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All but tests works

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This commit is contained in:
jvi
2020-09-07 13:47:09 +02:00
parent 8bf930b3c3
commit 437d22e460
9 changed files with 436 additions and 243 deletions
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11
pom.xml
View File

@@ -18,6 +18,12 @@
<artifactId>hapi-fhir-jpaserver-starter</artifactId>
<properties>
<java.version>11</java.version>
<maven.compiler.source>${java.version}</maven.compiler.source>
<maven.compiler.target>${java.version}</maven.compiler.target>
</properties>
<prerequisites>
<maven>3.6.0</maven>
</prerequisites>
@@ -293,8 +299,6 @@
</dependency>
<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-logging -->
<dependency>
<groupId>org.springframework.boot</groupId>
@@ -374,6 +378,9 @@
</overlay>
</overlays>
<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
<failOnMissingWebXml>false</failOnMissingWebXml>
</configuration>
</plugin>

5
src/main/java/ca/uhn/fhir/jpa/empi/EmpiConfig.java
View File

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.empi;
import ca.uhn.fhir.empi.api.IEmpiSettings;
import ca.uhn.fhir.empi.rules.config.EmpiRuleValidator;
import ca.uhn.fhir.empi.rules.config.EmpiSettings;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.HapiProperties;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
@@ -21,11 +22,11 @@ import java.io.IOException;
public class EmpiConfig {
@Bean
IEmpiSettings empiSettings(EmpiRuleValidator theEmpiRuleValidator) throws IOException {
IEmpiSettings empiSettings(EmpiRuleValidator theEmpiRuleValidator, AppProperties appProperties) throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("empi-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
return new EmpiSettings(theEmpiRuleValidator).setEnabled(HapiProperties.getEmpiEnabled()).setScriptText(json);
return new EmpiSettings(theEmpiRuleValidator).setEnabled(appProperties.getEmpi_enabled()).setScriptText(json);
}
}

