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[onFHIR](http://onfhir.io) is a FHIR compliant secure health data repository that you can use as a central data service for your FHIR compliant healthcare applications.
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You can use it as a standalone server, or you can extend it with your further custom FHIR Operations to build your own application layer in addition to having standard FHIR repository capabilities.
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onFHIR.io is using FHIR Infrastructure Resource definitions (CapabilityStatement, StructureDefinition, SearchParameter, etc.) to tailor
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the FHIR server to your specific FHIR capabilities you required; resource profiles, search parameters, FHIR interactions you wanted to support.
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> [!IMPORTANT]
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> **Rebranding Announcement**
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>
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> **onFHIR** has been officially rebranded as **Repofyr**. This change reflects our transition from a research-focused repository at [**SRDC**](https://srdc.com.tr) to a commercially supported product line by [**Pontegra**](https://pontegra.com).
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>
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> **Note on Technical Migration:** While the project identity has changed, the internal codebase - including package names (`io.onfhir`), configuration keys (e.g., `onfhir.conf`), and Maven coordinates - still uses the legacy `onfhir` naming. A full technical migration for these components is planned for future major releases.
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It is implemented with Scala, based on Akka and MongoDB.
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## Overview
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**Repofyr** is a FHIR-compliant, secure health data repository designed as a central data service for healthcare applications. It is implemented in **Scala**, built on the **Akka** framework, and utilizes **MongoDB** for high-performance persistence.
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Stable versions are released in [Maven Central](https://search.maven.org/search?q=io.onfhir) and snapshot versions in [Sonatype Snapshot Repository](https://oss.sonatype.org/content/repositories/snapshots/io/onfhir/).
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You can use Repofyr as a standalone server or extend it with custom FHIR Operations to build complex application layers. It uses FHIR Infrastructure Resource definitions (CapabilityStatement, StructureDefinition, SearchParameter, etc.) to tailor the server to your specific profile and search requirements.
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## TEMPORARY WARNING
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**On March 6, 2023, we forcefully rearranged the existing onfhir_2.13 branch as master. The old master has been branched has onfhir_2.12.**
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***Website:**[repofyr.io](https://repofyr.io)
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***Open Source Core:** Maintained by [SRDC](https://srdc.com.tr)
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## Basic Configuration
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You can copy and update **onfhir-core/src/main/resources/application.conf** file, which is the entrypoint configuration to configure onFHIR repository based on your needs.
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You can copy and update the **onfhir-core/src/main/resources/application.conf** file, which is the main entry-point configuration for tailoring the Repofyr repository to your needs.
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For logger configurations, check **onfhir-core/src/main/resources/logback.xml**
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For configuration of the FHIR API to be provided, you need to provide the followings;
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To configure the FHIR API to be provided, you need to supply the following:
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* A file providing your **Conformance statement** (FHIR Capability Statement - See http://hl7.org/fhir/capabilitystatement.html) that describes the capabilities of the FHIR server you want to provide
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* A folder including all your **Profile definitions** (FHIR StructureDefinition - See http://hl7.org/fhir/structuredefinition.html) including resource, data type and extension definitions that will be used in the FHIR server you want to provide
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* A folder including all your **Compartment definitions** (FHIR CompartmentDefinition - See http://hl7.org/fhir/compartmentdefinition.html) for all compartments that you want to support for search
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* A folder including all your **Search parameter definitions** (FHIR SearchParameter - See http://hl7.org/fhir/searchparameter.html) for all extra search parameters (apart from what is available from the base FHIR standard) that you define and support for your resources
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* A folder including all your **Value sets** (FHIR ValueSet - See http://hl7.org/fhir/valueset.html) that you define and refer in your resource profiles
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* A folder including all your **Operation definitions** (FHIR OperationDefinition - http://hl7.org/fhir/operationdefinition.html) that you define and refer from capability statement in operations part (For your OperationDefinitions write the full class path of your implementation of operation in OperationDefinition.name)
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You can also provide the zip file for FHIR base definitions (Validation package - 'validation-min.xml.zip') that you want to support specifically.
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onFHIR supports all stable and build versions of HL7 FHIR. In this project, we provide modules for the last 3 main versions that are configured automatically with standard definitions and special configurators:
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You can also provide the ZIP file for FHIR base definitions (validation package: `validation-min.xml.zip`) that you want to support specifically.
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Repofyr supports all stable and build versions of HL7 FHIR. In this project, we provide modules for the last three main versions, configured automatically with standard definitions and dedicated configurators:
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* R5 >> onfhir-server-r5
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* R4 >> onfhir-server-r4
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* STU3 >> onfhir-server-stu3
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## Prerequisites
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onFHIR requires a MongoDB database up and running. If you do not use the given docker containers, the MongoDB configuration parameters (host, port, dbname etc.)
