Welcome to Smile CDR

• Table of Contents 1.0
• Smile CDR Maturity Model 1.1
• Smile CDR Premium Solutions 1.2
• List of Features by Maturity 1.3
• Changelog (2022 Releases) 1.4
• Changelog (2021 Releases) 1.5
• Changelog (2020 Releases) 1.6
• Changelog (2019 Releases) 1.7
• Changelog (2018 Releases) 1.8
• Changelog (2017 Releases) 1.9

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: Kafka 3.6
• Message Broker: ActiveMQ 3.7
• Pre-Seeding Configuration and Data 3.8
• Upgrading Smile CDR 3.9
• Production Checklist 3.10
• Module Licensing 3.11

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
• Search Parameter Reindexing 6.11
• Searching for Data 6.12
• Creating Data 6.13
• Reading Data 6.14
• Updating Data 6.15
• Deleting Data 6.16
• Binary Data 6.17
• Request Tracing and Provenance 6.18
• FHIR Versions 6.19
• Versioned Resource References 6.20
• Tags, Profiles, and Security Labels 6.21
• Clinical Quality Language (CQL) 6.22
• Partitioning and Multitenancy 6.23
• Custom Resource Types 6.24
• Batch and Scheduled Jobs 6.25

FHIR Storage (Relational)

• FHIR Storage (Relational) Module 7.0
• Resource Storage Mode 7.1
• Performance Tuning 7.2
• Lucene Indexing 7.3
• Performance and Caching 7.4
• Chained Searching and Sorting 7.5
• MegaScale 7.6

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
• Topic Subscriptions 11.5

Interceptors

• Interceptors 12.0
• Starter Project 12.1
• Examples: FHIR Endpoints 12.2
• Examples: HL7v2 Endpoints 12.3
• Examples: FHIR Storage 12.4
• Examples: FHIR Gateway 12.5
• Examples: FHIR Client 12.6
• Examples: MDM 12.7
• Examples: Subscription 12.8
• Examples: Channel Import 12.9

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
• Consent Service: JavaScript API 15.13
• Consent Service: Java API 15.14
• Security Recipes 15.15
• Two Factor Authentication 15.16
• Troubleshooting Security 15.17

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
• MDM UI 22.6

Clinical Reasoning

• Overview 23.0
• CQL 23.1
• Care Gaps 23.2
• Measures 23.3

IG Support

• International Patient Summary (IPS) 24.0

Clustering

• Designing a Cluster 25.0
• Migration To 2020.02 25.1

Logging

• Overview 26.0
• Audit Log 26.1
• Transaction Log 26.2
• System Logging 26.3
• Troubleshooting Logs 26.4

HL7 v2.x Support

• Introduction 27.0
• Inbound Messaging 27.1
• FHIR-Based Terminology Translation 27.2
• Outbound Messaging 27.3
• Outbound Messaging: Transport 27.4
• Transactions 27.5
• Structure Definitions 27.6
• Segment Definitions 27.7
• Table Definitions 27.8
• Naming System Mapping 27.9
• Processing Results Feeds 27.10
• Protocol 27.11

CDA Exchange Module

• Introduction 28.0
• JavaScript Templates 28.1
• Rest API Operations 28.2
• Available Document and Section Types for CDA Export 28.3
• Available Document and Section Types for CDA Import 28.4
• JavaScript Hooks on CDA Import / Export 28.5
• Further Reading 28.6

Bulk Operations

• ETL Import Module 29.0
• FHIR Bulk Import Operation 29.1
• FHIR Bulk Export Operation 29.2

Additional Features

• Da Vinci Clinical Data Exchange (CDex) 30.0
• Da Vinci Health Record Exchange (HRex) 30.1

Monitoring

• Monitoring Basics 31.0
• Elastic APM Basics 31.1

Product Administration

• Batch Job Management 32.0
• Web Admin Console 32.1

JSON Admin Endpoints

• JSON Admin API 33.0
• Audit Log Endpoint 33.1
• Batch Job Endpoint 33.2
• Bulk Import Endpoint 33.3
• CDA Exchange Endpoint 33.4
• Metrics Endpoint 33.5
• Module Config Endpoint 33.6
• OpenID Connect Clients Endpoint 33.7
• OpenID Connect Servers Endpoint 33.8
• OpenID Connect Sessions Endpoint 33.9
• Runtime Status Endpoint 33.10
• System Config Endpoint 33.11
• Transaction Log Endpoint 33.12
• User Management Endpoint 33.13

Product Configuration

• HTTP Server Setup 34.0
• TLS and HTTPS Reference 34.1

Java Execution Environment

• Security Attributes 35.0
• Library Support 35.1
• Exception Handling 35.2
• Javadocs 35.3

