Add crystal library helm chart

charts/xchemlab/Chart.lock

@@ -5,6 +5,9 @@ dependencies:
 - name: compound-library
   repository: ""
   version: 0.0.1
+- name: crystal-library
+  repository: ""
+  version: 0.0.1
 - name: pin-packing
   repository: ""
   version: 0.0.3
@@ -35,5 +38,5 @@ dependencies:
 - name: oauth2-proxy
   repository: oci://registry-1.docker.io/bitnamicharts
   version: 3.7.4
-digest: sha256:37e0bc3ab1b7e071e600dc4e8416c4e98bed058f54fec0b1ee7b488f2eabe8d7
-generated: "2024-02-19T17:22:02.993010787Z"
+digest: sha256:e2987ea5e22dfa308a63f6f5e029d90bbc3cbd1c926161a2b72aa23ff7605825
+generated: "2024-03-05T14:33:24.387624369Z"

charts/xchemlab/Chart.yaml

@@ -6,7 +6,7 @@ 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: 0.7.0
+version: 0.8.0
 
 dependencies:
   - name: chimp-chomp
@@ -15,6 +15,9 @@ dependencies:
   - name: compound-library
     version: 0.0.1
     condition: compound-library.enabled
+  - name: crystal-library
+    version: 0.0.1
+    condition: crystal-library.enabled
   - name: pin-packing
     version: 0.0.3
     condition: pin-packing.enabled

charts/xchemlab/charts/chimp-chomp/Chart.yaml

@@ -12,4 +12,4 @@ version: 0.0.3
 # 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: "0.0.5"
+appVersion: "0.0.6"

charts/xchemlab/charts/compound-library/Chart.yaml

@@ -12,4 +12,4 @@ version: 0.0.1
 # 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: "0.0.5"
+appVersion: "0.0.6"

charts/xchemlab/charts/compound-library/templates/_helpers.tpl

@@ -1,7 +1,7 @@
 {{/*
 Expand the name of the chart.
 */}}
-{{- define "pinPacking.name" -}}
+{{- define "compoundLibrary.name" -}}
 {{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
 {{- end }}
 
@@ -10,7 +10,7 @@ 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 "pinPacking.fullname" -}}
+{{- define "compoundLibrary.fullname" -}}
 {{- if .Values.fullnameOverride }}
 {{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
 {{- else }}
@@ -26,16 +26,16 @@ If release name contains chart name it will be used as a full name.
 {{/*
 Create chart name and version as used by the chart label.
 */}}
-{{- define "pinPacking.chart" -}}
+{{- define "compoundLibrary.chart" -}}
 {{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
 {{- end }}
 
 {{/*
 Common labels
 */}}
-{{- define "pinPacking.labels" -}}
-helm.sh/chart: {{ include "pinPacking.chart" . }}
-{{ include "pinPacking.selectorLabels" . }}
+{{- define "compoundLibrary.labels" -}}
+helm.sh/chart: {{ include "compoundLibrary.chart" . }}
+{{ include "compoundLibrary.selectorLabels" . }}
 {{- if .Chart.AppVersion }}
 app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
 {{- end }}
@@ -45,15 +45,15 @@ app.kubernetes.io/managed-by: {{ .Release.Service }}
 {{/*
 Selector labels
 */}}
-{{- define "pinPacking.selectorLabels" -}}
-app.kubernetes.io/name: {{ include "pinPacking.name" . }}
+{{- define "compoundLibrary.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "compoundLibrary.name" . }}
 app.kubernetes.io/instance: {{ .Release.Name }}
 {{- end }}
 
 {{/*
 Create the name of the service account to use
 */}}
-{{- define "pinPacking.serviceAccountName" -}}
+{{- define "compoundLibrary.serviceAccountName" -}}
 {{- if .Values.serviceAccount.create }}
 {{- default (include "xchemlab.fullname" .) .Values.serviceAccount.name }}
 {{- else }}
@@ -64,7 +64,7 @@ Create the name of the service account to use
 {{/*
 Create the database URL string
 */}}
-{{- define "pinPacking.databaseURL" -}}
+{{- define "compoundLibrary.databaseURL" -}}
 {{- $host_parts := urlParse .Values.database.host }}
 {{- $raw_user_info := printf "%s:$DATABASE_PASSWORD" .Values.database.user }}
 {{- $url_parts := set $host_parts "userinfo" $raw_user_info }}

