From 482fc66a45c8f2822a7be0011b3b589053a3335e Mon Sep 17 00:00:00 2001 From: Kyle Burton Date: Thu, 6 Feb 2025 10:08:13 -0600 Subject: [PATCH] chore: Update services, remove unneeded services Update services for AL base image Remove unused services Remove unused sower jobs Remove jupyter --- .secrets.baseline | 17 +- .../manifest.json | 233 +----------------- 2 files changed, 9 insertions(+), 241 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 2b65476e8d..c5a4844c1c 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -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 @@ -7696,21 +7700,14 @@ "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": [ @@ -9561,5 +9558,5 @@ } ] }, - "generated_at": "2024-12-04T21:20:47Z" + "generated_at": "2025-02-06T16:08:12Z" } diff --git a/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json b/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json index 3833b83d43..17ee730dce 100644 --- a/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json +++ b/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json @@ -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", @@ -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": { @@ -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" }, @@ -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",