repository search by id (#353)

* repository search by id

* apply formatting

* separate InMemory test

* remove redundancy

* search by id update

* search by id update test

* search by id update test script

* reformat

* Fix repository and tests

* Fixes for repo api

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: JP <jonathan.percival@smilecdr.com>

cqf-fhir-api/src/main/java/org/opencds/cqf/fhir/api/Repository.java

@@ -451,7 +451,7 @@ <R extends IBaseResource, P extends IBaseParameters, T extends IBaseResource> R
      */
     default <P extends IBaseParameters, T extends IBaseResource> MethodOutcome invoke(
             Class<T> resourceType, String name, P parameters) {
-        return this.invoke(name, parameters, Collections.emptyMap());
+        return this.invoke(resourceType, name, parameters, Collections.emptyMap());
     }
 
     /**
@@ -520,7 +520,7 @@ <R extends IBaseResource, P extends IBaseParameters, I extends IIdType> R invoke
      * @return a MethodOutcome with a status code
      */
     default <P extends IBaseParameters, I extends IIdType> MethodOutcome invoke(I id, String name, P parameters) {
-        return this.invoke(name, parameters, Collections.emptyMap());
+        return this.invoke(id, name, parameters, Collections.emptyMap());
     }
 
     /**

cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/repository/InMemoryFhirRepository.java

@@ -3,9 +3,12 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.BundleBuilder;
 import ca.uhn.fhir.util.BundleUtil;
+import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -119,31 +122,56 @@ public <B extends IBaseBundle, T extends IBaseResource> B search(
             Map<String, List<IQueryParameterType>> searchParameters,
             Map<String, String> headers) {
         BundleBuilder builder = new BundleBuilder(this.context);
+        builder.setType("searchset");
+
+        var resourceIdMap = resourceMap.computeIfAbsent(resourceType.getSimpleName(), r -> new HashMap<>());
 
-        var resourceList = resourceMap
-                .computeIfAbsent(resourceType.getSimpleName(), r -> new HashMap<>())
-                .values();
         if (searchParameters == null || searchParameters.isEmpty()) {
-            resourceList.forEach(builder::addCollectionEntry);
-        } else {
-            var resourceMatcher = Repositories.getResourceMatcher(this.context);
-            for (var resource : resourceList) {
-                boolean include = true;
-                for (var nextEntry : searchParameters.entrySet()) {
-                    var paramName = nextEntry.getKey();
-                    if (!resourceMatcher.matches(paramName, nextEntry.getValue(), resource)) {
-                        include = false;
-                        break;
-                    }
+            resourceIdMap.values().forEach(builder::addCollectionEntry);
+            return (B) builder.getBundle();
+        }
+
+        Collection<IBaseResource> candidates;
+        if (searchParameters.containsKey("_id")) {
+            // We are consuming the _id parameter in this if statement
+            var idQueries = searchParameters.get("_id");
+            searchParameters.remove("_id");
+
+            // The _id param can be a list of ids
+            var idResources = new ArrayList<IBaseResource>(idQueries.size());
+            for (var idQuery : idQueries) {
+                var idToken = (TokenParam) idQuery;
+                // Need to construct the equivalent "UnqualifiedVersionless" id that the map is
+                // indexed by. If an id has a version it won't match. Need apples-to-apples Ids types
+                var id = Ids.newId(context, resourceType.getSimpleName(), idToken.getValue());
+                var r = resourceIdMap.get(id);
+                if (r != null) {
+                    idResources.add(r);
                 }
+            }
 
-                if (include) {
-                    builder.addCollectionEntry(resource);
+            candidates = idResources;
+        } else {
+            candidates = resourceIdMap.values();
+        }
+
+        // Apply the rest of the filters
+        var resourceMatcher = Repositories.getResourceMatcher(this.context);
+        for (var resource : candidates) {
+            boolean include = true;
+            for (var nextEntry : searchParameters.entrySet()) {
+                var paramName = nextEntry.getKey();
+                if (!resourceMatcher.matches(paramName, nextEntry.getValue(), resource)) {
+                    include = false;
+                    break;
                 }
             }
+
+            if (include) {
+                builder.addCollectionEntry(resource);
+            }
         }
 
-        builder.setType("searchset");
         return (B) builder.getBundle();
     }
 

cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/search/Searches.java

@@ -25,6 +25,14 @@ public static SearchBuilder builder() {
         return new SearchBuilder();
     }
 
+    public static Map<String, List<IQueryParameterType>> byId(String... ids) {
+        return builder().withTokenParam("_id", ids).build();
+    }
+
+    public static Map<String, List<IQueryParameterType>> byId(String id) {
+        return builder().withTokenParam("_id", id).build();
+    }
+
     public static Map<String, List<IQueryParameterType>> byCanonical(String canonical) {
         if (canonical.contains("|")) {
             var split = canonical.split("|");
@@ -108,14 +116,12 @@ public SearchBuilder withUriParam(String name, String value) {
             return this;
         }
 
-        SearchBuilder withTokenParam(String name, String value, String... values) {
+        SearchBuilder withTokenParam(String name, String... values) {
             if (this.values == null) {
                 this.values = new HashMap<>();
             }
 
             var params = new ArrayList<IQueryParameterType>(1 + values.length);
-            params.add(new TokenParam(value));
-
             for (var v : values) {
                 params.add(new TokenParam(v));
             }

cqf-fhir-utility/src/test/java/org/opencds/cqf/fhir/utility/repository/InMemoryRepositoryTest.java

@@ -0,0 +1,63 @@
+package org.opencds.cqf.fhir.utility.repository;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Encounter;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Library;
+import org.junit.jupiter.api.Test;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.utility.search.Searches;
+
+public class InMemoryRepositoryTest {
+
+    Repository repository;
+
+    public InMemoryRepositoryTest() {
+        repository = new InMemoryFhirRepository(FhirContext.forR4Cached());
+        repository.update(new Library().setId("Library/example1"));
+        repository.update(new Library().setUrl("http://example.com/123").setId("Library/example2"));
+        repository.update(new Encounter().setId("Encounter/example3"));
+    }
+
+    @Test
+    public void testRead() {
+        IBaseResource res = repository.read(Library.class, new IdType("Library/example1"), null);
+        assertEquals("example1", res.getIdElement().getIdPart());
+    }
+
+    @Test
+    public void testSearchWithId() {
+
+        var search = Searches.byId("example1");
+        var resources = repository.search(Bundle.class, Library.class, search);
+        // The _id parameter will be consumed if the index is being used.
+        assertTrue(search.isEmpty());
+        assertEquals(1, resources.getEntry().size());
+
+        search = Searches.byId("example3");
+        resources = repository.search(Bundle.class, Encounter.class, search);
+        assertTrue(search.isEmpty());
+        assertEquals(1, resources.getEntry().size());
+
+        search = Searches.byId("2345");
+        resources = repository.search(Bundle.class, Encounter.class, search);
+        assertTrue(search.isEmpty());
+        assertEquals(0, resources.getEntry().size());
+
+        search = Searches.byId("example1", "example2");
+        resources = repository.search(Bundle.class, Library.class, search);
+        assertTrue(search.isEmpty());
+        assertEquals(2, resources.getEntry().size());
+    }
+
+    @Test
+    public void testSearchWithUrl() {
+        var resources = repository.search(Bundle.class, Library.class, Searches.byUrl("http://example.com/123"));
+        assertEquals(1, resources.getEntry().size());
+    }
+}