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
• Development Forecast 1.4
• Changelog (2023 Releases) 1.5
• Changelog (2022 Releases) 1.6
• Changelog (2021 Releases) 1.7
• Changelog (2020 Releases) 1.8
• Changelog (2019 Releases) 1.9
• Changelog (2018 Releases) 1.10
• Changelog (2017 Releases) 1.11

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
• 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

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
• FHIR-Based Terminology Translation 28.6
• Further Reading 28.7

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
• Externalized Metrics 31.2

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

HFQL: Direct SQL Access

• HFQL/SQL Overview 34.0
• SQL Syntax 34.1
• SQL Syntax: Select 34.2
• SQL Syntax: Where 34.3
• SQL Syntax: Limitations 34.4
• SQL Syntax: Examples 34.5

Product Configuration

• HTTP Server Setup 35.0
• TLS and HTTPS Reference 35.1

Java Execution Environment

• Security Attributes 36.0
• Library Support 36.1
• Exception Handling 36.2
• Javadocs 36.3

JavaScript Execution Environment

• Introduction 37.0
• Specifying JavaScript in Configuration File 37.1
• Remote Debugging 37.2
• ECMA Modules (import) 37.3
• Converter API 37.4
• Environment API 37.5
• Exceptions API 37.6
• OAuth2 Exceptions API 37.7
• FHIR REST API 37.8
• FHIR Model API 37.9
• HL7 v2.x Mapping API 37.10
• HTTP API 37.11
• LDAP API 37.12
• Log API 37.13
• Composition Resource API 37.14
• Composition Section API 37.15
• TransactionBuilder API 37.16
• Util API 37.17
• UUID API 37.18
• XML API 37.19
• Callback Models 37.20

Database Administration

• Database Design 38.0
• Database Connection Pool 38.1
• Setting Up PostgreSQL 38.2
• Troubleshooting PostgreSQL 38.3
• Setting Up MySQL 38.4
• Setting Up MariaDB 38.5
• Setting Up Oracle 38.6
• Setting Up SQL Server (MSSQL) 38.7
• AWS IAM Authentication 38.8

Localization

• Localization 39.0
• Examples 39.1
• Available Localization Keys 39.2

Smile CDR CLI (smileutil)

• Introduction 40.0
• Bulk Import 40.1
• Create FHIR Package 40.2
• Execute Script Function 40.3
• Export ConceptMap to CSV 40.4
• HL7 v2.x Analyze Flat File 40.5
• HL7 v2.x Transmit Flat File 40.6
• Import CSV to ConceptMap 40.7
• Map and Upload CSV Bulk Import File 40.8
• Migrate Database 40.9
• Clear Database Migration Lock 40.10
• Module Config Properties Export 40.11
• Reindex Terminology 40.12
• Synchronize FHIR Servers 40.13
• Upgrade H2 Database File 40.14
• Upload Bundle Files 40.15
• Upload CSV Bulk Import File 40.16
• Upload Sample Dataset 40.17
• Upload Terminology 40.18
• Generate Realtime Export Schema 40.19
• Validate FHIR Resources 40.20

Apache Camel Integration

• Camel Module Overview 41.0
• Smile Camel Processors 41.1
• Smile Camel Converters 41.2

Modules

• JSON Admin API 42.0
• Web Admin Console 42.1
• CDA Exchange 42.2
• Channel Import 42.3
• Cluster Manager 42.4
• CQL 42.5
• Audit Log Persistence 42.6
• Transaction Log Persistence 42.7
• Digital Quality Measures (DQM) 42.8
• Documentation Templates and Rules (DTR) 42.9
• Enterprise Master Patient Index 42.10
• CDS Hooks Endpoint 42.11
• FHIR Gateway Endpoint 42.12
• FHIR REST Endpoint (All Versions) 42.13
• FHIR REST Endpoint (DSTU2 - Deprecated) 42.14
• FHIR REST Endpoint (DSTU3 - Deprecated) 42.15
• FHIR REST Endpoint (R4 - Deprecated) 42.16
• FHIRWeb Console 42.17
• HL7 v2.x Listening Endpoint 42.18
• HL7 v2.x Sending Endpoint 42.19
• Hybrid Providers Endpoint 42.20
• Package Registry Endpoint 42.21
• Subscription Websocket Endpoint 42.22
• ETL Importer 42.23
• MDM 42.24
• MDM UI 42.25
• Prior Auth CRD 42.26
• Narrative Generator 42.27
• FHIR Storage (DSTU2 RDBMS) 42.28
• FHIR Storage (R3 RDBMS) 42.29
• FHIR Storage (R4 RDBMS) 42.30
• FHIR Storage (R5 RDBMS) 42.31
• FHIR Storage (Mongo) 42.32
• Realtime Export 42.33
• LDAP Inbound Security 42.34
• Local Inbound Security 42.35
• SAML Inbound Security 42.36
• Scripted Inbound Security 42.37
• SMART Inbound Security 42.38
• SMART Outbound Security 42.39
• SMART App Host 42.40
• Subscription Matcher (All FHIR Versions) 42.41
• Subscription Matcher (DSTU2 - Deprecated) 42.42
• Subscription Matcher (DSTU3 - Deprecated) 42.43
• Subscription Matcher (R4 - Deprecated) 42.44
• appSphere 42.45
• Payer to Payer 42.46
• Amazon HealthLake Outbound REST Connector 42.47
• License 42.48
• Camel 42.49

