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Merge pull request #17 from chgl/develop
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feat: added option for running a custom cdm init job when installing
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@chgl
chgl authored Jan 11, 2021
2 parents 04adfdc + 5d21096 commit 6ab3353
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2 changes: 1 addition & 1 deletion charts/ohdsi/Chart.yaml
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Expand Up @@ -2,7 +2,7 @@ apiVersion: v2
name: ohdsi
description: A Helm chart for deploying OHDSI ATLAS and WebAPI.
type: application
version: 0.2.3
version: 0.3.0
home: https://github.com/OHDSI
keywords:
- ohdsi
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19 changes: 16 additions & 3 deletions charts/ohdsi/README.md
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Expand Up @@ -99,7 +99,7 @@ The following table lists the configurable parameters of the `ohdsi` chart and t
| atlas.webApiUrl | the base URL of the OHDSI WebAPI, e.g. https://example.com/WebAPI if this value is not set but `webapi.ingress.enabled=true`, then this URL is constructed from `webapi.ingress` | `""` |
| atlas.podAnnotations | | `{}` |
| atlas.podSecurityContext | | `{}` |
| atlas.securityContext | | `{"capabilities":{"drop":["ALL"]},"readOnlyRootFilesystem":false,"runAsNonRoot":true,"runAsUser":101}` |
| atlas.securityContext | ContainerSecurityContext for the Atlas container | `{"capabilities":{"drop":["ALL"]},"readOnlyRootFilesystem":false,"runAsNonRoot":true,"runAsUser":101}` |
| atlas.service.type | | `ClusterIP` |
| atlas.service.port | | `8080` |
| atlas.ingress.enabled | | `false` |
Expand All @@ -112,6 +112,15 @@ The following table lists the configurable parameters of the `ohdsi` chart and t
| atlas.tolerations | | `[]` |
| atlas.affinity | | `{}` |
| atlas.extraEnv | extra environment variables | `[]` |
| cdmInitJob.enabled | if enabled, create a Kubernetes Job running the specified container see [cdm-init-job.yaml](templates/cdm-init-job.yaml) for the env vars that are passed by default | `false` |
| cdmInitJob.image.registry | | `docker.io` |
| cdmInitJob.image.repository | | `docker/whalesay` |
| cdmInitJob.image.tag | | `latest` |
| cdmInitJob.image.pullPolicy | | `Always` |
| cdmInitJob.podAnnotations | annotations set on the cdm-init pod | `{}` |
| cdmInitJob.podSecurityContext | PodSecurityContext for the cdm-init pod | `{}` |
| cdmInitJob.securityContext | ContainerSecurityContext for the cdm-init container | `{}` |
| cdmInitJob.extraEnv | extra environment variables to set | `[]` |
| achilles.enabled | whether or not to enable the Achilles cron job | `true` |
| achilles.schedule | when to run the Achilles job. See <https://kubernetes.io/docs/concepts/workloads/controllers/cron-jobs/#cron-schedule-syntax> | `"@daily"` |
| achilles.image.registry | | `ghcr.io` |
Expand All @@ -122,8 +131,7 @@ The following table lists the configurable parameters of the `ohdsi` chart and t
| achilles.schemas.vocab | name of the schema containing the vocabulary. Equivalent to the Achilles `ACHILLES_VOCAB_SCHEMA` env var. | `"synpuf_vocab"` |
| achilles.schemas.res | name of the schema containing the cohort generation results. Equivalent to the Achilles `ACHILLES_RES_SCHEMA` env var. | `"synpuf_results"` |
| achilles.cdmVersion | version of the CDM. Equivalent to the Achilles `ACHILLES_CDM_VERSION` env var. | `"5.3.1"` |
| achilles.securityContext.runAsNonRoot | | `true` |
| achilles.securityContext.runAsUser | | `10001` |
| achilles.securityContext | ContainerSecurityContext for the Achilles container | `{"capabilities":{"drop":["ALL"]},"runAsNonRoot":true,"runAsUser":10001}` |

Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`. For example:

Expand All @@ -137,3 +145,8 @@ installing the chart. For example:
```console
$ helm install ohdsi chgl/ohdsi -n ohdsi --values values.yaml
```

## Initialize the CDM using a custom container

The `cdmInitJob` configuration parameter can be used to configure a
custom container that is run as a Kubernetes Job when the chart is installed.
5 changes: 5 additions & 0 deletions charts/ohdsi/README.tpl
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Expand Up @@ -61,3 +61,8 @@ installing the chart. For example:
```console
$ helm install {{ .Release.Name }} {{ .Repository.Name }}/{{ .Chart.Name }} -n {{ .Release.Namespace }}{{ with .Chart.Version }} --version={{.}}{{ end }} --values values.yaml
```

## Initialize the CDM using a custom container

The `cdmInitJob` configuration parameter can be used to configure a
custom container that is run as a Kubernetes Job when the chart is installed.
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