Backup/Restore commands

About the Feature

If you are using Bahmni with Docker Lite/Standard, then the bahmni -i command no longer exists. See this documentation instead: Performing a Backup / Restore of Container Data & Files (docker).
A training was conducted in Dec-2023, on how to perform a backup of all data from Bahmni on Centos V0.92/0.93. That will be very useful too. Please see the videos in the training guide here: Migrating Bahmni from CentOS to Docker (Training)
The page below is a bit outdated, although useful still to understand backup concepts.

This feature has been introduced in V0.88 of Bahmni. Please look at Known Issues with DB Backup and Restore in case there is an issue.

Bahmni has different artifacts in the system like patient documents, patient images, DB data etc. There is a possibility that unwanted events may happen such as hard drive failure or data loss due to some wrong SQL (eg: delete sql) mistakenly run by an user. Bahmni as a product should provide mechanism to backup all the artifacts so that if any unwanted event happen then we should be able to recover from the backup so that business continue as usual at the earliest.

Where to store / keep backup files

It is highly recommended that you keep the backup files in a separate external disk and away from the hospital location if possible – to avoid loss of all data in case of a Natural disaster like floods or earthquakes. You can provide the destination path for an external disk as long as you mount it successfully. It is also highly recommended to encrypt the external disk. Please refer Performing a Backup of Bahmni Data on USB or External Drive.

If you are more comfortable with perform your own direct backups, then you can also look at the following documentation on how to perform DB backups here:

MySQL backup: https://blog.devart.com/mysql-backup-tutorial.html
Postgres backup: https://www.postgresql.org/docs/current/backup-dump.html
Sample script on how to restore bahmni db: https://github.com/Bahmni/bahmni-scripts/tree/master/demo/db-backups/v0.93 (see dbRestore.sh)
For Patient Files, bahmni_config folder, etc, you will need to create your backups using cp or rcp commands.
You can then create a cron job to run the backup periodically. See this: https://www.geeksforgeeks.org/cron-command-in-linux-with-examples/

Right now Bahmni backup mechanism supports two categories name file backup and database backup. Below is the list of supported items

Patient images
Document images
Uploaded files
Uploaded lab results
PACS images
Report module generated files by Queue feature
MySQL databases
Postgres databases

Old Way of Backup and Restore

Old Way Backup

This will perform ONLY the DB backup and NOT of the other files (artifacts).

When the backup tools for MySQL and Postgres are not installed then the backup will fall back to old way of DB backups by using following commands. The following commands will achieve same as mentioned in old way of DB backups.

Please replace the inventory_file_name with appropriate file name. For example, in the below examples local is the inventory file name.

Full Openelis/clinlims DB Backup (Old way)

bahmni -i local backup --backup_type=db  --options=clinlims

Full Openerp DB Backupup (Old way)

bahmni -i local backup --backup_type=db  --options=openerp

Full Openmrs DB Backup (Old Way)

bahmni -i local backup --backup_type=db  --options=openmrs

Uninstall Backup Tools

If backrest tools are already installed, then uninstall them to perform oldway backup.
To uninstall pgsql backup tool, execute the following commands

sudo rm -f /usr/bin/pgbackrest
sudo rm -f /usr/bin/pg_backrest
sudo rm -rf /usr/lib/perl5/BackRest
sudo rm -rf /usr/share/perl5/BackRest
sudo rm -rf /usr/lib/perl5/pgBackRest
sudo rm -rf /usr/share/perl5/pgBackRest

To uninstall mysql backup tool, execute the following command
yum list installed | grep xtrabackup|xargs yum remove -y

Old Way Restore

Please replace the inventory_file_name with appropriate file name. For example, in the below examples local is the inventory file name.

Restore clinlims/openelis database

 bahmni -i local restore --restore_type=db --options=clinlims  --strategy=dump --restore_point=clinlims_dump_20170215-150418.sql.gz

Restore openerp database

 bahmni -i local restore --restore_type=db --options=openerp  --strategy=dump --restore_point=openerp_dump_20170215-150418.sql.gz

Restore openmrs db (old way)

bahmni -i local restore --restore_type=db --options=openmrs --strategy=dump   --restore_point=openmrs_dump_20170221084218.sql.gz

Complete / Full Backup

The backup tools for MySQL, Postgres and Artifacts have to be installed for the following commands. The Bahmni installation will take care of installing these tools based on provided configuration. Please refer Configure backup.

