issue #2143 - support custom compartment types via extension

The CompartmentDefinition resource has a required binding to a fixed list of compartment types. To support a custom compartments, we will now look for the `http://ibm.com/fhir/extension/custom-compartment-type` extension on this element (when it has no value). Additionally, I created a constant in fhir-core FHIRConstants for our base extension url and I updated all the different places we have extension urls to use it. Finally, I included a couple extra changes that I had sitting around for the FHIR Registry. If desired, I can split these out into a separate PR. Signed-off-by: Lee Surprenant <[email protected]>
LinuxForHealth · May 27, 2021 · 3a6f57d · 3a6f57d
1 parent 95123b0
commit 3a6f57d
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diff --git a/...avinci-pdex/src/test/java/com/ibm/fhir/ig/davinci/pdex/tool/SearchParameterAugmenter.java b/...avinci-pdex/src/test/java/com/ibm/fhir/ig/davinci/pdex/tool/SearchParameterAugmenter.java
@@ -15,6 +15,7 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import com.ibm.fhir.core.FHIRConstants;
 import com.ibm.fhir.model.format.Format;
 import com.ibm.fhir.model.generator.FHIRGenerator;
 import com.ibm.fhir.model.resource.SearchParameter;
@@ -35,7 +36,7 @@
  * to search parameters which always reference code values with a particular system
  */
 public class SearchParameterAugmenter {
-    private static final String IMPLICIT_SYSTEM_EXT_URL = "http://ibm.com/fhir/extension/implicit-system";
+    private static final String IMPLICIT_SYSTEM_EXT_URL = FHIRConstants.EXT_BASE + "implicit-system";
     private static final FHIRGenerator generator = FHIRGenerator.generator(Format.JSON, false);
 
     public static void main(String[] args) throws Exception {

diff --git a/.../fhir-ig-us-core/src/test/java/com/ibm/fhir/ig/us/core/tool/SearchParameterAugmenter.java b/.../fhir-ig-us-core/src/test/java/com/ibm/fhir/ig/us/core/tool/SearchParameterAugmenter.java
@@ -15,6 +15,7 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import com.ibm.fhir.core.FHIRConstants;
 import com.ibm.fhir.model.format.Format;
 import com.ibm.fhir.model.generator.FHIRGenerator;
 import com.ibm.fhir.model.resource.SearchParameter;
@@ -35,7 +36,7 @@
  * to search parameters which always reference code values with a particular system
  */
 public class SearchParameterAugmenter {
-    private static final String IMPLICIT_SYSTEM_EXT_URL = "http://ibm.com/fhir/extension/implicit-system";
+    private static final String IMPLICIT_SYSTEM_EXT_URL = FHIRConstants.EXT_BASE + "implicit-system";
     private static final FHIRGenerator generator = FHIRGenerator.generator(Format.JSON, false);
 
     public static void main(String[] args) throws Exception {

diff --git a/fhir-client/src/test/java/com/ibm/fhir/client/test/mains/JaxrsClientTestMain.java b/fhir-client/src/test/java/com/ibm/fhir/client/test/mains/JaxrsClientTestMain.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2016,2019
+ * (C) Copyright IBM Corp. 2016, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -38,54 +38,54 @@
 import com.ibm.fhir.provider.FHIRProvider;
 
