Add documentation

README.md

@@ -0,0 +1,4 @@
+# Aidbox helm charts
+
+- [aidbox](./aidbox)
+- [aidboxdb](./aidboxdb)

aidbox/Chart.yaml

@@ -1,6 +1,8 @@
 apiVersion: v2
 appVersion: edge
-description: Aidbox
+description: Aidbox FHIR server by HealthSamurai
+home: https://www.health-samurai.io/aidbox
+icon: https://aidbox.github.io/helm-charts/icon.png?1712669999
 name: aidbox
 type: application
-version: 0.1.1
+version: 0.1.4

aidbox/README.md

@@ -0,0 +1,82 @@
+# aidbox
+
+[Aidbox](https://docs.aidbox.app/) is an efficient and scalable FHIR server built to handle healthcare data effectively, empowering healthcare providers and developers alike with its comprehensive platform for storing, accessing, and exchanging healthcare information in accordance with FHIR standards.
+
+![Version: 0.1.4](https://img.shields.io/badge/Version-0.1.4-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: edge](https://img.shields.io/badge/AppVersion-edge-informational?style=flat-square)
+
+## Installation
+
+Prepare the configuration file. Please refer to the [Aidbox environment variables](https://docs.aidbox.app/reference/configuration/environment-variables) for details.
+
+```yaml
+host: <your host here, e.g. my.domain.tld>
+protocol: <http or https>
+
+config:
+  AIDBOX_FHIR_VERSION: <FHIR version, e.g. 4.0.0>
+  PGHOST: <PostgreSQL host to connect to>
+  PGDATABASE: <name of the database that is used to store resources>
+  PGUSER: <PostgreSQL user>
+  PGPASSWORD: <PostgreSQL password>
+  AIDBOX_CLIENT_ID: <root client resource id to create on startup>
+  AIDBOX_CLIENT_SECRET: <secret for the root client>
+  AIDBOX_ADMIN_ID: <root user resource id to create on startup>
+  AIDBOX_ADMIN_PASSWORD: <password for the root user>
+  AIDBOX_LICENSE: <license JWT obtained from the license server>
+```
+
+```console
+helm upgrade --install aidbox aidbox \
+  --repo https://aidbox.github.io/helm-charts \
+  --namespace aidbox --create-namespace \
+  --values /path/to/config/file
+```
+
+It will install the Aidbox in the `aidbox` namespace, creating that namespace if it doesn't already exist.
+
+## Values
+
+| Key | Type | Default | Description |
+|-----|------|---------|-------------|
+| autoscaling.enabled | bool | `false` |  |
+| autoscaling.maxReplicas | int | `100` |  |
+| autoscaling.minReplicas | int | `1` |  |
+| autoscaling.targetCPUUtilizationPercentage | int | `80` |  |
+| config | object | `{"AIDBOX_PORT":8080,"BOX_METRICS_PORT":8765,"PGPORT":5432}` | Aidbox config see [Aidbox environment variables](https://docs.aidbox.app/reference/configuration/environment-variables) for details |
+| fullnameOverride | string | `""` |  |
+| host | string | `"my.domain.tld"` | Host name Aidbox will be available at |
+| image.pullPolicy | string | `"IfNotPresent"` |  |
+| image.repository | string | `"healthsamurai/aidboxone"` |  |
+| image.tag | string | `""` |  |
+| ingress.annotations | object | `{}` |  |
+| ingress.className | string | `"nginx"` |  |
+| ingress.enabled | bool | `true` |  |
+| livenessProbe.failureThreshold | int | `10` |  |
+| livenessProbe.httpGet.path | string | `"/health"` |  |
+| livenessProbe.httpGet.port | string | `"api"` |  |
+| livenessProbe.periodSeconds | int | `10` |  |
+| nameOverride | string | `""` |  |
+| podAnnotations | object | `{}` |  |
+| podLabels | object | `{}` |  |
+| podSecurityContext | object | `{}` |  |
+| protocol | string | `"http"` | Protocol to be used to access Aidbox (http or https) |
+| readinessProbe.failureThreshold | int | `5` |  |
+| readinessProbe.httpGet.path | string | `"/health"` |  |
+| readinessProbe.httpGet.port | string | `"api"` |  |
+| readinessProbe.periodSeconds | int | `10` |  |
+| readinessProbe.successThreshold | int | `1` |  |
+| replicaCount | int | `1` |  |
+| resources.requests.cpu | string | `"500m"` |  |
+| resources.requests.memory | string | `"256Mi"` |  |
+| securityContext.runAsNonRoot | bool | `true` |  |
+| securityContext.runAsUser | int | `1000` |  |
+| service.apiPort | int | `80` |  |
+| service.metricsPort | int | `80` |  |
+| service.type | string | `"ClusterIP"` |  |
+| startupProbe.failureThreshold | int | `10` |  |
+| startupProbe.httpGet.path | string | `"/health"` |  |
+| startupProbe.httpGet.port | string | `"api"` |  |
+| startupProbe.initialDelaySeconds | int | `20` |  |
+| startupProbe.periodSeconds | int | `5` |  |
+| volumeMounts | list | `[]` |  |
+| volumes | list | `[]` |  |

