feat: add FHIR Ingestor CronJob for Sri Lanka production

k8s/environments/sri-lanka-production/argocd-apps/apps.yaml

@@ -400,6 +400,35 @@ spec:
         - values.yaml
         - ../../environments/sri-lanka-production/values/patient-scoring.yaml
   project: default
+  syncPolicy:
+    syncOptions:
+      - PruneLast=true
+      - CreateNamespace=true
+    automated:
+      prune: true
+      selfHeal: true
+
+---
+
+# FHIR Ingestor - Reconciles FHIR bundle data with Simple database (runs daily)
+apiVersion: argoproj.io/v1alpha1
+kind: Application
+metadata:
+  name: fhir-ingestor
+spec:
+  destination:
+    name: ''
+    namespace: simple-v1
+    server: 'https://kubernetes.default.svc'
+  source:
+    path: k8s/manifests/fhir-ingestor
+    repoURL: 'https://github.com/simpledotorg/container-deployment.git'
+    targetRevision: master
+    helm:
+      valueFiles:
+        - values.yaml
+        - ../../environments/sri-lanka-production/values/fhir-ingestor.yaml
+  project: default
   syncPolicy:
     syncOptions:
       - PruneLast=true

k8s/environments/sri-lanka-production/values/fhir-ingestor.yaml

@@ -0,0 +1,43 @@
+# FHIR Ingestor configuration for Sri Lanka Production
+
+image:
+  repository: simpledotorg/fhir-ingestor
+  tag: latest
+  pullPolicy: Always
+
+# Cron schedule: Daily at 2 AM Sri Lanka time (UTC+5:30)
+# 2 AM IST = 8:30 PM UTC previous day
+schedule: "30 20 * * *"
+
+# Operation mode
+operation: merger
+softDelete: true
+dryRun: false
+
+# FHIR data source - adjust based on how you provide FHIR data
+fhir:
+  localPath: "/data/fhir"
+  # If using S3:
+  # s3Bucket: "your-bucket-name"
+  # s3Key: "fhir-bundles/"
+
+# Database configuration (matches Simple server database)
+database:
+  secretName: "simple-pguser-simple"
+  host: "simple-primary"
+  port: "5432"
+  name: "simple_db_sri_lanka_production_001"
+
+# Pushgateway for metrics
+pushgateway:
+  enabled: true
+  namespace: "monitoring"
+
+# Resources
+resources:
+  requests:
+    memory: "512Mi"
+    cpu: "200m"
+  limits:
+    memory: "2Gi"
+    cpu: "1000m"

k8s/manifests/fhir-ingestor/Chart.yaml

@@ -0,0 +1,6 @@
+apiVersion: v2
+name: fhir-ingestor
+description: FHIR to Simple database reconciliation and merge tool
+type: application
+version: 0.1.0
+appVersion: "1.0.0"

