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reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["fhir","fhir-api","fhir-server","kafka"],"created_at":"2025-03-21T13:36:46.944Z","updated_at":"2026-01-12T15:29:15.822Z","avatar_url":"https://github.com/miracum.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FHIR Gateway\n\n![License](https://img.shields.io/github/license/miracum/fhir-gateway)\n[![OpenSSF Scorecard](https://api.securityscorecards.dev/projects/github.com/miracum/fhir-gateway/badge)](https://scorecard.dev/viewer/?uri=github.com/miracum/fhir-gateway)\n[![SLSA 3](https://slsa.dev/images/gh-badge-level3.svg)](https://slsa.dev)\n\nA thin layer between FHIR REST clients and resource processing pipelines.\n\n## Overview\n\n![Overview](docs/img/overview.png \"Overview\")\n\n## Run it\n\nThe recommended deployment is on Kubernetes. See \u003chttps://github.com/miracum/charts/tree/master/charts/fhir-gateway\u003e for\na Helm Chart.\n\nAn example for deploying using (Docker) Compose can be found in the [deploy folder](./deploy/README.md).\n\nAlso see the now archived \u003chttps://github.com/num-codex/num-knoten\u003e for an example end-to-end deployment.\n\n## Configuration\n\nTo configure your deployment, you can change the following environment variables:\n\n| Variable | Description | Default |\n|-----------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------|\n| SPRING_DATASOURCE_URL | JDBC URL of the Postgres DB to store the received FHIR resources, needs to be set to an empty variable if no PSQL db is to be connected to | jdbc:postgresql://fhir-db:5432/fhir |\n| SPRING_DATASOURCE_USERNAME | Username of the Postgres DB | postgres |\n| SPRING_DATASOURCE_PASSWORD | Password for the Postgres DB | postgres | \n| SERVICES_LOINC_CONVERSIONS_ENABLED | Wether LOINC harmonization should be enabled | false |\n| SERVICES_LOINC_CONVERSIONS_URL | URL of the [LOINC conversion service](https://github.com/miracum/loinc-conversion) | \u003chttp://loinc-converter:8080/conversions\u003e |\n| SERVICES_PSEUDONYMIZER_ENABLED | Whether pseudonymization should be enabled. | false |\n| SERVICES_PSEUDONYMIZER_URL | URL of the [FHIR Pseudonymizer service](https://github.com/miracum/fhir-pseudonymizer) | \u003chttp://fhir-pseudonymizer:8080/fhir\u003e |\n| SERVICES_FHIRSERVER_ENABLED | Wether storing resources in a downstream FHIR Server should be enabled | false |\n| SERVICES_FHIRSERVER_URL | URL of the FHIR server to send data to | \u003chttp://fhir-server:8080/fhir\u003e |\n| SERVICES_FHIRSERVER_AUTH_BASIC_ENABLED | Enable HTTP basic auth for sending data to FHIR server | false |\n| SERVICES_FHIRSERVER_AUTH_BASIC_USERNAME | HTTP basic auth username of the FHIR server to send data to | `\"\"` |\n| SERVICES_FHIRSERVER_AUTH_BASIC_PASSWORD | HTTP basic auth password of the FHIR server to send data to | `\"\"` |\n| SERVICES_PSQL_ENABLED | Wether storing resources in a PostgreSQL database should be enabled | false |\n| SERVICES_KAFKA_ENABLED | Wether Kafka should be enabled. Note Kafka options below | false |\n| SERVICES_KAFKA_PROCESSOR_ENABLED | Enable reading FHIR resources from, and writing them back to a Kafka cluster | false |\n| SERVICES_KAFKA_PROCESSOR_GENERATE_OUTPUT_TOPIC_MATCH_EXPRESSION | Allows for dynamically generating the Kafka output topic's name based on the input topic. Used to set a regular expression which is applied to the input topic and the first match is replaced with the value of `SERVICES_KAFKA_GENERATE_OUTPUT_TOPIC_REPLACE_WITH`. You can set this to `\"^\"` to add a prefix to the output topic. | `\"\"` |\n| SERVICES_KAFKA_PROCESSOR_CONSUME_ONLY | Only reads FHIR resources from a Kafka cluster without writing them back | false |\n| SERVICES_KAFKA_STORE_FROM_API_ENABLED | Wether storing resources in a Kafka topic should be enabled (only applicable for resources received by the FHIR Gateway's FHIR REST API | false |\n| SERVICES_KAFKA_STORE_FROM_API_OUTPUT_TOPIC | Name of the topic where resources received from API should be written to | fhir.gateway.ouput |\n\nFor the Kafka configuration and other configuration options,\nsee [application.yml](src/main/resources/application.yml).