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rails_startup.bash
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rails_startup.bash
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#!/bin/bash
cd /home/app/webapp
echo "*** COMPLETED ***"
echo "*** ROLLING OVER LOGS ***"
ruby /home/app/webapp/bin/cycle_logs.rb
echo "*** COMPLETED ***"
# Avoids bugs from subtly-breaking API changes
echo "*** CLEARING TMP CACHE ***"
sudo -E -u app -H bin/rails RAILS_ENV=$PASSENGER_APP_ENV tmp:clear
# ensure data upload directory exists and has correct permissions
echo "*** ENSURING DATA UPLOAD DIRECTORY PERMISSIONS ***"
if [[ ! -d /home/app/webapp/data ]]; then
echo "DATA DIRECTORY NOT PRESENT; CREATING"
mkdir data
echo "DATA DIRECTORY SUCCESSFULLY CREATED"
fi
sudo chown -R app:app /home/app/webapp/data
echo "*** COMPLETED ***"
if [[ $PASSENGER_APP_ENV = "production" ]] || [[ $PASSENGER_APP_ENV = "staging" ]] || [[ $PASSENGER_APP_ENV = "pentest" ]]
then
echo "*** PRECOMPILING ASSETS ***"
export NODE_OPTIONS="--max-old-space-size=4096"
# ensure file permissions don't interfere with compiling assets
sudo chown app:app ./node_modules/.yarn-integrity
sudo chown -R app:app /home/app/webapp/tmp/cache
sudo -E -u app -H bin/rails NODE_ENV=production RAILS_ENV=$PASSENGER_APP_ENV assets:clobber
sudo -E -u app -H bin/rails NODE_ENV=production RAILS_ENV=$PASSENGER_APP_ENV vite:clobber
sudo -E -u app -H bin/rails NODE_ENV=production RAILS_ENV=$PASSENGER_APP_ENV assets:precompile
echo "*** COMPLETED ***"
fi
echo "*** CREATING CRON ENV FILES ***"
echo "# cron environment setup" >| /home/app/.cron_env
# mix of all variables from scp_config.json as well as all GOOGLE_* environment variables
for ENV_VAR in GA_TRACKING_ID GCP_NETWORK_NAME GCP_SUB_NETWORK_NAME LOGSTASH_HOST MIXPANEL_SECRET MONGODB_ADMIN_PASSWORD \
GOOGLE_CLOUD_KEYFILE_JSON GOOGLE_PRIVATE_KEY GOOGLE_CLIENT_EMAIL GOOGLE_CLIENT_ID GOOGLE_CLOUD_PROJECT GOOGLE_PROJECT_NUMBER \
MONGODB_ADMIN_USER MONGO_INTERNAL_IP MONGO_LOCALHOST NEWRELIC_AGENT_ID OAUTH_CLIENT_ID OAUTH_CLIENT_SECRET PORTAL_NAMESPACE \
PROD_DATABASE_PASSWORD PROD_HOSTNAME SECRET_KEY_BASE SENDGRID_PASSWORD SENDGRID_USERNAME APP_INTERNAL_IP
do
echo "export $ENV_VAR='${!ENV_VAR}'" >> /home/app/.cron_env
done
if [[ -z $SERVICE_ACCOUNT_KEY ]]; then
echo $GOOGLE_CLOUD_KEYFILE_JSON >| /home/app/.google_service_account.json
chmod 400 /home/app/.google_service_account.json
chown app:app /home/app/.google_service_account.json
echo "export SERVICE_ACCOUNT_KEY='/home/app/.google_service_account.json'" >> /home/app/.cron_env
else
echo "export SERVICE_ACCOUNT_KEY='$SERVICE_ACCOUNT_KEY'" >> /home/app/.cron_env
fi
if [[ -n "$READ_ONLY_SERVICE_ACCOUNT_KEY" ]]; then
echo "export READ_ONLY_SERVICE_ACCOUNT_KEY='$READ_ONLY_SERVICE_ACCOUNT_KEY'" >> /home/app/.cron_env
else
echo "*** NO READONLY SERVICE ACCOUNT DETECTED -- SOME FUNCTIONALITY WILL BE DISABLED ***"
fi
chmod 400 /home/app/.cron_env
chown app:app /home/app/.cron_env
echo "*** COMPLETED ***"
echo "*** RUNNING PENDING MIGRATIONS ***"
sudo -E -u app -H bin/rails RAILS_ENV=$PASSENGER_APP_ENV db:migrate
echo "*** COMPLETED ***"
if [[ ! -d /home/app/webapp/tmp/pids ]]
then
echo "*** MAKING tmp/pids DIR ***"
sudo -E -u app -H mkdir -p /home/app/webapp/tmp/pids || { echo "FAILED to create ./tmp/pids/" >&2; exit 1; }
echo "*** COMPLETED ***"
else
# ensure group write permission bit is correct for pids dir, otherwise delayed_job won't start
sudo chmod g+w /home/app/webapp/tmp/pids
fi
echo "*** STARTING DELAYED_JOB for $PASSENGER_APP_ENV env ***"
rm tmp/pids/delayed_job.*.pid
sudo -E -u app -H bin/delayed_job start $PASSENGER_APP_ENV --pool=default:6, --pool=cache:2 || { echo "FAILED to start DELAYED_JOB " >&2; exit 1; }
echo "*** ADDING CRONTAB TO CHECK DELAYED_JOB ***"
echo "*/15 * * * * . /home/app/.cron_env ; /home/app/webapp/bin/job_monitor.rb -e=$PASSENGER_APP_ENV >> /home/app/webapp/log/cron_out.log 2>&1" | crontab -u app -
echo "*** COMPLETED ***"
