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single dockerfile behaves
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‎EverythingDockerfile‎

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# EverythingDockerfile - Multistage build combining all services
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# This combines mongodb, api, handler, ui, and telemetry into a single container
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# Stage 1: MongoDB base
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FROM mongo:4.4.15 AS mongodb-stage
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RUN apt-get update && apt-get install -y curl && rm -rf /var/lib/apt/lists/*
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# Stage 2: Neuroimaging tools and handler dependencies
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FROM neurodebian:nd20.04-non-free AS neuroimaging-stage
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SHELL ["/bin/bash", "-c"]
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt update && \
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apt-get update && apt-get upgrade -y
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RUN apt update && apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy bc
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RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \
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pip3 install quickshear mne mne-bids pypet2bids==1.4.1
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RUN apt-get install -y build-essential pkg-config cmake git pigz rename zstd libopenjp2-7 libgdcm-tools wget libopenblas-dev && \
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apt-get clean -y && apt-get autoclean -y && apt-get autoremove -y
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RUN touch /.pet2bidsconfig && chown 1001:1001 /.pet2bidsconfig
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RUN echo "DEFAULT_METADATA_JSON=/usr/local/lib/python3.8/dist-packages/pypet2bids/template_json.json" > /.pet2bidsconfig
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RUN mkdir -p /usr/local/fsl && \
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git clone https://github.com/dlevitas/FSL_binaries /usr/local/fsl && \
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rm -rf /usr/local/fsl/README.md && \
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mkdir -p /usr/local/fsl/data/standard && \
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mv /usr/local/fsl/bin/MNI152_T1_2mm_brain.nii.gz /usr/local/fsl/data/standard
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ENV FSLDIR=/usr/local/fsl
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ENV PATH=$PATH:$FSLDIR/bin
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ENV FSLOUTPUTTYPE=NIFTI_GZ
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RUN apt-get update \
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&& apt-get install -y ca-certificates curl gnupg \
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&& mkdir -p /etc/apt/keyrings \
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&& curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg
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ARG NODE_MAJOR=20
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RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list
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RUN apt-get update \
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&& apt-get install nodejs -y
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RUN cd /tmp && curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip \
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&& unzip /tmp/dcm2niix_lnx.zip \
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&& mv dcm2niix /usr/local/bin
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RUN mkdir -p /app
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# Get bids-specification from github
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RUN cd /app && git clone https://github.com/bids-standard/bids-specification && \
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cd bids-specification && git checkout 3537e9edbc81545614d3ee605c398361099b6977
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#install ROBEX
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ADD https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1 /
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RUN tar -xzf /ROBEXv12.linux64.tar.gz
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ENV PATH /ROBEX:$PATH
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ENV NODE_PATH $NVM_DIR/v$NODE_VERSION/lib/node_modules
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ENV PATH $NVM_DIR/v$NODE_VERSION/bin:$PATH
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#install bids-validator
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RUN npm install -g [email protected]
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RUN npm install -g [email protected]
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RUN git clone https://github.com/bids-standard/bids-validator
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# Stage 3: Node.js base for API and UI
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FROM node:20 AS nodejs-stage
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RUN npm install -g [email protected] pm2 typescript tsc-watch
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# Stage 4: Telemetry dependencies
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FROM neurodebian:nd20.04-non-free AS telemetry-stage
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SHELL ["/bin/bash", "-c"]
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ENV DEBIAN_FRONTEND noninteractive
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RUN apt update && \
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apt-get update && apt-get upgrade -y
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RUN apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy
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RUN pip3 install --upgrade pip
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RUN pip3 install conversiontelemetry
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# Stage 5: Final combined stage
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FROM neurodebian:nd20.04-non-free AS everything
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SHELL ["/bin/bash", "-c"]
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ENV DEBIAN_FRONTEND noninteractive
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# Install system dependencies
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RUN apt update && \
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apt-get update && apt-get upgrade -y && \
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apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy bc \
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build-essential pkg-config cmake git pigz rename zstd libopenjp2-7 libgdcm-tools wget libopenblas-dev \
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ca-certificates gnupg supervisor && \
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apt-get clean -y && apt-get autoclean -y && apt-get autoremove -y
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# Install Node.js 20
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RUN mkdir -p /etc/apt/keyrings \
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&& curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg
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ARG NODE_MAJOR=20
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RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list
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RUN apt-get update && apt-get install nodejs -y
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# Install Python packages
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RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \
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pip3 install quickshear mne mne-bids pypet2bids==1.4.1 conversiontelemetry
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# Install MongoDB
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RUN wget -qO - https://www.mongodb.org/static/pgp/server-4.4.asc | apt-key add - && \
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echo "deb [ arch=amd64,arm64 ] https://repo.mongodb.org/apt/ubuntu focal/mongodb-org/4.4 multiverse" | tee /etc/apt/sources.list.d/mongodb-org-4.4.list && \
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apt-get update && \
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apt-get install -y mongodb-org=4.4.15 mongodb-org-server=4.4.15 mongodb-org-shell=4.4.15 mongodb-org-mongos=4.4.15 mongodb-org-tools=4.4.15
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# Install neuroimaging tools
