Hail Search Service helm charts. (#19)

* add hail-search template * add volumne * mostly there * add some delays * failure thresholds * add config * cleanup * ws * Update values.yaml * Update values.yaml * use env vars * use env vars * undo env tpl * ws * missing quote * initContainers args * change to 5000 * use service port * update * Update values.yaml * remove non-public values * complete brain fart * Check for new samples upon chart install. (#22) * hail search re-deploy job * ws * rename annotation * rename * ws * use globals * add imagePullSecrets * add imagePullSecrets * rename global * dash does not work * skip if empty string provided
broadinstitute · Oct 5, 2023 · 54d7190 · 54d7190
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diff --git a/charts/hail-search/.helmignore b/charts/hail-search/.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/
diff --git a/charts/hail-search/Chart.yaml b/charts/hail-search/Chart.yaml
@@ -0,0 +1,27 @@
+apiVersion: v2
+name: hail-search
+description: A Helm chart for deploying the hail backend of Seqr, an open source software platform for rare disease genomics
+sources:
+  - https://github.com/broadinstitute/seqr
+  - https://github.com/broadinstitute/seqr-helm
+
+# 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: "ee4afa08ee1190ac05ef06543adcb1833f5e2e8e"
diff --git a/charts/hail-search/templates/_helpers.tpl b/charts/hail-search/templates/_helpers.tpl
@@ -0,0 +1,51 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "hail-search.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 "hail-search.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 "hail-search.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "hail-search.labels" -}}
+helm.sh/chart: {{ include "hail-search.chart" . }}
+{{ include "hail-search.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "hail-search.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "hail-search.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
diff --git a/charts/hail-search/templates/deployment.yaml b/charts/hail-search/templates/deployment.yaml
@@ -0,0 +1,74 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "hail-search.fullname" . }}
+  labels:
+    {{- include "hail-search.labels" . | nindent 4 }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      {{- include "hail-search.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      annotations:
+        checksum/datasetVersions: {{ print $.Values.datasetVersions | sha256sum }}
+      {{- with .Values.podAnnotations }}
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "hail-search.selectorLabels" . | nindent 8 }}
+    spec:
+      volumes:
+      - name: datasets
+        emptyDir:
+          # Default sizeLimit is 1/2 the total RAM of the Node.
+          medium: "Memory"
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 6 }}
+      {{- end }}
+      containers:
+        - name: {{ include "hail-search.fullname" . }}-pod
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          envFrom:
+            - configMapRef:
+                name: {{ include "hail-search.fullname" . }}
+          ports:
+            - name: http
+              containerPort: {{ .Values.service.port }}
+              protocol: TCP
+          livenessProbe:
+            initialDelaySeconds: 10
+            periodSeconds: 30
+            failureThreshold: 5
+            httpGet:
+              path: /status
+              port: http
+          readinessProbe:
+            initialDelaySeconds: 10
+            periodSeconds: 30
+            failureThreshold: 5
+            httpGet:
+              path: /status
+              port: http
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          volumeMounts:
+            - mountPath: {{ .Values.environment.DATASETS_DIR }}
+              name: datasets
+      restartPolicy: Always
+      dnsPolicy: ClusterFirst
+      {{- with .Values.initContainers}}
+      initContainers:
+        {{- tpl . $ | trim | nindent 8}}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- tpl . $ | nindent 8 }}
+      {{- end }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
diff --git a/charts/hail-search/templates/environment.yaml b/charts/hail-search/templates/environment.yaml
@@ -0,0 +1,10 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ include "hail-search.fullname" . }}
+  labels:
+    {{- include "hail-search.labels" . | nindent 4 }}
