Personal-Twin/hapi-fhir-jpaserver-starter
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Merge branch 'master' into kbd-20201125-cql-initial-impl

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This commit is contained in:
Kevin Dougan
2020-12-15 15:32:07 -05:00
parent 58bf8a100e 92656c80a2
commit ebe7e99c37
12 changed files with 365 additions and 50 deletions
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33
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -7,8 +7,10 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMap;
import org.hl7.fhir.r4.model.Bundle;
import org.springframework.boot.context.properties.ConfigurationProperties;
@@ -56,12 +58,14 @@ public class AppProperties {
private Boolean narrative_enabled = true;
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 Subscription subscription = new Subscription();
private Cors cors = 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() {
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;
}
public List<ImplementationGuide> getImplementationGuides() {
public Map<String, ImplementationGuide> getImplementationGuides() {
return implementationGuides;
}
public void setImplementationGuides(List<ImplementationGuide> implementationGuides) {
public void setImplementationGuides(Map<String, ImplementationGuide> implementationGuides) {
this.implementationGuides = implementationGuides;
}
@@ -372,11 +376,11 @@ public class AppProperties {
this.reuse_cached_search_results_millis = reuse_cached_search_results_millis;
}
public List<Tester> getTester() {
public Map<String, Tester> getTester() {
return tester;
}
public void setTester(List<Tester> tester) {
public void setTester(Map<String, Tester> tester) {
this.tester = tester;
}
@@ -390,6 +394,14 @@ 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("*");
@@ -456,7 +468,6 @@ public class AppProperties {
public static class Tester {
private String id = "home";
private String name = "Local Tester";
private String server_address = "http://localhost:8080/fhir";
private Boolean refuse_to_fetch_third_party_urls = true;
@@ -470,14 +481,6 @@ public class AppProperties {
this.fhir_version = fhir_version;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getName() {
return name;
}

21
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
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@@ -42,10 +42,7 @@ import org.springframework.http.HttpHeaders;
import org.springframework.web.cors.CorsConfiguration;
import javax.servlet.ServletException;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import java.util.*;
import java.util.stream.Collectors;
public class BaseJpaRestfulServer extends RestfulServer {
@@ -357,15 +354,21 @@ public class BaseJpaRestfulServer extends RestfulServer {
}
if (appProperties.getImplementationGuides() != null) {
List<AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
for (AppProperties.ImplementationGuide guide : guides) {
Map<String, AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
for (Map.Entry<String, AppProperties.ImplementationGuide> guide : guides.entrySet()) {
packageInstallerSvc.install(new PackageInstallationSpec()
.setPackageUrl(guide.getUrl())
.setName(guide.getName())
.setVersion(guide.getVersion())
.setPackageUrl(guide.getValue().getUrl())
.setName(guide.getValue().getName())
.setVersion(guide.getValue().getVersion())
.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 ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config;
import org.springframework.beans.factory.annotation.Autowired;
@@ -65,4 +66,18 @@ 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;
}
}
}

12
src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java
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@@ -36,15 +36,15 @@ public class FhirTesterConfig {
@Bean
public TesterConfig testerConfig(AppProperties appProperties) {
TesterConfig retVal = new TesterConfig();
appProperties.getTester().stream().forEach(t -> {
appProperties.getTester().entrySet().stream().forEach(t -> {
retVal
.addServer()
.withId(t.getId())
.withFhirVersion(t.getFhir_version())
.withBaseUrl(t.getServer_address())
.withName(t.getName());
.withId(t.getKey())
.withFhirVersion(t.getValue().getFhir_version())
.withBaseUrl(t.getValue().getServer_address())
.withName(t.getValue().getName());
retVal.setRefuseToFetchThirdPartyUrls(
t.getRefuse_to_fetch_third_party_urls());
t.getValue().getRefuse_to_fetch_third_party_urls());
});
return retVal;