Add support for uploading custom terminology using the

$upload-external-code-system operation

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java

@@ -165,6 +165,13 @@ public class ParametersUtil {
 
 	}
 
+	@SuppressWarnings("unchecked")
+	public static void addParameterToParametersCode(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
+		IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("code").newInstance();
+		value.setValue(theValue);
+		addParameterToParameters(theCtx, theParameters, theName, value);
+	}
+
 	@SuppressWarnings("unchecked")
 	public static void addParameterToParametersInteger(FhirContext theCtx, IBaseParameters theParameters, String theName, int theValue) {
 		IPrimitiveType<Integer> count = (IPrimitiveType<Integer>) theCtx.getElementDefinition("integer").newInstance();
@@ -184,6 +191,13 @@ public class ParametersUtil {
 		IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("string").newInstance();
 		value.setValue(theValue);
 		addParameterToParameters(theCtx, theParameters, theName, value);
+	}
+
+	@SuppressWarnings("unchecked")
+	public static void addParameterToParametersUri(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
+		IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("uri").newInstance();
+		value.setValue(theValue);
+		addParameterToParameters(theCtx, theParameters, theName, value);
 
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java

@@ -63,15 +63,21 @@ public class ValidateUtil {
 		}
 	}
 
+	public static void isNotNullOrThrowUnprocessableEntity(Object theObject, String theMessage, Object... theValues) {
+		if (theObject == null) {
+			throw new UnprocessableEntityException(String.format(theMessage, theValues));
+		}
+	}
+
 	public static void isNotTooLongOrThrowIllegalArgument(String theString, int theMaxLength, String theMessage) {
 		if (length(theString) > theMaxLength) {
 			throw new IllegalArgumentException(theMessage);
 		}
 	}
 
-	public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage) {
+	public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage, Object... theValues) {
 		if (theSuccess == false) {
-			throw new InvalidRequestException(theMessage);
+			throw new InvalidRequestException(String.format(theMessage, theValues));
 		}
 	}
 

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/ValidateUtilTest.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.util;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.fail;
 
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import org.junit.Test;
 
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -69,4 +70,18 @@ public class ValidateUtilTest {
 		}
 	}
 
+
+	@Test
+	public void testIsNotNull() {
+		ValidateUtil.isNotNullOrThrowUnprocessableEntity("aa", "");
+
+		try {
+			ValidateUtil.isNotNullOrThrowUnprocessableEntity(null, "The message %s", "123");
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("The message 123", e.getMessage());
+		}
+
+	}
+
 }

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java

@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.util.ParametersUtil;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
@@ -56,6 +57,7 @@ public class UploadTerminologyCommand extends BaseCommand {
 		addBaseUrlOption(options);
 		addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
 		addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
+		addOptionalOption(options, null, "custom", false, "Indicates that this upload uses the HAPI FHIR custom external terminology format");
 		addBasicAuthOption(options);
 		addVerboseLoggingOption(options);
 
@@ -78,23 +80,13 @@ public class UploadTerminologyCommand extends BaseCommand {
 		}
 
 		IGenericClient client = super.newClient(theCommandLine);
-		IBaseParameters inputParameters;
+		IBaseParameters inputParameters = ParametersUtil.newInstance(myFhirCtx);
-		if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
+		ParametersUtil.addParameterToParametersUri(myFhirCtx, inputParameters, "url", termUrl);
-			org.hl7.fhir.dstu3.model.Parameters p = new org.hl7.fhir.dstu3.model.Parameters();
+		for (String next : datafile) {
-			p.addParameter().setName("url").setValue(new org.hl7.fhir.dstu3.model.UriType(termUrl));
+			ParametersUtil.addParameterToParametersString(myFhirCtx, inputParameters, "localfile", next);
-			for (String next : datafile) {
+		}
-				p.addParameter().setName("localfile").setValue(new org.hl7.fhir.dstu3.model.StringType(next));
+		if (theCommandLine.hasOption("custom")) {
-			}
+			ParametersUtil.addParameterToParametersCode(myFhirCtx, inputParameters, "contentMode", "custom");
-			inputParameters = p;
-		} else if (ctx.getVersion().getVersion() == FhirVersionEnum.R4) {
-			org.hl7.fhir.r4.model.Parameters p = new org.hl7.fhir.r4.model.Parameters();
-			p.addParameter().setName("url").setValue(new org.hl7.fhir.r4.model.UriType(termUrl));
-			for (String next : datafile) {
-				p.addParameter().setName("localfile").setValue(new org.hl7.fhir.r4.model.StringType(next));
-			}
-			inputParameters = p;
-		} else {
-			throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
 		}
 
