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values.yaml
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3681 lines (3680 loc) · 231 KB
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ambassador:
jupyterNamespace: georget
arborist:
autoscaling:
enabled: true
maxReplicas: 2
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
image:
repository: quay.io/cdis/arborist
tag: "2025.03"
audit:
enabled: true
externalSecrets:
auditG3auto: georget-audit-g3auto
image:
repository: quay.io/cdis/audit-service
tag: "2025.03"
serviceAccount:
annotations:
eks.amazonaws.com/role-arn: arn:aws:iam::707767160287:role/devplanetv2--georget-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
cedar-wrapper:
enabled: true
image:
repository: quay.io/cdis/cedar-wrapper-service
tag: 0.6.0
dashboard:
dashboardConfig:
bucket: dashboard-707767160287-devplanetv1-gen3
prefix: georget.planx-pla.net
enabled: true
image:
repository: quay.io/cdis/gen3-statics
tag: "2024.12"
serviceAccount:
annotations:
eks.amazonaws.com/role-arn: arn:aws:iam::707767160287:role/devplanetv2--georget-helm--dashboard-access
etl:
esEndpoint: elasticsearch
mappings:
- aggregated_props:
- fn: count
name: _samples_count
path: samples
- fn: count
name: _aliquots_count
path: samples.aliquots
- fn: count
name: _submitted_methylations_count
path: samples.aliquots.submitted_methylation_files
- fn: count
name: _submitted_copy_number_files_on_aliquots_count
path: samples.aliquots.submitted_copy_number_files
- fn: count
name: _read_groups_count
path: samples.aliquots.read_groups
- fn: count
name: _submitted_aligned_reads_count
path: samples.aliquots.read_groups.submitted_aligned_reads_files
- fn: count
name: _submitted_unaligned_reads_count
path: samples.aliquots.read_groups.submitted_unaligned_reads_files
- fn: count
name: _submitted_copy_number_files_on_read_groups_count
path: samples.aliquots.read_groups.submitted_copy_number_files
- fn: count
name: _submitted_somatic_mutations_count
path: samples.aliquots.read_groups.submitted_somatic_mutations
doc_type: case
flatten_props:
- path: demographics
props:
- name: gender
value_mappings:
- female: F
- male: M
- name: race
value_mappings:
- american indian or alaskan native: Indian
- name: ethnicity
- name: year_of_birth
joining_props:
- index: file
join_on: case_id
props:
- fn: set
name: data_format
src: data_format
- fn: set
name: data_type
src: data_type
- fn: set
name: file_id
src: file_id
name: dev_case
props:
- name: submitter_id
- name: project_id
- name: disease_type
- name: primary_site
root: case
type: aggregator
- category: data_file
doc_type: file
injecting_props:
case:
props:
- fn: set
name: case_id
src: id
- name: project_id
name: dev_file
props:
- name: object_id
- name: md5sum
- name: file_name
- name: file_size
- name: data_format
- name: data_type
- name: state
root: None
target_nodes:
- name: slide_image
path: slides.samples.cases
type: collector
fence:
autoscaling:
enabled: true
maxReplicas: 2
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: true
externalSecrets:
createK8sGoogleAppSecrets: true
fenceConfig: georget-fence-config
fenceJwtKeys: georget-fence-jwt
image:
repository: quay.io/cdis/fence
tag: "2025.07"
fluentd:
enabled: true
image:
repository: fluent/fluentd-kubernetes-daemonset
tag: v1.15.3-debian-cloudwatch-1.0
global:
aws:
account: "707767160287"
awsEsProxyRole: devplanetv2-esproxy-sa
enabled: true
scheme: internal
hatchery_role: devplanetv2--georget-helm--hatchery-sa
secretStoreServiceAccount:
enabled: true
roleArn: arn:aws:iam::707767160287:role/devplanetv2-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/datadictionary/develop/schema.json
dispatcherJobNum: "10"
environment: georget
externalSecrets:
deploy: true
hostname: georget.planx-pla.net
manifestGlobalExtraValues:
client_creds_secret_name: georget-client-secret
client_id_key: ClientIdKey
client_secret_key: ClientSecretKey
es7: true
foo: bar
kube_bucket: kube_bucket.devplanetv1.gen3
logs_bucket: logs-devplanetv1-gen3
sync_from_dbgap: "False"
useryaml_s3path: s3://cdis-gen3-users/dev/user.yaml
portalApp: gitops
postgres:
dbCreate: false
revproxyArn: arn:aws:acm:us-east-1:707767160287:certificate/798e629d-05ee-4bc5-b51f-a86861f29b68
guppy:
autoscaling:
enabled: true
maxReplicas: 2
minReplicas: 1
targetCPUUtilizationPercentage: 40
enabled: false
esEndpoint: http://elasticsearch:9200
image:
repository: quay.io/cdis/guppy
tag: "2025.03"
