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
• Partitioning and Multitenancy 5.13
• Searching for Data 5.14
• Creating Data 5.15
• Reading Data 5.16
• Updating Data 5.17
• Deleting Data 5.18
• Binary Data 5.19
• Request Tracing and Provenance 5.20
• FHIR Versions 5.21
• Versioned Resource References 5.22
• Clinical Quality Language (CQL) 5.23

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
• Endpoint Validation 6.7
• Packages and Implementation Guides 6.8
• Remote Terminology Services 6.9

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

LiveBundle

• LiveBundle Overview 10.0
• LiveBundle API 10.1
• LiveBundle Rule Definition 10.2
• LiveBundle Keepers 10.3

Channel Import

• Channel Import Overview 11.0

Realtime Export

• Realtime Export Overview 12.0
• Realtime Export Rules Definition 12.1
• Using FHIRPath 12.2
• Debezium 12.3

Security

• Security in Smile CDR 13.0
• Authentication Protocols 13.1
• Authorization and Consent 13.2
• Inbound Security Module 13.3
• Local Inbound Security Module 13.4
• LDAP Inbound Security Module 13.5
• Scripted Inbound Security Module 13.6
• SAML Inbound Security Module 13.7
• Trusted Client Mode 13.8
• Roles and Permissions 13.9
• Callback Scripts 13.10
• Anonymous Access 13.11
• Consent Service 13.12
• Security Recipes 13.13
• Two Factor Authentication 13.14
• Troubleshooting Security 13.15

SMART on FHIR

• SMART on FHIR: Introduction 14.0
• SMART: Scopes 14.1
• SMART: Auth Flows 14.2
• SMART: Endpoints 14.3
• Client Management 14.4
• SMART: Smile CDR Support 14.5
• SMART Outbound Security: Module 14.6
• SMART Outbound Security: Skinning 14.7
• SMART: Federated OAuth2/OIDC Login 14.8
• SMART: Application Approval/Consent 14.9
• SMART Inbound Security Module 14.10
• SMART: Session Management 14.11
• SMART: Assigning Permissions 14.12
• SMART: Access Tokens 14.13
• SMART: User Profile Information 14.14
• FHIR Client Authentication 14.15

FHIR Hybrid Providers

• Hybrid Providers 15.0

CDS-Hooks

• CDS-Hooks 16.0

FHIR Gateway

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

EMPI

• Enterprise Master Patient Index 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

JSON Admin Endpoints

• JSON Admin API 26.0
• Audit Log Endpoint 26.1
• Batch Job Endpoint 26.2
• Bulk Import Endpoint 26.3
• CDA Exchange Endpoint 26.4
• Metrics Endpoint 26.5
• Module Config Endpoint 26.6
• OpenID Connect Clients Endpoint 26.7
• OpenID Connect Servers Endpoint 26.8
• Runtime Status Endpoint 26.9
• System Config Endpoint 26.10
• Transaction Log Endpoint 26.11
• User Management Endpoint 26.12

Product Configuration

• HTTP Server Setup 27.0
• TLS and HTTPS Reference 27.1

Java Execution Environment

• Security Attributes 28.0
• Library Support 28.1
• Exception Handling 28.2
• Javadocs 28.3

JavaScript Execution Environment

• Introduction 29.0
• Specifying JavaScript in Configuration File 29.1
• Converter API 29.2
• Environment API 29.3
• Exceptions API 29.4
• OAuth2 Exceptions API 29.5
• FHIR REST API 29.6
• FHIR Model API 29.7
• HL7 v2.x Mapping API 29.8
• HTTP API 29.9
• LDAP API 29.10
• Log API 29.11
• Composition Resource API 29.12
• Composition Section API 29.13
• TransactionBuilder API 29.14
• Util API 29.15
• UUID API 29.16
• XML API 29.17
• Callback Models 29.18

Database Administration

• Database Design 30.0
• Setting Up PostgreSQL 30.1
• Troubleshooting PostgreSQL 30.2
• Setting Up MySQL 30.3
• Setting Up MariaDB 30.4
• Setting Up Oracle 30.5
• Setting Up SQL Server (MSSQL) 30.6

Localization

• Localization 31.0
• Examples 31.1
• Available Localization Keys 31.2

Smile CDR CLI (smileutil)

• Introduction 32.0
• Execute Script Function 32.1
• Create FHIR Package 32.2
• Export ConceptMap to CSV 32.3
• HL7 v2.x Analyze Flat File 32.4
• HL7 v2.x Transmit Flat File 32.5
• Import CSV to ConceptMap 32.6
• Map and Upload CSV Bulk Import File 32.7
• Migrate Database 32.8
• Synchronize FHIR Servers 32.9
• Upload Bundle Files 32.10
• Upload CSV Bulk Import File 32.11
• Upload Sample Dataset 32.12
• Upload Terminology 32.13
• Validate FHIR Resources 32.14

