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fix(shell): all remaining shellcheck issues #459

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f159535
fix(shell): address all shellcheck warnings with -oall
kojiromike Jan 8, 2026
5cddb61
chore: remove defunct 7.0.5 container
kojiromike Jan 9, 2026
f4dba31
fix(shell): add -f flag support to auto_configure.php
kojiromike Jan 9, 2026
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24 changes: 20 additions & 4 deletions docker/openemr/7.0.4/auto_configure.php
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Original file line number Diff line number Diff line change
Expand Up @@ -21,11 +21,27 @@
$installSettings['no_root_db_access'] = 'BLANK';
$installSettings['development_translations'] = 'BLANK';
// Collect parameters(if exist) for installation configuration settings
// Supports two formats:
// php auto_configure.php key=value key=value ...
// php auto_configure.php -f "key=value key=value ..."
for ($i=1; $i < count($argv); $i++) {
$indexandvalue = explode("=", $argv[$i]);
$index = $indexandvalue[0];
$value = $indexandvalue[1] ?? '';
$installSettings[$index] = $value;
if ($argv[$i] == '-f' && isset($argv[$i+1])) {
// Handle -f flag: single string with space-separated key=value pairs
$configPairs = preg_split('/\s+/', trim($argv[$i+1]));
foreach ($configPairs as $pair) {
if (strpos($pair, '=') !== false) {
list($index, $value) = explode('=', $pair, 2);
$installSettings[$index] = $value;
}
}
$i++; // Skip the next argument (already processed)
} else {
// Handle standard key=value parameters
$indexandvalue = explode("=", $argv[$i]);
$index = $indexandvalue[0];
$value = $indexandvalue[1] ?? '';
$installSettings[$index] = $value;
}
}
// Convert BLANK settings to empty
$tempInstallSettings = array();
Expand Down
59 changes: 33 additions & 26 deletions docker/openemr/7.0.4/openemr.sh
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Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
#!/bin/sh
# shellcheck disable=SC2154,SC2310
# SC2154: Variables are passed as environment variables to the Docker container
# SC2310: Functions used in retry loops with set -e are intentional
# Allows customization of openemr credentials, preventing the need for manual setup
# (Note can force a manual setup by setting MANUAL_SETUP to 'yes')
# - Required settings for auto installation are MYSQL_HOST and MYSQL_ROOT_PASS
Expand Down Expand Up @@ -28,24 +31,25 @@ auto_setup() {
find . -not -perm 600 -exec chmod 600 {} \+

#create temporary file cache directory for auto_configure.php to use
TMP_FILE_CACHE_LOCATION="/tmp/php-file-cache"
mkdir ${TMP_FILE_CACHE_LOCATION}
TMP_FILE_CACHE_LOCATION='/tmp/php-file-cache'
mkdir "${TMP_FILE_CACHE_LOCATION}"

#create auto_configure.ini to be able to leverage opcache for operations
touch auto_configure.ini
echo "opcache.enable=1" >> auto_configure.ini
echo "opcache.enable_cli=1" >> auto_configure.ini
echo "opcache.file_cache=${TMP_FILE_CACHE_LOCATION}" >> auto_configure.ini
echo "opcache.file_cache_only=1" >> auto_configure.ini
echo "opcache.file_cache_consistency_checks=1" >> auto_configure.ini
echo "opcache.enable_file_override=1" >> auto_configure.ini
echo "opcache.max_accelerated_files=1000000" >> auto_configure.ini
{
echo 'opcache.enable=1'
echo 'opcache.enable_cli=1'
echo "opcache.file_cache=${TMP_FILE_CACHE_LOCATION}"
echo 'opcache.file_cache_only=1'
echo 'opcache.file_cache_consistency_checks=1'
echo 'opcache.enable_file_override=1'
echo 'opcache.max_accelerated_files=1000000'
} > auto_configure.ini

#run auto_configure
php auto_configure.php -c auto_configure.ini -f ${CONFIGURATION} || return 1
php auto_configure.php -c auto_configure.ini -f "${CONFIGURATION}" || return 1

