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Issue #2342 - add support for TerminologyCapabilities #2347

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merged 4 commits into from
May 12, 2021
Merged

Issue #2342 - add support for TerminologyCapabilities #2347

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cdaa93f
Issue #2342 - add support for TerminologyCapabilities
JohnTimm May 11, 2021
c7c5686
Issue #2342 - formatting
JohnTimm May 11, 2021
158c09b
Issue #2342 - more formatting
JohnTimm May 11, 2021
3d912e4
Issue #2342 - updates per PR comments
JohnTimm May 11, 2021
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24 changes: 24 additions & 0 deletions fhir-registry/src/main/java/com/ibm/fhir/registry/FHIRRegistry.java
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Original file line number Diff line number Diff line change
Expand Up @@ -165,6 +165,8 @@ public <T extends Resource> T getResource(String url, Class<T> resourceType) {
/**
* Get the resources for the given resource type
*
* <p>Use this method to get actual FHIR resources and not FHIR registry resources (metadata)
*
* @param resourceType
* the resource type
* @return
Expand All @@ -184,6 +186,28 @@ public <T extends Resource> Collection<T> getResources(Class<T> resourceType) {
return Collections.unmodifiableList(resources);
}

/**
* Get the registry resources for the given resource type
*
* <p>Use this method to get FHIR registry resources (metadata) and not actual FHIR resources
*
* @param resourceType
* the resource type
* @return
* the registry resources for the given resource type
* @throws IllegalArgumentException
* if the resource type is not a definitional resource type
*/
public Collection<FHIRRegistryResource> getRegistryResources(Class<? extends Resource> resourceType) {
Objects.requireNonNull(resourceType);
requireDefinitionalResourceType(resourceType);
List<FHIRRegistryResource> registryResources = new ArrayList<>();
for (FHIRRegistryResourceProvider provider : providers) {
registryResources.addAll(provider.getRegistryResources(resourceType));
}
return registryResources;
}

/**
* Get the search parameters with the given search parameter type (e.g. string, token, etc.)
*
Expand Down
109 changes: 101 additions & 8 deletions fhir-server/src/main/java/com/ibm/fhir/server/resources/Capabilities.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
Expand All @@ -34,9 +35,11 @@
import java.util.stream.Collectors;

import javax.ws.rs.Consumes;
import javax.ws.rs.DefaultValue;
import javax.ws.rs.GET;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.QueryParam;
import javax.ws.rs.core.CacheControl;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
Expand All @@ -54,10 +57,16 @@
import com.ibm.fhir.model.resource.CapabilityStatement.Rest;
import com.ibm.fhir.model.resource.CapabilityStatement.Rest.Resource.Interaction;
import com.ibm.fhir.model.resource.CapabilityStatement.Rest.Resource.Operation;
import com.ibm.fhir.model.resource.CodeSystem;
import com.ibm.fhir.model.resource.DomainResource;
import com.ibm.fhir.model.resource.OperationDefinition;
import com.ibm.fhir.model.resource.Resource;
import com.ibm.fhir.model.resource.SearchParameter;
import com.ibm.fhir.model.resource.TerminologyCapabilities;
import com.ibm.fhir.model.resource.TerminologyCapabilities.Closure;
import com.ibm.fhir.model.resource.TerminologyCapabilities.Expansion;
import com.ibm.fhir.model.resource.TerminologyCapabilities.Translation;
import com.ibm.fhir.model.resource.TerminologyCapabilities.ValidateCode;
import com.ibm.fhir.model.type.Canonical;
import com.ibm.fhir.model.type.Code;
import com.ibm.fhir.model.type.CodeableConcept;
Expand All @@ -67,6 +76,7 @@
import com.ibm.fhir.model.type.Markdown;
import com.ibm.fhir.model.type.Uri;
import com.ibm.fhir.model.type.code.CapabilityStatementKind;
import com.ibm.fhir.model.type.code.CodeSearchSupport;
import com.ibm.fhir.model.type.code.ConditionalDeleteStatus;
import com.ibm.fhir.model.type.code.ConditionalReadStatus;
import com.ibm.fhir.model.type.code.FHIRVersion;
Expand All @@ -79,6 +89,7 @@
import com.ibm.fhir.model.util.ModelSupport;
import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.registry.resource.FHIRRegistryResource;
import com.ibm.fhir.search.util.SearchUtil;
import com.ibm.fhir.server.FHIRBuildIdentifier;
import com.ibm.fhir.server.operation.FHIROperationRegistry;
Expand All @@ -96,6 +107,7 @@ public class Capabilities extends FHIRResource {
// Constants
private static final String FHIR_SERVER_NAME = "IBM FHIR Server";
private static final String FHIR_COPYRIGHT = "(C) Copyright IBM Corporation 2016, 2021";
private static final String FHIR_PUBLISHER = "IBM Corporation";
private static final String EXTENSION_URL = "http://ibm.com/fhir/extension";
private static final String BASE_CAPABILITY_URL = "http://hl7.org/fhir/CapabilityStatement/base";
private static final String BASE_2_CAPABILITY_URL = "http://hl7.org/fhir/CapabilityStatement/base2";
Expand All @@ -108,7 +120,6 @@ public class Capabilities extends FHIRResource {
private static final String ERROR_MSG = "Caught exception while processing 'metadata' request.";
private static final String ERROR_CONSTRUCTING = "An error occurred while constructing the Conformance statement.";

