Merge branch 'main' into federated_graph

backend/Cargo.toml

@@ -42,7 +42,7 @@ sea-orm = { version = "0.11.2", default-features = false, features = [
     "with-uuid",
 ] }
 sea-orm-migration = { version = "0.11.3" }
-serde = { version = "1.0.196" }
+serde = { version = "1.0.197" }
 thiserror = { version = "1.0.57" }
 tokio = { version = "1.35.1", features = ["macros", "rt-multi-thread"] }
 tracing = { version = "0.1.40" }

backend/chimp_chomp/Cargo.toml

@@ -10,7 +10,7 @@ clap = { workspace = true }
 derive_more = { workspace = true }
 dotenvy = { workspace = true }
 futures = { version = "0.3.30" }
-futures-timer = { version = "3.0.2" }
+futures-timer = { version = "3.0.3" }
 itertools = { workspace = true }
 lapin = { version = "2.3.1" }
 ndarray = { version = "0.15.6" }

backend/chimp_protocol/Cargo.toml

@@ -5,6 +5,6 @@ edition = "2021"
 
 [dependencies]
 serde = { workspace = true }
-serde_json = { version = "1.0.113" }
+serde_json = { version = "1.0.114" }
 url = { workspace = true, features = ["serde"] }
 uuid = { workspace = true, features = ["serde"] }

charts/xchemlab/Chart.lock

@@ -2,6 +2,9 @@ dependencies:
 - name: chimp-chomp
   repository: ""
   version: 0.0.3
+- name: compound-library
+  repository: ""
+  version: 0.0.1
 - name: pin-packing
   repository: ""
   version: 0.0.3
@@ -32,5 +35,5 @@ dependencies:
 - name: oauth2-proxy
   repository: oci://registry-1.docker.io/bitnamicharts
   version: 3.7.4
-digest: sha256:4b0ce326f2d48a9af560de0471ebf021e50fa0a9fba1f401bb11fdcdb28ef1d1
-generated: "2023-10-05T14:59:27.826614445+01:00"
+digest: sha256:37e0bc3ab1b7e071e600dc4e8416c4e98bed058f54fec0b1ee7b488f2eabe8d7
+generated: "2024-02-19T17:22:02.993010787Z"

charts/xchemlab/Chart.yaml

@@ -6,12 +6,15 @@ 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: 0.6.0
+version: 0.7.0
 
 dependencies:
   - name: chimp-chomp
     version: 0.0.3
     condition: chimp-chomp.enabled
+  - name: compound-library
+    version: 0.0.1
+    condition: compound-library.enabled
   - name: pin-packing
     version: 0.0.3
     condition: pin-packing.enabled

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

@@ -0,0 +1,15 @@
+apiVersion: v2
+name: compound-library
+description: A service for compounds 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: "0.0.5"

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

@@ -0,0 +1,73 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "pinPacking.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 "pinPacking.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 "pinPacking.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" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "pinPacking.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "pinPacking.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "pinPacking.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 "pinPacking.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/compound-library/templates/deployment.yaml

@@ -0,0 +1,63 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "pinPacking.fullname" . }}
+  labels:
+    {{- include "pinPacking.labels" . | nindent 4 }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      {{- include "pinPacking.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "pinPacking.selectorLabels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "pinPacking.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 "pinPacking.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/compound-library/templates/service.yaml

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

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

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

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

@@ -0,0 +1,43 @@
+nameOverride: ""
+fullnameOverride: ""
+
+image:
+  repository: ghcr.io/diamondlightsource/xchemlab-compound-library
+  pullPolicy: Always
+  tag: ""
+
+imagePullSecrets: []
+
+database:
+  host: ""
+  user: ""
+  password:
+    secretName: ""
+    secretKey: ""
+
+opa:
+  url: ""
+
+replicaCount: 1
+
+service:
+  type: ClusterIP
+  port: 80
+
+serviceAccount:
+  create: false
+  name: ""
+
+podAnnotations: {}
+
+podSecurityContext: {}
+
+securityContext: {}
+
+resources: {}
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}

charts/xchemlab/values.yaml

@@ -19,6 +19,17 @@ chimp-chomp:
       mountPath: /dls/labxchem
       mountPropagation: HostToContainer
 
+compound-library:
+  enabled: true
+  database:
+    host: postgres://postgresql-ha-pgpool
+    user: postgres
+    password:
+      secretName: postgres-passwords
+      secretKey: password
+  opa:
+    url: http://{{ .Release.Name }}-opa-kube-mgmt:8181
+
 pin-packing:
   enabled: true
   database:

frontend/package.json

@@ -5,7 +5,7 @@
   "devDependencies": {
     "@babel/core": "^7.23.9",
     "@graphql-codegen/cli": "^5.0.2",
-    "@graphql-codegen/client-preset": "^4.1.0",
+    "@graphql-codegen/client-preset": "^4.2.4",
     "@graphql-typed-document-node/core": "^3.2.0",
     "@pmmmwh/react-refresh-webpack-plugin": "^0.5.3",
     "@svgr/webpack": "^8.1.0",
@@ -22,9 +22,9 @@
     "case-sensitive-paths-webpack-plugin": "^2.4.0",
     "css-loader": "^6.10.0",
     "css-minimizer-webpack-plugin": "^6.0.0",
-    "dotenv": "^16.4.4",
+    "dotenv": "^16.4.5",
     "dotenv-expand": "^11.0.6",
-    "eslint": "8.56.0",
+    "eslint": "8.57.0",
     "eslint-config-react-app": "^7.0.1",
     "eslint-webpack-plugin": "^4.0.1",
     "file-loader": "^6.2.0",
@@ -50,7 +50,7 @@
     "typescript": "5.3.3",
     "web-vitals": "^3.5.2",
     "webpack": "^5.90.3",
-    "webpack-dev-server": "^4.6.0",
+    "webpack-dev-server": "^5.0.2",
     "webpack-manifest-plugin": "^5.0.0",
     "workbox-webpack-plugin": "^7.0.0"
   },