Welcome to Smile CDR

• Table of Contents 1.0
• Changelog (2021 Releases) 1.1
• Changelog (2020 Releases) 1.2
• Changelog (2019 Releases) 1.3
• Changelog (2018 Releases) 1.4
• Changelog (2017 Releases) 1.5

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 (Relational) Module 5.1
• FHIR Storage (MongoDB) Module 5.2
• FHIR Endpoint Module 5.3
• FHIRWeb Console 5.4
• OpenAPI / Swagger Support 5.5
• Lucene Indexing 5.6
• Performance and Caching 5.7
• Resource IDs 5.8
• Search Parameters 5.9
• Search Parameter Features 5.10
• Phonetic Search Parameters 5.11
• Custom Search Parameters 5.12
• Search Parameter Tuning 5.13
• Partitioning and Multitenancy 5.14
• Searching for Data 5.15
• Creating Data 5.16
• Reading Data 5.17
• Updating Data 5.18
• Deleting Data 5.19
• Binary Data 5.20
• Request Tracing and Provenance 5.21
• FHIR Versions 5.22
• Versioned Resource References 5.23
• Tags, Profiles, and Security Labels 5.24
• Clinical Quality Language (CQL) 5.25

Validation and Conformance

• Introduction 6.0
• Validation Support Repository 6.1
• Validation Support Repository Options 6.2
• Conformance Data 6.3
• Repository Validation 6.4
• Repository Validation: Java 6.5
• Repository Validation: Javascript 6.6
• Repository Validation: Validation Bean 6.7
• Endpoint Validation 6.8
• Packages and Implementation Guides 6.9
• Remote Terminology Services 6.10
• Suppressing Messages 6.11

Terminology

• Terminology Introduction 7.0
• Uploading Codes 7.1
• Terminology and Lucene Indexing 7.2
• ValueSet Expansion 7.3
• FHIR Response Terminology Mapping 7.4

Subscription

• Introduction 8.0
• Architecture 8.1
• Channel Types 8.2
• Delivery Options 8.3
• Manual Triggering 8.4

Interceptors

• Interceptors 9.0
• Starter Project 9.1
• Examples: FHIR Endpoints 9.2
• Examples: FHIR Storage 9.3
• Examples: FHIR Gateway 9.4

Channel Import

• Channel Import Overview 10.0

Realtime Export

• Realtime Export Overview 11.0
• Realtime Export Rules Definition 11.1
• Using FHIRPath 11.2
• Debezium 11.3

Security

• Security in Smile CDR 12.0
• Authentication Protocols 12.1
• Authorization and Consent 12.2
• Inbound Security Module 12.3
• Local Inbound Security Module 12.4
• LDAP Inbound Security Module 12.5
• Scripted Inbound Security Module 12.6
• SAML Inbound Security Module 12.7
• Trusted Client Mode 12.8
• Roles and Permissions 12.9
• Callback Scripts 12.10
• Anonymous Access 12.11
• Consent Service 12.12
• Security Recipes 12.13
• Two Factor Authentication 12.14
• Troubleshooting Security 12.15

SMART on FHIR

• SMART on FHIR: Introduction 13.0
• SMART: Scopes 13.1
• SMART: Auth Flows 13.2
• SMART: Endpoints 13.3
• Client Management 13.4
• SMART: Smile CDR Support 13.5
• SMART Outbound Security: Module 13.6
• SMART Outbound Security: Skinning 13.7
• SMART Outbound Security: Context Selection 13.8
• SMART: Federated OAuth2/OIDC Login 13.9
• SMART: Application Approval/Consent 13.10
• SMART Inbound Security Module 13.11
• SMART: Session Management 13.12
• SMART: Assigning Permissions 13.13
• SMART: Access Tokens 13.14
• SMART: User Profile Information 13.15
• FHIR Client Authentication 13.16

App Management Tools

• Introduction 14.0
• Getting Started 14.1
• Associated Module Configurations 14.2
• Client Creation and Configuration 14.3
• Other Configurations 14.4
• Developer Portal 14.5
• App Management Console 14.6
• App Gallery 14.7
• Appendix 14.8

FHIR Gateway

• FHIR Gateway Introduction 15.0
• Configuration: Initial Setup 15.1
• Configuration: Document 15.2

FHIR Hybrid Providers

• Hybrid Providers 16.0

LiveBundle

• LiveBundle Overview 17.0
• LiveBundle API 17.1
• LiveBundle Rule Definition 17.2
• LiveBundle Keepers 17.3

CDS-Hooks

• CDS-Hooks 18.0

Master Data Management

• MDM 19.0
• MDM Quickstart Guide 19.1
• MDM Survivorship Rules 19.2
• Upgrading from the EMPI module 19.3