 		if (theCommandLine.hasOption(VERBOSE_LOGGING_PARAM)) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java

@@ -50,15 +50,12 @@ import static org.apache.commons.lang3.StringUtils.length;
 	@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
 })
 public class TermConcept implements Serializable {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
-
-	private static final long serialVersionUID = 1L;
-
 	public static final int MAX_CODE_LENGTH = 500;
 	public static final int MAX_DESC_LENGTH = 400;
-
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
+	private static final long serialVersionUID = 1L;
 	@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
-	private Collection<TermConceptParentChildLink> myChildren;
+	private List<TermConceptParentChildLink> myChildren;
 
 	@Column(name = "CODEVAL", nullable = false, length = MAX_CODE_LENGTH)
 	@Fields({@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),})
@@ -178,7 +175,7 @@ public class TermConcept implements Serializable {
 		return b.isEquals();
 	}
 
-	public Collection<TermConceptParentChildLink> getChildren() {
+	public List<TermConceptParentChildLink> getChildren() {
 		if (myChildren == null) {
 			myChildren = new ArrayList<>();
 		}

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

@@ -160,6 +160,7 @@ public abstract class TerminologyUploaderProvider extends BaseJpaProvider {
 	public IBaseParameters uploadExternalCodeSystem(
 		HttpServletRequest theServletRequest,
 		@OperationParam(name = "url", min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
+		@OperationParam(name = "contentMode", min = 0, typeName = "code") IPrimitiveType<String> theContentMode,
 		@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theLocalFile,
 		@OperationParam(name = "package", min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> thePackage,
 		RequestDetails theRequestDetails
@@ -210,7 +211,7 @@ public abstract class TerminologyUploaderProvider extends BaseJpaProvider {
 					final String url = AttachmentUtil.getOrCreateUrl(myCtx, nextPackage).getValueAsString();
 
 					if (isBlank(url)) {
-						throw new UnprocessableEntityException("Package is missing mandatory url element");
+						throw new UnprocessableEntityException("Package is missing mandatory codeSystemUrl element");
 					}
 
 					localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
@@ -228,22 +229,27 @@ public abstract class TerminologyUploaderProvider extends BaseJpaProvider {
 				}
 			}
 
-			String url = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
+			String codeSystemUrl = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
-			url = defaultString(url);
+			codeSystemUrl = defaultString(codeSystemUrl);
 
+			String contentMode = theContentMode != null ? theContentMode.getValue() : null;
 			UploadStatistics stats;
-			switch (url) {
+			if ("custom".equals(contentMode)) {
-				case IHapiTerminologyLoaderSvc.SCT_URI:
+				stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
-					stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
+			} else {
-					break;
+				switch (codeSystemUrl) {
-				case IHapiTerminologyLoaderSvc.LOINC_URI:
+					case IHapiTerminologyLoaderSvc.SCT_URI:
-					stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
+						stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
-					break;
+						break;
-				case IHapiTerminologyLoaderSvc.IMGTHLA_URI:
+					case IHapiTerminologyLoaderSvc.LOINC_URI:
-					stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
+						stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
-					break;
+						break;
-				default:
+					case IHapiTerminologyLoaderSvc.IMGTHLA_URI:
-					throw new InvalidRequestException("Unknown URL: " + url);
+						stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
+						break;
+					default:
+						throw new InvalidRequestException("Unknown URL: " + codeSystemUrl);
+				}
 			}
 
 			IBaseParameters retVal = ParametersUtil.newInstance(myCtx);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java

