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
• FHIR Endpoint Customization 5.5
• Resource IDs 5.6
• Search Parameters 5.7
• Search Parameter Features 5.8
• Phonetic Search Parameters 5.9
• Custom Search Parameters 5.10
• Search Parameter Tuning 5.11
• Searching for Data 5.12
• Creating Data 5.13
• Reading Data 5.14
• Updating Data 5.15
• Deleting Data 5.16
• Binary Data 5.17
• Request Tracing and Provenance 5.18
• FHIR Versions 5.19
• Versioned Resource References 5.20
• Tags, Profiles, and Security Labels 5.21
• Clinical Quality Language (CQL) 5.22
• Partitioning and Multitenancy 5.23

FHIR Storage (Relational)

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

FHIR Storage (MongoDB)

• FHIR Storage (MongoDB) Module 7.0
• MongoDB Sharding / Partitioning 7.1

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
• Examples: MDM 11.5
• Examples: Subscription 11.6

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

Additional Features

• Da Vinci Clinical Data Exchange (CDex) 27.0

Monitoring

• Monitoring Basics 28.0
• Elastic APM Basics 28.1

Product Administration

• Batch Job Management 29.0

JSON Admin Endpoints

• JSON Admin API 30.0
• Audit Log Endpoint 30.1
• Batch Job Endpoint 30.2
• Bulk Import Endpoint 30.3
• CDA Exchange Endpoint 30.4
• Metrics Endpoint 30.5
• Module Config Endpoint 30.6
• OpenID Connect Clients Endpoint 30.7
• OpenID Connect Servers Endpoint 30.8
• OpenID Connect Sessions Endpoint 30.9
• Runtime Status Endpoint 30.10
• System Config Endpoint 30.11
• Transaction Log Endpoint 30.12
• User Management Endpoint 30.13

Product Configuration

• HTTP Server Setup 31.0
• TLS and HTTPS Reference 31.1

Java Execution Environment

• Security Attributes 32.0
• Library Support 32.1
• Exception Handling 32.2
• Javadocs 32.3

JavaScript Execution Environment

• Introduction 33.0
• Specifying JavaScript in Configuration File 33.1
• Remote Debugging 33.2
• Converter API 33.3
• Environment API 33.4
• Exceptions API 33.5
• OAuth2 Exceptions API 33.6
• FHIR REST API 33.7
• FHIR Model API 33.8
• HL7 v2.x Mapping API 33.9
• HTTP API 33.10
• LDAP API 33.11
• Log API 33.12
• Composition Resource API 33.13
• Composition Section API 33.14
• TransactionBuilder API 33.15
• Util API 33.16
• UUID API 33.17
• XML API 33.18
• Callback Models 33.19

Database Administration

• Database Design 34.0
• Database Connection Pool 34.1
• Setting Up PostgreSQL 34.2
• Troubleshooting PostgreSQL 34.3
• Setting Up MySQL 34.4
• Setting Up MariaDB 34.5
• Setting Up Oracle 34.6
• Setting Up SQL Server (MSSQL) 34.7

Localization

• Localization 35.0
• Examples 35.1
• Available Localization Keys 35.2

Smile CDR CLI (smileutil)

• Introduction 36.0
• Bulk Import 36.1
• Create FHIR Package 36.2
• Execute Script Function 36.3
• Export ConceptMap to CSV 36.4
• HL7 v2.x Analyze Flat File 36.5
• HL7 v2.x Transmit Flat File 36.6
• Import CSV to ConceptMap 36.7
• Map and Upload CSV Bulk Import File 36.8
• Migrate Database 36.9
• Reindex Terminology 36.10
• Synchronize FHIR Servers 36.11
• Upgrade H2 Database File 36.12
• Upload Bundle Files 36.13
• Upload CSV Bulk Import File 36.14
• Upload Sample Dataset 36.15
• Upload Terminology 36.16
• Validate FHIR Resources 36.17

Modules

• JSON Admin API 37.0
• Web Admin Console 37.1
• CDA Exchange 37.2
• Channel Import 37.3
• Cluster Manager 37.4
• Enterprise Master Patient Index 37.5
• CDS Hooks Endpoint 37.6
• FHIR Gateway Endpoint 37.7
• FHIR REST Endpoint (DSTU2) 37.8
• FHIR REST Endpoint (DSTU3) 37.9
• FHIR REST Endpoint (R4) 37.10
• FHIRWeb Console 37.11
• HL7 v2.x Listening Endpoint 37.12
• HL7 v2.x Sending Endpoint 37.13
• Hybrid Providers Endpoint 37.14
• Package Registry Endpoint 37.15
• Subscription Websocket Endpoint 37.16
• ETL Importer 37.17
• MDM 37.18
• Narrative Generator 37.19
• FHIR Storage (DSTU2 Relational) 37.20
• FHIR Storage (R3 Relational) 37.21
• FHIR Storage (Mongo) 37.22
• FHIR Storage (R4 Relational) 37.23
• Realtime Export 37.24
• LDAP Inbound Security 37.25
• Local Inbound Security 37.26
• SAML Inbound Security 37.27
• Scripted Inbound Security 37.28
• SMART Inbound Security 37.29
• SMART Outbound Security 37.30
• SMART App Host 37.31
• Subscription Matcher (All FHIR Versions) 37.32
• Subscription Matcher (DSTU2 - Deprecated) 37.33
• Subscription Matcher (DSTU3 - Deprecated) 37.34
• Subscription Matcher (R4 - Deprecated) 37.35
• appSphere 37.36
• Payer to Payer 37.37
• Amazon HealthLake Outbound REST Connector 37.38

