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Making various updates to ensure helm works with the new AL based images #213

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merged 3 commits into from
Nov 14, 2024
Merged

Making various updates to ensure helm works with the new AL based images #213

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48ed8a6
Making various updates to ensure helm works with the new AL based images
EliseCastle23 Nov 14, 2024
ff33419
disabling pidgin
EliseCastle23 Nov 14, 2024
e2c9cfc
updating requestor version
EliseCastle23 Nov 14, 2024
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12 changes: 6 additions & 6 deletions helm/gen3/Chart.yaml
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Expand Up @@ -48,7 +48,7 @@ dependencies:
repository: "file://../hatchery"
condition: hatchery.enabled
- name: indexd
version: 0.1.16
version: 0.1.17
repository: "file://../indexd"
condition: indexd.enabled
- name: manifestservice
Expand All @@ -60,7 +60,7 @@ dependencies:
repository: "file://../metadata"
condition: metadata.enabled
- name: peregrine
version: 0.1.15
version: 0.1.16
repository: "file://../peregrine"
condition: peregrine.enabled
- name: pidgin
Expand All @@ -72,15 +72,15 @@ dependencies:
repository: "file://../portal"
condition: portal.enabled
- name: requestor
version: 0.1.14
version: 0.1.15
repository: "file://../requestor"
condition: requestor.enabled
- name: revproxy
version: 0.1.18
repository: "file://../revproxy"
condition: revproxy.enabled
- name: sheepdog
version: 0.1.17
version: 0.1.18
repository: "file://../sheepdog"
condition: sheepdog.enabled
- name: ssjdispatcher
Expand All @@ -92,7 +92,7 @@ dependencies:
condition: sower.enabled
repository: "file://../sower"
- name: wts
version: 0.1.16
version: 0.1.17
repository: "file://../wts"
condition: wts.enabled
- name: gen3-network-policies
Expand Down Expand Up @@ -132,7 +132,7 @@ type: application
# This is the chart version. This version number should be incremented each time you make changes
# to the chart and its templates, including the app version.
# Versions are expected to follow Semantic Versioning (https://semver.org/)
version: 0.1.47
version: 0.1.48

# This is the version number of the application being deployed. This version number should be
# incremented each time you make changes to the application. Versions are not expected to
Expand Down
16 changes: 7 additions & 9 deletions helm/gen3/README.md
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@@ -1,6 +1,6 @@
# gen3

![Version: 0.1.47](https://img.shields.io/badge/Version-0.1.47-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)
![Version: 0.1.48](https://img.shields.io/badge/Version-0.1.48-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)

Helm chart to deploy Gen3 Data Commons

Expand Down Expand Up @@ -30,19 +30,19 @@ Helm chart to deploy Gen3 Data Commons
| file://../frontend-framework | frontend-framework | 0.1.4 |
| file://../guppy | guppy | 0.1.15 |
| file://../hatchery | hatchery | 0.1.11 |
| file://../indexd | indexd | 0.1.16 |
| file://../indexd | indexd | 0.1.17 |
| file://../manifestservice | manifestservice | 0.1.16 |
| file://../metadata | metadata | 0.1.15 |
| file://../neuvector | neuvector | 0.1.1 |
| file://../peregrine | peregrine | 0.1.15 |
| file://../peregrine | peregrine | 0.1.16 |
| file://../pidgin | pidgin | 0.1.12 |
| file://../portal | portal | 0.1.20 |
| file://../requestor | requestor | 0.1.14 |
| file://../requestor | requestor | 0.1.15 |
| file://../revproxy | revproxy | 0.1.18 |
| file://../sheepdog | sheepdog | 0.1.17 |
| file://../sheepdog | sheepdog | 0.1.18 |
| file://../sower | sower | 0.1.14 |
| file://../ssjdispatcher | ssjdispatcher | 0.1.12 |
| file://../wts | wts | 0.1.16 |
| file://../wts | wts | 0.1.17 |
| https://charts.bitnami.com/bitnami | postgresql | 11.9.13 |
| https://helm.elastic.co | elasticsearch | 7.10.2 |