@@ -39,6 +39,8 @@ public interface IHapiTerminologyLoaderSvc {
 
 	UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
 
+	UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
+
 	interface FileDescriptor {
 
 		String getFilename();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java

@@ -4,15 +4,19 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.jpa.term.custom.ConceptHandler;
+import ca.uhn.fhir.jpa.term.custom.HierarchyHandler;
 import ca.uhn.fhir.jpa.term.loinc.*;
 import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
 import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
 import ca.uhn.fhir.jpa.term.snomedct.SctHandlerRelationship;
 import ca.uhn.fhir.jpa.util.Counter;
+import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.ValidateUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Charsets;
 import org.apache.commons.csv.CSVFormat;
@@ -83,15 +87,19 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 	public static final String LOINC_GROUP_FILE = "Group.csv";
 	public static final String LOINC_GROUP_TERMS_FILE = "GroupLoincTerms.csv";
 	public static final String LOINC_PARENT_GROUP_FILE = "ParentGroup.csv";
+	public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
+	public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
+	public static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
+	public static final String CUSTOM_CODESYSTEM_XML = "codesystem.xml";
+
 	private static final int LOG_INCREMENT = 1000;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImpl.class);
 
 	@Autowired
 	private IHapiTerminologySvc myTermSvc;
-	@Autowired(required = false)
+
-	private IHapiTerminologySvcDstu3 myTermSvcDstu3;
+	// FYI: Hardcoded to R4 because that's what the term svc uses internally
-	@Autowired(required = false)
+	private final FhirContext myCtx = FhirContext.forR4();
-	private IHapiTerminologySvcR4 myTermSvcR4;
 
 	private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {
 
@@ -165,7 +173,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 					int nextLoggedCount = 0;
 					while (iter.hasNext()) {
 						CSVRecord nextRecord = iter.next();
-						if (nextRecord.isConsistent()==false) {
+						if (nextRecord.isConsistent() == false) {
 							continue;
 						}
 						theHandler.accept(nextRecord);
@@ -203,8 +211,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 			ourLog.info("Beginning IMGTHLA processing");
 
 			return processImgthlaFiles(descriptors, theRequestDetails);
-		}
+		} finally {
-		finally {
 			IOUtils.closeQuietly(descriptors);
 		}
 	}
@@ -229,15 +236,15 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 				LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV,
 				LOINC_IMAGING_DOCUMENT_CODES_FILE
 			);
-		descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
+			descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
 
 			List<String> optionalFilenameFragments = Arrays.asList(
 			);
-		descriptors.verifyOptionalFilesExist(optionalFilenameFragments);
+			descriptors.verifyOptionalFilesExist(optionalFilenameFragments);
 
-		ourLog.info("Beginning LOINC processing");
+			ourLog.info("Beginning LOINC processing");
 
-		return processLoincFiles(descriptors, theRequestDetails);
+			return processLoincFiles(descriptors, theRequestDetails);
 		}
 	}
 
