### Install GPG and Generate Key Pair

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Perform this one-time setup on the backup server to install GPG and generate a new key pair for encryption.

```bash
sudo apt-get install gnupg
gpg --gen-key
```

--------------------------------

### Run the Base Distro

Source: https://github.com/msf-ocg/lime-emr/blob/main/docs/README.md

After building, source the script to navigate to the correct directory and then start the demo environment. OpenMRS will be accessible at http://localhost:4001/openmrs.

```bash
source distro/target/go-to-scripts-dir.sh
./start-demo.sh
```

--------------------------------

### Frontend Configuration Inheritance Example

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Demonstrates how frontend configuration URLs are inherited and overridden from distro to site level using the SPA_CONFIG_URLS environment variable.

```properties
# Distro-level only:
SPA_CONFIG_URLS=/openmrs/spa/configs/msf-frontend-config.json

# Site-level (inherits distro + adds site overrides):
SPA_CONFIG_URLS=/openmrs/spa/configs/msf-frontend-config.json,/openmrs/spa/configs/msf-mosul-frontend-config.json
```

--------------------------------

### Build and Run New Site

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Command to build the new site module and start the demo script. This includes packaging the site and running its Docker environment.

```bash
./scripts/mvnw clean package -pl sites/newsite -am
cd sites/newsite/target/ozone-msf-newsite-<version>/run/docker/scripts
./start-demo.sh
```

--------------------------------

### Run Restore Backup Manually

Source: https://github.com/msf-ocg/lime-emr/wiki/Backups

Execute the restore backup script, specifying the paths to the full and incremental backup directories. This example also includes commands to stop and start a demo service, potentially related to the environment being restored.

```bash
bash restore_backup.sh --full /home/backup/full/2025-05-01_16-45-10/ --incremental /home/backup/incremental/2025-05-01_16-45-24/
export TRAEFIK="false" && ./stop-demo.sh
export TRAEFIK="false" && ./start-demo.sh
```

--------------------------------

### Build the Project with Maven

Source: https://github.com/msf-ocg/lime-emr/blob/main/docs/README.md

Execute this command to clean and package the project using the included Maven wrapper. Ensure Java 8+ and Maven 3.x are installed.

```bash
./scripts/mvnw clean package
```

--------------------------------

### Install Docker and Docker Compose on Ubuntu

Source: https://github.com/msf-ocg/lime-emr/wiki/Troubleshooting

Use these commands to update your package list and install the latest versions of Docker CE, Docker Compose, and related plugins on an Ubuntu system. Ensure you have the necessary permissions to run these commands.

```bash
sudo apt update
sudo apt install -y ca-certificates curl gnupg lsb-release

sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | \
  sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg

echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] \
  https://download.docker.com/linux/ubuntu \
  $(lsb_release -cs) stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt update
sudo apt install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
```

--------------------------------

### Run Bunia Site Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Navigate to the Bunia site's Docker scripts directory and run the start script to launch the site-specific configuration. This includes distro configuration plus Bunia overrides.

```bash
cd sites/bunia/target/ozone-msf-bunia-<version>/run/docker/scripts
./start-demo.sh

```

--------------------------------

### OpenFn Project State JSON Example

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Contains OpenFn project metadata, retention policies, and credential references. It maps credential names to their IDs and owners.

```json
{
  "id": "69066751-5f2c-459c-b42e-feba1c802383",
  "name": "msf-lime-mosul",
  "history_retention_period": 90,
  "dataclip_retention_period": 90,
  "project_credentials": {
    "owner@openfn.org-OpenMRS-Demo": {
      "id": "45634fcb-...",
      "name": "OpenMRS Demo",
      "owner": "owner@openfn.org"
    },
    "owner@openfn.org-MSF-DHIS2-UAT": {
      "id": "9716980f-...",
      "name": "MSF DHIS2 UAT",
      "owner": "owner@openfn.org"
    }
  }
}
```

