Personal-Twin/hapi-fhir-jpaserver-starter
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just need to merge the email TLS

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This commit is contained in:
Ken Stevens
2020-05-27 17:04:39 -04:00
parent f598dd8e1f
commit 0c9b9f7f77
10 changed files with 248 additions and 181 deletions
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9
pom.xml
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@@ -12,7 +12,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.0.0-SNAPSHOT</version>
<version>5.1.0-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -255,7 +255,12 @@
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<version>4.0.0-rc1</version>
<scope>test</scope>
</dependency>
</dependencies>
<packaging>war</packaging>

4
src/main/java/ca/uhn/fhir/jpa/starter/EmpiConfig.java
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@@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.empi.api.IEmpiSettings;
import ca.uhn.fhir.empi.rules.config.EmpiSettingsImpl;
import ca.uhn.fhir.empi.rules.config.EmpiSettings;
import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
import com.google.common.base.Charsets;
@@ -22,6 +22,6 @@ public class EmpiConfig {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("empi-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
return new EmpiSettingsImpl().setEnabled(HapiProperties.getEmpiEnabled()).setScriptText(json);
return new EmpiSettings().setEnabled(HapiProperties.getEmpiEnabled()).setScriptText(json);
}
}

9
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -201,11 +201,10 @@ public class FhirServerConfigCommon {
retVal.setSmtpServerPort(this.emailPort);
retVal.setSmtpServerUsername(this.emailUsername);
retVal.setSmtpServerPassword(this.emailPassword);
// FIXME KHS add these once this has merged in hapi
// retVal.setAuth(this.emailAuth);
// retVal.setStartTlsEnable(this.emailStartTlsEnable);
// retVal.setStartTlsRequired(this.emailStartTlsRequired);
// retVal.setQuitWait(this.emailQuitWait);
retVal.setAuth(this.emailAuth);
retVal.setStartTlsEnable(this.emailStartTlsEnable);
retVal.setStartTlsRequired(this.emailStartTlsRequired);
retVal.setQuitWait(this.emailQuitWait);
Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);

16
src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
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@@ -58,6 +58,10 @@ public class HapiProperties {
static final String SUBSCRIPTION_RESTHOOK_ENABLED = "subscription.resthook.enabled";
static final String SUBSCRIPTION_WEBSOCKET_ENABLED = "subscription.websocket.enabled";
static final String EMPI_ENABLED = "empi.enabled";
static final String PARTITIONING_ENABLED = "partitioning.enabled";
static final String PARTITIONING_CROSS_PARTITION_REFERENCE_MODE = "partitioning.cross_partition_reference_mode";
private static final String PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES = "partitioning.partitioning_include_in_search_hashes";
static final String ALLOWED_BUNDLE_TYPES = "allowed_bundle_types";
static final String TEST_PORT = "test.port";
static final String TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS = "tester.config.refuse_to_fetch_third_party_urls";
@@ -378,6 +382,18 @@ public class HapiProperties {
return HapiProperties.getBooleanProperty(EMPI_ENABLED, false);
}
public static Boolean getPartitioningEnabled() {
return HapiProperties.getBooleanProperty(PARTITIONING_ENABLED, false);
}
public static String getPartitioningCrossPartitionReferenceMode() {
return HapiProperties.getProperty(PARTITIONING_CROSS_PARTITION_REFERENCE_MODE, "NOT_ALLOWED");
}
public static Boolean getIncludePartitionInSearchHashes() {
return HapiProperties.getBooleanProperty(PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES, true);
}
public static Boolean getAllowContainsSearches() {
return HapiProperties.getBooleanProperty(ALLOW_CONTAINS_SEARCHES, true);
}

