Welcome to Smile CDR

• Table of Contents 1.0
• Smile CDR Maturity Model 1.1
• List of Features by Maturity 1.2
• Changelog (2022 Releases) 1.3
• Changelog (2021 Releases) 1.4
• Changelog (2020 Releases) 1.5
• Changelog (2019 Releases) 1.6
• Changelog (2018 Releases) 1.7
• Changelog (2017 Releases) 1.8

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 Failure Management 3.5
• Message Broker: ActiveMQ 3.6
• Message Broker: Kafka 3.7
• Pre-Seeding Configuration and Data 3.8
• Upgrading Smile CDR 3.9

Tutorial and Tour

• Preamble and Setup 4.0
• SMART on FHIR Apps 4.1
• Processing HL7 v2.x Feeds 4.2
• Federated OAuth2/OIDC Setup 4.3

The FHIR Standard

• FHIR Introduction 5.0
• FHIR CRUD Operations 5.1
• FHIR Searching Basics 5.2
• FHIR Search: References and Includes 5.3
• FHIR Search: Custom Search Parameters 5.4
• FHIR Transactions and Batches 5.5
• FHIRPath Expressions 5.6

FHIR Storage

• Concepts in Smile CDR 6.0
• FHIR Storage Modules 6.1
• FHIR Endpoint Module 6.2
• FHIRWeb Console 6.3
• OpenAPI / Swagger Support 6.4
• FHIR Endpoint Customization 6.5
• Resource IDs 6.6
• Search Parameters 6.7
• Search Parameter Features 6.8
• Phonetic Search Parameters 6.9
• Search Parameter Tuning 6.10
• Searching for Data 6.11
• Creating Data 6.12
• Reading Data 6.13
• Updating Data 6.14
• Deleting Data 6.15
• Binary Data 6.16
• Request Tracing and Provenance 6.17
• FHIR Versions 6.18
• Versioned Resource References 6.19
• Tags, Profiles, and Security Labels 6.20
• Clinical Quality Language (CQL) 6.21
• Partitioning and Multitenancy 6.22

FHIR Storage (Relational)

• FHIR Storage (Relational) Module 7.0
• Performance Tuning 7.1
• Lucene Indexing 7.2
• Performance and Caching 7.3

FHIR Storage (MongoDB)

• FHIR Storage (MongoDB) Module 8.0
• MongoDB Sharding / Partitioning 8.1

Validation and Conformance

• Introduction 9.0
• Validation Support Repository 9.1
• Validation Support Repository Options 9.2
• Conformance Data 9.3
• Repository Validation 9.4
• Repository Validation: Java 9.5
• Repository Validation: Javascript 9.6
• Repository Validation: Validation Bean 9.7
• Endpoint Validation 9.8
• Packages and Implementation Guides 9.9
• Package Registry Endpoint Module 9.10
• Remote Terminology Services 9.11
• Suppressing Messages 9.12
• Validation Performance 9.13
• Automatic Provenance Injection 9.14

Terminology

• Terminology Introduction 10.0
• Uploading Codes 10.1
• Terminology and Lucene Indexing 10.2
• ValueSet Expansion 10.3
• FHIR Response Terminology Mapping 10.4

Subscription

• Introduction 11.0
• Architecture 11.1
• Channel Types 11.2
• Delivery Options 11.3
• Manual Triggering 11.4

Interceptors

• Interceptors 12.0
• Starter Project 12.1
• Examples: FHIR Endpoints 12.2
• Examples: FHIR Storage 12.3
• Examples: FHIR Gateway 12.4
• Examples: FHIR Client 12.5
• Examples: MDM 12.6
• Examples: Subscription 12.7

Channel Import

• Channel Import Overview 13.0

Realtime Export

• Realtime Export Overview 14.0
• Realtime Export Rules Definition 14.1
• Using FHIRPath 14.2
• Debezium 14.3

Security

• Security in Smile CDR 15.0
• Authentication Protocols 15.1
• Authorization and Consent 15.2
• Inbound Security Module 15.3
• Local Inbound Security Module 15.4
• LDAP Inbound Security Module 15.5
• Scripted Inbound Security Module 15.6
• SAML Inbound Security Module 15.7
• Trusted Client Mode 15.8
• Roles and Permissions 15.9
• Callback Scripts 15.10
• Anonymous Access 15.11
• Consent Service 15.12
• Security Recipes 15.13
• Two Factor Authentication 15.14
• Troubleshooting Security 15.15