--------------------------------

### OpenFn Workflow Definition Example

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Defines OpenFn projects, workflows, jobs, triggers, and edges. This example shows a workflow with two jobs: Fetch-Metadata using the HTTP adaptor and Map-DHIS2-to-OpenMRS using the FHIR adaptor.

```yaml
workflows:
  wf1-dhis2-omrs-migration:
    name: wf1-dhis2-omrs-migration
    jobs:
      Fetch-Metadata:
        name: Fetch Metadata
        adaptor: "@openfn/language-http@6.5.1"
        body: |
          // JavaScript job code for data transformation
      Map-DHIS2-to-OpenMRS:
        name: Map DHIS2 to OpenMRS
        adaptor: "@openfn/language-fhir@1.0.0"
        body: |
          // FHIR-based mapping logic
```

--------------------------------

### New Site pom.xml Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Example pom.xml for a new site, specifying dependencies and packaging. It inherits from the distro artifact and requires specific Maven plugins for configuration management.

```xml
<groupId>com.ozonemsf</groupId>
<artifactId>ozone-msf-newsite</artifactId>
<version>1.0.0-SNAPSHOT</version>
<packaging>pom</packaging>

<dependencies>
  <dependency>
    <artifactId>ozone-msf-distro</artifactId>
    <groupId>com.ozonemsf</groupId>
    <version>1.0.0-SNAPSHOT</version>
    <type>zip</type>
  </dependency>
</dependencies>
```

--------------------------------

### OpenFn Adaptor Registry Cache Example

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

A local cache of available OpenFn adaptors and their versions to prevent repeated registry lookups and improve startup performance.

```json
[
  {
    "name": "@openfn/language-http",
    "versions": [{"version": "1.0.0"}, {"version": "6.5.1"}],
    "latest": "6.5.1"
  },
  {
    "name": "@openfn/language-dhis2",
    "versions": [...],
    "latest": "..."
  }
]
```

--------------------------------

### Run Mosul Site Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Navigate to the Mosul site's Docker scripts directory and run the start script to launch the site-specific configuration. This includes distro configuration plus Mosul overrides.

```bash
cd sites/mosul/target/ozone-msf-mosul-<version>/run/docker/scripts
./start-demo.sh

```

--------------------------------

### Run Matsapha Site Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Navigate to the Matsapha site's Docker scripts directory and run the start script to launch the site-specific configuration. This includes distro configuration plus Matsapha overrides.

```bash
cd sites/matsapha/target/ozone-msf-matsapha-<version>/run/docker/scripts
./start-demo.sh

```

--------------------------------

### Single-Command VPS Deployment Orchestrator

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

The deploy-lime.sh script automates the provisioning of a LIME EMR instance on a fresh Ubuntu VPS. It orchestrates four phases: security hardening, Docker installation, pulling bundled scripts, and starting the LIME instance.

```text
┌─────────────────────────────────────────────────────────────────┐
│                      deploy-lime.sh                             │
│                                                                 │
│  Phase 1 ──  VPS Security Hardening         (secure-vps.sh)    │
│  Phase 2 ──  Docker & Package Installation  (bundled_docker_…) │
│  Phase 3 ──  Pull Bundled-Docker Scripts    (pull_bundled_…)   │
│  Phase 4 ──  Start LIME Instance            (start-bundled-…)  │
│                                                                 │
│  Output:  Running LIME EMR on a hardened VPS with HTTPS         
└─────────────────────────────────────────────────────────────────┘
```

--------------------------------

### Run Base MSF Distribution

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Execute these commands to start the base MSF distribution, which includes organization-wide defaults. OpenMRS will be accessible at http://localhost:4001/openmrs.

```bash
source distro/target/go-to-scripts-dir.sh
./start-demo.sh

```

--------------------------------

### Run Iraq Country-Level Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Navigate to the Iraq country-level Docker scripts directory and run the start script to launch the configuration. This includes distro configuration plus Iraq overrides, without site-specific settings.

```bash
cd countries/iraq/target/ozone-msf-iraq-<version>/run/docker/scripts
./start-demo.sh

