devtoolsLibrary.source

#!/bin/sh

# defaults
: "${MYSQL_HOST:=}" \
  "${MYSQL_ROOT_PASS:=}" \
  "${SQL_DATA_DRIVE:=}"

prepareVariables() {
    CONFIGURATION="server=${MYSQL_HOST} rootpass=${MYSQL_ROOT_PASS} loginhost=%"
    # defaults
    CUSTOM_ROOT_USER=root
    CUSTOM_USER=openemr
    CUSTOM_PASSWORD=openemr
    CUSTOM_DATABASE=openemr
    CUSTOM_PORT=3306
    if [ -n "${MYSQL_ROOT_USER:-}" ]; then
        CONFIGURATION="${CONFIGURATION} root=${MYSQL_ROOT_USER}"
        CUSTOM_ROOT_USER="${MYSQL_ROOT_USER}"
    fi
    if [ -n "${MYSQL_USER:-}" ]; then
        CONFIGURATION="${CONFIGURATION} login=${MYSQL_USER}"
        CUSTOM_USER="${MYSQL_USER}"
    fi
    if [ -n "${MYSQL_PASS:-}" ]; then
        CONFIGURATION="${CONFIGURATION} pass=${MYSQL_PASS}"
        CUSTOM_PASSWORD="${MYSQL_PASS}"
    fi
    if [ -n "${MYSQL_DATABASE:-}" ]; then
        CONFIGURATION="${CONFIGURATION} dbname=${MYSQL_DATABASE}"
        CUSTOM_DATABASE="${MYSQL_DATABASE}"
    fi
    if [ -n "${MYSQL_PORT:-}" ]; then
        CONFIGURATION="${CONFIGURATION} port=${MYSQL_PORT}"
        CUSTOM_PORT="${MYSQL_PORT}"
    fi
    if [ -n "${OE_USER:-}" ]; then
        CONFIGURATION="${CONFIGURATION} iuser=${OE_USER}"
    fi
    if [ -n "${OE_PASS:-}" ]; then
        CONFIGURATION="${CONFIGURATION} iuserpass=${OE_PASS}"
    fi
    if [ -n "${ENCRYPTION_STRATEGY:-}" ]; then
        CONFIGURATION="${CONFIGURATION} encryption_strategy=${ENCRYPTION_STRATEGY}"
    fi
}

setGlobalSettings() {
    # Set requested openemr settings
    OPENEMR_SETTINGS=$(printenv | grep '^OPENEMR_SETTING_')
    [ -z "${OPENEMR_SETTINGS}" ] && return
    echo "${OPENEMR_SETTINGS}" |
    while IFS= read -r line; do
        SETTING_TEMP=$(echo "${line}" | cut -d "=" -f 1)
        # note am omitting the letter O on purpose
        # this guarantees that the field we want is the second field

        CORRECT_SETTING_TEMP=$(echo "${SETTING_TEMP}" | awk -F 'PENEMR_SETTING_' '{print $2}')
        VALUE_TEMP=$(echo "${line}" | awk -F "${CORRECT_SETTING_TEMP}=" '{print $2}')
        echo "Set ${CORRECT_SETTING_TEMP} to ${VALUE_TEMP}"
        mariadb --skip-ssl -u "${CUSTOM_USER}" --password="${CUSTOM_PASSWORD}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "UPDATE globals SET gl_value = '${VALUE_TEMP}' WHERE gl_name = '${CORRECT_SETTING_TEMP}'" "${CUSTOM_DATABASE}"
    done
}