aidbox/README.md.gotmpl

@@ -0,0 +1,38 @@
+{{ template "chart.header" . }}
+
+[Aidbox](https://docs.aidbox.app/) is an efficient and scalable FHIR server built to handle healthcare data effectively, empowering healthcare providers and developers alike with its comprehensive platform for storing, accessing, and exchanging healthcare information in accordance with FHIR standards.
+
+{{ template "chart.versionBadge" . }}{{ template "chart.typeBadge" . }}{{ template "chart.appVersionBadge" . }}
+
+## Installation
+
+Prepare the configuration file. Please refer to the [Aidbox environment variables](https://docs.aidbox.app/reference/configuration/environment-variables) for details.
+
+```yaml
+host: <your host here, e.g. my.domain.tld>
+protocol: <http or https>
+
+config:
+  AIDBOX_FHIR_VERSION: <FHIR version, e.g. 4.0.0>
+  PGHOST: <PostgreSQL host to connect to>
+  PGDATABASE: <name of the database that is used to store resources>
+  PGUSER: <PostgreSQL user>
+  PGPASSWORD: <PostgreSQL password>
+  AIDBOX_CLIENT_ID: <root client resource id to create on startup>
+  AIDBOX_CLIENT_SECRET: <secret for the root client>
+  AIDBOX_ADMIN_ID: <root user resource id to create on startup>
+  AIDBOX_ADMIN_PASSWORD: <password for the root user>
+  AIDBOX_LICENSE: <license JWT obtained from the license server>
+```
+
+
+```console
+helm upgrade --install aidbox aidbox \
+  --repo https://aidbox.github.io/helm-charts \
+  --namespace aidbox --create-namespace \
+  --values /path/to/config/file
+```
+
+It will install the Aidbox in the `aidbox` namespace, creating that namespace if it doesn't already exist.
+
+{{ template "chart.valuesSection" . }}

aidbox/templates/configmap.yaml

@@ -6,7 +6,9 @@ metadata:
     {{- include "aidbox.labels" . | nindent 4 }}
 data:
   {{- range $key, $val := .Values.config }}
+  {{- if and (ne $key "PGUSER") (ne $key "PGPASSWORD") (ne $key "AIDBOX_CLIENT_ID") (ne $key "AIDBOX_CLIENT_SECRET") (ne $key "AIDBOX_ADMIN_ID") (ne $key "AIDBOX_ADMIN_PASSWORD") (ne $key "AIDBOX_LICENSE") }}
   {{ $key }}: {{ $val | quote }}
   {{- end }}
-  AIDBOX_BASE_URL: {{ .Values.protocol }}://{{ .Values.host }}
+  {{- end }}
+  AIDBOX_BASE_URL: {{ required "missing protocol value" .Values.protocol }}://{{ required "missing host value" .Values.host }}
   PGHOST: {{ required "missing config PGHOST value" .Values.config.PGHOST | quote }}

aidbox/templates/deployment.yaml

@@ -15,7 +15,6 @@ spec:
     metadata:
       annotations:
         checksum/config: {{ toJson .Values.config | sha256sum }}
-        checksum/secrets: {{ toJson .Values.secrets | sha256sum }}
       labels:
         {{- include "aidbox.labels" . | nindent 8 }}
         {{- with .Values.podLabels }}