49
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
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@@ -2,6 +2,9 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.empi.provider.EmpiProviderDstu3;
import ca.uhn.fhir.empi.provider.EmpiProviderR4;
import ca.uhn.fhir.empi.rules.config.EmpiSettings;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
@@ -10,6 +13,8 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
@@ -37,11 +42,9 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import java.util.HashSet;
import java.util.TreeSet;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.springframework.context.ApplicationContext;
import org.springframework.http.HttpHeaders;
import org.springframework.web.cors.CorsConfiguration;
@@ -49,7 +52,9 @@ import org.springframework.web.cors.CorsConfiguration;
import javax.servlet.ServletException;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
import java.util.TreeSet;
public class JpaRestfulServer extends RestfulServer {
@@ -287,31 +292,7 @@ public class JpaRestfulServer extends RestfulServer {
}
// Validation
IValidatorModule validatorModule;
// FIXME KHS
/*
switch (fhirVersion) {
case DSTU2:
validatorModule = appCtx.getBean("myInstanceValidatorDstu2", IValidatorModule.class);
break;
case DSTU3:
validatorModule = appCtx.getBean("myInstanceValidatorDstu3", IValidatorModule.class);
break;
case R4:
validatorModule = appCtx.getBean("myInstanceValidatorR4", IValidatorModule.class);
break;
case R5:
validatorModule = appCtx.getBean("myInstanceValidatorR5", IValidatorModule.class);
break;
// These versions are not supported by HAPI FHIR JPA
case DSTU2_HL7ORG:
case DSTU2_1:
default:
validatorModule = null;
break;
}
*/
validatorModule = appCtx.getBean(IValidatorModule.class);
IValidatorModule validatorModule = appCtx.getBean(IValidatorModule.class);
if (validatorModule != null) {
if (HapiProperties.getValidateRequestsEnabled()) {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
@@ -351,11 +332,13 @@ public class JpaRestfulServer extends RestfulServer {
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
}
if (HapiProperties.getEmpiEnabled()) {
// FIXME KHS
if (HapiProperties.getPartitioningEnabled()) {
PartitionSettings partitionSettings = appCtx.getBean(PartitionSettings.class);
partitionSettings.setPartitioningEnabled(true);
PartitionSettings.CrossPartitionReferenceMode mode = PartitionSettings.CrossPartitionReferenceMode.valueOf(HapiProperties.getPartitioningCrossPartitionReferenceMode());
partitionSettings.setAllowReferencesAcrossPartitions(mode);
partitionSettings.setIncludePartitionInSearchHashes(HapiProperties.getIncludePartitionInSearchHashes());
registerProvider(appCtx.getBean(PartitionManagementProvider.class));
}
}
}

17
src/main/resources/empi-rules.json
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@@ -1,30 +1,33 @@
{
"resourceSearchParams" : [ {
"candidateSearchParams" : [ {
"resourceType" : "Patient",
"searchParam" : "birthdate"
}, {
"resourceType" : "All",
"resourceType" : "*",
"searchParam" : "identifier"
},{
"resourceType" : "Patient",
"searchParam" : "general-practitioner"
} ],
"filterSearchParams" : [ {
"resourceType" : "All",
"candidateFilterSearchParams" : [ {
"resourceType" : "*",
"searchParam" : "active",
"fixedValue" : "true"
} ],
"matchFields" : [ {
"name" : "given-name",
"resourceType" : "All",
"resourceType" : "*",
"resourcePath" : "name.given",
"metric" : "COSINE",
"matchThreshold" : 0.8
}, {
"name" : "last-name",
"resourceType" : "All",
"resourceType" : "*",
"resourcePath" : "name.family",
"metric" : "JARO_WINKLER",
"matchThreshold" : 0.8
}],
"weightMap" : {
"matchResultMap" : {
"given-name" : "POSSIBLE_MATCH",
"given-name,last-name" : "MATCH"
},

7
src/main/resources/hapi.properties
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@@ -148,7 +148,10 @@ email.password=
# Enable Websocket Subscription Channel
subscription.websocket.enabled=false
########
# EMPI
########
empi.enabled=false
# Partitioning
partitioning.enabled=false
partitioning.cross_partition_reference_mode=NOT_ALLOWED
partitioning.partitioning_include_in_search_hashes=true