@@ -257,6 +264,67 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		}
 	}
 
+	@Override
+	public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
+		try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
+			final Map<String, TermConcept> code2concept = new HashMap<>();
+			IRecordHandler handler;
+
+			Optional<String> codeSystemContent = loadFile(descriptors, CUSTOM_CODESYSTEM_JSON, CUSTOM_CODESYSTEM_XML);
+			CodeSystem codeSystem;
+			if (codeSystemContent.isPresent()) {
+				codeSystem = EncodingEnum
+					.detectEncoding(codeSystemContent.get())
+					.newParser(myCtx)
+					.parseResource(CodeSystem.class, codeSystemContent.get());
+				ValidateUtil.isTrueOrThrowInvalidRequest(theSystem.equalsIgnoreCase(codeSystem.getUrl()), "CodeSystem.url does not match the supplied system: %s", theSystem);
+				ValidateUtil.isTrueOrThrowInvalidRequest(CodeSystem.CodeSystemContentMode.NOTPRESENT.equals(codeSystem.getContent()), "CodeSystem.content does not match the expected value: %s", CodeSystem.CodeSystemContentMode.NOTPRESENT.toCode());
+			} else {
+				codeSystem = new CodeSystem();
+				codeSystem.setUrl(theSystem);
+				codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+			}
+
+			TermCodeSystemVersion csv = new TermCodeSystemVersion();
+
+			// Concept File
+			handler = new ConceptHandler(code2concept, csv);
+			iterateOverZipFile(descriptors, CUSTOM_CONCEPTS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+
+			// Hierarchy
+			if (descriptors.hasFile(CUSTOM_HIERARCHY_FILE)) {
+				handler = new HierarchyHandler(code2concept);
+				iterateOverZipFile(descriptors, CUSTOM_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+			}
+
+			// Add root concepts to CodeSystemVersion
+			for (TermConcept nextConcept : code2concept.values()) {
+				if (nextConcept.getParents().isEmpty()) {
+					csv.getConcepts().add(nextConcept);
+				}
+			}
+
+			IIdType target = storeCodeSystem(theRequestDetails, csv, codeSystem, null, null);
+			return new UploadStatistics(code2concept.size(), target);
+		}
+	}
+
+	private Optional<String> loadFile(LoadedFileDescriptors theDescriptors, String... theFilenames) {
+		for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
+			for (String nextFilename : theFilenames) {
+				if (next.getFilename().endsWith(nextFilename)) {
+					try {
+						String contents = IOUtils.toString(next.getInputStream(), Charsets.UTF_8);
+						return Optional.of(contents);
+					} catch (IOException e) {
+						throw new InternalErrorException(e);
+					}
+				}
+			}
+		}
+		return Optional.empty();
+	}
+
 	UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
 		final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
 		final Map<String, TermConcept> code2concept = new HashMap<>();
@@ -285,13 +353,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		for (FileDescriptor nextZipBytes : theDescriptors.getUncompressedFileDescriptors()) {
 			String nextFilename = nextZipBytes.getFilename();
 
-			if(!IMGTHLA_HLA_NOM_TXT.equals(nextFilename) && !nextFilename.endsWith("/" + IMGTHLA_HLA_NOM_TXT)
+			if (!IMGTHLA_HLA_NOM_TXT.equals(nextFilename) && !nextFilename.endsWith("/" + IMGTHLA_HLA_NOM_TXT)
 				&& !IMGTHLA_HLA_XML.equals(nextFilename) && !nextFilename.endsWith("/" + IMGTHLA_HLA_XML)) {
 				ourLog.info("Skipping unexpected file {}", nextFilename);
 				continue;
 			}
 
-			if(IMGTHLA_HLA_NOM_TXT.equals(nextFilename) || nextFilename.endsWith("/" + IMGTHLA_HLA_NOM_TXT)) {
+			if (IMGTHLA_HLA_NOM_TXT.equals(nextFilename) || nextFilename.endsWith("/" + IMGTHLA_HLA_NOM_TXT)) {
 				// process colon-delimited hla_nom.txt file
 				ourLog.info("Processing file {}", nextFilename);
 
@@ -309,20 +377,20 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 					}
 
 					LineNumberReader lnr = new LineNumberReader(reader);
-					while(lnr.readLine() != null) {}
+					while (lnr.readLine() != null) {
+					}
 					ourLog.warn("Lines read from {}:  {}", nextFilename, lnr.getLineNumber());
 
 				} catch (IOException e) {
 					throw new InternalErrorException(e);
-				}
+				} finally {
-				finally {
 					IOUtils.closeQuietly(reader);
 				}
 
 				foundHlaNom = true;
 			}
 
-			if(IMGTHLA_HLA_XML.equals(nextFilename) || nextFilename.endsWith("/" + IMGTHLA_HLA_XML)) {
+			if (IMGTHLA_HLA_XML.equals(nextFilename) || nextFilename.endsWith("/" + IMGTHLA_HLA_XML)) {
 				// process hla.xml file
 				ourLog.info("Processing file {}", nextFilename);
 
@@ -340,13 +408,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 					}
 
 					LineNumberReader lnr = new LineNumberReader(reader);
-					while(lnr.readLine() != null) {}
+					while (lnr.readLine() != null) {
+					}
 					ourLog.warn("Lines read from {}:  {}", nextFilename, lnr.getLineNumber());
 
