This commit is contained in:
akbermirage 2025-09-30 10:14:25 +06:00
commit cc8b5fb0d0
11 changed files with 502 additions and 56 deletions

283
.gitea/workflows/ci-cd.yaml Normal file
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name: FHIR IG CI/CD Pipeline
on:
push:
branches: [ main, develop ]
pull_request:
branches: [ main ]
env:
REGISTRY: git.dghs.gov.bd # Replace with your Gitea instance
IMAGE_NAME: gitadmin/bd-core-fhir-ig # Replace with your image name
jobs:
build-ig:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v3
with:
fetch-depth: 0 # Full history for proper IG building
- name: Install Docker CLI
run: |
apt-get update
apt-get install -y docker.io
docker --version
- name: Setup Docker Buildx
uses: docker/setup-buildx-action@v3
with:
install: true
- name: Build FHIR IG (Copy In/Out)
run: |
echo "Building FHIR IG using copy approach..."
# Create a container (don't start yet)
CONTAINER_ID=$(docker create \
hl7fhir/ig-publisher-base:latest \
/bin/bash -c "cp -r /home/publisher/ig /tmp/build && cd /tmp/build && _updatePublisher.sh -y && _genonce.sh")
echo "Container ID: $CONTAINER_ID"
# Copy all source files into the container
docker cp $(pwd)/. $CONTAINER_ID:/home/publisher/ig/
# Start and wait for completion
docker start -a $CONTAINER_ID
EXIT_CODE=$?
# Copy outputs back
echo "Copying outputs from container..."
docker cp $CONTAINER_ID:/tmp/build/output ./output || echo "Warning: No output directory"
docker cp $CONTAINER_ID:/tmp/build/fsh-generated ./fsh-generated || echo "No FSH generated files"
docker cp $CONTAINER_ID:/tmp/build/input-cache ./input-cache || echo "No input-cache"
docker cp $CONTAINER_ID:/tmp/build/temp ./temp || echo "No temp directory"
# Show container logs if failed
if [ $EXIT_CODE -ne 0 ]; then
echo "Build failed, showing container logs:"
docker logs $CONTAINER_ID
fi
# Cleanup
docker rm $CONTAINER_ID
# Verify
if [ ! -f "output/index.html" ]; then
echo "ERROR: Build failed - no index.html"
exit 1
fi
echo "✅ Build successful!"
- name: Verify IG Output
run: |
ls -la output/
if [ ! -f "output/index.html" ]; then
echo "ERROR: IG build failed - no index.html found"
exit 1
fi
echo "IG build successful!"
- name: Login to Gitea Container Registry
if: github.ref == 'refs/heads/main'
uses: docker/login-action@v3
with:
registry: ${{ env.REGISTRY }}
username: ${{ gitea.actor }}
password: ${{ secrets.ACCESS_TOKEN_GITEA }}
- name: Extract metadata
if: github.ref == 'refs/heads/main'
id: meta
uses: docker/metadata-action@v4
with:
images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
tags: |
type=ref,event=branch
type=ref,event=pr
type=sha,prefix={{branch}}-
type=raw,value=latest,enable={{is_default_branch}}
- name: Build and push Docker image
if: github.ref == 'refs/heads/main'
uses: docker/build-push-action@v6
with:
context: .
file: ./Dockerfile.serve
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
# cache-from: type=gha
# cache-to: type=gha,mode=max
deploy:
needs: build-ig
runs-on: ubuntu-latest
if: github.ref == 'refs/heads/main'
steps:
- name: Checkout repository
uses: actions/checkout@v3
- name: Deploy to server
uses: appleboy/ssh-action@v1.0.3
env:
REGISTRY: ${{ env.REGISTRY }}
IMAGE_NAME: ${{ env.IMAGE_NAME }}
IMAGE_TAG: latest
with:
host: ${{ secrets.DEPLOY_HOST }}
username: ${{ secrets.DEPLOY_USER }}
password: ${{ secrets.DEPLOY_PASSWORD }}
port: ${{ secrets.DEPLOY_PORT || 22 }}
envs: REGISTRY,IMAGE_NAME,IMAGE_TAG
script: |
# Create deployment directory if it doesn't exist
mkdir -p /opt/fhir-ig
cd /opt/fhir-ig
# Create docker-compose.prod.yml
cat > docker-compose.prod.yml << EOF
services:
fhir-ig:
image: \${REGISTRY}/\${IMAGE_NAME}:\${IMAGE_TAG:-latest}
