Added Dockerfiles for Murfey services and build context for Murfey frontend

.bumpversion.toml

@@ -12,3 +12,23 @@ replace = '__version__ = "{new_version}"'
 filename = "pyproject.toml"
 search = 'version = "{current_version}"'
 replace = 'version = "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "Helm/Chart.yaml"
+search = 'version: {current_version}'
+replace = 'version: {new_version}'
+
+[[tool.bumpversion.files]]
+filename = "Helm/charts/murfey-instrument-server-clem/Chart.yaml"
+search = 'version: {current_version}'
+replace = 'version: {new_version}'
+
+[[tool.bumpversion.files]]
+filename = "Helm/charts/murfey-rsync/Chart.yaml"
+search = 'version: {current_version}'
+replace = 'version: {new_version}'
+
+[[tool.bumpversion.files]]
+filename = "Helm/charts/murfey-server/Chart.yaml"
+search = 'version: {current_version}'
+replace = 'version: {new_version}'

.pre-commit-config.yaml

@@ -20,6 +20,7 @@ repos:
         name: Verifying JSON file syntax
       - id: check-yaml
         name: Verifying YAML file syntax
+        exclude: Helm/charts/.*?/templates/deployment\.yaml
         args: [--allow-multiple-documents]
       - id: check-toml
         name: Verifying TOML file syntax
@@ -103,4 +104,5 @@ repos:
     hooks:
       - id: prettier
         name: Formatting other file types according to Prettier
+        exclude: Helm/charts/.*?/templates/deployment\.yaml
         # types_or: [css, html, json, yaml]

Dockerfiles/murfey-instrument-server

@@ -0,0 +1,53 @@
+# Build command template
+# podman build --build-arg groupid=<groupid> --build-arg userid=<userid> --build-arg groupname=<groupname> --no-cache -f path/to/Dockerfiles/murfey-instrument-server -t murfey-instrument-server:<version> path/to/python-murfey
+
+# Set up the base image to build with
+FROM docker.io/library/python:3.12.8-slim-bullseye AS base
+
+# Install Vim in base image
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends \
+        rsync \
+        vim \
+        && \
+    apt-get autoremove && \
+    rm -rf /var/lib/apt/lists/*
+
+
+# Build Murfey in a branch image
+FROM base as build
+COPY ./ /python-murfey/
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends \
+        build-essential \
+        busybox \
+        net-tools \
+        libpq-dev \
+        && \
+    busybox --install && \
+    python -m venv /venv && \
+    /venv/bin/python -m pip install --upgrade \
+        pip \
+        build \
+        importlib-metadata && \
+    /venv/bin/python -m pip install /python-murfey[client,instrument-server]
+
+
+# Transfer completed Murfey build to base image
+FROM base
+
+# Define external build arguments
+ARG groupid
+ARG groupname
+ARG userid
+
+# Copy completed Murfey build across and set user and group permissions
+COPY --from=build /venv/ /venv/
+RUN groupadd -r -g "${groupid}" "${groupname}" && \
+    useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \
+    chown -R "${userid}":"${groupid}" /venv && \
+    chmod -R a+x /venv
+ENV PATH=/venv/bin:$PATH
+USER "${userid}":"${groupid}"

Dockerfiles/murfey-rsync

@@ -0,0 +1,14 @@
+# Template build command
+# podman build --build-arg groupid=<groupid> --build-arg userid=<userid> --build-arg groupname=<groupname> --no-cache -f path/to/Dockerfiles/murfey-rsync
+
+FROM docker.io/library/alpine:3.20
+# FROM alpine:3.14
+
+ARG groupid
+ARG groupname
+ARG userid
+
+# Add any system dependencies for the developer/build environment here
+RUN apk add --no-cache rsync && \
+    addgroup -S -g "${groupid}" "${groupname}" && \
+    adduser -S "${groupname}" -G "${groupname}" -u "${userid}" -s /bin/sh

Dockerfiles/murfey-server

@@ -0,0 +1,61 @@
+# Template build command
+# podman build --build-arg groupid=<groupid> --build-arg userid=<userid> --build-arg groupname=<groupname> --no-cache -f path/to/Dockerfiles/murfey-server -t murfey-server:<version> path/to/python-murfey
+
+# Set up the base image to build with
+FROM docker.io/library/python:3.12.8-slim-bullseye AS base
+
+# Install Vim and PostgreSQL dependencies in base image
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends \
+        libpq-dev \
+        vim \
+        && \
+    apt-get autoremove && \
+    rm -rf /var/lib/apt/lists/*
+
+
+# Build Murfey and IMOD in a branch image
+FROM base as build
+COPY ./ /python-murfey/
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends \
+        build-essential \
+        busybox \
+        curl \
+        net-tools \
+        && \
+    busybox --install && \
+    python -m venv /venv && \
+    /venv/bin/python -m pip install --upgrade \
+        pip \
+        build \
+        importlib-metadata \
+        psycopg2-binary \
+        && \
+    /venv/bin/python -m pip install /python-murfey[server] && \
+    curl https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_5.1.0_RHEL8-64_CUDA12.0.sh > imod_5.1.0_RHEL8-64_CUDA12.0.sh && \
+    chmod +x imod_5.1.0_RHEL8-64_CUDA12.0.sh && \
+    mkdir imod && \
+    ./imod_5.1.0_RHEL8-64_CUDA12.0.sh -dir imod -skip -y
+
+
+# Transfer completed builds to base image
+FROM base
+
+# Pass external build arguments to this stage
+ARG groupid
+ARG groupname
+ARG userid
+
+# Copy completed Murfey and IMOD builds across and set user and group permissions
+COPY --from=build /venv/ /venv/
+COPY --from=build /imod/ /imod/
+RUN groupadd -r -g "${groupid}" "${groupname}" && \
+    useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \
+    chown -R "${userid}":"${groupid}" /venv && \
+    chmod -R a+x /venv
+ENV PATH=/venv/bin:/imod/IMOD/bin:$PATH
+ENV IMOD_DIR=/imod/IMOD
+USER "${userid}":"${groupid}"