 				} catch (IOException e) {
 					throw new InternalErrorException(e);
-				}
+				} finally {
-				finally {
 					IOUtils.closeQuietly(reader);
 				}
 
@@ -553,11 +621,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 		return new UploadStatistics(code2concept.size(), target);
 	}
 
-	@VisibleForTesting
-	void setTermSvcDstu3ForUnitTest(IHapiTerminologySvcDstu3 theTermSvcDstu3) {
-		myTermSvcDstu3 = theTermSvcDstu3;
-	}
-
 	@VisibleForTesting
 	void setTermSvcForUnitTests(IHapiTerminologySvc theTermSvc) {
 		myTermSvc = theTermSvc;
@@ -571,38 +634,12 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 
 		IIdType retVal;
 		myTermSvc.setProcessDeferred(false);
-		if (myTermSvcDstu3 != null) {
+		retVal = myTermSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
-			retVal = myTermSvcDstu3.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
-		} else {
-			retVal = myTermSvcR4.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
-		}
 		myTermSvc.setProcessDeferred(true);
 
 		return retVal;
 	}
 
-
-	public static String firstNonBlank(String... theStrings) {
-		String retVal = "";
-		for (String nextString : theStrings) {
-			if (isNotBlank(nextString)) {
-				retVal = nextString;
-				break;
-			}
-		}
-		return retVal;
-	}
-
-	public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
-		TermConcept concept = id2concept.get(id);
-		if (concept == null) {
-			concept = new TermConcept();
-			id2concept.put(id, concept);
-			concept.setCodeSystemVersion(codeSystemVersion);
-		}
-		return concept;
-	}
-
 	static class LoadedFileDescriptors implements Closeable {
 
 		private List<File> myTemporaryFiles = new ArrayList<>();
@@ -651,6 +688,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 			}
 		}
 
+		boolean hasFile(String theFilename) {
+			return myUncompressedFileDescriptors
+				.stream()
+				.map(t -> t.getFilename().replaceAll(".*[\\\\/]", "")) // Strip the path from the filename
+				.anyMatch(t -> t.equals(theFilename));
+		}
+
 		@Override
 		public void close() {
 			for (File next : myTemporaryFiles) {
@@ -694,4 +738,25 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
 
 
 	}
+
+	public static String firstNonBlank(String... theStrings) {
+		String retVal = "";
+		for (String nextString : theStrings) {
+			if (isNotBlank(nextString)) {
+				retVal = nextString;
+				break;
+			}
+		}
+		return retVal;
+	}
+
+	public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
+		TermConcept concept = id2concept.get(id);
+		if (concept == null) {
+			concept = new TermConcept();
+			id2concept.put(id, concept);
+			concept.setCodeSystemVersion(codeSystemVersion);
+		}
+		return concept;
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/ConceptHandler.java

@@ -0,0 +1,63 @@
+package ca.uhn.fhir.jpa.term.custom;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.term.IRecordHandler;
+import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
+import org.apache.commons.csv.CSVRecord;
+import org.apache.commons.lang3.Validate;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Map;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
+
+public class ConceptHandler implements IRecordHandler {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ConceptHandler.class);
+	private final Map<String, TermConcept> myCode2Concept;
+	private final TermCodeSystemVersion myCodeSystemVersion;
+
+	public ConceptHandler(Map<String, TermConcept> theCode2concept, TermCodeSystemVersion theCodeSystemVersion) {
+		myCode2Concept = theCode2concept;
+		myCodeSystemVersion = theCodeSystemVersion;
+	}
+
+	@Override
+	public void accept(CSVRecord theRecord) {
+		String code = trim(theRecord.get("CODE"));
+		if (isNotBlank(code)) {
+			String display = trim(theRecord.get("DISPLAY"));
+
+			Validate.isTrue(!myCode2Concept.containsKey(code), "The code %s has appeared more than once", code);
+
+			TermConcept concept = TerminologyLoaderSvcImpl.getOrCreateConcept(myCodeSystemVersion, myCode2Concept, code);
+			concept.setCode(code);
+			concept.setDisplay(display);
+
+			myCode2Concept.put(code, concept);
+		}
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/HierarchyHandler.java