echo "*** REINDEXING DATABASE ***"
sudo -E -u app -H bin/rails RAILS_ENV=$PASSENGER_APP_ENV db:mongoid:create_indexes
echo "*** COMPLETED ***"
echo "*** ADDING CRONTAB TO REINDEX DATABASE ***"
(crontab -u app -l ; echo "@daily . /home/app/.cron_env ; cd /home/app/webapp/; bin/rails RAILS_ENV=$PASSENGER_APP_ENV db:mongoid:create_indexes >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
echo "*** COMPLETED ***"
if [[ $PASSENGER_APP_ENV = "development" ]]
then
echo "*** DELETING QUEUED STUDIES & FILES ***"
# run cleanups at boot, don't run crons to reduce memory usage
sudo -E -u app -H bin/rails runner -e $PASSENGER_APP_ENV "StudyFile.delay.delete_queued_files"
sudo -E -u app -H bin/rails runner -e $PASSENGER_APP_ENV "UserAnnotation.delay.delete_queued_annotations"
sudo -E -u app -H bin/rails runner -e $PASSENGER_APP_ENV "Study.delay.delete_queued_studies"
else
echo "*** ADDING CRONTAB TO DELETE FAILED UPLOADS, QUEUED STUDIES & FILES ***"
# check for failed uploads every 6 hours, run delete queues nightly
(crontab -u app -l ; echo "0 */6 * * * . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"UploadCleanupJob.find_and_remove_failed_uploads\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
(crontab -u app -l ; echo "0 1 * * * . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"Study.delete_queued_studies\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
(crontab -u app -l ; echo "0 1 * * * . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"StudyFile.delete_queued_files\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
(crontab -u app -l ; echo "0 1 * * * . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"UserAnnotation.delete_queued_annotations\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
# clean up cached failed ingest runs weekly
(crontab -u app -l ; echo "@weekly . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"FileParseService.clean_up_ingest_artifacts\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
fi
echo "*** COMPLETED ***"
if [[ $PASSENGER_APP_ENV = "production" ]]
then
echo "*** ADDING NIGHTLY ADMIN EMAIL ***"
(crontab -u app -l ; echo "55 23 * * * . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"SingleCellMailer.nightly_admin_report.deliver_now\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
echo "*** COMPLETED ***"
fi
if [[ $PASSENGER_APP_ENV != "production" ]]
then
echo "*** RESETTING DEFAULT INGEST DOCKER IMAGE ***"
sudo -E -u app -H bin/rails runner -e $PASSENGER_APP_ENV "AdminConfiguration.revert_ingest_docker_image"
echo "*** COMPLETED ***"
fi
echo "*** ADDING DAILY RESET OF USER DOWNLOAD QUOTAS ***"
(crontab -u app -l ; echo "@daily . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"DownloadQuotaService.reset_all_quotas\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
echo "*** COMPLETED ***"
echo "*** LOCALIZING USER ASSETS ***"
/home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV "UserAssetService.delay.localize_assets_from_remote"
echo "*** COMPLETED ***"
echo "*** ADDING REPORTING CRONS ***"
(crontab -u app -l ; echo "5 0 * * Sun . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"ReportTimePoint.create_point(ReportTimePoint::WEEKLY_RETURNING_USERS)\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
(crontab -u app -l ; echo "@daily . /home/app/.cron_env ; cd /home/app/webapp/; /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV \"AnalysisSubmission.update_running_submissions\" >> /home/app/webapp/log/cron_out.log 2>&1") | crontab -u app -
echo "*** COMPLETED ***"
# Improves performance for cluster scatter plots in Explore tab
echo "*** REFRESHING DEFAULT CLUSTER CACHE ***"
sudo -E -u app -H /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV "ClusterCacheService.delay(queue: :cache).cache_all_defaults"
echo "*** SENDING RESTART NOTIFICATION ***"
sudo -E -u app -H /home/app/webapp/bin/rails runner -e $PASSENGER_APP_ENV "AdminConfiguration.restart_notification"