container_name: fhir-ig-app
restart: unless-stopped
ports:
- "80:80"
environment:
- NODE_ENV=production
networks:
- fhir-ig-network
healthcheck:
test: ["CMD", "wget", "--no-verbose", "--tries=1", "--spider", "http://127.0.0.1/health"]
interval: 30s
timeout: 10s
retries: 3
start_period: 40s
logging:
driver: "json-file"
options:
max-size: "10m"
max-file: "3"
volumes:
- fhir-ig-logs:/var/log/nginx
networks:
fhir-ig-network:
driver: bridge
volumes:
fhir-ig-logs:
driver: local
EOF
# Create deployment script
cat > deploy.sh << 'DEPLOY_SCRIPT'
#!/bin/bash
set -e
# Configuration
COMPOSE_FILE="docker-compose.prod.yml"
SERVICE_NAME="fhir-ig"
BACKUP_DIR="/opt/backups/fhir-ig"
LOG_FILE="/var/log/fhir-ig-deploy.log"
# Create directories
mkdir -p "$BACKUP_DIR"
mkdir -p "$(dirname "$LOG_FILE")"
# Logging function
log() {
echo "$(date '+%Y-%m-%d %H:%M:%S') - $1" | tee -a "$LOG_FILE"
}
log "Starting deployment of BD Core FHIR IG..."
log "Registry: $REGISTRY"
log "Image: $IMAGE_NAME"
log "Tag: $IMAGE_TAG"
# Login to registry
echo "$GITEA_PASSWORD" | docker login $REGISTRY -u "$GITEA_USERNAME" --password-stdin
# Backup current container if it exists
if docker compose -f "$COMPOSE_FILE" ps --services --filter "status=running" | grep -q "$SERVICE_NAME"; then
log "Creating backup of current deployment..."
BACKUP_FILE="$BACKUP_DIR/backup-$(date +%Y%m%d-%H%M%S).tar.gz"
docker compose -f "$COMPOSE_FILE" exec -T "$SERVICE_NAME" tar -czf - -C /usr/share/nginx/html . > "$BACKUP_FILE" 2>/dev/null || log "Backup failed, continuing..."
fi
# Set environment variables for docker compose
export REGISTRY="$REGISTRY"
export IMAGE_NAME="$IMAGE_NAME"
export IMAGE_TAG="$IMAGE_TAG"
# Pull the latest image
log "Pulling latest image: $REGISTRY/$IMAGE_NAME:$IMAGE_TAG..."
docker pull "$REGISTRY/$IMAGE_NAME:$IMAGE_TAG"
# docker pull "\${REGISTRY}/\${IMAGE_NAME}:\${IMAGE_TAG}"
# Stop and remove old container
log "Stopping old container..."
docker compose -f "$COMPOSE_FILE" down || log "No existing container to stop"
# Start new container
log "Starting new container..."
docker compose -f "$COMPOSE_FILE" up -d
# Wait for container to be healthy
# log "Waiting for container to become healthy..."
# timeout=120
# elapsed=0
# healthy=false
# while [ $elapsed -lt $timeout ]; do
# if docker compose -f "$COMPOSE_FILE" ps --format json | grep -q '"Health":"healthy"'; then
# log "Container is healthy!"
# healthy=true
# break
# fi
# sleep 5
# elapsed=$((elapsed + 5))
# log "Waiting... ($elapsed/$timeout seconds)"
# done
# if [ "$healthy" = false ]; then
# log "ERROR: Container failed to become healthy within $timeout seconds"
# docker compose -f "$COMPOSE_FILE" logs --tail=50
# log "Rolling back..."
# docker compose -f "$COMPOSE_FILE" down
# exit 1
# fi
# Cleanup old images (keep last 3 versions)
log "Cleaning up old images..."
docker images "\${REGISTRY}/\${IMAGE_NAME}" --format "table {{.Repository}}:{{.Tag}}\t{{.CreatedAt}}" | tail -n +2 | sort -k2 -r | tail -n +4 | awk '{print $1}' | xargs -r docker rmi || log "No old images to clean"
# Cleanup old backups (keep only last 5)
log "Cleaning up old backups..."
ls -t "$BACKUP_DIR"/backup-*.tar.gz 2>/dev/null | tail -n +6 | xargs -r rm || log "No old backups to clean"
log "Deployment completed successfully!"
log "🌐 Service available at: http://$(hostname -I | awk '{print $1}')"
# Display final status
docker compose -f "$COMPOSE_FILE" ps
DEPLOY_SCRIPT
# Make deploy script executable
chmod +x deploy.sh
# Set registry credentials
export GITEA_USERNAME="${{ gitea.actor }}"
export GITEA_PASSWORD="${{ secrets.ACCESS_TOKEN_GITEA }}"
# Execute deployment
./deploy.sh

