How to configure HAPI-FHIR with MySQL?

[Avu]

Hello all,

I have set up the HAPI FHIR using Command line tools. Its working now. But I have to connect it with MySQL?

Guide me the required steps to be done. Thanks in advance

[James Agnew]

Hi Avu,

Unfortunately the CLI tool does not currently support databases other than Derby.

If you want to support MySQL you'll need to create a WAR project and configure it for MySQL. The hapi-fhir-jpaserver-example project can be a good starting point, but you'll have to switch the dialect and datasource properties to reflect MySQL.

Cheers,

James

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[Avu]

HI James,
I have gone through hapi-fhir-jpaserver-example from the link   "https://github.com/jamesagnew/hapi-fhir"

Then I imported it into eclipse as maven project and edited  FhirServerConfig.java  to configure with mysql. also I added maven dependency for tomcat server.
I used mvn install command,given me a war file under target folder.Finally i placed it in webapps directory.

http://localhost:8060/hapi-fhir-jpaserver-example/fhir/

gives me 404 error..

Were all my followed steps right??

[Kevin Mayfield]

I wrote some instructions for doing this with MySQL. https://www.openhealthhub.org/t/howto-build-a-health-database-and-fhir-api-server-in-15-mins-using-open-source/155

Sent from my iPhone

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[Avu]

Hi James/Kevin,

Please find the image and  I am bit confused about where the database connection has made??

Could you please explain it?

On Tuesday, March 7, 2017 at 2:11:04 PM UTC+5:30, Avu wrote:

[Kevin Mayfield]

In your FhirServerConfig file, what do you have for the DataSource Bean?

You should have something that looks like 

 Class<? extends Driver> driverClass = (Class<? extends Driver>) Class.forName("com.mysql.jdbc.Driver");

In addition in the jpaProperties you should have a line like:

extraProperties.put("hibernate.dialect", "org.hibernate.dialect.MySQLDialect");

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[marcelocabe...@gmail.com]

Hi all,
In my case I made a configuration to run JPA_Server with MySql. The engine required to adjust the same TimeZone inside MySql and the JDBC connector. Otherwise, Maven shows compilation errors.

This are the steps that I made:

1. Let's assume I created this database. By default I created an INNODB type

CREATE DATABASE dbhapi DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_general_ci;

CREATE USER 'fhirman' IDENTIFIED BY '******';

GRANT ALL ON dbhapi TO fhirman;

FLUSH PRIVILEGES;

2. In my.ini add this line and restart MySql:

default-time-zone = '+00:00'

3. Add the dependency in POM.XML

<dependency>

        <groupId>mysql</groupId>

        <artifactId>mysql-connector-java</artifactId>

        <version>6.0.5</version>

</dependency>

<!--

4. In FhirServerConfig.java
4a. Make sure you add this line:

import java.sql.*;

4b. Then modify the datasource()

public DataSource dataSource() {

   BasicDataSource retVal = new BasicDataSource();

      try {

            retVal.setDriver(new com.mysql.cj.jdbc.Driver());

          } catch (SQLException e) {

         // TODO Auto-generated catch block

            e.printStackTrace();

           }

retVal.setUrl("jdbc:mysql://localhost:3306/dbfhir?useSSL=false&serverTimezone=UTC");

 

         retVal.setUsername("fhirman");

         retVal.setPassword("******");

         return retVal;

        }

4c. On the jpaProperties, modify the line:

private Properties jpaProperties() {

  Properties extraProperties = new Properties();

  extraProperties.put("hibernate.dialect", "org.hibernate.dialect.MySQL5InnoDBDialect");

  extraProperties.put("hibernate.format_sql", "true");

  extraProperties.put("hibernate.show_sql", "false");

  extraProperties.put("hibernate.hbm2ddl.auto", "update");

  extraProperties.put("hibernate.jdbc.batch_size", "20");

  extraProperties.put("hibernate.cache.use_query_cache", "false");

  extraProperties.put("hibernate.cache.use_second_level_cache", "false");

  extraProperties.put("hibernate.cache.use_structured_entries", "false");

  extraProperties.put("hibernate.cache.use_minimal_puts", "false");

  extraProperties.put("hibernate.search.default.directory_provider", "filesystem");

  extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");

  extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

  //extraProperties.put("hibernate.search.default.worker.execution", "async");

return extraProperties;

Cheers,
Marcelo

[trantro...@gmail.com]

Hi Marcelo. Correct me if I'm wrong. You created Database and did not create any table right? And after modifying the project, you use cmd mvn install again to make a new *.war, right?

[Marcelo Cabello]

From version JPA-STARTER is much easier to configure the database:

datasource.driver=com.mysql.cj.jdbc.Driver
datasource.url=jdbc:mysql://localhost:3306/<database name>?useSSL=false&useLegacyDatetimeCode=false&serverTimezone=UTC
datasource.username=<user>
datasource.password=<password>

Cheers!

Marcelo

[Octavian Ianculescu]

Just FYI that besides the setup above within the JPA-STARTER project, on UNIX file-systems it also looks mysql schema needs to be case-insensitive in order for Hibernate to properly work and create the FHIR schema in mysql.
See https://dev.mysql.com/doc/refman/5.7/en/identifier-case-sensitivity.html

Setting lower_case_table_names=1 for a fresh mysql 5.7 docker container did the trick for me.

[James Agnew]

Hi Octavian,

Thanks for the sharing! Any chance you could submit a PR against the README to add these instructions?

Cheers,

James

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[Tomomi Yamano]

Hi,

Thank you for your share. 

I am also working on this, though. Has this instruction been added in Readme?

Best,