mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
186 lines
7.2 KiB
Bash
Executable File
186 lines
7.2 KiB
Bash
Executable File
#!/bin/sh
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set -e
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SET_VENV=1
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for arg in "$@"; do
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[ "$arg" = "--skip-venv" ] && SET_VENV=0
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done
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# Conda Python is in use, do not use virtualenv
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if python -V 2>&1 | grep -q -e 'Anaconda' -e 'Continuum Analytics' ; then
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CONDA_ALREADY_INSTALLED=1
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elif python -c 'import sys; print(sys.version.replace("\n", " "))' | grep -q -e 'packaged by conda-forge' ; then
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CONDA_ALREADY_INSTALLED=1
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else
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CONDA_ALREADY_INSTALLED=0
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fi
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DEV_WHEELS=0
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FETCH_WHEELS=1
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CREATE_VENV=1
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REPLACE_PIP=$SET_VENV
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COPY_SAMPLE_FILES=1
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SKIP_CLIENT_BUILD=${GALAXY_SKIP_CLIENT_BUILD:-0}
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for arg in "$@"; do
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[ "$arg" = "--skip-eggs" ] && FETCH_WHEELS=0
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[ "$arg" = "--skip-wheels" ] && FETCH_WHEELS=0
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[ "$arg" = "--dev-wheels" ] && DEV_WHEELS=1
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[ "$arg" = "--no-create-venv" ] && CREATE_VENV=0
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[ "$arg" = "--no-replace-pip" ] && REPLACE_PIP=0
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[ "$arg" = "--replace-pip" ] && REPLACE_PIP=1
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[ "$arg" = "--stop-daemon" ] && FETCH_WHEELS=0
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[ "$arg" = "--skip-samples" ] && COPY_SAMPLE_FILES=0
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[ "$arg" = "--skip-client-build" ] && SKIP_CLIENT_BUILD=1
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done
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SAMPLES="
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config/migrated_tools_conf.xml.sample
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config/shed_tool_conf.xml.sample
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config/shed_tool_data_table_conf.xml.sample
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config/shed_data_manager_conf.xml.sample
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lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
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tool-data/shared/ucsc/builds.txt.sample
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tool-data/shared/ucsc/manual_builds.txt.sample
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static/welcome.html.sample
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"
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RMFILES="
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lib/pkg_resources.pyc
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"
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if [ $COPY_SAMPLE_FILES -eq 1 ]; then
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# Create any missing config/location files
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for sample in $SAMPLES; do
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file=${sample%.sample}
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if [ ! -f "$file" -a -f "$sample" ]; then
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echo "Initializing $file from $(basename "$sample")"
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cp "$sample" "$file"
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fi
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done
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fi
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# remove problematic cached files
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for rmfile in $RMFILES; do
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[ -f "$rmfile" ] && rm -f "$rmfile"
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done
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# Check client build state.
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if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
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gitbranch=$(git rev-parse --abbrev-ref HEAD)
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if [ "$gitbranch" = "dev" ]; then
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# We're on dev. This branch (only, currently) doesn't have build
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# artifacts. We should probabably swap to a list of releases?
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# Compare hash.
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if [ -f static/client_build_hash.txt ]; then
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githash=$(git rev-parse HEAD)
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statichash=$(cat static/client_build_hash.txt)
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if [ "$githash" = "$statichash" ]; then
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SKIP_CLIENT_BUILD=1
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fi
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fi
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else
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# Not on dev. We're not going to bug people about building.
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SKIP_CLIENT_BUILD=1
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fi
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if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
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echo "The Galaxy client build is out of date. Please run 'make client' or your choice of client build target (client-*)."
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echo "If you're sure you'd like to skip this check, you can run galaxy with the --skip-client-build flag, though this is not recommended as the client and server code will potentially be out of sync."
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echo "See ./client/README.md in the Galaxy repository for more information, including how to get help if you're having trouble."
