Personal-Twin/hapi-fhir-jpaserver-starter
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Added support for $lastn operation and fixed Elasticsearch indexing.

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This commit is contained in:
ianmarshall
2020-12-04 15:50:43 -05:00
parent 329a7f3293
commit 2e2bdaed67
9 changed files with 272 additions and 0 deletions
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10
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -62,6 +62,8 @@ public class AppProperties {
private Partitioning partitioning = null;
private List<ImplementationGuide> implementationGuides = null;
private Boolean lastn_enabled = false;
public Integer getDefer_indexing_for_codesystems_of_size() {
return defer_indexing_for_codesystems_of_size;
}
@@ -382,6 +384,14 @@ public class AppProperties {
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 {
private Boolean allow_Credentials = true;
private List<String> allowed_origin = ImmutableList.of("*");

6
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
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@@ -360,6 +360,12 @@ public class BaseJpaRestfulServer extends RestfulServer {
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL));
}
}
if (appProperties.getLastn_enabled()) {
daoConfig.setLastNEnabled(true);
}
}

60
src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java
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@@ -1,5 +1,8 @@
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.ConfigurableEnvironment;
import org.springframework.core.env.EnumerablePropertySource;
@@ -35,9 +38,66 @@ public class EnvironmentHelper {
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;
}
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,
String aKeyPrefix) {
Map<String, Object> result = new HashMap<>();

15
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java
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@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.*;
@@ -63,4 +64,18 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
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;
}
}
}

15
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java
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@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
@@ -66,4 +67,18 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
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;
}
}
}

16
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java
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@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.BaseJavaConfigR5;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
@@ -66,4 +67,19 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
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;
}
}
}

1
src/main/resources/application.yaml
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@@ -120,6 +120,7 @@ hapi:
# startTlsEnable:
# startTlsRequired:
# quitWait:
# lastn_enabled: true
#