feature HAPI FHIR

helm/gen3/Chart.yaml

@@ -104,6 +104,17 @@ dependencies:
   repository: "https://charts.bitnami.com/bitnami"
   condition: global.dev
 
+# helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/
+# adds the hapi-fhir-jpaserver chart to the list of charts that can be installed
+- name: hapi-fhir-jpaserver
+  version: 0.17.1
+  repository: "https://hapifhir.github.io/hapi-fhir-jpaserver-starter/"
+  condition: global.dev
+- name: hapi-fhir-db-init
+  version: 0.1.0
+  repository: "file://../hapi-fhir-db-init"
+  condition: global.dev
+
 # A chart can be either an 'application' or a 'library' chart.
 #
 # Application charts are a collection of templates that can be packaged into versioned archives
@@ -117,7 +128,7 @@ 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: 0.1.19
+version: 0.1.20
 
 # 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

helm/hapi-fhir-db-init/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

helm/hapi-fhir-db-init/Chart.yaml

@@ -0,0 +1,30 @@
+apiVersion: v2
+name: hapi-fhir-db-init
+description: A Helm chart for Kubernetes
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+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: 0.1.0
+
+# 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
+# follow Semantic Versioning. They should reflect the version the application is using.
+# It is recommended to use it with quotes.
+appVersion: "1.16.0"
+
+
+dependencies:
+  - name: hapi-fhir-jpaserver
+    version: 0.17.1
+    repository: "https://hapifhir.github.io/hapi-fhir-jpaserver-starter/"

helm/hapi-fhir-db-init/templates/NOTES.txt

@@ -0,0 +1 @@
+# TODO

helm/hapi-fhir-db-init/templates/_helpers.tpl

@@ -0,0 +1,62 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "hapi-fhir-db-init.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "hapi-fhir-db-init.fullname" -}}
+{{- if .Values.fullnameOverride }}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- $name := default .Chart.Name .Values.nameOverride }}
+{{- if contains $name .Release.Name }}
+{{- .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
+{{- end }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "hapi-fhir-db-init.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "hapi-fhir-db-init.labels" -}}
+helm.sh/chart: {{ include "hapi-fhir-db-init.chart" . }}
+{{ include "hapi-fhir-db-init.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "hapi-fhir-db-init.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "hapi-fhir-db-init.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "hapi-fhir-db-init.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "hapi-fhir-db-init.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}

helm/hapi-fhir-db-init/templates/db-init.yaml

@@ -0,0 +1,6 @@
+{{ include "common.db-secret" . }}
+---
+{{ include "common.db_setup_job" . }}
+---
+{{ include "common.db_setup_sa" . }}
+---

helm/hapi-fhir-db-init/values.yaml

@@ -0,0 +1,31 @@
+# Global configuration
+
+# -- (map) Postgres database configuration. If db does not exist in postgres cluster and dbCreate is set ot true then these databases will be created for you
+postgres:
+  # (bool) Whether the database should be restored from s3. Default to global.postgres.dbRestore
+  dbRestore: false
+  # -- (bool) Whether the database should be created. Default to global.postgres.dbCreate
+  dbCreate:
+  # -- (string) Hostname for postgres server. This is a service override, defaults to global.postgres.host
+  host:
+  # -- (string) Database name for postgres. This is a service override, defaults to <serviceName>-<releaseName>
+  database:
+  # -- (string) Username for postgres. This is a service override, defaults to <serviceName>-<releaseName>
+  username:
+  # -- (string) Port for Postgres.
+  port: "5432"
+  # -- (string) Password for Postgres. Will be autogenerated if left empty.
+  password:
+  # -- (string) Will create a Database for the individual service to help with developing it.
+  separate: false
+
+# -- (map) External Secrets settings.
+externalSecrets:
+  # -- (string) Will override the name of the aws secrets manager secret. Default is "Values.global.environment-.Chart.Name-creds"
+  dbcreds:
+# -- (map) Secret information for External Secrets.
+secrets:
+  # -- (str) AWS access key ID. Overrides global key.
+  awsAccessKeyId:
+  # -- (str) AWS secret access key ID. Overrides global key.
+  awsSecretAccessKey:

helm/revproxy/gen3.nginx.conf/hapi-fhir-jpaserver-service.conf

@@ -0,0 +1,10 @@
+location /fhir/ {
+    proxy_connect_timeout 600s;
+    proxy_send_timeout 600s;
+    proxy_read_timeout 600s;
+    send_timeout 600s;
+
+#   maintain the /fhir prefix in the proxied request
+    proxy_pass http://local-hapi-fhir-jpaserver.$namespace.svc.cluster.local:8080;
+}
+