```

--------------------------------

### Build LIME EMR Project

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Use this command to clean and package the LIME EMR project. Ensure you have Java 8+ and Maven 3.x installed.

```bash
./scripts/mvnw clean package

```

--------------------------------

### Example Form JSON Structure

Source: https://github.com/msf-ocg/lime-emr/blob/main/docs/translations.md

This JSON structure represents a form definition, including its name, description, version, and pages with sections and questions. It serves as a reference for creating translation files.

```json
{
  "name": "F13-PNC",
  "description": "Postnatal Care Form",
  "version": "1",
  "published": true,
  "uuid": "",
  "processor": "EncounterFormProcessor",
  "encounter": "Maternal Health",
  "encounterType": "dd528487-82a5-4082-9c72-ed246bd49591",
  "retired": false,
  "referencedForms": [],
  "pages": [
    {
      "label": "Postnatal Care",
      "sections": [
        {
          "label": "General information",
          "isExpanded": false,
          "questions": [
            {
              "id": "typeOfConsultation",
              "label": "Type of consultation",
              "type": "obs",
              "required": false,
              "questionOptions": {
                "rendering": "radio",
                "concept": "typeOfConsultation",
                "answers": [
                  {
                    "label": "Admission",
                    "concept": "admission"
                  },
                  {
                    "label": "Follow up",
                    "concept": "followUp"
                  },
                  {
                    "label": "Discharge",
                    "concept": "discharge"
                  }
                ]
              }
            },
            {
              "id": "caretakersName",
              "label": "Caretaker's name",
              "type": "obs",
              "required": false,
              "questionOptions": {
                "rendering": "text",
                "concept": "caretakersName"
              }
            }
          ]
        }
      ]
    }
  ]
}
```

--------------------------------

### Run a Specific Site Demo

Source: https://github.com/msf-ocg/lime-emr/blob/main/docs/README.md

Navigate to the specific site's Docker scripts directory and run the start-demo script to launch a particular site's environment. Replace <version> with the actual version number.

```bash
# Mosul (Iraq)
cd sites/mosul/target/ozone-msf-mosul-<version>/run/docker/scripts
./start-demo.sh
```

```bash
# Matsapha (Eswatini)
cd sites/matsapha/target/ozone-msf-matsapha-<version>/run/docker/scripts
./start-demo.sh
```

```bash
# Bunia (DRC)
cd sites/bunia/target/ozone-msf-bunia-<version>/run/docker/scripts
./start-demo.sh
```

--------------------------------

### Build and Restart OpenMRS with Initializer

Source: https://github.com/msf-ocg/lime-emr/blob/main/docs/content-management.md

After adding the OCL ZIP file, build the OpenMRS project and restart the relevant site or distribution to load the concepts.

```bash
./scripts/mvnw clean package
# then start the relevant site or distro
```

--------------------------------

### Perform Manual PostgreSQL Backup

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

This command creates a manual backup of the OpenFn PostgreSQL database. Replace `hello` and `lightning_prod` with your specific database user and name if they differ.

```bash
docker exec openfn-postgresql pg_dump \
  -U hello lightning_prod \
  | gzip > openfn_backup_$(date +%Y%m%d).sql.gz
```

--------------------------------

### Enable HTTPS with Traefik

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Enable HTTPS for LIME EMR by setting the TRAEFIK environment variable and running the start script. This configures Traefik as a reverse proxy with automatic SSL certificates.

```bash
export TRAEFIK="true" && ./start-demo.sh
```