217
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -4,8 +4,11 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.api.config.DaoConfig.ClientIdStrategyEnum;
import ca.uhn.fhir.rest.api.EncodingEnum;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r4.model.Bundle;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.boot.context.properties.EnableConfigurationProperties;
import org.springframework.context.annotation.Configuration;
@@ -16,7 +19,7 @@ import org.springframework.context.annotation.Configuration;
@EnableConfigurationProperties
public class AppProperties {
private Boolean empi_enabled = false;
private Boolean allow_cascading_deletes = false;
private Boolean allow_contains_searches = true;
private Boolean allow_external_references = false;
@@ -24,7 +27,6 @@ public class AppProperties {
private Boolean allow_override_default_search_params = true;
private Boolean allow_placeholder_references = true;
private Boolean auto_create_placeholder_reference_targets = true;
private Integer default_page_size = 20;
private Boolean enable_index_missing_fields = false;
private Boolean enforce_referential_integrity_on_delete = true;
private Boolean enforce_referential_integrity_on_write = true;
@@ -35,23 +37,79 @@ public class AppProperties {
private Boolean graphql_enabled = true;
private Boolean binary_storage_enabled = true;
private Boolean bulk_export_enabled = true;
private Integer max_binary_size = 104857600;
private Boolean default_pretty_print = true;
private Integer default_page_size = 20;
private Integer max_binary_size = null;
private Integer max_page_size = Integer.MAX_VALUE;
private Integer retain_cached_searches_mins = 60;
private Long retain_cached_searches_mins = 60L;
private Long reuse_cached_search_results_millis = 60000L;
private String server_address = null;
private EncodingEnum default_encoding = EncodingEnum.JSON;
private FhirVersionEnum fhir_version = FhirVersionEnum.R4;
private ClientIdStrategyEnum client_id_strategy = ClientIdStrategyEnum.ALPHANUMERIC;
private List<String> supported_resource_types = new ArrayList<>();
private List<Bundle.BundleType> allowed_bundle_types = null;
private Validation validation = new Validation();
private List<Tester> tester = new ArrayList<>();
private Logger logger = new Logger();
private Subscription subscription = new Subscription();
private Cors cors = null;
private Partitioning partitioning = null;
public Partitioning getPartitioning() {
return partitioning;
}
public void setPartitioning(Partitioning partitioning) {
this.partitioning = partitioning;
}
public Boolean getEmpi_enabled() {
return empi_enabled;
}
public void setEmpi_enabled(Boolean empi_enabled) {
this.empi_enabled = empi_enabled;
}
public Cors getCors() {
return cors;
}
public void setCors(Cors cors) {
this.cors = cors;
}
public List<Bundle.BundleType> getAllowed_bundle_types() {
return allowed_bundle_types;
}
public void setAllowed_bundle_types(List<Bundle.BundleType> allowed_bundle_types) {
this.allowed_bundle_types = allowed_bundle_types;
}
public String getServer_address() {
return server_address;
}
public void setServer_address(String server_address) {
this.server_address = server_address;
}
public Subscription getSubscription() {
return subscription;
}
public Boolean getDefault_pretty_print() {
return default_pretty_print;
}
public void setDefault_pretty_print(Boolean default_pretty_print) {
this.default_pretty_print = default_pretty_print;
}
public void setSubscription(Subscription subscription) {
this.subscription = subscription;
}
@@ -64,6 +122,13 @@ public class AppProperties {
this.validation = validation;
}
public List<String> getSupported_resource_types() {
return supported_resource_types;
}
