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Merge pull request #71 from MattMorgis/master

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PostgreSQL Support
This commit is contained in:
Sean McIlvenna
2019-12-25 11:02:33 -08:00
committed by GitHub
parent e1b1fbf16a 7ca00a7325
commit 607f43f5f0
3 changed files with 50 additions and 462 deletions
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68
README.md
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@@ -8,13 +8,13 @@ Note that this project is specifically intended for end users of the HAPI FHIR J
In order to use this sample, you should have: In order to use this sample, you should have:
* [This project](https://github.com/hapifhir/hapi-fhir-jpaserver-starter) checked out. You may wish to create a GitHub Fork of the project and check that out instead so that you can customize the project and save the results to GitHub. - [This project](https://github.com/hapifhir/hapi-fhir-jpaserver-starter) checked out. You may wish to create a GitHub Fork of the project and check that out instead so that you can customize the project and save the results to GitHub.
* Oracle Java (JDK) installed: Minimum JDK8 or newer. - Oracle Java (JDK) installed: Minimum JDK8 or newer.
* Apache Maven build tool (newest version) - Apache Maven build tool (newest version)
# Running Locally # Running Locally
The easiest way to run this server is to run it directly in Maven using a built-in Jetty server. To do this, change `src/main/resources/hapi.properties` `server_address` and `server.base` with the values commented out as *For Jetty, use this* and then execute the following command: The easiest way to run this server is to run it directly in Maven using a built-in Jetty server. To do this, change `src/main/resources/hapi.properties` `server_address` and `server.base` with the values commented out as _For Jetty, use this_ and then execute the following command:
``` ```
mvn jetty:run mvn jetty:run
@@ -25,28 +25,40 @@ Then, browse to the following link to use the server:
[http://localhost:8080/hapi-fhir-jpaserver/](http://localhost:8080/hapi-fhir-jpaserver/) [http://localhost:8080/hapi-fhir-jpaserver/](http://localhost:8080/hapi-fhir-jpaserver/)
If you need to run this server on a different port (using Maven), you can change the port in the run command as follows: If you need to run this server on a different port (using Maven), you can change the port in the run command as follows:
``` ```
mvn -Djetty.port=8888 jetty:run mvn -Djetty.port=8888 jetty:run
``` ```
And replacing 8888 with the port of your choice. And replacing 8888 with the port of your choice.
# Configuration # Configuration
Much of this HAPI starter project can be configured using the properties file in *src/main/resources/hapi.properties*. By default, this starter project is configured to use Derby as the database. Much of this HAPI starter project can be configured using the properties file in _src/main/resources/hapi.properties_. By default, this starter project is configured to use Derby as the database.
## MySql ## MySql
To configure the starter app to use MySQL, instead of the default Derby, update the hapi.properties file to have the following: To configure the starter app to use MySQL, instead of the default Derby, update the hapi.properties file to have the following:
* datasource.driver=com.mysql.jdbc.Driver - datasource.driver=com.mysql.jdbc.Driver
* datasource.url=jdbc:mysql://localhost:3306/hapi_dstu3 - datasource.url=jdbc:mysql://localhost:3306/hapi_dstu3
* hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect - hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect
* datasource.username=admin - datasource.username=admin
* datasource.password=admin - datasource.password=admin
Because the integration tests within the project rely on the default Derby database configuration, it is important to either explicity skip the integration tests during the build process, i.e., `mvn install -DskipTests`, or delete the tests altogether. Failure to skip or delete the tests once you've configured MySQL for the datasource.driver, datasource.url, and hibernate.dialect as outlined above will result in build errors and compilation failure. ## PostgreSQL
It is important to use MySQL5Dialect when using MySQL version 5+. To configure the starter app to use PostgreSQL, instead of the default Derby, update the hapi.properties file to have the following:
- datasource.driver=org.postgresql.Driver
- datasource.url=jdbc:postgresql://localhost:5432/hapi_dstu3
- hibernate.dialect=org.hibernate.dialect.PostgreSQL95Dialect
- datasource.username=admin
- datasource.password=admin
Because the integration tests within the project rely on the default Derby database configuration, it is important to either explicity skip the integration tests during the build process, i.e., `mvn install -DskipTests`, or delete the tests altogether. Failure to skip or delete the tests once you've configured PostgreSQL for the datasource.driver, datasource.url, and hibernate.dialect as outlined above will result in build errors and compilation failure.
It is important to use PostgreSQL95Dialect when using PostgreSQL version 10+.
# Customizing The Web Testpage UI # Customizing The Web Testpage UI
@@ -79,20 +91,20 @@ Again, browse to the following link to use the server (note that the port 8080 m
# Deploy with docker compose # Deploy with docker compose
Docker compose is a simple option to build and deploy container. To deploy with docker compose, you should build the project Docker compose is a simple option to build and deploy container. To deploy with docker compose, you should build the project
with ```mvn clean install``` and then bring up the containers with ```docker-compose up -d --build```. The server can be with `mvn clean install` and then bring up the containers with `docker-compose up -d --build`. The server can be
reached at http://localhost:8080/hapi-fhir-jpaserver/. reached at http://localhost:8080/hapi-fhir-jpaserver/.
