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chore: Update services, remove unneeded services
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Update services for AL base image

Remove unused services

Remove unused sower jobs

Remove jupyter
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@k-burt-uch
k-burt-uch committed Feb 6, 2025
1 parent 12b4528 commit 482fc66
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Showing 2 changed files with 9 additions and 241 deletions.
17 changes: 7 additions & 10 deletions .secrets.baseline
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Expand Up @@ -75,6 +75,10 @@
{
"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
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"filename": "preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json",
"hashed_secret": "0447a636536df0264b2000403fbefd69f603ceb1",
"is_verified": false,
"line_number": 102
"line_number": 90
},
{
"type": "Secret Keyword",
"filename": "preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json",
"hashed_secret": "ca253d1c9dece2da0d6fb24ded7bdb849a475966",
"is_verified": false,
"line_number": 108
},
{
"type": "Secret Keyword",
"filename": "preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json",
"hashed_secret": "7120244dce59930b75711144fda4b1f6d78e4865",
"is_verified": false,
"line_number": 217
"line_number": 96
}
],
"preprod.healdata.org/dashboard/Public/notebooks/JCOIN-MOUD_accessibility_analysis_02092022.html": [
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}
]
},
"generated_at": "2024-12-04T21:20:47Z"
"generated_at": "2025-02-06T16:08:12Z"
}
233 changes: 2 additions & 231 deletions preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
"autodeploy": "yes"
},
"versions": {
"access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2025.01",
"access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:1.6.0",
"arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2025.01",
"audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2025.01",
"awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2025.01",
Expand All @@ -16,20 +16,13 @@
"indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2025.01",
"peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2025.01",
"revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2025.01",
"sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2025.01",
"sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:5.2.0",
"metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2025.01",
"portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2025.01",
"fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
"spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2025.01",
"tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2025.01",
"guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2025.01",
"sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2025.01",
"hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2025.01",
"ambassador": "quay.io/datawire/ambassador:1.4.2",
"wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2025.01",
"manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2025.01",
"ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2025.01",
"dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2025.01",
"metadata-delete-expired-objects": "quay.io/cdis/metadata-delete-expired-objects:2025.01"
},
"google": {
Expand All @@ -38,11 +31,6 @@
"indexd": {
"arborist": "true"
},
"ssjdispatcher": {
"job_images": {
"indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2025.01"
}
},
"arborist": {
"deployment_version": "2"
},
Expand Down Expand Up @@ -178,225 +166,8 @@
}
],
"restart_policy": "Never"
},
{
"name": "ingest-metadata-manifest",
"action": "ingest-metadata-manifest",
"activeDeadlineSeconds": 86400,
"serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov",
"container": {
"name": "job-task",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2025.01",
"pull_policy": "Always",
"env": [
{
"name": "GEN3_HOSTNAME",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "hostname"
}
}
}
],
"volumeMounts": [
{
"name": "creds-volume",
"readOnly": true,
"mountPath": "/creds.json",
"subPath": "creds.json"
}
],
"cpu-limit": "1",
"memory-limit": "1Gi"
},
"volumes": [
{
"name": "creds-volume",
"secret": {
"secretName": "sower-jobs-g3auto"
}
}
],
"restart_policy": "Never"
},
{
"name": "get-dbgap-metadata",
"action": "get-dbgap-metadata",
"serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov",
"container": {
"name": "job-task",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2025.01",
"pull_policy": "Always",
"env": [],
"volumeMounts": [
{
"name": "creds-volume",
"readOnly": true,
"mountPath": "/creds.json",
"subPath": "creds.json"
}
],
"cpu-limit": "1",
"memory-limit": "1Gi"
},
"volumes": [
{
"name": "creds-volume",
"secret": {
"secretName": "sower-jobs-g3auto"
}
}
],
"restart_policy": "Never"
},
{
"name": "manifest-indexing",
"action": "index-object-manifest",
"activeDeadlineSeconds": 86400,
"serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov",
"container": {
"name": "job-task",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2025.01",
"pull_policy": "Always",
"env": [
{
"name": "GEN3_HOSTNAME",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "hostname"
}
}
}
],
"volumeMounts": [
{
"name": "sower-jobs-creds-volume",
"readOnly": true,
"mountPath": "/creds.json",
"subPath": "creds.json"
}
],
"cpu-limit": "1",
"memory-limit": "1Gi"
},
"volumes": [
{
"name": "sower-jobs-creds-volume",
"secret": {
"secretName": "sower-jobs-g3auto"
}
}
],
"restart_policy": "Never"
},
{
"name": "manifest-merging",
"action": "merge-manifests",
"activeDeadlineSeconds": 86400,
"serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov",
"container": {
"name": "job-task",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cdis/manifest-merging:2025.01",
"pull_policy": "Always",
"env": [
{
"name": "GEN3_HOSTNAME",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "hostname"
}
}
}
],
"volumeMounts": [
{
"name": "sower-jobs-creds-volume",
"readOnly": true,
"mountPath": "/creds.json",
"subPath": "creds.json"
}
],
"cpu-limit": "1",
"memory-limit": "1Gi"
},
"volumes": [
{
"name": "sower-jobs-creds-volume",
"secret": {
"secretName": "sower-jobs-g3auto"
}
}
],
"restart_policy": "Never"
},
{
"name": "indexd-manifest",
"action": "download-indexd-manifest",
"activeDeadlineSeconds": 86400,
"serviceAccountName": "jobs-preprod-gen3-biodatacatalyst-nhlbi-nih-gov",
"container": {
"name": "job-task",
"image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2025.01",
"pull_policy": "Always",
"env": [
{
"name": "GEN3_HOSTNAME",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "hostname"
}
}
}
],
"volumeMounts": [
{
"name": "sower-jobs-creds-volume",
"readOnly": true,
"mountPath": "/creds.json",
"subPath": "creds.json"
}
],
"cpu-limit": "1",
"memory-limit": "1Gi"
},
"volumes": [
{
"name": "sower-jobs-creds-volume",
"secret": {
"secretName": "sower-jobs-g3auto"
}
}
],
"restart_policy": "Never"
}
],
"jupyterhub": {
"enabled": "yes",
"containers": [
{
"name": "Bioinfo - Python/R",
"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"
}
]
},
"global": {
"environment": "stageprod",
"hostname": "preprod.gen3.biodatacatalyst.nhlbi.nih.gov",
Expand Down

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