Merge branch 'master' into kbd-20201125-cql-initial-impl
This commit is contained in:
24
.github/workflows/maven.yml
vendored
Normal file
24
.github/workflows/maven.yml
vendored
Normal file
@@ -0,0 +1,24 @@
|
|||||||
|
# This workflow will build a Java project with Maven
|
||||||
|
# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
|
||||||
|
|
||||||
|
name: Java CI with Maven
|
||||||
|
|
||||||
|
on:
|
||||||
|
push:
|
||||||
|
branches: [ master ]
|
||||||
|
pull_request:
|
||||||
|
branches: [ master ]
|
||||||
|
|
||||||
|
jobs:
|
||||||
|
build:
|
||||||
|
|
||||||
|
runs-on: ubuntu-latest
|
||||||
|
|
||||||
|
steps:
|
||||||
|
- uses: actions/checkout@v2
|
||||||
|
- name: Set up JDK 11
|
||||||
|
uses: actions/setup-java@v1
|
||||||
|
with:
|
||||||
|
java-version: 11
|
||||||
|
- name: Build with Maven
|
||||||
|
run: mvn -B package --file pom.xml
|
||||||
40
README.md
40
README.md
@@ -233,7 +233,20 @@ Again, browse to the following link to use the server (note that the port 8080 m
|
|||||||
|
|
||||||
[http://localhost:8080/](http://localhost:8080/)
|
[http://localhost:8080/](http://localhost:8080/)
|
||||||
|
|
||||||
If you would like it to be hosted at eg. hapi-fhir-jpaserver, eg. http://localhost:8080/hapi-fhir-jpaserver/ - then rename the WAR file to ```hapi-fhir-jpaserver.war```.
|
You will then be able access the JPA server e.g. using http://localhost:8080/fhir/metadata.
|
||||||
|
|
||||||
|
If you would like it to be hosted at eg. hapi-fhir-jpaserver, eg. http://localhost:8080/hapi-fhir-jpaserver/ or http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata - then rename the WAR file to ```hapi-fhir-jpaserver.war``` and adjust the overlay configuration accordingly e.g.
|
||||||
|
|
||||||
|
```yaml
|
||||||
|
tester:
|
||||||
|
-
|
||||||
|
id: home
|
||||||
|
name: Local Tester
|
||||||
|
server_address: 'http://localhost:8080/hapi-fhir-jpaserver/fhir'
|
||||||
|
refuse_to_fetch_third_party_urls: false
|
||||||
|
fhir_version: R4
|
||||||
|
```
|
||||||
|
|
||||||
|
|
||||||
## Deploy with docker compose
|
## Deploy with docker compose
|
||||||
|
|
||||||
@@ -321,3 +334,28 @@ elasticsearch.password=SomePassword
|
|||||||
elasticsearch.required_index_status=YELLOW
|
elasticsearch.required_index_status=YELLOW
|
||||||
elasticsearch.schema_management_strategy=CREATE
|
elasticsearch.schema_management_strategy=CREATE
|
||||||
```
|
```
|
||||||
|
|
||||||
|
## Enabling LastN
|
||||||
|
|
||||||
|
Set `hapi.fhir.lastn_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable the $lastn operation on this server. Note that the $lastn operation relies on Elasticsearch, so for $lastn to work, indexing must be enabled using Elasticsearch.
|
||||||
|
|
||||||
|
## Example of a Dockerfile based on distroless images (for lower footprint and improved security)
|
||||||
|
|
||||||
|
```code
|
||||||
|
FROM maven:3.6.3-jdk-11-slim as build-hapi
|
||||||
|
WORKDIR /tmp/hapi-fhir-jpaserver-starter
|
||||||
|
|
||||||
|
COPY pom.xml .