In order to use another port, change the `ports` parameter In order to use another port, change the `ports` parameter
inside ``docker-compose.yml`` to ```8888:8080```, where 8888 is a port of your choice. inside `docker-compose.yml` to `8888:8080`, where 8888 is a port of your choice.
The docker compose set also includes my MySQL database, if you choose to use MySQL instead of derby, change the following The docker compose set also includes my MySQL database, if you choose to use MySQL instead of derby, change the following
properties in hapi.properties: properties in hapi.properties:
* datasource.driver=com.mysql.jdbc.Driver - datasource.driver=com.mysql.jdbc.Driver
* datasource.url=jdbc:mysql://hapi-fhir-mysql:3306/hapi - datasource.url=jdbc:mysql://hapi-fhir-mysql:3306/hapi
* hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect - hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect
* datasource.username=admin - datasource.username=admin
* datasource.password=admin - datasource.password=admin
# Running hapi-fhir-jpaserver-example in Tomcat from IntelliJ # Running hapi-fhir-jpaserver-example in Tomcat from IntelliJ
@@ -114,7 +126,7 @@ Add a Run Configuration for running hapi-fhir-jpaserver-example under Tomcat
- Uncheck the "After launch" checkbox - Uncheck the "After launch" checkbox
- On the "Deployment" tab, click the green + - On the "Deployment" tab, click the green +
- Select "Artifact" - Select "Artifact"
- Select "hapi-fhir-jpaserver-example:war" - Select "hapi-fhir-jpaserver-example:war"
- In "Application context" type /hapi - In "Application context" type /hapi
Run the configuration. Run the configuration.
@@ -130,13 +142,13 @@ It is important to use MySQL5Dialect when using MySQL version 5+.
# Enabling Subscriptions # Enabling Subscriptions
The server may be configured with subscription support by enabling properties in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file: The server may be configured with subscription support by enabling properties in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file:
* `subscription.resthook.enabled` - Enables REST Hook subscriptions, where the server will make an outgoing connection to a remote REST server - `subscription.resthook.enabled` - Enables REST Hook subscriptions, where the server will make an outgoing connection to a remote REST server
* `subscription.email.enabled` - Enables email subscriptions. Note that you must also provide the connection details for a usable SMTP server. - `subscription.email.enabled` - Enables email subscriptions. Note that you must also provide the connection details for a usable SMTP server.
* `subscription.websocket.enabled` - Enables websocket subscriptions. With this enabled, your server will accept incoming websocket connections on the following URL (this example uses the default context path and port, you may need to tweak depending on your deployment environment): [ws://localhost:8080/hapi-fhir-jpaserver/websocket](ws://localhost:8080/hapi-fhir-jpaserver/websocket) - `subscription.websocket.enabled` - Enables websocket subscriptions. With this enabled, your server will accept incoming websocket connections on the following URL (this example uses the default context path and port, you may need to tweak depending on your deployment environment): [ws://localhost:8080/hapi-fhir-jpaserver/websocket](ws://localhost:8080/hapi-fhir-jpaserver/websocket)
# Using ElasticSearch # Using ElasticSearch
@@ -151,4 +163,4 @@ elasticsearch.username=SomeUsername
elasticsearch.password=SomePassword elasticsearch.password=SomePassword
elasticsearch.required_index_status=YELLOW elasticsearch.required_index_status=YELLOW
elasticsearch.schema_management_strategy=CREATE elasticsearch.schema_management_strategy=CREATE
``` ```

14
pom.xml
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@@ -1,5 +1,5 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" <project xmlns="http://maven.apache.org/POM/4.0.0"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<!-- <!--
@@ -36,6 +36,12 @@
<artifactId>mysql-connector-java</artifactId> <artifactId>mysql-connector-java</artifactId>
<version>8.0.11</version> <version>8.0.11</version>
</dependency> </dependency>
<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>42.2.9</version>
</dependency>
<!-- Needed for Email subscriptions --> <!-- Needed for Email subscriptions -->
<dependency> <dependency>
@@ -213,8 +219,8 @@
<groupId>org.eclipse.jetty</groupId> <groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId> <artifactId>jetty-webapp</artifactId>
<scope>test</scope> <scope>test</scope>
</dependency> </dependency>
<!-- <!--
<dependency> <dependency>
<groupId>com.helger</groupId> <groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId> <artifactId>ph-schematron</artifactId>

430
pom.xml.orig
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@@ -1,430 +0,0 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<!--
Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management.
You do not need to use this in your own projects, so the "parent" tag and it's
contents below may be removed
if you are using this file as a basis for your own project.