19
src/main/resources/logback.xml
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@@ -9,6 +9,25 @@
</encoder>
</appender>
<appender name="EMPI_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter"><level>DEBUG</level></filter>
<file>${smile.basedir}/log/empi-troubleshooting.log</file>
<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
<fileNamePattern>${smile.basedir}/log/empi-troubleshooting.log.%i.gz</fileNamePattern>
<minIndex>1</minIndex>
<maxIndex>9</maxIndex>
</rollingPolicy>
<triggeringPolicy class="ch.qos.logback.core.rolling.SizeBasedTriggeringPolicy">
<maxFileSize>5MB</maxFileSize>
</triggeringPolicy>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n${log.stackfilter.pattern}</pattern>
</encoder>
</appender>
<logger name="ca.uhn.fhir.log.empi_troubleshooting" level="TRACE">
<appender-ref ref="EMPI_TROUBLESHOOTING"/>
</logger>
<root level="INFO">
<appender-ref ref="STDOUT" />
</root>

37
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
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@@ -8,6 +8,7 @@ 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 ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.BundleUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
import org.eclipse.jetty.websocket.api.Session;
@@ -17,6 +18,8 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Person;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Subscription;
import org.junit.AfterClass;
import org.junit.BeforeClass;
@@ -24,11 +27,16 @@ import org.junit.Test;
import java.net.URI;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.awaitility.Awaitility.await;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
public class ExampleServerR4IT {
@@ -43,6 +51,7 @@ public class ExampleServerR4IT {
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr4");
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R4");
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
HapiProperties.setProperty(HapiProperties.EMPI_ENABLED, "true");
ourCtx = FhirContext.forR4();
}
@@ -57,6 +66,28 @@ public class ExampleServerR4IT {
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
// Test EMPI
// Wait until the EMPI message has been processed
await().until(() -> getPeople().size() > 0);
List<Person> persons = getPeople();
// Verify a Person was created that links to our Patient
Optional<String> personLinkToCreatedPatient = persons.stream()
.map(Person::getLink)
.flatMap(Collection::stream)
.map(Person.PersonLinkComponent::getTarget)
.map(Reference::getReference)
.filter(pid -> id.toUnqualifiedVersionless().getValue().equals(pid))
.findAny();
assertTrue(personLinkToCreatedPatient.isPresent());
}
private List<Person> getPeople() {
Bundle bundle = ourClient.search().forResource(Person.class).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
return BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Person.class);
}
@Test
@@ -78,7 +109,7 @@ public class ExampleServerR4IT {
IIdType mySubscriptionId = methodOutcome.getId();
// Wait for the subscription to be activated
waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
await().until(() -> activeSubscriptionCount() == 3);
/*
* Attach websocket
@@ -117,6 +148,10 @@ public class ExampleServerR4IT {
ourClient.delete().resourceById(mySubscriptionId).execute();
}
private int activeSubscriptionCount() {
return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();

22
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java
View File

@@ -14,7 +14,13 @@ import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Subscription;
import org.hl7.fhir.r5.model.SubscriptionTopic;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
@@ -62,7 +68,7 @@ public class ExampleServerR5IT {
/*
* Create topic
*/
Topic topic = new Topic();
SubscriptionTopic topic = new SubscriptionTopic();
topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
/*
@@ -71,14 +77,12 @@ public class ExampleServerR5IT {
Subscription subscription = new Subscription();
subscription.getTopic().setResource(topic);
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
channel.getType().addCoding()
.setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
.setCode("websocket");
channel.getPayload().setContentType("application/json");
subscription.setChannel(channel);
subscription.setContentType("application/json");
Coding channelType = new Coding().setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
.setCode("websocket");;
subscription.setChannelType(channelType);
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();