public void setSupported_resource_types(List<String> supported_resource_types) {
this.supported_resource_types = supported_resource_types;
}
public Logger getLogger() {
return logger;
@@ -262,11 +327,11 @@ public class AppProperties {
this.max_page_size = max_page_size;
}
public Integer getRetain_cached_searches_mins() {
public Long getRetain_cached_searches_mins() {
return retain_cached_searches_mins;
}
public void setRetain_cached_searches_mins(Integer retain_cached_searches_mins) {
public void setRetain_cached_searches_mins(Long retain_cached_searches_mins) {
this.retain_cached_searches_mins = retain_cached_searches_mins;
}
@@ -286,6 +351,29 @@ public class AppProperties {
this.tester = tester;
}
public static class Cors {
private Boolean allow_Credentials = true;
private List<String> allowed_origin = new ArrayList<>();//List.of("*");
public List<String> getAllowed_origin() {
return allowed_origin;
}
public void setAllowed_origin(List<String> allowed_origin) {
this.allowed_origin = allowed_origin;
}
public Boolean getAllow_Credentials() {
return allow_Credentials;
}
public void setAllow_Credentials(Boolean allow_Credentials) {
this.allow_Credentials = allow_Credentials;
}
}
public static class Logger {
private String name = "fhirtest.access";
@@ -398,16 +486,22 @@ public class AppProperties {
}
}
public static class Partitioning {
private Boolean partitioning_include_in_search_hashes = false;
public Boolean getPartitioning_include_in_search_hashes() {
return partitioning_include_in_search_hashes;
}
public void setPartitioning_include_in_search_hashes(Boolean partitioning_include_in_search_hashes) {
this.partitioning_include_in_search_hashes = partitioning_include_in_search_hashes;
}
}
public static class Subscription {
public Boolean getEmail_enabled() {
return email_enabled;
}
public void setEmail_enabled(Boolean email_enabled) {
this.email_enabled = email_enabled;
}
public Boolean getResthook_enabled() {
return resthook_enabled;
}
@@ -424,8 +518,101 @@ public class AppProperties {
this.websocket_enabled = websocket_enabled;
}
private Boolean email_enabled = false;
private Boolean resthook_enabled = false;
private Boolean websocket_enabled = false;
private Email email = null;
public Email getEmail() {
return email;
}
public void setEmail(Email email) {
this.email = email;
}
public static class Email {
public String getFrom() {
return from;
}
public void setFrom(String from) {
this.from = from;
}
public String getHost() {
return host;
}
public void setHost(String host) {
this.host = host;
}
public Integer getPort() {
return port;
}
public void setPort(Integer port) {
this.port = port;
}
public String getUsername() {
return username;
}
public void setUsername(String username) {
this.username = username;
}
public String getPassword() {
return password;
}
public void setPassword(String password) {
this.password = password;
}
public Boolean getAuth() {
return auth;
}
public void setAuth(Boolean auth) {
this.auth = auth;
}
public Boolean getStartTlsEnable() {
return startTlsEnable;
}
public void setStartTlsEnable(Boolean startTlsEnable) {
this.startTlsEnable = startTlsEnable;
}
public Boolean getStartTlsRequired() {
return startTlsRequired;
}
public void setStartTlsRequired(Boolean startTlsRequired) {
this.startTlsRequired = startTlsRequired;
}
public Boolean getQuitWait() {
return quitWait;
}
public void setQuitWait(Boolean quitWait) {
this.quitWait = quitWait;
}
private String from;
private String host;
private Integer port = 25;
private String username;
private String password;
private Boolean auth = false;
private Boolean startTlsEnable = false;
private Boolean startTlsRequired = false;
private Boolean quitWait = false;
}
}
}