-->
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<<<<<<< HEAD
<version>4.1.0</version>
=======
<version>4.0.3</version>
>>>>>>> master
</parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId>
<prerequisites>
<maven>3.5.0</maven>
</prerequisites>
<dependencies>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-api</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-client</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>8.0.11</version>
</dependency>
<!-- Needed for Email subscriptions -->
<dependency>
<groupId>com.sun.mail</groupId>
<artifactId>javax.mail</artifactId>
<exclusions>
<exclusion>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
</exclusion>
</exclusions>
</dependency>
<!--
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
</dependency>
-->
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</exclusion>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- This dependency is used for the "FHIR Tester" web app overlay -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<type>war</type>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
<scope>provided</scope>
</dependency>
<!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
is used here, but log4j would also be fine. -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise the following can be omitted. -->
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
</dependency>
<!-- Used for CORS support -->
<!-- Spring Web is used to deploy the server to a web container. -->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
</dependency>
<!-- You may not need this if you are deploying to an application server which provides database connection pools itself. -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- This example uses H2 embedded database. If you are using another database such as Mysql or Oracle, you may omit the following dependencies and replace them with an appropriate database client
dependency for your database platform. -->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
</dependency>
<!-- webjars -->
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
<version>3.3.7</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>Eonasdan-bootstrap-datetimepicker</artifactId>
<version>4.17.43</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>font-awesome</artifactId>
<version>5.8.2</version>
</dependency>
<dependency>
<groupId>org.webjars.bower</groupId>
<artifactId>awesome-bootstrap-checkbox</artifactId>
<version>1.0.1</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>jstimezonedetect</artifactId>
<version>1.0.6</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>select2</artifactId>
<version>4.0.3</version>
</dependency>
<dependency>
<groupId>org.webjars.bower</groupId>
<artifactId>jquery</artifactId>
<version>3.3.1</version>
</dependency>
<dependency>
<groupId>org.webjars.bower</groupId>
<artifactId>moment</artifactId>
<version>2.15.1</version>
</dependency>
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
<scope>test</scope>
</dependency>
<!--
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
</exclusions>
</dependency>
-->
<!--
For some reason JavaDoc crashed during site generation unless we have this dependency
-->
<dependency>
<groupId>javax.interceptor</groupId>
<artifactId>javax.interceptor-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<packaging>war</packaging>
<name>HAPI FHIR JPA Server - Starter Project</name>
<repositories>
<repository>
<id>oss-snapshots</id>
<snapshots>
<enabled>false</enabled>
</snapshots>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
</repositories>
<build>
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver.war -->
<finalName>hapi-fhir-jpaserver</finalName>
<plugins>
<!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>9.4.8.v20180619</version>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
<!-- Tell Maven which Java source version you want to use -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifestEntries>
<Build-Time>${maven.build.timestamp}</Build-Time>
</manifestEntries>
</archive>
<overlays>
<overlay>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
</overlay>
</overlays>
<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
</configuration>
</plugin>
<!-- This is to run the integration tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<executions>
<execution>
<id>default</id>
<phase>verify</phase>
<goals>
<goal>check</goal>
</goals>
<inherited>true</inherited>
</execution>
</executions>
<configuration>
<failBuildInCaseOfConflict>true</failBuildInCaseOfConflict>
<checkTestClasspath>false</checkTestClasspath>
<!--
<printEqualFiles>false</printEqualFiles>
<failBuildInCaseOfDifferentContentConflict>true</failBuildInCaseOfDifferentContentConflict>
<failBuildInCaseOfEqualContentConflict>true</failBuildInCaseOfEqualContentConflict>
<failBuildInCaseOfConflict>true</failBuildInCaseOfConflict>
<checkCompileClasspath>true</checkCompileClasspath>
<checkRuntimeClasspath>false</checkRuntimeClasspath>
<skip>false</skip>
<quiet>false</quiet>
<preferLocal>true</preferLocal>
<useResultFile>true</useResultFile>
<resultFileMinClasspathCount>2</resultFileMinClasspathCount>
<resultFile>${project.build.directory}/duplicate-finder-result.xml</resultFile>
-->
<!--
<ignoredDependencies>
<dependency>
<groupId>javax.el</groupId>
<artifactId>javax.el-api</artifactId>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>javax.activation-api</artifactId>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</dependency>
<dependency>
<groupId>org.jscience</groupId>
<artifactId>jscience</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>annotations</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbynet</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
<dependency>
<groupId>org.checkerframework</groupId>
<artifactId>checker-compat-qual</artifactId>
</dependency>
</ignoredDependencies>
-->
<ignoredResourcePatterns>
<ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>
<ignoredResourcePattern>.*\.html$</ignoredResourcePattern>
</ignoredResourcePatterns>
</configuration>
</plugin>
</plugins>
</build>
</project>