JavaScript Execution Environment

• Introduction 36.0
• Specifying JavaScript in Configuration File 36.1
• Remote Debugging 36.2
• Converter API 36.3
• Environment API 36.4
• Exceptions API 36.5
• OAuth2 Exceptions API 36.6
• FHIR REST API 36.7
• FHIR Model API 36.8
• HL7 v2.x Mapping API 36.9
• HTTP API 36.10
• LDAP API 36.11
• Log API 36.12
• Composition Resource API 36.13
• Composition Section API 36.14
• TransactionBuilder API 36.15
• Util API 36.16
• UUID API 36.17
• XML API 36.18
• Callback Models 36.19

Database Administration

• Database Design 37.0
• Database Connection Pool 37.1
• Setting Up PostgreSQL 37.2
• Troubleshooting PostgreSQL 37.3
• Setting Up MySQL 37.4
• Setting Up MariaDB 37.5
• Setting Up Oracle 37.6
• Setting Up SQL Server (MSSQL) 37.7
• AWS IAM Authentication 37.8

Localization

• Localization 38.0
• Examples 38.1
• Available Localization Keys 38.2

Smile CDR CLI (smileutil)

• Introduction 39.0
• Bulk Import 39.1
• Create FHIR Package 39.2
• Execute Script Function 39.3
• Export ConceptMap to CSV 39.4
• HL7 v2.x Analyze Flat File 39.5
• HL7 v2.x Transmit Flat File 39.6
• Import CSV to ConceptMap 39.7
• Map and Upload CSV Bulk Import File 39.8
• Migrate Database 39.9
• Clear Database Migration Lock 39.10
• Module Config Properties Export 39.11
• Reindex Terminology 39.12
• Synchronize FHIR Servers 39.13
• Upgrade H2 Database File 39.14
• Upload Bundle Files 39.15
• Upload CSV Bulk Import File 39.16
• Upload Sample Dataset 39.17
• Upload Terminology 39.18
• Generate Realtime Export Schema 39.19
• Validate FHIR Resources 39.20

Modules

• JSON Admin API 40.0
• Web Admin Console 40.1
• CDA Exchange 40.2
• Channel Import 40.3
• Cluster Manager 40.4
• CQL 40.5
• Audit Log Persistence 40.6
• Transaction Log Persistence 40.7
• Digital Quality Measures (DQM) 40.8
• Documentation Templates and Rules (DTR) 40.9
• Enterprise Master Patient Index 40.10
• CDS Hooks Endpoint 40.11
• FHIR Gateway Endpoint 40.12
• FHIR REST Endpoint (All Versions) 40.13
• FHIR REST Endpoint (DSTU2 - Deprecated) 40.14
• FHIR REST Endpoint (DSTU3 - Deprecated) 40.15
• FHIR REST Endpoint (R4 - Deprecated) 40.16
• FHIRWeb Console 40.17
• HL7 v2.x Listening Endpoint 40.18
• HL7 v2.x Sending Endpoint 40.19
• Hybrid Providers Endpoint 40.20
• Package Registry Endpoint 40.21
• Subscription Websocket Endpoint 40.22
• ETL Importer 40.23
• MDM 40.24
• MDM UI 40.25
• Narrative Generator 40.26
• FHIR Storage (DSTU2 RDBMS) 40.27
• FHIR Storage (R3 RDBMS) 40.28
• FHIR Storage (R4 RDBMS) 40.29
• FHIR Storage (R5 RDBMS) 40.30
• FHIR Storage (Mongo) 40.31
• Realtime Export 40.32
• LDAP Inbound Security 40.33
• Local Inbound Security 40.34
• SAML Inbound Security 40.35
• Scripted Inbound Security 40.36
• SMART Inbound Security 40.37
• SMART Outbound Security 40.38
• SMART App Host 40.39
• Subscription Matcher (All FHIR Versions) 40.40
• Subscription Matcher (DSTU2 - Deprecated) 40.41
• Subscription Matcher (DSTU3 - Deprecated) 40.42
• Subscription Matcher (R4 - Deprecated) 40.43
• appSphere 40.44
• Payer to Payer 40.45
• Amazon HealthLake Outbound REST Connector 40.46
• License 40.47
• Camel 40.48

