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 (2023 Releases) 1.4
• Changelog (2022 Releases) 1.5
• Changelog (2021 Releases) 1.6
• Changelog (2020 Releases) 1.7
• Changelog (2019 Releases) 1.8
• Changelog (2018 Releases) 1.9
• Changelog (2017 Releases) 1.10

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
• Processing HL7 v2.x Feeds 4.1
• Federated OAuth2/OIDC Setup 4.2

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
• Resource Versions and Versioned 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
• Pointcuts 12.1
• Starter Project 12.2
• Examples: FHIR Endpoints 12.3
• Examples: HL7v2 Endpoints 12.4
• Examples: FHIR Storage 12.5
• Examples: FHIR Gateway 12.6
• Examples: FHIR Client 12.7
• Examples: MDM 12.8
• Examples: Subscription 12.9
• Examples: Channel Import 12.10
• Examples: Cluster Manager 12.11

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
• MDM Blocklist Definition 22.7

Clinical Reasoning

• Overview 23.0
• CQL 23.1
• Care Gaps 23.2
• Measures 23.3
• QPP Report Builder 23.4
• PlanDefinitions 23.5
• Questionnaires 23.6

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
• Custom Logging 26.5

HL7 v2.x Support

• Introduction 27.0
• Inbound Messaging 27.1
• FHIR-Based Terminology Translation 27.2
• Outbound Messaging 27.3
• Outbound: Default Resource Conversion 27.4
• Outbound: Custom Resource Conversion 27.5
• Outbound: Verbatim Messaging 27.6
• Outbound: Transport 27.7
• Transactions 27.8
• Structure Definitions 27.9
• Segment Definitions 27.10
• Table Definitions 27.11
• Naming System Mapping 27.12
• Processing Results Feeds 27.13
• Protocol 27.14

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

CDA Exchange Module v2

• Introduction 29.0
• JavaScript Templates 29.1
• Rest API Operations 29.2
• Available Document and Section Types for CDA Export 29.3
• Available Document and Section Types for CDA Import 29.4
• JavaScript Hooks on CDA Import / Export 29.5
• FHIR-Based Terminology Translation 29.6
• Further Reading 29.7

Bulk Operations

• ETL Import Module 30.0
• FHIR Bulk Import Operation 30.1
• FHIR Bulk Export Operation 30.2

Additional Features

• Da Vinci Clinical Data Exchange (CDex) 31.0
• Da Vinci Health Record Exchange (HRex) 31.1

Monitoring

• Monitoring Basics 32.0
• Elastic APM Basics 32.1
• Externalized Metrics 32.2

Product Administration

• Batch Job Management 33.0
• Web Admin Console 33.1

JSON Admin Endpoints

• JSON Admin API 34.0
• Audit Log Endpoint 34.1
• Batch Job Endpoint 34.2
• Bulk Import Endpoint 34.3
• CDA Exchange Endpoint 34.4
• Metrics Endpoint 34.5
• Module Config Endpoint 34.6
• OpenID Connect Clients Endpoint 34.7
• OpenID Connect Servers Endpoint 34.8
• OpenID Connect Sessions Endpoint 34.9
• Runtime Status Endpoint 34.10
• System Config Endpoint 34.11
• Transaction Log Endpoint 34.12
• User Management Endpoint 34.13

HFQL: Direct SQL Access

• HFQL/SQL Overview 35.0
• SQL Syntax 35.1
• SQL Syntax: Select 35.2
• SQL Syntax: Where 35.3
• SQL Syntax: Limitations 35.4
• SQL Syntax: Examples 35.5

Product Configuration

• HTTP Server Setup 36.0
• TLS and HTTPS Reference 36.1

Java Execution Environment

• Security Attributes 37.0
• Library Support 37.1
• Exception Handling 37.2
• Javadocs 37.3

JavaScript Execution Environment

• Introduction 38.0
• Specifying JavaScript in Configuration File 38.1
• Remote Debugging 38.2
• ECMA Modules (import) 38.3
• Converter API 38.4
• Environment API 38.5
• Exceptions API 38.6
• OAuth2 Exceptions API 38.7
• FHIR REST API 38.8
• FHIR Model API 38.9
• HL7 v2.x Mapping API 38.10
• HTTP API 38.11
• LDAP API 38.12
• Log API 38.13
• Composition Resource API 38.14
• Composition Section API 38.15
• TransactionBuilder API 38.16
• Util API 38.17
• UUID API 38.18
• XML API 38.19
• Callback Models 38.20

Database Administration

• Database Design 39.0
• Database Connection Pool 39.1
• Setting Up PostgreSQL 39.2
• Troubleshooting PostgreSQL 39.3
• Setting Up MySQL 39.4
• Setting Up MariaDB 39.5
• Setting Up Oracle 39.6
• Setting Up SQL Server (MSSQL) 39.7
• AWS IAM Authentication 39.8