2
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
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@@ -34,7 +34,7 @@ public class Application {
ServletRegistrationBean registrationBean = new ServletRegistrationBean();
registrationBean.setServlet(dispatcherServlet);
registrationBean.addUrlMappings("/*");
registrationBean.addUrlMappings("/hapi-fhir-jpaserver/*", "/*");
registrationBean.setLoadOnStartup(1);
return registrationBean;

181
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
View File

@@ -4,7 +4,6 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.IDaoRegistry;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
@@ -12,56 +11,36 @@ import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.IJpaSystemProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.provider.*;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
import ca.uhn.fhir.jpa.provider.r5.JpaConformanceProviderR5;
import ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.*;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
import java.util.TreeSet;
import javax.servlet.ServletException;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta;
import com.google.common.base.Strings;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.springframework.aop.framework.Advised;
import org.springframework.aop.support.AopUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.http.HttpHeaders;
import org.springframework.web.cors.CorsConfiguration;
import javax.servlet.ServletException;
import java.util.*;
import java.util.stream.Collectors;
public class BaseJpaRestfulServer extends RestfulServer {
AppProperties hapiProperties;
@Autowired
DaoRegistry daoRegistry;
@@ -81,8 +60,35 @@ public class BaseJpaRestfulServer extends RestfulServer {
@Autowired
IJpaSystemProvider jpaSystemProvider;
public BaseJpaRestfulServer(AppProperties appProperties) {
this.hapiProperties = appProperties;
@Autowired
IInterceptorBroadcaster interceptorBroadcaster;
@Autowired
DatabaseBackedPagingProvider databaseBackedPagingProvider;
@Autowired
IInterceptorService interceptorService;
@Autowired
IValidatorModule validatorModule;
@Autowired
Optional<GraphQLProvider> graphQLProvider;
@Autowired
BulkDataExportProvider bulkDataExportProvider;
@Autowired
PartitionManagementProvider partitionManagementProvider;
@Autowired
BinaryStorageInterceptor binaryStorageInterceptor;
@Autowired
AppProperties appProperties;
public BaseJpaRestfulServer() {
}
private static final long serialVersionUID = 1L;
@@ -92,26 +98,18 @@ public class BaseJpaRestfulServer extends RestfulServer {
protected void initialize() throws ServletException {
super.initialize();
ApplicationContext appCtx = (ApplicationContext) getServletContext()
.getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
/*
* Create a FhirContext object that uses the version of FHIR
* specified in the properties file.
*/
// Customize supported resource types
Set<String> supportedResourceTypes = HapiProperties.getSupportedResourceTypes();
List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
if (!supportedResourceTypes.isEmpty() && !supportedResourceTypes.contains("SearchParameter")) {
supportedResourceTypes.add("SearchParameter");
}
if (!supportedResourceTypes.isEmpty()) {
daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
}
setFhirContext(fhirSystemDao.getContext());
registerProviders(resourceProviders.createProviders());
registerProvider(jpaSystemProvider);
@@ -160,7 +158,10 @@ public class BaseJpaRestfulServer extends RestfulServer {
/*
* ETag Support
*/
setETagSupport(HapiProperties.getEtagSupport());
if(appProperties.getEtag_support_enabled() == false)
setETagSupport(ETagSupportEnum.DISABLED);
/*
* This server tries to dynamically generate narratives
@@ -171,12 +172,12 @@ public class BaseJpaRestfulServer extends RestfulServer {
/*
* Default to JSON and pretty printing
*/
setDefaultPrettyPrint(HapiProperties.getDefaultPrettyPrint());
setDefaultPrettyPrint(appProperties.getDefault_pretty_print());
/*
* Default encoding
*/
setDefaultResponseEncoding(HapiProperties.getDefaultEncoding());
setDefaultResponseEncoding(appProperties.getDefault_encoding());
/*
* This configures the server to page search results to and from
@@ -185,7 +186,7 @@ public class BaseJpaRestfulServer extends RestfulServer {
* but makes the server much more scalable.
*/
setPagingProvider(appCtx.getBean(DatabaseBackedPagingProvider.class));
setPagingProvider(databaseBackedPagingProvider);
/*
* This interceptor formats the output using nice colourful
@@ -195,7 +196,7 @@ public class BaseJpaRestfulServer extends RestfulServer {
ResponseHighlighterInterceptor responseHighlighterInterceptor = new ResponseHighlighterInterceptor();
this.registerInterceptor(responseHighlighterInterceptor);
if (HapiProperties.isFhirPathFilterInterceptorEnabled()) {
if (appProperties.getFhirpath_interceptor_enabled()) {
registerInterceptor(new FhirPathFilterInterceptor());
}
@@ -203,10 +204,10 @@ public class BaseJpaRestfulServer extends RestfulServer {
* Add some logging for each request
*/
LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
loggingInterceptor.setLoggerName(HapiProperties.getLoggerName());
loggingInterceptor.setMessageFormat(HapiProperties.getLoggerFormat());
loggingInterceptor.setErrorMessageFormat(HapiProperties.getLoggerErrorFormat());
loggingInterceptor.setLogExceptions(HapiProperties.getLoggerLogExceptions());
loggingInterceptor.setLoggerName(appProperties.getLogger().getName());
loggingInterceptor.setMessageFormat(appProperties.getLogger().getFormat());
loggingInterceptor.setErrorMessageFormat(appProperties.getLogger().getError_format());
loggingInterceptor.setLogExceptions(appProperties.getLogger().getLog_exceptions());
this.registerInterceptor(loggingInterceptor);
/*
@@ -215,8 +216,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
* this doesn't always work. If you are setting links in your search bundles that
