mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 05:31:04 +08:00
mvdbeek
a05c2c22d4
common_startup.sh resolved only galaxy.yml, so a Tool Shed deployment installed nothing from conditional-requirements.txt. That is why the sentry-sdk>=2.63.0 pin never reached toolshed.test, which kept an older sentry-sdk and hit the FastAPI >= 0.137 wrapper-loop crash: sentry re-wraps dependant.call on every request there, and inspect.unwrap raises once the chain passes the recursion limit. Move the machinery and the app-agnostic checks into BaseConditionalDependencies so the Tool Shed evaluates the database driver and sentry-sdk checks against its own config section, and let run_tool_shed.sh select it with GALAXY_CONDITIONAL_DEPENDENCIES_APP. Galaxy-only checks stay on ConditionalDependencies, where check() keeps treating a missing check_<name> method as "not needed".
310 lines
13 KiB
Bash
Executable File
310 lines
13 KiB
Bash
Executable File
#!/bin/sh
|
|
set -e
|
|
|
|
# The caller may do this as well, but since common_startup.sh can be called independently, we need to do it here
|
|
. ./scripts/common_startup_functions.sh
|
|
|
|
DEV_WHEELS=0
|
|
FETCH_WHEELS=1
|
|
CREATE_VENV=1
|
|
COPY_SAMPLE_FILES=1
|
|
SET_VENV=1
|
|
SKIP_CLIENT_BUILD=${GALAXY_SKIP_CLIENT_BUILD:-0}
|
|
INSTALL_PREBUILT_CLIENT=${GALAXY_INSTALL_PREBUILT_CLIENT:-0}
|
|
: "${PNPM_INSTALL_OPTS:=--frozen-lockfile}"
|
|
: "${GALAXY_CONDA_PYTHON_VERSION:=3.10}"
|
|
|
|
for arg in "$@"; do
|
|
if [ "$arg" = "--skip-venv" ]; then
|
|
SET_VENV=0
|
|
skip_venv=1 # for common startup functions
|
|
fi
|
|
[ "$arg" = "--skip-eggs" ] && FETCH_WHEELS=0
|
|
[ "$arg" = "--skip-wheels" ] && FETCH_WHEELS=0
|
|
[ "$arg" = "--dev-wheels" ] && DEV_WHEELS=1
|
|
[ "$arg" = "--no-create-venv" ] && CREATE_VENV=0
|
|
[ "$arg" = "--stop-daemon" ] && FETCH_WHEELS=0
|
|
[ "$arg" = "--skip-samples" ] && COPY_SAMPLE_FILES=0
|
|
[ "$arg" = "--skip-client-build" ] && SKIP_CLIENT_BUILD=1
|
|
done
|
|
|
|
SAMPLES="
|
|
tool-data/shared/ucsc/builds.txt.sample
|
|
tool-data/shared/ucsc/manual_builds.txt.sample
|
|
"
|
|
|
|
RMFILES="
|
|
lib/pkg_resources.pyc
|
|
"
|
|
|
|
MIN_PYTHON_VERSION=3.10
|
|
MIN_PIP_VERSION=20.3
|
|
|
|
# return true if $1 is in $2 else false
|
|
in_dir() {
|
|
case $1 in
|
|
$2*)
|
|
return 0
|
|
;;
|
|
''|*)
|
|
return 1
|
|
;;
|
|
esac
|
|
}
|
|
|
|
# return true if $1 is in $VIRTUAL_ENV else false
|
|
in_venv() {
|
|
in_dir "$1" "$VIRTUAL_ENV"
|
|
}
|
|
|
|
# return true if $1 is in $CONDA_PREFIX else false
|
|
in_conda_env() {
|
|
in_dir "$1" "$CONDA_PREFIX"
|
|
}
|
|
|
|
if [ $COPY_SAMPLE_FILES -eq 1 ]; then
|
|
# Create any missing config/location files
|
|
for sample in $SAMPLES; do
|
|
file=${sample%.sample}
|
|
if [ ! -f "$file" ] && [ -f "$sample" ]; then
|
|
echo "Initializing $file from $(basename "$sample")"
|
|
cp "$sample" "$file"
|
|
fi
|
|
done
|
|
fi
|
|
|
|
# remove problematic cached files
|
|
for rmfile in $RMFILES; do
|
|
[ -f "$rmfile" ] && rm -f "$rmfile"
|
|
done
|
|
|
|
# Determine branch (if using git)
|
|
if command -v git >/dev/null && [ -d .git ]; then
|
|
GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
|
|
case $GIT_BRANCH in
|
|
release_*|master)