SMART on FHIR

• SMART on FHIR: Introduction 16.0
• SMART: Scopes 16.1
• SMART: Auth Flows 16.2
• SMART: Endpoints 16.3
• Client Management 16.4
• OIDC Keystores 16.5
• SMART: Smile CDR Support 16.6
• SMART Outbound Security: Module 16.7
• SMART Outbound Security: Skinning 16.8
• SMART Outbound Security: Context Selection 16.9
• SMART Outbound Security: SAML Bridging 16.10
• SMART: Federated OAuth2/OIDC Login 16.11
• SMART: Application Approval/Consent 16.12
• SMART Inbound Security Module 16.13
• SMART: Session Management 16.14
• SMART: Assigning Permissions 16.15
• SMART: Access Tokens 16.16
• SMART: User Profile Information 16.17
• FHIR Client Authentication 16.18

appSphere

• Introduction 17.0
• Getting Started 17.1
• Associated Module Configurations 17.2
• Client Creation and Configuration 17.3
• Other Configurations 17.4
• Developer Portal 17.5
• App Management Console 17.6
• App Gallery 17.7
• Appendix 17.8

FHIR Gateway

• FHIR Gateway Introduction 18.0
• Configuration: Initial Setup 18.1
• Configuration: Document 18.2

FHIR Hybrid Providers

• Hybrid Providers 19.0
• REST Custom Operations 19.1

LiveBundle

• LiveBundle Overview 20.0
• LiveBundle API 20.1
• LiveBundle Rule Definition 20.2
• LiveBundle Keepers 20.3

CDS Hooks

• CDS Hooks 21.0

Master Data Management

• MDM 22.0
• MDM Quickstart Guide 22.1
• MDM Rule Definition 22.2
• Using EIDs in MDM Rule Definition 22.3
• MDM Survivorship Rules 22.4
• Upgrading from the EMPI module 22.5

Clustering

• Designing a Cluster 23.0
• Migration To 2020.02 23.1

Logging

• Overview 24.0
• Audit Log 24.1
• Transaction Log 24.2
• System Logging 24.3
• Troubleshooting Logs 24.4

HL7 v2.x Support

• Introduction 25.0
• Inbound Messaging 25.1
• Outbound Messaging 25.2
• Outbound Messaging: Transport 25.3
• Transactions 25.4
• Structure Definitions 25.5
• Segment Definitions 25.6
• Table Definitions 25.7
• Naming System Mapping 25.8
• Processing Results Feeds 25.9
• Protocol 25.10

CDA Exchange Module

• Introduction 26.0
• JavaScript Templates 26.1
• Rest API Operations 26.2
• Available Document and Section Types for CDA Export 26.3
• Available Document and Section Types for CDA Import 26.4
• Further Reading 26.5

Bulk Operations

• ETL Import Module 27.0
• FHIR Bulk Import Operation 27.1
• FHIR Bulk Export Operation 27.2

Additional Features

• Da Vinci Clinical Data Exchange (CDex) 28.0
• Da Vinci Health Record Exchange (HRex) 28.1

Monitoring

• Monitoring Basics 29.0
• Elastic APM Basics 29.1

Product Administration

• Batch Job Management 30.0

JSON Admin Endpoints

• JSON Admin API 31.0
• Audit Log Endpoint 31.1
• Batch Job Endpoint 31.2
• Bulk Import Endpoint 31.3
• CDA Exchange Endpoint 31.4
• Metrics Endpoint 31.5
• Module Config Endpoint 31.6
• OpenID Connect Clients Endpoint 31.7
• OpenID Connect Servers Endpoint 31.8
• OpenID Connect Sessions Endpoint 31.9
• Runtime Status Endpoint 31.10
• System Config Endpoint 31.11
• Transaction Log Endpoint 31.12
• User Management Endpoint 31.13

Product Configuration

• HTTP Server Setup 32.0
• TLS and HTTPS Reference 32.1

Java Execution Environment

• Security Attributes 33.0
• Library Support 33.1
• Exception Handling 33.2
• Javadocs 33.3

