A PostgreSQL Interface for FHIR Data

There are a vast number of PostgreSQL clients available on the Internet. From standard Drivers to BI and Analytics tools, PostgreSQL is a popular interface for data access. Using the SQL Gateway included in our ODBC Drivers, you can now create PostgreSQL entry-points that you can connect to from any standard client.

To access FHIR data as a PostgreSQL database on Windows, use the CData SQL Gateway, the ODBC Driver for FHIR, and the MySQL foreign data wrapper from EnterpriseDB. In this article, we compile the foreign data wrapper in Visual Studio, install it as an extension, and query FHIR data from PostgreSQL Server.

Configure the Connection to FHIR

If you have not already, first specify connection properties in an ODBC DSN (data source name). This is the last step of the driver installation. You can use the Microsoft ODBC Data Source Administrator to create and configure ODBC DSNs.

Set URL to the Service Base URL of the FHIR server. This is the address where the resources are defined in the FHIR server you would like to connect to. Set ConnectionType to a supported connection type. Set ContentType to the format of your documents. Set AuthScheme based on the authentication requirements for your FHIR server.

Generic, Azure-based, AWS-based, and Google-based FHIR server implementations are supported.

Sample Service Base URLs

• Generic: http://my_fhir_server/r4b/
• Azure: https://MY_AZURE_FHIR.azurehealthcareapis.com/
• AWS: https://healthlake.REGION.amazonaws.com/datastore/DATASTORE_ID/r4/
• Google: https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID/fhir/

Generic FHIR Instances

The product supports connections to custom instances of FHIR. Authentication to custom FHIR servers is handled via OAuth (read more about OAuth in the Help documentation. Before you can connect to custom FHIR instances, you must set ConnectionType to Generic.

Start the Remoting Service

The MySQL remoting service is a daemon process that listens for clients' incoming MySQL connections. See the setup guide in the SQL Gateway overview to configure the MySQL Remoting service in the CData SQL Gateway.

Build the MySQL Foreign Data Wrapper

The Foreign Data Wrapper can be installed as an extension to PostgreSQL, without recompiling PostgreSQL. If you are running PostgreSQL on a Unix-based system, you can use the PostgreSQL Extension Network (PGXN) to install the FDW, mysql_fdw. If you are running PostgreSQL on Windows, compile the extension to ensure that you are working with the latest version. Follow the steps below to make the necessary modifications to build the extension from Visual Studio:

Obtain Prerequisites

To build the foreign data wrapper, do the following:

• Install PostgreSQL. This example uses an installation of PostgreSQL 9.4.
• If you are using a 64-bit installation of PostgreSQL, obtain libintl.h from the PostgreSQL source. The 64-bit PostgreSQL installer does not currently include libintl.h.
• Obtain the source for the mysql_fdw foreign data wrapper from EnterpriseDB.
• Install MySQL Connector C. This example uses an installation of MySQL Connector C 6.1.

Configure a Project

After you have obtained the necessary software and source code, you are ready to compile the extension with Visual Studio. Follow the steps below to create a project using the mysql_fdw source:

1. In Visual Studio, create a new empty C++ project.
2. In Solution Explorer, right-click Source Files and click Add -> Existing Item. In the file explorer, select all of the .c and .h files from the mysql_fdw source.

Follow the steps below to configure your project:

1. If you are building for a 64-bit system, click Build -> Configuration Manager and in Active Solution Platform select x64.
2. Right-click your project and click Properties.
3. In the Configuration menu, select All Configurations.
4. In Configuration Properties -> General -> Configuration Type, select Dynamic Library.
5. In Configuration Properties -> C/C++ -> Code Generation -> Enable C++ Exceptions, select No.
6. In Configuration Properties -> C/C++ -> Advanced -> Compile As, select Compile as C Code.
7. In Linker -> Manifest File -> Generate Manifest, select No.

Follow the steps below to add the required dependencies:

1. In Linker -> Input -> Additional Dependencies, select Edit and enter the following: postgres.lib libmysql.lib WS2_32.lib Secur32.lib Additionally, ensure that Inherit From Parent or Project Defaults is checked.
2. In Linker -> General -> Additional Library Directories, select Edit and add the path to the lib folder in your PostgreSQL installation.
3. In Linker -> General -> Link Library Dependencies, select No.
4. To complete the configuration of your project, add the necessary includes: In C/C++ -> General -> Additional Include Directories, add the following folders in the following order: MyMySQLConnectorCInstallation\include MyPostgreSQLInstallation\MyPostgreSQLVersion\include\server\port\win32_msvc MyPostgreSQLInstallation\MyPostgreSQLVersion\include\server\port\win32 MyPostgreSQLInstallation\MyPostgreSQLVersion\include\server MyPostgreSQLInstallation\MyPostgreSQLVersion\include

Configure mysql_fdw for Windows

After setting up a project, make the following changes to build mysql_fdw in Visual Studio:

1. In mysql_fdw.c, add the following defines: #define dlsym(lib, name) (void*)GetProcAddress((HMODULE)lib, name) #define dlopen(libname, unused) LoadLibraryEx(libname, NULL, 0)
2. In the mysql_load_library definition, delete the following line: mysql_dll_handle = dlopen(_MYSQL_LIBNAME, RTLD_LAZY | RTLD_DEEPBIND);
3. Add the following line in the mysql_load_library definition to replace the assignment of mysql_dll_handle for a Windows build: mysql_dll_handle = dlopen("libmysql.dll", 0);
4. Prepend the call to the mysql_fdw_handler function with the __declspec(dllexport) keyword to export the function from the DLL: __declspec(dllexport) extern Datum mysql_fdw_handler(PG_FUNCTION_ARGS);
5. In option.c, prepend the declaration of the mysql_fdw_validator function with the __declspec(dllexport) keyword to export the function from the DLL: __declspec(dllexport) extern Datum mysql_fdw_validator(PG_FUNCTION_ARGS);

You can now select the Release configuration and build.

Install the Extension

After you have compiled the DLL, follow the steps below to install the extension:

1. Add the path to the lib folder for MySQL Connector C to the PATH environment variable of the machine running PostgreSQL.
2. Copy the DLL from the RElease folder for your project into the lib subfolder of your PostgreSQL installation.
3. In the folder containing the mysql_fdw csource files, copy myswl_fdw--1.0.sql and mysql_fdw.control into the extension folder under the share folder of your PostgreSQL installation. For example: C:\Program Files\PostgreSQL\9.4\share\extension.

Query FHIR Data as a PostgreSQL Database

After you have installed the extension, follow the steps below to start executing queries to FHIR data:

1. Log into your PostgreSQL database. For example: C:\> psql -U postgres
2. Load the extension for the database: postgres=#CREATE EXTENSION mysql_fdw;
3. Create a server object for FHIR data: postgres=# CREATE SERVER FHIR FOREIGN DATA WRAPPER mysql_fdw OPTIONS (host '127.0.0.1', port '3306');
4. Create a user mapping for the username and password of a user known to the MySQL remoting service. Below are the credentials for the user in the sample configuration of the service: postgres=# CREATE USER MAPPING for postgres SERVER FHIR OPTIONS (username 'admin', password 'test');
5. Create the local schema: postgres=# CREATE SCHEMA FHIR_db;
6. Import all the tables in the FHIR database you defined: postgres=# IMPORT FOREIGN SCHEMA "CData FHIR Sys" FROM SERVER FHIR INTO FHIR_db;

You can now execute SELECT commands to FHIR: