Welcome to Smile CDR

• Table of Contents 1.0
• Changelog 1.1

Getting Started

• Basic Concepts 2.0
• Platform Requirements 2.1

Installation

• Installing Smile CDR 3.0
• Docker Container Installation 3.1
• Unix Service Installation 3.2
• Tuning your Installation 3.3
• Message Brokers 3.4
• Message Broker: ActiveMQ 3.5
• Message Broker: Kafka 3.6
• Upgrading Smile CDR 3.7

Tutorial and Tour

• Preamble and Setup 4.0
• FHIR Basics 4.1
• FHIR Search Queries 4.2
• FHIR CRUD Operations 4.3
• SMART on FHIR Apps 4.4
• Processing HL7 v2.x Feeds 4.5

FHIR Storage

• Concepts in Smile CDR 5.0
• FHIR Storage (Relational) Module 5.1
• FHIR Storage (MongoDB) Module 5.2
• FHIR Endpoint Module 5.3
• FHIRWeb Console 5.4
• Lucene Indexing 5.5
• Performance and Caching 5.6
• Resource IDs 5.7
• Search Parameters 5.8
• Subscription 5.9
• Terminology 5.10
• Multitenancy 5.11
• Searching for Data 5.12
• Updating Data 5.13
• Deleting Data 5.14
• Interceptors 5.15
• Binary Data 5.16
• Request Tracing and Provenance 5.17

LiveBundle

• LiveBundle Overview 6.0
• LiveBundle API 6.1
• LiveBundle Rule Definition 6.2
• LiveBundle Keepers 6.3

Security

• Security in Smile CDR 7.0
• Authorization and Consent 7.1
• Inbound Security Module 7.2
• Local Inbound Security Module 7.3
• LDAP Inbound Security Module 7.4
• Scripted Inbound Security Module 7.5
• Trusted Client Mode 7.6
• Roles and Permissions 7.7
• Callback Scripts 7.8
• SMART on FHIR: Introduction 7.9
• SMART: Scopes 7.10
• SMART: Auth Flows 7.11
• SMART: Endpoints 7.12
• SMART: Smile CDR Support 7.13
• SMART Outbound Security Module 7.14
• SMART Inbound Security Module 7.15
• SMART: Session Management 7.16
• SMART: Assigning Permissions 7.17
• Anonymous Access 7.18
• Consent Service 7.19
• Security Recipes 7.20
• Two Factor Authentication 7.21
• Troubleshooting Security 7.22

FHIR Hybrid Providers

• Hybrid Providers 8.0

FHIR Gateway

• FHIR Gateway 9.0

Master Data Management

• EMPI Mode 10.0

Clustering

• Designing a Cluster 11.0
• Migration To 2020.02 11.1

Logging

• Overview 12.0
• Audit Log 12.1
• Transaction Log 12.2
• System Logging 12.3
• Troubleshooting Logs 12.4

HL7 v2.x Support

• Introduction 13.0
• Inbound Messaging 13.1
• Outbound Messaging 13.2
• Transactions 13.3
• Structure Definitions 13.4
• Segment Definitions 13.5
• Table Definitions 13.6
• Naming System Mapping 13.7
• Processing Results Feeds 13.8
• Protocol 13.9

CDA Exchange Module

• Introduction 14.0
• JavaScript Templates 14.1
• Rest API Operations 14.2
• Available Document and Section Types 14.3
• Further Reading 14.4

Bulk Operations

• ETL Import Module 15.0
• FHIR Bulk Export Operation 15.1

Monitoring

• Monitoring Basics 16.0
• Elastic APM Basics 16.1

JSON Admin Endpoints

• JSON Admin API 17.0
• Audit Log Endpoint 17.1
• Bulk Import Endpoint 17.2
• CDA Exchange Endpoint 17.3
• Metrics Endpoint 17.4
• Module Config Endpoint 17.5
• OpenID Connect Clients Endpoint 17.6
• OpenID Connect Servers Endpoint 17.7
• Runtime Status Endpoint 17.8
• Transaction Log Endpoint 17.9
• User Management Endpoint 17.10

Product Configuration

• HTTP Server Setup 18.0

Java Execution Environment

• Security Attributes 19.0

JavaScript Execution Environment

• Introduction 20.0
• Converter API 20.1
• Environment API 20.2
• Exceptions API 20.3
• FHIR REST API 20.4
• FHIR Model API 20.5
• HL7 v2.x Mapping API 20.6
• HTTP API 20.7
• Log API 20.8
• Composition Resource API 20.9
• Composition Section API 20.10
• TransactionBuilder API 20.11
• Util API 20.12
• UUID API 20.13
• Callback Models 20.14

Database Administration

• Database Design 21.0
• Setting Up PostgreSQL 21.1
• Troubleshooting PostgreSQL 21.2
• Setting Up MySQL 21.3
• Setting Up MariaDB 21.4
• Setting Up Oracle 21.5
• Setting Up SQL Server (MSSQL) 21.6