resetOpenemr() {
    echo "Remove database"
    mariadb --skip-ssl -f -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "DROP DATABASE ${CUSTOM_DATABASE}"
    echo "Remove database user"
    mariadb --skip-ssl -f -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "Drop user '${CUSTOM_USER}'@'%';FLUSH PRIVILEGES;"
    echo "Reset couchdb"
    rsync --delete --recursive --links /couchdb/original/data /couchdb/
    echo "Remove files"
    rm -fr /var/www/localhost/htdocs/openemr/sites/*
    rsync --delete --recursive --links --exclude .git /openemr/sites /var/www/localhost/htdocs/openemr/
    chmod 666 /var/www/localhost/htdocs/openemr/sites/default/sqlconf.php
    chown -R apache /var/www/localhost/htdocs/openemr/
}

installOpenemr() {
    echo "Re-installing OpenEMR"
    cp /root/auto_configure.php /var/www/localhost/htdocs/
    php /var/www/localhost/htdocs/auto_configure.php -f "${CONFIGURATION}"
    rm -f /var/www/localhost/htdocs/auto_configure.php
}

demoData() {
    echo "Install demo data"
    mariadb-dump --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" --add-drop-table --no-data "${CUSTOM_DATABASE}" | grep ^DROP | awk ' BEGIN { print "SET FOREIGN_KEY_CHECKS=0;" } { print $0 } END { print "SET FOREIGN_KEY_CHECKS=1;" } ' | mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" "${CUSTOM_DATABASE}"
    mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" "${CUSTOM_DATABASE}" < /root/demo_5_0_0_5.sql
    upgradeOpenEMR 5.0.0
    changeEncodingCollation utf8mb4 utf8mb4_general_ci
}

# parameter 1 is original version
upgradeOpenEMR() {
    sed -e "s@!empty(\$_POST\['form_submit'\])@true@" < /var/www/localhost/htdocs/openemr/sql_upgrade.php > /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
    sed -i "s@\$form_old_version = \$_POST\['form_old_version'\];@\$form_old_version = '${1}';@" /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
    sed -i "1s@^@<?php \$_GET['site'] = 'default'; ?>@" /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
    php -f /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
    rm -f /var/www/localhost/htdocs/openemr/sql_upgrade_temp.php
}

sqlDataDrive() {
    echo "Installing sql data from drive"
    [ -n "${SQL_DATA_DRIVE}" ] || return 0
    (
        cd "${SQL_DATA_DRIVE}" || exit
        # Loop over all sql files inside of the current directory
        for f in *.sql ; do
            echo "Loading sql data from ${f}"
            mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" "${CUSTOM_DATABASE}" < "${f}"
        done
    )
}

# parameter 1 is identifier
backupOpenemr() {
    mkdir -p "/snapshots/${1}"
    mariadb-dump --skip-ssl --ignore-table="${CUSTOM_DATABASE}".onsite_activity_view --hex-blob -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" "${CUSTOM_DATABASE}" > "/snapshots/${1}/backup.sql"
    rsync --delete --recursive --links /var/www/localhost/htdocs/openemr/sites "/snapshots/${1}/"
    rsync --delete --recursive --links /couchdb/data "/snapshots/${1}/"
    tar -C /snapshots -czf "${1}.tgz" "${1}"
    rm -fr "/snapshots/${1}"
}

# parameter 1 is identifier
restoreOpenemr() (
    cd /snapshots || exit
    tar -C /snapshots -xzf "${1}.tgz"
    # need to empty the database before the restore database import
    mariadb-dump --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" --add-drop-table --no-data "${CUSTOM_DATABASE}" |
        grep ^DROP |
        awk ' BEGIN { print "SET FOREIGN_KEY_CHECKS=0;" } { print $0 } END { print "SET FOREIGN_KEY_CHECKS=1;" } ' |
        mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" "${CUSTOM_DATABASE}"
    mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" "${CUSTOM_DATABASE}" < "/snapshots/${1}/backup.sql"
    # note keeping same sqlconf.php in case snapshot is from somewhere else (ie. such as the demo farm) with different credentials
    sqlconf=$(cat /var/www/localhost/htdocs/openemr/sites/default/sqlconf.php)
    rsync --delete --recursive --links "/snapshots/${1}/sites" /var/www/localhost/htdocs/openemr/
    echo "${sqlconf}" > /var/www/localhost/htdocs/openemr/sites/default/sqlconf.php
    chown -R apache /var/www/localhost/htdocs/openemr/
    if [ -d "/snapshots/${1}/data" ]; then
        rsync --delete --recursive --links "/snapshots/${1}/data" /couchdb/
    fi
    rm -fr "/snapshots/${1}"
)

