Welcome to Smile CDR
- Table of Contents 1.0
- Smile CDR Maturity Model 1.1
- List of Features by Maturity 1.2
- Changelog (2022 Releases) 1.3
- Changelog (2021 Releases) 1.4
- Changelog (2020 Releases) 1.5
- Changelog (2019 Releases) 1.6
- Changelog (2018 Releases) 1.7
- Changelog (2017 Releases) 1.8
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: ActiveMQ 3.6
- Message Broker: Kafka 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
- Searching for Data 6.11
- Creating Data 6.12
- Reading Data 6.13
- Updating Data 6.14
- Deleting Data 6.15
- Binary Data 6.16
- Request Tracing and Provenance 6.17
- FHIR Versions 6.18
- Versioned Resource References 6.19
- Tags, Profiles, and Security Labels 6.20
- Clinical Quality Language (CQL) 6.21
- Partitioning and Multitenancy 6.22
- Custom Resource Types 6.23
FHIR Storage (Relational)
- FHIR Storage (Relational) Module 7.0
- Performance Tuning 7.1
- Lucene Indexing 7.2
- Performance and Caching 7.3
- Chained Searching and Sorting 7.4
- MegaScale 7.5
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
Interceptors
- Interceptors 12.0
- Starter Project 12.1
- Examples: FHIR Endpoints 12.2
- Examples: FHIR Storage 12.3
- Examples: FHIR Gateway 12.4
- Examples: FHIR Client 12.5
- Examples: MDM 12.6
- Examples: Subscription 12.7
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
Clinical Reasoning
IG Support
Clustering
Logging
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
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
Product Configuration
Java Execution Environment
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
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
- Audit Log Persistence 40.5
- Digital Quality Measures (DQM) 40.6
- Enterprise Master Patient Index 40.7
- CDS Hooks Endpoint 40.8
- FHIR Gateway Endpoint 40.9
- FHIR REST Endpoint (DSTU2) 40.10
- FHIR REST Endpoint (DSTU3) 40.11
- FHIR REST Endpoint (R4) 40.12
- FHIRWeb Console 40.13
- HL7 v2.x Listening Endpoint 40.14
- HL7 v2.x Sending Endpoint 40.15
- Hybrid Providers Endpoint 40.16
- Package Registry Endpoint 40.17
- Subscription Websocket Endpoint 40.18
- ETL Importer 40.19
- MDM 40.20
- Narrative Generator 40.21
- FHIR Storage (DSTU2 Relational) 40.22
- FHIR Storage (R3 Relational) 40.23
- FHIR Storage (Mongo) 40.24
- FHIR Storage (R4 Relational) 40.25
- Realtime Export 40.26
- LDAP Inbound Security 40.27
- Local Inbound Security 40.28
- SAML Inbound Security 40.29
- Scripted Inbound Security 40.30
- SMART Inbound Security 40.31
- SMART Outbound Security 40.32
- SMART App Host 40.33
- Subscription Matcher (All FHIR Versions) 40.34
- Subscription Matcher (DSTU2 - Deprecated) 40.35
- Subscription Matcher (DSTU3 - Deprecated) 40.36
- Subscription Matcher (R4 - Deprecated) 40.37
- appSphere 40.38
- Payer to Payer 40.39
- Amazon HealthLake Outbound REST Connector 40.40
- License 40.41
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
- Capability Statement (metadata) 41.10
- CDA Generation 41.11
- CDA Import 41.12
- CDA JavaScript Execution Scripts 41.13
- CDS Hooks Definitions 41.14
- Channel Import 41.15
- Channel Retry 41.16
- Kafka 41.17
- Cluster Manager Maintenance 41.18
- Message Broker 41.19
- Cluster Level Security 41.20
- Credentials 41.21
- Cross-Origin Resource Sharing (CORS) 41.22
- Database 41.23
- Da Vinci Health Record Exchange 41.24
- DQM 41.25
- Email Configuration 41.26
- ETL Import: CSV Properties 41.27
- ETL Import: Source 41.28
- FHIR Binary Storage 41.29
- FHIR Bulk Operations 41.30
- Capability Statement 41.31
- FHIR Configuration 41.32
- Consent Service 41.33
- FHIR Endpoint Conversion 41.34
- Interceptors 41.35
- FHIR Endpoint Partitioning 41.36
- Resource Providers 41.37
- FHIR Endpoint Security 41.38
