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tieneupintieneupin
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Added Dockerfiles and Helm charts needed to build and deploy containers to run a Murfey data transfer and processing environment
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‎.bumpversion.toml‎

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

‎.pre-commit-config.yaml‎

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

‎Dockerfiles/murfey-instrument-server‎

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

‎Dockerfiles/murfey-rsync‎

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

‎Dockerfiles/murfey-server‎

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

‎Helm/Chart.yaml‎

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

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

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apiVersion: v1
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name: murfey-instrument-server-clem
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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
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version: 0.16.9

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

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

‎Helm/charts/murfey-rsync/Chart.yaml‎

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apiVersion: v1
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name: murfey-rsync
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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
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version: 0.16.9

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

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

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