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should be passed to onFHIR through either application.conf file or as runtime parameters. The parameter names can be seen in the provided application.conf file.
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Repofyr requires a MongoDB database up and running. If you do not use the provided Docker containers, the MongoDB configuration parameters (host, port, dbname, etc.)
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should be passed to Repofyr through either the `application.conf` file or runtime parameters. Parameter names can be seen in the provided `application.conf` file.
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## Build & Run
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You need to run the below command to build fhir-repository. This will compile
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Run the command below to build Repofyr. This will compile
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your code, execute unit tests and create a single standalone jar with all the dependencies:
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```
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$ mvn package
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$ mvn package -DskipTests=true
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```
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Executable standalone jars **target/onfhir-server-standalone.jar** will be created under each onfhir-server for
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different FHIR version. Executing the following command will run the onRHI server for that version with nearly whole FHIR
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Executable standalone JARs (**target/onfhir-server-standalone.jar**) will be created under each `onfhir-server-*` module for
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different FHIR versions. Executing the following command will run the Repofyr server for that version with nearly complete FHIR
resolution methods; Signed JWT tokens and OAuth2.0 Token Introspection. You can use them by configurations or implement a new module.
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* Custom Audit Handler (Implementing**io.onfhir.audit.ICustomAuditHandler**): In default, you can configure onFHIR
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to store FHIR AuditEvent records to its own local repository, or a remote FHIR server running as a seperate audit repository.
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If you want to create audit events/logs in different format and send them to a custom audit repository (ElasticSearch+Kibana, etc),
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You can extend Repofyr by implementing certain custom mechanisms:
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* Custom Authorizer (implementing**io.onfhir.authz.IAAuthorizer**): By default(if configured), Repofyr
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supports the authorization mechanism defined by the [SMART on FHIR](https://docs.smarthealthit.org/authorization/) initiative,
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which is based on OAuth 2.0 Bearer Token authorization. If you need a custom authorization mechanism with a different set of
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scopes (permissions), you can implement an authorizer module and register it with Repofyr.
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* Custom Token Resolver (implementing**io.onfhir.authz.ITokenResolver**): Repofyr supports two default token
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resolution methods: signed JWT tokens and OAuth 2.0 token introspection. You can use them via configuration or implement a new module.
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* Custom Audit Handler (implementing**io.onfhir.audit.ICustomAuditHandler**): By default, you can configure Repofyr
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to store FHIR AuditEvent records in its own local repository, or in a remote FHIR server running as a separate audit repository.
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If you want to create audit events/logs in a different format and send them to a custom audit repository (Elasticsearch + Kibana, etc.),
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you can extend this interface with your module and register it.
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* Further FHIR Operations: You can implement custom FHIR Operations by extending **io.onfhir.api.service.FHIROperationHandlerService** and
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* Further FHIR Operations: You can implement custom FHIR operations by extending **io.onfhir.api.service.FHIROperationHandlerService** and
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preparing an OperationDefinition file describing the input and output parameters of the operation. You then need to provide a Map[String, String]
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of the (operation URL -> the class name of the module) that you implemented by extending FHIROperationHandlerService.
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* External Akka Routes: You can also implement non-FHIR REST services for your server and register them to onFHIR.
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of the (operation URL -> the class name of the module) that you implemented by extending FHIROperationHandlerService.
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* External Akka Routes: You can also implement non-FHIR REST services for your server and register them with Repofyr.
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```
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object Boot extends App {
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//Initialize onfhir for R4
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//Initialize Onfhir for R4
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var onfhir =
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Onfhir.apply(
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fhirConfigurator = new FhirR4Configurator(),
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customAuditHandler = new MyAuditHandler(),
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externalRoutes = ...my non-fhir routes
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)
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//Start it
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//Start it
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onfhir.start
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}
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```
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### Docker
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We also provide a simple docker setup for onFHIR under 'docker' folder. It provides a docker-compose file with
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two containers; one for MongoDB database and one for onFHIR application. You can run it with our sample onFHIR setup given with 'sample-setup' directory.
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You can copy the 'onfhir-server-standalone.jar' file to this sample-setup directory and run the sample setup as it is with the following command;
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We also provide a simple Docker setup for Repofyr under the `docker` folder. It includes a `docker-compose` file with
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two containers: one for MongoDB and one for the Repofyr application. You can run it with our sample Repofyr setup in the `sample-setup` directory.
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You can copy the `onfhir-server-standalone.jar` file to this `sample-setup` directory and run the sample setup as is with the following command:
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