Expand Down Expand Up @@ -167,7 +167,7 @@ Helm chart to deploy Gen3 Data Commons
| neuvector.policies.include | bool | `false` | |
| neuvector.policies.policyMode | string | `"Monitor"` | |
| peregrine.enabled | bool | `true` | Whether to deploy the peregrine subchart. |
| pidgin.enabled | bool | `true` | Whether to deploy the pidgin subchart. |
| pidgin.enabled | bool | `false` | Whether to deploy the pidgin subchart. |
| portal.enabled | bool | `true` | Whether to deploy the portal subchart. |
| postgresql | map | `{"primary":{"persistence":{"enabled":false}}}` | To configure postgresql subchart Disable persistence by default so we can spin up and down ephemeral environments |
| postgresql.primary.persistence.enabled | bool | `false` | Option to persist the dbs data. |
Expand All @@ -181,5 +181,3 @@ Helm chart to deploy Gen3 Data Commons
| ssjdispatcher.enabled | bool | `false` | Whether to deploy the ssjdispatcher subchart. |
| wts.enabled | bool | `true` | Whether to deploy the wts subchart. |

----------------------------------------------
Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)
2 changes: 1 addition & 1 deletion helm/gen3/values.yaml
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Expand Up @@ -238,7 +238,7 @@ peregrine:

pidgin:
# -- (bool) Whether to deploy the pidgin subchart.
enabled: true
enabled: false

portal:
# -- (bool) Whether to deploy the portal subchart.
Expand Down
2 changes: 1 addition & 1 deletion helm/indexd/Chart.yaml
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Expand Up @@ -15,7 +15,7 @@ type: application
# This is the chart version. This version number should be incremented each time you make changes
# to the chart and its templates, including the app version.
# Versions are expected to follow Semantic Versioning (https://semver.org/)
version: 0.1.16
version: 0.1.17

# This is the version number of the application being deployed. This version number should be
# incremented each time you make changes to the application. Versions are not expected to
Expand Down
4 changes: 1 addition & 3 deletions helm/indexd/README.md
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@@ -1,6 +1,6 @@
# indexd

![Version: 0.1.16](https://img.shields.io/badge/Version-0.1.16-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)
![Version: 0.1.17](https://img.shields.io/badge/Version-0.1.17-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)

A Helm chart for gen3 indexd

Expand Down Expand Up @@ -107,5 +107,3 @@ A Helm chart for gen3 indexd
| volumeMounts | list | `[{"mountPath":"/var/www/indexd/local_settings.py","name":"config-volume","readOnly":true,"subPath":"local_settings.py"}]` | Volumes to mount to the container. |
| volumes | list | `[{"configMap":{"name":"indexd-uwsgi"},"name":"uwsgi-config"},{"name":"config-volume","secret":{"secretName":"indexd-settings"}}]` | Volumes to attach to the pod |

----------------------------------------------
Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)
15 changes: 11 additions & 4 deletions helm/indexd/templates/pre-install.yaml
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Expand Up @@ -82,8 +82,15 @@ spec:
# Script always succeeds if it runs (echo exits with 0)
# indexd image does not include jq, so use python
- |
echo 'python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}'
python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}"
echo 'python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}'
python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}"
if command -v python &> /dev/null; then
echo 'python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}'
python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}"
echo 'python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}'
python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}"
else
echo 'poetry run python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}'
poetry run python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}"
echo 'poetry run python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}'
poetry run python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}"
fi
restartPolicy: Never
2 changes: 1 addition & 1 deletion helm/observability/Chart.yaml
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Expand Up @@ -15,7 +15,7 @@ type: application
# This is the chart version. This version number should be incremented each time you make changes
# to the chart and its templates, including the app version.
# Versions are expected to follow Semantic Versioning (https://semver.org/)
version: 0.1.1
version: 0.1.2

# This is the version number of the application being deployed. This version number should be
# incremented each time you make changes to the application. Versions are not expected to
Expand Down
4 changes: 1 addition & 3 deletions helm/observability/README.md
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@@ -1,6 +1,6 @@
# lgtma-chart

![Version: 0.1.1](https://img.shields.io/badge/Version-0.1.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 1.0.0](https://img.shields.io/badge/AppVersion-1.0.0-informational?style=flat-square)
![Version: 0.1.2](https://img.shields.io/badge/Version-0.1.2-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 1.0.0](https://img.shields.io/badge/AppVersion-1.0.0-informational?style=flat-square)

