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
• Localization 3.10

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

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
• Lucene Indexing 5.5
• Performance and Caching 5.6
• Resource IDs 5.7
• Search Parameters 5.8
• Search Parameter Features 5.9
• Phonetic Search Parameters 5.10
• Custom Search Parameters 5.11
• Partitioning and Multitenancy 5.12
• Searching for Data 5.13
• Creating Data 5.14
• Reading Data 5.15
• Updating Data 5.16
• Deleting Data 5.17
• Binary Data 5.18
• Request Tracing and Provenance 5.19
• FHIR Versions 5.20
• Versioned Resource References 5.21
• Clinical Quality Language (CQL) 5.22

Validation and Conformance

• Introduction 6.0
• Validation Support Repository 6.1
• Conformance Data 6.2
• Repository Validation 6.3
• Repository Validation: Java 6.4
• Repository Validation: Javascript 6.5
• Endpoint Validation 6.6
• Packages and Implementation Guides 6.7
• Remote Terminology Services 6.8

Terminology

• Terminology Introduction 7.0
• Uploading Codes 7.1
• Searching for Codes 7.2

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: Federated OAuth2/OIDC Login 14.7
• SMART: Application Approval/Consent 14.8
• SMART Inbound Security Module 14.9
• SMART: Session Management 14.10
• SMART: Assigning Permissions 14.11
• SMART: Access Tokens 14.12

FHIR Hybrid Providers

• Hybrid Providers 15.0

CDS-Hooks

• CDS-Hooks 16.0

FHIR Gateway

• FHIR Gateway Introduction 17.0
• Configuration 17.1

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
• Bulk Import Endpoint 26.2
• CDA Exchange Endpoint 26.3
• Metrics Endpoint 26.4
• Module Config Endpoint 26.5
• OpenID Connect Clients Endpoint 26.6
• OpenID Connect Servers Endpoint 26.7
• Runtime Status Endpoint 26.8
• Transaction Log Endpoint 26.9
• User Management Endpoint 26.10

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

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

Smile CDR CLI (smileutil)

• Introduction 31.0
• Execute Script Function 31.1
• Create FHIR Package 31.2
• Export ConceptMap to CSV 31.3
• HL7 v2.x Analyze Flat File 31.4
• HL7 v2.x Transmit Flat File 31.5
• Import CSV to ConceptMap 31.6
• Migrate Database 31.7
• Synchronize FHIR Servers 31.8
• Upload Bundle Files 31.9
• Upload CSV Bulk Import File 31.10
• Upload Sample Dataset 31.11
• Upload Terminology 31.12
• Validate FHIR Resources 31.13

Modules

• CDA Exchange 32.0
• Channel Import 32.1
• Cluster Manager 32.2
• MDM 32.3
• ETL Importer 32.4
• FHIR REST Endpoint (DSTU2) 32.5
• FHIR REST Endpoint (R3) 32.6
• FHIR Storage (DSTU2 Relational) 32.7
• FHIR Storage (R3 Relational) 32.8
• Subscription Matcher (R3) 32.9
• Subscription Matcher (R4) 32.10
• FHIRWeb Console 32.11
• HL7 v2.x Listening Endpoint 32.12
• HL7 v2.x Sending Endpoint 32.13
• JSON Admin API 32.14
• LDAP Inbound Security 32.15
• Local Inbound Security 32.16
• Scripted Inbound Security 32.17
• SMART App Host 32.18
• SMART Inbound Security 32.19
• Realtime Export 32.20
• SMART Outbound Security 32.21
• Web Admin Console 32.22

Configuration Categories

• Web Admin Console Settings 33.0
• Authentication Callback Scripts 33.1
• Auth: General for APIs 33.2
• User Authentication 33.3
• Auth: HTTP Basic 33.4
• Auth: OpenID Connect 33.5
• Browser Syntax Highlighting 33.6
• Capability Statement (metadata) 33.7
• Channel Import 33.8
• Channel Retry 33.9
• Cluster Manager Subscription Messaging 33.10
• Cluster Manager Maintenance 33.11
• Cluster Manager Message Broker 33.12
• Cluster Manager Kafka 33.13
• Credentials 33.14
• Cross-Origin Resource Sharing (CORS) 33.15
• Database 33.16
• ETL Import: CSV Properties 33.17
• ETL Import: Source 33.18
• FHIR Binary Storage 33.19
• FHIR Bulk Operations 33.20
• FHIR Configuration 33.21
• FHIR Consent Service 33.22
• FHIR LiveBundle Service 33.23
• FHIR Endpoint Conversion 33.24
• FHIR Endpoint Security 33.25
• Interceptors 33.26
• FHIR Endpoint Partitioning and Multitenancy 33.27
• FHIR Gateway Config 33.28
• FHIR MDM Server 33.29
• FHIR Storage Partitioning and Multitenancy 33.30
• Package Registry 33.31
• Versioned References 33.32
• FHIR Performance 33.33
• FHIR Performance Tracing 33.34
• FHIR Realtime Export 33.35
• FHIR Resource Types 33.36
• FHIR REST Endpoint 33.37
• FHIR Search 33.38
• FHIR Interceptors 33.39
• FHIR Repository Validation 33.40
• FHIR Subscription Persistence 33.41
• FHIR Subscription Delivery 33.42
• FHIR Validation Services 33.43
• HL7 v2.x to FHIR Mapper - Forced Namespace Mode 33.44
• HL7 v2.x to FHIR Mapper - General 33.45
• HL7 v2.x Mapper - Medications 33.46
• HL7 v2.x to FHIR Mapper - OBR 33.47
• HL7 v2.x to FHIR Mapper - OBSERVATION Group 33.48
• HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 33.49
• HL7 v2.x to FHIR Mapper - PV1 33.50
• HL7 v2.x Listener Script 33.51
• HL7 v2.x MLLP Listener 33.52
• FHIR to HL7 v2.x Mapper Script 33.53
• HL7 v2.x MLLP Sender 33.54
• HTTP Access Log 33.55
• HTTP Listener 33.56
• HTTP Request Pool 33.57
• HTTP Security 33.58
• Hybrid Providers Definitions 33.59
• Initial User Seeding 33.60
• JSON Web KeySet (JWKS) 33.61
• LDAP Authentication 33.62
• Lucene FullText Indexing 33.63
• Narrative Generator 33.64
• MDM 33.65
• OpenID Connect (OIC) 33.66
• Realtime Export 33.67
• Request Validating 33.68
• Security Inbound Script 33.69
• Inbound SMART on FHIR Authentication 33.70
• Inbound SMART on FHIR Endpoints 33.71
• OpenID Connect Token Validation 33.72
• SAML Provider 33.73
• OAuth2/OIDC Federation 33.74
• SMART Authorization 33.75
• SMART Definitions Seeding 33.76
• Sessions 33.77
• SMART Outbound Security: Callback Script 33.78
• SMART Outbound Security: CODAP 33.79
• SMART Outbound Security: Login Skin 33.80
• Two Factor Authentication 33.81
• TLS / SSL (Encryption) 33.82
• Trusted Client 33.83
• Transaction Log 33.84
• Miscellaneous Categories 33.85

Product Reference

• Enumerated Types 34.0

Appendix

• Preparing a Linux Host 35.0
• Production Checklist 35.1
• Installing Smile CDR, NGINX and PostgreSQL in a Docker Stack 35.2
• Deploying a Kubernetes Managed Cluster 35.3
• Password Hashing Algorithms 35.4
• Resource Paths 35.5
• JWT Signature Algorithms 35.6