In order to backup all the possible files and databases, please use the below mentioned command.

bahmni -i <inventory_file_name> backup --backup_type=all --options=all

Please replace the inventory_file_name with appropriate file name. For Example, in the below example local is the inventory file name.

Command to backup everything (databases, files)

  bahmni -i local backup --backup_type=all --options=all

Schedule Backup:

In order to schedule a backup one can use --schedule option available in command line which adds cron entry for the user to run the command as per schedule.

Example Scenario

--schedule "30 2 * * 0" is an example schedule option that can be added to any of the backup commands. The backup in this case is scheduled for every Sunday 2.30 am

Sample command

 bahmni -i <inventory_file_name> backup --backup_type=<file/db> --options=<options_possible> --strategy=<strategy> --schedule "* * * * *"

Example Scheduling Full Backup command for Openmrs Database

  bahmni -i local backup --backup_type=db --options=openmrs --strategy=full --schedule "30 2 * * 0"


    # Use the hash sign to prefix a comment
    # +---------------- minute (0 - 59)
    # |  +------------- hour (0 - 23)
    # |  |  +---------- day of month (1 - 31)
    # |  |  |  +------- month (1 - 12)
    # |  |  |  |  +---- day of week (0 - 7) (Sunday=0 or 7)
    # |  |  |  |  |
    # *  *  *  *  *  command to be executed

Mysql Backup:

Taking Backup of all the Mysql Databases with single command is not supported yet.

There are different configurations for mysql database backup command as mentioned below

Key	Default value	Available options	Mandatory
backup_type	all	This value should be db for database backup	No
options	all	This Value can be either openmrs or bahmni-reports while taking mysql database backup.	No
strategy	full	Possible values are full, incr.	No

Mysql Full Backup

One can take full backup of particular mysql database by mentioning the database name.

For example, in the below sample command DBName should be replaced with the actual database name. Possible values supported right now are "openmrs" or "bahmni-reports".

Sample command for Full backup of MySQL database

  bahmni -i <inventory_file_name> backup --backup_type=db --options=<DBName>

Please replace the inventory_file_name with appropriate file name and DBName with the database name. For example, in the below examples local is the inventory file name.

Openmrs Database Full Backup

bahmni -i local backup --backup_type=db --options=openmrs

Bahmni Reports Database Full Backup

bahmni -i local backup --backup_type=db --options=bahmni_reports

Mysql Incremental Backup:

Apart from the full backup, there is an option to take incremental backup. In case of incremental backup, strategy should be "incr"

Sample Command for Incremental Backup

bahmni -i <inventory_file_name> backup --backup_type=db --options=<DBName>  --strategy=incr

Please replace the inventory_file_name with appropriate file name and DBName with the database name. For example, in the below examples local is the inventory file name.

Openmrs Database Incremental Backup

  bahmni -i local backup --backup_type=db --options=openmrs  --strategy=incr

Bahmni Reports Database Incremental Backup

  bahmni -i local backup --backup_type=db --options=bahmni_reports  --strategy=incr

Mysql Database Restore:

Restoring all the mysql databases with single command is not supported yet.

One can restore to any point (either full or incremental) in database given that the chosen restore points/files are available in configured restore path.

How to find restore path ?

Restore Path is configured in /etc/bahmni-backrest.conf file. More about the configurations, please read Configure backup

Sample Mysql restore command

bahmni -i <inventory_file_name> restore --restore_type=db --options=<DBName> --strategy=<dump/pitr> --restore_point=<Backup foldername>

Please replace the inventory_file_name with appropriate file name and DBName with the database name (either openmrs or bahmni_reports). For example, in the below examples local is the inventory file name.

There are different configurations for mysql database backup command as mentioned below. Please note that there are no default values for the below configurations

Key

Description

Mandatory

restore_type

Value should be "db" (in case of database restore)

Yes

options

Available options for mysql database restore are "openmrs" or "bahmni_reports"

Yes

strategy

Two types of strategies are available as explained below.

Strategy	Description
pitr	If the restore point value is the folder name of the backup.
dump	If the restore point value is database entire dump gunzip file.

Yes

restore_point

Value should be folder name of the backup file(It could be either incr/full).
If the strategy is dump, then value should be dump file name.