Localization

• Localization 40.0
• Examples 40.1
• Available Localization Keys 40.2

Smile CDR CLI (smileutil)

• Introduction 41.0
• Bulk Import 41.1
• Create FHIR Package 41.2
• Execute Script Function 41.3
• Export ConceptMap to CSV 41.4
• HL7 v2.x Analyze Flat File 41.5
• HL7 v2.x Transmit Flat File 41.6
• Import CSV to ConceptMap 41.7
• Map and Upload CSV Bulk Import File 41.8
• Migrate Database 41.9
• Clear Database Migration Lock 41.10
• Module Config Properties Export 41.11
• Reindex Terminology 41.12
• Synchronize FHIR Servers 41.13
• Upgrade H2 Database File 41.14
• Upload Bundle Files 41.15
• Upload CSV Bulk Import File 41.16
• Upload Sample Dataset 41.17
• Upload Terminology 41.18
• Generate Realtime Export Schema 41.19
• Validate FHIR Resources 41.20

Apache Camel Integration

• Camel Module Overview 42.0
• Smile Camel Processors 42.1
• Smile Camel Converters 42.2

Modules

• JSON Admin API 43.0
• Web Admin Console 43.1
• CDA Exchange 43.2
• Channel Import 43.3
• Cluster Manager 43.4
• CQL 43.5
• Audit Log Persistence 43.6
• Transaction Log Persistence 43.7
• Digital Quality Measures (DQM) 43.8
• Documentation Templates and Rules (DTR) 43.9
• Enterprise Master Patient Index 43.10
• CDS Hooks Endpoint 43.11
• FHIR Gateway Endpoint 43.12
• FHIR REST Endpoint (All Versions) 43.13
• FHIR REST Endpoint (DSTU2 - Deprecated) 43.14
• FHIR REST Endpoint (DSTU3 - Deprecated) 43.15
• FHIR REST Endpoint (R4 - Deprecated) 43.16
• FHIRWeb Console 43.17
• HL7 v2.x Listening Endpoint 43.18
• HL7 v2.x Listening Endpoint (Deprecated) 43.19
• HL7 v2.x Sending Endpoint 43.20
• Hybrid Providers Endpoint 43.21
• Package Registry Endpoint 43.22
• Subscription Websocket Endpoint 43.23
• ETL Importer 43.24
• MDM 43.25
• MDM UI 43.26
• Prior Auth CRD 43.27
• Prior Auth Support 43.28
• Narrative Generator 43.29
• FHIR Storage (DSTU2 RDBMS) 43.30
• FHIR Storage (R3 RDBMS) 43.31
• FHIR Storage (R4 RDBMS) 43.32
• FHIR Storage (R5 RDBMS) 43.33
• FHIR Storage (Mongo) 43.34
• Realtime Export 43.35
• LDAP Inbound Security 43.36
• Local Inbound Security 43.37
• SAML Inbound Security 43.38
• Scripted Inbound Security 43.39
• SMART Inbound Security 43.40
• SMART Outbound Security 43.41
• Subscription Matcher (All FHIR Versions) 43.42
• Subscription Matcher (DSTU2 - Deprecated) 43.43
• Subscription Matcher (DSTU3 - Deprecated) 43.44
• Subscription Matcher (R4 - Deprecated) 43.45
• appSphere 43.46
• Payer to Payer 43.47
• Amazon HealthLake Outbound REST Connector 43.48
• License 43.49
• Camel 43.50