 public class JaxrsClientTestMain {
-    
+
     public static void main(String[] args) throws Exception {
         Patient patient = buildPatient();
         System.out.println("\nJSON:");
-        
+
         FHIRGenerator.generator( Format.JSON, false).generate(patient, System.out);
         System.out.println("\nXML:");
         FHIRGenerator.generator( Format.XML, false).generate(patient, System.out);
-        
+
         Client client = ClientBuilder.newBuilder()
                 .register(new FHIRProvider(RuntimeType.CLIENT))
                 .build();
-        
+
         WebTarget target = client.target("http://localhost:9080/fhir-server/api/v4");
         Entity<Patient> entity = Entity.entity(patient, FHIRMediaType.APPLICATION_FHIR_XML);
         Response response = target.path("Patient").request().post(entity, Response.class);
-        
+
         if (Response.Status.CREATED.getStatusCode() == response.getStatus()) {
             System.out.println("");
             System.out.println(response.getStatus());
             System.out.println(response.getStatusInfo().getReasonPhrase());
             String location = response.getLocation().toString();
             System.out.println("location: " + location);
-            
+
             String id = location.substring(location.lastIndexOf("/") + 1);
             response = target.path("Patient/" + id).request(FHIRMediaType.APPLICATION_FHIR_JSON).get();
             patient = response.readEntity(Patient.class);
             System.out.println("\nJSON:");
             FHIRGenerator.generator( Format.JSON, false).generate(patient, System.out);
             System.out.println("\nXML:");
             FHIRGenerator.generator( Format.XML, false).generate(patient, System.out);
-                        
+
             Observation observation = buildObservation(id);
             System.out.println("\nJSON:");
             FHIRGenerator.generator( Format.JSON, false).generate(observation, System.out);
             System.out.println("\nXML:");
             FHIRGenerator.generator( Format.XML, false).generate(observation, System.out);
-            
+
             Entity<Observation> observationEntity = Entity.entity(observation, FHIRMediaType.APPLICATION_FHIR_JSON);
             response = target.path("Observation").request().post(observationEntity, Response.class);
-            
+
             if (Response.Status.CREATED.getStatusCode() == response.getStatus()) {
                 System.out.println("");
                 System.out.println(response.getStatus());
                 System.out.println(response.getStatusInfo().getReasonPhrase());
                 location = response.getLocation().toString();
                 System.out.println("location: " + location);
-                
+
                 response = target.path("Observation").queryParam("subject", "Patient/" + id).request(FHIRMediaType.APPLICATION_FHIR_JSON).get();
                 Bundle bundle = response.readEntity(Bundle.class);
                 System.out.println("\nJSON:");
@@ -105,7 +105,7 @@ public static void main(String[] args) throws Exception {
             System.out.println(response.readEntity(String.class));
         }
     }
-    
+
     public static Patient buildPatient() {
         Patient patient = Patient.builder().name(HumanName.builder()
                         .family(string("Doe"))
@@ -114,12 +114,12 @@ public static Patient buildPatient() {
                 .telecom(ContactPoint.builder().system(ContactPointSystem.PHONE)
                         .use(ContactPointUse.HOME).value(string("555-1234")).build())
                 .extension(Extension.builder().url("http://ibm.com/fhir/extension/Patient/favorite-color")
-                        .value(string("blue")).build()).build();        
+                        .value(string("blue")).build()).build();
         return patient;
     }
-    
+
     public static Observation buildObservation(String patientId) {
-        Observation observation = Observation.builder().status(ObservationStatus.FINAL).bodySite( 
+        Observation observation = Observation.builder().status(ObservationStatus.FINAL).bodySite(
                 CodeableConcept.builder().coding(Coding.builder().code(Code.of("55284-4"))
                         .system(Uri.of("http://loinc.org")).build())
                         .text(string("Blood pressure systolic & diastolic")).build())
@@ -135,8 +135,8 @@ public static Observation buildObservation(String patientId) {
                         .system(Uri.of("http://loinc.org")).build())
                         .text(string("Diastolic")).build())
                         .value(Quantity.builder().value(Decimal.of(93.7)).unit(string("mmHg")).build()).build())
-             .build();           
+             .build();
 
         return observation;
-    } 
+    }
 }
diff --git a/fhir-core/src/main/java/com/ibm/fhir/core/FHIRConstants.java b/fhir-core/src/main/java/com/ibm/fhir/core/FHIRConstants.java
@@ -37,6 +37,8 @@ public class FHIRConstants {
 
     public static final String UPDATE_IF_MODIFIED_HEADER = "X-FHIR-UPDATE-IF-MODIFIED";
 
+    public static final String EXT_BASE = "http://ibm.com/fhir/extension/";
+
     /**
      * General parameter names that can be used with any FHIR interaction.
      *

diff --git a/...stence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/impl/FHIRPersistenceJDBCImpl.java b/...stence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/impl/FHIRPersistenceJDBCImpl.java
@@ -1334,7 +1334,7 @@ private FHIRPersistenceNotSupportedException buildNotSupportedException(String m
                 .severity(IssueSeverity.FATAL)
                 .code(IssueType.NOT_SUPPORTED.toBuilder()
                         .extension(Extension.builder()
-                            .url("http://ibm.com/fhir/extension/not-supported-detail")
+                            .url(FHIRConstants.EXT_BASE + "not-supported-detail")
                             .value(Code.of("interaction"))
                             .build())
                         .build())