--------------------------------

### New Site Directory Structure

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Illustrates the required directory structure for a new site, including configuration files for OpenMRS, OpenFn, and other components.

```text
sites/newsite/
├── pom.xml
├── assembly.xml
└── configs/
    ├── openmrs/
    │   ├── frontend_config/
    │   │   └── msf-newsite-frontend-config.json
    │   └── initializer_config/
    │       ├── addresshierarchy/         # Site-specific address hierarchy CSV + XML
    │       ├── locations/                # Facility location definitions
    │       ├── idgen/                    # Patient ID generation schemes
    │       ├── visittypes/               # Visit type definitions
    │       ├── appointmentservicedefinitions/
    │       └── ...                       # Any other overrides
    └── openfn/
        ├── newsite-project.yaml          # OpenFn workflow definitions
        ├── projectState.json             # OpenFn credentials and project metadata
        ├── adaptor_registry_cache.json   # Cached OpenFn adaptor versions
        └── version.txt
```

--------------------------------

### New Site assembly.xml Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

The assembly.xml file for a new site, which is typically identical across sites and defines how the final ZIP artifact is assembled.

```xml
<assembly>
  <id>zip</id>
  <formats><format>zip</format></formats>
  <includeBaseDirectory>false</includeBaseDirectory>
  <fileSets>
    <fileSet>
      <outputDirectory>.</outputDirectory>
      <directory>${project.build.directory}/${project.artifactId}-${project.version}</directory>
    </fileSet>
  </fileSets>
</assembly>
```

--------------------------------

### Create Backup Directory

Source: https://github.com/msf-ocg/lime-emr/blob/main/docs/restic_backup.md

Create and set permissions for the local directory where Restic will store backups.

```bash
sudo mkdir -p ~/backups/restic_data

# Set appropriate permissions
sudo chmod 700 ~/backups/restic_data

# Change ownership if needed
sudo chown $USER:$USER ~/backups/restic_data
```

--------------------------------

### Restore and Reset Database Scripts

Source: https://github.com/msf-ocg/lime-emr/wiki/Go-Live

Execute SQL scripts to restore a backup, reset the database, and create users. Ensure correct database credentials and file paths are used.

```bash
zcat -v LIME-EMR-Tooling/Backups/Mosul/mosul__20250508_140058.sql.gz  | docker exec -i ozone-msf-mosul-mysql-1 /usr/bin/mysql -u root --password='dbpassword' openmrs -v
```

```bash
cat -v LIME-EMR-Tooling/Procedures/Reset\ Database/reset_db.sql | docker exec -i ozone-msf-mosul-mysql-1 /usr/bin/mysql -u openmrs --password='dbpassword' openmrs -v
```

```bash
cat -v LIME-EMR-Tooling/Users/Mosul_Users_202503172205.sql | docker exec -i ozone-msf-mosul-mysql-1 /usr/bin/mysql -u openmrs --password='dbpassword' openmrs -v
```

--------------------------------

### Create Backup Directory for Restic

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Create and set permissions for the Restic backup directory. Ensure it is owned by the current user.

```bash
sudo mkdir -p ~/backups/restic_data
sudo chmod 700 ~/backups/restic_data
sudo chown $USER:$USER ~/backups/restic_data
```

--------------------------------

### Encrypt Backup File with GPG

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Encrypt a backup file using GPG. Replace `"Your Name"` with the name associated with your GPG key.

```bash
gpg --encrypt --recipient "Your Name" openmrs_backup_20250101.sql.gz
```

--------------------------------

### Build Bundled Docker Images

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Build bundled Docker images using Maven. Use the `-Pbundled-docker` profile for standard builds and add `-Pproduction` for production tags.

```bash
./scripts/mvnw clean package -Pbundled-docker
```

```bash
./scripts/mvnw clean package -Pbundled-docker -Pproduction
```

--------------------------------

### Perform Manual MySQL/MariaDB Backup

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Use this command to create a manual backup of the OpenMRS MySQL/MariaDB database. Ensure you replace `<password>` with your actual database password.

```bash
docker exec openmrs-db /usr/bin/mysqldump \
  --max_allowed_packet=512M \
  -u openmrs --password='<password>' \
  openmrs --skip-lock-tables --single-transaction --skip-triggers \
  | gzip > openmrs_backup_$(date +%Y%m%d).sql.gz
```