- Endpoint Terminology 41.39
- FHIR Gateway Configuration 41.40
- FHIR Interceptors 41.41
- LiveBundle Service 41.42
- FHIR MDM Server 41.43
- FHIR Performance 41.44
- FHIR Performance Tracing 41.45
- FHIR Realtime Export 41.46
- Repository Validation 41.47
- FHIR Resource Types 41.48
- FHIR REST Endpoint 41.49
- FHIR Search 41.50
- Custom Resource Types 41.51
- IG Support 41.52
- MegaScale 41.53
- FHIR Storage Module Scheduled Tasks 41.54
- FHIR Validation Services 41.55
- FHIR Storage Package Registry 41.56
- FHIR Storage Partitioning 41.57
- Versioned References 41.58
- FHIR Subscription Delivery 41.59
- FHIR Subscription Persistence 41.60
- Amazon HealthLake REST Endpoint 41.61
- HL7 v2.x Mapper - Contained Resource 41.62
- HL7 v2.x Mapper - DG1 41.63
- HL7 v2.x Mapper - Forced Namespace Mode 41.64
- HL7 v2.x Mapper - General 41.65
- HL7 v2.x Mapper - Medications 41.66
- HL7 v2.x Mapper - OBR 41.67
- HL7 v2.x to FHIR Mapper - OBSERVATION Group 41.68
- HL7 v2.x to FHIR Mapper - ORDER_OBSERVATION Group 41.69
- HL7 v2.x Mapper - PID 41.70
- HL7 v2.x Mapper - PV1 41.71
- HL7 v2.x Listener Script 41.72
- HL7 v2.x MLLP Listener 41.73
- HL7 v2.x MLLP Sender 41.74
- FHIR to HL7 v2.x Mapper Script 41.75
- HL7 v2.x Outbound Mapping 41.76
- Da Vinci Health Record Exchange (HRex) 41.77
- HTTP Access Log 41.78
- HTTP Listener 41.79
- HTTP Request Pool 41.80
- HTTP Security 41.81
- Hybrid Providers Definitions 41.82
- Initial User Seeding 41.83
- JavaScript Execution Environment 41.84
- JSON Web KeySet (JWKS) 41.85
- LDAP Authentication 41.86
- Smile CDR License 41.87
- Lucene FullText Indexing 41.88
- MDM 41.89
- Narrative Generator 41.90
- OpenID Connect Token Validation 41.91
- OpenID Connect (OIDC) 41.92
- Payer to Payer 41.93
- Privacy Security Notice 41.94
- Provenance Injection 41.95
- Realtime Export 41.96
- Endpoint Validation: Request Validating 41.97
- Scheduler Configuration 41.98
- Search Parameter Seeding 41.99
- SAML Provider 41.100
- Security Inbound Script 41.101
- Inbound SMART on FHIR Authentication 41.102
- Inbound SMART on FHIR Endpoints 41.103
- OAuth2/OIDC Federation 41.104
- SMART Callback Script 41.105
- Cross-Organizational Data Access Profile 41.106
- SMART Login Skin 41.107
- SMART Login Terms of Service 41.108
- SMART Authorization 41.109
- SMART Definitions Seeding 41.110
- Sessions 41.111
- Two Factor Authentication 41.112
- TLS / SSL (Encryption) 41.113
- Transaction Log 41.114
- Trusted Client 41.115
- User Self Registration 41.116
Product Reference
Amazon HealthLake Outbound REST Connector
ExperimentalPremium
Appendix
Table of Contents
MegaScale
7.5MegaScaleExperimental
MegaScale is a new and experimental 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.
7.5.1Architecture
In MegaScale mode, a single FHIR Endpoint module is paired with a single FHIR Storage (RDBMS) module. Incoming FHIR requests include a tenant identifier which specifies the target database. This architecture is shown in the diagram below.
7.5.2Limitations
This section lists the known limitations on this feature.
Partition Styles
- Only the Request Tenant (REQUEST_TENANT) mode may be used as a Request Partition Selection Mode.
FHIR Interactions
The following FHIR interactions have been tested:
- Create/Update
- Search
- $validate
- $expunge – Expunge everything is verified to work, but will only expunge everything for a single MegaScale database at a time
No other features, operations, or interactions have been tested or are expected to work with MegaScale.
Cross-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.
7.5.3Configuration
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.
7.5.4Connection Provider Interceptor
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.