private static final Object PRESENT = new Object();
private static final String CAPABILITY_STATEMENT_CACHE_NAME = "com.ibm.fhir.server.resources.Capabilities.statementCache";

// Constructor
Expand All @@ -118,25 +129,31 @@ public Capabilities() throws Exception {

@GET
@Path("metadata")
public Response capabilities() {
public Response capabilities(@QueryParam("mode") @DefaultValue("full") String mode) {
log.entering(this.getClass().getName(), "capabilities()");
try {
Date startTime = new Date();
checkInitComplete();

if (!isValidMode(mode)) {
throw new IllegalArgumentException("Invalid mode parameter: must be one of [full, normative, terminology]");
}

// Defaults to 60 minutes (or what's in the fhirConfig)
int cacheTimeout = FHIRConfigHelper.getIntProperty(PROPERTY_CAPABILITY_STATEMENT_CACHE, 60);
Configuration configuration = Configuration.of(Duration.of(cacheTimeout, ChronoUnit.MINUTES));

Map<Object, CapabilityStatement> cacheAsMap = CacheManager.getCacheAsMap(CAPABILITY_STATEMENT_CACHE_NAME, configuration);
CapabilityStatement capabilityStatement = cacheAsMap.computeIfAbsent(PRESENT, k -> computeCapabilityStatement());
Map<String, Resource> cacheAsMap = CacheManager.getCacheAsMap(CAPABILITY_STATEMENT_CACHE_NAME, configuration);
Resource capabilityStatement = cacheAsMap.computeIfAbsent(mode, k -> computeCapabilityStatement(mode));

RestAuditLogger.logMetadata(httpServletRequest, startTime, new Date(), Response.Status.OK);

CacheControl cacheControl = new CacheControl();
cacheControl.setPrivate(true);
cacheControl.setMaxAge(60 * cacheTimeout);
return Response.ok().entity(capabilityStatement).cacheControl(cacheControl).build();
} catch (IllegalArgumentException e) {
return exceptionResponse(e, Response.Status.BAD_REQUEST);
} catch (RuntimeException e) {
FHIROperationException foe = buildRestException(ERROR_CONSTRUCTING, IssueType.EXCEPTION);
if (e.getCause() != null) {
Expand All @@ -153,14 +170,90 @@ public Response capabilities() {
}
}

private CapabilityStatement computeCapabilityStatement() {
private boolean isValidMode(String mode) {
return "full".equals(mode) || "normative".equals(mode) || "terminology".equals(mode);
}

private Resource computeCapabilityStatement(String mode) {
try {
return buildCapabilityStatement();
switch (mode) {
case "terminology":
return buildTerminologyCapabilities();
case "full":
case "normative":
default:
return buildCapabilityStatement();
}
} catch (Exception e) {
throw new RuntimeException(e);
}
}

private TerminologyCapabilities buildTerminologyCapabilities() {
FHIRBuildIdentifier buildInfo = new FHIRBuildIdentifier();
String buildDescription = FHIR_SERVER_NAME + " version " + buildInfo.getBuildVersion() + " build id " + buildInfo.getBuildId() + "";
return TerminologyCapabilities.builder()
.status(PublicationStatus.ACTIVE)
.date(DateTime.now(ZoneOffset.UTC))
.kind(CapabilityStatementKind.INSTANCE)
.version(string(buildInfo.getBuildVersion()))
.name(string(FHIR_SERVER_NAME))
.description(Markdown.of(buildDescription))
.copyright(Markdown.of(FHIR_COPYRIGHT))
.publisher(string(FHIR_PUBLISHER))
.software(TerminologyCapabilities.Software.builder()
.name(string(FHIR_SERVER_NAME))
.version(string(buildInfo.getBuildVersion()))
.id(buildInfo.getBuildId())
.build())
.codeSystem(buildCodeSystem())
.expansion(Expansion.builder()
.hierarchical(com.ibm.fhir.model.type.Boolean.FALSE)
.paging(com.ibm.fhir.model.type.Boolean.FALSE)
.incomplete(com.ibm.fhir.model.type.Boolean.FALSE)
.textFilter(Markdown.of("Text searching is not supported"))
.build())
.codeSearch(CodeSearchSupport.ALL)
.validateCode(ValidateCode.builder()
.translations(com.ibm.fhir.model.type.Boolean.FALSE)
.build())
.translation(Translation.builder()
.needsMap(com.ibm.fhir.model.type.Boolean.TRUE)
.build())
.closure(Closure.builder()
.translation(com.ibm.fhir.model.type.Boolean.FALSE)
.build())
.build();
}

