HAPI FHIR Simple Server as Spring Boot deploying to Tomcat
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rbhman
Jan 21, 2021, 4:49:38 PM1/21/21
to HAPI FHIR
Has anyone built a HAPI FHIR Simple Server as Spring Boot and then successfully deployed to Tomcat?
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.2.2.RELEASE</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<groupId>xxx</groupId>
<artifactId>yyy</artifactId>
<version>1.0</version>
<packaging>war</packaging>
<name>zzz</name>
<repositories>
<!-- Oracle driver has been downloaded manually and installed in this local repo.
Note that this repo must also be excluded in individual developers
.m2/settings.xml so that Nexus does not flag it as non-updated -->
<repository>
<id>local.maven</id>
<name>local.cr.maven</name>
<url>file:${project.basedir}/maven_repository</url>
</repository>
</repositories>
<dependencies>
<!-- Spring Boot -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-configuration-processor</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jdbc</artifactId>
</dependency>
<!-- HAPI-FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-starter</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.3</version>
</dependency>
<!-- Needed for JEE/Servlet support -->
<!-- <dependency>-->
<!-- <groupId>javax.servlet</groupId>-->
<!-- <artifactId>javax.servlet-api</artifactId>-->
<!-- <version>3.0.1</version>-->
<!-- <scope>provided</scope>-->
<!-- </dependency>-->
<dependency>
<groupId>com.oracle</groupId>
<artifactId>ojdbc8</artifactId>
<version>12.2.0.1</version>
</dependency>
<!-- Needed by junit -->
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<!--
Tell Maven which Java source version you want to use
-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>9.4.7.v20170914</version>
</plugin>
</plugins>
</build>
</project>
I've had a hard time with this. I can successfully do the following:
- Create a Spring Boot/Hapi FHIR Simple Server that uses Spring configuration annotation etc. to obtain data sources, connect to a DB, create FHIR resources, make RESTful FHIR queries against them etc. Note that my application class (extending SpringBootServletInitializer) has both main() and configure() methods so that it can run from Spring or as a WAR.
- This works fine in my (IntelliJ) IDE when started as a Spring Boot launch config. Note also that the pom uses a provided embedded server (spring-boot-tomcat-starter.)
- The same app fails however when started as a Tomcat launch config. I can confirm that upon startup, the app's configure() method invokes my application servlet (extending HAPI FHIR RestfulServer) and the Spring config classes are properly injected and available in my servlet. The problem seems to be though that the servlet is then immediately instantiated/initialized a second time (in short, from catalina.startup to javax.servlet to RestfulServer). This time, the Spring Boot data sources etc. are all null, since presumably the servlet was somehow instatiated from the HAPI-FHIR framework - as a new() class as opposed to injected by Spring.
- The same problem occurs when I deploy to a remote Tomcat server.
Does my servlet have to be a POJO? Or can I continue somehow to enjoy Spring Boot features while deploying to a Tomcat server? Do I somehow have to integrate with the HAPI-FHIR Spring config?
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.2.2.RELEASE</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<groupId>xxx</groupId>
<artifactId>yyy</artifactId>
<version>1.0</version>
<packaging>war</packaging>
<name>zzz</name>
<repositories>
<!-- Oracle driver has been downloaded manually and installed in this local repo.