#remove temporary file cache directory and auto_configure.ini
rm -r ${TMP_FILE_CACHE_LOCATION}
rm -r "${TMP_FILE_CACHE_LOCATION}"
rm auto_configure.ini

echo "OpenEMR configured."
Expand Down Expand Up @@ -75,7 +79,7 @@ fi
if [ "${SWARM_MODE}" = "yes" ]; then
# atomically test for leadership
set -o noclobber
{ > /var/www/localhost/htdocs/openemr/sites/docker-leader ; } &> /dev/null || AUTHORITY=no
{ : > /var/www/localhost/htdocs/openemr/sites/docker-leader ; } > /dev/null 2>&1 || AUTHORITY=no
set +o noclobber

if [ "${AUTHORITY}" = "no" ] &&
Expand Down Expand Up @@ -241,18 +245,18 @@ if

if ${UPGRADE_YES}; then
# Need to do the upgrade
echo "Attempting upgrade"
echo 'Attempting upgrade'
c=${DOCKER_VERSION_SITES}
while [ "${c}" -le "${DOCKER_VERSION_ROOT}" ]; do
if [ "${c}" -gt "${DOCKER_VERSION_SITES}" ] ; then
echo "Start: Processing fsupgrade-${c}.sh upgrade script"
sh /root/fsupgrade-${c}.sh
sh "/root/fsupgrade-${c}.sh"
echo "Completed: Processing fsupgrade-${c}.sh upgrade script"
fi
c=$(( c + 1 ))
done
echo -n ${DOCKER_VERSION_ROOT} > /var/www/localhost/htdocs/openemr/sites/default/docker-version
echo "Completed upgrade"
printf '%s' "${DOCKER_VERSION_ROOT}" > /var/www/localhost/htdocs/openemr/sites/default/docker-version
echo 'Completed upgrade'
fi
fi

Expand All @@ -269,8 +273,8 @@ if [ "${REDIS_SERVER}" != "" ] &&
# version 5.3.7 .
if [ "${PHPREDIS_BUILD}" != "" ]; then
apk update
apk del --no-cache php${PHP_VERSION_ABBR}-redis
apk add --no-cache git php${PHP_VERSION_ABBR}-dev php${PHP_VERSION_ABBR}-pecl-igbinary gcc make g++
apk del --no-cache "php${PHP_VERSION_ABBR}-redis"
apk add --no-cache git "php${PHP_VERSION_ABBR}-dev" "php${PHP_VERSION_ABBR}-pecl-igbinary" gcc make g++
mkdir /tmpredis
cd /tmpredis
git clone https://github.com/phpredis/phpredis.git
Expand All @@ -282,11 +286,12 @@ if [ "${REDIS_SERVER}" != "" ] &&
phpize83
# note for php 8.3, needed to change from './configure --enable-redis-igbinary' to:
./configure --with-php-config=/usr/bin/php-config83 --enable-redis-igbinary
make -j $(nproc --all)
nproc_count=$(nproc --all)
make -j "${nproc_count}"
make install
echo "extension=redis" > /etc/php${PHP_VERSION_ABBR}/conf.d/20_redis.ini
echo 'extension=redis' > "/etc/php${PHP_VERSION_ABBR}/conf.d/20_redis.ini"
rm -fr /tmpredis/phpredis
apk del --no-cache git php${PHP_VERSION_ABBR}-dev gcc make g++
apk del --no-cache git "php${PHP_VERSION_ABBR}-dev" gcc make g++
cd /var/www/localhost/htdocs/openemr
fi

Expand Down Expand Up @@ -327,7 +332,7 @@ if [ "${REDIS_SERVER}" != "" ] &&

# Configure PHP to use Redis for sessions via conf.d include file
{
printf 'session.save_handler = redis\n'
echo 'session.save_handler = redis'
printf 'session.save_path = "%s"\n' "${REDIS_PATH}"
} > "/etc/php${PHP_VERSION_ABBR}/conf.d/redis-session.ini"

Expand Down Expand Up @@ -436,14 +441,16 @@ if [ "${XDEBUG_IDE_KEY}" != "" ] ||
sh xdebug.sh
#also need to turn off opcache since it can not be turned on with xdebug
if [ ! -f /etc/php-opcache-jit-configured ]; then
echo "opcache.enable=0" >> /etc/php${PHP_VERSION_ABBR}/php.ini
echo 'opcache.enable=0' >> "/etc/php${PHP_VERSION_ABBR}/php.ini"
touch /etc/php-opcache-jit-configured
fi
else
# Configure opcache jit if Xdebug is not being used (note opcache is already on, so just need to add setting(s) to php.ini that are different from the default setting(s))
if [ ! -f /etc/php-opcache-jit-configured ]; then
echo "opcache.jit=tracing" >> /etc/php${PHP_VERSION_ABBR}/php.ini
echo "opcache.jit_buffer_size=100M" >> /etc/php${PHP_VERSION_ABBR}/php.ini
{
echo 'opcache.jit=tracing'
echo 'opcache.jit_buffer_size=100M'
} >> "/etc/php${PHP_VERSION_ABBR}/php.ini"
touch /etc/php-opcache-jit-configured
fi
fi
Expand Down
21 changes: 11 additions & 10 deletions docker/openemr/7.0.4/ssl.sh
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
#!/bin/sh
# shellcheck disable=SC2154
# SC2154: Variables are passed as environment variables to the Docker container
#
# configures SSL
# optionally configures Let's Encrypt
Expand All @@ -25,28 +27,27 @@ if [ ! -f /etc/ssl/docker-selfsigned-configured ]; then
fi