# parameter 1 is character set
# parameter 2 is collation
# shellcheck disable=SC2016
changeEncodingCollation() {
    mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e 'SELECT concat("ALTER DATABASE `",TABLE_SCHEMA,"` CHARACTER SET = '"${1}"' COLLATE = '"${2}"';") as _sql FROM `information_schema`.`TABLES` where `TABLE_SCHEMA` like "'"${CUSTOM_DATABASE}"'" and `TABLE_TYPE`="BASE TABLE" group by `TABLE_SCHEMA`;' |
        grep '^ALTER' |
        mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}"
    mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e 'SELECT concat("ALTER TABLE `",TABLE_SCHEMA,"`.`",TABLE_NAME,"` CONVERT TO CHARACTER SET '"${1}"' COLLATE '"${2}"';") as _sql FROM `information_schema`.`TABLES` where `TABLE_SCHEMA` like "'"${CUSTOM_DATABASE}"'" and `TABLE_TYPE`="BASE TABLE" group by `TABLE_SCHEMA`, `TABLE_NAME`;' |
        grep '^ALTER' |
        mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}"
}

forceHttps() {
    sed -i 's@#RewriteEngine On@ RewriteEngine On@' /etc/apache2/conf.d/openemr.conf
    sed -i 's@#RewriteCond %{HTTPS} off@ RewriteCond %{HTTPS} off@' /etc/apache2/conf.d/openemr.conf
    # shellcheck disable=SC2016
    sed -i 's@#RewriteRule (\.\*) https://%{HTTP_HOST}/\$1 \[R,L\]@ RewriteRule (.*) https://%{HTTP_HOST}/$1 [R,L]@' /etc/apache2/conf.d/openemr.conf
}

unForceHttps() {
    sed -i 's@[^#]RewriteEngine On@#RewriteEngine On@' /etc/apache2/conf.d/openemr.conf
    sed -i 's@[^#]RewriteCond %{HTTPS} off@#RewriteCond %{HTTPS} off@' /etc/apache2/conf.d/openemr.conf
    # shellcheck disable=SC2016
    sed -i 's@[^#]RewriteRule (\.\*) https://%{HTTP_HOST}/\$1 \[R,L\]@#RewriteRule (.*) https://%{HTTP_HOST}/$1 [R,L]@' /etc/apache2/conf.d/openemr.conf
}