Smile CDR CLI (smileutil)

• Introduction 22.0
• Execute Script Function 22.1
• Export ConceptMap to CSV 22.2
• HL7 v2.x Analyze Flat File 22.3
• HL7 v2.x Transmit Flat File 22.4
• Import CSV to ConceptMap 22.5
• Migrate Database 22.6
• Synchronize FHIR Servers 22.7
• Upload Bundle Files 22.8
• Upload CSV Bulk Import File 22.9
• Upload Sample Dataset 22.10
• Upload Terminology 22.11
• Validate FHIR Resources 22.12

Modules

• CDA Exchange 23.0
• Cluster Manager 23.1
• ETL Importer 23.2
• FHIR REST Endpoint (DSTU2) 23.3
• FHIR REST Endpoint (R3) 23.4
• FHIR Storage (DSTU2 Relational) 23.5
• FHIR Storage (R3 Relational) 23.6
• Subscription Matcher (R3) 23.7
• Subscription Matcher (R4) 23.8
• FHIRWeb Console 23.9
• HL7 v2.x Listening Endpoint 23.10
• HL7 v2.x Sending Endpoint 23.11
• JSON Admin API 23.12
• LDAP Inbound Security 23.13
• Local Inbound Security 23.14
• Scripted Inbound Security 23.15
• SMART App Host 23.16
• SMART Inbound Security 23.17
• SMART Outbound Security 23.18
• Web Admin Console 23.19

Configuration Categories

• Web Admin Console Settings 24.0
• Authentication Callback Scripts 24.1
• Auth: General for APIs 24.2
• Auth: General for Web 24.3
• Auth: HTTP Basic 24.4
• Auth: OpenID Connect 24.5
• Browser Syntax Highlighting 24.6
• Capability Statement (metadata) 24.7
• Cluster Manager Subscription Messaging 24.8
• Cluster Manager Maintenance 24.9
• Cluster Manager Message Broker 24.10
• Cluster Manager Kafka 24.11
• Credentials 24.12
• Cross-Origin Resource Sharing (CORS) 24.13
• Database 24.14
• ETL Import: CSV Properties 24.15
• ETL Import: Source 24.16
• FHIR Binary Storage 24.17
• FHIR Bulk Operations 24.18
• FHIR Configuration 24.19
• FHIR Consent Service 24.20
• FHIR LiveBundle Service 24.21
• FHIR EMPI Server 24.22
• FHIR Endpoint Conversion 24.23
• FHIR Endpoint Security 24.24
• Interceptors 24.25
• FHIR Gateway Target 24.26
• FHIR Gateway Cache 24.27
• FHIR Multitenancy 24.28
• FHIR Performance 24.29
• FHIR Performance Tracing 24.30
• FHIR Resource Types 24.31
• FHIR REST Endpoint 24.32
• FHIR Search 24.33
• FHIR Interceptors 24.34
• FHIR Subscription Persistence 24.35
• FHIR Subscription Delivery 24.36
• FHIR Validation: Remote Terminology Service 24.37
• HL7 v2.x to FHIR Mapper - Forced Namespace Mode 24.38
• HL7 v2.x to FHIR Mapper - General 24.39
• HL7 v2.x Mapper - Medications 24.40
• HL7 v2.x to FHIR Mapper - OBR 24.41
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 24.42
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 24.43
• HL7 v2.x to FHIR Mapper - PV1 24.44
• HL7 v2.x Listener Script 24.45
• HL7 v2.x MLLP Listener 24.46
• FHIR to HL7 v2.x Mapper Script 24.47
• HL7 v2.x MLLP Sender 24.48
• HTTP Access Log 24.49
• HTTP Listener 24.50
• HTTP Request Pool 24.51
• HTTP Security 24.52
• Hybrid Providers Definitions 24.53
• Initial User Seeding 24.54
• JSON Web KeySet (JWKS) 24.55
• LDAP Authentication 24.56
• Lucene FullText Indexing 24.57
• Narrative Generator 24.58
• OpenID Connect (OIC) 24.59
• Request Validating 24.60
• Inbound SMART on FHIR Authentication 24.61
• Inbound SMART on FHIR Endpoints 24.62
• Security Inbound Script 24.63
• SMART Authorization 24.64
• Sessions 24.65
• SMART Outbound Security: Callback Script 24.66
• SMART Outbound Security: CODAP 24.67
• SMART Outbound Security: Login Skin 24.68
• Two Factor Authentication 24.69
• TLS / SSL (Encryption) 24.70
• Trusted Client 24.71
• Trusted Client 24.72
• Miscellaneous Categories 24.73

Product Reference

• Enumerated Types 25.0

Appendix

• Preparing a Linux Host 26.0
• Production Checklist 26.1
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 26.2
• Deploying a Kubernetes Managed Cluster 26.3
• Password Hashing Algorithms 26.4
• JWT Signature Algorithms 26.5