|
||||||
|
RUN mvn -ntp dependency:go-offline
|
||||||
|
|
||||||
|
COPY src/ /tmp/hapi-fhir-jpaserver-starter/src/
|
||||||
|
RUN mvn clean package spring-boot:repackage -Pboot
|
||||||
|
|
||||||
|
FROM gcr.io/distroless/java:11
|
||||||
|
|
||||||
|
COPY --from=build-hapi /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
|
||||||
|
|
||||||
|
EXPOSE 8080
|
||||||
|
WORKDIR /app
|
||||||
|
CMD ["main.war"]
|
||||||
|
```
|
||||||
|
|||||||
7
pom.xml
7
pom.xml
@@ -184,37 +184,30 @@
|
|||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.webjars</groupId>
|
<groupId>org.webjars</groupId>
|
||||||
<artifactId>Eonasdan-bootstrap-datetimepicker</artifactId>
|
<artifactId>Eonasdan-bootstrap-datetimepicker</artifactId>
|
||||||
<version>4.17.43</version>
|
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.webjars</groupId>
|
<groupId>org.webjars</groupId>
|
||||||
<artifactId>font-awesome</artifactId>
|
<artifactId>font-awesome</artifactId>
|
||||||
<version>5.8.2</version>
|
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.webjars.bower</groupId>
|
<groupId>org.webjars.bower</groupId>
|
||||||
<artifactId>awesome-bootstrap-checkbox</artifactId>
|
<artifactId>awesome-bootstrap-checkbox</artifactId>
|
||||||
<version>1.0.1</version>
|
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.webjars</groupId>
|
<groupId>org.webjars</groupId>
|
||||||
<artifactId>jstimezonedetect</artifactId>
|
<artifactId>jstimezonedetect</artifactId>
|
||||||
<version>1.0.6</version>
|
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.webjars</groupId>
|
<groupId>org.webjars</groupId>
|
||||||
<artifactId>select2</artifactId>
|
<artifactId>select2</artifactId>
|
||||||
<version>4.0.3</version>
|
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.webjars.bower</groupId>
|
<groupId>org.webjars.bower</groupId>
|
||||||
<artifactId>jquery</artifactId>
|
<artifactId>jquery</artifactId>
|
||||||
<version>3.3.1</version>
|
|
||||||
</dependency>
|
</dependency>
|
||||||
<dependency>
|
<dependency>
|
||||||
<groupId>org.webjars.bower</groupId>
|
<groupId>org.webjars.bower</groupId>
|
||||||
<artifactId>moment</artifactId>
|
<artifactId>moment</artifactId>
|
||||||
<version>2.15.1</version>
|
|
||||||
</dependency>
|
</dependency>
|
||||||
|
|
||||||
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
|
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
|
||||||
|
|||||||
@@ -7,8 +7,10 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
|
|||||||
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
import java.util.Map;
|
||||||
|
|
||||||
import com.google.common.collect.ImmutableList;
|
import com.google.common.collect.ImmutableList;
|
||||||
|
import com.google.common.collect.ImmutableMap;
|
||||||
import org.hl7.fhir.r4.model.Bundle;
|
import org.hl7.fhir.r4.model.Bundle;
|
||||||
|
|
||||||
import org.springframework.boot.context.properties.ConfigurationProperties;
|
import org.springframework.boot.context.properties.ConfigurationProperties;
|
||||||
@@ -56,12 +58,14 @@ public class AppProperties {
|
|||||||
private Boolean narrative_enabled = true;
|
private Boolean narrative_enabled = true;
|
||||||
|
|
||||||
private Validation validation = new Validation();
|
private Validation validation = new Validation();
|
||||||
private List<Tester> tester = ImmutableList.of(new Tester());
|
private Map<String, Tester> tester = ImmutableMap.of("home", new Tester());
|
||||||
private Logger logger = new Logger();
|
private Logger logger = new Logger();
|
||||||
private Subscription subscription = new Subscription();
|
private Subscription subscription = new Subscription();
|
||||||
private Cors cors = null;
|
private Cors cors = null;
|
||||||
private Partitioning partitioning = null;
|
private Partitioning partitioning = null;
|
||||||
private List<ImplementationGuide> implementationGuides = null;
|
private Map<String, ImplementationGuide> implementationGuides = null;
|
||||||
|
|
||||||
|
private Boolean lastn_enabled = false;
|
||||||
|
|
||||||
