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
• 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
• FHIRPath Expressions 4.6
• Federated OAuth2/OIDC Setup 4.7

FHIR Storage

• Concepts in Smile CDR 5.0
• FHIR Storage Modules 5.1
• FHIR Endpoint Module 5.2
• FHIRWeb Console 5.3
• OpenAPI / Swagger Support 5.4
• Resource IDs 5.5
• Search Parameters 5.6
• Search Parameter Features 5.7
• Phonetic Search Parameters 5.8
• Custom Search Parameters 5.9
• Search Parameter Tuning 5.10
• Searching for Data 5.11
• Creating Data 5.12
• Reading Data 5.13
• Updating Data 5.14
• Deleting Data 5.15
• Binary Data 5.16
• Request Tracing and Provenance 5.17
• FHIR Versions 5.18
• Versioned Resource References 5.19
• Tags, Profiles, and Security Labels 5.20
• Clinical Quality Language (CQL) 5.21

FHIR Storage (Relational)

• FHIR Storage (Relational) Module 6.0
• Performance Tuning 6.1
• Lucene Indexing 6.2
• Performance and Caching 6.3
• Partitioning and Multitenancy 6.4

FHIR Storage (MongoDB)

• FHIR Storage (MongoDB) Module 7.0

Validation and Conformance

• Introduction 8.0
• Validation Support Repository 8.1
• Validation Support Repository Options 8.2
• Conformance Data 8.3
• Repository Validation 8.4
• Repository Validation: Java 8.5
• Repository Validation: Javascript 8.6
• Repository Validation: Validation Bean 8.7
• Endpoint Validation 8.8
• Packages and Implementation Guides 8.9
• Remote Terminology Services 8.10
• Suppressing Messages 8.11
• Validation Performance 8.12
• Automatic Provenance Injection 8.13

Terminology

• Terminology Introduction 9.0
• Uploading Codes 9.1
• Terminology and Lucene Indexing 9.2
• ValueSet Expansion 9.3
• FHIR Response Terminology Mapping 9.4

Subscription

• Introduction 10.0
• Architecture 10.1
• Channel Types 10.2
• Delivery Options 10.3
• Manual Triggering 10.4

Interceptors

• Interceptors 11.0
• Starter Project 11.1
• Examples: FHIR Endpoints 11.2
• Examples: FHIR Storage 11.3
• Examples: FHIR Gateway 11.4

Channel Import

• Channel Import Overview 12.0

Realtime Export

• Realtime Export Overview 13.0
• Realtime Export Rules Definition 13.1
• Using FHIRPath 13.2
• Debezium 13.3

Security

• Security in Smile CDR 14.0
• Authentication Protocols 14.1
• Authorization and Consent 14.2
• Inbound Security Module 14.3
• Local Inbound Security Module 14.4
• LDAP Inbound Security Module 14.5
• Scripted Inbound Security Module 14.6
• SAML Inbound Security Module 14.7
• Trusted Client Mode 14.8
• Roles and Permissions 14.9
• Callback Scripts 14.10
• Anonymous Access 14.11
• Consent Service 14.12
• Security Recipes 14.13
• Two Factor Authentication 14.14
• Troubleshooting Security 14.15

SMART on FHIR

• SMART on FHIR: Introduction 15.0
• SMART: Scopes 15.1
• SMART: Auth Flows 15.2
• SMART: Endpoints 15.3
• Client Management 15.4
• OIDC Keystores 15.5
• SMART: Smile CDR Support 15.6
• SMART Outbound Security: Module 15.7
• SMART Outbound Security: Skinning 15.8
• SMART Outbound Security: Context Selection 15.9
• SMART: Federated OAuth2/OIDC Login 15.10
• SMART: Application Approval/Consent 15.11
• SMART Inbound Security Module 15.12
• SMART: Session Management 15.13
• SMART: Assigning Permissions 15.14
• SMART: Access Tokens 15.15
• SMART: User Profile Information 15.16
• FHIR Client Authentication 15.17

appSphere

• Introduction 16.0
• Getting Started 16.1
• Associated Module Configurations 16.2
• Client Creation and Configuration 16.3
• Other Configurations 16.4
• Developer Portal 16.5
• App Management Console 16.6
• App Gallery 16.7
• Appendix 16.8

FHIR Gateway

• FHIR Gateway Introduction 17.0
• Configuration: Initial Setup 17.1
• Configuration: Document 17.2

FHIR Hybrid Providers

• Hybrid Providers 18.0

LiveBundle

• LiveBundle Overview 19.0
• LiveBundle API 19.1
• LiveBundle Rule Definition 19.2
• LiveBundle Keepers 19.3

CDS Hooks

• CDS Hooks 20.0

Master Data Management

• MDM 21.0
• MDM Quickstart Guide 21.1
• MDM Survivorship Rules 21.2
• Upgrading from the EMPI module 21.3

Clustering

• Designing a Cluster 22.0
• Migration To 2020.02 22.1

Logging

• Overview 23.0
• Audit Log 23.1
• Transaction Log 23.2
• System Logging 23.3
• Troubleshooting Logs 23.4