JavaScript Execution Environment

• Introduction 34.0
• Specifying JavaScript in Configuration File 34.1
• Remote Debugging 34.2
• Converter API 34.3
• Environment API 34.4
• Exceptions API 34.5
• OAuth2 Exceptions API 34.6
• FHIR REST API 34.7
• FHIR Model API 34.8
• HL7 v2.x Mapping API 34.9
• HTTP API 34.10
• LDAP API 34.11
• Log API 34.12
• Composition Resource API 34.13
• Composition Section API 34.14
• TransactionBuilder API 34.15
• Util API 34.16
• UUID API 34.17
• XML API 34.18
• Callback Models 34.19

Database Administration

• Database Design 35.0
• Database Connection Pool 35.1
• Setting Up PostgreSQL 35.2
• Troubleshooting PostgreSQL 35.3
• Setting Up MySQL 35.4
• Setting Up MariaDB 35.5
• Setting Up Oracle 35.6
• Setting Up SQL Server (MSSQL) 35.7
• AWS IAM Authentication 35.8

Localization

• Localization 36.0
• Examples 36.1
• Available Localization Keys 36.2

Smile CDR CLI (smileutil)

• Introduction 37.0
• Bulk Import 37.1
• Create FHIR Package 37.2
• Execute Script Function 37.3
• Export ConceptMap to CSV 37.4
• HL7 v2.x Analyze Flat File 37.5
• HL7 v2.x Transmit Flat File 37.6
• Import CSV to ConceptMap 37.7
• Map and Upload CSV Bulk Import File 37.8
• Migrate Database 37.9
• Module Config Properties Export 37.10
• Reindex Terminology 37.11
• Synchronize FHIR Servers 37.12
• Upgrade H2 Database File 37.13
• Upload Bundle Files 37.14
• Upload CSV Bulk Import File 37.15
• Upload Sample Dataset 37.16
• Upload Terminology 37.17
• Validate FHIR Resources 37.18

Modules

• JSON Admin API 38.0
• Web Admin Console 38.1
• CDA Exchange 38.2
• Channel Import 38.3
• Cluster Manager 38.4
• Enterprise Master Patient Index 38.5
• CDS Hooks Endpoint 38.6
• FHIR Gateway Endpoint 38.7
• FHIR REST Endpoint (DSTU2) 38.8
• FHIR REST Endpoint (DSTU3) 38.9
• FHIR REST Endpoint (R4) 38.10
• FHIRWeb Console 38.11
• HL7 v2.x Listening Endpoint 38.12
• HL7 v2.x Sending Endpoint 38.13
• Hybrid Providers Endpoint 38.14
• Package Registry Endpoint 38.15
• Subscription Websocket Endpoint 38.16
• ETL Importer 38.17
• MDM 38.18
• Narrative Generator 38.19
• FHIR Storage (DSTU2 Relational) 38.20
• FHIR Storage (R3 Relational) 38.21
• FHIR Storage (Mongo) 38.22
• FHIR Storage (R4 Relational) 38.23
• Realtime Export 38.24
• LDAP Inbound Security 38.25
• Local Inbound Security 38.26
• SAML Inbound Security 38.27
• Scripted Inbound Security 38.28
• SMART Inbound Security 38.29
• SMART Outbound Security 38.30
• SMART App Host 38.31
• Subscription Matcher (All FHIR Versions) 38.32
• Subscription Matcher (DSTU2 - Deprecated) 38.33
• Subscription Matcher (DSTU3 - Deprecated) 38.34
• Subscription Matcher (R4 - Deprecated) 38.35
• appSphere 38.36
• Payer to Payer 38.37
• Amazon HealthLake Outbound REST Connector 38.38