diff --git a/fhir-registry/src/main/java/com/ibm/fhir/registry/FHIRRegistry.java b/fhir-registry/src/main/java/com/ibm/fhir/registry/FHIRRegistry.java
@@ -22,6 +22,7 @@
 import java.util.Set;
 import java.util.concurrent.CopyOnWriteArrayList;
 import java.util.logging.Logger;
+import java.util.stream.Collectors;
 
 import com.ibm.fhir.model.resource.DomainResource;
 import com.ibm.fhir.model.resource.Resource;
@@ -177,13 +178,10 @@ public <T extends Resource> T getResource(String url, Class<T> resourceType) {
     public <T extends Resource> Collection<T> getResources(Class<T> resourceType) {
         Objects.requireNonNull(resourceType);
         requireDefinitionalResourceType(resourceType);
-        List<T> resources = new ArrayList<>();
-        for (FHIRRegistryResourceProvider provider : providers) {
-            for (FHIRRegistryResource registryResource : provider.getRegistryResources(resourceType)) {
-                resources.add(resourceType.cast(registryResource.getResource()));
-            }
-        }
-        return Collections.unmodifiableList(resources);
+        return providers.parallelStream()
+                .flatMap(p -> p.getRegistryResources(resourceType).stream())
+                .map(rr -> resourceType.cast(rr.getResource()))
+                .collect(Collectors.collectingAndThen(Collectors.toList(), Collections::unmodifiableList));
     }
 
     /**

diff --git a/fhir-registry/src/main/java/com/ibm/fhir/registry/resource/FHIRRegistryResource.java b/fhir-registry/src/main/java/com/ibm/fhir/registry/resource/FHIRRegistryResource.java
@@ -111,8 +111,8 @@ public boolean isDefaultVersion() {
         return defaultVersion;
     }
 
-    public Resource getResource() {
-        return resource;
+    public <T extends Resource> T getResource() {
+        return (T) resource;
     }
 
     public <T extends FHIRRegistryResource> boolean is(Class<T> registryResourceType) {

diff --git a/fhir-search/src/main/java/com/ibm/fhir/search/SearchConstants.java b/fhir-search/src/main/java/com/ibm/fhir/search/SearchConstants.java
@@ -15,6 +15,7 @@
 import java.util.Map;
 import java.util.Set;
 
+import com.ibm.fhir.core.FHIRConstants;
 import com.ibm.fhir.model.type.Code;
 import com.ibm.fhir.model.type.Coding;
 import com.ibm.fhir.model.type.Uri;
@@ -94,8 +95,7 @@ private SearchConstants() {
     // _has
     public static final String HAS = "_has";
 
-    public static final String BASE_SYSTEM_EXT_URL = "http://ibm.com/fhir/extension/";
-    public static final String IMPLICIT_SYSTEM_EXT_URL = BASE_SYSTEM_EXT_URL + "implicit-system";
+    public static final String IMPLICIT_SYSTEM_EXT_URL = FHIRConstants.EXT_BASE + "implicit-system";
 
     // Extracted search parameter suffix for :identifier modifier
     public static final String IDENTIFIER_MODIFIER_SUFFIX = ":identifier";

diff --git a/fhir-search/src/main/java/com/ibm/fhir/search/compartment/CompartmentUtil.java b/fhir-search/src/main/java/com/ibm/fhir/search/compartment/CompartmentUtil.java
@@ -14,8 +14,11 @@
 import java.util.Objects;
 import java.util.Set;
 
+import com.ibm.fhir.core.FHIRConstants;
 import com.ibm.fhir.model.resource.CompartmentDefinition;
 import com.ibm.fhir.model.resource.CompartmentDefinition.Resource;
+import com.ibm.fhir.model.type.code.CompartmentType;
+import com.ibm.fhir.model.util.FHIRUtil;
 import com.ibm.fhir.registry.FHIRRegistry;
 import com.ibm.fhir.search.exception.FHIRSearchException;
 import com.ibm.fhir.search.exception.SearchExceptionUtil;
@@ -36,6 +39,9 @@
  * Call {@link #init()} to initialize static members and avoid a slight performance hit on first use.
  */
 public class CompartmentUtil {
+    // The URL of the compartment subtype extension...useful for defining new compartments
+    public static final String CUSTOM_COMPARTMENT_TYPE_EXT = FHIRConstants.EXT_BASE + "custom-compartment-type";
+
     // Map of Compartment name to CompartmentCache
     private static final Map<String, CompartmentCache> compartmentMap = new HashMap<>();
 