Modules

• JSON Admin API 33.0
• Web Admin Console 33.1
• CDA Exchange 33.2
• Channel Import 33.3
• Cluster Manager 33.4
• Enterprise Master Patient Index 33.5
• CDS Hooks Endpoint 33.6
• FHIR Gateway Endpoint 33.7
• FHIR REST Endpoint (DSTU2) 33.8
• FHIR REST Endpoint (DSTU3) 33.9
• FHIR REST Endpoint (R4) 33.10
• FHIRWeb Console 33.11
• HL7 v2.x Listening Endpoint 33.12
• HL7 v2.x Sending Endpoint 33.13
• Hybrid Providers Endpoint 33.14
• Package Registry Endpoint 33.15
• Subscription Websocket Endpoint 33.16
• ETL Importer 33.17
• MDM 33.18
• Narrative Generator 33.19
• FHIR Storage (DSTU2 Relational) 33.20
• FHIR Storage (R3 Relational) 33.21
• FHIR Storage (Mongo) 33.22
• FHIR Storage (R4 Relational) 33.23
• Realtime Export 33.24
• LDAP Inbound Security 33.25
• Local Inbound Security 33.26
• SAML Inbound Security 33.27
• Scripted Inbound Security 33.28
• SMART Inbound Security 33.29
• SMART Outbound Security 33.30
• SMART App Host 33.31
• Subscription Matcher (All FHIR Versions) 33.32
• Subscription Matcher (DSTU2 - Deprecated) 33.33
• Subscription Matcher (DSTU3 - Deprecated) 33.34
• Subscription Matcher (R4 - Deprecated) 33.35
• Application Gallery 33.36

Configuration Categories

• Web Admin Console Settings 34.0
• App Gallery 34.1
• Authentication Callback Scripts 34.2
• Auth: General for APIs 34.3
• User Authentication 34.4
• Auth: HTTP Basic 34.5
• Auth: OpenID Connect 34.6
• Browser Syntax Highlighting 34.7
• Capability Statement (metadata) 34.8
• CDS Hooks 34.9
• Channel Import 34.10
• Channel Retry 34.11
• Cluster Manager Maintenance 34.12
• Cluster Manager Message Broker 34.13
• Cluster Manager Kafka 34.14
• Credentials 34.15
• Cross-Origin Resource Sharing (CORS) 34.16
• Database 34.17
• ETL Import: CSV Properties 34.18
• ETL Import: Source 34.19
• FHIR Binary Storage 34.20
• FHIR Bulk Operations 34.21
• FHIR Configuration 34.22
• FHIR Capability Statement 34.23
• FHIR Consent Service 34.24
• FHIR Endpoint Terminology 34.25
• FHIR LiveBundle Service 34.26
• FHIR Endpoint Conversion 34.27
• FHIR Endpoint Security 34.28
• Interceptors 34.29
• FHIR Endpoint Partitioning and Multitenancy 34.30
• FHIR Gateway Config 34.31
• FHIR MDM Server 34.32
• FHIR Storage Partitioning and Multitenancy 34.33
• FHIR Storage Package Registry 34.34
• Versioned References 34.35
• FHIR Performance 34.36
• FHIR Performance Tracing 34.37
• FHIR Realtime Export 34.38
• FHIR Resource Types 34.39
• FHIR REST Endpoint 34.40
• FHIR Search 34.41
• FHIR Interceptors 34.42
• FHIR Repository Validation 34.43
• FHIR Subscription Persistence 34.44
• FHIR Subscription Delivery 34.45
• FHIR Validation Services 34.46
• HL7 v2.x to FHIR Mapper - Forced Namespace Mode 34.47
• HL7 v2.x to FHIR Mapper - General 34.48
• HL7 v2.x Mapper - Medications 34.49
• HL7 v2.x to FHIR Mapper - OBR 34.50
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 34.51
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 34.52
• HL7 v2.x to FHIR Mapper - PV1 34.53
• HL7 v2.x Listener Script 34.54
• HL7 v2.x MLLP Listener 34.55
• FHIR to HL7 v2.x Mapper Script 34.56
• HL7 v2.x MLLP Sender 34.57
• HTTP Access Log 34.58
• HTTP Listener 34.59
• HTTP Request Pool 34.60
• HTTP Security 34.61
• Hybrid Providers Definitions 34.62
• Initial User Seeding 34.63
• JSON Web KeySet (JWKS) 34.64
• LDAP Authentication 34.65
• Lucene FullText Indexing 34.66
• Narrative Generator 34.67
• Master Data Management 34.68
• OpenID Connect (OIDC) 34.69
• Realtime Export 34.70
• Request Validating 34.71
• Security Inbound Script 34.72
• Inbound SMART on FHIR Authentication 34.73
• Inbound SMART on FHIR Endpoints 34.74
• OpenID Connect Token Validation 34.75
• SAML Provider 34.76
• OAuth2/OIDC Federation 34.77
• SMART Authorization 34.78
• SMART Definitions Seeding 34.79
• Sessions 34.80
• SMART Outbound Security: Callback Script 34.81
• SMART Outbound Security: CODAP 34.82
• SMART Outbound Security: Login Skin 34.83
• SMART Outbound Security: Terms of Service 34.84
• Two Factor Authentication 34.85
• TLS / SSL (Encryption) 34.86
• Trusted Client 34.87
• Transaction Log 34.88
• User Self Registration 34.89

Product Reference

• Enumerated Types 35.0

Appendix

• Preparing a Linux Host 36.0
• Production Checklist 36.1
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 36.2
• Deploying a Kubernetes Managed Cluster 36.3
• Password Hashing Algorithms 36.4
• Resource Paths 36.5
• JWT Signature Algorithms 36.6
• Inferno Considerations 36.7