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FHIRBase

Open source relational storage for FHIR targeting real production.

Build Status

Powered by Health Samurai

Sponsored by:

choice-hs.com

Live Demo

Here is an interactive demo, which is build with FHIRPlace & FHIRFace by-products.

Motivation

While crafting Health IT systems you begin to understand a value of properly chosen domain model. FHIR is an open source new generation lightweight standard for health data interoperability, which (we hope) could be used as a foundationan for Health IT systems. FHIR is based on a concept of resource.

FHIR® is a next generation standards framework created by HL7. FHIR combines the best features of HL7 Version 2, Version 3 and CDA® product lines while leveraging the latest web standards and applying a tight focus on implementability.

Also we learned that data is a heart of any information system, and should be reliably managed. PostgreSQL is battle proved open source database, which supports structured documents (jsonb), while preserving ACID guaranties and richness of SQL query language.

PostgreSQL is a powerful, open source object-relational database system. It has more than 15 years of active development and a proven architecture that has earned it a strong reputation for reliability, data integrity, and correctness.

Here is list of PostgreSQL features we use:

We actively collaborate with PostgreSQL lead developers to craft production ready storage for FHIR.

TODO: about fhirb, VODKA and jsquery

Why we are doing this inside database?

We decided to implement most of FHIR specification inside database for scalability reason (all data operations is done efficiently in databse).

This approach also gives you possibility use FHIRBase from your prefered lang/platform (.NET, java, ruby, nodejs etc). We implemented FHIR compliant server in clojure, with small amount of code - FHIRPlace.

And there is option to break FHIR specification abstraction (if required) and go into database by generic SQL interface and complete your business task.

Features

TODO:

Overview

We heavily use PostgreSQL inheritance feature, for polymorphic operations.

Here are base tables:

To store resource data:

  • resource - for current resources
  • resource_history - for resource historical versions
  • tag - for tags
  • tag_history - tags history

There are some "index" tables by one for each search parameter type and one for indexing all resource references, which are populated in sync with resource data and provide fast FHIR search queries:

  • search_string
  • search_token
  • search_date
  • search_reference
  • search_quantity
  • references

For each resource type FHIRbase generate set of tables (which inherit from base tables). This is done, to separate dataspaces for each resource, so they are not messed and can guarantee performance proportional to amount of data for particular type of resource.

Note: Same trick is used by PostgreSQL for partitioning.

  • "{{lower(ResourceType)}}" (...) INHERITS (resource)

  • "{{lower(ResourceType)}}_history" (...) INHERITS (resource_history)

  • "{{lower(ResourceType)}}_tag" (...) INHERITS (tag)

  • "{{lower(ResourceType)}}_tag_history" (...) INHERITS tag_history

  • "{{lower(ResourceType)}}_sort" (...)

  • "{{lower(ResourceType)}}_search_string" (...)

  • "{{lower(ResourceType)}}_search_token" (...)

  • "{{lower(ResourceType)}}_search_date" (...)

  • "{{lower(ResourceType)}}_search_reference" (...)

  • "{{lower(ResourceType)}}_search_quantity" (...)

  • "{{lower(ResourceType)}}_references" (...)

For more information see source code:

Installation

Prefered way is docker - https://docker.com.

Install docker.

Here is auto builded public image of fhirbase:

To install fhirbase:

sudo docker.io run -d --name=fhirbase -t -p <mylocalport>:5432 fhirbase/fhirbase:latest

# check by connecting to database
psql -U fhirbase -h localhost -p <mylocalport> fhirbase
password> fhirbase

# or you can connect with your postgresql client: 
# user:fhirbase, password: fhirbase, host: localhost, port:<mylocalport>

Build

Requirements:

You can download postgresql 9.4 pre-release or build Postgresql from source on debian/ubuntu and create local user cluster with:

source local_cfg.sh && ./install-postgres

NOTE: you can tune configuration in local_cfg.sh.

You can install FHIRBase:

source local_cfg.sh
echo 'CREATE DATABASE mydb' | psql postgres
psql mydb < fhirbase--1.0.sql

TODO: test script to verify installation

API

Most of FHIR complaint operations could be done with FHIRBase procedures, which guaranties data integrity and do heavy job for you. All procedures have first parameter _cfg jsonb with configuration params. Now there is only one paramenter [base] (Service Root URL): {"base":"http:/myserver"}

FUNCTION fhir_read(_cfg jsonb, type varchar, id uuid)

Read the current state of the resource Return bundle with only one entry for uniformity;

FUNCTION fhir_create(_cfg jsonb, type varchar, resource jsonb, tags jsonb)

Create a new resource with a server assigned id Return bundle with newly entry;

FUNCTION fhir_vread(_cfg jsonb, type varchar, id uuid, vid uuid)

Read specific version of resource with type Returns bundle with one entry;

FUNCTION fhir_update(_cfg jsonb, type varchar, id uuid, vid uuid, resource jsonb, tags jsonb)

Update resource, creating new version Returns bundle with one entry;

FUNCTION fhir_delete(_cfg jsonb, type varchar, id uuid)

DELETE resource by its id AND return deleted version Return bundle with one deleted version entry ;

FUNCTION fhir_history(_cfg jsonb, type varchar, id uuid, params jsonb)

Retrieve the changes history for a particular resource with logical id (id) Return bundle with entries representing versions;

FUNCTION fhir_search(_cfg jsonb, type varchar, params jsonb)

Search in resources with type by params Returns bundle with entries;

FUNCTION fhir_conformance(_cfg jsonb)

Returns conformance resource jsonb;

Contribution

  • Star us on github
  • Create an issue – for a bug report or enhancment
  • Contribute to FHIRBase − see dev/README.md

Development

Development details see in dev/README.md

License

Copyright © 2014 health samurai

FHIRbase are released under the terms of the MIT license