary-artifacts/heal_dictionary/1.1.0/schema.json + dispatcherJobNum: "10" + environment: healprod + externalSecrets: + deploy: true + createSlackWebhookSecret: true + slackWebhookSecretName: healprod-slack-webhook + frontendRoot: gen3ff + hostname: healdata.org + fenceURL: https://healdata.org/user + manifestGlobalExtraValues: + document_url: https://heal.github.io/platform-documentation + kube_bucket: kube-healprod-gen3 + logs_bucket: logs-healprod-gen3 + tierAccessLevel: libre + portalApp: gitops + dataUploadBucket: healprod-default-205252583234-upload + postgres: + dbCreate: false + revproxyArn: arn:aws:acm:us-east-1:205252583234:certificate/f87abeee-47ce-47cd-a3ca-b3f76b34c845 hatchery: + hotNode: + enabled: true + availabilityZones: + - us-east-1c replicaCount: 4 autoscaling: enabled: false @@ -165,1516 +169,1311 @@ hatchery: stataG3auto: stata-workspace-gen3-license-healdata image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery - tag: '2.7.1' + tag: "2026.01" hatchery: json: |- { "pricing": { - "cpu": 0.04048, - "memory": 0.004445 + "cpu": 0.04048, + "memory": 0.004445 }, "user-namespace": "jupyter-pods", "sub-dir": "/lw-workspace", "user-volume-size": "10Gi", "pay-models-dynamodb-table": "bmh-admin-portal-backend-bmhworkspacetableD4D73E43-1SZM8FA8IP6F", "default-pay-model": { - "bmh_workspace_id": "blanket_billing_eks", - "region": "us-east-1", - "account_id": "252835817747", - "workspace_type": "healworkspaces", - "hard-limit": 5, - "soft-limit": 4 + "bmh_workspace_id": "blanket_billing_eks", + "region": "us-east-1", + "local": true, + "workspace_type": "healworkspaces", + "hard-limit": 5, + "soft-limit": 4 }, "license-user-maps-dynamodb-table": "gen3-license-user-maps-prod-heal", "license-user-maps-global-secondary-index": "activeUsersIndex", "sidecar": { + "cpu-limit": "1.0", + "memory-limit": "256Mi", + "image": "quay.io/cdis/ecs-ws-sidecar:0.3.1", + "env": { + "NAMESPACE": "healprod-helm", + "GEN3_ENDPOINT": "healdata.org", + "HOSTNAME": "healdata.org", + "USER_UID": "1010" + }, + "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": "256Mi", - "image": "quay.io/cdis/ecs-ws-sidecar:0.3.2", + "memory-limit": "2Gi", + "name": "JupyterLab with Python and R Kernels", + "image": "quay.io/cdis/heal-notebooks:generic_rkernel__518649830a512a48eb4727ffa56d3a87b08d427c", "env": { - "NAMESPACE": "healprod-helm", - "GEN3_ENDPOINT": "healdata.org", - "HOSTNAME": "healdata.org", - "USER_UID": "1010" + "FRAME_ANCESTORS": "https://healdata.org" }, - "args": [], + "args": [ + "--JupyterNotebookApp.base_url=/lw-workspace/proxy/", + "--JupyterNotebookApp.default_url=/lab/tree/heal-welcome.md", + "--JupyterNotebookApp.password=''", + "--JupyterNotebookApp.token=''", + "--JupyterNotebookApp.ip='*'", + "--JupyterNotebookApp.notebook_dir='/home/jovyan'", + "--JupyterNotebookApp.shutdown_no_activity_timeout=5400", + "--JupyterNotebookApp.quit_button=False" + ], "command": [ - "/bin/bash", - "./sidecar.sh" + "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/$IAM/; rm /home/$IAM/pd/data; wget -O /data/external_data_download.ipynb https://raw.githubusercontent.com/uc-cdis/heal-platform-sdk/refs/heads/master/notebooks/external_data_download.ipynb; true" ], - "lifecycle-pre-stop": [ - "su", - "-c", - "echo test", - "-s", - "/bin/sh", - "root" - ] + "user-uid": 1010, + "fs-gid": 100, + "user-volume-location": "/home/jovyan/pd", + "gen3-volume-location": "/home/jovyan/.gen3" }, - "containers": [ - { - "target-port": 8888, - "cpu-limit": "1.0", - "memory-limit": "2Gi", - "name": "JupyterLab with Python and R Kernels", - "image": "quay.io/cdis/heal-notebooks:generic_rkernel__518649830a512a48eb4727ffa56d3a87b08d427c", - "env": { - "FRAME_ANCESTORS": "https://healdata.org" + { + "target-port": 8888, + "cpu-limit": "1.0", + "memory-limit": "2Gi", + "name": "JupyterLab with User-Licensed Stata", + "image": "quay.io/cdis/jupyter-pystata-user-licensed:3.1.1", + "env": { + "FRAME_ANCESTORS": "https://healdata.org" + }, + "args": [ + "--JupyterNotebookApp.base_url=/lw-workspace/proxy/", + "--JupyterNotebookApp.default_url=/lab/tree/welcome.html", + "--JupyterNotebookApp.password=''", + "--JupyterNotebookApp.token=''", + "--JupyterNotebookApp.ip='*'", + "--JupyterNotebookApp.notebook_dir='/home/jovyan'", + "--JupyterNotebookApp.shutdown_no_activity_timeout=3600", + "--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/$IAM/; rm /home/$IAM/pd/data; true" + ], + "user-uid": 1010, + "fs-gid": 100, + "user-volume-location": "/home/jovyan/pd", + "gen3-volume-location": "/home/jovyan/.gen3" + }, + { + "target-port": 8888, + "cpu-limit": "1.0", + "memory-limit": "2Gi", + "name": "JupyterLab with Shared Stata License", + "image": 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"file_name": "buprenorphine-and-methadone-during-covid-19-research-protocol-02072022.pdf", + "commons_url": "jcoin.datacommons.io", + "object_id": "dg.6VTS/7744b857-c8cc-49e2-b8e9-7574c0241c71" + } + ], + "authz": "/programs/NIDA/projects/PDAPS", + "data_availability": "available", + "study_url": "https://pdaps.org/datasets/increasing-access-to-buprenorphine-and-methadone-during-covid-19", + "dataset_1_type": "Codebook", + "dataset_2_type": "Data", + "dataset_4_type": "Report", + "dataset_3_type": "Protocol", + "dataset_1_title": "buprenorphine-and-methadone-during-covid-19-codebook-020222.pdf", + "dataset_2_title": "buprenorphine-and-methadone-during-covid-19-data-020222.xlsx", + "dataset_4_title": "buprenorphine-and-methadone-during-covid-19-report-02102022.pdf", + "dataset_3_title": "buprenorphine-and-methadone-during-covid-19-research-protocol-02072022.pdf" } + } } - aggMdsDefaultDataDictField: variable_level_metadata - aggMdsNamespace: healprod-helm - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - esEndpoint: http://elasticsearch:9200 - externalSecrets: - metadataG3auto: healprod-metadata-g3auto - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service - tag: "2026.01" - useAggMds: true - schedule: 0 9 * * * - suspendCronjob: false -mutatingWebhook: + } + } + aggMdsDefaultDataDictField: variable_level_metadata + aggMdsNamespace: healprod-helm + replicaCount: 4 + autoscaling: enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 + enabled: true + esEndpoint: http://elasticsearch:9200 + externalSecrets: + metadataG3auto: healprod-metadata-g3auto + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service + tag: "2026.01" + useAggMds: true + schedule: 0 9 * * * + suspendCronjob: false +mutatingWebhook: + enabled: false peregrine: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine - tag: "2026.01" + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine + tag: "2026.01" portal: - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 + enabled: true + customConfig: enabled: true - customConfig: - enabled: true - dir: healprod/healdata.org/values/portal/ - repo: https://github.com/uc-cdis/gen3-gitops.git - branch: master - gitops: - gen3Bundle: heal - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal - tag: "2026.01" + dir: healprod/healdata.org/values/portal/ + repo: https://github.com/uc-cdis/gen3-gitops.git + branch: master + gitops: + gen3Bundle: heal + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal + tag: "2026.01" requestor: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor - tag: "2026.01" + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor + tag: "2026.01" revproxy: - enabled: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx - tag: "2026.01" - ingress: - aws: - group: healprod - replicaCount: 4 + enabled: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx + tag: "2026.01" + ingress: + aws: + group: healprod + replicaCount: 4 sheepdog: enabled: true image: @@ -1682,65 +1481,65 @@ sheepdog: tag: '2026.01' replicaCount: 1 sower: - serviceAccount: - create: true - name: sower-service-account - enabled: true - externalSecrets: - createK8sPelicanServiceSecret: true - createK8sSowerJobsSecret: true - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower - tag: "2026.01" - sowerConfig: - - action: batch-export - activeDeadlineSeconds: 600 - container: - cpu-limit: "1" - env: - - name: GEN3_HOSTNAME - valueFrom: - configMapKeyRef: - key: hostname - name: manifest-global - - name: BUCKET - value: healdata-org-batch-export-bucket - image: quay.io/cdis/batch-export:2026.01 - labels: - internet: "yes" - memory-limit: 1Gi - name: job-task - pull_policy: Always - name: batch-export - restart_policy: Never - serviceAccountName: sower-service-account + serviceAccount: + create: true + name: sower-service-account + enabled: true + externalSecrets: + createK8sPelicanServiceSecret: true + createK8sSowerJobsSecret: true + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower + tag: "2026.01" + sowerConfig: + - action: batch-export + activeDeadlineSeconds: 600 + container: + cpu-limit: "1" + env: + - name: GEN3_HOSTNAME + valueFrom: + configMapKeyRef: + key: hostname + name: manifest-global + - name: BUCKET + value: healdata-org-batch-export-bucket + image: quay.io/cdis/batch-export:2026.01 + labels: + internet: "yes" + memory-limit: 1Gi + name: job-task + pull_policy: Always + name: batch-export + restart_policy: Never + serviceAccountName: sower-service-account ssjdispatcher: - gen3Namespace: healprod-helm - serviceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/gen3_service/healprod--default--ssj - jobServiceAccount: - annotations: - eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/gen3_service/healprod--default--ssj-job - enabled: true - externalSecrets: - credsFile: healprod-ssjdispatcher-creds - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher - tag: "2026.01" - indexing: quay.io/cdis/indexs3client:2026.01 + gen3Namespace: healprod-helm + serviceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/gen3_service/healprod--default--ssj + jobServiceAccount: + annotations: + eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/gen3_service/healprod--default--ssj-job + enabled: true + externalSecrets: + credsFile: healprod-ssjdispatcher-creds + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher + tag: "2026.01" + indexing: quay.io/cdis/indexs3client:2026.01 wts: - replicaCount: 4 - autoscaling: - enabled: false - maxReplicas: 3 - minReplicas: 2 - targetCPUUtilizationPercentage: 40 - enabled: true - externalSecrets: - createWtsOidcClientSecret: false - wtsG3auto: healprod-wts-g3auto - wtsOidcClient: healprod-wts-client-secret - image: - repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service - tag: "2026.01" + replicaCount: 4 + autoscaling: + enabled: false + maxReplicas: 3 + minReplicas: 2 + targetCPUUtilizationPercentage: 40 + enabled: true + externalSecrets: + createWtsOidcClientSecret: false + wtsG3auto: healprod-wts-g3auto + wtsOidcClient: healprod-wts-client-secret + image: + repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service + tag: "2026.01" From 603d9073cb167da982ec6e83f20a641e0c46202a Mon Sep 17 00:00:00 2001 From: Aidan Hilt Date: Tue, 24 Feb 2026 13:26:23 -0500 Subject: [PATCH 4/6] Fix YAML formatting issue --- healprod/healdata.org/values/values.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/healprod/healdata.org/values/values.yaml b/healprod/healdata.org/values/values.yaml index a9588564c..f6adf4d9a 100644 --- a/healprod/healdata.org/values/values.yaml +++ b/healprod/healdata.org/values/values.yaml @@ -1498,10 +1498,10 @@ sower: cpu-limit: "1" env: - name: GEN3_HOSTNAME - valueFrom: - configMapKeyRef: - key: hostname - name: manifest-global + valueFrom: + configMapKeyRef: + key: hostname + name: manifest-global - name: BUCKET value: healdata-org-batch-export-bucket image: quay.io/cdis/batch-export:2026.01 From 33bc0ff9e8c3302313a491109e24cf0a5c4a34b3 Mon Sep 17 00:00:00 2001 From: Aidan Hilt Date: Tue, 24 Feb 2026 13:27:47 -0500 Subject: [PATCH 5/6] More YAML formatting fixes --- .secrets.baseline | 575 +---------------------- healprod/healdata.org/values/values.yaml | 4 +- 2 files changed, 7 insertions(+), 572 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 06680929a..24aec93aa 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -90,6 +90,10 @@ { "path": "detect_secrets.filters.allowlist.is_line_allowlisted" }, + { + "path": "detect_secrets.filters.common.is_baseline_file", + "filename": ".secrets.baseline" + }, { "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies", "min_level": 2 @@ -172,575 +176,6 @@ "line_number": 1305 } ], - "healprod/healdata.org/values/values.yaml": [ - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "a63133a51a782d2fc02b5453d9e4b8d97311edf9", - "is_verified": false, - "line_number": 710 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "e268aefcb792ce6a57d1133c8fa48095525ea529", - "is_verified": false, - "line_number": 713 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "c8c6d6c462b1cf551b73730c34d1e023575a88dc", - "is_verified": false, - "line_number": 720 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "42702f9e49552d91607038925ad0fca153756cc9", - "is_verified": false, - "line_number": 727 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "1daece92f86cbaa6e9e0a1279a125a393576fd40", - "is_verified": false, - "line_number": 734 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "49c19ac2e140df87e67f22f362ba39f783e093b8", - "is_verified": false, - "line_number": 753 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "39ef2666d50ef83983d1c4196c6e0fa086cd9144", - "is_verified": false, - "line_number": 756 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "17fc3763345b8c2780d429de102fb0e411c9711b", - "is_verified": false, - "line_number": 763 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "12cd3610b2685ccc60c2c32b2f198201ce63204b", - "is_verified": false, - "line_number": 770 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "d64e3cc4e2e87a699af44fcff567bdff597c0376", - "is_verified": false, - "line_number": 777 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": 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- }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "f1565b2bf1a1d9a827d196c42b86808d43fd3c5c", - "is_verified": false, - "line_number": 994 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "2e3c3459ae07130e7bd32755740431d73dee1bf5", - "is_verified": false, - "line_number": 1001 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "d856b7d922db2a8f3b995509b18b1df9731a1b01", - "is_verified": false, - "line_number": 1008 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "68f3e1f89974ee0a254ba5ad8e21f3875507de6f", - "is_verified": false, - "line_number": 1029 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "a70714f6811ca1984285a274d803d397a854f437", - "is_verified": false, - "line_number": 1032 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "6fc3b39e677ed0674bb766d511036cb644061b25", - "is_verified": false, - "line_number": 1039 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "59fd8c3f61f33197f02003e856946037d304692d", - "is_verified": false, - "line_number": 1046 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "cfc071d4b772406b421d6c11107af0452c7791a3", - "is_verified": false, - "line_number": 1053 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "6497035d007fbb86db29830a98375a2d07441e26", - "is_verified": false, - "line_number": 1072 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "60d65b9cd0ae04bf2d25698255f9fe9c97b5a9b3", - "is_verified": false, - "line_number": 1075 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "36690c5f0476bf03772314800d25b8439bf0bc27", - "is_verified": false, - "line_number": 1082 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "e6792e08a82410fff9037572786261320ce41799", - "is_verified": false, - "line_number": 1089 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "4b3732ebb3fde431f4f3754c3e37cfbfd39ebc75", - "is_verified": false, - "line_number": 1096 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "e301ed844716902def444c1ce6224999da4b5443", - "is_verified": false, - "line_number": 1115 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "1677089ffb27fe27f8eb47b005d595adb249eaba", - "is_verified": false, - "line_number": 1118 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "5c4e740e6edcce4b32ba215f376c46ff685f84ba", - "is_verified": false, - "line_number": 1125 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "e42f676bca01cfa08a9dd66221ba4c1c965f8d4a", - "is_verified": false, - "line_number": 1132 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "f2b5ccaff2ce715767e90ba4ee942cb49c269e04", - "is_verified": false, - "line_number": 1139 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "4829156f57536223a66876c11203f0232f16b0ba", - "is_verified": false, - "line_number": 1158 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "f6f71352db31c6a057b4f37e9dda102366e5e2ff", - "is_verified": false, - "line_number": 1161 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "df8364d52aabf1d380a99bfb0ef6d6a34de461a6", - "is_verified": false, - "line_number": 1168 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "632db2776362cbd194bcecda2f3a011ef09f0e5d", - "is_verified": false, - "line_number": 1175 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "2bfc4e00f3a391f240d8cb6702b2daba2ef5fb26", - "is_verified": false, - "line_number": 1182 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "93ef759d083104f19ae77c221f76a7d8a679a710", - "is_verified": false, - "line_number": 1204 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "25988519ec331829f445662006767e0dd0abc130", - "is_verified": false, - "line_number": 1211 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "43b25a71a5cf1293710ba14ba6ab577a1ae35563", - "is_verified": false, - "line_number": 