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{{DISPLAYTITLE:Devops:Install OpenMRS SDK}}<languages/>
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= 1 Installation OpenMRS 3.X =
Installation of Open Medical Record System.
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source: https://o3-docs.openmrs.org/docs/recipes/set-up-o3-instance
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Notice:
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Run on Virtual Machine (virtualbox) with Debian 12 kde 20 GB hard drive. Used the whole disk not separate home.
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The installation with everything took 11GB.
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== 1.1 Prerequisites for installing OpenMRS SDK ==
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Requires a running installation of Debian 12 with username and password: openmrs
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Look at [[Special:MyLanguage/install virtualbox|install virtualbox]] in Debian 12
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The setup I have used on the virtual machine in VirtualBox:
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The example uses a 20GB virtual disk -> select "Pre-allocate Full size" -> RAM 6 GB (6144 MB) -> Number of cores: 4
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Settings -> System -> Processor -> Enable Nested VT-x/AMD-v
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Note: VT-X/AMD-v supports virtual machines by making them run more efficiently by leveraging hardware capabilities.
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Debian netinstall -> guided partitioning -> used whole disk -> all on same partition -> replaced gnome with kde -> added ssh server -> installed.
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Installed VBoxGuestAdditions.iso -> See [[Special:MyLanguage/Install virtualbox#2 Install VBoxGuestAdditions in virtualbox|Install VBoxGuestAddtions]] for how to install.
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=== 1.2 Install Apache Maven MariaDB and Java 11 ===
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installation of apache maven, java 11 and mariadb
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<code>wget -O - https://apt.corretto.aws/corretto.key | sudo gpg --dearmor -o /usr/share/keyrings/corretto-keyring.gpg && echo "deb [signed-by=/usr/share/keyrings/corretto-keyring.gpg] https://apt.corretto.aws stable main" | sudo tee /etc/apt/sources.list.d/corretto.list</code>
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NOTE: Enter the password openmrs when you get this as shown below:
 <- 100%[=============================================>] 2.40K --.-KB/s on 0s
 2025-01-29 21:32:01 (104 MB/s) - written to standard output channel [2459/2459After the password is entered, you get this in return:
 
  <code>deb [signed-by=/usr/share/keyrings/corretto-keyring.gpg] https://apt.corretto.aws stable main</code>
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==== 1.3 Install java from amazon, mariadb and maven Apache module ====
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It  brings in quite a bit
 
  <code>sudo apt install java-11-amazon-corretto-jdk mariadb-server maven -y</code>
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==== '''1.4 Configure mariadb''' ====
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sudo mariadb -u root -p
  enter the root password:
Enter the superuser password on the OS
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All this is full commentary on what happens with full feedback
 <code>Welcome to the MariaDB monitor.  Commands end with ; or \g.
   
   Your MariaDB connection id is 31
   
   Server version: 10.11.6-MariaDB-0+deb12u1 Debian 12
   
   Copyright (c) 2000, 2018, Oracle, MariaDB Corporation Ab and others.
   
   Type 'help;' or '\h' for help. Type '\c' to clear the current input statement
   
   .
   
   MariaDB [(none)]> ALTER USER 'root'@'localhost' IDENTIFIED BY 'openmrs';  
   
   Query OK, 0 rows affected (0,011 sec)
   
   MariaDB [(none)]> GRANT ALL PRIVILEGES ON *.* TO 'root'@'localhost' IDENTIFIED BY 'openmrs';
   
   Query OK, 0 rows affected (0,025 sec)
   
   
   MariaDB [(none)]> FLUSH PRIVILEGES;
   
   Query OK, 0 rows affected (0,002 sec)
   
   MariaDB [(none)]> exit;  
   
   Bye</code>
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===== 1.4.1 Check if new login with user openmrs works =====
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sudo mariadb -u root -p
 Enter password:
 exit;
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===== 1.4.2 Not mandatory: To reset the database and start from scratch: =====
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Source: https://dba.stackexchange.com/questions/261932/how-to-reset-mariadb-into-a-fresh-install-state
 <code>sudo systemctl stop mysql 
 sudo rm -rf /var/lib/mysql/* 
 sudo -u mysql mysql_install_db 
 sudo systemctl start mysql</code>
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== 2 Set up the OpenMRS SDK ==
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=== '''2.1 Install OpenMRS SDK''' ===
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Run the following command to install OpenMRS SDK. If you have already installed the SDK, you can skip this step.
 <code>mvn org.openmrs.maven.plugins:openmrs-sdk-maven-plugin:setup-sdk</code>
Note: You will be asked if you want to send anonymous usage statistics:
 
  <code>Would you be willing to help us improve SDK by sending us once in a while anonymous usage statistics (you can always change your mind by going to sdk-stats.properties and setting statsEnabled to false) [Y/n]:</code>
Press n for no
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==== 2.2 Setup OpenMRS SDK ====
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Run the following command to setup the OpenMRS SDK:
 <code>mvn openmrs-sdk:setup</code>
The command walks us through some questions:
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==== '''Select server id (server name): openmrs-sdk''' ====
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Setting up a new server...
 