--------------------------------

### Configuration Inheritance Diagram

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Visual representation of the LIME EMR's three-level configuration inheritance model, showing how Distro, Country, and Site configurations are layered.

```mermaid
%%{init: {'theme':'forest'}}%%
flowchart TD
    subgraph Inheritance["Configuration Inheritance"]
        direction TB
        OZONE["Ozone HIS (Parent Platform)"] --> DISTRO["Distro: MSF Base Config"]
        DISTRO --> COUNTRY["Country: e.g., Iraq"]
        DISTRO --> SITE_A["Site: e.g., Mosul"]
        DISTRO --> SITE_B["Site: e.g., Matsapha"]
        DISTRO --> SITE_C["Site: e.g., Bunia"]
    end

    subgraph Build["Build & Deploy"]
        direction TB
        GH["GitHub Repository"] -->|Maven build| ARTIFACTS["ZIP Artifacts + Docker Images"]
        ARTIFACTS -->|GitHub Actions deploy| SERVER["Execution Server"]
    end

    Inheritance --> Build
```

--------------------------------

### Run Full Backup Manually

Source: https://github.com/msf-ocg/lime-emr/wiki/Backups

Execute the full backup script directly from the command line for immediate backup operations.

```bash
bash full_backup.sh
```

--------------------------------

### Build Bundled Docker Images

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Activate the bundled-docker Maven profile to build and push pre-configured Docker images to Docker Hub. This command packages all necessary components for deployment.

```bash
./scripts/mvnw clean package -Pbundled-docker
```

--------------------------------

### Configure Follow-up Table Columns

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Define the columns for the follow-up table by editing the `obs-table-horizontal-widget` configuration in the frontend config. Add concept UUIDs to the `data` array to specify which concepts to display.

```json
"obs-table-horizontal-widget": {
  "title": "My Follow-up Table",
  "oldestFirst": true,
  "editable": true,
  "encounterTypeToCreateUuid": "<encounter-type-uuid>",
  "data": [
    {"concept": "<concept-uuid-1>"},
    {"concept": "<concept-uuid-2>"}
  ]
}
```

--------------------------------

### List Available Restic Snapshots

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Execute this command within the backup container to view a list of all available snapshots for restoration.

```bash
docker exec backup restic snapshots
```

--------------------------------

### Add Custom System Task

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Define custom system tasks by adding rows to the `systemtasks.csv` file located in `configs/openmrs/initializer_config/systemtasks/`. Ensure all required columns are populated.

```csv
Uuid,Name,Title,Description,Priority,Default Assignee Role,Rationale
a1b2c3d4-e5f6-...,check-wound-dressing,Check wound dressing,Monitoring > Wound Care,Medium,Nurse,
```

--------------------------------

### Add OCL ZIP to Distribution Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/docs/content-management.md

Place the exported OCL ZIP file in the appropriate configuration directory for the Initializer module to load concepts automatically on OpenMRS startup.

```bash
distro/configs/openmrs/initializer_config/ocl/    # for distro-level concepts
sites/<site>/configs/openmrs/initializer_config/ocl/    # for site-specific concepts
```

--------------------------------

### Copy Initializer Config with Content-Package Structure in POM

Source: https://github.com/msf-ocg/lime-emr/blob/main/setting_up_new_site.md

Add an antrun execution in pom.xml to copy initializer_config files, structuring them with the artifact name as a subfolder for correct override order.

```xml
<execution>
  <id>Copy local initializer_config with content-package structure</id>
  <phase>process-resources</phase>
  <goals>
    <goal>run</goal>
  </goals>
  <configuration>
    <target>
      <mkdir dir="${project.build.directory}/${project.artifactId}-${project.version}/distro/configs/openmrs/initializer_config"/>
      <copy todir="${project.build.directory}/${project.artifactId}-${project.version}/distro/configs/openmrs/initializer_config">
        <fileset dir="${project.basedir}/configs/openmrs/initializer_config"/>
        <mapper type="regexp"
                from="^([^/]+)/(.+$"
                to="\1/${project.artifactId}/\2"/>
      </copy>
    </target>
  </configuration>
</execution>
```