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@ -1,23 +0,0 @@
name: Deploy on production
on:
push:
branches:
- main
jobs:
deploy:
runs-on: ubuntu-latest
steps:
- name: Deploy by SSH to production environment
uses: appleboy/ssh-action@master
with:
host: ${{ secrets.PRODUCTION_SSH_HOST }}
username: ${{ secrets.PRODUCTION_SSH_USERNAME }}
password: ${{ secrets.PRODUCTION_SSH_PASSWORD }}
port: ${{ secrets.PRODUCTION_SSH_PORT }}
script: |
cd /home/mishealth/BD-Core-FHIR-IG
git pull origin main
docker run --rm -v $(pwd):/home/publisher/ig hl7fhir/ig-publisher-base:latest /home/publisher/ig/_genonce.sh
rsync -av output/ /var/www/html
sudo systemctl restart nginx

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Dockerfile.serve Normal file
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# Multi-stage build for serving FHIR IG output
FROM nginx:alpine
# Copy the built IG output to nginx html directory
# (Uncomment and adjust the path if needed)
COPY output/ /usr/share/nginx/html/
# Copy custom nginx configuration
COPY nginx.conf /etc/nginx/nginx.conf
# Create a non-root user for security
RUN addgroup -g 1001 -S nginx-user && \
adduser -S -D -H -u 1001 -h /var/cache/nginx -s /sbin/nologin -G nginx-user -g nginx-user nginx-user
# Set proper permissions for Nginx directories
RUN chown -R nginx-user:nginx-user /usr/share/nginx/html && \
chown -R nginx-user:nginx-user /var/cache/nginx && \
chown -R nginx-user:nginx-user /var/log/nginx && \
chown -R nginx-user:nginx-user /etc/nginx/conf.d
# Fix Nginx PID permission issue
RUN mkdir -p /var/cache/nginx/run && \
chown -R nginx-user:nginx-user /var/cache/nginx/run
# Update nginx.conf to point PID to writable location
# Ensure your nginx.conf has:
# pid /var/cache/nginx/run/nginx.pid;
# Switch to non-root user
USER nginx-user
# Health check
# HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \
# CMD curl -f http://localhost/ || exit 1
EXPOSE 80
# Start Nginx in foreground
# CMD ["nginx", "-g", "daemon off;"]
CMD ["nginx", "-g", "daemon off;", "-c", "/etc/nginx/nginx.conf"]

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@ -1,14 +1,39 @@
# sample-ig
A sample, template-driven implementation guide that provides a starting environment to use a base for defining new IGs
# Bangladesh Core FHIR Implementation Guide (BD-Core-FHIR-IG)
The **Bangladesh Core FHIR Implementation Guide (IG)** defines the national baseline for health data exchange in Bangladesh.
It ensures that health information systems can share and understand data consistently, supporting the goals of the **Bangladesh Digital Health Blueprint**.
See https://build.fhir.org/ig/FHIR/sample-ig/
👉 Published IG: [https://fhir.dghs.gov.bd](https://fhir.dghs.gov.bd)
---
## FHIR Foundation Project Statement
## Purpose
* Maintainers: Grahame Grieve / Lloyd Mckenzie
* Issues / Discussion: Use github issues
* License: Creative Commons Public Domain
* Contribution Policy: Make PRs. PRs have to build ok with the latest IG Publisher
* Security Information: There should be no security issues here - it's all static content. Can report issues with the standard github repotring method
- Provide a **national reference** for stakeholders building digital health solutions.
- Ensure alignment with **international FHIR standards**, making future **cross-border health information exchange** possible.
- Promote **patient-centered data exchange**, reducing duplication and improving continuity of care.
---
## Using This IG
- **For Health System Developers:**
Use the defined **profiles, value sets, and code systems** in this IG when designing or integrating digital health applications. This ensures interoperability with other systems in Bangladesh and beyond.
- **For Policymakers and Implementers:**
Treat this IG as the **standard reference** for system requirements, data flows, and exchange formats when planning or evaluating digital health projects.
- **For Vendors and Partners:**
Align your solutions with this IG to ensure **compliance with national standards** and **seamless integration** with Bangladeshs digital health ecosystem.
---
## Contributions
Feedback and contributions are welcome. Issues can be raised through this repository to suggest improvements or alignments.
---
## License
This project is released under the [Creative Commons Public Domain License](https://creativecommons.org/publicdomain/).