Configuration Categories

• Web Admin Console Settings 38.0
• appSphere 38.1
• Payer Config 38.2
• Initial appSphere Seeding 38.3
• Authentication Callback Scripts 38.4
• Auth: General for APIs 38.5
• User Authentication 38.6
• Auth: HTTP Basic 38.7
• Auth: OpenID Connect 38.8
• Browser Syntax Highlighting 38.9
• Capability Statement (metadata) 38.10
• CDA Generation 38.11
• CDA Import 38.12
• CDS Hooks Definitions 38.13
• Channel Import 38.14
• Channel Retry 38.15
• Kafka 38.16
• Smile CDR License 38.17
• Cluster Manager Maintenance 38.18
• Message Broker 38.19
• Cluster Level Security 38.20
• Credentials 38.21
• Cross-Origin Resource Sharing (CORS) 38.22
• Database 38.23
• Email Configuration 38.24
• ETL Import: CSV Properties 38.25
• ETL Import: Source 38.26
• FHIR Binary Storage 38.27
• FHIR Bulk Operations 38.28
• Capability Statement 38.29
• FHIR Configuration 38.30
• Consent Service 38.31
• FHIR Endpoint Conversion 38.32
• Interceptors 38.33
• FHIR Endpoint Partitioning 38.34
• Resource Providers 38.35
• FHIR Endpoint Security 38.36
• Endpoint Terminology 38.37
• FHIR Gateway Configuration 38.38
• FHIR Interceptors 38.39
• LiveBundle Service 38.40
• FHIR MDM Server 38.41
• FHIR Performance 38.42
• FHIR Performance Tracing 38.43
• FHIR Realtime Export 38.44
• Repository Validation 38.45
• FHIR Resource Types 38.46
• FHIR REST Endpoint 38.47
• FHIR Search 38.48
• FHIR Storage Module Scheduled Tasks 38.49
• FHIR Validation Services 38.50
• FHIR Storage Package Registry 38.51
• FHIR Storage Partitioning 38.52
• Versioned References 38.53
• FHIR Subscription Delivery 38.54
• FHIR Subscription Persistence 38.55
• Amazon HealthLake REST Endpoint 38.56
• HL7 v2.x Mapper - Contained Resource 38.57
• HL7 v2.x Mapper - DG1 38.58
• HL7 v2.x Mapper - Forced Namespace Mode 38.59
• HL7 v2.x Mapper - General 38.60
• HL7 v2.x Mapper - Medications 38.61
• HL7 v2.x Mapper - OBR 38.62
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 38.63
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 38.64
• HL7 v2.x Mapper - PID 38.65
• HL7 v2.x Mapper - PV1 38.66
• HL7 v2.x Listener Script 38.67
• HL7 v2.x MLLP Listener 38.68
• HL7 v2.x MLLP Sender 38.69
• FHIR to HL7 v2.x Mapper Script 38.70
• HL7 v2.x Outbound Mapping 38.71
• HTTP Access Log 38.72
• HTTP Listener 38.73
• HTTP Request Pool 38.74
• HTTP Security 38.75
• Hybrid Providers Definitions 38.76
• Initial User Seeding 38.77
• JavaScript Execution Environment 38.78
• JSON Web KeySet (JWKS) 38.79
• LDAP Authentication 38.80
• Lucene FullText Indexing 38.81
• MDM 38.82
• Narrative Generator 38.83
• OpenID Connect Token Validation 38.84
• OpenID Connect (OIDC) 38.85
• Payer to Payer 38.86
• Privacy Security Notice 38.87
• Provenance Injection 38.88
• Realtime Export 38.89
• Endpoint Validation: Request Validating 38.90
• Search Parameter Seeding 38.91
• SAML Provider 38.92
• Security Inbound Script 38.93
• Inbound SMART on FHIR Authentication 38.94
• Inbound SMART on FHIR Endpoints 38.95
• OAuth2/OIDC Federation 38.96
• SMART Callback Script 38.97
• Cross-Organizational Data Access Profile 38.98
• SMART Login Skin 38.99
• SMART Login Terms of Service 38.100
• SMART Authorization 38.101
• SMART Definitions Seeding 38.102
• Sessions 38.103
• Two Factor Authentication 38.104
• TLS / SSL (Encryption) 38.105
• Transaction Log 38.106
• Trusted Client 38.107
• User Self Registration 38.108

Product Reference

• Enumerated Types 39.0

Amazon HealthLake Outbound REST Connector

• Introduction 40.0
• Getting Started 40.1
• Data Management and Transfer 40.2

Appendix

• Preparing a Linux Host 41.0
• Production Checklist 41.1
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 41.2
• Deploying a Kubernetes Managed Cluster 41.3
• Password Hashing Algorithms 41.4
• Resource Paths 41.5
• JWT Signature Algorithms 41.6
• Inferno Considerations 41.7