 '''Specify server id (-DserverId) (default: 'server'): openmrs-sdk'''
Give the server the name: openmrs-sdk
 
 '''You can setup the following distributions:'''
 1) Reference Application 2.x
 
 2) Reference Application 3.x
 
 3) Platform
 
 4) Other...
 
 Which one do you choose? [1/2/3/4]: 2
 
 '''Select option 2 “Reference Application 3.x”'''
'''Please choose a Reference Application 3.x version:'''
 
 1) 3.3.0-SNAPSHOT
 
 2) 3.2.1
 
 3) 3.1.1
 
 4) 3.0.0
 
 Which one do you choose? [1/2/3/4]: 2
'''Note: Select 3.2.1. (choice 2). The choice number for 3.2.1 might change when the sdk is updated.'''
 '''<code>What port would you like your server to use? (default: '8080'):</code>'''
press enter to answer yes to the default answer which is 8080
 If you want to enable remote debugging by default when running the server''','''specify the port number here (e.g. 1044). Leave blank to disable debugging. 
 
 (Do not do this on a production server) (default: 'no debugging'):
'''Press enter to select the default no-debugging response'''
 '''Which database would you like to use?:'''
 1) MySQL 5.6 and above (requires pre-installed MySQL 5.6 and above)
 
 2) MySQL 8.4.1 and above in SDK docker container (requires pre-installed Docker)
 
 3) Existing docker container (requires pre-installed Docker)
 
 4) PostgreSQL 8.2 and above
 
 Which one do you choose? [1/2/3/4]: 1
'''Answer number 1 to select the correct database type.'''
 The distribution requires a MySQL database. Please specify database uri (-DdbUri) (default: 'jdbc:mysql://localhost:3306/@DBNAME@'):
'''Press enter to accept suggested value''' 
 When asked to specify your database username, specify whatever you chose when setting up your MySQL installation (defaults to root).
 
 Please specify database username (-DdbUser) (default: 'root'):
'''Press enter to accept the default value root'''
 You will be asked to enter the database password:
 
 Please specify database password (-DdbPassword):
Enter the password '''openmrs'''
 Connected to the database.
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'''Select the java version the openmrs server should use:'''
 Note: JDK 1.8 or above is needed for platform version 2.6.14.
 
 Which JDK would you like to use to run this server?:
 
 1) JAVA_HOME (currently: /usr/lib/jvm/java-11-amazon-corretto)
 
 2) Other...
 
 Which one do you choose? [1/2]: 1
'''Select option 1 to select java 11 which we installed instead.'''
 [INFO] Server configured successfully, path: /home/openmrs/openmrs/openmrs-sdk
 
 [INFO] --------------------------------------------------------------------
 
 [INFO] '''BUILD SUCCESS'''
 
 [INFO] --------------------------------------------------------------------
 
 [INFO] Total time:  26:00 min
 
 [INFO] Finished at: 2025-02-11T15:04:44+01:00
 
 [INFO] --------------------------------------------------------------------
'''Hooray, now the openmrs-sdk is finished building.'''
 2.3 Add config files
Run one command at a time: creates the two files adressConfiguration.xml and addresshierarchy.csv
 