Configuration Categories

• Web Admin Console Settings 39.0
• appSphere 39.1
• Payer Config 39.2
• Initial appSphere Seeding 39.3
• Authentication Callback Scripts 39.4
• Auth: General for APIs 39.5
• User Authentication 39.6
• Auth: HTTP Basic 39.7
• Auth: OpenID Connect 39.8
• Browser Syntax Highlighting 39.9
• Capability Statement (metadata) 39.10
• CDA Generation 39.11
• CDA Import 39.12
• CDS Hooks Definitions 39.13
• Channel Import 39.14
• Channel Retry 39.15
• Kafka 39.16
• Smile CDR License 39.17
• Cluster Manager Maintenance 39.18
• Message Broker 39.19
• Cluster Level Security 39.20
• Credentials 39.21
• Cross-Origin Resource Sharing (CORS) 39.22
• Database 39.23
• Email Configuration 39.24
• ETL Import: CSV Properties 39.25
• ETL Import: Source 39.26
• FHIR Binary Storage 39.27
• FHIR Bulk Operations 39.28
• Capability Statement 39.29
• FHIR Configuration 39.30
• Consent Service 39.31
• FHIR Endpoint Conversion 39.32
• Interceptors 39.33
• FHIR Endpoint Partitioning 39.34
• Resource Providers 39.35
• FHIR Endpoint Security 39.36
• Endpoint Terminology 39.37
• FHIR Gateway Configuration 39.38
• FHIR Interceptors 39.39
• LiveBundle Service 39.40
• FHIR MDM Server 39.41
• FHIR Performance 39.42
• FHIR Performance Tracing 39.43
• FHIR Realtime Export 39.44
• Repository Validation 39.45
• FHIR Resource Types 39.46
• FHIR REST Endpoint 39.47
• FHIR Search 39.48
• FHIR Storage Module Scheduled Tasks 39.49
• FHIR Validation Services 39.50
• FHIR Storage Package Registry 39.51
• FHIR Storage Partitioning 39.52
• Versioned References 39.53
• FHIR Subscription Delivery 39.54
• FHIR Subscription Persistence 39.55
• Amazon HealthLake REST Endpoint 39.56
• HL7 v2.x Mapper - Contained Resource 39.57
• HL7 v2.x Mapper - DG1 39.58
• HL7 v2.x Mapper - Forced Namespace Mode 39.59
• HL7 v2.x Mapper - General 39.60
• HL7 v2.x Mapper - Medications 39.61
• HL7 v2.x Mapper - OBR 39.62
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 39.63
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 39.64
• HL7 v2.x Mapper - PID 39.65
• HL7 v2.x Mapper - PV1 39.66
• HL7 v2.x Listener Script 39.67
• HL7 v2.x MLLP Listener 39.68
• HL7 v2.x MLLP Sender 39.69
• FHIR to HL7 v2.x Mapper Script 39.70
• HL7 v2.x Outbound Mapping 39.71
• Da Vinci Health Record Exchange (HRex) 39.72
• HTTP Access Log 39.73
• HTTP Listener 39.74
• HTTP Request Pool 39.75
• HTTP Security 39.76
• Hybrid Providers Definitions 39.77
• Initial User Seeding 39.78
• JavaScript Execution Environment 39.79
• JSON Web KeySet (JWKS) 39.80
• LDAP Authentication 39.81
• Lucene FullText Indexing 39.82
• MDM 39.83
• Narrative Generator 39.84
• OpenID Connect Token Validation 39.85
• OpenID Connect (OIDC) 39.86
• Payer to Payer 39.87
• Privacy Security Notice 39.88
• Provenance Injection 39.89
• Realtime Export 39.90
• Endpoint Validation: Request Validating 39.91
• Search Parameter Seeding 39.92
• SAML Provider 39.93
• Security Inbound Script 39.94
• Inbound SMART on FHIR Authentication 39.95
• Inbound SMART on FHIR Endpoints 39.96
• OAuth2/OIDC Federation 39.97
• SMART Callback Script 39.98
• Cross-Organizational Data Access Profile 39.99
• SMART Login Skin 39.100
• SMART Login Terms of Service 39.101
• SMART Authorization 39.102
• SMART Definitions Seeding 39.103
• Sessions 39.104
• Two Factor Authentication 39.105
• TLS / SSL (Encryption) 39.106
• Transaction Log 39.107
• Trusted Client 39.108
• User Self Registration 39.109

Product Reference

• Enumerated Types 40.0

Amazon HealthLake Outbound REST Connector

• Introduction 41.0
• Getting Started 41.1
• Data Management and Transfer 41.2

Appendix

• Preparing a Linux Host 42.0
• Production Checklist 42.1
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 42.2
• Deploying a Kubernetes Managed Cluster 42.3
• Password Hashing Algorithms 42.4
• Resource Paths 42.5
• JWT Signature Algorithms 42.6
• Inferno Considerations 42.7