HL7 v2.x Support

• Introduction 24.0
• Inbound Messaging 24.1
• Outbound Messaging 24.2
• Outbound Messaging: Transport 24.3
• Transactions 24.4
• Structure Definitions 24.5
• Segment Definitions 24.6
• Table Definitions 24.7
• Naming System Mapping 24.8
• Processing Results Feeds 24.9
• Protocol 24.10

CDA Exchange Module

• Introduction 25.0
• JavaScript Templates 25.1
• Rest API Operations 25.2
• Available Document and Section Types for CDA Export 25.3
• Available Document and Section Types for CDA Import 25.4
• Further Reading 25.5

Bulk Operations

• ETL Import Module 26.0
• FHIR Bulk Import Operation 26.1
• FHIR Bulk Export Operation 26.2

Monitoring

• Monitoring Basics 27.0
• Elastic APM Basics 27.1

Product Administration

• Batch Job Management 28.0

JSON Admin Endpoints

• JSON Admin API 29.0
• Audit Log Endpoint 29.1
• Batch Job Endpoint 29.2
• Bulk Import Endpoint 29.3
• CDA Exchange Endpoint 29.4
• Metrics Endpoint 29.5
• Module Config Endpoint 29.6
• OpenID Connect Clients Endpoint 29.7
• OpenID Connect Servers Endpoint 29.8
• OpenID Connect Sessions Endpoint 29.9
• Runtime Status Endpoint 29.10
• System Config Endpoint 29.11
• Transaction Log Endpoint 29.12
• User Management Endpoint 29.13

Product Configuration

• HTTP Server Setup 30.0
• TLS and HTTPS Reference 30.1

Java Execution Environment

• Security Attributes 31.0
• Library Support 31.1
• Exception Handling 31.2
• Javadocs 31.3

JavaScript Execution Environment

• Introduction 32.0
• Specifying JavaScript in Configuration File 32.1
• Remote Debugging 32.2
• Converter API 32.3
• Environment API 32.4
• Exceptions API 32.5
• OAuth2 Exceptions API 32.6
• FHIR REST API 32.7
• FHIR Model API 32.8
• HL7 v2.x Mapping API 32.9
• HTTP API 32.10
• LDAP API 32.11
• Log API 32.12
• Composition Resource API 32.13
• Composition Section API 32.14
• TransactionBuilder API 32.15
• Util API 32.16
• UUID API 32.17
• XML API 32.18
• Callback Models 32.19

Database Administration

• Database Design 33.0
• Database Connection Pool 33.1
• Setting Up PostgreSQL 33.2
• Troubleshooting PostgreSQL 33.3
• Setting Up MySQL 33.4
• Setting Up MariaDB 33.5
• Setting Up Oracle 33.6
• Setting Up SQL Server (MSSQL) 33.7

Localization

• Localization 34.0
• Examples 34.1
• Available Localization Keys 34.2

Smile CDR CLI (smileutil)

• Introduction 35.0
• Bulk Import 35.1
• Create FHIR Package 35.2
• Execute Script Function 35.3
• Export ConceptMap to CSV 35.4
• HL7 v2.x Analyze Flat File 35.5
• HL7 v2.x Transmit Flat File 35.6
• Import CSV to ConceptMap 35.7
• Map and Upload CSV Bulk Import File 35.8
• Migrate Database 35.9
• Reindex Terminology 35.10
• Synchronize FHIR Servers 35.11
• Upgrade H2 Database File 35.12
• Upload Bundle Files 35.13
• Upload CSV Bulk Import File 35.14
• Upload Sample Dataset 35.15
• Upload Terminology 35.16
• Validate FHIR Resources 35.17

Modules

• JSON Admin API 36.0
• Web Admin Console 36.1
• CDA Exchange 36.2
• Channel Import 36.3
• Cluster Manager 36.4
• Enterprise Master Patient Index 36.5
• Amazon HealthLake Connection 36.6
• CDS Hooks Endpoint 36.7
• FHIR Gateway Endpoint 36.8
• FHIR REST Endpoint (DSTU2) 36.9
• FHIR REST Endpoint (DSTU3) 36.10
• FHIR REST Endpoint (R4) 36.11
• FHIRWeb Console 36.12
• HL7 v2.x Listening Endpoint 36.13
• HL7 v2.x Sending Endpoint 36.14
• Hybrid Providers Endpoint 36.15
• Package Registry Endpoint 36.16
• Subscription Websocket Endpoint 36.17
• ETL Importer 36.18
• MDM 36.19
• Narrative Generator 36.20
• FHIR Storage (DSTU2 Relational) 36.21
• FHIR Storage (R3 Relational) 36.22
• FHIR Storage (Mongo) 36.23
• FHIR Storage (R4 Relational) 36.24
• Realtime Export 36.25
• LDAP Inbound Security 36.26
• Local Inbound Security 36.27
• SAML Inbound Security 36.28
• Scripted Inbound Security 36.29
• SMART Inbound Security 36.30
• SMART Outbound Security 36.31
• SMART App Host 36.32
• Subscription Matcher (All FHIR Versions) 36.33
• Subscription Matcher (DSTU2 - Deprecated) 36.34
• Subscription Matcher (DSTU3 - Deprecated) 36.35
• Subscription Matcher (R4 - Deprecated) 36.36
• appSphere 36.37
• Payer to Payer 36.38