* just refer to "localhost", you might want to use a server address strategy:
*/
String serverAddress = HapiProperties.getServerAddress();
if (serverAddress != null && serverAddress.length() > 0) {
String serverAddress = appProperties.getServer_address();
if (!Strings.isNullOrEmpty(serverAddress)) {
setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
}
@@ -228,21 +229,21 @@ public class BaseJpaRestfulServer extends RestfulServer {
* with this feature.
*/
if (false) { // <-- DISABLED RIGHT NOW
registerProvider(appCtx.getBean(TerminologyUploaderProvider.class));
//registerProvider(appCtx.getBean(TerminologyUploaderProvider.class));
}
// If you want to enable the $trigger-subscription operation to allow
// manual triggering of a subscription delivery, enable this provider
if (false) { // <-- DISABLED RIGHT NOW
SubscriptionTriggeringProvider retriggeringProvider = appCtx
/* 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
if (HapiProperties.getCorsEnabled()) {
if (appProperties.getCors() != null) {
CorsConfiguration config = new CorsConfiguration();
config.addAllowedHeader(HttpHeaders.ORIGIN);
config.addAllowedHeader(HttpHeaders.ACCEPT);
@@ -252,17 +253,15 @@ public class BaseJpaRestfulServer extends RestfulServer {
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("X-Requested-With");
config.addAllowedHeader("Prefer");
String allAllowedCORSOrigins = HapiProperties.getCorsAllowedOrigin();
Arrays.stream(allAllowedCORSOrigins.split(",")).forEach(o -> {
config.addAllowedOrigin(o);
});
config.addAllowedOrigin(HapiProperties.getCorsAllowedOrigin());
List<String> allAllowedCORSOrigins = appProperties.getCors().getAllowed_origin();
allAllowedCORSOrigins.forEach(config::addAllowedOrigin);
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(
Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
config.setAllowCredentials(HapiProperties.getCorsAllowedCredentials());
config.setAllowCredentials(appProperties.getCors().getAllow_Credentials());
// Create the interceptor and register it
CorsInterceptor interceptor = new CorsInterceptor(config);
@@ -271,40 +270,35 @@ public class BaseJpaRestfulServer extends RestfulServer {
// If subscriptions are enabled, we want to register the interceptor that
// will activate them and match results against them
if (HapiProperties.getSubscriptionWebsocketEnabled() ||
HapiProperties.getSubscriptionEmailEnabled() ||
HapiProperties.getSubscriptionRestHookEnabled()) {
if (appProperties.getSubscription() != null) {
// Subscription debug logging
IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
}
// Cascading deletes
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
if (HapiProperties.getAllowCascadingDeletes()) {
if (appProperties.getAllow_cascading_deletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx,
daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
// Binary Storage
if (HapiProperties.isBinaryStorageEnabled()) {
BinaryStorageInterceptor binaryStorageInterceptor = appCtx
.getBean(BinaryStorageInterceptor.class);
if (appProperties.getBinary_storage_enabled()) {
getInterceptorService().registerInterceptor(binaryStorageInterceptor);
}
// Validation
IValidatorModule validatorModule = appCtx.getBean(IValidatorModule.class);
if (validatorModule != null) {
if (HapiProperties.getValidateRequestsEnabled()) {
if (appProperties.getValidation().getRequests_enabled()) {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
if (HapiProperties.getValidateResponsesEnabled()) {
if (appProperties.getValidation().getResponses_enabled()) {
ResponseValidatingInterceptor interceptor = new ResponseValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
@@ -313,52 +307,33 @@ public class BaseJpaRestfulServer extends RestfulServer {
}
// GraphQL
if (HapiProperties.getGraphqlEnabled()) {
if (appProperties.getGraphql_enabled()) {
if (fhirVersion.isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
registerProvider(appCtx.getBean(GraphQLProvider.class));
registerProvider(graphQLProvider.get());
}
}
if (!HapiProperties.getAllowedBundleTypes().isEmpty()) {
String allowedBundleTypesString = HapiProperties.getAllowedBundleTypes();
Set<String> allowedBundleTypes = new HashSet<>();
Arrays.stream(allowedBundleTypesString.split(",")).forEach(o -> {
BundleType type = BundleType.valueOf(o);
allowedBundleTypes.add(type.toCode());
});
DaoConfig config = daoConfig;
config.setBundleTypesAllowedForStorage(
Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
if (appProperties.getAllowed_bundle_types() != null) {
daoConfig.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream().map(BundleType::toCode).collect(Collectors.toSet()));
}
// Bulk Export
if (HapiProperties.getBulkExportEnabled()) {
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
if (appProperties.getBulk_export_enabled()) {
registerProvider(bulkDataExportProvider);
}
// Partitioning
if (HapiProperties.getPartitioningMultitenancyEnabled()) {
if (appProperties.getPartitioning() != null) {
registerInterceptor(new RequestTenantPartitionInterceptor());
setTenantIdentificationStrategy(new UrlBaseTenantIdentificationStrategy());
registerProviders(appCtx.getBean(PartitionManagementProvider.class));
registerProviders(partitionManagementProvider);
}
if (HapiProperties.getClientIdStrategy() == DaoConfig.ClientIdStrategyEnum.ANY) {
if (appProperties.getClient_id_strategy() == DaoConfig.ClientIdStrategyEnum.ANY) {
daoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);
daoConfig.setResourceClientIdStrategy(HapiProperties.getClientIdStrategy());
daoConfig.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
}
}
protected <T> T getBeanWithoutProxy(Object bean) {
if (AopUtils.isAopProxy(bean) && bean instanceof Advised) {
try {
return (T) ((Advised) bean).getTargetSource().getTarget();
} catch (Exception e) {
throw new RuntimeException(e);
}
}
return (T)bean;
}
}

