Personal-Twin/hapi-fhir-jpaserver-starter
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- fixed issue on ui regarding pagination of results by configuring refuseToFetchThirdPartyUrls

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- updated fhir version to R4 and used mysql as datasource with docs updated
- transferred jetty plugin to be viewable on intellij
- disabled oss snapshots
- replaced corsFilter based on new hapi docs
This commit is contained in:
Jessie James Cosare
2019-03-08 13:22:25 +08:00
parent 6907ae34ba
commit c5bfade9ce
7 changed files with 119 additions and 89 deletions
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11
README.md
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@@ -56,10 +56,13 @@ Much of this HAPI starter project can be configured using the properties file in
## 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 with MySQL, use the commands below to add user and database:
* datasource.driver=com.mysql.jdbc.Driver ```
* datasource.url=jdbc:mysql://localhost:3306/hapi_dstu3 CREATE USER 'fhirUser'@'localhost' IDENTIFIED BY 'fhirPass';
* hibernate.dialect=org.hibernate.dialect.MySQL5Dialect CREATE DATABASE fhir_r4;
GRANT ALL PRIVILEGES ON fhir_r4.* to 'fhirUser'@'localhost';
FLUSH PRIVILEGES;
```
It is important to use MySQL5Dialect when using MySQL version 5+. It is important to use MySQL5Dialect when using MySQL version 5+.

47
pom.xml
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@@ -24,7 +24,7 @@
<repository> <repository>
<id>oss-snapshots</id> <id>oss-snapshots</id>
<snapshots> <snapshots>
<enabled>true</enabled> <enabled>false</enabled>
</snapshots> </snapshots>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url> <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository> </repository>
@@ -111,16 +111,11 @@
</dependency> </dependency>
<!-- Used for CORS support --> <!-- Used for CORS support -->
<dependency> <!--<dependency>-->
<groupId>org.ebaysf.web</groupId> <!--<groupId>org.eclipse.jetty</groupId>-->
<artifactId>cors-filter</artifactId> <!--<artifactId>jetty-servlets</artifactId>-->
<exclusions> <!--<version>9.4.12.v20180830</version>-->
<exclusion> <!--</dependency>-->
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
</exclusions>
</dependency>
<!-- Spring Web is used to deploy the server to a web container. --> <!-- Spring Web is used to deploy the server to a web container. -->
<dependency> <dependency>
@@ -207,24 +202,20 @@
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver.war --> <!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver.war -->
<finalName>hapi-fhir-jpaserver</finalName> <finalName>hapi-fhir-jpaserver</finalName>
<!-- 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. -->
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>9.4.8.v20180619</version>
<configuration>
<webApp>
<contextPath>/</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins> <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>/</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
<!-- Tell Maven which Java source version you want to use --> <!-- Tell Maven which Java source version you want to use -->
<plugin> <plugin>
<groupId>org.apache.maven.plugins</groupId> <groupId>org.apache.maven.plugins</groupId>

1
src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java
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@@ -43,6 +43,7 @@ public class FhirTesterConfig {
.withFhirVersion(HapiProperties.getFhirVersion()) .withFhirVersion(HapiProperties.getFhirVersion())
.withBaseUrl(HapiProperties.getServerAddress()) .withBaseUrl(HapiProperties.getServerAddress())
.withName(HapiProperties.getServerName()); .withName(HapiProperties.getServerName());
retVal.setRefuseToFetchThirdPartyUrls(HapiProperties.getTesterConfigRefustToFetchThirdPartyUrls());
return retVal; return retVal;
} }

5
src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
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@@ -39,6 +39,7 @@ public class HapiProperties {
static final String SUBSCRIPTION_EMAIL_ENABLED = "subscription.email.enabled"; static final String SUBSCRIPTION_EMAIL_ENABLED = "subscription.email.enabled";
static final String SUBSCRIPTION_RESTHOOK_ENABLED = "subscription.resthook.enabled"; static final String SUBSCRIPTION_RESTHOOK_ENABLED = "subscription.resthook.enabled";
static final String TEST_PORT = "test.port"; static final String TEST_PORT = "test.port";
static final String TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS = "tester.config.refuse_to_fetch_third_party_urls";
private static Properties properties; private static Properties properties;
@@ -249,6 +250,10 @@ public class HapiProperties {
return HapiProperties.getIntegerProperty(TEST_PORT, 0); return HapiProperties.getIntegerProperty(TEST_PORT, 0);
} }
public static Boolean getTesterConfigRefustToFetchThirdPartyUrls() {
return HapiProperties.getBooleanProperty(TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS, false);
}
public static String getServerBase() { public static String getServerBase() {
return HapiProperties.getProperty(SERVER_BASE, "/fhir"); return HapiProperties.getProperty(SERVER_BASE, "/fhir");
} }

33
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