Configuration Categories

• Web Admin Console Settings 43.0
• appSphere 43.1
• Payer Config 43.2
• Initial appSphere Seeding 43.3
• Authentication Callback Scripts 43.4
• Auth: General for APIs 43.5
• User Authentication 43.6
• Auth: HTTP Basic 43.7
• Auth: OpenID Connect 43.8
• Browser Syntax Highlighting 43.9
• Camel 43.10
• Capability Statement (metadata) 43.11
• Care Gaps 43.12
• CDA Generation 43.13
• CDA Import 43.14
• CDA Interceptors 43.15
• CDA JavaScript Execution Scripts 43.16
• CDA Terminology 43.17
• CDS Hooks Definitions 43.18
• Channel Import 43.19
• Channel Retry 43.20
• Kafka 43.21
• Cluster Manager Maintenance 43.22
• Message Broker 43.23
• Cluster Level Security 43.24
• CQL 43.25
• Credentials 43.26
• Cross-Origin Resource Sharing (CORS) 43.27
• Database 43.28
• Da Vinci Health Record Exchange 43.29
• DQM 43.30
• DTR 43.31
• Email Configuration 43.32
• Encounter Start CDS hook configuration 43.33
• MDM UI 43.34
• ETL Import: CSV Properties 43.35
• ETL Import: Source 43.36
• FHIR Binary Storage 43.37
• FHIR Bulk Operations 43.38
• Capability Statement 43.39
• FHIR Configuration 43.40
• Consent Service 43.41
• FHIR Endpoint Conversion 43.42
• FHIR Endpoint HFQL Support 43.43
• Interceptors 43.44
• FHIR Endpoint Partitioning 43.45
• Resource Providers 43.46
• FHIR Endpoint Security 43.47
• Endpoint Terminology 43.48
• FHIR Gateway Configuration 43.49
• FHIR Interceptors 43.50
• LiveBundle Service 43.51
• FHIR MDM Server 43.52
• FHIR Performance 43.53
• FHIR Performance Tracing 43.54
• FHIR Realtime Export 43.55
• Repository Validation 43.56
• FHIR Resource Types 43.57
• FHIR REST Endpoint 43.58
• FHIR Search 43.59
• Custom Resource Types 43.60
• IG Support 43.61
• MegaScale 43.62
• FHIR Storage Module Conditional Updates 43.63
• FHIR Storage Module Scheduled Tasks 43.64
• FHIR Validation Services 43.65
• FHIR Storage Package Registry 43.66
• FHIR Storage Partitioning 43.67
• Versioned References 43.68
• FHIR Subscription Delivery 43.69
• FHIR Subscription Persistence 43.70
• Amazon HealthLake REST Endpoint 43.71
• HL7 v2.x Mapper - Contained Resource 43.72
• HL7 v2.x Mapper - DG1 43.73
• HL7 v2.x Mapper - Forced Namespace Mode 43.74
• HL7 v2.x Mapper - General 43.75
• HL7 v2.x Mapper - Medications 43.76
• HL7 v2.x Mapper - OBR 43.77
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 43.78
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 43.79
• HL7 v2.x Mapper - PID 43.80
• HL7 v2.x Mapper - PV1 43.81
• Listener Interceptors 43.82
• HL7 v2.x Listener Script 43.83
• HL7 v2.x MLLP Listener 43.84
• HL7 v2.x MLLP Sender 43.85
• FHIR to HL7 v2.x Mapper Script 43.86
• HL7 v2.x Outbound Mapping 43.87
• Da Vinci Health Record Exchange (HRex) 43.88
• HTTP Access Log 43.89
• HTTP Listener 43.90
• HTTP Request Pool 43.91
• HTTP Security 43.92
• Hybrid Providers Definitions 43.93
• Initial User Seeding 43.94
• JavaScript Execution Environment 43.95
• JSON Web KeySet (JWKS) 43.96
• LDAP Authentication 43.97
• Smile CDR License 43.98
• Lucene FullText Indexing 43.99
• MDM 43.100
• Narrative Generator 43.101
• OpenID Connect Token Validation 43.102
• OpenID Connect (OIDC) 43.103
• Order Sign CDS hook configuration 43.104
• Payer to Payer 43.105
• Prior Authorization Coverage Requirement Discovery 43.106
• Privacy Security Notice 43.107
• Provenance Injection 43.108
• Realtime Export 43.109
• Endpoint Validation: Request Validating 43.110
• Scheduler Configuration 43.111
• Search Parameter Seeding 43.112
• SAML Provider 43.113
• Security Inbound Script 43.114
• Inbound SMART on FHIR Authentication 43.115
• Inbound SMART on FHIR Endpoints 43.116
• OAuth2/OIDC Federation 43.117
• SMART Callback Script 43.118
• Cross-Organizational Data Access Profile 43.119
• SMART Login Skin 43.120
• SMART Login Terms of Service 43.121
• SMART Authorization 43.122
• SMART Definitions Seeding 43.123
• Sessions 43.124
• Two Factor Authentication 43.125
• TLS / SSL (Encryption) 43.126
• Transaction Log 43.127
• Trusted Client 43.128
• User Self Registration 43.129

Product Reference

• Enumerated Types 44.0

Amazon HealthLake Outbound REST Connector

• Introduction 45.0
• Getting Started 45.1
• Data Management and Transfer 45.2

Appendix

• Preparing a Linux Host 46.0
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 46.1
• Deploying a Kubernetes Managed Cluster 46.2
• Password Hashing Algorithms 46.3
• Resource Paths 46.4
• JWT Signature Algorithms 46.5
• Inferno Considerations 46.6