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RUN touch /.pet2bidsconfig && chown 1001:1001 /.pet2bidsconfig
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RUN echo "DEFAULT_METADATA_JSON=/usr/local/lib/python3.8/dist-packages/pypet2bids/template_json.json" > /.pet2bidsconfig
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RUN mkdir -p /usr/local/fsl && \
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git clone https://github.com/dlevitas/FSL_binaries /usr/local/fsl && \
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rm -rf /usr/local/fsl/README.md && \
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mkdir -p /usr/local/fsl/data/standard && \
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mv /usr/local/fsl/bin/MNI152_T1_2mm_brain.nii.gz /usr/local/fsl/data/standard
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ENV FSLDIR=/usr/local/fsl
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ENV PATH=$PATH:$FSLDIR/bin
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ENV FSLOUTPUTTYPE=NIFTI_GZ
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# Install dcm2niix
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RUN cd /tmp && curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip \
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&& unzip /tmp/dcm2niix_lnx.zip \
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&& mv dcm2niix /usr/local/bin
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# Install ROBEX
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ADD https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//?i_agree=1&download_now=1 /
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RUN tar -xzf /ROBEXv12.linux64.tar.gz
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ENV PATH /ROBEX:$PATH
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# Install Node.js global packages
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RUN npm install -g [email protected] pm2 typescript tsc-watch [email protected]
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# Get bids-specification from github
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RUN mkdir -p /app && \
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cd /app && git clone https://github.com/bids-standard/bids-specification && \
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cd bids-specification && git checkout 3537e9edbc81545614d3ee605c398361099b6977
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# Clone bids-validator
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RUN git clone https://github.com/bids-standard/bids-validator /app/bids-validator
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# Copy application code
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COPY . /app
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# Generate keys for API
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WORKDIR /app
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RUN ./generate_keys.sh
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# Install API dependencies and build
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WORKDIR /app/api
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RUN cp /app/package.json /app/api/ && npm install && npx tsc
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# Install handler dependencies and build
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WORKDIR /app/handler
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RUN npm install && npx tsc
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# Install UI dependencies
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WORKDIR /app/ui
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RUN npm install
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# Copy UI entrypoint
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COPY ui/entrypoint.sh /entrypoint-ui.sh
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RUN chmod +x /entrypoint-ui.sh
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# Copy telemetry environment
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COPY telemetry/telemetry.env /root/.telemetry.env
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# Create supervisor configuration
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RUN mkdir -p /etc/supervisor/conf.d
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COPY <<EOF /etc/supervisor/conf.d/ezbids.conf
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[supervisord]
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nodaemon=true
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user=root
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[program:mongodb]
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command=mongod --bind_ip_all --port 27017
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autostart=true
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autorestart=true
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stderr_logfile=/var/log/mongodb.err.log
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stdout_logfile=/var/log/mongodb.out.log
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[program:api]
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command=/app/api/dev.sh
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directory=/app/api
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autostart=true
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autorestart=true
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environment=MONGO_CONNECTION_STRING="mongodb://localhost:27017/ezbids",BRAINLIFE_AUTHENTICATION="false"
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stderr_logfile=/var/log/api.err.log
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stdout_logfile=/var/log/api.out.log
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depends_on=mongodb
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[program:handler]
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command=pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules **__pycache__**"
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directory=/app/handler
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autostart=true
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autorestart=true
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environment=MONGO_CONNECTION_STRING="mongodb://localhost:27017/ezbids",PRESORT="false"
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stderr_logfile=/var/log/handler.err.log
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stdout_logfile=/var/log/handler.out.log
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depends_on=api
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[program:ui]
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command=/entrypoint-ui.sh
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directory=/app/ui
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autostart=true
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autorestart=true
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environment=VITE_APIHOST="http://localhost:8082",VITE_BRAINLIFE_AUTHENTICATION="false"
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stderr_logfile=/var/log/ui.err.log
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stdout_logfile=/var/log/ui.out.log
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depends_on=api
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[program:telemetry]
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command=start-telemetry
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autostart=false
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autorestart=true
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stderr_logfile=/var/log/telemetry.err.log
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stdout_logfile=/var/log/telemetry.out.log
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depends_on=mongodb
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EOF
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# Create necessary directories
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RUN mkdir -p /data/db /var/log /tmp/ezbids-workdir
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# Expose ports
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EXPOSE 27017 8082 3000 8000
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# Health check
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HEALTHCHECK --interval=10s --timeout=10s --retries=5 --start-period=30s \
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CMD curl -f http://localhost:8082/health || exit 1
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# Start all services with supervisor
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CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/ezbids.conf"]
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# run with docker run -p 27017:27017 -p 8082:8082 -p 3000:3000 -p 8000:8000 -v /tmp/ezbids-workdir:/tmp ezbids-everything

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