88
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
View File

@@ -8,6 +8,7 @@ import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
import com.google.common.base.Strings;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hl7.fhir.dstu2.model.Subscription;
import org.springframework.beans.factory.annotation.Autowired;
@@ -20,6 +21,7 @@ import org.thymeleaf.util.Validate;
import java.lang.reflect.InvocationTargetException;
import java.sql.Driver;
import java.util.Optional;
/**
* This is the primary configuration file for the example server
@@ -30,23 +32,6 @@ public class FhirServerConfigCommon {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
private Boolean subscriptionRestHookEnabled = HapiProperties.getSubscriptionRestHookEnabled();
private Boolean subscriptionEmailEnabled = HapiProperties.getSubscriptionEmailEnabled();
private String emailFrom = HapiProperties.getEmailFrom();
private Boolean emailEnabled = HapiProperties.getEmailEnabled();
private String emailHost = HapiProperties.getEmailHost();
private Integer emailPort = HapiProperties.getEmailPort();
private String emailUsername = HapiProperties.getEmailUsername();
private String emailPassword = HapiProperties.getEmailPassword();
private Boolean emailAuth = HapiProperties.getEmailAuth();
private Boolean emailStartTlsEnable = HapiProperties.getEmailStartTlsEnable();
private Boolean emailStartTlsRequired = HapiProperties.getEmailStartTlsRequired();
private Boolean emailQuitWait = HapiProperties.getEmailQuitWait();
@Autowired
private ApplicationContext appContext;
@@ -58,24 +43,25 @@ public class FhirServerConfigCommon {
ourLog.info("Server configured to " + (appProperties.getAllow_placeholder_references() ? "allow" : "deny") + " placeholder references");
ourLog.info("Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny") + " overriding default search params");
if (this.emailEnabled) {
ourLog.info("Server is configured to enable email with host '" + this.emailHost + "' and port " + this.emailPort.toString());
ourLog.info("Server will use '" + this.emailFrom + "' as the from email address");
if (appProperties.getSubscription().getEmail() != null) {
AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
ourLog.info("Server is configured to enable email with host '" + email.getHost() + "' and port " + email.getPort());
ourLog.info("Server will use '" + email.getFrom() + "' as the from email address");
if (this.emailUsername != null && this.emailUsername.length() > 0) {
ourLog.info("Server is configured to use username '" + this.emailUsername + "' for email");
if (!Strings.isNullOrEmpty(email.getUsername())) {
ourLog.info("Server is configured to use username '" + email.getUsername() + "' for email");
}
if (this.emailPassword != null && this.emailPassword.length() > 0) {
if (!Strings.isNullOrEmpty(email.getPassword())) {
ourLog.info("Server is configured to use a password for email");
}
}
if (this.subscriptionRestHookEnabled) {
if (appProperties.getSubscription().getResthook_enabled()) {
ourLog.info("REST-hook subscriptions enabled");
}
if (this.subscriptionEmailEnabled) {
if (appProperties.getSubscription().getEmail() != null) {
ourLog.info("Email subscriptions enabled");
}
}
@@ -96,7 +82,8 @@ public class FhirServerConfigCommon {
retVal.setAllowExternalReferences(appProperties.getAllow_external_references());
retVal.setExpungeEnabled(appProperties.getExpunge_enabled());
retVal.setAutoCreatePlaceholderReferenceTargets(appProperties.getAllow_placeholder_references());
retVal.setEmailFromAddress(this.emailFrom);
if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
retVal.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
Integer maxFetchSize = appProperties.getMax_page_size();
retVal.setFetchSizeDefaultMaximum(maxFetchSize);
@@ -106,15 +93,17 @@ public class FhirServerConfigCommon {
retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
Long retainCachedSearchesMinutes = HapiProperties.getExpireSearchResultsAfterMins();