Helm/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+name: murfey-services
+description: Umbrella Helm chart for deploying the servers and daemons needed to enable Murfey to transfer and process data
+version: 0.16.9
+dependencies:
+  - name: murfey-instrument-server-clem
+  - name: murfey-server
+  - name: murfey-rsync

Helm/charts/murfey-instrument-server-clem/Chart.yaml

@@ -0,0 +1,4 @@
+apiVersion: v1
+name: murfey-instrument-server-clem
+description: Helm chart for deploying a Murfey instrument server, which executes orders to detect, modify, and transfer files on the instrument PC, and notifies the backend server about transferred files
+version: 0.16.9

Helm/charts/murfey-instrument-server-clem/templates/deployment.yaml

@@ -0,0 +1,68 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.appName }}
+  namespace: {{ .Values.global.namespace }}
+  labels:
+    app: {{ .Values.appName }}
+spec:
+  type: LoadBalancer
+  externalTrafficPolicy: Cluster
+  ports:
+    {{- toYaml .Values.servicePorts | nindent 2 }}
+  selector:
+    app: {{ .Values.appName }}
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Values.appName }}
+  namespace: {{ .Values.global.namespace }}
+  labels:
+    app: {{ .Values.appName }}
+spec:
+  replicas: {{ .Values.replicas }}
+  selector:
+    matchLabels:
+      app: {{ .Values.appName }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.appName }}
+    spec:
+      securityContext:
+        runAsUser: {{ .Values.global.runAsUser }}
+        runAsGroup: {{ .Values.global.runAsGroup }}
+      volumes:
+        # Mount config files from secrets
+        - name: murfey-client-config
+          secret:
+            secretName: {{ .Values.global.murfeyClientConfigCLEMSecretName }}
+            items:
+              - key: {{ .Values.global.murfeyClientConfigCLEMFileName }}
+                path: .murfey
+        # Mount data directories
+        {{- toYaml .Values.extraVolumes | nindent 8 }}
+      containers:
+        - name: {{ .Values.appName }}
+          image: {{ .Values.image }}
+          imagePullPolicy: Always
+          securityContext:
+            privileged: false
+          volumeMounts:
+            # Mount Murfey client config
+            - name: murfey-client-config
+              mountPath: /murfey/config/.murfey
+              subPath: .murfey
+              readOnly: false
+            # Mount data directories
+            {{- toYaml .Values.extraVolumeMounts | nindent 12 }}
+          env:
+            - name: MURFEY_CLIENT_CONFIG_HOME
+              value: "/tmp"
+          ports:
+            - containerPort: {{ .Values.containerPort }}
+          command:
+            {{- toYaml .Values.command | nindent 12 }}
+          args:
+            {{- toYaml .Values.args | nindent 12 }}

Helm/charts/murfey-rsync/Chart.yaml

@@ -0,0 +1,4 @@
+apiVersion: v1
+name: murfey-rsync
+description: Helm chart for deploying an rsync daemon, which is responsible for executing the transfer of files from the client storage directory to the server storage system
+version: 0.16.9

Helm/charts/murfey-rsync/templates/deployment.yaml

@@ -0,0 +1,62 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.appName }}
+spec:
+  ports:
+    {{- toYaml .Values.servicePorts | nindent 2 }}
+  selector:
+    app: {{ .Values.appName }}
+  type: ClusterIP
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Values.appName }}
+  namespace: {{ .Values.global.namespace }}
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: {{ .Values.appName }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.appName }}
+    spec:
+      securityContext:
+        runAsUser: {{ .Values.global.runAsUser }}
+        runAsGroup: {{ .Values.global.runAsGroup }}
+      volumes:
+        - name: rsyncd-conf
+          secret:
+            secretName: {{ .Values.global.rsyncConfigSecretName }}
+            items:
+              - key: {{ .Values.global.rsyncConfigFileName }}
+                path: rsyncd.conf
+        # Mount data directories
+        {{- toYaml .Values.extraVolumes | nindent 8 }}
+      containers:
+        - name: {{ .Values.appName }}
+          image: {{ .Values.image }}
+          imagePullPolicy: Always
+          resources:
+            requests:
+              cpu: {{ .Values.cpuRequest }}
+            limits:
+              cpu: {{ .Values.cpuLimit }}
+              memory: {{ .Values.memoryLimit }}
+          volumeMounts:
+            # Mount rsync config files
+            - name: rsyncd-conf
+              mountPath: /murfey/rsync/rsyncd.conf
+              subPath: rsyncd.conf
+              readOnly: true
+            # Mount data directories
+            {{- toYaml .Values.extraVolumeMounts | nindent 12 }}
+          ports:
+            - containerPort: {{ .Values.containerPort }}
+          command:
+            {{- toYaml .Values.command | nindent 12 }}
+          args:
+            {{- toYaml .Values.args | nindent 12 }}

Helm/charts/murfey-server/Chart.yaml

@@ -0,0 +1,4 @@
+apiVersion: v1
+name: murfey-server
+description: Helm chart for deploying a Murfey backend server, which is responsible for orchestrating the data transfer and processing workflow between the client PC and the storage system
+version: 0.16.9