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Merge pull request #18 from chgl/develop
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ohdsi fixes
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@chgl
chgl committed Jan 12, 2021
2 parents 6ab3353 + 875703c commit adf9859
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Showing 7 changed files with 49 additions and 16 deletions.
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: 0.3.0
version: 0.3.1
home: https://github.com/OHDSI
keywords:
- ohdsi
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10 changes: 5 additions & 5 deletions charts/ohdsi/README.md
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Expand Up @@ -69,11 +69,11 @@ The following table lists the configurable parameters of the `ohdsi` chart and t
| webApi.image.repository | | `chgl/ohdsi/webapi` |
| webApi.image.tag | | `2.8.0-snapshot` |
| webApi.image.pullPolicy | | `Always` |
| webApi.db.host | | `"db"` |
| webApi.db.port | | `5432` |
| webApi.db.database | | `"ohdsi"` |
| webApi.db.username | | `"postgres"` |
| webApi.db.password | | `"postgres"` |
| webApi.db.host | database hostname | `"host.example.com"` |
| webApi.db.port | port used to connect to the postgres DB | `5432` |
| webApi.db.database | name of the database inside. If postgresql.enabled=true, then postgresql.postgresqlDatabase is used | `"ohdsi"` |
| webApi.db.username | username used to connect to the DB. Note that this name is currently used even if postgresql.enabled=true | `"postgres"` |
| webApi.db.password | the database password. Only used if postgresql.enabled=false, otherwise the secret created by the postgresql chart is used | `"postgres"` |
| webApi.db.existingSecret | name of an existing secret containing the password to the DB. | `""` |
| webApi.db.existingSecretKey | name of the key in `webApi.db.existingSecret` to use as the password to the DB. | `"postgresql-postgres-password"` |
| webApi.podAnnotations | annotations applied to the WebAPI pod | `{}` |
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14 changes: 10 additions & 4 deletions charts/ohdsi/templates/achilles-cronjob.yaml
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Expand Up @@ -20,16 +20,22 @@ spec:
{{- toYaml . | nindent 12 }}
{{- end }}
automountServiceAccountToken: false
{{- with .podSecurityContext}}
securityContext:
{{- toYaml .podSecurityContext | nindent 12 }}
{{- toYaml . | nindent 12 }}
{{- end }}
containers:
- name: achilles-cron
securityContext:
{{- toYaml .securityContext | nindent 16 }}
image: "{{ .image.registry }}/{{ .image.repository }}:{{ .image.tag }}"
imagePullPolicy: {{ .image.pullPolicy }}
{{- with .securityContext}}
securityContext:
{{- toYaml . | nindent 16 }}
{{- end }}
{{- with .resources}}
resources:
{{- toYaml .resources | nindent 16 }}
{{- toYaml . | nindent 16 }}
{{- end }}
env:
- name: ACHILLES_DB_URI
value: {{ include "ohdsi.webapi.jdbcUrl" $ | replace "jdbc:" ""}}
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14 changes: 11 additions & 3 deletions charts/ohdsi/templates/atlas-deployment.yaml
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Expand Up @@ -33,12 +33,16 @@ spec:
{{- toYaml . | nindent 8 }}
{{- end }}
automountServiceAccountToken: false
{{- with .podSecurityContext}}
securityContext:
{{- toYaml .podSecurityContext | nindent 8 }}
{{- toYaml . | nindent 8 }}
{{- end }}
containers:
- name: atlas
{{- with .securityContext}}
securityContext:
{{- toYaml .securityContext | nindent 12 }}
{{- toYaml . | nindent 12 }}
{{- end }}
image: "{{ .image.registry }}/{{ .image.repository }}:{{ .image.tag }}"
imagePullPolicy: {{ .image.pullPolicy }}
ports:
Expand All @@ -63,8 +67,10 @@ spec:
timeoutSeconds: {{ .readinessProbe.timeoutSeconds }}
successThreshold: {{ .readinessProbe.successThreshold }}
failureThreshold: {{ .readinessProbe.failureThreshold }}
{{- with .resources}}
resources:
{{- toYaml .resources | nindent 12 }}
{{- toYaml . | nindent 12 }}
{{- end }}
env:
{{- if .webApiUrl }}
- name: WEBAPI_URL
Expand All @@ -74,6 +80,8 @@ spec:
{{- $host := (index $.Values.webApi.ingress.hosts 0) }}
{{- $path := index (index $.Values.webApi.ingress.hosts 0).paths 0 }}
value: http{{ if $.Values.webApi.ingress.tls }}s{{ end }}://{{ $host.host }}{{ $path }}
{{- else }}
[]
{{- end }}
{{- if .extraEnv }}
{{- toYaml .extraEnv | nindent 12 }}
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16 changes: 15 additions & 1 deletion charts/ohdsi/templates/cdm-init-job.yaml
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Expand Up @@ -30,8 +30,10 @@ spec:
{{- toYaml . | nindent 8 }}
{{- end }}
automountServiceAccountToken: false
{{- with .securityContext }}
securityContext:
{{- toYaml .podSecurityContext | nindent 8 }}
{{- toYaml . | nindent 8 }}
{{- end }}
containers:
- name: cdm-init
image: "{{ .image.registry }}/{{ .image.repository }}:{{ .image.tag }}"
Expand All @@ -51,15 +53,27 @@ spec:
- name: PGUSER
value: {{ $.Values.webApi.db.username }}
- name: PGHOST
{{- if $.Values.postgresql.enabled }}
{{- $fullname := ( include "ohdsi.fullname" $ ) }}
{{- $pgServiceName := ( printf "%s-%s" $fullname "postgresql") }}
value: "{{ $pgServiceName }}"
{{- else }}
value: {{ $.Values.webApi.db.host }}
{{- end }}
- name: PGPORT
value: {{ $.Values.webApi.db.port | quote }}
- name: PGDATABASE
{{- if $.Values.postgresql.enabled }}
value: {{ $.Values.postgresql.postgresqlDatabase }}
{{- else }}
value: {{ $.Values.webApi.db.database }}
{{- end }}
- name: WEBAPI_URL
{{- if $.Values.atlas.webApiUrl }}
value: {{ $.Values.atlas.webApiUrl }}
{{- else }}
value: "http://{{ include "ohdsi.fullname" $ }}-webapi:{{ $.Values.webApi.service.port }}/WebAPI"
{{- end }}
{{- if .extraEnv }}
{{- toYaml .extraEnv | nindent 12 }}
{{- end }}
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2 changes: 1 addition & 1 deletion charts/ohdsi/templates/webapi-db-secret.yaml
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@@ -1,5 +1,5 @@
{{- if .Values.webApi.enabled }}
{{- if not .Values.postgresql.enabled -}}
{{- if and (not .Values.postgresql.enabled) (not .Values.webApi.db.existingSecret) -}}
apiVersion: v1
kind: Secret
metadata:
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7 changes: 6 additions & 1 deletion charts/ohdsi/values.yaml
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Expand Up @@ -63,10 +63,15 @@ webApi:
pullPolicy: Always

db:
host: "db"
# database hostname
host: "host.example.com"
# port used to connect to the postgres DB
port: 5432
# name of the database inside. If postgresql.enabled=true, then postgresql.postgresqlDatabase is used
database: "ohdsi"
# username used to connect to the DB. Note that this name is currently used even if postgresql.enabled=true
username: "postgres"
# the database password. Only used if postgresql.enabled=false, otherwise the secret created by the postgresql chart is used
password: "postgres"
# name of an existing secret containing the password to the DB.
existingSecret: ""
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