Yes

Mysql Dump Restore

One can restore the database by providing dump gunzip file.

Openmrs Database Dump Restore

bahmni -i local restore --restore_type=db --options=openmrs --strategy=dump   --restore_point=openmrs_dump_20170221084218.sql.gz

Mysql Full Restore

One can restore the database by providing full backup file.

Openmrs Database FULL PITR (Point In Time Restore)

bahmni -i local restore --restore_type=db --options=openmrs --strategy=pitr   --restore_point=20170220103125_full

Bahmni Reports Database FULL PITR (Point In Time Restore)

bahmni -i local restore --restore_type=db --options=bahmni_reports --strategy=pitr   --restore_point=20170220103125_full

In above examples, please replace 20170220103125_full (in case of full restore) with appropriate backup folder name available in the configured restore path and local with relevant inventory file name.

If the file is not available in the restore path, it is expected that the restore command will fail.

Mysql Incremental Restore

One can restore the database by providing incremental backup file.

Openmrs Database INCREMENTAL PITR (Point In Time Restore)

bahmni -i local restore --restore_type=db --options=openmrs --strategy=pitr   --restore_point=20170330103125_incr

Bahmni Reports Database INCREMENTAL PITR (Point In Time Restore)

bahmni -i local restore --restore_type=db --options=bahmni_reports --strategy=pitr   --restore_point=20170330103125_incr

In above examples, please replace 20170330103125_incr (in case of incremental restore) with appropriate backup folder name available in the configured restore path and local with relevant inventory file name.

If the file is not available in the restore path, it is expected that the restore command will fail.

Pgsql Database Backup:

In this approach of taking backup of postgres database, we can't take individual postgres database backup (like clinlims or openerp).

There are different configurations for postgres database backup command as mentioned below

Key	Default value	Available options	Mandatory
backup_type	all	This value should be db for database backup	No
options	all	This Value can be either postgres while taking pgsql database backup.	No
strategy	full	Possible values are full, incr.	No

Postgres Full Backup

One can take full backup of particular postgres database by mentioning the database name under options which is postgres.

Sample command for Full backup of Postgres database

  bahmni -i <inventory_file_name> backup --backup_type=db --options=<DBName>

Please replace the inventory_file_name with appropriate file name and DBName with the database name (postgres). For example, in the below examples local is the inventory file name.

Postgres Databases Full Backup

bahmni -i local backup --backup_type=db --options=postgres

If the file is not available in the restore path, it is expected that the restore command will fail.

Postgres Incremental Backup:

Apart from the full backup, there is an option to take incremental backup. In case of incremental backup, strategy should be "incr"

Sample Command for Incremental Backup

bahmni -i <inventory_file_name> backup --backup_type=db --options=<DBName>  --strategy=incr

Please replace the inventory_file_name with appropriate file name and DBName with the database name. For example, in the below examples local is the inventory file name.

Postgres Database Incremental Backup

  bahmni -i local backup --backup_type=db --options=postgres  --strategy=incr

If the file is not available in the restore path, it is expected that the restore command will fail.

Pgsql Database Restore:

One can restore the entire pgsql backup at a time. In case of restoring an empty postgres database, first the db has to be restored using a full backup and then the desired incremental backup has to be applied on it.

In the newer way of restoring the pgsql backup, we can't restore individual databases (for elis and erp).

Pgsql restore

bahmni -i <inventory_file_name> restore --restore_type=db --options=postgres --strategy=<pitr/dump>     --restore_point=<DB backup folder name>

There are different configurations for pgsql database backup command as mentioned below. Please note that there are no default values for the below configurations

Key

Description

Mandatory

restore_type

Value should be "db" (in case of database restore)

Yes

options

value in case of pitr startegy is "postgres".
value in case of dump strategy is "clinlims" or "openerp".

Yes

strategy

Two types of strategies are available as explained below.

Strategy	Description
pitr	If the restore point value is the folder name of the backup.
dump	If the restore point value is database entire dump gunzip file.

Yes

restore_point

Value should be folder name of the backup file(It could be either incr/full).
If the strategy is dump, then value should be dump file name.

Yes

Postgres Dump Restore

Please replace the inventory_file_name with appropriate file name. For example, in the below examples local is the inventory file name.

Openerp Dump Restore

One can restore the database by providing dump gunzip file.