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ig.ini
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# ini file for the Implementation Guide publisher
# see comments below for instructions
ig = input/myig.xml
ig = fsh-generated/resources/ImplementationGuide-bd.fhir.core.json
template = #bd-national-template
##########################
@ -41,7 +41,7 @@ examples:
# other parameters are defined in the ImplementationGuide resource:
# https://confluence.hl7.org/display/FHIR/Implementation+Guide+Parameters
# for more documentation on implementation guides and templates, see the FHIR Guidance ImplementationGuide
# for more documentation on implementation guides and templates, see the FHIR Guidance ImplementationGuide
# http://build.fhir.org/ig/FHIR/ig-guidance
output = /var/www/html

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@ -0,0 +1,84 @@
Profile: BDObservationProfile
Id: bd-observation
Parent: Observation
Title: "Bangladesh Observation Profile"
Description: "Bangladesh Observation Profile"
* ^url = "https://fhir.dghs.gov.bd/core/StructureDefinition/bd-observation"
* ^version = "1.0.0"
* ^status = #active
* identifier 1..* MS
* identifier.value 1..1
* status 1..1
* partOf 0..*
* category 1..* MS
* category from http://hl7.org/fhir/ValueSet/observation-category (required)
* category ^definition = "Type of category"
* category ^comment = "E.g. vital, physical examination"
* code 1..1 MS
* code from http://hl7.org/fhir/ValueSet/observation-codes (required)
* code ^definition = "Type of test/measurement"
* code ^comment = "E.g., Hb, RBS, CBC"
// Subject: Reference to Patient Profile (Required)
* subject 1..1 MS
* subject.reference 1..1 MS
* subject.display 1..1 MS
* subject.identifier 0..1
* subject ^definition = "Reference to Patient Profile"
* subject ^comment = "EX: http://mci.mcishr.dghs.gov.bd/api/v1/patients/98002412586"
* encounter 1..1 MS
* encounter.reference 1..1 MS
* encounter ^definition = "Reference to Patient Profile"
* encounter ^comment = "EX: uuid:34c38499-58ab-41e0-8e94-c3931491ad0e - bundle encounter uuid from local"
* performer 1..*
* performer.reference 1..1
// Value[x]: Result value (Optional, but constrained)
* value[x] 0..1
* value[x] ^definition = "Result value (Quantity, string, code, boolean, etc.)"
* valueQuantity 0..1
* valueQuantity ^comment = "If numeric, must include UCUM unit"
* valueQuantity.system 0..1
* valueQuantity.code 0..1
* valueString 0..1
* valueCodeableConcept 0..1
* valueBoolean 0..1
* valueInteger 0..1
* valueRange 0..1
* valueRatio 0..1
* valueSampledData 0..1
* valueTime 0..1
* valueDateTime 0..1
* valuePeriod 0..1
* interpretation 0..*
* interpretation from http://hl7.org/fhir/ValueSet/observation-interpretation (required)
* interpretation ^definition = "Type of test/measurement"
* interpretation ^comment = "E.g.: High, low, normal, etc"
* method 0..1
* method from http://hl7.org/fhir/ValueSet/observation-methods (required)
* method ^definition = "Type of observation method"
* method ^comment = "E.g.: Technique, Total measurement"
// Issued: Date/time result was issued (Optional)
* issued 0..1
* issued ^definition = "Date/time result was issued"
// Reference Range: Normal reference range (Optional)
* referenceRange 0..*
* referenceRange ^definition = "Normal reference range"
* referenceRange ^comment = "Optional"
// Specimen: Specimen used for the observation (Optional)
* specimen 0..1
* specimen ^definition = "Specimen used for the observation"
* specimen ^comment = "Optional"

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@ -0,0 +1,8 @@
Profile: BDLocation
Id: bd-location
Parent: Location
Title: "Location of Immunization for Bangladesh"
Description: "Address for Bangladesh Standard"
* address 1..1
* address only BDAddress