1218 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "f7fddcb97ba38b1ca1979eb1de3088b812bdd834", - "is_verified": false, - "line_number": 1225 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "b11396ee35dd076a7f08a2d02bfcdb9fd2c0b3ee", - "is_verified": false, - "line_number": 1244 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "b364e8eafbf161dc1789e1e099be2c07f7690ecb", - "is_verified": false, - "line_number": 1247 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "0b2a961e1f852d93ee413d2dbcfe2e09637ae92a", - "is_verified": false, - "line_number": 1254 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "9860b5f9b5478bdb72cfeb2a6f40c7eb7106755e", - "is_verified": false, - "line_number": 1261 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "a709cddb975dedf3c0a6931a710937206f734758", - "is_verified": false, - "line_number": 1268 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "f720282990073f87db353f82c9fe11bb5fd17330", - "is_verified": false, - "line_number": 1287 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "cfe6faa430f539de6a804046e9f92f97c5573431", - "is_verified": false, - "line_number": 1290 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "5c0e0176bf11adac3253cca8c4c2fe350f59eb73", - "is_verified": false, - "line_number": 1297 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "79cde8590d0dedc41f2c0f1fdca767f0f5f6b2aa", - "is_verified": false, - "line_number": 1304 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "35358c7055a2a6a8997239918588e01ed6ae1392", - "is_verified": false, - "line_number": 1311 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "5a2cf84d549c25cf8c117adc380e8d501b6c3c82", - "is_verified": false, - "line_number": 1330 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "2ab98077a4a68016d72b75f4d22fef06db6fd605", - "is_verified": false, - "line_number": 1333 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "68463d5b987ed3868e08bd30c3ec5be831b952b7", - "is_verified": false, - "line_number": 1340 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "ef62359609ac68617f0a01a4419a3dbd9af64f5c", - "is_verified": false, - "line_number": 1347 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "963db3117b5c98e3645a9cdd9d77df9e5feb1302", - "is_verified": false, - "line_number": 1354 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "8ed37aa21f5c9f21ade6e4dd2527bfde5c71ff87", - "is_verified": false, - "line_number": 1373 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "e128ecc842f57ce57e883cc0ab67eaac557c520e", - "is_verified": false, - "line_number": 1376 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "3bcefddae71fd94340005f4b81c06ff1644a9643", - "is_verified": false, - "line_number": 1383 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "d4f7da97231deec20a5de30a8f9ec36cda85cf9c", - "is_verified": false, - "line_number": 1390 - }, - { - "type": "Hex High Entropy String", - "filename": "healprod/healdata.org/values/values.yaml", - "hashed_secret": "499dd9a0da3623a288ad3c2bb6c08c787a4750f5", - "is_verified": false, - "line_number": 1397 - } - ], "icgc/icgc.bionimbus.org/values/values.yaml": [ { "type": "Secret Keyword", @@ -805,5 +240,5 @@ } ] }, - "generated_at": "2026-02-24T17:55:37Z" + "generated_at": "2026-02-24T18:27:40Z" } diff --git a/healprod/healdata.org/values/values.yaml b/healprod/healdata.org/values/values.yaml index f6adf4d9a..7de065eb2 100644 --- a/healprod/healdata.org/values/values.yaml +++ b/healprod/healdata.org/values/values.yaml @@ -1478,7 +1478,7 @@ sheepdog: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog - tag: '2026.01' + tag: "2026.01" replicaCount: 1 sower: serviceAccount: @@ -1503,7 +1503,7 @@ sower: key: hostname name: manifest-global - name: BUCKET - value: healdata-org-batch-export-bucket + value: healdata-org-batch-export-bucket image: quay.io/cdis/batch-export:2026.01 labels: internet: "yes" From 337fca4a16c2828f53f0c7e079b4b594794254ca Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Tue, 24 Feb 2026 15:14:50 -0600 Subject: [PATCH 6/6] restore hatchery and sidecar --- healprod/healdata.org/values/values.yaml | 64 ++++++++++++------------ 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/healprod/healdata.org/values/values.yaml b/healprod/healdata.org/values/values.yaml index d3d70b95d..4714407dc 100644 --- a/healprod/healdata.org/values/values.yaml +++ b/healprod/healdata.org/values/values.yaml @@ -13,14 +13,14 @@ arborist: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist - tag: '2026.02' + tag: "2026.02" audit: enabled: true externalSecrets: auditG3auto: healprod-audit-g3auto image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service - tag: '2026.02' + tag: "2026.02" serviceAccount: annotations: eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--audit-sqs-receiver @@ -48,7 +48,7 @@ dashboard: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics - tag: '2026.02' + tag: "2026.02" serviceAccount: annotations: eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--dashboard-access @@ -75,7 +75,7 @@ fence: fenceJwtKeys: healprod-fence-jwt image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence - tag: '2026.02' + tag: "2026.02" FENCE_CONFIG_PUBLIC: S3_BUCKETS: healprod-default-205252583234-upload: @@ -169,37 +169,37 @@ hatchery: stataG3auto: stata-workspace-gen3-license-healdata image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery - tag: "2026.01" + tag: "2.7.1" hatchery: json: |- { "pricing": { - "cpu": 0.04048, - "memory": 0.004445 + "cpu": 0.04048, + "memory": 0.004445 }, "user-namespace": "jupyter-pods", "sub-dir": "/lw-workspace", "user-volume-size": "10Gi", "pay-models-dynamodb-table": "bmh-admin-portal-backend-bmhworkspacetableD4D73E43-1SZM8FA8IP6F", "default-pay-model": { - "bmh_workspace_id": "blanket_billing_eks", - "region": "us-east-1", - "local": true, - "workspace_type": "healworkspaces", - "hard-limit": 5, - "soft-limit": 4 + "bmh_workspace_id": "blanket_billing_eks", + "region": "us-east-1", + "local": true, + "workspace_type": "healworkspaces", + "hard-limit": 5, + "soft-limit": 4 }, "license-user-maps-dynamodb-table": "gen3-license-user-maps-prod-heal", "license-user-maps-global-secondary-index": "activeUsersIndex", "sidecar": { - "cpu-limit": "1.0", - "memory-limit": "256Mi", - "image": "quay.io/cdis/ecs-ws-sidecar:0.3.1", - "env": { - "NAMESPACE": "healprod-helm", - "GEN3_ENDPOINT": "healdata.org", - "HOSTNAME": "healdata.org", - "USER_UID": "1010" + "cpu-limit": "1.0", + "memory-limit": "256Mi", + "image": "quay.io/cdis/ecs-ws-sidecar:0.3.2", + "env": { + "NAMESPACE": "healprod-helm", + "GEN3_ENDPOINT": "healdata.org", + "HOSTNAME": "healdata.org", + "USER_UID": "1010" }, "args": [], "command": [ @@ -389,14 +389,14 @@ indexd: serviceCreds: healprod-indexd-service-creds image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd - tag: '2026.02' + tag: "2026.02" manifestservice: enabled: true externalSecrets: manifestserviceG3auto: healprod-manifestservice-g3auto image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice - tag: '2026.02' + tag: "2026.02" serviceAccount: annotations: eks.amazonaws.com/role-arn: arn:aws:iam::205252583234:role/healprod--healprod-helm--manifest-service-sa @@ -1431,7 +1431,7 @@ metadata: metadataG3auto: healprod-metadata-g3auto image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service - tag: '2026.02' + tag: "2026.02" useAggMds: true schedule: 0 9 * * * suspendCronjob: false @@ -1441,7 +1441,7 @@ peregrine: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine - tag: '2026.02' + tag: "2026.02" portal: replicaCount: 4 autoscaling: @@ -1459,17 +1459,17 @@ portal: gen3Bundle: heal image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal - tag: '2026.02' + tag: "2026.02" requestor: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor - tag: '2026.02' + tag: "2026.02" revproxy: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx - tag: '2026.02' + tag: "2026.02" ingress: aws: group: healprod @@ -1478,7 +1478,7 @@ sheepdog: enabled: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog - tag: '2026.02' + tag: "2026.02" replicaCount: 1 sower: serviceAccount: @@ -1490,7 +1490,7 @@ sower: createK8sSowerJobsSecret: true image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower - tag: '2026.02' + tag: "2026.02" sowerConfig: - action: batch-export activeDeadlineSeconds: 600 @@ -1526,7 +1526,7 @@ ssjdispatcher: credsFile: healprod-ssjdispatcher-creds image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher - tag: '2026.02' + tag: "2026.02" indexing: quay.io/cdis/indexs3client:2026.02 wts: replicaCount: 4 @@ -1542,4 +1542,4 @@ wts: wtsOidcClient: healprod-wts-client-secret image: repository: 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service - tag: '2026.02' + tag: "2026.02"