Configuration Categories

• Web Admin Console Settings 41.0
• appSphere 41.1
• Payer Config 41.2
• Initial appSphere Seeding 41.3
• Authentication Callback Scripts 41.4
• Auth: General for APIs 41.5
• User Authentication 41.6
• Auth: HTTP Basic 41.7
• Auth: OpenID Connect 41.8
• Browser Syntax Highlighting 41.9
• Camel 41.10
• Capability Statement (metadata) 41.11
• Care Gaps 41.12
• CDA Generation 41.13
• CDA Import 41.14
• CDA JavaScript Execution Scripts 41.15
• CDS Hooks Definitions 41.16
• Channel Import 41.17
• Channel Retry 41.18
• Kafka 41.19
• Cluster Manager Maintenance 41.20
• Message Broker 41.21
• Cluster Level Security 41.22
• CQL 41.23
• Credentials 41.24
• Cross-Origin Resource Sharing (CORS) 41.25
• Database 41.26
• Da Vinci Health Record Exchange 41.27
• DQM 41.28
• DTR 41.29
• Email Configuration 41.30
• MDM UI 41.31
• ETL Import: CSV Properties 41.32
• ETL Import: Source 41.33
• FHIR Binary Storage 41.34
• FHIR Bulk Operations 41.35
• Capability Statement 41.36
• FHIR Configuration 41.37
• Consent Service 41.38
• FHIR Endpoint Conversion 41.39
• Interceptors 41.40
• FHIR Endpoint Partitioning 41.41
• Resource Providers 41.42
• FHIR Endpoint Security 41.43
• Endpoint Terminology 41.44
• FHIR Gateway Configuration 41.45
• FHIR Interceptors 41.46
• LiveBundle Service 41.47
• FHIR MDM Server 41.48
• FHIR Performance 41.49
• FHIR Performance Tracing 41.50
• FHIR Realtime Export 41.51
• Repository Validation 41.52
• FHIR Resource Types 41.53
• FHIR REST Endpoint 41.54
• FHIR Search 41.55
• Custom Resource Types 41.56
• IG Support 41.57
• MegaScale 41.58
• FHIR Storage Module Scheduled Tasks 41.59
• FHIR Validation Services 41.60
• FHIR Storage Package Registry 41.61
• FHIR Storage Partitioning 41.62
• Versioned References 41.63
• FHIR Subscription Delivery 41.64
• FHIR Subscription Persistence 41.65
• Amazon HealthLake REST Endpoint 41.66
• HL7 v2.x Mapper - Contained Resource 41.67
• HL7 v2.x Mapper - DG1 41.68
• HL7 v2.x Mapper - Forced Namespace Mode 41.69
• HL7 v2.x Mapper - General 41.70
• HL7 v2.x Mapper - Medications 41.71
• HL7 v2.x Mapper - OBR 41.72
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 41.73
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 41.74
• HL7 v2.x Mapper - PID 41.75
• HL7 v2.x Mapper - PV1 41.76
• Listener Interceptors 41.77
• HL7 v2.x Listener Script 41.78
• HL7 v2.x MLLP Listener 41.79
• HL7 v2.x MLLP Sender 41.80
• FHIR to HL7 v2.x Mapper Script 41.81
• HL7 v2.x Outbound Mapping 41.82
• Da Vinci Health Record Exchange (HRex) 41.83
• HTTP Access Log 41.84
• HTTP Listener 41.85
• HTTP Request Pool 41.86
• HTTP Security 41.87
• Hybrid Providers Definitions 41.88
• Initial User Seeding 41.89
• JavaScript Execution Environment 41.90
• JSON Web KeySet (JWKS) 41.91
• LDAP Authentication 41.92
• Smile CDR License 41.93
• Lucene FullText Indexing 41.94
• MDM 41.95
• Narrative Generator 41.96
• OpenID Connect Token Validation 41.97
• OpenID Connect (OIDC) 41.98
• Payer to Payer 41.99
• Privacy Security Notice 41.100
• Provenance Injection 41.101
• Realtime Export 41.102
• Endpoint Validation: Request Validating 41.103
• Scheduler Configuration 41.104
• Search Parameter Seeding 41.105
• SAML Provider 41.106
• Security Inbound Script 41.107
• Inbound SMART on FHIR Authentication 41.108
• Inbound SMART on FHIR Endpoints 41.109
• OAuth2/OIDC Federation 41.110
• SMART Callback Script 41.111
• Cross-Organizational Data Access Profile 41.112
• SMART Login Skin 41.113
• SMART Login Terms of Service 41.114
• SMART Authorization 41.115
• SMART Definitions Seeding 41.116
• Sessions 41.117
• Two Factor Authentication 41.118
• TLS / SSL (Encryption) 41.119
• Transaction Log 41.120
• Trusted Client 41.121
• User Self Registration 41.122

Product Reference

• Enumerated Types 42.0

Amazon HealthLake Outbound REST Connector

Premium

• Introduction 43.0
• Getting Started 43.1
• Data Management and Transfer 43.2

Appendix

• Preparing a Linux Host 44.0
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 44.1
• Deploying a Kubernetes Managed Cluster 44.2
• Password Hashing Algorithms 44.3
• Resource Paths 44.4
• JWT Signature Algorithms 44.5
• Inferno Considerations 44.6