Note that this repo must also be excluded in individual developers
.m2/settings.xml so that Nexus does not flag it as non-updated -->
<repository>
<id>local.maven</id>
<name>local.cr.maven</name>
<url>file:${project.basedir}/maven_repository</url>
</repository>
</repositories>
<dependencies>
<!-- Spring Boot -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-configuration-processor</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jdbc</artifactId>
</dependency>
<!-- HAPI-FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-starter</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.3</version>
</dependency>
<!-- Needed for JEE/Servlet support -->
<!-- <dependency>-->
<!-- <groupId>javax.servlet</groupId>-->
<!-- <artifactId>javax.servlet-api</artifactId>-->
<!-- <version>3.0.1</version>-->
<!-- <scope>provided</scope>-->
<!-- </dependency>-->
<dependency>
<groupId>com.oracle</groupId>
<artifactId>ojdbc8</artifactId>
<version>12.2.0.1</version>
</dependency>
<!-- Needed by junit -->
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<!--
Tell Maven which Java source version you want to use
-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>9.4.7.v20170914</version>
</plugin>
</plugins>
</build>
</project>
revathi vadlamudi
Feb 8, 2021, 2:41:49 PM2/8/21
to HAPI FHIR
Hi,
When connected with Tomcat and spring boot application, tomcat starts with out errors, but when called restService to create Patient getDAO() method returns null. Someone help me how to overcome below error
POM.xml
<?xml version="1.0" encoding="UTF-8"?>
<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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.4.2</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<groupId>com.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>0.0.1-SNAPSHOT</version>
<name>HapiFhir</name>
<description>Hapi FHIR project for Spring Boot</description>
<properties>
<java.version>11</java.version>
</properties>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-jdbc</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-configuration-processor</artifactId>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jdbc</artifactId>
</dependency>
<!-- <dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-autoconfigure</artifactId>
</dependency>
--> <dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<scope>runtime</scope>
</dependency>
<!-- Hibernate -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>5.2.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>5.2.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>5.2.0</version>
</dependency>
<!-- <dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-autoconfigure</artifactId>
<version>5.2.0</version>
</dependency> -->
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
</plugins>
</build>
</project>
ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method: java.lang.NullPointerException
at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:250) ~[hapi-fhir-server-5.2.0.jar:na]
at ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBinding.invokeServer(BaseOutcomeReturningMethodBinding.java:154) ~[hapi-fhir-server-5.2.0.jar:na]
at ca.uhn.fhir.rest.server.method.CreateMethodBinding.invokeServer(CreateMethodBinding.java:41) ~[hapi-fhir-server-5.2.0.jar:na]
at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:1052) ~[hapi-fhir-server-5.2.0.jar:na]
at ca.uhn.fhir.rest.server.RestfulServer.doPost(RestfulServer.java:377) ~[hapi-fhir-server-5.2.0.jar:na]
at ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1749) ~[hapi-fhir-server-5.2.0.jar:na]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:733) ~[tomcat-embed-core-9.0.41.jar:4.0.FR]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) ~[tomcat-embed-websocket-9.0.41.jar:9.0.41]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100) ~[spring-web-5.3.3.jar:5.3.3]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.3.3.jar:5.3.3]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.springframework.web.filter.FormContentFilter.doFilterInternal(FormContentFilter.java:93) ~[spring-web-5.3.3.jar:5.3.3]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.3.3.jar:5.3.3]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201) ~[spring-web-5.3.3.jar:5.3.3]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) ~[spring-web-5.3.3.jar:5.3.3]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:542) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:143) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:374) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:888) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1597) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[na:na]
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[na:na]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) ~[tomcat-embed-core-9.0.41.jar:9.0.41]
at java.base/java.lang.Thread.run(Thread.java:834) ~[na:na]
Caused by: java.lang.reflect.InvocationTargetException: null
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:na]
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
at java.base/java.lang.reflect.Method.invoke(Method.java:566) ~[na:na]
at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:245) ~[hapi-fhir-server-5.2.0.jar:na]
... 39 common frames omitted
Caused by: java.lang.NullPointerException: null
at ca.uhn.fhir.jpa.provider.r5.JpaResourceProviderR5.create(JpaResourceProviderR5.java:71) ~[hapi-fhir-jpaserver-base-5.2.0.jar:na]
... 44 common frames omitted
James Agnew
Feb 8, 2021, 2:51:35 PM2/8/21
to revathi vadlamudi, HAPI FHIR
If you are looking to use the HAPI FHIR JPA server, I'd recommend just forking the JPA Starter: https://github.com/hapifhir/hapi-fhir-jpaserver-starter
Cheers,
James
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