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
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)
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
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 Hybrid Providers
LiveBundle
- LiveBundle Overview 20.0
- LiveBundle API 20.1
- LiveBundle Rule Definition 20.2
- LiveBundle Keepers 20.3
CDS Hooks
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
Clustering
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
Additional Features
Monitoring
Product Administration
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
Java Execution Environment
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
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
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
Amazon HealthLake Outbound REST Connector
Appendix
Table of Contents
MegaScale
7.6.1MegaScaleTrial
MegaScale is a new feature. It has a number of limitations and will not be suitable for many use cases. See Limitations below.
MegaScale is a mechanism for storing virtually unlimited amounts of data in a single FHIR server. It uses multiple database instances to create discrete pools of data which are logically separate, but are managed under a single Smile CDR FHIR Storage (RDBMS) module.
In its simplest terms, a MegaScale-enabled server can be thought of as a multitenant repository where each tenant is hosted in a separate database instance.
Using this strategy can be helpful in cases such as:
- The total amount of data to be stored exceeds the natural limit of a single instance of the database technology being used
- Data needs to be kept physically separate due to privacy or legal rules.
7.6.2ArchitectureTrial
In MegaScale mode, one or more FHIR Endpoint modules are combined with a single FHIR Storage (RDBMS) module. Incoming FHIR requests include a tenant identifier which maps to a particular partition, which then specifies the target database. This architecture is shown in the diagram below.
7.6.3LimitationsTrial
This section lists the known limitations on this feature.
7.6.3.1Partition Styles
- Only the Request Tenant (REQUEST_TENANT) mode may be used as a Request Partition Selection Mode.
7.6.3.2FHIR Interactions
The following FHIR interactions have been tested:
- Create/Update
- Search
- $validate
- $expunge – Expunge everything is verified to work, and will only expunge everything for a single MegaScale database at a time.
- $delete-expunge – Delete expunge is verified to work, and will only delete and expunge for a single MegaScale database at a time.
No other features, operations, or interactions have been tested or are expected to work with MegaScale.
7.6.3.3Cross-Partition References
If Cross-Partition References are enabled, it will be possible to create references that cross partition and database boundaries. In a MegaScale-enabled repository, these references rely on a soft-reference that is stored in the source partition that redirects the server to the target partition.
These references may be used for _include processing, but do not support chained searches or _revinclude processing.
7.6.4ConfigurationTrial
To enable MegaScale mode, the following settings must be set.
On the FHIR Storage (RDBMS) module:
- Partitioning Enabled must be set to
true. - At least one partition must be created. See Seeding Partitions.
- Partition Selection Mode must be set to
REQUEST_TENANT. - MegaScale Enabled must be set to
true. - A Connection Provider Interceptor must be set (see below).
On the FHIR Endpoint module:
- Tenant Identification Strategy must be set to
URL_BASED.
7.6.5Connection Provider InterceptorTrial
MegaScale connection details are supplied using a Java Smile CDR Interceptor using the STORAGE_MEGASCALE_PROVIDE_DB_INFO pointcut.
See Example: MegaScale Connection Provider to see how this pointcut can be used. This example is also available in the Interceptor Starter Project.