private List<TerminologyCapabilities.CodeSystem> buildCodeSystem() {
Map<String, List<TerminologyCapabilities.CodeSystem.Version>> versionMap = new LinkedHashMap<>();

for (FHIRRegistryResource registryResource : FHIRRegistry.getInstance().getRegistryResources(CodeSystem.class)) {
String url = registryResource.getUrl();
FHIRRegistryResource.Version version = registryResource.getVersion();

List<TerminologyCapabilities.CodeSystem.Version> versions = versionMap.computeIfAbsent(url, k -> new ArrayList<>());
if (!FHIRRegistryResource.NO_VERSION.equals(version)) {
versions.add(TerminologyCapabilities.CodeSystem.Version.builder()
.code(string(version.toString()))
.build());
}
}

List<TerminologyCapabilities.CodeSystem> codeSystems = new ArrayList<>(versionMap.keySet().size());

for (String url : versionMap.keySet()) {
List<TerminologyCapabilities.CodeSystem.Version> versions = versionMap.get(url);
codeSystems.add(TerminologyCapabilities.CodeSystem.builder()
.uri(Canonical.of(url))
.version(versions)
.build());
}

return codeSystems;
}

/**
* Builds a CapabilityStatement resource instance which describes this server.
*
Expand Down Expand Up @@ -390,7 +483,7 @@ private CapabilityStatement buildCapabilityStatement() throws Exception {
CapabilityStatement conformance = CapabilityStatement.builder()
.status(PublicationStatus.ACTIVE)
.date(DateTime.now(ZoneOffset.UTC))
.kind(CapabilityStatementKind.CAPABILITY)
.kind(CapabilityStatementKind.INSTANCE)
.fhirVersion(FHIRVersion.VERSION_4_0_1)
.format(format)
.patchFormat(Code.of(FHIRMediaType.APPLICATION_JSON_PATCH),
Expand All @@ -400,7 +493,7 @@ private CapabilityStatement buildCapabilityStatement() throws Exception {
.name(string(FHIR_SERVER_NAME))
.description(Markdown.of(buildDescription))
.copyright(Markdown.of(FHIR_COPYRIGHT))
.publisher(string("IBM Corporation"))
.publisher(string(FHIR_PUBLISHER))
.software(CapabilityStatement.Software.builder()
.name(string(FHIR_SERVER_NAME))
.version(string(buildInfo.getBuildVersion()))
Expand Down
10 changes: 5 additions & 5 deletions fhir-server/src/test/java/com/ibm/fhir/server/test/CapabilitiesTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ void testBuildCapabilityStatement_resources_omitted() throws Exception {
FHIRRequestContext.get().setOriginalRequestUri("http://example.com/metadata");
CapabilitiesChild c = new CapabilitiesChild();

Response capabilities = c.capabilities();
Response capabilities = c.capabilities("full");
CapabilityStatement capabilityStatement = capabilities.readEntity(CapabilityStatement.class);

assertEquals(capabilityStatement.getRest().size(), 1, "Number of REST Elements");
Expand All @@ -60,7 +60,7 @@ void testBuildCapabilityStatement_resources_empty() throws Exception {
FHIRRequestContext.get().setOriginalRequestUri("http://example.com/metadata");
CapabilitiesChild c = new CapabilitiesChild();

Response capabilities = c.capabilities();
Response capabilities = c.capabilities("full");
CapabilityStatement capabilityStatement = capabilities.readEntity(CapabilityStatement.class);

assertEquals(capabilityStatement.getRest().size(), 1, "Number of REST Elements");
Expand All @@ -75,7 +75,7 @@ void testBuildCapabilityStatement_resources_filtered() throws Exception {
FHIRRequestContext.get().setOriginalRequestUri("http://example.com/metadata");
CapabilitiesChild c = new CapabilitiesChild();

Response capabilities = c.capabilities();
Response capabilities = c.capabilities("full");
CapabilityStatement capabilityStatement = capabilities.readEntity(CapabilityStatement.class);

assertEquals(capabilityStatement.getRest().size(), 1, "Number of REST Elements");
Expand Down Expand Up @@ -121,9 +121,9 @@ public CapabilitiesChild() throws Exception {
}

@Override
public Response capabilities() {
public Response capabilities(String mode) {
httpServletRequest = new MockHttpServletRequest();
return super.capabilities();
return super.capabilities(mode);
}
}
}