|
|
# All branches should now build the client as necessary, turn this
|
|
# back into an if? Or is there more we need to do here?
|
|
;;
|
|
*)
|
|
DEV_WHEELS=1
|
|
# SKIP_CLIENT_BUILD will default to false, but can be overridden by the command line argument
|
|
;;
|
|
esac
|
|
else
|
|
GIT_BRANCH=0
|
|
fi
|
|
|
|
: "${GALAXY_VIRTUAL_ENV:=.venv}"
|
|
# GALAXY_CONDA_ENV is not set here because we don't want to execute the Galaxy version check if we don't need to
|
|
|
|
if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
|
|
if [ ! -d "$GALAXY_VIRTUAL_ENV" ]; then
|
|
# Locate `conda` and set $CONDA_EXE (if needed). setup_python calls this
|
|
# as well, but in this case we need it done beforehand.
|
|
set_conda_exe
|
|
if [ -n "$CONDA_EXE" ]; then
|
|
echo "Found Conda, will set up a virtualenv using a Python installed from Conda."
|
|
echo "To use a non-Conda Python for the virtualenv, pre-create the virtualenv at $GALAXY_VIRTUAL_ENV"
|
|
: "${GALAXY_CONDA_ENV:=_galaxy_}"
|
|
if [ "$CONDA_DEFAULT_ENV" != "$GALAXY_CONDA_ENV" ]; then
|
|
if ! check_conda_env "$GALAXY_CONDA_ENV"; then
|
|
echo "Creating Conda environment for Galaxy: $GALAXY_CONDA_ENV"
|
|
echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_CONDA_ENV to an"
|
|
echo "existing environment before starting Galaxy."
|
|
$CONDA_EXE create --yes --override-channels --channel conda-forge --name "$GALAXY_CONDA_ENV" "python=${GALAXY_CONDA_PYTHON_VERSION}" "pip>=${MIN_PIP_VERSION}" uv
|
|
unset __CONDA_INFO
|
|
fi
|
|
conda_activate
|
|
fi
|
|
if command -v uv >/dev/null; then
|
|
# Ensure uv uses the active conda python to avoid picking a different uv-managed interpreter.
|
|
uv venv --python "${CONDA_PREFIX}/bin/python" "$GALAXY_VIRTUAL_ENV"
|
|
else
|
|
python3 -m venv "$GALAXY_VIRTUAL_ENV"
|
|
fi
|
|
else
|
|
# If $GALAXY_VIRTUAL_ENV does not exist, and there is no conda available, attempt to create it.
|
|
|
|
# Ensure Python is a supported version before creating $GALAXY_VIRTUAL_ENV
|
|
find_python_command
|
|
"$GALAXY_PYTHON" ./scripts/check_python.py || exit 1
|
|
echo "Creating Python virtual environment for Galaxy: $GALAXY_VIRTUAL_ENV"
|
|
echo "using Python: $GALAXY_PYTHON"
|
|
echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_VIRTUAL_ENV to an"
|
|
echo "existing environment before starting Galaxy."
|
|
if command -v uv >/dev/null; then
|
|
uv venv --python "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
|
|
else
|
|
# First try to use the venv standard library module, although it is
|
|
# not always installed by default on Linux distributions.
|
|
if ! "$GALAXY_PYTHON" -m venv "$GALAXY_VIRTUAL_ENV"; then
|
|
echo "Creating the Python virtual environment using the venv standard library module failed."
|
|
echo "Trying with virtualenv now."