  <code>cp openmrs/openmrs-sdk/configuration/addresshierarchy/addressConfiguration-core_demo.xml openmrs/openmrs-sdk/configuration/addresshierarchy/addressConfiguration.xml</code>
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<code>cp openmrs/openmrs-sdk/configuration/addresshierarchy/addresshierarchy-core_demo.csv openmrs/openmrs-sdk/configuration/addresshierarchy/addresshierarchy.csv</code>
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NOTE: in the commands above, replace openmrs-sdk if you selected another server-id.
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== 3 Start the OpenMRS SDK ==
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Run the following command to start the SDK:
 <code>mvn openmrs-sdk:run -DserverId=openmrs-sdk</code>
NOTE: It often takes more than 10 minutes to run through the installation, maybe as much as 30 minutes.
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After a while you see this message in the console:
  OpenMRS is ready for you at <nowiki>http://localhost:8080/openmrs/</nowiki>
  feb. 11, 2025 3:07:23 P.M. org.apache.coyote.AbstractProtocol start
  INFO: Starting ProtocolHandler ["http-nio-8080"]
You can now access http://localhost:8080/openmrs/spa in a browser to continue the rest of the installation.
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'''Note that the address changes after installation, so go to: http://localhost:8080/openmrs/spa again in the web browser of the virtual machine.'''
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== 4 Log in to the front page ==
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Go to:  http://localhost:8080/openmrs/spa
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Login with: admin
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Password: Admin123
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Select locaton
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As a test, select: '''Outpatient clinic''' (Poliklinikk)
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For now: Don't remember the location until next time
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==== 4.1 Links ====
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The guides:https://openmrs.atlassian.net/wiki/spaces/docs/pages/26936930/O3+Setup+Configuration+Deployment#O3Setup,Configuration&Deployment-SetupOpenMRS3WithOpenMRSSDK
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older guide: https://o3-docs.openmrs.org/docs/recipes/set-up-o3-instance
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https://openmrs.jfrog.io/ui/native/releases/org/openmrs/distro-emr-configuration/
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==== 4.2 Error correction Not mandatory ====
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If you get this error message in the internet browser:
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'''Invalid or Missing CSRF Token. Try Going Back and Refresh the page after clearing the browser cache.'''
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Do the following:
 <code>pico openmrs/openmrs-o3-test/tmp/openmrs/WEB-INF/csrfguard.properties</code>
Change from:
  <code>'''org.owasp.csrfguard.Enabled''' = true</code>
to:
  <code>'''org.owasp.csrfguard.Enabled''' = false</code>
restart openmrs
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== 5 Backup database ==
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=== '''5.1 Full backup of database with mariadb-backup:''' ===
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Note: If you have already done a full backup once, you can proceed with incremental FIXME (internal link) backups.
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In the virtual machine where the openmrs database is running, create a folder to backup the database to:
 
 mkdir -p backup/openmrs-database
The folder is now created
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=== '''5.2 Take a full backup of the entire database''' ===
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mariadb-dump -u root -p --all-databases > backup/openmrs-database/openmrs_full_backup_$(date +%F_%R).sql
Enter the database password when prompted.
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In this example, the password is: openmrs
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To confirm the database is fully backed up to backup/openmrs database with time stamps, do:
 openmrs@openmrs:~$ ls -l backup/openmrs-database/
 totalt 11008
 -rw-r--r-- 1 openmrs openmrs 11271689 feb.  28 13:09 openmrs_full_backup_2025-02-28_13:09.sql
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==== 5.2.1 Copy the backup to another machine: ====
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Om the machine you want to send the backup to, create a folder to store the backup in.
 mkdir -p backup/openmrs-database
The folder is created
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Retrieve the database backup with scp:
 scp openmrs@192.168.0.181:/home/openmrs/backup/openmrs-database/openmrs_full_backup_2025-02-28_13:09.sql backup/openmrs-database/
Verify the database backup is copied to the other machine:
 ls -l backup/openmrs-database/
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total 11008
 
 -rw-r--r-- 1 openmrs openmrs 11271689 feb.  28 13:19 openmrs_full_backup_2025-02-28_13:09.sql
See also: https://openmrs.atlassian.net/wiki/search?text=backup for more articles on backing up the database.
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=== 5.3 Incremental backup of the database ===
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Incremental backup takes a backup of the changes as opposed to a full backup. This saves space, especially on larger databases.
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You must have a [https://wiki.pc-aid.no/Devops:Install_OpenMRS_SDK#5.1_Full_backup_of_database_with_mariadb-backup: full backup] of the database to run an incremental backup.
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sources: https://mariadb.com/kb/en/incremental-backup-and-restore-with-mariabackup/
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=== 5.4 Useful tips about mariadb database: ===
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===== 5.4.1 Reset root password: =====
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Stop the database
 sudo systemctl stop mariadb.service
Start MySQL/MariaDB in Safe Mode with the command:
 mariadbd-safe --skip-grant-tables &
You can now log in to MySQL/MariaDB as root without having to enter a password:
 mariadb -u root
Reset the MySQL/MariaDB password with the following command. Change my-new-password to a secure password.
 UPDATE user SET password=PASSWORD("my-new-password") WHERE user='root';
Reload the privilege tables:
 FLUSH PRIVILEGES;
Exit the MySQL/MariaDB client:
 quit;
Shut down MySQL/MariaDB:
 mariadb-admin -u root -p shutdown
Start MySQL/MariaDB:
 sudo systemctl start mariadb.service
source:https://www.ionos.com/digitalguide/hosting/technical-matters/reset-mysql-mariadb-root-password/
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