\n\n### Running without database persistence\n\nBy default, the FHIR gateway persists any received FHIR resource in a PostgreSQL database.\nTo run without persistence, the following variables both need to be set:\n\n- `SPRING_SERVICE_PSQL_ENABLED=\"false\"`\n- `SPRING_SQL_INIT_MODE=\"never\"`\n\nthis allows the gateway to start without the database.\n\n## Supported Operations\n\nThe FHIR Gateway is not a fully-fledged FHIR server and only supports a subset of the RESTful server\ninteractions.\n\n### POST/PUT\n\nThe Gateway only supports persisting resources that are HTTP POSTed as FHIR Bundles using\nthe [update-as-create](https://www.hl7.org/fhir/http.html#upsert) semantics.\nSee [bundle.json](tests/e2e/data/bundle.json) for an example.\n\n### DELETE\n\nFHIR Bundles containing `DELETE` requests are also handled and will result in deleting the resource\nspecified in the request URL. Note that the resources are marked as `is_deleted` in the Gateway's\nPostgreSQL DB instead of being physically deleted.\n\nNote that neither conditional creates nor deletes are supported. While this works:\n\n```json\n{\n \"request\": {\n \"method\": \"DELETE\",\n \"url\": \"Patient/234\"\n }\n}\n```\n\nThis does not:\n\n```json\n{\n \"request\": {\n \"method\": \"DELETE\",\n \"url\": \"Patient?identifier=123456\"\n }\n}\n```\n\n## Development\n\nStart all fixtures to run the FHIR GW:\n\n```sh\ndocker compose \\\n -f dev/docker-compose.dev.yml \\\n -f dev/docker-compose.gw-deps.yml \\\n -f dev/docker-compose.exposed.yml up\n```\n\nThis contains a few optional services: Kafka, a FHIR server, FHIR Pseudonymizer, Vfps. You might simplify the\ndocker-compose.dev.yml and only include relevant components for development.\n\nRun the FHIR Gateway from your terminal:\n\n```sh\n./gradlew :bootRun\n```\n\nBy default, this runs using Kafka as a source of FHIR resources to process. You can view the generated Kafka topics\nat \u003chttp://localhost:9000/ui/kafka/topic\u003e.\n\n## Database Tuning\n\n### Partitioning\n\nIf the size of the `resources` table is expected to grow significantly, you can leverage\npartitioning to split the stored resources by type. Run the following **before** starting the\nFHIR-Gateway to create the `resources` table with partitions for the most common resource types:\n\n```postgresql\nCREATE TABLE resources (\n id SERIAL,\n fhir_id VARCHAR(64) NOT NULL,\n type VARCHAR(64) NOT NULL,\n data JSONB NOT NULL,\n created_at TIMESTAMP NOT NULL DEFAULT NOW(),\n last_updated_at TIMESTAMP NOT NULL DEFAULT NOW(),\n is_deleted BOOLEAN NOT NULL DEFAULT FALSE,\n CONSTRAINT fhir_id_unique UNIQUE (fhir_id, type)\n) PARTITION BY LIST (type);\n\nCREATE TABLE resources_patient PARTITION OF resources FOR VALUES IN ('Patient');\nCREATE TABLE resources_encounter PARTITION OF resources FOR VALUES IN ('Encounter');\nCREATE TABLE resources_condition PARTITION OF resources FOR VALUES IN ('Condition');\nCREATE TABLE resources_observation PARTITION OF resources FOR VALUES IN ('Observation');\nCREATE TABLE resources_medication PARTITION OF resources FOR VALUES IN ('Medication');\nCREATE TABLE resources_medication_statement PARTITION OF resources FOR VALUES IN ('MedicationStatement');\nCREATE TABLE resources_medication_administration PARTITION OF resources FOR VALUES IN ('MedicationAdministration');\nCREATE TABLE resources_procedure PARTITION OF resources FOR VALUES IN ('Procedure');\nCREATE TABLE resources_others PARTITION OF resources DEFAULT;\n\nCREATE INDEX resource_id_idx ON resources (id);\nCREATE INDEX resource_type_idx ON resources (type);\nCREATE INDEX last_updated_at_idx ON resources (last_updated_at DESC);\n```\n\nBe sure to set `SPRING_SQL_INIT_MODE=never` before starting the FHIR GW.\n\nThis isn't part of the default initialization schema, but may become the default as part of the next\nmajor release.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmiracum%2Ffhir-gateway","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmiracum%2Ffhir-gateway","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmiracum%2Ffhir-gateway/lists"}