aidbox/templates/secrets.yaml

@@ -5,13 +5,12 @@ metadata:
   labels:
     {{- include "aidbox.labels" . | nindent 4 }}
 data:
-  {{- range $key, $val := .Values.secrets }}
-  {{ $key }}: {{ required (printf "missing secret %s value" $key) $val | b64enc }}
-  {{- end }}
-
-  {{- with .Values.secrets }}
-  {{- if not .AIDBOX_LICENSE }}
-  AIDBOX_LICENSE_ID: {{ required "missing secret AIDBOX_LICENSE or AIDBOX_LICENSE_ID value" .AIDBOX_LICENSE_ID | b64enc }}
-  AIDBOX_LICENSE_KEY: {{ required "missing secret AIDBOX_LICENSE or AIDBOX_LICENSE_KEY value" .AIDBOX_LICENSE_KEY | b64enc }}
-  {{- end }}
+  {{- with .Values.config }}
+  AIDBOX_ADMIN_ID: {{ required "missing AIDBOX_ADMIN_ID value" .AIDBOX_ADMIN_ID | b64enc }}
+  AIDBOX_ADMIN_PASSWORD: {{ required "missing AIDBOX_ADMIN_PASSWORD value" .AIDBOX_ADMIN_PASSWORD | b64enc }}
+  AIDBOX_CLIENT_ID: {{ required "missing AIDBOX_CLIENT_ID value" .AIDBOX_CLIENT_ID | b64enc }}
+  AIDBOX_CLIENT_SECRET: {{ required "missing AIDBOX_CLIENT_SECRET value" .AIDBOX_CLIENT_SECRET | b64enc }}
+  AIDBOX_LICENSE: {{ required "missing AIDBOX_LICENSE value" .AIDBOX_LICENSE | b64enc }}
+  PGUSER: {{ required "missing PGUSER value" .PGUSER | b64enc }}
+  PGPASSWORD: {{ required "missing PGPASSWORD value" .PGPASSWORD | b64enc }}
   {{- end }}

aidbox/values.yaml

@@ -1,27 +1,15 @@
+# -- Host name Aidbox will be available at
 host: my.domain.tld
+# -- Protocol to be used to access Aidbox (http or https)
 protocol: http
 
+# -- Aidbox config
+# see [Aidbox environment variables](https://docs.aidbox.app/reference/configuration/environment-variables) for details
 config:
-  AIDBOX_BOX_ID: aidbox
   AIDBOX_PORT: 8080
-  BOX_INSTANCE_NAME: aidbox
   BOX_METRICS_PORT: 8765
-  PGDATABASE: aidbox
   PGPORT: 5432
 
-secrets:
-  AIDBOX_ADMIN_ID: admin
-  AIDBOX_ADMIN_PASSWORD: ""
-  AIDBOX_CLIENT_ID: admin
-  AIDBOX_CLIENT_SECRET: ""
-  # AIDBOX_LICENSE: ""
-  # or
-  # AIDBOX_LICENSE_ID: ""
-  # AIDBOX_LICENSE_KEY: ""
-  PGUSER: ""
-  PGPASSWORD: ""
-
-
 image:
   repository: healthsamurai/aidboxone
   pullPolicy: IfNotPresent

aidboxdb/Chart.yaml

@@ -1,6 +1,8 @@
 apiVersion: v2
 appVersion: "16.1"
-description: AidboxDB
+description: AidboxDB is based on the official PostgreSQL and adapted to work with Aidbox.
+home: https://www.health-samurai.io/aidbox
+icon: https://aidbox.github.io/helm-charts/icon.png?1712669999
 name: aidboxdb
 type: application
-version: 0.1.1
+version: 0.1.4

aidboxdb/README.md

@@ -0,0 +1,57 @@
+# aidboxdb
+
+[AidboxDB](https://docs.aidbox.app/storage-1/aidboxdb-image) is a specialized version of the open-source PostgreSQL database, tailored for use as the data storage backend for Aidbox. It serves various purposes, including initializing and operating as a master database for Aidbox, functioning as a streaming replica, optimizing FHIR search queries, and supporting backup and maintenance functionalities.
+
+![Version: 0.1.4](https://img.shields.io/badge/Version-0.1.4-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 16.1](https://img.shields.io/badge/AppVersion-16.1-informational?style=flat-square)
+
+## Installation with the PostgreSQL default credentials
+
+```console
+helm upgrade --install aidboxdb aidboxdb \
+  --repo https://aidbox.github.io/helm-charts \
+  --namespace postgres --create-namespace
+```
+
+It will install the AidboxDB with default credentials in the `postgres` namespace, creating that namespace if it doesn't already exist.
+
+## Installation using custom PostgreSQL config and/or environment variables
+
+Create values YAML like
+
+```yaml
+config: |-
+  max_wal_size = '4GB'
+  shared_buffers = '2GB'
+
+env:
+  POSTGRES_USER: superuser
+  POSTGRES_PASSWORD: strongpassword
+```
+
+and apply it
+
+```console
+helm upgrade --install aidboxdb aidboxdb \
+  --repo https://aidbox.github.io/helm-charts \
+  --namespace postgres --create-namespace \
+  --values /path/to/values.yaml
+```
+
+## Values
+
+| Key | Type | Default | Description |
+|-----|------|---------|-------------|
+| config | string | `"max_wal_size = '4GB'\nshared_buffers = '2GB'"` | PostgreSQL config |
+| env | object | [AidboxDB environment variables](https://docs.aidbox.app/reference/configuration/environment-variables/aidboxdb-environment-variables) | Environment variables |
+| fullnameOverride | string | `""` |  |
+| image.pullPolicy | string | `"IfNotPresent"` |  |
+| image.repository | string | `"healthsamurai/aidboxdb"` |  |
+| image.tag | string | `""` | Overrides the image tag whose default is the chart appVersion. Has one-to-one mapping to the PostgreSQL version. |
+| imagePullSecrets | list | `[]` |  |
+| nameOverride | string | `""` |  |
+| podSecurityContext | object | `{}` |  |
+| securityContext | object | `{}` |  |
+| storage.className | string | `""` | Storage className to use |
+| storage.size | string | `"300Gi"` | Storage volume size request |
+| volumeMounts | list | `[]` | Additional volume mounts |
+| volumes | list | `[]` | Additional volumes |