--------------------------------

### Restore Manual PostgreSQL Backup

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

This command restores a manual SQL dump to the OpenFn PostgreSQL database. Ensure the backup file `openfn_backup_20250101.sql.gz` exists.

```bash
gunzip < openfn_backup_20250101.sql.gz | docker exec -i openfn-postgresql psql -U hello lightning_prod
```

--------------------------------

### Root pom.xml Module Registration

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Shows how to register a new site module within the root pom.xml file to include it in the multi-module build.

```xml
<modules>
  <module>distro</module>
  <module>countries/iraq</module>
  <module>sites/mosul</module>
  <module>sites/matsapha</module>
  <module>sites/newsite</module>    <!-- Add this line -->
</modules>
```

--------------------------------

### Configure Backup Script Logging

Source: https://github.com/msf-ocg/lime-emr/wiki/Backups

Redirect the standard output and standard error of the backup and restore scripts to a central log file for monitoring and troubleshooting.

```bash
/home/lime/full_backup.sh >> /var/log/backup.log 2>&1
/home/lime/incremental_backup.sh >> /var/log/backup.log 2>&1
/home/lime/restore_backup.sh >> /var/log/backup.log 2>&1
```

--------------------------------

### Maven Execution to Copy Distro Resources

Source: https://github.com/msf-ocg/lime-emr/blob/main/setting_up_new_site.md

This Maven execution configuration is used to copy metadata files from the distro directory to the build output. It allows for excluding specific configuration files and directories that are not needed for the site.

```xml
<execution>
  <!-- Copy Ozone MSF files -->
  <id>Copy Ozone MSF files</id>
  <phase>process-resources</phase>
  <goals>
    <goal>copy-resources</goal>
  </goals>
  <configuration>
    <outputDirectory>
      ${project.build.directory}/${project.artifactId}-${project.version}</outputDirectory>
    <overwrite>true</overwrite>
    <resources>
      <resource>
        <directory>${project.build.directory}/ozone-msf-distro</directory>
        <excludes>
          <exclude>distro/configs/**/addresshierarchy/*.*</exclude>
          <exclude>distro/configs/**/addresshierarchy/**/*.*</exclude>
          <exclude>distro/configs/**/locations/**/*.*</exclude>
          <exclude>distro/configs/**/idgen/**/*.*</exclude>
          <exclude>distro/configs/**/visittypes/**/*.*</exclude>
          <exclude>distro/configs/**/appointmentservicedefinitions/**/*.*</exclude>
          <exclude>distro/configs/**/appointmentservicetypes/**/*.*</exclude>
          <exclude>distro/ozone-info.json</exclude>
        </excludes>
      </resource>
    </resources>
  </configuration>
</execution>
```

--------------------------------

### Exclude App from Build Entirely (Distro-Level)

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Exclude a frontend app from the build for all sites by adding it to the `frontendModuleExcludes` array in the `spa-assemble-config.json` file.

```json
{
  "frontendModuleExcludes": [
    "@openmrs/esm-some-app"
  ]
}
```

--------------------------------

### Run All E2E Tests Locally

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Execute all end-to-end tests locally using the yarn command. Ensure your environment variables are correctly set in the .env file.

```bash
yarn test:e2e
```

--------------------------------

### Set Java 8 Environment Variables

Source: https://github.com/msf-ocg/lime-emr/blob/main/java8_profile_config.txt

Configures the JAVA_HOME and PATH environment variables for Java 8. Ensure the JDK path is correct for your system.

```bash
export JAVA_HOME="/Library/Java/JavaVirtualMachines/temurin-8.jdk/Contents/Home"
export PATH="$JAVA_HOME/bin:$PATH"
```

--------------------------------

### Restore Manual MySQL/MariaDB Backup

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

This command restores a manual SQL dump to the OpenMRS database. Ensure the backup file `openmrs_backup_20250101.sql.gz` exists and replace `<password>` if necessary.

```bash
gunzip < openmrs_backup_20250101.sql.gz | docker exec -i openmrs-db mysql -u openmrs --password='<password>' openmrs
```