charts/xchemlab/charts/compound-library/templates/deployment.yaml

@@ -1,28 +1,28 @@
 apiVersion: apps/v1
 kind: Deployment
 metadata:
-  name: {{ include "pinPacking.fullname" . }}
+  name: {{ include "compoundLibrary.fullname" . }}
   labels:
-    {{- include "pinPacking.labels" . | nindent 4 }}
+    {{- include "compoundLibrary.labels" . | nindent 4 }}
 spec:
   replicas: {{ .Values.replicaCount }}
   selector:
     matchLabels:
-      {{- include "pinPacking.selectorLabels" . | nindent 6 }}
+      {{- include "compoundLibrary.selectorLabels" . | nindent 6 }}
   template:
     metadata:
       {{- with .Values.podAnnotations }}
       annotations:
         {{- toYaml . | nindent 8 }}
       {{- end }}
       labels:
-        {{- include "pinPacking.selectorLabels" . | nindent 8 }}
+        {{- include "compoundLibrary.selectorLabels" . | nindent 8 }}
     spec:
       {{- with .Values.imagePullSecrets }}
       imagePullSecrets:
         {{- toYaml . | nindent 8 }}
       {{- end }}
-      serviceAccountName: {{ include "pinPacking.serviceAccountName" . }}
+      serviceAccountName: {{ include "compoundLibrary.serviceAccountName" . }}
       securityContext:
         {{- toYaml .Values.podSecurityContext | nindent 8 }}
       containers:
@@ -40,7 +40,7 @@ spec:
                   name: {{ .Values.database.password.secretName }}
                   key: {{ .Values.database.password.secretKey }}
             - name: DATABASE_URL
-              value: {{ include "pinPacking.databaseURL" . }}
+              value: {{ include "compoundLibrary.databaseURL" . }}
             - name: OPA_URL
               value: {{ tpl .Values.opa.url . }}
           ports:

charts/xchemlab/charts/compound-library/templates/service.yaml

@@ -1,9 +1,9 @@
 apiVersion: v1
 kind: Service
 metadata:
-  name: {{ include "pinPacking.fullname" . }}
+  name: {{ include "compoundLibrary.fullname" . }}
   labels:
-    {{- include "pinPacking.labels" . | nindent 4 }}
+    {{- include "compoundLibrary.labels" . | nindent 4 }}
 spec:
   type: {{ .Values.service.type }}
   ports:
@@ -12,4 +12,4 @@ spec:
       protocol: TCP
       name: http
   selector:
-    {{- include "pinPacking.selectorLabels" . | nindent 4 }}
+    {{- include "compoundLibrary.selectorLabels" . | nindent 4 }}

charts/xchemlab/charts/compound-library/templates/serviceaccount.yaml

@@ -2,9 +2,9 @@
 apiVersion: v1
 kind: ServiceAccount
 metadata:
-  name: {{ include "pinPacking.serviceAccountName" . }}
+  name: {{ include "compoundLibrary.serviceAccountName" . }}
   labels:
-    {{- include "pinPacking.labels" . | nindent 4 }}
+    {{- include "compoundLibrary.labels" . | nindent 4 }}
   {{- with .Values.serviceAccount.annotations }}
   annotations:
     {{- toYaml . | nindent 4 }}

charts/xchemlab/charts/crystal-library/Chart.yaml

@@ -0,0 +1,15 @@
+apiVersion: v2
+name: crystal-library
+description: A service for crystals currently available in the XChem lab
+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: 0.0.1
+
+# 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: "0.0.6"

charts/xchemlab/charts/crystal-library/templates/_helpers.tpl

@@ -0,0 +1,73 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "crystalLibrary.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 "crystalLibrary.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 "crystalLibrary.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "crystalLibrary.labels" -}}
+helm.sh/chart: {{ include "crystalLibrary.chart" . }}
+{{ include "crystalLibrary.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "crystalLibrary.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "crystalLibrary.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "crystalLibrary.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "xchemlab.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create the database URL string
+*/}}
+{{- define "crystalLibrary.databaseURL" -}}
+{{- $host_parts := urlParse .Values.database.host }}
+{{- $raw_user_info := printf "%s:$DATABASE_PASSWORD" .Values.database.user }}
+{{- $url_parts := set $host_parts "userinfo" $raw_user_info }}
+{{- $raw_database_url := urlJoin $url_parts }}
+{{- replace "$DATABASE_PASSWORD" "$(DATABASE_PASSWORD)" $raw_database_url }}
+{{- end }}

charts/xchemlab/charts/crystal-library/templates/deployment.yaml

@@ -0,0 +1,63 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "crystalLibrary.fullname" . }}
+  labels:
+    {{- include "crystalLibrary.labels" . | nindent 4 }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      {{- include "crystalLibrary.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "crystalLibrary.selectorLabels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "crystalLibrary.serviceAccountName" . }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      containers:
+        - name: {{ .Chart.Name }}
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          args: 
+            - serve
+          env:
+            - name: DATABASE_PASSWORD
+              valueFrom:
+                secretKeyRef:
+                  name: {{ .Values.database.password.secretName }}
+                  key: {{ .Values.database.password.secretKey }}
+            - name: DATABASE_URL
+              value: {{ include "crystalLibrary.databaseURL" . }}
+            - name: OPA_URL
+              value: {{ tpl .Values.opa.url . }}
+          ports:
+            - name: http
+              containerPort: {{ .Values.service.port }}
+              protocol: TCP
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}

charts/xchemlab/charts/crystal-library/templates/service.yaml

@@ -0,0 +1,15 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "crystalLibrary.fullname" . }}
+  labels:
+    {{- include "crystalLibrary.labels" . | nindent 4 }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    {{- include "crystalLibrary.selectorLabels" . | nindent 4 }}

charts/xchemlab/charts/crystal-library/templates/serviceaccount.yaml

@@ -0,0 +1,12 @@
+{{- if .Values.serviceAccount.create -}}
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: {{ include "crystalLibrary.serviceAccountName" . }}
+  labels:
+    {{- include "crystalLibrary.labels" . | nindent 4 }}
+  {{- with .Values.serviceAccount.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+{{- end }}