Long retainCachedSearchesMinutes = appProperties.getRetain_cached_searches_mins();
retVal.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
if(appProperties.getSubscription() != null) {
// Subscriptions are enabled by channel type
if (appProperties.getSubscription().getResthook_enabled()) {
ourLog.info("Enabling REST-hook subscriptions");
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
}
if (appProperties.getSubscription().getEmail_enabled()) {
if (appProperties.getSubscription().getEmail() != null) {
ourLog.info("Enabling email subscriptions");
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
}
@@ -122,6 +111,7 @@ public class FhirServerConfigCommon {
ourLog.info("Enabling websocket subscriptions");
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
}
}
retVal.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
@@ -133,7 +123,7 @@ public class FhirServerConfigCommon {
PartitionSettings retVal = new PartitionSettings();
// Partitioning
if (HapiProperties.getPartitioningMultitenancyEnabled()) {
if (appProperties.getPartitioning() != null) {
retVal.setPartitioningEnabled(true);
}
@@ -147,14 +137,15 @@ public class FhirServerConfigCommon {
modelConfig.setAllowContainsSearches(appProperties.getAllow_contains_searches());
modelConfig.setAllowExternalReferences(appProperties.getAllow_external_references());
modelConfig.setDefaultSearchParamsCanBeOverridden(appProperties.getAllow_override_default_search_params());
modelConfig.setEmailFromAddress(this.emailFrom);
if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
modelConfig.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
// You can enable these if you want to support Subscriptions from your server
if (this.subscriptionRestHookEnabled) {
if (appProperties.getSubscription() != null && appProperties.getSubscription().getResthook_enabled() != null) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
if (this.subscriptionEmailEnabled) {
if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
@@ -181,34 +172,33 @@ public class FhirServerConfigCommon {
@Lazy
@Bean
public IBinaryStorageSvc binaryStorageSvc() {
public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {
DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
if (HapiProperties.getMaxBinarySize() != null) {
binaryStorageSvc.setMaximumBinarySize(HapiProperties.getMaxBinarySize());
if (appProperties.getMax_binary_size() != null) {
binaryStorageSvc.setMaximumBinarySize(appProperties.getMax_binary_size());
}
return binaryStorageSvc;
}
@Bean()
public IEmailSender emailSender() {
if (this.emailEnabled) {
public IEmailSender emailSender(AppProperties appProperties, Optional<SubscriptionDeliveryHandlerFactory> subscriptionDeliveryHandlerFactory) {
if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
JavaMailEmailSender retVal = new JavaMailEmailSender();
retVal.setSmtpServerHostname(this.emailHost);
retVal.setSmtpServerPort(this.emailPort);
retVal.setSmtpServerUsername(this.emailUsername);
retVal.setSmtpServerPassword(this.emailPassword);
retVal.setAuth(this.emailAuth);
retVal.setStartTlsEnable(this.emailStartTlsEnable);
retVal.setStartTlsRequired(this.emailStartTlsRequired);
retVal.setQuitWait(this.emailQuitWait);
SubscriptionDeliveryHandlerFactory subscriptionDeliveryHandlerFactory = appContext.getBean(SubscriptionDeliveryHandlerFactory.class);
Validate.notNull(subscriptionDeliveryHandlerFactory, "No subscription delivery handler");
subscriptionDeliveryHandlerFactory.setEmailSender(retVal);
AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
retVal.setSmtpServerHostname(email.getHost());
retVal.setSmtpServerPort(email.getPort());
retVal.setSmtpServerUsername(email.getUsername());
retVal.setSmtpServerPassword(email.getPassword());
retVal.setAuth(email.getAuth());
retVal.setStartTlsEnable(email.getStartTlsEnable());
retVal.setStartTlsRequired(email.getStartTlsRequired());
retVal.setQuitWait(email.getQuitWait());
if(subscriptionDeliveryHandlerFactory.isPresent())
subscriptionDeliveryHandlerFactory.get().setEmailSender(retVal);
return retVal;
}