public Integer getDefer_indexing_for_codesystems_of_size() {
|
public Integer getDefer_indexing_for_codesystems_of_size() {
|
||||||
return defer_indexing_for_codesystems_of_size;
|
return defer_indexing_for_codesystems_of_size;
|
||||||
@@ -71,11 +75,11 @@ public class AppProperties {
|
|||||||
this.defer_indexing_for_codesystems_of_size = defer_indexing_for_codesystems_of_size;
|
this.defer_indexing_for_codesystems_of_size = defer_indexing_for_codesystems_of_size;
|
||||||
}
|
}
|
||||||
|
|
||||||
public List<ImplementationGuide> getImplementationGuides() {
|
public Map<String, ImplementationGuide> getImplementationGuides() {
|
||||||
return implementationGuides;
|
return implementationGuides;
|
||||||
}
|
}
|
||||||
|
|
||||||
public void setImplementationGuides(List<ImplementationGuide> implementationGuides) {
|
public void setImplementationGuides(Map<String, ImplementationGuide> implementationGuides) {
|
||||||
this.implementationGuides = implementationGuides;
|
this.implementationGuides = implementationGuides;
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -372,11 +376,11 @@ public class AppProperties {
|
|||||||
this.reuse_cached_search_results_millis = reuse_cached_search_results_millis;
|
this.reuse_cached_search_results_millis = reuse_cached_search_results_millis;
|
||||||
}
|
}
|
||||||
|
|
||||||
public List<Tester> getTester() {
|
public Map<String, Tester> getTester() {
|
||||||
return tester;
|
return tester;
|
||||||
}
|
}
|
||||||
|
|
||||||
public void setTester(List<Tester> tester) {
|
public void setTester(Map<String, Tester> tester) {
|
||||||
this.tester = tester;
|
this.tester = tester;
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -390,6 +394,14 @@ public class AppProperties {
|
|||||||
this.narrative_enabled = narrative_enabled;
|
this.narrative_enabled = narrative_enabled;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public Boolean getLastn_enabled() {
|
||||||
|
return lastn_enabled;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setLastn_enabled(Boolean lastn_enabled) {
|
||||||
|
this.lastn_enabled = lastn_enabled;
|
||||||
|
}
|
||||||
|
|
||||||
public static class Cors {
|
public static class Cors {
|
||||||
private Boolean allow_Credentials = true;
|
private Boolean allow_Credentials = true;
|
||||||
private List<String> allowed_origin = ImmutableList.of("*");
|
private List<String> allowed_origin = ImmutableList.of("*");
|
||||||
@@ -456,7 +468,6 @@ public class AppProperties {
|
|||||||
|
|
||||||
public static class Tester {
|
public static class Tester {
|
||||||
|
|
||||||
private String id = "home";
|
|
||||||
private String name = "Local Tester";
|
private String name = "Local Tester";
|
||||||
private String server_address = "http://localhost:8080/fhir";
|
private String server_address = "http://localhost:8080/fhir";
|
||||||
private Boolean refuse_to_fetch_third_party_urls = true;
|
private Boolean refuse_to_fetch_third_party_urls = true;
|
||||||
@@ -470,14 +481,6 @@ public class AppProperties {
|
|||||||
this.fhir_version = fhir_version;
|
this.fhir_version = fhir_version;
|
||||||
}
|
}
|
||||||
|
|
||||||
public String getId() {
|
|
||||||
return id;
|
|
||||||
}
|
|
||||||
|
|
||||||
public void setId(String id) {
|
|
||||||
this.id = id;
|
|
||||||
}
|
|
||||||
|
|
||||||
public String getName() {
|
public String getName() {
|
||||||
return name;
|
return name;
|
||||||
}
|
}
|
||||||
|
|||||||
@@ -42,10 +42,7 @@ import org.springframework.http.HttpHeaders;
|
|||||||
import org.springframework.web.cors.CorsConfiguration;
|
import org.springframework.web.cors.CorsConfiguration;
|
||||||
|
|
||||||
import javax.servlet.ServletException;
|
import javax.servlet.ServletException;
|
||||||
import java.util.Arrays;
|
import java.util.*;
|
||||||
import java.util.Collections;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.Optional;
|
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
public class BaseJpaRestfulServer extends RestfulServer {
|