@@ -76,7 +82,10 @@ public static final void buildMaps(Map<String, CompartmentCache> compMap, Map<St
 
         Collection<CompartmentDefinition> definitions = FHIRRegistry.getInstance().getResources(CompartmentDefinition.class);
         for (CompartmentDefinition compartmentDefinition : definitions) {
-            String compartmentName = compartmentDefinition.getCode().getValue();
+            CompartmentType type = compartmentDefinition.getCode();
+
+            String compartmentName = type.hasValue() ? type.getValue()
+                    : FHIRUtil.getExtensionStringValue(type, CUSTOM_COMPARTMENT_TYPE_EXT);
 
             // The cached object (a smaller/lighter lookup resource) used for point lookups
             CompartmentCache compartmentDefinitionCache = new CompartmentCache();
@@ -131,7 +140,7 @@ public static List<String> getCompartmentResourceTypeInclusionCriteria(final Str
     }
 
     /**
-     * checks that the compartment is valid, and throws and exception if, not
+     * checks that the compartment is valid and throws an exception if not
      *
      * @param compartment
      * @throws FHIRSearchException
@@ -144,7 +153,7 @@ public static void checkValidCompartment(final String compartment) throws FHIRSe
     }
 
     /**
-     * checks that the compartment and resource are valid, and throws and exception if, not
+     * checks that the compartment and resource are valid and throws an exception if not
      *
      * @param compartment
      * @throws FHIRSearchException

diff --git a/fhir-search/src/main/java/com/ibm/fhir/search/util/SearchUtil.java b/fhir-search/src/main/java/com/ibm/fhir/search/util/SearchUtil.java
@@ -6,6 +6,8 @@
 
 package com.ibm.fhir.search.util;
 
+import static com.ibm.fhir.model.util.ModelSupport.FHIR_STRING;
+
 import java.io.FileNotFoundException;
 import java.math.BigDecimal;
 import java.net.URISyntaxException;
@@ -43,6 +45,7 @@
 import com.ibm.fhir.model.resource.ValueSet;
 import com.ibm.fhir.model.type.Canonical;
 import com.ibm.fhir.model.type.Code;
+import com.ibm.fhir.model.type.Element;
 import com.ibm.fhir.model.type.Reference;
 import com.ibm.fhir.model.type.Uri;
 import com.ibm.fhir.model.type.code.IssueSeverity;
@@ -2587,24 +2590,46 @@ public static Map<String, Set<CompartmentReference>> extractCompartmentParameter
                         }
 
                         for (FHIRPathNode node : nodes) {
-                            Reference reference = node.asElementNode().element().as(Reference.class);
-                            ReferenceValue rv = ReferenceUtil.createReferenceValueFrom(reference, baseUrl);
-                            if (rv.getType() != ReferenceType.DISPLAY_ONLY && rv.getType() != ReferenceType.INVALID) {
-
-                                // Check that the target resource type of the reference matches one of the
-                                // target resource types in the compartment definition.
-                                final String compartmentName = rv.getTargetResourceType();
-                                if (paramEntry.getValue().contains(compartmentName)) {
-                                    // Add this reference to the set of references we're collecting for each compartment
-                                    CompartmentReference cref = new CompartmentReference(searchParm, compartmentName, rv.getValue());
-                                    Set<CompartmentReference> references = result.computeIfAbsent(compartmentName, k -> new HashSet<>());
-                                    references.add(cref);
+                            String compartmentName = null;
+                            String compartmentId = null;
+
+                            Element element = node.asElementNode().element();
+                            if (element.is(Reference.class)) {
+                                Reference reference = element.as(Reference.class);
+                                ReferenceValue rv = ReferenceUtil.createReferenceValueFrom(reference, baseUrl);
+                                if (rv.getType() != ReferenceType.DISPLAY_ONLY && rv.getType() != ReferenceType.INVALID) {
+                                    compartmentName = rv.getTargetResourceType();
+                                    compartmentId = rv.getValue();
+
+                                    // Check that the target resource type of the reference matches one of the
+                                    // target resource types in the compartment definition.
+                                    if (!paramEntry.getValue().contains(compartmentName)) {
+                                        if (log.isLoggable(Level.FINE)) {
+                                            log.fine("Skipping reference with value " + reference.getReference() + ";"
+                                                    + " target resource type does not match any of the allowed compartment types: " + paramEntry);
+                                        }
+                                        continue;
+                                    }
+                                }
+                            } else if (element.is(FHIR_STRING)) {
+                                if (paramEntry.getValue().size() != 1) {
+                                    log.warning("CompartmentDefinition inclusion criteria must be of type Reference unless they have 1 and only 1 resource target");
+                                    continue;
                                 }
+                                compartmentName = paramEntry.getValue().iterator().next();
+                                compartmentId = element.as(FHIR_STRING).getValue();
                             }
+
+                            // Add this reference to the set of references we're collecting for each compartment
+                            CompartmentReference cref = new CompartmentReference(searchParm, compartmentName, compartmentId);
+                            Set<CompartmentReference> references = result.computeIfAbsent(compartmentName, k -> new HashSet<>());
+                            references.add(cref);
                         }
                     } else if (!useStoredCompartmentParam()) {
-                       log.warning("Compartment parameter not found: [" + resourceType + "] '" + searchParm + "'. This will stop compartment searches from working correctly.");
+                       log.warning("Compartment parameter not found: [" + resourceType + "] '" + searchParm + "'. "
+                               + "This will stop compartment searches from working correctly.");
                     }
+
                 }
             }
         } catch (Exception e) {

