pick up new docker-compose standards (openemr#483)

Co-authored-by: Michael A. Smith <michael@smith-li.com>

Author: jesdynf

packages/express/README.md

@@ -31,16 +31,16 @@ In a couple of minutes, once OpenEMR has finished the final setup procedures, it
 ### General
 
 * Need access to the containers? Connect to user `ubuntu`, sudo to root, and...
-  * Apache: `docker exec -it $(docker ps | grep _openemr | cut -f 1 -d " ") /bin/sh`
-  * MySQL: `docker exec -it $(docker ps | grep mysql | cut -f 1 -d " ") /bin/bash`
+  * Apache: `docker compose exec openemr /bin/sh`
+  * MySQL: `docker compose exec mysql /bin/bash`
 * Visit container volume: `docker volume ls`, `cd $(docker volume inspect <volume_name> | jq -r ".[0].Mountpoint")`
 
 #### Set Local Timezone
 
 1. See http://php.net/manual/en/timezones.php for the PHP timezone for your region.
 2. `sudo bash`
-3. `docker exec $(docker ps | grep _openemr | cut -f 1 -d " ") sed -i 's^;date.timezone\ =^date.timezone = <your timezone>^' /etc/php7/php.ini`
-4. `docker restart $(docker ps | grep _openemr | cut -f 1 -d " ")`
+3. `docker compose exec openemr sed -i 's^;date.timezone\ =^date.timezone = <your timezone>^' /etc/php7/php.ini`
+4. `docker compose restart openemr`
 
 ### HIPAA Compliance
 

packages/express/ami/ami-rekey.sh

@@ -33,21 +33,24 @@ if [[ -f /etc/appliance-unlocked ]]; then
 fi
 
 # wait a while for services to start
-until docker container ls | grep openemr/openemr >& /dev/null
+# shellcheck disable=SC2312
+until docker container ls | grep openemr/openemr -q
 do
     sleep 5
 done
 
-until docker top $(docker ps | grep _openemr | cut -f 1 -d " ") | grep httpd &> /dev/null
+# shellcheck disable=SC2312
+until docker top "$(docker ps | grep -- -openemr | cut -f 1 -d " ")" | grep -q httpd
 do
     sleep 3
 done
 
 # reset password
-docker exec $(docker ps | grep _openemr | cut -f 1 -d " ") /root/unlock_admin.sh $(curl http://169.254.169.254/latest/meta-data/instance-id)
+# shellcheck disable=SC2312
+docker compose exec openemr /root/unlock_admin.sh "$(curl http://169.254.169.254/latest/meta-data/instance-id)"
 
 # reset SSL
-docker exec $(docker ps | grep _openemr | cut -f 1 -d " ") /bin/sh -c 'rm -f /etc/ssl/private/* /etc/ssl/docker-selfsigned-configured'
+docker compose exec openemr /bin/sh -c 'rm -f /etc/ssl/private/* /etc/ssl/docker-selfsigned-configured'
 docker restart lightsail_openemr_1
 
 # let's never speak of this again

packages/launchpad/README.md

@@ -17,16 +17,16 @@ Follow our [Getting Started Guide](https://www.open-emr.org/wiki/index.php/Googl
 ### General
 
 * Need access to the containers? Connect to user `ubuntu`, sudo to root, and...
-  * Apache: `docker exec -it $(docker ps | grep _openemr | cut -f 1 -d " ") /bin/sh`
-  * MySQL: `docker exec -it $(docker ps | grep mysql | cut -f 1 -d " ") /bin/bash`
+  * Apache: `docker compose exec openemr /bin/sh`
+  * MySQL: `docker compose exec mysql /bin/bash`
 * Visit container volume: `docker volume ls`, `cd $(docker volume inspect <volume_name> | jq -r ".[0].Mountpoint")`
 
 #### Set Local Timezone
 
 1. See http://php.net/manual/en/timezones.php for the PHP timezone for your region.
 2. `sudo bash`
-3. `docker exec $(docker ps | grep _openemr | cut -f 1 -d " ") sed -i 's^;date.timezone\ =^date.timezone = <your timezone>^' /etc/php7/php.ini`
-4. `docker restart $(docker ps | grep _openemr | cut -f 1 -d " ")`
+3. `docker compose exec openemr sed -i 's^;date.timezone\ =^date.timezone = <your timezone>^' /etc/php7/php.ini`
+4. `docker compose restart openemr`
 