public class BaseJpaRestfulServer extends RestfulServer {
|
||||||
@@ -357,15 +354,21 @@ public class BaseJpaRestfulServer extends RestfulServer {
|
|||||||
}
|
}
|
||||||
|
|
||||||
if (appProperties.getImplementationGuides() != null) {
|
if (appProperties.getImplementationGuides() != null) {
|
||||||
List<AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
|
Map<String, AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
|
||||||
for (AppProperties.ImplementationGuide guide : guides) {
|
for (Map.Entry<String, AppProperties.ImplementationGuide> guide : guides.entrySet()) {
|
||||||
packageInstallerSvc.install(new PackageInstallationSpec()
|
packageInstallerSvc.install(new PackageInstallationSpec()
|
||||||
.setPackageUrl(guide.getUrl())
|
.setPackageUrl(guide.getValue().getUrl())
|
||||||
.setName(guide.getName())
|
.setName(guide.getValue().getName())
|
||||||
.setVersion(guide.getVersion())
|
.setVersion(guide.getValue().getVersion())
|
||||||
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL));
|
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL));
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (appProperties.getLastn_enabled()) {
|
||||||
|
daoConfig.setLastNEnabled(true);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@@ -1,5 +1,8 @@
|
|||||||
package ca.uhn.fhir.jpa.starter;
|
package ca.uhn.fhir.jpa.starter;
|
||||||
|
|
||||||
|
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
|
||||||
|
import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
|
||||||
|
import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
|
||||||
import org.springframework.core.env.CompositePropertySource;
|
import org.springframework.core.env.CompositePropertySource;
|
||||||
import org.springframework.core.env.ConfigurableEnvironment;
|
import org.springframework.core.env.ConfigurableEnvironment;
|
||||||
import org.springframework.core.env.EnumerablePropertySource;
|
import org.springframework.core.env.EnumerablePropertySource;
|
||||||
@@ -35,9 +38,66 @@ public class EnvironmentHelper {
|
|||||||
properties.put(values[0], values[1]);
|
properties.put(values[0], values[1]);
|
||||||
});
|
});
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null
|
||||||
|
&& environment.getProperty("elasticsearch.enabled", Boolean.class) == true ){
|
||||||
|
ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
|
||||||
|
ElasticsearchIndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", ElasticsearchIndexStatus.class);
|
||||||
|
if (requiredIndexStatus == null) {
|
||||||
|
builder.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW);
|
||||||
|
} else {
|
||||||
|
builder.setRequiredIndexStatus(requiredIndexStatus);
|
||||||
|
}
|
||||||
|
|
||||||
|
builder.setRestUrl(getElasticsearchServerUrl(environment));
|
||||||
|
builder.setUsername(getElasticsearchServerUsername(environment));
|
||||||
|
builder.setPassword(getElasticsearchServerPassword(environment));
|
||||||
|
IndexSchemaManagementStrategy indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", IndexSchemaManagementStrategy.class);
|
||||||
|
if (indexSchemaManagementStrategy == null) {
|
||||||
|
builder.setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE);
|
||||||
|
} else {
|
||||||
|
builder.setIndexSchemaManagementStrategy(indexSchemaManagementStrategy);
|
||||||
|
}
|
||||||
|
// pretty_print_json_log: false
|
||||||
|
Boolean refreshAfterWrite = environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class);
|
||||||
|
if (refreshAfterWrite == null) {
|
||||||
|
builder.setDebugRefreshAfterWrite(false);
|
||||||
|
} else {
|
||||||
|
builder.setDebugRefreshAfterWrite(refreshAfterWrite);
|
||||||
|
}
|
||||||
|
// pretty_print_json_log: false
|
||||||
|
Boolean prettyPrintJsonLog = environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class);
|
||||||
|
if (prettyPrintJsonLog == null) {
|
||||||
|
builder.setDebugPrettyPrintJsonLog(false);
|
||||||
|
} else {
|
||||||
|
builder.setDebugPrettyPrintJsonLog(prettyPrintJsonLog);
|
||||||
|
}
|
||||||
|
