Merge branch 'main' of https://git.dghs.gov.bd/gitadmin/BD-Core-FHIR-IG

.gitea/workflows/ci-cd.yaml

@@ -0,0 +1,283 @@
+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

.gitea/workflows/deploy.yaml

@@ -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

Dockerfile.serve

@@ -0,0 +1,41 @@
+# 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"]

README.md

@@ -1,14 +1,39 @@
-# sample-ig
+# Bangladesh Core FHIR Implementation Guide (BD-Core-FHIR-IG)
-A sample, template-driven implementation guide that provides a starting environment to use a base for defining new IGs
 
+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
+- Provide a **national reference** for stakeholders building digital health solutions.  
-* Issues / Discussion: Use github issues
+- Ensure alignment with **international FHIR standards**, making future **cross-border health information exchange** possible.  
-* License: Creative Commons Public Domain
+- Promote **patient-centered data exchange**, reducing duplication and improving continuity of care.  
-* 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 
+---
+
+## 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 Bangladesh’s 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/).

ig.ini

@@ -2,7 +2,7 @@
 # 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
 

input/fsh/ovserbation-profile.fsh

@@ -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"

input/fsh/profile/BDLocation.fsh

@@ -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

input/fsh/profile/BDMedicationRequest.fsh

@@ -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) or boolean
-* reported[x] only Reference(BDOrganization)
+* requester only Reference(BDPractitioner or BDOrganization)
+* priorPrescription only Reference(BDMedicationRequest)
+* basedOn only Reference(BDMedicationRequest or ServiceRequest or CarePlan or ImmunizationRecommendation)

input/fsh/profile/immunization-profile.fsh

@@ -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 1..1
-// * patient ^definition = "The patient receiving the vaccine"
+* patient ^definition = "The patient receiving the vaccine"
-// * patient from BDPatientProfile
+* 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 0..1
-// * location ^definition = "Location where vaccine was administered"
+* location ^definition = "Location where vaccine was administered"
-// * location only BDAddress
+* 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
+* doseQuantity.system = "http://unitsofmeasure.org"
-* ^url = "http://unitsofmeasure.org"
 
-* performer 0..* 
+* performer 0..*
 * performer ^definition = "Individual who performed the immunization"
-//* performer from BD Practitioner Profile
+* performer.actor only Reference(BDPractitioner)
-* ^url = "https://fhir.dghs.gov.bd/core/StructureDefinition/bd-practitioner"
 
 * 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)

nginx.conf

@@ -0,0 +1,27 @@
+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;
+
+    }
+}

sushi-config.yaml

@@ -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