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@ -7,8 +7,6 @@ Parent: MedicationRequest
Title: "Medication Request Profile for Bangladesh-V2"
Description: "Profile of MedicationRequest Bangladesh Standard V2"
* identifier 1..*
* medication[x] 1..1 MS
* medication[x] only Reference(BDMedication) or CodeableConcept
@ -16,8 +14,10 @@ Description: "Profile of MedicationRequest Bangladesh Standard V2"
// TODO: BDEncounter referencing
* authoredOn 1..1
* requester 1..1
* reported[x] 1..1
* requester 1..1
* requester only Reference(BDPractitioner)
* reported[x] only Reference(BDOrganization)
* reported[x] only Reference(BDOrganization) or boolean
* requester only Reference(BDPractitioner or BDOrganization)
* priorPrescription only Reference(BDMedicationRequest)
* basedOn only Reference(BDMedicationRequest or ServiceRequest or CarePlan or ImmunizationRecommendation)

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@ -1,7 +1,7 @@
// @Name: Profile
// @Description: Immunization Profile of the Bangladeshi Patient.
// @Description: Immunization Profile of the Bangladeshi Patient.
Profile: BDImmunizationProfile
Id: bd-immunization
Parent: Immunization
@ -28,7 +28,7 @@ Description: "Bangladesh Immunization Profile"
* manufacturer ^definition = "Vaccine manufacturer"
* ^url = "https://fhir.dghs.gov.bd/core/StructureDefinition/bd-organization"
* lotNumber 0..1
* lotNumber 0..1
* lotNumber ^short = "Vaccine Lot Number"
* lotNumber ^definition = "Vaccine lot or batch number"
@ -36,19 +36,19 @@ Description: "Bangladesh Immunization Profile"
* expirationDate ^short = "Expiration Date"
* expirationDate ^definition = "Expiration date of vaccine lot"
// * patient 1..1
// * patient ^definition = "The patient receiving the vaccine"
// * patient from BDPatientProfile
* patient 1..1
* patient ^definition = "The patient receiving the vaccine"
* patient only Reference(BDPatientProfile)
* encounter 1..1
* encounter ^definition = "Encounter during which vaccine was administered"
//* encounter from BD Encounter Profile
* encounter only Reference(BDEncounterProfile)
* occurrence[x] 1..1
* occurrence[x] 1..1
// * location 0..1
// * location ^definition = "Location where vaccine was administered"
// * location only BDAddress
* location 0..1
* location ^definition = "Location where vaccine was administered"
* location only Reference(BDLocation)
* site 0..1
* site ^definition = "Body site of administration"
@ -60,14 +60,15 @@ Description: "Bangladesh Immunization Profile"
* doseQuantity 0..1
* doseQuantity ^definition = "Amount of vaccine administered"
//* doseQuantity from UCUM Units
* ^url = "http://unitsofmeasure.org"
* doseQuantity.system = "http://unitsofmeasure.org"
* performer 0..*
* performer 0..*
* performer ^definition = "Individual who performed the immunization"
//* performer from BD Practitioner Profile
* ^url = "https://fhir.dghs.gov.bd/core/StructureDefinition/bd-practitioner"
* performer.actor only Reference(BDPractitioner)
* reaction 0..*
* reaction ^definition = "Adverse reaction following immunization"
* reaction.detail only Reference(Observation)
//TODO: change to BDObservation after creating the profile
* reaction.detail only Reference(Observation)
//TODO change to BDObservation after creating the profile
* reasonReference only Reference(Condition or Observation or DiagnosticReport)

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nginx.conf Normal file
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pid /var/cache/nginx/run/nginx.pid;
events {
worker_connections 1024;
}
http {
include /etc/nginx/mime.types;
default_type application/octet-stream;
# Logging
log_format main '$remote_addr - $remote_user [$time_local] "$request" '
'$status $body_bytes_sent "$http_referer" '
'"$http_user_agent" "$http_x_forwarded_for"';
access_log /var/log/nginx/access.log main;
error_log /var/log/nginx/error.log warn;
server {
listen 80;
server_name _;
root /usr/share/nginx/html;
index index.html;
}
}

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@ -10,7 +10,7 @@ version: 0.2.0
fhirVersion: 4.0.1
copyrightYear: 2025+
releaseLabel: CI Build
FSHOnly: true
FSHOnly: false
publisher:
name: Directorate General of Health Services (DGHS), Bangladesh
url: https://dghs.gov.bd