aidboxdb/README.md.gotmpl

@@ -0,0 +1,41 @@
+{{ template "chart.header" . }}
+
+[AidboxDB](https://docs.aidbox.app/storage-1/aidboxdb-image) is a specialized version of the open-source PostgreSQL database, tailored for use as the data storage backend for Aidbox. It serves various purposes, including initializing and operating as a master database for Aidbox, functioning as a streaming replica, optimizing FHIR search queries, and supporting backup and maintenance functionalities.
+
+{{ template "chart.versionBadge" . }}{{ template "chart.typeBadge" . }}{{ template "chart.appVersionBadge" . }}
+
+## Installation with the PostgreSQL default credentials
+
+```console
+helm upgrade --install aidboxdb aidboxdb \
+  --repo https://aidbox.github.io/helm-charts \
+  --namespace postgres --create-namespace
+```
+
+It will install the AidboxDB with default credentials in the `postgres` namespace, creating that namespace if it doesn't already exist.
+
+## Installation using custom PostgreSQL config and/or environment variables
+
+Create values YAML like
+
+```yaml
+config: |-
+  max_wal_size = '4GB'
+  shared_buffers = '2GB'
+
+env:
+  POSTGRES_USER: superuser
+  POSTGRES_PASSWORD: strongpassword
+```
+
+and apply it
+
+```console
+helm upgrade --install aidboxdb aidboxdb \
+  --repo https://aidbox.github.io/helm-charts \
+  --namespace postgres --create-namespace \
+  --values /path/to/values.yaml
+```
+
+
+{{ template "chart.valuesSection" . }}

aidboxdb/templates/configmap-env.yaml

@@ -5,5 +5,8 @@ metadata:
   labels:
     {{- include "aidboxdb.labels" . | nindent 4 }}
 data:
-  PGDATA: /data/pg
-  POSTGRES_DB: postgres
+  {{- range $key, $val := .Values.env }}
+  {{- if and (not (eq $key "POSTGRES_USER")) (not (eq $key "POSTGRES_PASSWORD")) }}
+  {{ $key }}: {{ $val | quote }}
+  {{- end }}
+  {{- end }}

aidboxdb/templates/configmap-files.yaml

@@ -7,8 +7,6 @@ metadata:
 data:
   postgres.conf: |-
     listen_addresses = '*'
-    shared_buffers = {{ .Values.config.shared_buffers | squote }}
-    max_wal_size = {{ .Values.config.max_wal_size | squote }}
     pg_stat_statements.max = 500
     pg_stat_statements.save = false
     pg_stat_statements.track = top
@@ -19,3 +17,4 @@ data:
     wal_log_hints = on
     archive_command = 'wal-g wal-push %p'
     restore_command = 'wal-g wal-fetch %f %p'
+    {{- .Values.config | nindent 4 }}

aidboxdb/templates/persistentvolumeclaim.yaml

@@ -9,7 +9,7 @@ spec:
     - ReadWriteOnce
   resources:
     requests:
-      storage: {{ required "missing storageSize value" .Values.storageSize }}
-  {{- if .Values.storageClassName }}
-  storageClassName: {{ .Values.storageClassName }}
+      storage: {{ required "missing storage.size value" .Values.storage.size }}
+  {{- if .Values.storage.className }}
+  storageClassName: {{ .Values.storage.className }}
   {{- end }}

aidboxdb/templates/secrets.yaml

@@ -6,5 +6,5 @@ metadata:
     {{- include "aidboxdb.labels" . | nindent 4 }}
 type: Opaque
 data:
-  POSTGRES_PASSWORD: {{ required "missing env.PGPASSWORD value" .Values.env.PGPASSWORD | b64enc }}
-  POSTGRES_USER: {{ required "missing env.PGUSER value" .Values.env.PGUSER | b64enc }}
+  POSTGRES_PASSWORD: {{ required "missing env.POSTGRES_PASSWORD value" .Values.env.POSTGRES_PASSWORD | b64enc }}
+  POSTGRES_USER: {{ required "missing env.POSTGRES_USER value" .Values.env.POSTGRES_USER | b64enc }}