Allow absolute links for refs with an identifier (#5295)

* Allow absolute links for refs with an identifier

* Add changelog

* Update hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5295-fix-absolute-refs-with-identifier.yaml

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>

* Remove redundant class

* Review comments

---------

Co-authored-by: Kevin Dougan SmileCDR <72025369+KevinDougan-SmileCDR@users.noreply.github.com>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5295-fix-absolute-refs-with-identifier.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5295
+title: "A regression in the HAPI FHIR 6.6.0 JPA server meant that absolute resource
+    references which also contained an identifier were rejected even if the server
+    was configured to allow absolute references. This has been corrected."

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java

@@ -64,6 +64,7 @@ import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.IdType;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import java.util.ArrayList;
@@ -692,8 +693,20 @@ public class SearchParamExtractorService {
 			return;
 		}
 
-		final boolean hasNoIdentifier = !nextReference.hasIdentifier();
+		String baseUrl = nextId.getBaseUrl();
-		final String baseUrl = hasNoIdentifier ? nextId.getBaseUrl() : null;
+
+		// If this is a conditional URL, the part after the question mark
+		// can include URLs (e.g. token system URLs) and these really confuse
+		// the IdType parser because a conditional URL isn't actually a valid
+		// FHIR ID. So in order to truly determine whether we're dealing with
+		// an absolute reference, we strip the query part and reparse
+		// the reference.
+		int questionMarkIndex = nextId.getValue().indexOf('?');
+		if (questionMarkIndex != -1) {
+			IdType preQueryId = new IdType(nextId.getValue().substring(0, questionMarkIndex - 1));
+			baseUrl = preQueryId.getBaseUrl();
+		}
+
 		String typeString = nextId.getResourceType();
 		if (isBlank(typeString)) {
 			String msg = "Invalid resource reference found at path[" + path + "] - Does not contain resource type - "

hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirSystemDaoTransactionR5Test.java

@@ -20,12 +20,14 @@ import org.junit.jupiter.params.provider.CsvSource;
 import org.junit.jupiter.params.provider.ValueSource;
 
 import javax.annotation.Nonnull;
+import java.io.IOException;
 import java.util.UUID;
 
 import static org.apache.commons.lang3.StringUtils.countMatches;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.endsWith;
+import static org.hamcrest.Matchers.in;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -40,6 +42,7 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 		myStorageSettings.setMatchUrlCacheEnabled(defaults.isMatchUrlCacheEnabled());
 		myStorageSettings.setDeleteEnabled(defaults.isDeleteEnabled());
 		myStorageSettings.setInlineResourceTextBelowSize(defaults.getInlineResourceTextBelowSize());
+		myStorageSettings.setAllowExternalReferences(defaults.isAllowExternalReferences());
 	}
 
 
@@ -503,6 +506,17 @@ public class FhirSystemDaoTransactionR5Test extends BaseJpaR5Test {
 	}
 
 
+	@Test
+	public void testExternalReference() throws IOException {
+		myStorageSettings.setAllowExternalReferences(true);
+
+		Bundle input = loadResourceFromClasspath(Bundle.class, "docref-test-bundle.json");
+		Bundle output = mySystemDao.transaction(mySrd, input);
+		assertEquals(1, output.getEntry().size());
+	}
+
+
+
 	@Test
 	public void testConditionalDeleteAndConditionalUpdateOnSameResource_MultipleMatchesAlreadyExist() {
 

hapi-fhir-jpaserver-test-r5/src/test/resources/docref-test-bundle.json

@@ -0,0 +1,27 @@
+{
+    "resourceType": "Bundle",
+    "type": "transaction",
+    "entry": [
+        {
+            "fullUrl": "Provenance/1.2.40.0.13.1.1.584109161.20230630175432428.38899",
+            "resource": {
+                "resourceType": "Provenance",
+                "id": "1.2.40.0.13.1.1.584109161.20230630175432428.38899",
+                "entity": [
+                    {
+                        "what": {
+                            "reference": "https://somehost:8443/mhd/r4/responder/DocumentReference/urn:oid:1.2.40.0.13.1.1.584109161.20230630175432428.38899",
+                            "identifier": {
+                                "value": "urn:oid:1.2.40.0.13.1.1.584109161.20230630175432428.38899"
+                            }
+                        }
+                    }
+                ]
+            },
+            "request": {
+                "method": "PUT",
+                "url": "Provenance/1.2.40.0.13.1.1.584109161.20230630175432428.38899"
+            }
+        }
+    ]
+}