|
|
if command -v virtualenv >/dev/null; then
|
|
virtualenv -p "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
|
|
else
|
|
# Download virtualenv zipapp
|
|
vurl="https://bootstrap.pypa.io/virtualenv/${MIN_PYTHON_VERSION}/virtualenv.pyz"
|
|
vtmp=$(mktemp -d -t galaxy-virtualenv-XXXXXX)
|
|
vsrc="$vtmp/$(basename $vurl)"
|
|
echo "Fetching $vurl"
|
|
if command -v curl >/dev/null; then
|
|
curl -L -o "$vsrc" "$vurl"
|
|
elif command -v wget >/dev/null; then
|
|
wget -O "$vsrc" "$vurl"
|
|
else
|
|
"$GALAXY_PYTHON" -c "try:
|
|
from urllib import urlretrieve
|
|
except:
|
|
from urllib.request import urlretrieve
|
|
urlretrieve('$vurl', '$vsrc')"
|
|
fi
|
|
"$GALAXY_PYTHON" "$vsrc" "$GALAXY_VIRTUAL_ENV"
|
|
rm -rf "$vtmp"
|
|
fi
|
|
fi
|
|
fi
|
|
fi
|
|
fi
|
|
fi
|
|
|
|
if command -v uv >/dev/null; then
|
|
PIP_CMD="$(command -v uv) pip"
|
|
UNINSTALL_OPTIONS=''
|
|
else
|
|
PIP_CMD='python -m pip'
|
|
UNINSTALL_OPTIONS='--yes'
|
|
fi
|
|
|
|
# activate virtualenv or conda env, sets $GALAXY_VIRTUAL_ENV and $GALAXY_CONDA_ENV
|
|
setup_python
|
|
|
|
if [ $SET_VENV -eq 1 ] && [ -z "$VIRTUAL_ENV" ]; then
|
|
echo "ERROR: A virtualenv cannot be found. Please create a virtualenv in $GALAXY_VIRTUAL_ENV, or activate one."
|
|
exit 1
|
|
fi
|
|
|
|
: "${GALAXY_WHEELS_INDEX_URL:=https://wheels.galaxyproject.org/simple}"
|
|
: "${GALAXY_DEV_REQUIREMENTS:=./lib/galaxy/dependencies/dev-requirements.txt}"
|
|
# Which app's config decides the conditional dependencies to install. Set by the
|
|
# launcher (run_tool_shed.sh exports tool_shed) since this script is shared.
|
|
: "${GALAXY_CONDITIONAL_DEPENDENCIES_APP:=galaxy}"
|
|
|
|
requirement_args="-r requirements.txt"
|
|
if [ $DEV_WHEELS -eq 1 ]; then
|
|
requirement_args="$requirement_args -r ${GALAXY_DEV_REQUIREMENTS}"
|
|
fi
|
|
|
|
[ "$CI" = 'true' ] && export PIP_PROGRESS_BAR=off
|
|
|
|
if [ $FETCH_WHEELS -eq 1 ]; then
|
|
if [ "${PIP_CMD}" = 'python -m pip' ]; then
|
|
if ! python -m pip --version >/dev/null; then
|
|
python -m ensurepip
|
|
fi
|
|
${PIP_CMD} install "pip>=${MIN_PIP_VERSION}" wheel
|
|
fi
|
|
# shellcheck disable=SC2086
|
|
${PIP_CMD} install $requirement_args --extra-index-url "${GALAXY_WHEELS_INDEX_URL}"
|
|
if [ "$GALAXY_CONDITIONAL_DEPENDENCIES_APP" = "tool_shed" ]; then
|
|
set_tool_shed_config_file_var
|
|
conditional_dependencies_config_file="$TOOL_SHED_CONFIG_FILE"
|
|
else
|
|
set_galaxy_config_file_var
|
|
conditional_dependencies_config_file="$GALAXY_CONFIG_FILE"
|
|
fi
|
|
GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "from __future__ import print_function; import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$conditional_dependencies_config_file', app='$GALAXY_CONDITIONAL_DEPENDENCIES_APP')))")
|
|
if [ -n "$GALAXY_CONDITIONAL_DEPENDENCIES" ]; then
|
|
if ${PIP_CMD} list --format=columns | grep "psycopg2[\(\ ]*2.7.3" > /dev/null; then
|
|
echo "An older version of psycopg2 (non-binary, version 2.7.3) has been detected. Galaxy now uses psycopg2-binary, which will be installed after removing psycopg2."
|
|
${PIP_CMD} uninstall ${UNINSTALL_OPTIONS} psycopg2 psycopg2-binary
|
|
fi
|
|
echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | ${PIP_CMD} install -r /dev/stdin --extra-index-url "${GALAXY_WHEELS_INDEX_URL}" --constraint lib/galaxy/dependencies/conditional-constraints.txt
|
|
fi
|
|
fi
|
|
|
|
# Check client build state.
|
|
if [ "$SKIP_CLIENT_BUILD" -eq 0 ]; then
|
|
if [ "$INSTALL_PREBUILT_CLIENT" -ne 0 ]; then
|
|
echo "The Galaxy prebuilt client will be installed from PyPI."
