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chore(qa): Prepare manifest for TheAnvil staging environments (stagin…
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…g) (#1116)

* chore(qa): Prepare manifest for TheAnvil staging environments (staging)

* reverting undesired changes

Co-authored-by: Marcelo Costa <marceloc@uchicago.edu>
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@themarcelor
themarcelor and Marcelo Costa authored Mar 11, 2020
1 parent 23bcdb2 commit 5ac8046
Showing 1 changed file with 237 additions and 24 deletions.
261 changes: 237 additions & 24 deletions staging.theanvil.io/manifest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,27 +7,25 @@
"autodeploy": "yes"
},
"versions": {
"arborist": "quay.io/cdis/arborist:2.3.2",
"arranger-adminapi": "quay.io/cdis/arranger-server:master",
"arranger-dashboard": "quay.io/cdis/arranger-dashboard:master",
"arborist": "quay.io/cdis/arborist:2020.02",
"aws-es-proxy": "abutaha/aws-es-proxy:0.8",
"fence": "quay.io/cdis/fence:4.11.0",
"fence": "quay.io/cdis/fence:2020.02",
"fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
"guppy": "quay.io/cdis/guppy:0.3.10",
"hatchery": "quay.io/cdis/hatchery:0.1.0",
"guppy": "quay.io/cdis/guppy:2020.02",
"hatchery": "quay.io/cdis/hatchery:2020.02",
"ambassador": "quay.io/datawire/ambassador:0.60.3",
"indexd": "quay.io/cdis/indexd:2.1.0",
"manifestservice": "quay.io/cdis/manifestservice:0.2.0",
"peregrine": "quay.io/cdis/peregrine:2.1.1",
"pidgin": "quay.io/cdis/pidgin:1.0.0",
"portal": "quay.io/cdis/data-portal:2.22.6",
"indexd": "quay.io/cdis/indexd:2020.02",
"manifestservice": "quay.io/cdis/manifestservice:2020.02",
"peregrine": "quay.io/cdis/peregrine:2020.02",
"pidgin": "quay.io/cdis/pidgin:2020.02",
"portal": "quay.io/cdis/data-portal:2020.02",
"revproxy": "quay.io/cdis/nginx:1.15.5-ctds",
"sheepdog": "quay.io/cdis/sheepdog:1.1.10",
"sower": "quay.io/cdis/sower:0.3.0",
"spark": "quay.io/cdis/gen3-spark:1.0.0",
"tube": "quay.io/cdis/tube:0.3.18",
"ssjdispatcher": "quay.io/cdis/ssjdispatcher:0.0.6",
"wts": "quay.io/cdis/workspace-token-service:0.2.0"
"sheepdog": "quay.io/cdis/sheepdog:2020.02",
"sower": "quay.io/cdis/sower:2020.02",
"spark": "quay.io/cdis/gen3-spark:2020.02",
"tube": "quay.io/cdis/tube:2020.02",
"ssjdispatcher": "quay.io/cdis/ssjdispatcher:2020.02",
"wts": "quay.io/cdis/workspace-token-service:2020.02"
},
"global": {
"environment": "anvilstaging",
Expand All @@ -45,12 +43,78 @@
"tier_access_limit": 50,
"public_datasets": true
},
"sower": [
{
"name": "pelican-export",
"action": "export",
"container": {
"name": "job-task",
"image": "quay.io/cdis/pelican-export:2020.02",
"pull_policy": "Always",
"env": [
{
"name": "DICTIONARY_URL",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "dictionary_url"
}
}
},
{
"name": "GEN3_HOSTNAME",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "hostname"
}
}
},
{
"name": "ROOT_NODE",
"value": "subject"
}
],
"volumeMounts": [
{
"name": "pelican-creds-volume",
"readOnly": true,
"mountPath": "/pelican-creds.json",
"subPath": "config.json"
},
{
"name": "peregrine-creds-volume",
"readOnly": true,
"mountPath": "/peregrine-creds.json",
"subPath": "creds.json"
}
],
"cpu-limit": "1",
"memory-limit": "12Gi"
},
"volumes": [
{
"name": "pelican-creds-volume",
"secret": {
"secretName": "pelicanservice-g3auto"
}
},
{
"name": "peregrine-creds-volume",
"secret": {
"secretName": "peregrine-creds"
}
}
],
"restart_policy": "Never"
}
],
"google": {
"enabled": "no"
"enabled": "yes"
},
"ssjdispatcher": {
"job_images": {
"indexing": "quay.io/cdis/indexs3client:0.0.3"
"indexing": "quay.io/cdis/indexs3client:2020.02"
}
},
"arborist": {
Expand All @@ -67,8 +131,7 @@
"type": "file"
}
],
"auth_filter_field": "auth_resource_path",
"enable_encrypt_whitelist": false
"auth_filter_field": "auth_resource_path"
},
"hatchery": {
"user-namespace": "jupyter-pods",
Expand All @@ -77,7 +140,7 @@
"sidecar": {
"cpu-limit": "1.0",
"memory-limit": "512Mi",
"image": "quay.io/cdis/gen3fuse-sidecar:chore_sidecar",
"image": "quay.io/cdis/gen3fuse-sidecar:2020.02",
"env": {
"NAMESPACE": "default",
"HOSTNAME": "staging.theanvil.io"
Expand Down Expand Up @@ -110,6 +173,138 @@
"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
}
]
},
Expand All @@ -121,6 +316,18 @@
"cpu": 0.5,
"memory": "256M",
"image": "quay.io/occ_data/jupyternotebook:1.9.0"
},
{
"name": "Bioinfo - Python/R",
"cpu": 1,
"memory": "1024M",
"image": "quay.io/occ_data/jupyternotebook:1.9.0"
},
{
"name": "Helium COPD Demo",
"cpu": 1,
"memory": "1024M",
"image": "ananyak8srenci/autoencoder-copd-demo:1d33030cef16"
}
]
},
Expand Down Expand Up @@ -211,8 +418,14 @@
},
"fence": {
"strategy": "auto",
"min": 4,
"max": 8,
"min": 5,
"max": 15,
"targetCpu": 40
},
"presigned-url-fence": {
"strategy": "auto",
"min": 2,
"max": 5,
"targetCpu": 40
},
"indexd": {
Expand Down

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