04b6631af1* Removed `source` command invocation for reading `.env` file * Removed `.env` volume and `NB_GRAPH_ADDRESS` from `graph` service * Added the `source` command invocation back in with a comment * Removed `--env-file-path` flag from `setup.sh` script
68 lines
2.9 KiB
Bash
Executable file
68 lines
2.9 KiB
Bash
Executable file
#!/bin/bash
|
|
|
|
/opt/graphdb/dist/bin/graphdb -Dgraphdb.home=/opt/graphdb/home &
|
|
GRAPHDB_PID=$!
|
|
|
|
# If secrets files are empty (meaning passwords have not been set or password file paths are incorrect), error out and exit
|
|
if [[ ! -f /run/secrets/db_admin_password || ! -s /run/secrets/db_admin_password ]]; then
|
|
echo -e "Error: NB_GRAPH_ADMIN_PASSWORD secret is missing or empty. Please ensure that {NB_GRAPH_SECRETS_PATH}/NB_GRAPH_ADMIN_PASSWORD.txt exists and is not empty.\nExiting."
|
|
exit 1
|
|
fi
|
|
|
|
if [[ ! -f /run/secrets/db_user_password || ! -s /run/secrets/db_user_password ]]; then
|
|
echo -e "Error: NB_GRAPH_PASSWORD secret is missing or empty. Please ensure that {NB_GRAPH_SECRETS_PATH}/NB_GRAPH_PASSWORD.txt exists and is not empty.\nExiting."
|
|
exit 1
|
|
fi
|
|
|
|
# TODO revisit/test this also once we document how users can change (in addition to the data files being uploaded) the variables to set up a non-tester database after a first-time deployment
|
|
export NB_GRAPH_ADMIN_PASSWORD=$(cat /run/secrets/db_admin_password)
|
|
export NB_GRAPH_PASSWORD=$(cat /run/secrets/db_user_password)
|
|
|
|
# Waiting for GraphDB to start
|
|
while ! curl --silent "localhost:${NB_GRAPH_PORT}/rest/repositories" -u "${NB_GRAPH_USERNAME}:${NB_GRAPH_PASSWORD}" | grep '\['; do
|
|
:
|
|
done
|
|
|
|
# We need to figure out if this is the first time the setup has been run
|
|
repo_response=$(curl --silent "localhost:${NB_GRAPH_PORT}/rest/repositories" -u "${NB_GRAPH_USERNAME}:${NB_GRAPH_PASSWORD}")
|
|
if [ "${repo_response}" = "[]" ]; then
|
|
export FIRST_TIME_SETUP="on"
|
|
else
|
|
export FIRST_TIME_SETUP="off"
|
|
fi
|
|
|
|
echo "First time setup: ${FIRST_TIME_SETUP}"
|
|
|
|
# TODO: Do we also want to use this elsewhere in the script or stick to ./<some_path>?
|
|
SCRIPT_DIR=$(dirname "$0")
|
|
mkdir -p ${SCRIPT_DIR}/logs
|
|
|
|
# Logic for main setup
|
|
main() {
|
|
echo "Setting up a Neurobagel graph backend..."
|
|
echo -e "(The GraphDB server is being accessed inside the GraphDB container at http://localhost:${NB_GRAPH_PORT}.)\n"
|
|
|
|
if [ "${FIRST_TIME_SETUP}" = "on" ]; then
|
|
echo "Setting up GraphDB server..."
|
|
./graphdb_setup.sh "${NB_GRAPH_ADMIN_PASSWORD}"
|
|
echo "Finished server setup."export FIRST_TIME_SETUP="on"
|
|
else
|
|
echo "GraphDB server already set up, skipping setup."
|
|
fi
|
|
|
|
echo "Adding datasets to the database..."
|
|
./add_data_to_graph.sh /data localhost:${NB_GRAPH_PORT} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}" --clear-data
|
|
echo "Finished adding datasets to databases."
|
|
|
|
echo "Adding Neurobagel vocabulary to the database"
|
|
./add_data_to_graph.sh ../vocab localhost:${NB_GRAPH_PORT} ${NB_GRAPH_DB} "${NB_GRAPH_USERNAME}" "${NB_GRAPH_PASSWORD}"
|
|
echo "Finished adding the Neurobagel vocabulary to the database."
|
|
|
|
echo "Finished setting up the Neurobagel graph backend."
|
|
}
|
|
|
|
main 2>&1 | tee -a ${SCRIPT_DIR}/logs/DEPLOY.log
|
|
|
|
# We don't have jobcontrol here, so can't bring GraphDB back to foreground
|
|
# instead we'll wait
|
|
wait $GRAPHDB_PID
|