@@ -0,0 +1,58 @@
+package ca.uhn.fhir.jpa.term.custom;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.jpa.term.IRecordHandler;
+import ca.uhn.fhir.util.ValidateUtil;
+import org.apache.commons.csv.CSVRecord;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Map;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
+
+public class HierarchyHandler implements IRecordHandler {
+
+	private final Map<String, TermConcept> myCode2Concept;
+
+	public HierarchyHandler(Map<String, TermConcept> theCode2concept) {
+		myCode2Concept = theCode2concept;
+	}
+
+	@Override
+	public void accept(CSVRecord theRecord) {
+		String parent = trim(theRecord.get("PARENT"));
+		String child = trim(theRecord.get("CHILD"));
+		if (isNotBlank(parent) && isNotBlank(child)) {
+
+			TermConcept parentConcept = myCode2Concept.get(parent);
+			ValidateUtil.isNotNullOrThrowUnprocessableEntity(parentConcept, "Parent code %s not found", parent);
+			TermConcept childConcept = myCode2Concept.get(child);
+			ValidateUtil.isNotNullOrThrowUnprocessableEntity(childConcept, "Child code %s not found", child);
+
+			parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
+		}
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/BaseLoaderTest.java

@@ -0,0 +1,58 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.runner.RunWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+@RunWith(MockitoJUnitRunner.class)
+abstract class BaseLoaderTest {
+
+	@Mock
+	protected RequestDetails mySrd;
+	@Captor
+	protected ArgumentCaptor<List<ConceptMap>> myConceptMapCaptor;
+	@Captor
+	protected ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
+	@Captor
+	protected ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
+	@Captor
+	protected ArgumentCaptor<CodeSystem> mySystemCaptor;
+
+	Map<String, ConceptMap> extractConceptMaps() {
+		Map<String, ConceptMap> conceptMaps = new HashMap<>();
+		for (ConceptMap next : myConceptMapCaptor.getAllValues().get(0)) {
+			conceptMaps.put(next.getId(), next);
+		}
+		return conceptMaps;
+	}
+
+	Map<String, TermConcept> extractConcepts() {
+		Map<String, TermConcept> concepts = new HashMap<>();
+		for (TermConcept next : myCsvCaptor.getValue().getConcepts()) {
+			concepts.put(next.getCode(), next);
+		}
+		return concepts;
+	}
+
+	Map<String, ValueSet> extractValueSets() {
+		Map<String, ValueSet> valueSets = new HashMap<>();
+		for (ValueSet next : myValueSetsCaptor.getValue()) {
+			valueSets.put(next.getId(), next);
+		}
+		return valueSets;
+	}
+
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcCustomTest.java

