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Merge branch 'main' into feature/datashield

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This commit is contained in:
patrickskowronekdkfz
2024-03-19 09:52:40 +01:00
committed by GitHub
parent ec6f9302a1 8ea7da64b7
commit 4fac079aec
9 changed files with 77 additions and 46 deletions
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22
lib/functions.sh
View File

@ -155,6 +155,28 @@ setHostname() {
fi
}
# This function optimizes the usage of memory through blaze, according to the official performance tuning guide:
# https://github.com/samply/blaze/blob/master/docs/tuning-guide.md
# Short summary of the adjustments made:
# - set blaze memory cap to a quarter of the system memory
# - set db block cache size to a quarter of the system memory
# - limit resource count allowed in blaze to 1,25M per 4GB available system memory
optimizeBlazeMemoryUsage() {
if [ -z "$BLAZE_MEMORY_CAP" ]; then
system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
export BLAZE_MEMORY_CAP=$(("$system_memory_in_mb"/4));
fi
if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
available_system_memory_chuncks=$((BLAZE_MEMORY_CAP / 1000))
if [ $available_system_memory_chuncks -eq 0 ]; then
log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
export BLAZE_RESOURCE_CACHE_CAP=128000;
else
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chuncks * 312500))
fi
fi
}
# Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
# Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
createEncryptedPostgresBackup(){

45
lib/prerequisites.sh
View File

@ -67,29 +67,30 @@ log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
source /etc/bridgehead/${PROJECT}.conf
source ${PROJECT}/vars
set +e
SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
RET=$?
set -e
if [ $RET -ne 0 ]; then
log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
log WARN "Unable to check clock skew due to previous error."
else
log INFO "Checking clock skew ..."
if [ "${PROJECT}" != "minimal" ]; then
set +e
SERVERTIME="$(https_proxy=$HTTPS_PROXY_FULL_URL curl -m 5 -s -I $BROKER_URL_FOR_PREREQ 2>&1 | grep -i -e '^Date: ' | sed -e 's/^Date: //i')"
RET=$?
set -e
if [ $RET -ne 0 ]; then
log WARN "Unable to connect to Samply.Beam broker at $BROKER_URL_FOR_PREREQ. Please check your proxy settings.\nThe currently configured proxy was \"$HTTPS_PROXY_URL\". This error is normal when using proxy authentication."
log WARN "Unable to check clock skew due to previous error."
else
log INFO "Checking clock skew ..."
SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
MYTIME=$(date +%s)
SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
SKEW=$(echo $SKEW | awk -F- '{print $NF}')
SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
if [ $SKEW -ge 300 ]; then
report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
exit 1
elif [ $SKEW -ge 60 ]; then
log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
fi
SERVERTIME_AS_TIMESTAMP=$(date --date="$SERVERTIME" +%s)
MYTIME=$(date +%s)
SKEW=$(($SERVERTIME_AS_TIMESTAMP - $MYTIME))
SKEW=$(echo $SKEW | awk -F- '{print $NF}')
SYNCTEXT="For example, consider entering a correct NTP server (e.g. your institution's Active Directory Domain Controller in /etc/systemd/timesyncd.conf (option NTP=) and restart systemd-timesyncd."
if [ $SKEW -ge 300 ]; then
report_error 5 "Your clock is not synchronized (${SKEW}s off). This will cause Samply.Beam's certificate will fail. Please setup time synchronization. $SYNCTEXT"
exit 1
elif [ $SKEW -ge 60 ]; then
log WARN "Your clock is more than a minute off (${SKEW}s). Consider syncing to a time server. $SYNCTEXT"
fi
fi
fi
checkPrivKey() {
if [ -e /etc/bridgehead/pki/${SITE_ID}.priv.pem ]; then
log INFO "Success - private key found."
@ -100,7 +101,7 @@ checkPrivKey() {
return 0
}
if [[ "$@" =~ "noprivkey" ]]; then
if [[ "$@" =~ "noprivkey" || "${PROJECT}" != "minimal" ]]; then
log INFO "Skipping check for private key for now."
else
checkPrivKey || exit 1