diff --git a/fhir-server-test/src/test/java/com/ibm/fhir/server/test/SearchExtensionsTest.java b/fhir-server-test/src/test/java/com/ibm/fhir/server/test/SearchExtensionsTest.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2017, 2020
+ * (C) Copyright IBM Corp. 2017, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -17,6 +17,7 @@
 
 import org.testng.annotations.Test;
 
+import com.ibm.fhir.core.FHIRConstants;
 import com.ibm.fhir.core.FHIRMediaType;
 import com.ibm.fhir.model.generator.exception.FHIRGeneratorException;
 import com.ibm.fhir.model.resource.Bundle;
@@ -34,7 +35,7 @@
 import com.ibm.fhir.model.type.Uri;
 
 public class SearchExtensionsTest extends FHIRServerTestBase {
-    private static final String EXTENSION_BASE_URL = "http://ibm.com/fhir/extension/Patient/";
+    private static final String EXTENSION_BASE_URL = FHIRConstants.EXT_BASE + "Patient/";
 
     private static final boolean DEBUG_SEARCH = false;
 

diff --git a/fhir-server/src/main/java/com/ibm/fhir/server/operation/spi/AbstractOperation.java b/fhir-server/src/main/java/com/ibm/fhir/server/operation/spi/AbstractOperation.java
@@ -14,6 +14,7 @@
 
 import org.owasp.encoder.Encode;
 
+import com.ibm.fhir.core.FHIRConstants;
 import com.ibm.fhir.exception.FHIROperationException;
 import com.ibm.fhir.model.resource.OperationDefinition;
 import com.ibm.fhir.model.resource.OperationOutcome;
@@ -29,7 +30,6 @@
 import com.ibm.fhir.model.type.code.ResourceType;
 import com.ibm.fhir.model.util.FHIRUtil;
 import com.ibm.fhir.model.util.ModelSupport;
-import com.ibm.fhir.server.util.FHIRRestHelper;
 
 public abstract class AbstractOperation implements FHIROperation {
     protected final OperationDefinition definition;
@@ -186,7 +186,7 @@ private FHIROperationException buildUnsupportedResourceTypeException(String reso
                 .severity(IssueSeverity.FATAL)
                 .code(IssueType.NOT_SUPPORTED.toBuilder()
                         .extension(Extension.builder()
-                            .url(FHIRRestHelper.EXTENSION_URL +  "/not-supported-detail")
+                            .url(FHIRConstants.EXT_BASE + "not-supported-detail")
                             .value(Code.of("resource"))
                             .build())
                         .build())
-Original file line number
+Diff line change
@@ Expand Up / @@ -37,6 +37,8 @@ public class FHIRConstants { @@
         public static final String UPDATE_IF_MODIFIED_HEADER = "X-FHIR-UPDATE-IF-MODIFIED";
+        public static final String EXT_BASE = "http://ibm.com/fhir/extension/";
         /**
          * General parameter names that can be used with any FHIR interaction.
          *
@@ Expand Down @@