@@ -0,0 +1,115 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.util.TestUtil;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+@RunWith(MockitoJUnitRunner.class)
+public class TerminologyLoaderSvcCustomTest extends BaseLoaderTest {
+	private TerminologyLoaderSvcImpl mySvc;
+
+	@Mock
+	private IHapiTerminologySvc myTermSvc;
+
+	private ZipCollectionBuilder myFiles;
+
+
+	@Before
+	public void before() {
+		mySvc = new TerminologyLoaderSvcImpl();
+		mySvc.setTermSvcForUnitTests(myTermSvc);
+
+		myFiles = new ZipCollectionBuilder();
+	}
+
+	@Test
+	public void testLoadComplete() throws Exception {
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CODESYSTEM_JSON);
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_HIERARCHY_FILE);
+
+		// Actually do the load
+		mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
+
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		Map<String, TermConcept> concepts = extractConcepts();
+
+		// Verify codesystem
+		assertEquals("http://example.com/labCodes", mySystemCaptor.getValue().getUrl());
+		assertEquals(CodeSystem.CodeSystemContentMode.NOTPRESENT, mySystemCaptor.getValue().getContent());
+		assertEquals("Example Lab Codes", mySystemCaptor.getValue().getName());
+
+		// Root code
+		TermConcept code;
+		assertEquals(2, concepts.size());
+		code = concepts.get("CHEM");
+		assertEquals("CHEM", code.getCode());
+		assertEquals("Chemistry", code.getDisplay());
+
+		assertEquals(2, code.getChildren().size());
+		assertEquals("HB", code.getChildren().get(0).getChild().getCode());
+		assertEquals("Hemoglobin", code.getChildren().get(0).getChild().getDisplay());
+		assertEquals("NEUT", code.getChildren().get(1).getChild().getCode());
+		assertEquals("Neutrophils", code.getChildren().get(1).getChild().getDisplay());
+
+	}
+
+	@Test
+	public void testLoadWithNoCodeSystem() throws Exception {
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
+
+		// Actually do the load
+		mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
+
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		Map<String, TermConcept> concepts = extractConcepts();
+
+		// Verify codesystem
+		assertEquals("http://example.com/labCodes", mySystemCaptor.getValue().getUrl());
+		assertEquals(CodeSystem.CodeSystemContentMode.NOTPRESENT, mySystemCaptor.getValue().getContent());
+
+	}
+
+	/**
+	 * No hierarchy file supplied
+	 */
+	@Test
+	public void testLoadCodesOnly() throws Exception {
+		myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
+
+		// Actually do the load
+		mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
+
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		Map<String, TermConcept> concepts = extractConcepts();
+
+		TermConcept code;
+
+		// Root code
+		assertEquals(5, concepts.size());
+		code = concepts.get("CHEM");
+		assertEquals("CHEM", code.getCode());
+		assertEquals("Chemistry", code.getDisplay());
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImgthlaTest.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.jpa.term;
 
-import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
@@ -8,9 +7,7 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
-import org.junit.runner.RunWith;
 import org.mockito.Mock;
-import org.mockito.junit.MockitoJUnitRunner;
 
 import java.io.IOException;
 
@@ -18,19 +15,12 @@ import static org.hamcrest.Matchers.containsString;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.fail;
 
-@RunWith(MockitoJUnitRunner.class)
+public class TerminologyLoaderSvcImgthlaTest extends BaseLoaderTest {
-public class TerminologyLoaderSvcImgthlaTest {
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImgthlaTest.class);
 	private TerminologyLoaderSvcImpl mySvc;
 
 	@Mock
 	private IHapiTerminologySvc myTermSvc;
 
-	@Mock
-	private IHapiTerminologySvcDstu3 myTermSvcDstu3;
-
-	@Mock
-	private RequestDetails details;
 	private ZipCollectionBuilder myFiles;
 
 
@@ -38,7 +28,6 @@ public class TerminologyLoaderSvcImgthlaTest {
 	public void before() {
 		mySvc = new TerminologyLoaderSvcImpl();
 		mySvc.setTermSvcForUnitTests(myTermSvc);
-		mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
 
 		myFiles = new ZipCollectionBuilder();
 	}
@@ -49,7 +38,7 @@ public class TerminologyLoaderSvcImgthlaTest {
 
 		// Actually do the load
 		try {
-			mySvc.loadImgthla(myFiles.getFiles(), details);
+			mySvc.loadImgthla(myFiles.getFiles(), mySrd);
 			fail("Expected \"not yet fully implemented\" InternalErrorException");
 		} catch(InternalErrorException e) {
 			// for now, expect "not yet fully implemented" exception
@@ -65,7 +54,7 @@ public class TerminologyLoaderSvcImgthlaTest {
 		addImgthlaMandatoryFilesToZip(myFiles);
 
 		// Actually do the load
-		mySvc.loadImgthla(myFiles.getFiles(), details);
+		mySvc.loadImgthla(myFiles.getFiles(), mySrd);
 
 		// TODO:  verify the code system was loaded correctly (similarly to TerminologyLoaderSvcLoincTest.testLoadLoincMandatoryFilesOnly)
 	}
@@ -76,7 +65,7 @@ public class TerminologyLoaderSvcImgthlaTest {
 