if [ "${DOMAIN}" != "" ]; then
if [ "${EMAIL}" != "" ]; then
EMAIL="-m ${EMAIL}"
else
echo "WARNING: SETTING AN EMAIL VIA \$EMAIL is HIGHLY RECOMMENDED IN ORDER TO"
echo " RECEIVE ALERTS FROM LETSENCRYPT ABOUT YOUR SSL CERTIFICATE."
if [ "${EMAIL}" = "" ]; then
# shellcheck disable=SC2016
echo 'WARNING: SETTING AN EMAIL VIA $EMAIL is HIGHLY RECOMMENDED IN ORDER TO'
echo ' RECEIVE ALERTS FROM LETSENCRYPT ABOUT YOUR SSL CERTIFICATE.'
fi
# if a domain has been set, set up LE and target those certs

if ! [ -f /etc/letsencrypt/live/${DOMAIN}/fullchain.pem ]; then
if ! [ -f "/etc/letsencrypt/live/${DOMAIN}/fullchain.pem" ]; then
/usr/sbin/httpd -k start
sleep 2
certbot certonly --webroot -n -w /var/www/localhost/htdocs/openemr/ -d ${DOMAIN} ${EMAIL} --agree-tos
certbot certonly --webroot -n -w /var/www/localhost/htdocs/openemr/ -d "${DOMAIN}" ${EMAIL:+-m} ${EMAIL:+"${EMAIL}"} --agree-tos
/usr/sbin/httpd -k stop
echo "1 23 * * * certbot renew -q --post-hook \"httpd -k graceful\"" >> /etc/crontabs/root
echo '1 23 * * * certbot renew -q --post-hook "httpd -k graceful"' >> /etc/crontabs/root
fi

# run letsencrypt as a daemon and reference the correct cert
if [ ! -f /etc/ssl/docker-letsencrypt-configured ]; then
rm -f /etc/ssl/certs/webserver.cert.pem
rm -f /etc/ssl/private/webserver.key.pem
ln -s /etc/letsencrypt/live/${DOMAIN}/fullchain.pem /etc/ssl/certs/webserver.cert.pem
ln -s /etc/letsencrypt/live/${DOMAIN}/privkey.pem /etc/ssl/private/webserver.key.pem
ln -s "/etc/letsencrypt/live/${DOMAIN}/fullchain.pem" /etc/ssl/certs/webserver.cert.pem
ln -s "/etc/letsencrypt/live/${DOMAIN}/privkey.pem" /etc/ssl/private/webserver.key.pem
touch /etc/ssl/docker-letsencrypt-configured
fi

Expand Down
112 changes: 35 additions & 77 deletions docker/openemr/7.0.4/upgrade/fsupgrade-1.sh
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Original file line number Diff line number Diff line change
@@ -1,103 +1,61 @@
#!/bin/sh
# Upgrade number 1 for OpenEMR docker
# From prior version 5.0.1 (needed for the sql upgrade script).
priorOpenemrVersion="5.0.1"
priorOpenemrVersion='5.0.1'

echo "Start: Upgrade to docker-version 1"
echo 'Start: Upgrade to docker-version 1'

# Perform codebase upgrade on each directory in sites/
for dir in $(find /var/www/localhost/htdocs/openemr/sites/* -maxdepth 0 -type d ); do
sitename=$(basename "${dir}")
for dir in /var/www/localhost/htdocs/openemr/sites/*/; do
sitename=${dir%/}
sitename=${sitename##*/}