builder.apply(properties);
|
||||||
|
}
|
||||||
|
|
||||||
return properties;
|
return properties;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public static String getElasticsearchServerUrl(ConfigurableEnvironment environment) {
|
||||||
|
return environment.getProperty("elasticsearch.rest_url", String.class);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String getElasticsearchServerUsername(ConfigurableEnvironment environment) {
|
||||||
|
return environment.getProperty("elasticsearch.username");
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String getElasticsearchServerPassword(ConfigurableEnvironment environment) {
|
||||||
|
return environment.getProperty("elasticsearch.password");
|
||||||
|
}
|
||||||
|
|
||||||
|
public static Boolean isElasticsearchEnabled(ConfigurableEnvironment environment) {
|
||||||
|
if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null) {
|
||||||
|
return environment.getProperty("elasticsearch.enabled", Boolean.class);
|
||||||
|
} else {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv,
|
public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv,
|
||||||
String aKeyPrefix) {
|
String aKeyPrefix) {
|
||||||
Map<String, Object> result = new HashMap<>();
|
Map<String, Object> result = new HashMap<>();
|
||||||
|
|||||||
@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter;
|
|||||||
import ca.uhn.fhir.context.ConfigurationException;
|
import ca.uhn.fhir.context.ConfigurationException;
|
||||||
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
|
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
|
||||||
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
|
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
|
||||||
|
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
|
||||||
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
|
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
|
||||||
import org.springframework.beans.factory.annotation.Autowired;
|
import org.springframework.beans.factory.annotation.Autowired;
|
||||||
import org.springframework.context.annotation.*;
|
import org.springframework.context.annotation.*;
|
||||||
@@ -63,4 +64,18 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
|
|||||||
return retVal;
|
return retVal;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Bean()
|
||||||
|
public ElasticsearchSvcImpl elasticsearchSvc() {
|
||||||
|
if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
|
||||||
|
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
|
||||||
|
String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":"));
|
||||||
|
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
|
||||||
|
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
|
||||||
|
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));
|
||||||
|
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
|
||||||
|
} else {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter;
|
|||||||
import ca.uhn.fhir.context.ConfigurationException;
|
import ca.uhn.fhir.context.ConfigurationException;
|
||||||
import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
|
import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
|
||||||
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
|
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
|
||||||
|
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
|
||||||
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
|
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
|
||||||
import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config;
|
import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config;
|
||||||
import org.springframework.beans.factory.annotation.Autowired;
|
import org.springframework.beans.factory.annotation.Autowired;
|
||||||
@@ -65,4 +66,18 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
|
|||||||
return retVal;
|
return retVal;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Bean()
|
||||||
|
public ElasticsearchSvcImpl elasticsearchSvc() {
|
||||||