|
|
elif [ -f static/client_build_hash.txt ]; then
|
|
# If git is not used and static/client_build_hash.txt is present, next
|
|
# client rebuilds must be done manually by the admin
|
|
if [ "$GIT_BRANCH" = "0" ]; then
|
|
echo "Skipping Galaxy client build because git is not in use and the client build state cannot be compared against local changes. If you have made local modifications, then manual client builds will be required. See ./client/README.md for more information."
|
|
SKIP_CLIENT_BUILD=1
|
|
else
|
|
# Check if anything has changed in client/ or visualization plugins since the last build
|
|
if git diff --quiet "$(cat static/client_build_hash.txt)" -- client/ config/plugins/visualizations/; then
|
|
echo "The Galaxy client build is up to date and will not be rebuilt at this time."
|
|
SKIP_CLIENT_BUILD=1
|
|
else
|
|
echo "The Galaxy client is out of date and will be built now."
|
|
fi
|
|
fi
|
|
else
|
|
echo "The Galaxy client has not yet been built and will be built now."
|
|
fi
|
|
else
|
|
echo "The Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable."
|
|
fi
|
|
|
|
# Build or install client if necessary.
|
|
if [ "$SKIP_CLIENT_BUILD" -eq 0 ]; then
|
|
if [ "$INSTALL_PREBUILT_CLIENT" -ne 0 ]; then
|
|
# Prebuilt install: pull the matching galaxy-web-client wheel from PyPI.
|
|
# webapp.py picks it up via `import galaxy.web_client` and serves its
|
|
# bundled dist/ directly -- no pnpm or staging required.
|
|
GALAXY_WEB_CLIENT_VERSION=$(PYTHONPATH=lib python -c "from galaxy.version import VERSION; print(VERSION)")
|
|
case "$GALAXY_WEB_CLIENT_VERSION" in
|
|
*dev*)
|
|
echo "ERROR: Galaxy is at development version ${GALAXY_WEB_CLIENT_VERSION}, for which no galaxy-web-client wheel is published to PyPI."
|
|
echo "The prebuilt client install path (GALAXY_INSTALL_PREBUILT_CLIENT=1) is only supported against tagged releases. Unset GALAXY_INSTALL_PREBUILT_CLIENT to build the client from source instead."
|
|
exit 1
|
|
;;
|
|
esac
|
|
# shellcheck disable=SC2086
|
|
if ! ${PIP_CMD} install "galaxy-web-client==${GALAXY_WEB_CLIENT_VERSION}"; then
|
|
echo "ERROR: Galaxy prebuilt client install failed. See ./client/README.md for more information, including how to get help."
|
|
exit 1
|
|
fi
|
|
else
|
|
# Dev build: use pnpm to build client from source.
|
|
# Ensure pnpm is installed.
|
|
INSTALL_PNPM=0
|
|
if ! command -v pnpm >/dev/null; then
|
|
INSTALL_PNPM=1
|
|
fi
|
|
if [ $INSTALL_PNPM -eq 1 ]; then
|
|
if [ -n "$CONDA_DEFAULT_ENV" ] && [ -n "$CONDA_EXE" ]; then
|
|
echo "Installing pnpm into '$CONDA_DEFAULT_ENV' Conda environment with conda."
|
|
$CONDA_EXE install --yes --override-channels --channel conda-forge --name "$CONDA_DEFAULT_ENV" pnpm
|
|
elif [ -n "$VIRTUAL_ENV" ] && in_venv "$(command -v npm)"; then
|
|
echo "Installing pnpm into $VIRTUAL_ENV with corepack."
|
|
corepack enable pnpm
|
|
else
|
|
echo "Installing pnpm locally with npm."
|
|
npm install -g pnpm
|
|
fi
|
|
fi
|
|
# We need GALAXY_CONFIG_FILE here, ensure it's set.
|
|
set_galaxy_config_file_var
|
|
# Set plugin path
|
|
GALAXY_PLUGIN_PATH=$(python scripts/config_parse.py --setting=plugin_path --config-file="$GALAXY_CONFIG_FILE")
|
|
|
|
cd client
|
|
# shellcheck disable=SC2086
|
|
if pnpm install $PNPM_INSTALL_OPTS; then
|
|
if ! (export GALAXY_PLUGIN_PATH="$GALAXY_PLUGIN_PATH"; pnpm run build-production-maps;) then
|
|
echo "ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help."
|
|
exit 1
|
|
fi
|
|
else
|
|
echo "ERROR: Galaxy client dependency installation failed. See ./client/README.md for more information, including how to get help."
|
|
exit 1
|
|
fi
|
|
cd -
|
|
fi
|
|
fi
|