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@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum; import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.dao.DaoConfig; import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao; import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.model.interceptor.executor.InterceptorService;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2; import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2; import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider; import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
@@ -14,17 +15,22 @@ import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4; import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4; import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.subscription.SubscriptionInterceptorLoader;
import ca.uhn.fhir.jpa.subscription.module.interceptor.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.model.dstu2.composite.MetaDt; import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator; import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy; import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.IResourceProvider; import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer; import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor; import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.hl7.fhir.dstu3.model.Bundle; import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta; import org.hl7.fhir.dstu3.model.Meta;
import org.springframework.context.annotation.AnnotationConfigApplicationContext; import org.springframework.context.annotation.AnnotationConfigApplicationContext;
import org.springframework.web.cors.CorsConfiguration;
import javax.servlet.ServletException; import javax.servlet.ServletException;
import java.util.Arrays;
import java.util.List; import java.util.List;
public class JpaRestfulServer extends RestfulServer { public class JpaRestfulServer extends RestfulServer {
@@ -173,6 +179,33 @@ public class JpaRestfulServer extends RestfulServer {
SubscriptionTriggeringProvider retriggeringProvider = appCtx.getBean(SubscriptionTriggeringProvider.class); SubscriptionTriggeringProvider retriggeringProvider = appCtx.getBean(SubscriptionTriggeringProvider.class);
registerProvider(retriggeringProvider); registerProvider(retriggeringProvider);
} }
// Define your CORS configuration. This is an example
// showing a typical setup. You should customize this
// to your specific needs
CorsConfiguration config = new CorsConfiguration();
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("Origin");
config.addAllowedHeader("Accept");
config.addAllowedHeader("X-Requested-With");
config.addAllowedHeader("Content-Type");
config.addAllowedOrigin("*");
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH"));
// Create the interceptor and register it
CorsInterceptor interceptor = new CorsInterceptor(config);
registerInterceptor(interceptor);
// Enable the use of subscriptions
SubscriptionInterceptorLoader subscriptionInterceptorLoader = appCtx.getBean(SubscriptionInterceptorLoader.class);
subscriptionInterceptorLoader.registerInterceptors();
// Subscription debug logging
InterceptorService interceptorService = (InterceptorService) appCtx.getBean("interceptorService");
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
} }
} }

13
src/main/resources/hapi.properties
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@@ -1,7 +1,7 @@
# Adjust this to set the version of FHIR supported by this server. See # Adjust this to set the version of FHIR supported by this server. See
# FhirVersionEnum for a list of available constants. # FhirVersionEnum for a list of available constants.
fhir_version=DSTU3 fhir_version=R4
# This is the address that the FHIR server will report as its own address. # This is the address that the FHIR server will report as its own address.
# If this server will be deployed (for example) to an internet accessible # If this server will be deployed (for example) to an internet accessible
@@ -25,16 +25,16 @@ logger.name=fhirtest.access
logger.format=Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}] logger.format=Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]
logger.error_format=ERROR - ${requestVerb} ${requestUrl} logger.error_format=ERROR - ${requestVerb} ${requestUrl}
logger.log_exceptions=true logger.log_exceptions=true
datasource.driver=org.apache.derby.jdbc.EmbeddedDriver datasource.driver=com.mysql.cj.jdbc.Driver
datasource.url=jdbc:derby:directory:target/jpaserver_derby_files;create=true datasource.url=jdbc:mysql://localhost:3306/fhir_r4
datasource.username= datasource.username=fhirUser
datasource.password= datasource.password=fhirPass
server.name=Local Tester server.name=Local Tester
server.id=home server.id=home
test.port= test.port=
subscription.email.enabled=true subscription.email.enabled=true
subscription.resthook.enabled=true subscription.resthook.enabled=true
hibernate.dialect=ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect hibernate.dialect=org.hibernate.dialect.MySQL5Dialect
hibernate.search.model_mapping=ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory hibernate.search.model_mapping=ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory
hibernate.format_sql=false hibernate.format_sql=false
hibernate.show_sql=false hibernate.show_sql=false
@@ -47,3 +47,4 @@ hibernate.cache.use_minimal_puts=false
hibernate.search.default.directory_provider=filesystem hibernate.search.default.directory_provider=filesystem
hibernate.search.default.indexBase=target/lucenefiles hibernate.search.default.indexBase=target/lucenefiles