indices:
- index: dev_case
type: case
hatchery:
enabled: true
image:
repository: quay.io/cdis/hatchery
tag: test_updates-to-cost
json: |
{
"user-namespace": "jupyter-pods-georget",
"sub-dir": "/lw-workspace",
"user-volume-size": "10Gi",
"default-pay-model": {
"workspace_type": "Trial Workspace",
"local": true
},
"license-user-maps-dynamodb-table": "gen3-license-user-maps",
"license-user-maps-global-secondary-index": "activeUsersIndex",
"default-hard-limit": 10,
"default-soft-limit": 5,
"sidecar": {
"cpu-limit": "1.0",
"memory-limit": "256Mi",
"image": "quay.io/cdis/ecs-ws-sidecar:master",
"env": {
"NAMESPACE": "georget"
},
"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": "(Generic) Jupyter Notebook with R Kernel",
"image": "quay.io/cdis/jupyter-superslim-r:master",
"env": {"FRAME_ANCESTORS": "https://georget.planx-pla.net"},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''",
"--NotebookApp.ip='*'",
"--NotebookApp.notebook_dir='/home/jovyan'",
"--NotebookApp.shutdown_no_activity_timeout=3600",
"--NotebookApp.quit_button=False",
"--Application.log_level=DEBUG",
"--NotebookApp.log_level=DEBUG",
"--JupyterApp.log_level=DEBUG",
"--Session.debug=True"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100,
"user-volume-location": "/home/jovyan/pd"
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "2Gi",
"name": "(Generic, User-licensed) Stata Notebook ",
"image": "quay.io/cdis/stata-heal:master",
"env": {},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''",
"--NotebookApp.quit_button=False"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"(while true; do [ -d ~/pd ] && [ -f ~/pd/stata.lic ] && cp ~/pd/stata.lic /usr/local/stata17/; sleep 1; done) & export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100,
"user-volume-location": "/home/jovyan/pd"
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "2Gi",
"name": "(Generic, Limited Gen3-licensed) Stata Notebook",
"image": "quay.io/cdis/stata-heal:gen3-licensed",
"env": {},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''",
"--NotebookApp.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/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100,
"user-volume-location": "/home/jovyan/pd"
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "2Gi",
"name": "(Tutorial) JCOIN Tracking Opioid Stigma Notebook",
"image": "quay.io/cdis/heal-notebooks:jcoin__177f89f0fab8a13c606c68bab0b953aa3fed4b71",
"env": {
"FRAME_ANCESTORS": "https://georget.planx-pla.net"
},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''",
"--NotebookApp.quit_button=False"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100,
"user-volume-location": "/home/jovyan/pd"
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "2Gi",
"name": "(Tutorial) Bacpac Synthetic Data Analysis Notebook",
"image": "quay.io/cdis/heal-notebooks:bacpac__10670ad79b4488cfa9f1b3681ce52bc3f1139b5a",
"env": {
"FRAME_ANCESTORS": "https://georget.planx-pla.net"
},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''",
"--NotebookApp.quit_button=False"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100,
"user-volume-location": "/home/jovyan/pd"
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "2Gi",
"name": "(Tutorial) Opioid Prevalence And Overdoses Notebook",
"image": "quay.io/cdis/heal-notebooks:cdcdea__2c94886708fbf7454b6e54f64eb844886d0c3a93",
"env": {
"FRAME_ANCESTORS": "https://georget.planx-pla.net"
},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''",
"--NotebookApp.quit_button=False"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100,
"user-volume-location": "/home/jovyan/pd"
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "2Gi",
"name": "(Tutorial) Opioid Overdose Trajectories Notebook",
"image": "quay.io/cdis/heal-notebooks:cdcwonder__fd15dab0198c6dd0da71e6806ac690c7c8632fa7",
"env": {
"FRAME_ANCESTORS": "https://georget.planx-pla.net"
},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''",
"--NotebookApp.quit_button=False"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
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jupyterhub:
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image:
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manifestservice:
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externalSecrets:
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image:
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