# parameter 1 is identifier
setupClientCert() {
    if [ ! -d "/certs/${1}" ]; then
        mkdir -p "/certs/${1}"
    fi
    cp "/certs/${1}.zip" "/certs/${1}/"
    (
        cd "/certs/${1}" &&
        unzip "${1}.zip"
    )
    # server certificate
    cp "/certs/${1}/Server.crt" /etc/ssl/certs/customclientbased.cert.pem
    rm -f /etc/ssl/certs/webserver.cert.pem
    ln -s /etc/ssl/certs/customclientbased.cert.pem /etc/ssl/certs/webserver.cert.pem
    # server key
    cp "/certs/${1}/Server.key" /etc/ssl/private/customclientbased.key.pem
    rm -f /etc/ssl/private/webserver.key.pem
    ln -s /etc/ssl/private/customclientbased.key.pem /etc/ssl/private/webserver.key.pem
    # ca certificate
    cp "/certs/${1}/CertificateAuthority.crt" /etc/ssl/certs/CAcustomclientbased.cert.pem
    rm -f /etc/ssl/certs/CAcustomclientbasedwebserver.cert.pem
    ln -s /etc/ssl/certs/CAcustomclientbased.cert.pem /etc/ssl/certs/CAcustomclientbasedwebserver.cert.pem
    # ca key
    cp "/certs/${1}/CertificateAuthority.key" /etc/ssl/private/CAcustomclientbased.key.pem
    rm -f /etc/ssl/private/CAcustomclientbasedwebserver.key.pem
    ln -s /etc/ssl/private/CAcustomclientbased.key.pem /etc/ssl/private/CAcustomclientbasedwebserver.key.pem
    # cleanup
    rm -fr "/certs/${1}"
    # configure apache
    sed -i "s@#SSLVerifyClient@ SSLVerifyClient@" /etc/apache2/conf.d/openemr.conf
    sed -i "s@#SSLVerifyDepth@ SSLVerifyDepth@" /etc/apache2/conf.d/openemr.conf
    sed -i "s@#SSLOptions@ SSLOptions@" /etc/apache2/conf.d/openemr.conf
    sed -i "s@#SSLCACertificateFile@ SSLCACertificateFile@" /etc/apache2/conf.d/openemr.conf
    # configure openemr
    mariadb --skip-ssl -u "${CUSTOM_USER}" --password="${CUSTOM_PASSWORD}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "UPDATE globals SET gl_value = 1 WHERE gl_name = 'is_client_ssl_enabled'" "${CUSTOM_DATABASE}"
    mariadb --skip-ssl -u "${CUSTOM_USER}" --password="${CUSTOM_PASSWORD}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "UPDATE globals SET gl_value = '/etc/ssl/certs/CAcustomclientbasedwebserver.cert.pem' WHERE gl_name = 'certificate_authority_crt'" "${CUSTOM_DATABASE}"
    mariadb --skip-ssl -u "${CUSTOM_USER}" --password="${CUSTOM_PASSWORD}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "UPDATE globals SET gl_value = '/etc/ssl/private/CAcustomclientbasedwebserver.key.pem' WHERE gl_name = 'certificate_authority_key'" "${CUSTOM_DATABASE}"
}

toggleOnSelfSignedCert() {
    # server certificate
    rm -f /etc/ssl/certs/webserver.cert.pem
    ln -s /etc/ssl/certs/selfsigned.cert.pem /etc/ssl/certs/webserver.cert.pem
    # server key
    rm -f /etc/ssl/private/webserver.key.pem
    ln -s /etc/ssl/private/selfsigned.key.pem /etc/ssl/private/webserver.key.pem
    # configure apache
    sed -i "s@[^#]SSLVerifyClient@#SSLVerifyClient@" /etc/apache2/conf.d/openemr.conf
    sed -i "s@[^#]SSLVerifyDepth@#SSLVerifyDepth@" /etc/apache2/conf.d/openemr.conf
    sed -i "s@[^#]SSLOptions@#SSLOptions@" /etc/apache2/conf.d/openemr.conf
    sed -i "s@[^#]SSLCACertificateFile@#SSLCACertificateFile@" /etc/apache2/conf.d/openemr.conf
    # configure openemr
    mariadb --skip-ssl -u "${CUSTOM_USER}" --password="${CUSTOM_PASSWORD}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "UPDATE globals SET gl_value = 0 WHERE gl_name = 'is_client_ssl_enabled'" "${CUSTOM_DATABASE}"
    mariadb --skip-ssl -u "${CUSTOM_USER}" --password="${CUSTOM_PASSWORD}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "UPDATE globals SET gl_value = '' WHERE gl_name = 'certificate_authority_crt'" "${CUSTOM_DATABASE}"
    mariadb --skip-ssl -u "${CUSTOM_USER}" --password="${CUSTOM_PASSWORD}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "UPDATE globals SET gl_value = '' WHERE gl_name = 'certificate_authority_key'" "${CUSTOM_DATABASE}"
}