 ### HIPAA Compliance
 

packages/launchpad/vm/vm-rekey.sh

@@ -36,10 +36,11 @@ fi
 sleep 15
 
 # reset password
-docker exec $(docker ps | grep _openemr | cut -f 1 -d " ") /root/unlock_admin.sh $(curl -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/attributes/openemr_admin_password)
+# shellcheck disable=SC2312
+docker compose exec openemr /root/unlock_admin.sh "$(curl -H "Metadata-Flavor: Google" http://metadata.google.internal/computeMetadata/v1/instance/attributes/openemr_admin_password)"
 
 # reset SSL
-docker exec $(docker ps | grep _openemr | cut -f 1 -d " ") /bin/sh -c 'rm -rf /etc/ssl/private/*'
+docker compose exec openemr /bin/sh -c 'rm -rf /etc/ssl/private/*'
 docker restart lightsail_openemr_1
 
 # let's never speak of this again

packages/lightsail/README.md

@@ -50,7 +50,7 @@ To install, run the same launch script, make sure you're provided inbound access
   * You will need network access, don't try to build from a private IP without NAT egress.
   * Check the process list, make sure `auto_configure.php` isn't running before you attempt to log in.
 * Need access to the containers? Log into root, and...
-  * Apache: `docker exec -it $(docker ps | grep _openemr | cut -f 1 -d " ") /bin/sh`
+  * Apache: `docker exec -it $(docker ps | grep -- -openemr | cut -f 1 -d " ") /bin/sh`
   * MySQL: `docker exec -it $(docker ps | grep mysql | cut -f 1 -d " ") /bin/bash`
 * Visit container volume: `docker volume ls`, `cd $(docker volume inspect <volume_name> | jq -r ".[0].Mountpoint")`
 * Run a quick backup? `/etc/cron.daily/duplicity-backups` as root.
@@ -103,7 +103,7 @@ If you're seeking to install a feature release (to upgrade from `5.0.0` to `5.0.
 #!/bin/sh
 
 PATCHFILE=5-0-1-Patch-4.zip
-OE_INSTANCE=$(docker ps | grep _openemr | cut -f 1 -d " ")
+OE_INSTANCE=$(docker ps | grep -- -openemr | cut -f 1 -d " ")
 
 /etc/cron.daily/duplicity-backups
 # running OpenEMR Standard? don't forget to make an RDS snapshot

packages/lightsail/ingestion.sh

@@ -8,21 +8,22 @@
 # Three: You'll want a /lot/ of room to unpack. An eight-gig instance won't cut it.
 
 mkdir /tmp/backup-ingestion
-cd /tmp/backup-ingestion
-tar -xf $1 -C /tmp/backup-ingestion/ --no-same-owner
+cd /tmp/backup-ingestion || exit 1
+tar -xf "$1" -C /tmp/backup-ingestion/ --no-same-owner
 
-DOCKERID=$(docker ps | grep _openemr | cut -f 1 -d " ")
+# shellcheck disable=2312
+DOCKERID=$(docker ps | grep -- -openemr | cut -f 1 -d " ")
 
 # retrieve site
 mkdir webroot
 tar -zxf openemr.tar.gz -C webroot
 rm openemr.tar.gz
 find webroot -type d -name 'node_modules' -exec rm -rf {} +
-docker cp ${DOCKERID}:/var/www/localhost/htdocs/openemr/sites/default/sqlconf.php webroot/sites/default
-docker cp webroot ${DOCKERID}:/tmp/oe-recovery
+docker cp "${DOCKERID}:/var/www/localhost/htdocs/openemr/sites/default/sqlconf.php" webroot/sites/default
+docker cp webroot "${DOCKERID}:/tmp/oe-recovery"
 
 # straighten out internal permissions
-docker exec -i $(docker ps | grep _openemr | cut -f 1 -d " ") /bin/sh -s << "EOF"
+docker exec -i "${DOCKERID}" /bin/sh -s << "EOF"
 cd /var/www/localhost/htdocs/openemr/sites
 chown -R apache:root default-recovery
 chmod -R 400 default-recovery
@@ -35,13 +36,14 @@ EOF
 
 # restore database
 gzip -d openemr.sql.gz
-echo 'USE openemr;' | cat - openemr.sql | docker exec -i ${DOCKERID} /bin/sh -c 'mysql -h"$MYSQL_HOST" -u"$MYSQL_USER" -p"$MYSQL_PASS"'
+# shellcheck disable=2312
+echo 'USE openemr;' | cat - openemr.sql | docker exec -i "${DOCKERID}" /bin/sh -c 'mysql -h"$MYSQL_HOST" -u"$MYSQL_USER" -p"$MYSQL_PASS"'
 rm openemr.sql
 
 # swift kick to PHP
-docker restart ${DOCKERID}
+docker restart "${DOCKERID}"
 
-cd /root
+cd /root || exit 1
 rm -rf /tmp/backup-ingestion
 
 echo Restore operation complete!

packages/lightsail/patch.md

@@ -45,7 +45,7 @@ Script to be run:
 # Note that you may be copying over your own custom files so BEWARE!
 # For multi-site also uncomment the 3 commented docker exec lines below. 
  