A Helm chart for deploying the LGTM stack with additional resources

Expand Down Expand Up @@ -307,5 +307,3 @@ A Helm chart for deploying the LGTM stack with additional resources
| lgtm.role.arn | string | `nil` | The arn of the aws role to associate with the service account that will be used for Loki and Mimir. Documentation on IRSA setup https://docs.aws.amazon.com/eks/latest/userguide/iam-roles-for-service-accounts.html |
| lgtm.tempo.enabled | bool | `false` | Enable or disable tempo. |

----------------------------------------------
Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)
2 changes: 1 addition & 1 deletion helm/observability/SETUP.md
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Expand Up @@ -117,7 +117,7 @@ This Helm chart comes equipped with built-in Gen3 alerts, defined in the 'alerti
### Built-in Gen3 Dashboards
We'll soon be releasing Gen3 dashboards, providing users with Gen3-specific visualizations. Please check back here to see if they have been released.
You can utilize Gen3-specific visualizations by visiting our [grafana-dashboards repo](https://github.com/uc-cdis/grafana-dashboards).
## Configuring Mimir
Expand Down
2 changes: 1 addition & 1 deletion helm/peregrine/Chart.yaml
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Expand Up @@ -15,7 +15,7 @@ type: application
# This is the chart version. This version number should be incremented each time you make changes
# to the chart and its templates, including the app version.
# Versions are expected to follow Semantic Versioning (https://semver.org/)
version: 0.1.15
version: 0.1.16

# This is the version number of the application being deployed. This version number should be
# incremented each time you make changes to the application. Versions are not expected to
Expand Down
6 changes: 2 additions & 4 deletions helm/peregrine/README.md
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@@ -1,6 +1,6 @@
# peregrine

![Version: 0.1.15](https://img.shields.io/badge/Version-0.1.15-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)
![Version: 0.1.16](https://img.shields.io/badge/Version-0.1.16-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)

A Helm chart for gen3 Peregrine service

Expand Down Expand Up @@ -99,8 +99,6 @@ A Helm chart for gen3 Peregrine service
| serviceAccount.create | bool | `true` | Specifies whether a service account should be created. |
| serviceAccount.name | string | `""` | The name of the service account |
| tolerations | list | `[]` | Tolerations for the pods |
| volumeMounts | list | `[{"mountPath":"/var/www/peregrine/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"}]` | Volumes to mount to the container. |
| volumeMounts | list | `[{"mountPath":"/var/www/peregrine/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"},{"mountPath":"peregrine/bin/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"}]` | Volumes to mount to the container. |
| volumes | list | `[{"emptyDir":{},"name":"shared-data"},{"name":"config-volume","secret":{"secretName":"peregrine-secret"}}]` | Volumes to attach to the container. |

----------------------------------------------
Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)
4 changes: 4 additions & 0 deletions helm/peregrine/values.yaml
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Expand Up @@ -222,6 +222,10 @@ volumeMounts:
readOnly: true
mountPath: "/var/www/peregrine/settings.py"
subPath: "settings.py"
- name: "config-volume"
readOnly: true
mountPath: "peregrine/bin/settings.py"
subPath: "settings.py"

# Values to determine the labels that are used for the deployment, pod, etc.
# -- (string) Valid options are "production" or "dev". If invalid option is set- the value will default to "dev".
Expand Down
2 changes: 1 addition & 1 deletion helm/requestor/Chart.yaml
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Expand Up @@ -15,7 +15,7 @@ type: application
# This is the chart version. This version number should be incremented each time you make changes
# to the chart and its templates, including the app version.
# Versions are expected to follow Semantic Versioning (https://semver.org/)
version: 0.1.14
version: 0.1.15

# This is the version number of the application being deployed. This version number should be
# incremented each time you make changes to the application. Versions are not expected to
Expand Down
4 changes: 1 addition & 3 deletions helm/requestor/README.md
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@@ -1,6 +1,6 @@
# requestor

![Version: 0.1.14](https://img.shields.io/badge/Version-0.1.14-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)
![Version: 0.1.15](https://img.shields.io/badge/Version-0.1.15-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)

A Helm chart for gen3 Requestor Service

Expand Down Expand Up @@ -114,5 +114,3 @@ A Helm chart for gen3 Requestor Service
| strategy.rollingUpdate.maxUnavailable | int | `0` | Maximum amount of pods that can be unavailable during the update. |
| volumeMounts | list | `nil` | Volumes to mount to the container. |