|
if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
|
||||||
|
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
|
||||||
|
String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":"));
|
||||||
|
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
|
||||||
|
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
|
||||||
|
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));
|
||||||
|
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
|
||||||
|
} else {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter;
|
|||||||
import ca.uhn.fhir.context.ConfigurationException;
|
import ca.uhn.fhir.context.ConfigurationException;
|
||||||
import ca.uhn.fhir.jpa.config.BaseJavaConfigR5;
|
import ca.uhn.fhir.jpa.config.BaseJavaConfigR5;
|
||||||
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
|
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
|
||||||
|
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
|
||||||
import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
|
import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
|
||||||
import org.springframework.beans.factory.annotation.Autowired;
|
import org.springframework.beans.factory.annotation.Autowired;
|
||||||
import org.springframework.context.annotation.Bean;
|
import org.springframework.context.annotation.Bean;
|
||||||
@@ -66,4 +67,19 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
|
|||||||
return retVal;
|
return retVal;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Bean()
|
||||||
|
public ElasticsearchSvcImpl elasticsearchSvc() {
|
||||||
|
if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
|
||||||
|
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
|
||||||
|
String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":"));
|
||||||
|
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
|
||||||
|
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
|
||||||
|
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));
|
||||||
|
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
|
||||||
|
} else {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
@@ -36,15 +36,15 @@ public class FhirTesterConfig {
|
|||||||
@Bean
|
@Bean
|
||||||
public TesterConfig testerConfig(AppProperties appProperties) {
|
public TesterConfig testerConfig(AppProperties appProperties) {
|
||||||
TesterConfig retVal = new TesterConfig();
|
TesterConfig retVal = new TesterConfig();
|
||||||
appProperties.getTester().stream().forEach(t -> {
|
appProperties.getTester().entrySet().stream().forEach(t -> {
|
||||||
retVal
|
retVal
|
||||||
.addServer()
|
.addServer()
|
||||||
.withId(t.getId())
|
.withId(t.getKey())
|
||||||
.withFhirVersion(t.getFhir_version())
|
.withFhirVersion(t.getValue().getFhir_version())
|
||||||
.withBaseUrl(t.getServer_address())
|
.withBaseUrl(t.getValue().getServer_address())
|
||||||
.withName(t.getName());
|
.withName(t.getValue().getName());
|
||||||
retVal.setRefuseToFetchThirdPartyUrls(
|
retVal.setRefuseToFetchThirdPartyUrls(
|
||||||
t.getRefuse_to_fetch_third_party_urls());
|
t.getValue().getRefuse_to_fetch_third_party_urls());
|
||||||
|
|
||||||
});
|
});
|
||||||
return retVal;
|
return retVal;
|
||||||
|
|||||||
@@ -1,6 +1,7 @@
|
|||||||
spring:
|
spring:
|
||||||
datasource:
|
datasource:
|
||||||
url: 'jdbc:h2:file:./target/database/h2'
|
url: 'jdbc:h2:file:./target/database/h2'
|
||||||
|
#url: jdbc:h2:mem:test_mem
|
||||||
username: sa
|
username: sa
|
||||||
password: null
|
password: null
|
||||||
driverClassName: org.h2.Driver
|
driverClassName: org.h2.Driver
|
||||||
@@ -33,13 +34,15 @@ hapi:
|
|||||||
fhir_version: R4
|
fhir_version: R4
|
||||||
# defer_indexing_for_codesystems_of_size: 101
|
# defer_indexing_for_codesystems_of_size: 101
|
||||||
#implementationguides:
|
#implementationguides:
|
||||||
# -
|
#example from registry (packages.fhir.org)
|
||||||
# url: https://build.fhir.org/ig/hl7dk/dk-medcom/branches/corrections/package.tgz
|
#swiss:
|
||||||
# name: dk.fhir.ig.medcom-core
|