# parameter 1 is number of random patients to create and import
# parameter 2 has to be either "true" or "false" and is for the development setting in the import_ccda.php script call
importRandomPatients() {
    echo "Setting up for following number of random patients (each patient will take several seconds): ${1}"
    echo "Development mode: ${2}"
    (
        if [ ! -d /root/synthea ]; then
            echo "Setting up synthea first"
            apk update
            apk add openjdk11-jre
            mkdir /root/synthea
            cd /root/synthea || exit
            wget https://github.com/synthetichealth/synthea/releases/download/master-branch-latest/synthea-with-dependencies.jar
        fi
        rm -fr /root/synthea/output
        cd /root/synthea &&
            java -jar synthea-with-dependencies.jar --exporter.fhir.export false --exporter.ccda.export true --generate.only_alive_patients true -p "${1}"
    )
    sed -i "s@exit;@//exit;@" /var/www/localhost/htdocs/openemr/contrib/util/ccda_import/import_ccda.php
    php /var/www/localhost/htdocs/openemr/contrib/util/ccda_import/import_ccda.php --sourcePath=/root/synthea/output/ccda --site=default --openemrPath=/var/www/localhost/htdocs/openemr --isDev="${2}"
    sed -i "s@//exit;@exit;@" /var/www/localhost/htdocs/openemr/contrib/util/ccda_import/import_ccda.php
    echo "Completed run for following number of random patients: ${1}"
}

# parameter 1 is number of multisites to create
generateMultisiteBank() {
    echo "Setting up a multisite bank with following number of multisites (labeled run1, run2, run3, ...): run1...run${1}"
    # Activate newer versions of InstallerAuto that support environment variable activation.
    export OPENEMR_ENABLE_INSTALLER_AUTO=1
    # Activate older versions of InstallerAuto that require `sed` activation.
    sed -i "s@exit;@//exit;@" /var/www/localhost/htdocs/openemr/contrib/util/installScripts/InstallerAuto.php
    a=1
    while [ "${a}" -le "${1}" ]; do
        run="run${a}"
        echo "dropping ${run} sql database, sql user, and directory if they already exist (just ignore any errors that are displayed)"
        mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "DROP DATABASE ${run}"
        mariadb --skip-ssl -u "${CUSTOM_ROOT_USER}" --password="${MYSQL_ROOT_PASS}" -h "${MYSQL_HOST}" -P "${CUSTOM_PORT}" -e "DROP USER '${run}'"
        rm -fr "/var/www/localhost/htdocs/openemr/sites/${run}"
        rm /tmp/setup_dump.sql
        echo "adding ${run} multisite"
        php /var/www/localhost/htdocs/openemr/contrib/util/installScripts/InstallerAuto.php rootpass="${MYSQL_ROOT_PASS}" server="${MYSQL_HOST}" port="${CUSTOM_PORT}" loginhost=% "login=${run}" "pass=${run}" "dbname=${run}" "site=${run}" source_site_id=default clone_database=yes
        chown -R apache "/var/www/localhost/htdocs/openemr/sites/${run}"
        find "/var/www/localhost/htdocs/openemr/sites/${run}" -type d -print0 | xargs -0 chmod 500
        find "/var/www/localhost/htdocs/openemr/sites/${run}" -type f -print0 | xargs -0 chmod 400
        find "/var/www/localhost/htdocs/openemr/sites/${run}/documents" -type d -print0 | xargs -0 chmod 700
        find "/var/www/localhost/htdocs/openemr/sites/${run}/documents" -type f -print0 | xargs -0 chmod 700
        echo "completed adding ${run} multisite"
        a=$(( a + 1 ))
    done
    sed -i "s@//exit;@exit;@" /var/www/localhost/htdocs/openemr/contrib/util/installScripts/InstallerAuto.php
    echo "Completed setting up a multisite bank with following number of multisites (labeled run1, run2, run3, ...): run1...run${1}"
}