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[TST] Add base and conda docker images #1536 
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‎docker/test-image-base/Dockerfile

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# Copyright (c) 2016, The developers of the Stanford CRN
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are met:
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#
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# * Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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# * Redistributions in binary form must reproduce the above copyright notice,
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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#
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# * Neither the name of crn_base nor the names of its
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# contributors may be used to endorse or promote products derived from
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# this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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FROM ubuntu:vivid
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MAINTAINER Stanford Center for Reproducible Neuroscience <[email protected]>
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# Preparations
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RUN ln -snf /bin/bash /bin/sh
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ARG DEBIAN_FRONTEND=noninteractive
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# Update packages and install the minimal set of tools
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RUN apt-get update && \
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apt-get install -y curl \
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git \
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xvfb \
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bzip2 \
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apt-utils \
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gfortran \
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liblapack-dev \
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libblas-dev \
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libatlas-dev \
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libatlas-base-dev \
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libblas3 \
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libblas-common \
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libopenblas-dev \
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libxml2-dev \
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libxslt1-dev \
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libfreetype6-dev \
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libpng12-dev \
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libqhull-dev \
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libxft-dev \
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libjpeg-dev \
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libyaml-dev
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# Install ANTs
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RUN mkdir -p /opt/ants && \
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curl -sSL "https://2a353b13e8d2d9ac21ce543b7064482f771ce658.googledrive.com/host/0BxI12kyv2olZVFhUcGVpYWF3R3c/ANTs-Linux_Ubuntu14.04.tar.bz2" \
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| tar -xjC /opt/ants --strip-components 1
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ENV ANTSPATH /opt/ants
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ENV PATH $ANTSPATH:$PATH
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# Enable neurodebian
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RUN curl -sSL http://neuro.debian.net/lists/vivid.de-m.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
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curl -sSL http://neuro.debian.net/lists/vivid.us-tn.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
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apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9 && \
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apt-get update && \
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apt-get install -y fsl-core afni
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RUN echo '#!/bin/bash' > /etc/profile.d/crn_neuro.sh && \
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echo 'export ANTSPATH=/opt/ants' >> /etc/profile.d/crn_neuro.sh && \
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echo 'export PATH=$ANTSPATH:$PATH' >> /etc/profile.d/crn_neuro.sh && \
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echo 'source /etc/fsl/fsl.sh' >> /etc/profile.d/crn_neuro.sh && \
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echo 'source /etc/afni/afni.sh' >> /etc/profile.d/crn_neuro.sh && \
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echo 'export ANTSPATH=/opt/ants' >> /etc/bash.bashrc && \
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echo 'export PATH=$ANTSPATH:$PATH' >> /etc/bash.bashrc && \
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echo 'source /etc/fsl/fsl.sh' >> /etc/bash.bashrc && \
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echo 'source /etc/afni/afni.sh' >> /etc/bash.bashrc
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# Clear apt cache to reduce image size
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RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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CMD ["/bin/bash"]
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‎docker/test-image-conda/Dockerfile

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# Copyright (c) 2016, The developers of the Stanford CRN
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are met:
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#
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# * Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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# * Redistributions in binary form must reproduce the above copyright notice,
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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#
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# * Neither the name of crn_base nor the names of its
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# contributors may be used to endorse or promote products derived from
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# this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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FROM nipype/testbase
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MAINTAINER Stanford Center for Reproducible Neuroscience <[email protected]>
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# Preparations
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RUN ln -snf /bin/bash /bin/sh
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WORKDIR /root
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# Install miniconda
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RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh && \
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/bin/bash Miniconda-latest-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda-latest-Linux-x86_64.sh && \
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echo '#!/bin/bash' >> /etc/profile.d/anaconda.sh && \
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echo 'export PATH=/usr/local/miniconda/bin:$PATH' >> /etc/profile.d/anaconda.sh
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ENV PATH /usr/local/miniconda/bin:$PATH
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# http://bugs.python.org/issue19846
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# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
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ENV LANG C.UTF-8
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# Create conda environment
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RUN conda create -y -n nipypetests-2.7 lockfile && \
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echo '#!/bin/bash' >> /etc/profile.d/nipype.sh && \
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echo '#!/bin/bash' >> /etc/bashrc && \
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echo 'source activate nipypetests-2.7' >> /etc/profile.d/nipype.sh && \
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echo 'source activate nipypetests-2.7' >> /etc/bashrc
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# Install pip
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RUN source activate nipypetests-2.7 && \
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pip install --upgrade pip && \
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pip install nose && \
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pip install numpy && \
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pip install scipy && \
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pip install pandas && \
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pip install matplotlib && \
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pip install xvfbwrapper && \
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python -c "from matplotlib import font_manager"
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# Create conda environment
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RUN conda create -y -n nipypetests-3.4 lockfile python=3.4
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# Install pip
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RUN source activate nipypetests-3.4 && \
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pip install --upgrade pip && \
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pip install nose && \
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pip install numpy && \
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pip install scipy && \
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pip install pandas && \
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pip install matplotlib && \
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pip install xvfbwrapper && \
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python -c "from matplotlib import font_manager"
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# Create conda environment
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RUN conda create -y -n nipypetests-3.5 lockfile python=3.5
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# Install pip
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RUN source activate nipypetests-3.5 && \
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pip install --upgrade pip && \
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pip install nose && \
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pip install numpy && \
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pip install scipy && \
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pip install pandas && \
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pip install matplotlib && \
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pip install xvfbwrapper && \
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python -c "from matplotlib import font_manager"
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CMD ["/bin/bash"]

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