hibernate.search.lucene_version=LUCENE_CURRENT hibernate.search.lucene_version=LUCENE_CURRENT
tester.config.refuse_to_fetch_third_party_urls=false

98
src/main/webapp/WEB-INF/web.xml
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@@ -37,69 +37,65 @@
</init-param> </init-param>
<load-on-startup>2</load-on-startup> <load-on-startup>2</load-on-startup>
</servlet> </servlet>
<servlet-mapping>
<servlet-name>spring</servlet-name>
<url-pattern>/</url-pattern>
</servlet-mapping>
<servlet> <servlet>
<servlet-name>fhirServlet</servlet-name> <servlet-name>fhirServlet</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.starter.JpaRestfulServer</servlet-class> <servlet-class>ca.uhn.fhir.jpa.starter.JpaRestfulServer</servlet-class>
<load-on-startup>1</load-on-startup> <load-on-startup>1</load-on-startup>
</servlet> </servlet>
<servlet-mapping> <servlet-mapping>
<servlet-name>fhirServlet</servlet-name> <servlet-name>fhirServlet</servlet-name>
<url-pattern>/fhir/*</url-pattern> <url-pattern>/fhir/*</url-pattern>
</servlet-mapping> </servlet-mapping>
<servlet-mapping>
<servlet-name>spring</servlet-name>
<url-pattern>/</url-pattern>
</servlet-mapping>
<!-- This filters provide support for Cross Origin Resource Sharing (CORS) --> <!-- This filters provide support for Cross Origin Resource Sharing (CORS) -->
<filter> <!--<filter>-->
<filter-name>CORS Filter</filter-name> <!--<filter-name>CORS Filter</filter-name>-->
<filter-class>org.ebaysf.web.cors.CORSFilter</filter-class> <!--<filter-class>org.eclipse.jetty.servlets.CrossOriginFilter</filter-class>-->
<init-param> <!--<init-param>-->
<description>A comma separated list of allowed origins. Note: An '*' cannot be used for an allowed origin when using credentials.</description> <!--<description>A comma separated list of allowed origins. Note: An '*' cannot be used for an allowed origin when using credentials.</description>-->
<param-name>cors.allowed.origins</param-name> <!--<param-name>cors.allowed.origins</param-name>-->
<param-value>*</param-value> <!--<param-value>*</param-value>-->
</init-param> <!--</init-param>-->
<init-param> <!--<init-param>-->
<description>A comma separated list of HTTP verbs, using which a CORS request can be made.</description> <!--<description>A comma separated list of HTTP verbs, using which a CORS request can be made.</description>-->
<param-name>cors.allowed.methods</param-name> <!--<param-name>cors.allowed.methods</param-name>-->
<param-value>GET,POST,PUT,DELETE,OPTIONS</param-value> <!--<param-value>GET,POST,PUT,DELETE,OPTIONS</param-value>-->
</init-param> <!--</init-param>-->
<init-param> <!--<init-param>-->
<description>A comma separated list of allowed headers when making a non simple CORS request.</description> <!--<description>A comma separated list of allowed headers when making a non simple CORS request.</description>-->
<param-name>cors.allowed.headers</param-name> <!--<param-name>cors.allowed.headers</param-name>-->
<param-value>Accept,Access-Control-Request-Headers,Access-Control-Request-Method,Cache-Control,Content-Type,Origin,Prefer,X-FHIR-Starter,X-Requested-With</param-value> <!--<param-value>Accept,Access-Control-Request-Headers,Access-Control-Request-Method,Cache-Control,Content-Type,Origin,Prefer,X-FHIR-Starter,X-Requested-With</param-value>-->
</init-param> <!--</init-param>-->
<init-param> <!--<init-param>-->
<description>A comma separated list non-standard response headers that will be exposed to XHR2 object.</description> <!--<description>A comma separated list non-standard response headers that will be exposed to XHR2 object.</description>-->
<param-name>cors.exposed.headers</param-name> <!--<param-name>cors.exposed.headers</param-name>-->
<param-value>Location,Content-Location</param-value> <!--<param-value>Location,Content-Location</param-value>-->
</init-param> <!--</init-param>-->
<init-param> <!--<init-param>-->
<description>A flag that suggests if CORS is supported with cookies</description> <!--<description>A flag that suggests if CORS is supported with cookies</description>-->
<param-name>cors.support.credentials</param-name> <!--<param-name>cors.support.credentials</param-name>-->
<param-value>true</param-value> <!--<param-value>true</param-value>-->
</init-param> <!--</init-param>-->
<init-param> <!--<init-param>-->
<description>A flag to control logging</description> <!--<description>A flag to control logging</description>-->
<param-name>cors.logging.enabled</param-name> <!--<param-name>cors.logging.enabled</param-name>-->
<param-value>true</param-value> <!--<param-value>true</param-value>-->
</init-param> <!--</init-param>-->
<init-param> <!--<init-param>-->
<description>Indicates how long (in seconds) the results of a preflight request can be cached in a preflight result cache.</description> <!--<description>Indicates how long (in seconds) the results of a preflight request can be cached in a preflight result cache.</description>-->
<param-name>cors.preflight.maxage</param-name> <!--<param-name>cors.preflight.maxage</param-name>-->
<param-value>300</param-value> <!--<param-value>300</param-value>-->
</init-param> <!--</init-param>-->
</filter> <!--</filter>-->
<filter-mapping> <!--<filter-mapping>-->
<filter-name>CORS Filter</filter-name> <!--<filter-name>CORS Filter</filter-name>-->
<url-pattern>/*</url-pattern> <!--<url-pattern>/*</url-pattern>-->
</filter-mapping> <!--</filter-mapping>-->
</web-app> </web-app>