11
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
View File

@@ -2,16 +2,21 @@ package ca.uhn.fhir.jpa.starter;
import javax.servlet.ServletException;
import javax.servlet.annotation.WebServlet;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Import;
@WebServlet(urlPatterns = {"/fhir/*"})
@WebServlet(urlPatterns = {"/hapi-fhir-jpaserver/fhir/*"})
@Import(AppProperties.class)
public class JpaRestfulServer extends BaseJpaRestfulServer {
@Autowired
AppProperties appProperties;
private static final long serialVersionUID = 1L;
public JpaRestfulServer(AppProperties appProperties) {
super(appProperties);
public JpaRestfulServer() {
super();
}
@Override

133
src/main/resources/application.yaml
View File

@@ -1,6 +1,6 @@
spring:
datasource:
url: 'jdbc:h2:file:./target/database/h2dflkjglkj'
url: 'jdbc:h2:file:./target/database/h2'
username: sa
password: null
driverClassName: org.h2.Driver
@@ -10,42 +10,57 @@ spring:
active: r4
hapi:
fhir:
allow_cascading_deletes: true
allow_contains_searches: true
allow_external_references: true
allow_multiple_delete: true
allow_override_default_search_params: true
allow_placeholder_references: true
auto_create_placeholder_reference_targets: false
default_encoding: JSON
default_page_size: 20
enable_index_missing_fields: false
enforce_referential_integrity_on_delete: false
enforce_referential_integrity_on_write: false
etag_support_enabled: true
expunge_enabled: true
daoconfig_client_id_strategy: null
fhirpath_interceptor_enabled: false
filter_search_enabled: true
graphql_enabled: true
logger:
error_format: 'ERROR - ${requestVerb} ${requestUrl}'
format: >-
Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
Operation[${operationType} ${operationName} ${idOrResourceName}]
UA[${requestHeader.user-agent}] Params[${requestParameters}]
ResponseEncoding[${responseEncodingNoDefault}]
log_exceptions: true
name: fhirtest.access
max_binary_size: 104857600
max_page_size: 200
retain_cached_searches_mins: 60
reuse_cached_search_results_millis: 60000
#supported_resource_types:
# - Patient
# - Observation
# allow_cascading_deletes: true
# allow_contains_searches: true
# allow_external_references: true
# allow_multiple_delete: true
# allow_override_default_search_params: true
# allow_placeholder_references: true
# auto_create_placeholder_reference_targets: false
# default_encoding: JSON
# default_pretty_print: true
# default_page_size: 20
# enable_index_missing_fields: false
# enforce_referential_integrity_on_delete: false
# enforce_referential_integrity_on_write: false
# etag_support_enabled: true
# expunge_enabled: true
# daoconfig_client_id_strategy: null
# fhirpath_interceptor_enabled: false
# filter_search_enabled: true
# graphql_enabled: true
#partitioning:
# cross_partition_reference_mode: true
# multitenancy_enabled: true
# partitioning_include_in_search_hashes: true
#cors:
# allow_Credentials: true
# Supports multiple, comma separated allowed origin entries
# cors.allowed_origin=http://localhost:8080,https://localhost:8080,https://fhirtest.uhn.ca
# allowed_origin:
# - '*'
# logger:
# error_format: 'ERROR - ${requestVerb} ${requestUrl}'
# format: >-
# Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
# Operation[${operationType} ${operationName} ${idOrResourceName}]
# UA[${requestHeader.user-agent}] Params[${requestParameters}]
# ResponseEncoding[${responseEncodingNoDefault}]
# log_exceptions: true
# name: fhirtest.access
# max_binary_size: 104857600
# max_page_size: 200
# retain_cached_searches_mins: 60
# reuse_cached_search_results_millis: 60000
tester:
-
id: home
name: Local Tester
server_address: 'http://localhost:8080/fhir'
server_address: 'http://localhost:8080/hapi-fhir-jpaserver/fhir'
refuse_to_fetch_third_party_urls: false
fhir_version: R4
-
@@ -54,23 +69,35 @@ hapi:
server_address: "http://hapi.fhir.org/baseR4"
refuse_to_fetch_third_party_urls: false
fhir_version: R4
validation:
requests_enabled: true
responses_enabled: true
binary_storage_enabled: true
bulk_export_enabled: true
partitioning_multitenancy_enabled:
subscription:
email_enabled: false
resthook_enabled: false
websocket_enabled: false
elasticsearch:
debug:
pretty_print_json_log: false
refresh_after_write: false
enabled: false
password: SomePassword
required_index_status: YELLOW
rest_url: 'http://localhost:9200'
schema_management_strategy: CREATE
username: SomeUsername
# validation:
# requests_enabled: true
# responses_enabled: true
# binary_storage_enabled: true
# bulk_export_enabled: true
# partitioning_multitenancy_enabled:
# subscription:
# resthook_enabled: false
# websocket_enabled: false
# email:
# from: some@test.com
# host: google.com
# port:
# username:
# password:
# auth:
# startTlsEnable:
# startTlsRequired:
# quitWait:
#
#elasticsearch:
# debug:
# pretty_print_json_log: false
# refresh_after_write: false
# enabled: false
# password: SomePassword
# required_index_status: YELLOW
# rest_url: 'http://localhost:9200'
# schema_management_strategy: CREATE
# username: SomeUsername

9
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java
View File

@@ -26,10 +26,10 @@ public class ExampleServerDstu2IT {
private static Server ourServer;
static {
HapiProperties.forceReload();
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "DSTU2");
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr2");
ourCtx = FhirContext.forDstu2();
System.setProperty("spring.profiles.active", "dstu2");
System.setProperty("spring.batch.job.enabled", "false");
System.setProperty("spring.datasource.url", "jdbc:h2:mem:dbr2");
}
@Test
@@ -60,7 +60,8 @@ public class ExampleServerDstu2IT {
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/hapi-fhir-jpaserver");
webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
webAppContext.setParentLoaderPriority(true);