Fix to code delta CSV encoding

hapi-fhir-jpaserver-base/pom.xml

@@ -608,7 +608,7 @@
 			<scope>compile</scope>
 		</dependency>
 
-	</dependencies>
+    </dependencies>
 
 
 	<properties>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java

@@ -53,9 +53,14 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.InputStream;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
 
 public class TerminologyUploaderProvider extends BaseJpaProvider {
 
@@ -226,9 +231,9 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 			b.append(ConceptHandler.DISPLAY);
 			b.append("\n");
 			for (Map.Entry<String, String> nextEntry : codes.entrySet()) {
-				b.append(nextEntry.getKey());
+				b.append(csvEscape(nextEntry.getKey()));
 				b.append(",");
-				b.append(defaultString(nextEntry.getValue()));
+				b.append(csvEscape(nextEntry.getValue()));
 				b.append("\n");
 			}
 			byte[] bytes = b.toString().getBytes(Charsets.UTF_8);
@@ -245,9 +250,9 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 			b.append(HierarchyHandler.PARENT);
 			b.append("\n");
 			for (Map.Entry<String, String> nextEntry : codeToParentCodes.entries()) {
-				b.append(nextEntry.getKey());
+				b.append(csvEscape(nextEntry.getKey()));
 				b.append(",");
-				b.append(defaultString(nextEntry.getValue()));
+				b.append(csvEscape(nextEntry.getValue()));
 				b.append("\n");
 			}
 			byte[] bytes = b.toString().getBytes(Charsets.UTF_8);
@@ -354,7 +359,6 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 		return retVal;
 	}
 
-
 	private static class FileBackedFileDescriptor implements ITermLoaderSvc.FileDescriptor {
 		private final File myNextFile;
 
@@ -376,4 +380,13 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
 			}
 		}
 	}
+
+	private static String csvEscape(String theValue) {
+		return '"' +
+			theValue
+				.replace("\"", "\"\"")
+				.replace("\n", "\\n")
+				.replace("\r", "") +
+			'"';
+	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/TerminologyUploaderProviderR4Test.java

@@ -1,8 +1,12 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
+import ca.uhn.fhir.jpa.entity.TermCodeSystem;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
+import ca.uhn.fhir.model.api.annotation.SimpleSetter;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
@@ -21,6 +25,7 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Optional;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
@@ -253,6 +258,67 @@ public class TerminologyUploaderProviderR4Test extends BaseResourceProviderR4Tes
 		);
 	}
 
+	@Test
+	public void testApplyDeltaAdd_UsingCodeSystemWithComma() throws IOException {
+
+		// Create initial codesystem
+		{
+			CodeSystem codeSystem = new CodeSystem();
+			codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+			codeSystem.setUrl("https://good.health");
+
+			LoggingInterceptor interceptor = new LoggingInterceptor(true);
+			ourClient.registerInterceptor(interceptor);
+			ourClient
+				.create()
+				.resource(codeSystem)
+				.execute();
+			ourClient.unregisterInterceptor(interceptor);
+		}
+
+		// Add a child with a really long description
+		Parameters outcome;
+		{
+			Parameters inputBundle = loadResourceFromClasspath(Parameters.class, "/term-delta-json.json");
+
+			LoggingInterceptor interceptor = new LoggingInterceptor(true);
+			ourClient.registerInterceptor(interceptor);
+			outcome = ourClient
+				.operation()
+				.onType(CodeSystem.class)
+				.named(JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD)
+				.withParameters(inputBundle)
+				.execute();
+			ourClient.unregisterInterceptor(interceptor);
+		}
+
+		String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
+		ourLog.info(encoded);
+		assertThat(encoded, stringContainsInOrder(
+			"\"name\": \"conceptCount\"",
+			"\"valueInteger\": 2",
+			"\"name\": \"target\"",
+			"\"reference\": \"CodeSystem/"
+		));
+
+		assertHierarchyContains(
+			"1111222233 seq=0",
+			" 1111222234 seq=0"
+		);
+
+		runInTransaction(()->{
+			TermCodeSystem codeSystem = myTermCodeSystemDao.findByCodeSystemUri("https://good.health");
+			TermCodeSystemVersion version = codeSystem.getCurrentVersion();
+			TermConcept code = myTermConceptDao.findByCodeSystemAndCode(version, "1111222233").get();
+			assertEquals("Some label for the parent - with a dash too", code.getDisplay());
+
+			code = myTermConceptDao.findByCodeSystemAndCode(version, "1111222234").get();
+			assertEquals("Some very very very very very looooooong child label with a coma, another one, one more, more and final one", code.getDisplay());
+		});
+	}
+
+
+
 	@Test
 	public void testApplyDeltaAdd_UsingCodeSystemWithVeryLongDescription() {
 

hapi-fhir-jpaserver-base/src/test/resources/term-delta-json.json

@@ -0,0 +1,30 @@
+{
+	"resourceType": "Parameters",
+	"parameter": [
+		{
+			"name": "system",
+			"valueUri": "https://good.health"
+		},
+		{
+			"name": "codeSystem",
+			"resource": {
+				"resourceType": "CodeSystem",
+				"status": "active",
+				"content": "not-present",
+				"url": "https://good.health",
+				"concept": [
+					{
+						"code": "1111222233",
+						"display": "Some label for the parent - with a dash too",
+						"concept": [
+							{
+								"code": "1111222234",
+								"display": "Some very very very very very looooooong child label with a coma, another one, one more, more and final one"
+							}
+						]
+					}
+				]
+			}
+		}
+	]
+}