#name: swiss.mednet.fhir
|
||||||
#version: 0.8.0
|
#version: 0.8.0
|
||||||
# -
|
#example not from registry
|
||||||
|
#ips_1_0_0:
|
||||||
|
#url: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
|
||||||
#name: hl7.fhir.uv.ips
|
#name: hl7.fhir.uv.ips
|
||||||
# version: 0.3.0
|
#version: 1.0.0
|
||||||
|
|
||||||
#supported_resource_types:
|
#supported_resource_types:
|
||||||
# - Patient
|
# - Patient
|
||||||
@@ -91,14 +94,14 @@ hapi:
|
|||||||
# retain_cached_searches_mins: 60
|
# retain_cached_searches_mins: 60
|
||||||
# reuse_cached_search_results_millis: 60000
|
# reuse_cached_search_results_millis: 60000
|
||||||
tester:
|
tester:
|
||||||
-
|
|
||||||
id: home
|
home:
|
||||||
name: Local Tester
|
name: Local Tester
|
||||||
server_address: 'http://localhost:8080/fhir'
|
server_address: 'http://localhost:8080/fhir'
|
||||||
refuse_to_fetch_third_party_urls: false
|
refuse_to_fetch_third_party_urls: false
|
||||||
fhir_version: R4
|
fhir_version: R4
|
||||||
-
|
|
||||||
id: global
|
global:
|
||||||
name: Global Tester
|
name: Global Tester
|
||||||
server_address: "http://hapi.fhir.org/baseR4"
|
server_address: "http://hapi.fhir.org/baseR4"
|
||||||
refuse_to_fetch_third_party_urls: false
|
refuse_to_fetch_third_party_urls: false
|
||||||
@@ -122,6 +125,7 @@ hapi:
|
|||||||
# startTlsEnable:
|
# startTlsEnable:
|
||||||
# startTlsRequired:
|
# startTlsRequired:
|
||||||
# quitWait:
|
# quitWait:
|
||||||
|
# lastn_enabled: true
|
||||||
|
|
||||||
|
|
||||||
#
|
#
|
||||||
|
|||||||
@@ -0,0 +1,144 @@
|
|||||||
|
package ca.uhn.fhir.jpa.starter;
|
||||||
|
|
||||||
|
import ca.uhn.fhir.context.ConfigurationException;
|
||||||
|
import ca.uhn.fhir.context.FhirContext;
|
||||||
|
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
|
||||||
|
import ca.uhn.fhir.rest.client.api.IGenericClient;
|
||||||
|
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
|
||||||
|
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
|
||||||
|
import org.hl7.fhir.instance.model.api.IIdType;
|
||||||
|
import org.hl7.fhir.r4.model.Bundle;
|
||||||
|
import org.hl7.fhir.r4.model.DateTimeType;
|
||||||
|
import org.hl7.fhir.r4.model.IntegerType;
|
||||||
|
import org.hl7.fhir.r4.model.Observation;
|
||||||
|
import org.hl7.fhir.r4.model.Parameters;
|
||||||
|
import org.hl7.fhir.r4.model.Patient;
|
||||||
|
import org.hl7.fhir.r4.model.StringType;
|
||||||
|
import org.junit.jupiter.api.BeforeAll;
|
||||||
|
import org.junit.jupiter.api.BeforeEach;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith;
|
||||||
|
import org.springframework.beans.factory.annotation.Autowired;
|
||||||
|
import org.springframework.boot.test.context.SpringBootTest;
|
||||||
|
import org.springframework.boot.test.util.TestPropertyValues;
|
||||||
|
import org.springframework.boot.web.server.LocalServerPort;
|
||||||
|
import org.springframework.context.ApplicationContextInitializer;
|
||||||
|
import org.springframework.context.ConfigurableApplicationContext;
|
||||||
|
import org.springframework.test.context.ContextConfiguration;
|
||||||
|
import org.springframework.test.context.junit.jupiter.SpringExtension;
|
||||||
|
import pl.allegro.tech.embeddedelasticsearch.EmbeddedElastic;
|
||||||
|
import pl.allegro.tech.embeddedelasticsearch.PopularProperties;
|
||||||
|
|
||||||
|
import javax.annotation.PreDestroy;
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.GregorianCalendar;
|
||||||
|
import java.util.UUID;
|
||||||
|
import java.util.concurrent.TimeUnit;
|
||||||
|
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
|
|
||||||
|
@ExtendWith(SpringExtension.class)
|
||||||
|
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
|
||||||
|
{
|
||||||
|
"spring.batch.job.enabled=false",
|
||||||
|
"spring.datasource.url=jdbc:h2:mem:dbr4",
|
||||||
|
"hapi.fhir.fhir_version=r4",
|
||||||
|
"hapi.fhir.lastn_enabled=true",
|
||||||
|
"elasticsearch.enabled=true",
|
||||||
|
// Because the port is set randomly, we will set the rest_url using the Initializer.