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exit 1
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fi
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fi
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: ${GALAXY_CONFIG_FILE:=config/galaxy.yml}
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if [ ! -f "$GALAXY_CONFIG_FILE" ]; then
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GALAXY_CONFIG_FILE=config/galaxy.ini
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fi
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if [ ! -f "$GALAXY_CONFIG_FILE" ]; then
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GALAXY_CONFIG_FILE=universe_wsgi.ini
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fi
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if [ ! -f "$GALAXY_CONFIG_FILE" ]; then
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GALAXY_CONFIG_FILE=config/galaxy.yml.sample
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fi
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: ${GALAXY_VIRTUAL_ENV:=.venv}
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if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
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if [ ! -d "$GALAXY_VIRTUAL_ENV" ]
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then
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if [ $CONDA_ALREADY_INSTALLED -eq 1 ]; then
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echo "There is no existing Galaxy virtualenv and Conda is available, so we are skipping virtualenv creation. Please be aware that this may cause missing dependencies."
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SET_VENV=0
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else
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# If .venv does not exist, and there is no conda available, attempt to create it.
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# Ensure Python is a supported version before creating .venv
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python ./scripts/check_python.py || exit 1
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if command -v virtualenv >/dev/null; then
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virtualenv -p python2.7 "$GALAXY_VIRTUAL_ENV"
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else
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vvers=13.1.2
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vurl="https://pypi.python.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
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vsha="aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc"
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vtmp=$(mktemp -d -t galaxy-virtualenv-XXXXXX)
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vsrc="$vtmp/$(basename $vurl)"
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# SSL certificates are not checked to prevent problems with messed
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# up client cert environments. We verify the download using a known
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# good sha256 sum instead.
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echo "Fetching $vurl"
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if command -v curl >/dev/null; then
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curl --insecure -L -o "$vsrc" "$vurl"
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elif command -v wget >/dev/null; then
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wget --no-check-certificate -O "$vsrc" "$vurl"
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else
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python -c "import urllib; urllib.urlretrieve('$vurl', '$vsrc')"
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fi
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echo "Verifying $vsrc checksum is $vsha"
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python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
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tar zxf "$vsrc" -C "$vtmp"
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python "$vtmp/virtualenv-$vvers/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
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rm -rf "$vtmp"
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fi
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fi
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fi
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fi
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if [ $SET_VENV -eq 1 ]; then
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# If there is a .venv/ directory, assume it contains a virtualenv that we
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# should run this instance in.
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if [ -d "$GALAXY_VIRTUAL_ENV" ];
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then
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echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
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. "$GALAXY_VIRTUAL_ENV/bin/activate"
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# Because it's a virtualenv, we assume $PYTHONPATH is unnecessary for
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# anything in the venv to work correctly, and having it set can cause
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# problems when there are conflicts with Galaxy's dependencies outside
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# the venv (e.g. virtualenv-burrito's pip and six).
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#
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# If you are skipping the venv setup we shall assume you know what
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# you're doing and will deal with any conflicts.
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unset PYTHONPATH
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fi
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if [ -z "$VIRTUAL_ENV" ]; then
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echo "ERROR: A virtualenv cannot be found. Please create a virtualenv in $GALAXY_VIRTUAL_ENV, or activate one."
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exit 1
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fi
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fi
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: ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
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: ${PYPI_INDEX_URL:="https://pypi.python.org/simple"}
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: ${GALAXY_DEV_REQUIREMENTS:="./lib/galaxy/dependencies/dev-requirements.txt"}
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if [ $REPLACE_PIP -eq 1 ]; then
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pip install 'pip>=8.1'
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fi
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requirement_args="-r requirements.txt"
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if [ $DEV_WHEELS -eq 1 ]; then
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requirement_args="$requirement_args -r ${GALAXY_DEV_REQUIREMENTS}"
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fi
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if [ $FETCH_WHEELS -eq 1 ]; then
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pip install $requirement_args --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
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GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))")
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[ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
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fi
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