Configuration Categories

• Web Admin Console Settings 44.0
• appSphere 44.1
• Payer Config 44.2
• Initial appSphere Seeding 44.3
• Authentication Callback Scripts 44.4
• Auth: General for APIs 44.5
• User Authentication 44.6
• Auth: HTTP Basic 44.7
• Auth: OpenID Connect 44.8
• Browser Syntax Highlighting 44.9
• Camel 44.10
• Capability Statement (metadata) 44.11
• Care Gaps 44.12
• CDA Generation 44.13
• CDA Import 44.14
• CDA Interceptors 44.15
• CDA JavaScript Execution Scripts 44.16
• CDA Terminology 44.17
• CDS Hooks Definitions 44.18
• CDS Hooks On FHIR 44.19
• Channel Import 44.20
• Channel Retry 44.21
• Kafka 44.22
• Cluster Manager Maintenance 44.23
• Message Broker 44.24
• Cluster Level Security 44.25
• CQL 44.26
• Credentials 44.27
• Cross-Origin Resource Sharing (CORS) 44.28
• Database 44.29
• Da Vinci Health Record Exchange 44.30
• DQM 44.31
• DTR 44.32
• Email Configuration 44.33
• Encounter Start CDS hook configuration 44.34
• MDM UI 44.35
• ETL Import: CSV Properties 44.36
• ETL Import: Source 44.37
• FHIR Binary Storage 44.38
• FHIR Bulk Operations 44.39
• Capability Statement 44.40
• FHIR Configuration 44.41
• Consent Service 44.42
• FHIR Endpoint Conversion 44.43
• FHIR Endpoint HFQL Support 44.44
• FHIR Endpoint Partitioning 44.45
• Resource Providers 44.46
• FHIR Endpoint Security 44.47
• Endpoint Terminology 44.48
• FHIR Gateway Configuration 44.49
• FHIR Interceptors 44.50
• LiveBundle Service 44.51
• FHIR MDM Server 44.52
• FHIR Performance 44.53
• FHIR Performance Tracing 44.54
• FHIR Realtime Export 44.55
• Repository Validation 44.56
• FHIR Resource Types 44.57
• FHIR REST Endpoint 44.58
• FHIR Search 44.59
• Custom Resource Types 44.60
• IG Support 44.61
• MegaScale 44.62
• FHIR Storage Module Conditional Updates 44.63
• FHIR Storage Module Scheduled Tasks 44.64
• FHIR Validation Services 44.65
• FHIR Storage Package Registry 44.66
• FHIR Storage Partitioning 44.67
• Versioned References 44.68
• FHIR Subscription Delivery 44.69
• FHIR Subscription Persistence 44.70
• Amazon HealthLake REST Endpoint 44.71
• HL7 v2.x Mapper - Contained Resource 44.72
• HL7 v2.x Mapper - DG1 44.73
• HL7 v2.x Mapper - Forced Namespace Mode 44.74
• HL7 v2.x Mapper - General 44.75
• HL7 v2.x Mapper - Medications 44.76
• HL7 v2.x Mapper - OBR 44.77
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 44.78
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 44.79
• HL7 v2.x Mapper - PID 44.80
• HL7 v2.x Mapper - PV1 44.81
• Listener Interceptors 44.82
• HL7 v2.x Listener Script 44.83
• HL7 v2.x Listening Endpoint 44.84
• HL7 v2.x MLLP Listener 44.85
• HL7 v2.x MLLP Sender 44.86
• FHIR to HL7 v2.x Mapper Script 44.87
• HL7 v2.x Outbound Mapping 44.88
• Da Vinci Health Record Exchange (HRex) 44.89
• HTTP Access Log 44.90
• HTTP Listener 44.91
• HTTP Request Pool 44.92
• HTTP Security 44.93
• Hybrid Providers Definitions 44.94
• Initial User Seeding 44.95
• JavaScript Execution Environment 44.96
• JSON Web KeySet (JWKS) 44.97
• LDAP Authentication 44.98
• Smile CDR License 44.99
• Lucene FullText Indexing 44.100
• MDM 44.101
• Narrative Generator 44.102
• OpenID Connect Token Validation 44.103
• OpenID Connect (OIDC) 44.104
• Order Sign CDS hook configuration 44.105
• Payer to Payer 44.106
• Prior Authorization Coverage Requirement Discovery 44.107
• Prior Authorization Support 44.108
• Privacy Security Notice 44.109
• Provenance Injection 44.110
• Quality Payment Program (QPP) 44.111
• Realtime Export 44.112
• Endpoint Validation: Request Validating 44.113
• Scheduler Configuration 44.114
• Search Parameter Seeding 44.115
• SAML Provider 44.116
• Security Inbound Script 44.117
• Inbound SMART on FHIR Authentication 44.118
• Inbound SMART on FHIR Endpoints 44.119
• OAuth2/OIDC Federation 44.120
• SMART Callback Script 44.121
• Cross-Organizational Data Access Profile 44.122
• SMART Login Skin 44.123
• SMART Login Terms of Service 44.124
• SMART Authorization 44.125
• SMART Definitions Seeding 44.126
• Sessions 44.127
• Two Factor Authentication 44.128
• TLS / SSL (Encryption) 44.129
• Transaction Log 44.130
• Trusted Client 44.131
• User Self Registration 44.132

Product Reference

• Enumerated Types 45.0

Amazon HealthLake Outbound REST Connector

• Introduction 46.0
• Getting Started 46.1
• Data Management and Transfer 46.2

Appendix

• Preparing a Linux Host 47.0
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 47.1
• Deploying a Kubernetes Managed Cluster 47.2
• Password Hashing Algorithms 47.3
• Resource Paths 47.4
• JWT Signature Algorithms 47.5
• Inferno Considerations 47.6