|
||||||
|
// "elasticsearch.rest_url='http://localhost:9200'",
|
||||||
|
"elasticsearch.username=SomeUsername",
|
||||||
|
"elasticsearch.password=SomePassword"
|
||||||
|
})
|
||||||
|
@ContextConfiguration(initializers = ElasticsearchLastNR4IT.Initializer.class)
|
||||||
|
public class ElasticsearchLastNR4IT {
|
||||||
|
|
||||||
|
private IGenericClient ourClient;
|
||||||
|
private FhirContext ourCtx;
|
||||||
|
|
||||||
|
private static final String ELASTIC_VERSION = "6.5.4";
|
||||||
|
private static EmbeddedElastic embeddedElastic;
|
||||||
|
|
||||||
|
@Autowired
|
||||||
|
private ElasticsearchSvcImpl myElasticsearchSvc;
|
||||||
|
|
||||||
|
@BeforeAll
|
||||||
|
public static void beforeClass() {
|
||||||
|
|
||||||
|
embeddedElastic = null;
|
||||||
|
try {
|
||||||
|
embeddedElastic = EmbeddedElastic.builder()
|
||||||
|
.withElasticVersion(ELASTIC_VERSION)
|
||||||
|
.withSetting(PopularProperties.TRANSPORT_TCP_PORT, 0)
|
||||||
|
.withSetting(PopularProperties.HTTP_PORT, 0)
|
||||||
|
.withSetting(PopularProperties.CLUSTER_NAME, UUID.randomUUID())
|
||||||
|
.withStartTimeout(60, TimeUnit.SECONDS)
|
||||||
|
.build()
|
||||||
|
.start();
|
||||||
|
} catch (IOException | InterruptedException e) {
|
||||||
|
throw new ConfigurationException(e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
@PreDestroy
|
||||||
|
public void stop() {
|
||||||
|
embeddedElastic.stop();
|
||||||
|
}
|
||||||
|
|
||||||
|
@LocalServerPort
|
||||||
|
private int port;
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testLastN() throws IOException {
|
||||||
|
|
||||||
|
Patient pt = new Patient();
|
||||||
|
pt.addName().setFamily("Lastn").addGiven("Arthur");
|
||||||
|
IIdType id = ourClient.create().resource(pt).execute().getId().toUnqualifiedVersionless();
|
||||||
|
|
||||||
|
Observation obs = new Observation();
|
||||||
|
obs.getSubject().setReferenceElement(id);
|
||||||
|
String observationCode = "testobservationcode";
|
||||||
|
String codeSystem = "http://testobservationcodesystem";
|
||||||
|
obs.getCode().addCoding().setCode(observationCode).setSystem(codeSystem);
|
||||||
|
obs.setValue(new StringType(observationCode));
|
||||||
|
Date effectiveDtm = new GregorianCalendar().getTime();
|
||||||
|
obs.setEffective(new DateTimeType(effectiveDtm));
|
||||||
|
obs.getCategoryFirstRep().addCoding().setCode("testcategorycode").setSystem("http://testcategorycodesystem");
|
||||||
|
IIdType obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless();
|
||||||
|
|
||||||
|
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||||
|
|
||||||
|
Parameters output = ourClient.operation().onType(Observation.class).named("lastn")
|
||||||
|
.withParameter(Parameters.class, "max", new IntegerType(1))
|
||||||
|
.andParameter("subject", new StringType("Patient/" + id.getIdPart()))
|
||||||
|
.execute();
|
||||||
|
Bundle b = (Bundle) output.getParameter().get(0).getResource();
|
||||||
|
assertEquals(1, b.getTotal());
|
||||||
|
assertEquals(obsId, b.getEntry().get(0).getResource().getIdElement().toUnqualifiedVersionless());
|
||||||
|
}
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
void beforeEach() {
|
||||||
|
|
||||||
|
ourCtx = FhirContext.forR4();
|
||||||
|
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
|
||||||
|
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
|
||||||
|
String ourServerBase = "http://localhost:" + port + "/fhir/";
|
||||||
|
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
|
||||||
|
ourClient.registerInterceptor(new LoggingInterceptor(true));
|
||||||
|
}
|
||||||
|
|
||||||
|
static class Initializer
|
||||||
|
implements ApplicationContextInitializer<ConfigurableApplicationContext> {
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void initialize(
|
||||||
|
ConfigurableApplicationContext configurableApplicationContext) {
|
||||||
|
// Since the port is dynamically generated, replace the URL with one that has the correct port
|
||||||
|
TestPropertyValues.of("elasticsearch.rest_url=http://localhost:" + embeddedElastic.getHttpPort())
|
||||||
|
.applyTo(configurableApplicationContext.getEnvironment());
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
Reference in New Issue
Block a user