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Merge pull request #559 from uc-cdis/fix/sparse-checkout
Enhance config puller with detailed logging and support for empty dir
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‎helm/frontend-framework/Chart.yaml‎

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# This is the chart version. This version number should be incremented each time you make changes
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# to the chart and its templates, including the app version.
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# Versions are expected to follow Semantic Versioning (https://semver.org/)
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version: 0.1.23
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version: 0.1.24
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# This is the version number of the application being deployed. This version number should be
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# incremented each time you make changes to the application. Versions are not expected to

‎helm/frontend-framework/README.md‎

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# frontend-framework
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![Version: 0.1.23](https://img.shields.io/badge/Version-0.1.23-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: develop](https://img.shields.io/badge/AppVersion-develop-informational?style=flat-square)
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![Version: 0.1.24](https://img.shields.io/badge/Version-0.1.24-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: develop](https://img.shields.io/badge/AppVersion-develop-informational?style=flat-square)
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A Helm chart for the gen3 frontend framework
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## Requirements
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| Repository | Name | Version |
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|------------|------|---------|
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| file://../common | common | 0.1.31 |
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| file://../common | common | 0.1.34 |
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## Values
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| customConfig.dir | string | `""` | directory to pull to the configuration from (e.g. gen3.datacommons.io/gen3ff) |
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| customConfig.enabled | bool | `false` | |
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| customConfig.repo | string | `"https://github.com/uc-cdis/commons-frontend-app.git"` | Repository for the config for CDIS this is cdis-manifest |
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| env | list | `[]` | List of environment variables to add to the deployment. |
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| env | list | `{"DATACOMMONS":"","DATADOG_APPLICATION_ID":"","DATADOG_CLIENT_TOKEN":""}` | List of environment variables to add to the deployment. |
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| fullnameOverride | string | `""` | Override the full name of the deployment. |
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| global | map | `{"autoscaling":{"averageCPUValue":"500m","averageMemoryValue":"500Mi","enabled":false,"maxReplicas":10,"minReplicas":1},"aws":{"awsAccessKeyId":null,"awsSecretAccessKey":null,"enabled":false},"dev":true,"dictionaryUrl":"https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json","dispatcherJobNum":10,"environment":"default","hostname":"localhost","kubeBucket":"kube-gen3","logsBucket":"logs-gen3","minAvailable":1,"netPolicy":{"enabled":false},"pdb":false,"portalApp":"gitops","postgres":{"dbCreate":true,"master":{"host":null,"password":null,"port":"5432","username":"postgres"}},"publicDataSets":true,"revproxyArn":"arn:aws:acm:us-east-1:123456:certificate","tierAccessLevel":"libre","topologySpread":{"enabled":false,"maxSkew":1,"topologyKey":"topology.kubernetes.io/zone"},"userYamlS3Path":"s3://cdis-gen3-users/test/user.yaml"}` | Global configuration options. |
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| global.aws | map | `{"awsAccessKeyId":null,"awsSecretAccessKey":null,"enabled":false}` | AWS configuration |

‎helm/frontend-framework/templates/deployment.yaml‎

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- /bin/sh
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- -c
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- |
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echo "Starting config puller"
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echo "Starting config puller initContainer"
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mkdir -p /tmp/repo
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cd /tmp/repo
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# Clone with sparse checkout and filter
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echo "Starting config puller"
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echo "Cloning repo: ${GIT_REPO} (branch: ${GIT_BRANCH}) into /tmp/repo"
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git clone --depth 1 --branch ${GIT_BRANCH} --filter=blob:none --sparse ${GIT_REPO} /tmp/repo
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cd /tmp/repo
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git sparse-checkout set ${CONFIG_DIR}
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echo "Done cloning config"
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# Handle empty CONFIG_DIR (root checkout)
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if [ -z "${CONFIG_DIR}" ]; then
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echo "CONFIG_DIR is empty → disabling sparse checkout (full repo will be used)"
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git sparse-checkout disable
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else
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echo "CONFIG_DIR='${CONFIG_DIR}' → enabling sparse checkout for this path"
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git sparse-checkout set ${CONFIG_DIR}
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fi
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echo "Repository ready, starting file copy"
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{{- if .Values.customConfig.dir }}
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echo "Using customConfig.dir='{{ .Values.customConfig.dir }}'"
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echo "Copying config from /tmp/repo/{{ .Values.customConfig.dir }}/config → /gen3/config"
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cp -r /tmp/repo/{{ .Values.customConfig.dir }}/config/* /gen3/config
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echo "Copying public from /tmp/repo/{{ .Values.customConfig.dir }}/public → /gen3/public"
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cp -r /tmp/repo/{{ .Values.customConfig.dir }}/public/* /gen3/public
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{{- else }}
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echo "No customConfig.dir set → using repo root directories"
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echo "Copying config from /tmp/repo/config → /gen3/config"
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cp -r /tmp/repo/config/* /gen3/config
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echo "Copying public from /tmp/repo/public → /gen3/public"
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cp -r /tmp/repo/public/* /gen3/public
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echo "Done copying config"
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{{- end }}
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echo "Config puller completed successfully"
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volumeMounts:
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- name: config-volume
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mountPath: /gen3/config

‎helm/frontend-framework/values.yaml‎

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branch: main
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# -- (list) List of environment variables to add to the deployment.
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env: []
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env:
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DATADOG_APPLICATION_ID: ""
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DATADOG_CLIENT_TOKEN: ""
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DATACOMMONS: ""
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# -- (map) Node selector to apply to the pod
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nodeSelector: {}

‎helm/gen3/Chart.yaml‎

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repository: file://../etl
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condition: etl.enabled
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- name: frontend-framework
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version: 0.1.23
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version: 0.1.24
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repository: "file://../frontend-framework"
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condition: frontend-framework.enabled
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- name: fence
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# to the chart and its templates, including the app version.
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# Versions are expected to follow Semantic Versioning (https://semver.org/)
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version: 0.3.21
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version: 0.3.22
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# This is the version number of the application being deployed. This version number should be
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# incremented each time you make changes to the application. Versions are not expected to

‎helm/gen3/README.md‎

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# gen3
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![Version: 0.3.21](https://img.shields.io/badge/Version-0.3.21-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
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![Version: 0.3.22](https://img.shields.io/badge/Version-0.3.22-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
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Helm chart to deploy Gen3 Data Commons
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| file://../embedding-management-service | embedding-management-service | 0.1.4 |
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| file://../etl | etl | 0.1.22 |
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| file://../fence | fence | 0.1.73 |
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| file://../frontend-framework | frontend-framework | 0.1.23 |
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| file://../frontend-framework | frontend-framework | 0.1.24 |
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| file://../funnel | funnel | 0.1.13 |
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| file://../gen3-analysis | gen3-analysis | 0.1.9 |
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| file://../gen3-network-policies | gen3-network-policies | 0.1.3 |

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