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Chore/stage version review (#1374)
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* chore(stage-version-review): updated stage versions/config to match preprod

* chore(stage-version-review): updated stage versions/config to match preprod

* chore(stage-version-review): updated stage versions/config to match preprod

Co-authored-by: Edward Malinowski <edwardmalinowski@Edwards-MacBook-Pro.local.cdis>
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emalinowski and Edward Malinowski authored Apr 20, 2020
1 parent f628043 commit 0276c0c
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Showing 7 changed files with 264 additions and 225 deletions.
2 changes: 1 addition & 1 deletion staging.gen3.biodatacatalyst.nhlbi.nih.gov/README.md
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Expand Up @@ -17,4 +17,4 @@ AWS-only commons do not require.

* stagingdatastage/apis-configs/fence_google_app_creds_secret.json and fence_google_storage_creds_secret.json have creds for Google service accounts that fence uses to give access to Google storage - needed to copy those 2 files over from dcp, and update the secrets
* stagingdatastage/apis_configs/fence-config.yaml has a `CIRRUS_CONFIG` section that requires setup - `CIRRUS` is the name of our internal library for talking to Google
* also in fence-config.yaml (small change) - `ENABLED_IDENTITY_PROVIDERS` should just be `google` - commented out the `fence` provider that we currently only ever use for DbGap mediated authentication
* also in fence-config.yaml (small change) - `ENABLED_IDENTITY_PROVIDERS` should just be `google` - commented out the `fence` provider that we currently only ever use for DbGap mediated authentication
10 changes: 1 addition & 9 deletions staging.gen3.biodatacatalyst.nhlbi.nih.gov/etlMapping.yaml
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Expand Up @@ -37,13 +37,9 @@ mappings:
- name: vte_case_status
- name: vte_followup_start_age
- name: vte_prior_history
- path: diagnoses
props:
- name: metabolic_syndrome_diagnosis
sorted_by: updated_datetime, desc
- path: blood_pressure_test
props:
- name: diastolic_blood_pressure
- name: bp_systolic
- name: bp_diastolic
- path: medication_records
props:
Expand Down Expand Up @@ -84,10 +80,6 @@ mappings:
path: demographics
src: ethnicity
fn: set
- name: age_at_enrollment
path: demographics
src: age_at_enrollment
fn: set
- name: _samples_count
path: samples
fn: count
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183 changes: 4 additions & 179 deletions staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json
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Expand Up @@ -13,13 +13,13 @@
"indexd": "quay.io/cdis/indexd:2.6.1",
"peregrine": "quay.io/cdis/peregrine:3.0.0",
"pidgin": "quay.io/cdis/pidgin:1.0.0",
"revproxy": "quay.io/cdis/nginx:1.15.5-ctds",
"revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
"sheepdog": "quay.io/cdis/sheepdog:3.0.0",
"portal": "quay.io/cdis/data-portal:2.24.3",
"portal": "quay.io/cdis/data-portal:2.24.10",
"fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
"spark": "quay.io/cdis/gen3-spark:1.0.0",
"tube": "quay.io/cdis/tube:0.3.18",
"guppy": "quay.io/cdis/guppy:0.3.14",
"guppy": "quay.io/cdis/guppy:0.4.1",
"sower": "quay.io/cdis/sower:0.3.0",
"hatchery": "quay.io/cdis/hatchery:0.1.0",
"ambassador": "quay.io/datawire/ambassador:0.60.3",
Expand Down Expand Up @@ -99,181 +99,6 @@
"restart_policy": "Never"
}
],
"hatchery": {
"user-namespace": "jupyter-pods-staging",
"sub-dir": "/lw-workspace",
"user-volume-size": "500Gi",
"sidecar": {
"cpu-limit": "1.0",
"memory-limit": "256Mi",
"image": "quay.io/cdis/gen3fuse-sidecar:0.1.4",
"env": {
"NAMESPACE":"staging",
"HOSTNAME": "staging.gen3.biodatacatalyst.nhlbi.nih.gov"
},
"args": [],
"command": [
"/bin/bash",
"/sidecarDockerrun.sh"
],
"lifecycle-pre-stop": [
"su",
"-c",
"echo test",
"-s",
"/bin/sh",
"root"
]
},
"containers": [
{
"target-port": 8787,
"cpu-limit": "1.0",
"memory-limit": "512Mi",
"name": "R Studio",
"image": "heliumdatastage/rstudio-server:1",
"env": {
"DISABLE_AUTH": "true"
},
"args": [],
"path-rewrite": "/",
"use-tls": "false",
"ready-probe": "/"
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "512Mi",
"name": "Jupyter Notebook Bio Python",
"image": "quay.io/occ_data/jupyternotebook:1.9.0",
"env": {},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''"
],
"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; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100,
"user-volume-location": "/home/jovyan/pd"
},
{
"target-port": 8888,
"cpu-limit": "4.0",
"memory-limit": "15512Mi",
"name": "Jupyter Notebook Power Python",
"image": "quay.io/occ_data/jupyternotebook:1.7.2",
"env": {},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100,
"user-volume-location": "/home/jovyan/pd"
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "8096Mi",
"name": "Helium Autoencoder Demo",
"image": "quay.io/cdis/auntoencoder-copd-demo:latest",
"env": {},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "8096Mi",
"name": "Helium Tensorflow-Pytorch",
"image": "heliumdatastage/tensorflow-pytorch-ext:1",
"env": {},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100
},
{
"target-port": 8888,
"cpu-limit": "1.0",
"memory-limit": "8096Mi",
"name": "Helium CIP Demo",
"image": "heliumdatastage/jup-cip:v1",
"env": {},
"args": [
"--NotebookApp.base_url=/lw-workspace/proxy/",
"--NotebookApp.password=''",
"--NotebookApp.token=''"
],
"command": [
"start-notebook.sh"
],
"path-rewrite": "/lw-workspace/proxy/",
"use-tls": "false",
"ready-probe": "/lw-workspace/proxy/",
"lifecycle-post-start": [
"/bin/sh",
"-c",
"export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"
],
"user-uid": 1000,
"fs-gid": 100
}
]
},
"jupyterhub": {
"enabled": "yes",
"containers": [
Expand Down Expand Up @@ -301,7 +126,7 @@
"environment": "stagingdatastage",
"hostname": "staging.gen3.biodatacatalyst.nhlbi.nih.gov",
"revproxy_arn": "arn:aws:acm:us-east-1:895962626746:certificate/1876fa51-031e-4aa9-ab95-7da182a52c7f",
"dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/gtexdictionary/3.3.9/schema.json",
"dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/gtexdictionary/3.4.7/schema.json",
"portal_app": "gitops",
"kube_bucket": "kube-stageprod-gen3",
"logs_bucket": "logs-stageprod-gen3",
Expand Down
7 changes: 7 additions & 0 deletions staging.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/fence/fence-config-public.yaml
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@@ -0,0 +1,7 @@
########################################################################################
# OPTIONAL CONFIGURATIONS #
########################################################################################

# For displaying a privacy policy to users, we can either link to the URL specified by
# PRIVACY_POLICY_URL, or default to the `static/privacy_policy.md` file in fence.
PRIVACY_POLICY_URL: 'https://biodatacatalyst.nhlbi.nih.gov/privacy/'
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