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ClickHouse version of import users script #1317

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ClickHouse version of import users script #1317

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0689a96
change import-users script to be clickhouse only
jamesqo Apr 8, 2026
4643c85
replace usage of clickhouse CLI with the clickhouse-connect library
jamesqo Apr 8, 2026
664a630
wip
jamesqo Apr 8, 2026
8f19f8a
convert script from python2 to python3
jamesqo Apr 8, 2026
8abfae6
more details on authorities
jamesqo Apr 8, 2026
239c95e
batch query for authorities
jamesqo Apr 8, 2026
e942ce7
remove the clickhouse suffix
jamesqo Apr 23, 2026
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21 changes: 1 addition & 20 deletions import-scripts/import-portal-users.sh
100755 → 100644
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Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,6 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/import-portal-users.lock"
SMTP_SERVER=`cat $MAIL_SMTP_SERVER`
GENIE_BLUE_DATABASE_PROPERTIES_FILENAME="portal.properties.genie.blue"
GENIE_GREEN_DATABASE_PROPERTIES_FILENAME="portal.properties.genie.green"
GENIE_BLUE_CLICKHOUSE_CLIENT_CONFIG_FILEPATH="/data/portal-cron/pipelines-credentials/clickhouse_client_genie_blue_config.yaml"
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@jamesqo jamesqo Apr 21, 2026

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removed these lines as we're no longer using the clickhouse CLI

GENIE_GREEN_CLICKHOUSE_CLIENT_CONFIG_FILEPATH="/data/portal-cron/pipelines-credentials/clickhouse_client_genie_green_config.yaml"
CLICKHOUSE_COMMANDS_PENDING_DIRPATH="/data/portal-cron/tmp/import-users-genie/pending_clickhouse_commands"
CLICKHOUSE_COMMANDS_COMPLETED_DIRPATH="/data/portal-cron/tmp/import-users-genie/completed_clickhouse_commands"
CLICKHOUSE_BINARY_FILEPATH="/home/cbioportal_importer/tools/clickhouse/bin/clickhouse"
GET_DATABASE_CURRENTLY_IN_PRODUCTION_SCRIPT="$PORTAL_HOME/scripts/get_database_currently_in_production.sh"
MANAGE_DATABASE_TOOL_PROPERTIES_FILEPATH="$PORTAL_HOME/pipelines-credentials/manage_genie_database_update_tools.properties"
CURRENT_DATABASE_OUTPUT_FILEPATH=$(mktemp $PORTAL_HOME/tmp/import-portal-users/get_current_database_output.txt.XXXXXX)
Expand All @@ -29,32 +24,18 @@ MY_FLOCK_FILEPATH="/data/portal-cron/cron-lock/import-portal-users.lock"
rm -f $CURRENT_DATABASE_OUTPUT_FILEPATH
if [ ${current_production_database_color:0:5} == "green" ] ; then
GENIE_PRODUCTION_DATABASE_PROPERTIES_FILENAME="$GENIE_GREEN_DATABASE_PROPERTIES_FILENAME"
GENIE_CLICKHOUSE_CLIENT_CONFIG_FILEPATH="$GENIE_GREEN_CLICKHOUSE_CLIENT_CONFIG_FILEPATH"
else
if [ ${current_production_database_color:0:4} == "blue" ] ; then
GENIE_PRODUCTION_DATABASE_PROPERTIES_FILENAME="$GENIE_BLUE_DATABASE_PROPERTIES_FILENAME"
GENIE_CLICKHOUSE_CLIENT_CONFIG_FILEPATH="$GENIE_BLUE_CLICKHOUSE_CLIENT_CONFIG_FILEPATH"
else
echo "error : Failed to properly detect the current production database for genie" >> "$USERSGENIELOGFILENAME"
fi
fi

echo "### Starting import" >> "$USERSGENIELOGFILENAME"
date >> "$USERSGENIELOGFILENAME"
$PYTHON_BINARY $PORTAL_HOME/scripts/importUsers.py --port 3306 --secrets-file $PIPELINES_CONFIG_HOME/google-docs/client_secrets.json --creds-file $PIPELINES_CONFIG_HOME/google-docs/creds.dat --properties-file $PIPELINES_CONFIG_HOME/properties/import-users/${GENIE_PRODUCTION_DATABASE_PROPERTIES_FILENAME} --send-email-confirm true --sender GENIE --ssl-ca $PORTAL_HOME/pipelines-credentials/pipelines-genie-db-aws-rds-combined-ca-bundle.pem --gmail-username $GMAIL_USERNAME --gmail-password $GMAIL_PASSWORD --smtp-server $SMTP_SERVER >> "$USERSGENIELOGFILENAME" 2>&1
$PYTHON3_BINARY $PORTAL_HOME/scripts/importUsers.py --secrets-file $PIPELINES_CONFIG_HOME/google-docs/client_secrets.json --creds-file $PIPELINES_CONFIG_HOME/google-docs/creds.dat --properties-file $PIPELINES_CONFIG_HOME/properties/import-users/${GENIE_PRODUCTION_DATABASE_PROPERTIES_FILENAME} --send-email-confirm true --sender GENIE --gmail-username $GMAIL_USERNAME --gmail-password $GMAIL_PASSWORD --smtp-server $SMTP_SERVER >> "$USERSGENIELOGFILENAME" 2>&1
CGDS_GENIE_IMPORT_STATUS=$?
clickhouse_commands_filepath=$(ls ${CLICKHOUSE_COMMANDS_PENDING_DIRPATH}/*.sql 2>/dev/null | head -n 1)
if [ $CGDS_GENIE_IMPORT_STATUS -eq 0 ] && [ -f "$clickhouse_commands_filepath" ] ; then
echo "executing clickhouse commands from $clickhouse_commands_filepath" >> "$USERSGENIELOGFILENAME"
date >> "$USERSGENIELOGFILENAME"
"$CLICKHOUSE_BINARY_FILEPATH" client --config-file="$GENIE_CLICKHOUSE_CLIENT_CONFIG_FILEPATH" --multiquery < "$clickhouse_commands_filepath"
CLICKHOUSE_IMPORT_STATUS=$?
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if [ $CLICKHOUSE_IMPORT_STATUS -eq 0 ] ; then
mv "$clickhouse_commands_filepath" "$CLICKHOUSE_COMMANDS_COMPLETED_DIRPATH"
else
$CGDS_GENIE_IMPORT_STATUS=2 # failure flag
fi
fi

PIPELINES_EMAIL_LIST="cbioportal-pipelines@cbioportal.org"
FAILED_DATABASES=""
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