----------------------------------------------
Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)
2 changes: 1 addition & 1 deletion helm/requestor/templates/deployment.yaml
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Expand Up @@ -152,4 +152,4 @@ spec:
args:
- "-c"
- |
/env/bin/alembic upgrade head
poetry run alembic upgrade head || /env/bin/alembic upgrade head
2 changes: 1 addition & 1 deletion helm/sheepdog/Chart.yaml
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Expand Up @@ -15,7 +15,7 @@ type: application
# This is the chart version. This version number should be incremented each time you make changes
# to the chart and its templates, including the app version.
# Versions are expected to follow Semantic Versioning (https://semver.org/)
version: 0.1.17
version: 0.1.18

# This is the version number of the application being deployed. This version number should be
# incremented each time you make changes to the application. Versions are not expected to
Expand Down
6 changes: 2 additions & 4 deletions helm/sheepdog/README.md
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# sheepdog

![Version: 0.1.17](https://img.shields.io/badge/Version-0.1.17-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)
![Version: 0.1.18](https://img.shields.io/badge/Version-0.1.18-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)

A Helm chart for gen3 Sheepdog Service

Expand Down Expand Up @@ -105,7 +105,5 @@ A Helm chart for gen3 Sheepdog Service
| strategy.rollingUpdate.maxSurge | int | `1` | Number of additional replicas to add during rollout. |
| strategy.rollingUpdate.maxUnavailable | int | `0` | Maximum amount of pods that can be unavailable during the update. |
| terminationGracePeriodSeconds | int | `50` | sheepdog transactions take forever - try to let the complete before termination |
| volumeMounts | list | `[{"mountPath":"/var/www/sheepdog/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"}]` | Volumes to mount to the container. |
| volumeMounts | list | `[{"mountPath":"/var/www/sheepdog/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"},{"mountPath":"sheepdog/bin/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"}]` | Volumes to mount to the container. |

----------------------------------------------
Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)
17 changes: 12 additions & 5 deletions helm/sheepdog/templates/deployment.yaml
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Expand Up @@ -49,6 +49,7 @@ spec:
initContainers:
- name: sheepdog-init
image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
imagePullPolicy: {{ .Values.image.pullPolicy }}
env:
- name: DICTIONARY_URL
value: {{ .Values.dictionaryUrl }}
Expand Down Expand Up @@ -93,11 +94,17 @@ spec:
# sheepdog sets up core data model now,
# but suffers from a race condition doing it ...
#
echo datamodel_postgres_admin create-all -U "${PGUSER}" -P XXXXXXX -H "${PGHOST}" -D "${PGDB}"
datamodel_postgres_admin create-all -U "${PGUSER}" -P "${PGPASSWORD}" -H "${PGHOST}" -D "${PGDB}"

echo python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}" --password XXXXX --host "${PGHOST}" --database "${PGDB}"
python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}" --password "${PGPASSWORD}" --host "${PGHOST}" --database "${PGDB}"
if command -v python &> /dev/null; then
echo datamodel_postgres_admin create-all -U "${PGUSER}" -P XXXXXXX -H "${PGHOST}" -D "${PGDB}"
datamodel_postgres_admin create-all -U "${PGUSER}" -P "${PGPASSWORD}" -H "${PGHOST}" -D "${PGDB}"
echo python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}" --password XXXXX --host "${PGHOST}" --database "${PGDB}"
python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}" --password "${PGPASSWORD}" --host "${PGHOST}" --database "${PGDB}"
else
echo poetry run datamodel_postgres_admin create-all -U "${PGUSER}" -P XXXXXXX -H "${PGHOST}" -D "${PGDB}"
poetry run datamodel_postgres_admin create-all -U "${PGUSER}" -P "${PGPASSWORD}" -H "${PGHOST}" -D "${PGDB}"
echo poetry run python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}" --password XXXXX --host "${PGHOST}" --database "${PGDB}"
poetry run python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}" --password "${PGPASSWORD}" --host "${PGHOST}" --database "${PGDB}"
fi
containers:
- name: sheepdog
image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
Expand Down
4 changes: 4 additions & 0 deletions helm/sheepdog/values.yaml
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Expand Up @@ -188,6 +188,10 @@ volumeMounts:
readOnly: true
mountPath: "/var/www/sheepdog/settings.py"
subPath: "settings.py"
- name: "config-volume"
readOnly: true
mountPath: "sheepdog/bin/settings.py"
subPath: "settings.py"

# -- (map) Resource requests and limits for the containers in the pod
resources:
Expand Down
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