Clustering

• Designing a Cluster 20.0
• Migration To 2020.02 20.1

Logging

• Overview 21.0
• Audit Log 21.1
• Transaction Log 21.2
• System Logging 21.3
• Troubleshooting Logs 21.4

HL7 v2.x Support

• Introduction 22.0
• Inbound Messaging 22.1
• Outbound Messaging 22.2
• Transactions 22.3
• Structure Definitions 22.4
• Segment Definitions 22.5
• Table Definitions 22.6
• Naming System Mapping 22.7
• Processing Results Feeds 22.8
• Protocol 22.9

CDA Exchange Module

• Introduction 23.0
• JavaScript Templates 23.1
• Rest API Operations 23.2
• Available Document and Section Types 23.3
• Further Reading 23.4

Bulk Operations

• ETL Import Module 24.0
• FHIR Bulk Export Operation 24.1

Monitoring

• Monitoring Basics 25.0
• Elastic APM Basics 25.1

Product Administration

• Batch Job Management 26.0

JSON Admin Endpoints

• JSON Admin API 27.0
• Audit Log Endpoint 27.1
• Batch Job Endpoint 27.2
• Bulk Import Endpoint 27.3
• CDA Exchange Endpoint 27.4
• Metrics Endpoint 27.5
• Module Config Endpoint 27.6
• OpenID Connect Clients Endpoint 27.7
• OpenID Connect Servers Endpoint 27.8
• OpenID Connect Sessions Endpoint 27.9
• Runtime Status Endpoint 27.10
• System Config Endpoint 27.11
• Transaction Log Endpoint 27.12
• User Management Endpoint 27.13

Product Configuration

• HTTP Server Setup 28.0
• TLS and HTTPS Reference 28.1

Java Execution Environment

• Security Attributes 29.0
• Library Support 29.1
• Exception Handling 29.2
• Javadocs 29.3

JavaScript Execution Environment

• Introduction 30.0
• Specifying JavaScript in Configuration File 30.1
• Converter API 30.2
• Environment API 30.3
• Exceptions API 30.4
• OAuth2 Exceptions API 30.5
• FHIR REST API 30.6
• FHIR Model API 30.7
• HL7 v2.x Mapping API 30.8
• HTTP API 30.9
• LDAP API 30.10
• Log API 30.11
• Composition Resource API 30.12
• Composition Section API 30.13
• TransactionBuilder API 30.14
• Util API 30.15
• UUID API 30.16
• XML API 30.17
• Callback Models 30.18

Database Administration

• Database Design 31.0
• Setting Up PostgreSQL 31.1
• Troubleshooting PostgreSQL 31.2
• Setting Up MySQL 31.3
• Setting Up MariaDB 31.4
• Setting Up Oracle 31.5
• Setting Up SQL Server (MSSQL) 31.6

Localization

• Localization 32.0
• Examples 32.1
• Available Localization Keys 32.2

Smile CDR CLI (smileutil)

• Introduction 33.0
• Execute Script Function 33.1
• Create FHIR Package 33.2
• Export ConceptMap to CSV 33.3
• HL7 v2.x Analyze Flat File 33.4
• HL7 v2.x Transmit Flat File 33.5
• Import CSV to ConceptMap 33.6
• Map and Upload CSV Bulk Import File 33.7
• Migrate Database 33.8
• Synchronize FHIR Servers 33.9
• Upload Bundle Files 33.10
• Upload CSV Bulk Import File 33.11
• Upload Sample Dataset 33.12
• Upload Terminology 33.13
• Validate FHIR Resources 33.14

Modules

• JSON Admin API 34.0
• Web Admin Console 34.1
• CDA Exchange 34.2
• Channel Import 34.3
• Cluster Manager 34.4
• Enterprise Master Patient Index 34.5
• CDS Hooks Endpoint 34.6
• FHIR Gateway Endpoint 34.7
• FHIR REST Endpoint (DSTU2) 34.8
• FHIR REST Endpoint (DSTU3) 34.9
• FHIR REST Endpoint (R4) 34.10
• FHIRWeb Console 34.11
• HL7 v2.x Listening Endpoint 34.12
• HL7 v2.x Sending Endpoint 34.13
• Hybrid Providers Endpoint 34.14
• Package Registry Endpoint 34.15
• Subscription Websocket Endpoint 34.16
• ETL Importer 34.17
• MDM 34.18
• Narrative Generator 34.19
• FHIR Storage (DSTU2 Relational) 34.20
• FHIR Storage (R3 Relational) 34.21
• FHIR Storage (Mongo) 34.22
• FHIR Storage (R4 Relational) 34.23
• Realtime Export 34.24
• LDAP Inbound Security 34.25
• Local Inbound Security 34.26
• SAML Inbound Security 34.27
• Scripted Inbound Security 34.28
• SMART Inbound Security 34.29
• SMART Outbound Security 34.30
• SMART App Host 34.31
• Subscription Matcher (All FHIR Versions) 34.32
• Subscription Matcher (DSTU2 - Deprecated) 34.33
• Subscription Matcher (DSTU3 - Deprecated) 34.34
• Subscription Matcher (R4 - Deprecated) 34.35
• App Management Tools 34.36