--------------------------------

### Run Specific E2E Login Tests

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Execute only the end-to-end login tests locally. This is useful for quickly verifying authentication flows.

```bash
yarn test:login
```

--------------------------------

### Runtime Services Diagram

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Diagram illustrating the runtime services of LIME EMR, including OpenMRS, OpenFn, databases, and supporting infrastructure like Traefik and Keycloak.

```mermaid
%%{init: {'theme':'forest'}}%%
flowchart LR
    subgraph Services["Runtime Services"]
        direction TB
        OPENMRS_BE["OpenMRS Backend (Java 8)"]
        OPENMRS_FE["OpenMRS Frontend (ESM)"]
        MYSQL["MySQL"]
        OPENFN["OpenFn Lightning"]
        POSTGRES["PostgreSQL"]
        TRAEFIK["Traefik (SSL)"]
        KEYCLOAK["Keycloak (OAuth2)"]
    end

    OPENMRS_FE -->|REST API| OPENMRS_BE
    OPENMRS_BE --> MYSQL
    OPENFN --> POSTGRES
    OPENFN -->|FHIR / REST| OPENMRS_BE
    OPENFN -->|Tracker API| DHIS2["DHIS2"]
    TRAEFIK -->|SSL termination| OPENMRS_FE
    TRAEFIK --> OPENFN
    KEYCLOAK -->|OAuth2| OPENMRS_BE
```

--------------------------------

### Replicate Backup Data with Rsync

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

For ongoing file-level replication of backup data, use `rsync`. This command synchronizes the local backup directory with the remote server, deleting extraneous files on the destination.

```bash
rsync -a --delete ~/backups/restic_data/ backup@remote-server:/backups/restic_data/
```

--------------------------------

### Set GitHub Authentication Token

Source: https://github.com/msf-ocg/lime-emr/wiki/Troubleshooting

Export your GitHub fine-grained token as an environment variable to authenticate with private repositories when using scripts like `get_lime.sh`. Replace 'your_github_token_here' with your actual token.

```bash
export GITHUB_AUTH_TOKEN=your_github_token_here
```

--------------------------------

### Run Incremental Backup Manually

Source: https://github.com/msf-ocg/lime-emr/wiki/Backups

Execute the incremental backup script directly from the command line for immediate incremental backup operations.

```bash
bash incremental_backup.sh
```

--------------------------------

### OpenMRS Docker Compose Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/scripts/docker-compose-files.txt

Sets up the OpenMRS service, including its database and application configurations. It typically extends common configurations.

```yaml
services:
  openmrs:
    image: openmrs/openmrs-reference-app:latest
    container_name: openmrs
    ports:
      - "8080:8080"
    depends_on:
      - postgres
    environment:
      DB_HOST: postgres
      DB_PORT: 5432
      DB_NAME: emr
      DB_USER: emr
      DB_PASSWORD: emr

```

--------------------------------

### Backup Docker Compose Configuration

Source: https://github.com/msf-ocg/lime-emr/blob/main/scripts/docker-compose-files.txt

Configures the backup service, likely for database or application data. This file specifies the services required for performing backups.

```yaml
services:
  backup:
    image: ubuntu:latest
    container_name: backup
    volumes:
      - ./backup-scripts:/scripts
    command: /bin/bash /scripts/backup.sh

```

--------------------------------

### Maven GitHub Packages Credentials

Source: https://github.com/msf-ocg/lime-emr/blob/main/README.md

Configure your Maven settings to authenticate with GitHub Packages. Replace YOUR_GITHUB_USERNAME and YOUR_GITHUB_TOKEN with your actual credentials.

```xml
<servers>
  <server>
    <id>msf-ocg-github-lime-emr</id>
    <username>YOUR_GITHUB_USERNAME</username>
    <password>YOUR_GITHUB_TOKEN</password>
  </server>
</servers>
```