+data:
+  {{- with .Values.environment }}
+    {{- toYaml . | nindent 2 }}
+  {{- end }}
diff --git a/charts/hail-search/templates/service.yaml b/charts/hail-search/templates/service.yaml
@@ -0,0 +1,15 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "hail-search.fullname" . }}
+  labels:
+    {{- include "hail-search.labels" . | nindent 4 }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    {{- include "hail-search.selectorLabels" . | nindent 4 }}
diff --git a/charts/hail-search/values.yaml b/charts/hail-search/values.yaml
@@ -0,0 +1,70 @@
+# Default values for hail-search.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 4
+
+image:
+  repository: gcr.io/seqr-project/seqr-hail-search
+  pullPolicy: Always
+  # -- The docker image tag to pull from the repository
+  # tag: "gcloud-dev"
+
+imagePullSecrets: []
+nameOverride: ""
+fullnameOverride: ""
+
+podAnnotations: {}
+
+service:
+  type: ClusterIP
+  port: 5000
+
+resources: 
+  {}
+
+# default environment variables
+environment:
+  DATASETS_DIR: '/datasets'
+
+initContainers: |-
+  {{- range $path, $version := .Values.global.hail_search.datasetVersions -}}
+  {{ if $version }}
+  - name: sync-datasets-{{ $path }}
+    image: gcr.io/google.com/cloudsdktool/google-cloud-cli:latest
+    command: ['gsutil', '-m', 'rsync', '-r', '{{ $.Values.global.hail_search.sourceDatasetsDir }}/{{ $path }}/runs/{{ $version }}', '{{ $.Values.environment.DATASETS_DIR }}/{{ $path }}']
+    volumeMounts:
+      - mountPath: {{ $.Values.environment.DATASETS_DIR }}
+        name: datasets
+  {{ end }}
+  {{ end }}
+
+# Prefer to be scheduled away from other hail-search pods and seqr application pods
+affinity: |-
+  podAntiAffinity:
+    preferredDuringSchedulingIgnoredDuringExecution:
+      - weight: 1.0
+        podAffinityTerm:
+          labelSelector:
+            matchLabels:
+              {{- include "hail-search.selectorLabels"  . | nindent 12 }}
+          topologyKey: "kubernetes.io/hostname"
+      - weight: 1.0
+        podAffinityTerm:
+          labelSelector:
+            matchExpressions:
+              - key: "name"
+                operator: In
+                values:
+                - seqr
+          topologyKey: "kubernetes.io/hostname"
+
+nodeSelector: 
+  {}
+
+global:
+  hail_search:
+    sourceDatasetsDir: ''
+    datasetVersions:
+      GRCh37/SNV_INDEL: ''
+      GRCh38/SNV_INDEL: ''
diff --git a/charts/seqr/templates/check-for-new-samples-from-pipeline.yaml b/charts/seqr/templates/check-for-new-samples-from-pipeline.yaml
@@ -0,0 +1,44 @@
+{{- range $path, $version := .Values.global.hail_search.datasetVersions -}}
+{{ if $version }}
+apiVersion: batch/v1
+kind: Job
+metadata:
+  name: {{ include "seqr.fullname" $ }}-check-new-samples-job
+  labels:
+    {{- include "seqr.labels" $ | nindent 4 }}
+  annotations:
+    "helm.sh/hook": post-install, post-upgrade
+    "helm.sh/hook-weight": "-1"
+    "helm.sh/hook-delete-policy": before-hook-creation,hook-succeeded
+    {{- with $.Values.podAnnotations }}
+      {{- toYaml . | nindent 4 }}
+    {{- end }}
+spec:
+  template:
+    metadata:
+      labels:
+        {{- include "seqr.labels" $ | nindent 8 }}
+    spec:
+      {{- with $.Values.volumes }}
+      volumes:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      restartPolicy: Never
+      {{- with $.Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 6 }}
+      {{- end }}
+      containers:
+        - name: {{ include "seqr.fullname" $ }}-check-new-samples-job-pod
+          image: {{ $.Values.image.repository }}:{{ $.Values.image.tag | default $.Chart.AppVersion }}
+          imagePullPolicy: {{ $.Values.image.pullPolicy }}
+          {{- with $.Values.volumeMounts }}
+          volumeMounts:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          command: ["python", "manage.py", "check_for_new_samples_from_pipeline", "{{ $path }}", "{{ $version }}"]
+      {{- with $.Values.deployment_sidecars }}
+        {{- tpl . $ | nindent 6 }}
+      {{- end }}
+{{ end }}
+{{ end }}
diff --git a/charts/seqr/values.yaml b/charts/seqr/values.yaml
@@ -181,3 +181,10 @@ run_seqr_database_migration: false
 redis:
   # -- enables or disables redis deployment using this chart
   enabled: false
+
+global:
+  hail_search:
+    sourceDatasetsDir: ''
+    datasetVersions:
+      GRCh37/SNV_INDEL: ''
+      GRCh38/SNV_INDEL: ''