Configuration Categories

• Web Admin Console Settings 35.0
• App Management Tools 35.1
• Initial App Management Tools Seeding 35.2
• App Management Tools Email Server 35.3
• Authentication Callback Scripts 35.4
• Auth: General for APIs 35.5
• User Authentication 35.6
• Auth: HTTP Basic 35.7
• Auth: OpenID Connect 35.8
• Browser Syntax Highlighting 35.9
• Capability Statement (metadata) 35.10
• CDA Generation 35.11
• CDS Hooks 35.12
• Channel Import 35.13
• Channel Retry 35.14
• Cluster Manager Maintenance 35.15
• Cluster Manager Message Broker 35.16
• Cluster Manager Kafka 35.17
• Credentials 35.18
• Cross-Origin Resource Sharing (CORS) 35.19
• Database 35.20
• ETL Import: CSV Properties 35.21
• ETL Import: Source 35.22
• FHIR Binary Storage 35.23
• FHIR Bulk Operations 35.24
• FHIR Configuration 35.25
• FHIR Capability Statement 35.26
• FHIR Consent Service 35.27
• FHIR Endpoint Terminology 35.28
• FHIR LiveBundle Service 35.29
• FHIR Endpoint Conversion 35.30
• FHIR Endpoint Security 35.31
• Interceptors 35.32
• FHIR Endpoint Partitioning and Multitenancy 35.33
• FHIR Gateway Config 35.34
• FHIR MDM Server 35.35
• FHIR Storage Partitioning and Multitenancy 35.36
• FHIR Storage Package Registry 35.37
• Versioned References 35.38
• FHIR Performance 35.39
• FHIR Performance Tracing 35.40
• FHIR Storage Scheduled Tasks 35.41
• FHIR Realtime Export 35.42
• FHIR Resource Types 35.43
• FHIR REST Endpoint 35.44
• FHIR Search 35.45
• FHIR Interceptors 35.46
• FHIR Repository Validation 35.47
• FHIR Subscription Persistence 35.48
• FHIR Subscription Delivery 35.49
• FHIR Validation Services 35.50
• HL7 v2.x to FHIR Mapper - Forced Namespace Mode 35.51
• HL7 v2.x to FHIR Mapper - General 35.52
• HL7 v2.x Mapper - Medications 35.53
• HL7 v2.x to FHIR Mapper - OBR 35.54
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 35.55
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 35.56
• HL7 v2.x to FHIR Mapper - PV1 35.57
• HL7 v2.x Listener Script 35.58
• HL7 v2.x MLLP Listener 35.59
• FHIR to HL7 v2.x Mapper Script 35.60
• HL7 v2.x Outbound Mapping 35.61
• HL7 v2.x MLLP Sender 35.62
• HTTP Access Log 35.63
• HTTP Listener 35.64
• HTTP Request Pool 35.65
• HTTP Security 35.66
• Hybrid Providers Definitions 35.67
• Initial User Seeding 35.68
• JSON Web KeySet (JWKS) 35.69
• LDAP Authentication 35.70
• Lucene FullText Indexing 35.71
• Narrative Generator 35.72
• Master Data Management 35.73
• OpenID Connect (OIDC) 35.74
• Realtime Export 35.75
• Request Validating 35.76
• Search Parameter Seeding 35.77
• Security Inbound Script 35.78
• Inbound SMART on FHIR Authentication 35.79
• Inbound SMART on FHIR Endpoints 35.80
• OpenID Connect Token Validation 35.81
• SAML Provider 35.82
• OAuth2/OIDC Federation 35.83
• SMART Authorization 35.84
• SMART Definitions Seeding 35.85
• Sessions 35.86
• SMART Outbound Security: Callback Script 35.87
• SMART Outbound Security: CODAP 35.88
• SMART Outbound Security: Login Skin 35.89
• SMART Outbound Security: Terms of Service 35.90
• Two Factor Authentication 35.91
• TLS / SSL (Encryption) 35.92
• Trusted Client 35.93
• Transaction Log 35.94
• User Self Registration 35.95

Product Reference

• Enumerated Types 36.0

Appendix

• Preparing a Linux Host 37.0
• Production Checklist 37.1
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 37.2
• Deploying a Kubernetes Managed Cluster 37.3
• Password Hashing Algorithms 37.4
• Resource Paths 37.5
• JWT Signature Algorithms 37.6
• Inferno Considerations 37.7