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Fix failing integration tests #11246

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Fix failing integration tests #11246

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f0bcc5a
fix parse db params
onursumer Dec 3, 2024
c1d0517
add legacy datasource params to the application properties
onursumer Dec 4, 2024
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6 changes: 5 additions & 1 deletion .github/workflows/integration-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,11 @@ jobs:
cat $PORTAL_SOURCE_DIR/src/main/resources/application.properties | \
sed 's|spring.datasource.mysql.url=.*|spring.datasource.mysql.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|' | \
sed 's|spring.datasource.mysql.username=.*|spring.datasource.mysql.username=cbio_user|' | \
sed 's|spring.datasource.mysql.password=.*|spring.datasource.mysql.password=somepassword|' \
sed 's|spring.datasource.mysql.password=.*|spring.datasource.mysql.password=somepassword|' | \
sed 'a spring.datasource.driver-class-name=com.mysql.jdbc.Driver' | \
sed 'a spring.datasource.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false' | \
sed 'a spring.datasource.username=cbio_user' | \
sed 'a spring.datasource.password=somepassword' \
Comment on lines +48 to +51
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This is a workaround to add legacy properties which are needed by migrate.py script. This is required for now because migration script is in the separate cbioportal-core repo.

> application.properties
- name: 'Copy cgds.sql file into Docker Compose'
run: cp ./cbioportal/src/main/resources/db-scripts/cgds.sql ./cbioportal-docker-compose/data/.
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12 changes: 6 additions & 6 deletions docker/web-and-data/docker-entrypoint.sh
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Expand Up @@ -23,7 +23,7 @@ parse_db_params_from_config_and_command_line() {
else
PROPERTIES_FILE=$BAKED_IN_WAR_CONFIG_FILE
fi
for param in db.host spring.datasource.username db.portal_db_name spring.datasource.password spring.datasource.url; do
for param in db.host spring.datasource.mysql.username db.portal_db_name spring.datasource.mysql.password spring.datasource.mysql.url; do
if $(parse_db_params_from_command_line $@ | grep -q $param); then
prop=$(parse_db_params_from_command_line $@ | grep "^$param" || [[ $? == 1 ]])
else
Expand All @@ -37,7 +37,7 @@ parse_db_params_from_config_and_command_line() {
after_equal_sign="${prop#*=}"
updated_before_equal_sign="${before_equal_sign//./_}"
prop="${updated_before_equal_sign}=${after_equal_sign}"
if [[ $param == spring.datasource.url ]]
if [[ $param == spring.datasource.mysql.url ]]
then
# Remove the parameters (?...) from the connection URL.
echo $(sed -r "s/^([^=]+)=([^\?]+).*/\1=\2/" <<< $prop)
Expand Down Expand Up @@ -79,9 +79,9 @@ check_db_connection() {
eval "$(parse_connection_string $db_connection_string)"
fi

if [[ -n $spring_datasource_url ]]
if [[ -n $spring_datasource_mysql_url ]]
then
eval "$(parse_connection_string $spring_datasource_url)"
eval "$(parse_connection_string $spring_datasource_mysql_url)"
fi

if [ -z ${db_port+x} ] # is $db_port unset?
Expand All @@ -93,11 +93,11 @@ check_db_connection() {
fi
fi

while ! mysqladmin ping -s -h$(echo ${db_host} | cut -d: -f1) -P${db_port} -u${spring_datasource_username} -p${spring_datasource_password};
while ! mysqladmin ping -s -h$(echo ${db_host} | cut -d: -f1) -P${db_port} -u${spring_datasource_mysql_username} -p${spring_datasource_mysql_password};
do
sleep 5s;
if [ -n "$SHOW_DEBUG_INFO" ] && [ "$SHOW_DEBUG_INFO" != "false" ]; then
echo mysqladmin ping -s -h$(echo ${db_host} | cut -d: -f1) -P${db_port} -u${spring_datasource_username} -p${spring_datasource_password}
echo mysqladmin ping -s -h$(echo ${db_host} | cut -d: -f1) -P${db_port} -u${spring_datasource_mysql_username} -p${spring_datasource_mysql_password}
fi
echo "Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect..."
done
Expand Down
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