k8s/manifests/fhir-ingestor/templates/cronjob.yaml

@@ -0,0 +1,132 @@
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: fhir-ingestor-cronjob
+  labels:
+    app.kubernetes.io/name: fhir-ingestor
+spec:
+  schedule: "{{ .Values.schedule }}"
+  concurrencyPolicy: Forbid
+  successfulJobsHistoryLimit: 3
+  failedJobsHistoryLimit: 3
+  jobTemplate:
+    spec:
+      backoffLimit: 2
+      template:
+        metadata:
+          labels:
+            app.kubernetes.io/name: fhir-ingestor
+            app.kubernetes.io/component: cronjob
+        spec:
+          {{- with .Values.podSecurityContext }}
+          securityContext:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          restartPolicy: OnFailure
+          containers:
+          - name: fhir-ingestor
+            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+            imagePullPolicy: {{ .Values.image.pullPolicy }}
+            command:
+            - /bin/bash
+            - -c
+            - |
+              set -e
+
+              echo "============================================"
+              echo "FHIR Ingestor CronJob Started"
+              echo "============================================"
+              echo "Operation: {{ .Values.operation }}"
+              echo "Database Host: ${DB_HOST}:${DB_PORT}"
+              echo "Database Name: ${DB_NAME}"
+              {{- if .Values.softDelete }}
+              echo "Soft Delete: enabled"
+              {{- end }}
+              {{- if .Values.dryRun }}
+              echo "Dry Run: enabled"
+              {{- end }}
+              echo "============================================"
+
+              # Construct DATABASE_URL from environment variables
+              export SIMPLE_DATABASE_URL="postgres://${DB_USER}:${DB_PASSWORD}@${DB_HOST}:${DB_PORT}/${DB_NAME}"
+
+              cd /app
+
+              {{- if eq .Values.operation "merger" }}
+              # Run merger
+              echo "Running FHIR merger..."
+              python -m app.merger {{ .Values.fhir.localPath }} \
+                {{- if .Values.softDelete }}
+                --soft-delete \
+                {{- end }}
+                {{- if .Values.dryRun }}
+                --dry-run \
+                {{- end }}
+
+              {{- else if eq .Values.operation "gap_analysis" }}
+              # Run gap analysis
+              echo "Running FHIR gap analysis..."
+              python -m app.gap_analysis {{ .Values.fhir.localPath }} --json
+              {{- end }}
+
+              echo "============================================"
+              echo "FHIR Ingestor CronJob Completed!"
+              echo "============================================"
+            env:
+            {{- if .Values.pushgateway.enabled }}
+            - name: PUSHGATEWAY_URL
+              value: "http://prometheus-pushgateway.{{ .Values.pushgateway.namespace }}.svc.cluster.local:9091"
+            {{- end }}
+            - name: DB_USER
+              valueFrom:
+                secretKeyRef:
+                  name: {{ .Values.database.secretName }}
+                  key: user
+            - name: DB_PASSWORD
+              valueFrom:
+                secretKeyRef:
+                  name: {{ .Values.database.secretName }}
+                  key: password
+            - name: DB_HOST
+              value: "{{ .Values.database.host }}"
+            - name: DB_PORT
+              value: "{{ .Values.database.port }}"
+            - name: DB_NAME
+              value: "{{ .Values.database.name }}"
+            - name: LOG_LEVEL
+              value: "INFO"
+            {{- if .Values.fhir.s3Bucket }}
+            - name: S3_BUCKET
+              value: "{{ .Values.fhir.s3Bucket }}"
+            - name: S3_KEY
+              value: "{{ .Values.fhir.s3Key }}"
+            {{- end }}
+            {{- with .Values.extraEnv }}
+            {{- toYaml . | nindent 12 }}
+            {{- end }}
+            resources:
+              {{- toYaml .Values.resources | nindent 14 }}
+            {{- if .Values.fhir.localPath }}
+            volumeMounts:
+            - name: fhir-data
+              mountPath: {{ .Values.fhir.localPath }}
+              readOnly: true
+            {{- end }}
+          {{- if .Values.fhir.localPath }}
+          volumes:
+          - name: fhir-data
+            persistentVolumeClaim:
+              claimName: fhir-data-pvc
+          {{- end }}
+          {{- with .Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.affinity }}
+          affinity:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.tolerations }}
+          tolerations:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}

k8s/manifests/fhir-ingestor/values.yaml

@@ -0,0 +1,68 @@
+image:
+  repository: simpledotorg/fhir-ingestor
+  pullPolicy: Always
+  tag: latest
+
+# Cron schedule: Daily at 2 AM UTC
+# Format: minute hour day-of-month month day-of-week
+schedule: "0 2 * * *"
+
+# Operation mode: "merger" or "gap_analysis"
+operation: merger
+
+# Enable soft delete (only for merger operation)
+softDelete: true
+
+# Dry run mode (no actual DB writes)
+dryRun: false
+
+# FHIR data source
+fhir:
+  # S3 bucket containing FHIR bundles
+  s3Bucket: ""
+  # S3 key/path to FHIR data (can be zip file or prefix)
+  s3Key: ""
+  # Or use a local/mounted path
+  localPath: "/data/fhir"
+
+# Database configuration
+database:
+  # Postgres Operator creates this secret automatically
+  secretName: "simple-pguser-simple"
+  # Use direct connection to primary (not pgpool) for data ingestion
+  host: "simple-primary"
+  port: "5432"
+  name: "simple"
+
+# AWS credentials for S3 access (if using S3)
+aws:
+  # Secret containing AWS credentials
+  secretName: ""
+  # Or use IAM role (recommended in EKS)
+  useIAMRole: true
+
+# Pushgateway configuration for metrics
+pushgateway:
+  enabled: true
+  namespace: "monitoring"
+
+# Resource limits
+resources:
+  requests:
+    memory: "256Mi"
+    cpu: "100m"
+  limits:
+    memory: "1Gi"
+    cpu: "500m"
+
+# Node selection
+nodeSelector: {}
+affinity: {}
+tolerations: []
+
+# Pod security context
+podSecurityContext:
+  fsGroup: 9999
+
+# Additional environment variables
+extraEnv: []