# Ensure have all directories
echo "Start: Ensure have all directories in ${sitename}"
if [ ! -d ${dir}/documents/certificates ]; then
mkdir -p ${dir}/documents/certificates
fi
if [ ! -d ${dir}/documents/couchdb ]; then
mkdir -p ${dir}/documents/couchdb
fi
if [ ! -d ${dir}/documents/custom_menus/patient_menus ]; then
mkdir -p ${dir}/documents/custom_menus/patient_menus
fi
if [ ! -d ${dir}/documents/edi ]; then
mkdir -p ${dir}/documents/edi
fi
if [ ! -d ${dir}/documents/era ]; then
mkdir -p ${dir}/documents/era
fi
if [ ! -d ${dir}/documents/letter_templates ]; then
mkdir -p ${dir}/documents/letter_templates
fi
if [ ! -d ${dir}/documents/logs_and_misc/methods ]; then
mkdir -p ${dir}/documents/logs_and_misc/methods
fi
if [ ! -d ${dir}/documents/mpdf/pdf_tmp ]; then
mkdir -p ${dir}/documents/mpdf/pdf_tmp
fi
if [ ! -d ${dir}/documents/onsite_portal_documents/templates ]; then
mkdir -p ${dir}/documents/onsite_portal_documents/templates
fi
if [ ! -d ${dir}/documents/procedure_results ]; then
mkdir -p ${dir}/documents/procedure_results
fi
if [ ! -d ${dir}/documents/smarty/gacl ]; then
mkdir -p ${dir}/documents/smarty/gacl
fi
if [ ! -d ${dir}/documents/smarty/main ]; then
mkdir -p ${dir}/documents/smarty/main
fi
if [ ! -d ${dir}/documents/temp ]; then
mkdir -p ${dir}/documents/temp
fi
mkdir -p "${dir}documents/certificates" \
"${dir}documents/couchdb" \
"${dir}documents/custom_menus/patient_menus" \
"${dir}documents/edi" \
"${dir}documents/era" \
"${dir}documents/letter_templates" \
"${dir}documents/logs_and_misc/methods" \
"${dir}documents/mpdf/pdf_tmp" \
"${dir}documents/onsite_portal_documents/templates" \
"${dir}documents/procedure_results" \
"${dir}documents/smarty/gacl" \
"${dir}documents/smarty/main" \
"${dir}documents/temp"
echo "Completed: Ensure have all directories in ${sitename}"

# Update new directory structure
# Move contents to new location (silently skip if dir missing/empty), then remove old dir
echo "Start: Update new directory structure in ${sitename}"
if [ -d ${dir}/era ]; then
if [ "$(ls ${dir}/era)" ]; then
mv -f ${dir}/era/* ${dir}/documents/era/
fi
rm -rf ${dir}/era
fi
if [ -d ${dir}/edi ]; then
if [ "$(ls ${dir}/edi)" ]; then
mv -f ${dir}/edi/* ${dir}/documents/edi/
fi
rm -rf ${dir}/edi
fi
if [ -d ${dir}/letter_templates ]; then
if [ "$(ls ${dir}/letter_templates)" ]; then
if [ -f ${dir}/letter_templates/custom_pdf.php ]; then
mv -f ${dir}/letter_templates/custom_pdf.php ${dir}/
fi
mv -f ${dir}/letter_templates/* ${dir}/documents/letter_templates/
fi
rm -rf ${dir}/letter_templates
fi
if [ -d ${dir}/procedure_results ]; then
if [ "$(ls ${dir}/procedure_results)" ]; then
mv -f ${dir}/procedure_results/* ${dir}/documents/procedure_results/
fi
rm -rf ${dir}/procedure_results
fi
mv -f "${dir}era"/* "${dir}documents/era/" 2>/dev/null || true
rm -rf "${dir}era/"
mv -f "${dir}edi"/* "${dir}documents/edi/" 2>/dev/null || true
rm -rf "${dir}edi/"
mv -f "${dir}letter_templates/custom_pdf.php" "${dir}" 2>/dev/null || true
mv -f "${dir}letter_templates"/* "${dir}documents/letter_templates/" 2>/dev/null || true
rm -rf "${dir}letter_templates/"
mv -f "${dir}procedure_results"/* "${dir}documents/procedure_results/" 2>/dev/null || true
rm -rf "${dir}procedure_results/"
echo "Completed: Update new directory structure in ${sitename}"

# Clear smarty cache
echo "Start: Clear smarty cache in ${sitename}"
rm -fr ${dir}/documents/smarty/gacl/*
rm -fr ${dir}/documents/smarty/main/*
rm -fr "${dir}documents/smarty/gacl"/* "${dir}documents/smarty/main"/*
echo "Completed: Clear smarty cache in ${sitename}"
done

# Fix permissions
echo "Start: Fix permissions"
echo 'Start: Fix permissions'
chown -R apache:root /var/www/localhost/htdocs/openemr/sites/
echo "Completed: Fix permissions"
echo 'Completed: Fix permissions'

# Perform database upgrade on each directory in sites/
for dirdata in $(find /var/www/localhost/htdocs/openemr/sites/* -maxdepth 0 -type d ); do
sitename=$(basename "${dirdata}")
for dir in /var/www/localhost/htdocs/openemr/sites/*/; do
sitename=${dir%/}
sitename=${sitename##*/}

# Upgrade database
echo "Start: Upgrade database for ${sitename} from ${priorOpenemrVersion}"
Expand All @@ -111,4 +69,4 @@ for dirdata in $(find /var/www/localhost/htdocs/openemr/sites/* -maxdepth 0 -typ
echo "Completed: Upgrade database for ${sitename} from ${priorOpenemrVersion}"
done

echo "Completed: Upgrade to docker-version 1"
echo 'Completed: Upgrade to docker-version 1'
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