Openerp Database Dump Restore

bahmni -i local restore --restore_type=db --options=openerp --strategy=dump   --restore_point=openerp_dump_20170221084218.sql.gz

Openelis Dump Restore

OpenELIS (clinlims) Database Dump Restore

bahmni -i local restore --restore_type=db --options=openerp --strategy=dump   --restore_point=openerp_dump_20170221084218.sql.gz

Postgres Full Restore

One can restore the database by providing full backup file.

Postgres Database FULL PITR (Point In Time Restore)

bahmni -i local restore --restore_type=db --options=postgres --strategy=pitr  --restore_point=20170221-120904F

In above examples, please replace 20170221-120904F (in case of full restore) with appropriate backup folder name available in the configured restore path and local with relevant inventory file name.

If the file is not available in the restore path, it is expected that the restore command will fail.

Postgres Incremental Restore

One can restore the database by providing incremental backup file.

Postgres Database Incremental PITR (Point In Time Restore)

bahmni -i local restore --restore_type=db --options=postgres --strategy=pitr   --restore_point= 20170221-121423F_20170222-124131I

In above examples, please replace 20170221-121423F_20170222-124131I (in case of incremental restore) with appropriate backup folder name available in the configured restore path and local with relevant inventory file name.

If the file is not available in the restore path, it is expected that the restore command will fail.

Artifacts Backup

We can either take backup of all artifacts or individual artifacts. There are different configurations available as listed below

Key

Description

Mandatory

backup_type

This Value should be "file" incase of artifact backup

yes

options

all available values are listed below

Value	Description
all	backup all artifacts
patient_images	backup patient images only
document_images	backup document images only
uploaded-files	backup uploaded files only
uploaded_results	backup uploaded results only
reports	backup reports only
pacs_images	backup pacs images only

yes

Artifacts Full Backup

Please replace local with appropriate inventory file name. For example, in the below examples local is the inventory file name.

Command to backup all artifacts

bahmni -i local backup --backup_type=file  --options=all

Artifacts Individual/Specific Backup

Please replace the inventory_file_name with appropriate file name and artifact_name with the relevant value.

Backup specific files

bahmni -i <inventory_file_name> backup --backup_type=file  --options=<artifact_name>

Commands to Backup specific files

bahmni -i local backup --backup_type=file  --options="patient_images" //for patient images
bahmni -i local backup --backup_type=file  --options="document_images" //for document images
bahmni -i local backup --backup_type=file  --options="uploaded-files" //for uploaded files
bahmni -i local backup --backup_type=file  --options="uploaded_results" //for uploaded results
bahmni -i local backup --backup_type=file  --options="reports" //for reports
bahmni -i local backup --backup_type=file  --options="pacs_images" //for pacs images

Backing up multiple artifacts (giving comma separated values without using all) is not supported right now. But, this can be achieved with a custom script with all the individual/specific backup commands.

Artifacts Restore

We can either restore all artifacts or individual artifacts.There are different configurations available as listed below

Key

Description

Mandatory

restore_type

This Value should be "file" incase of artifact restore

yes

options

all available values are listed below

Value	Description
all	restore all artifacts
patient_images	restore patient images only
document_images	restore document images only
uploaded-files	restore uploaded files only
uploaded_results	restore uploaded results only
reports	restore reports only
pacs_images	restore pacs images only

yes

Artifacts Full Restore

Please replace local with appropriate inventory file name. For example, in the below examples local is the inventory file name.

Command to restore all artifacts

bahmni -i local restore --restore_type=file  --options=all

Artifacts Individual/Specific Restore

Please replace the inventory_file_name with appropriate file name and artifact_name with the relevant value.

Restore specific files

bahmni -i <inventory_file_name> restore --restore_type=file  --options=<artifact_name>

Example Commands to Restore specific files

bahmni -i local restore --restore_type=file --options="patient_images" //for patient images
bahmni -i local restore --restore_type=file  --options="document_images" //for document images
bahmni -i local backup --restore_type=file  --options="uploaded-files" //for uploaded files
bahmni -i local restore --restore_type=file  --options="uploaded_results" //for uploaded results
bahmni -i local restore --restore_type=file  --options="reports" //for reports
bahmni -i local restore --restore_type=file  --options="pacs_images" //for pacs images

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