-OE_INSTANCE=$(docker ps | grep _openemr | cut -f 1 -d " ")
+OE_INSTANCE=$(docker ps | grep -- -openemr | cut -f 1 -d " ")
 #docker exec -it "$OE_INSTANCE" sh -c 'curl -L https://raw.githubusercontent.com/openemr/openemr/v7_0_0_2/admin.php > /var/www/localhost/htdocs/openemr/admin.php'
 docker exec -it "$OE_INSTANCE" sh -c 'curl -L https://raw.githubusercontent.com/openemr/openemr/v7_0_0_2/sql_patch.php > /var/www/localhost/htdocs/openemr/sql_patch.php'
 docker exec -it "$OE_INSTANCE" sh -c 'curl -L https://www.open-emr.org/patch/7-0-0-Patch-2.zip > /var/www/localhost/htdocs/openemr/7-0-0-Patch-2.zip'
@@ -81,7 +81,7 @@ Create a cleanup script to delete sensitive scripts.
 /etc/cron.daily/duplicity-backups
 
 #delete upgrade files that have served their purpose
-OE_INSTANCE=$(docker ps | grep _openemr | cut -f 1 -d " ")
+OE_INSTANCE=$(docker ps | grep -- -openemr | cut -f 1 -d " ")
 docker exec "$OE_INSTANCE" rm -f /var/www/localhost/htdocs/openemr/admin.php /var/www/localhost/htdocs/openemr/sql_patch.php /var/www/localhost/htdocs/openemr/7-0-0-Patch-2.zip
 
 # comment below line to avoid deleting the patch script created above

packages/lightsail/upgrade.md

@@ -75,7 +75,7 @@ sed -i 's/5.0.0/5.0.1/' docker-compose.yml
 #!/bin/sh
 
 # retrieve files deleted for security
-OE_INSTANCE=$(docker ps | grep _openemr | cut -f 1 -d " ")
+OE_INSTANCE=$(docker ps | grep -- -openemr | cut -f 1 -d " ")
 docker exec -it $OE_INSTANCE sh -c 'curl -L https://raw.githubusercontent.com/openemr/openemr/v5_0_1/sql_upgrade.php > /var/www/localhost/htdocs/openemr/sql_upgrade.php'
 docker exec -it $OE_INSTANCE sh -c 'curl -L https://raw.githubusercontent.com/openemr/openemr/v5_0_1/acl_upgrade.php > /var/www/localhost/htdocs/openemr/acl_upgrade.php'
 docker exec $OE_INSTANCE chown apache:root /var/www/localhost/htdocs/openemr/sql_upgrade.php /var/www/localhost/htdocs/openemr/acl_upgrade.php
@@ -97,6 +97,6 @@ Navigate to `http://<your-instance>/sql_upgrade.php` and select `5.0.0`.
 /etc/cron.daily/duplicity-backups
 
 #delete upgrade files that have served their purpose
-OE_INSTANCE=$(docker ps | grep _openemr | cut -f 1 -d " ")
+OE_INSTANCE=$(docker ps | grep -- -openemr | cut -f 1 -d " ")
 docker exec $OE_INSTANCE rm -f /var/www/localhost/htdocs/openemr/sql_upgrade.php /var/www/localhost/htdocs/openemr/acl_upgrade.php
 ```

packages/standard/README.md

@@ -6,7 +6,7 @@
 
 ## Administration
 
-* Access the OpenEMR container: `sudo -i -- sh -c 'docker exec -it $(docker ps | grep _openemr | cut -f 1 -d " ") /bin/sh'`
+* Access the OpenEMR container: `sudo -i -- sh -c 'docker exec -it $(docker ps | grep -- -openemr | cut -f 1 -d " ") /bin/sh'`
 * Visit container volume: `docker volume ls`, `cd $(docker volume inspect <volume_name> | jq -r ".[0].Mountpoint")`
 * Open mysql shell
     1. Ssh into the EC2.