Configuration Categories

• Web Admin Console Settings 37.0
• appSphere 37.1
• Payer Config 37.2
• Initial appSphere Seeding 37.3
• Authentication Callback Scripts 37.4
• Auth: General for APIs 37.5
• User Authentication 37.6
• Auth: HTTP Basic 37.7
• Auth: OpenID Connect 37.8
• Browser Syntax Highlighting 37.9
• Capability Statement (metadata) 37.10
• CDA Generation 37.11
• CDA Import 37.12
• CDS Hooks Definitions 37.13
• Channel Import 37.14
• Channel Retry 37.15
• Kafka 37.16
• Cluster Manager Maintenance 37.17
• Message Broker 37.18
• Cluster Level Security 37.19
• Credentials 37.20
• Cross-Origin Resource Sharing (CORS) 37.21
• Database 37.22
• Email Configuration 37.23
• ETL Import: CSV Properties 37.24
• ETL Import: Source 37.25
• FHIR Binary Storage 37.26
• FHIR Bulk Operations 37.27
• Capability Statement 37.28
• FHIR Configuration 37.29
• Consent Service 37.30
• FHIR Endpoint Conversion 37.31
• Interceptors 37.32
• FHIR Endpoint Partitioning 37.33
• Custom Resource Providers 37.34
• FHIR Endpoint Security 37.35
• Endpoint Terminology 37.36
• FHIR Gateway Configuration 37.37
• FHIR Interceptors 37.38
• LiveBundle Service 37.39
• FHIR MDM Server 37.40
• FHIR Performance 37.41
• FHIR Performance Tracing 37.42
• FHIR Realtime Export 37.43
• Repository Validation 37.44
• FHIR Resource Types 37.45
• FHIR REST Endpoint 37.46
• FHIR Search 37.47
• FHIR Storage Module Scheduled Tasks 37.48
• FHIR Validation Services 37.49
• FHIR Storage Package Registry 37.50
• FHIR Storage Partitioning 37.51
• Versioned References 37.52
• FHIR Subscription Delivery 37.53
• FHIR Subscription Persistence 37.54
• Amazon HealthLake REST Endpoint 37.55
• HL7 v2.x Mapper - Contained Resource 37.56
• HL7 v2.x Mapper - DG1 37.57
• HL7 v2.x Mapper - Forced Namespace Mode 37.58
• HL7 v2.x Mapper - General 37.59
• HL7 v2.x Mapper - Medications 37.60
• HL7 v2.x Mapper - OBR 37.61
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 37.62
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 37.63
• HL7 v2.x Mapper - PID 37.64
• HL7 v2.x Mapper - PV1 37.65
• HL7 v2.x Listener Script 37.66
• HL7 v2.x MLLP Listener 37.67
• HL7 v2.x MLLP Sender 37.68
• FHIR to HL7 v2.x Mapper Script 37.69
• HL7 v2.x Outbound Mapping 37.70
• HTTP Access Log 37.71
• HTTP Listener 37.72
• HTTP Request Pool 37.73
• HTTP Security 37.74
• Hybrid Providers Definitions 37.75
• Initial User Seeding 37.76
• JavaScript Execution Environment 37.77
• JSON Web KeySet (JWKS) 37.78
• LDAP Authentication 37.79
• Lucene FullText Indexing 37.80
• MDM 37.81
• Narrative Generator 37.82
• OpenID Connect Token Validation 37.83
• OpenID Connect (OIDC) 37.84
• Provenance Injection 37.85
• Realtime Export 37.86
• Endpoint Validation: Request Validating 37.87
• Search Parameter Seeding 37.88
• SAML Provider 37.89
• Security Inbound Script 37.90
• Inbound SMART on FHIR Authentication 37.91
• Inbound SMART on FHIR Endpoints 37.92
• OAuth2/OIDC Federation 37.93
• SMART Callback Script 37.94
• Cross-Organizational Data Access Profile 37.95
• SMART Login Skin 37.96
• SMART Login Terms of Service 37.97
• SMART Authorization 37.98
• SMART Definitions Seeding 37.99
• Sessions 37.100
• Two Factor Authentication 37.101
• TLS / SSL (Encryption) 37.102
• Transaction Log 37.103
• Trusted Client 37.104
• User Self Registration 37.105

Product Reference

• Enumerated Types 38.0

AWS / Amazon Support

• HealthLake Export module 39.0

Appendix

• Preparing a Linux Host 40.0
• Production Checklist 40.1
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 40.2
• Deploying a Kubernetes Managed Cluster 40.3
• Password Hashing Algorithms 40.4
• Resource Paths 40.5
• JWT Signature Algorithms 40.6
• Inferno Considerations 40.7