 		// Actually do the load
 		try {
-			mySvc.loadImgthla(myFiles.getFiles(), details);
+			mySvc.loadImgthla(myFiles.getFiles(), mySrd);
 			fail("Expected UnprocessableEntityException");
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input:"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.term;
 
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.term.loinc.*;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
@@ -15,46 +14,28 @@ import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
-import org.junit.runner.RunWith;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Captor;
 import org.mockito.Mock;
-import org.mockito.junit.MockitoJUnitRunner;
 
 import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 
-import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.*;
-import static org.hamcrest.Matchers.containsString;
-import static org.hamcrest.Matchers.empty;
 import static org.junit.Assert.*;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 
-@RunWith(MockitoJUnitRunner.class)
+public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
-public class TerminologyLoaderSvcLoincTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcLoincTest.class);
 	private TerminologyLoaderSvcImpl mySvc;
 
 	@Mock
 	private IHapiTerminologySvc myTermSvc;
-
-	@Mock
-	private IHapiTerminologySvcDstu3 myTermSvcDstu3;
-
-	@Captor
-	private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
 	@Captor
 	private ArgumentCaptor<CodeSystem> mySystemCaptor;
-	@Mock
+
-	private RequestDetails details;
-	@Captor
-	private ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
-	@Captor
-	private ArgumentCaptor<List<ConceptMap>> myConceptMapCaptor;
 	private ZipCollectionBuilder myFiles;
 
 
@@ -62,43 +43,18 @@ public class TerminologyLoaderSvcLoincTest {
 	public void before() {
 		mySvc = new TerminologyLoaderSvcImpl();
 		mySvc.setTermSvcForUnitTests(myTermSvc);
-		mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
 
 		myFiles = new ZipCollectionBuilder();
 	}
 
-	private Map<String, ConceptMap> extractConceptMaps() {
-		Map<String, ConceptMap> conceptMaps = new HashMap<>();
-		for (ConceptMap next : myConceptMapCaptor.getAllValues().get(0)) {
-			conceptMaps.put(next.getId(), next);
-		}
-		return conceptMaps;
-	}
-
-	private Map<String, TermConcept> extractConcepts() {
-		Map<String, TermConcept> concepts = new HashMap<>();
-		for (TermConcept next : myCsvCaptor.getValue().getConcepts()) {
-			concepts.put(next.getCode(), next);
-		}
-		return concepts;
-	}
-
-	private Map<String, ValueSet> extractValueSets() {
-		Map<String, ValueSet> valueSets = new HashMap<>();
-		for (ValueSet next : myValueSetsCaptor.getValue()) {
-			valueSets.put(next.getId(), next);
-		}
-		return valueSets;
-	}
-
 	@Test
 	public void testLoadLoinc() throws Exception {
 		addLoincMandatoryFilesToZip(myFiles);
 
 		// Actually do the load
-		mySvc.loadLoinc(myFiles.getFiles(), details);
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
 
-		verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		Map<String, TermConcept> concepts = extractConcepts();
 		Map<String, ValueSet> valueSets = extractValueSets();
 		Map<String, ConceptMap> conceptMaps = extractConceptMaps();
@@ -347,9 +303,9 @@ public class TerminologyLoaderSvcLoincTest {
 		addLoincMandatoryFilesToZip(myFiles);
 
 		// Actually do the load
-		mySvc.loadLoinc(myFiles.getFiles(), details);
+		mySvc.loadLoinc(myFiles.getFiles(), mySrd);
 
-		verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+		verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
 		Map<String, TermConcept> concepts = extractConcepts();
 		Map<String, ValueSet> valueSets = extractValueSets();
 		Map<String, ConceptMap> conceptMaps = extractConceptMaps();
@@ -371,7 +327,7 @@ public class TerminologyLoaderSvcLoincTest {
 
 		// Actually do the load
 		try {
-			mySvc.loadLoinc(myFiles.getFiles(), details);
+			mySvc.loadLoinc(myFiles.getFiles(), mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input:"));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcSnomedCtTest.java

@@ -4,39 +4,36 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.ConceptMap;
-import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
-import org.junit.runner.RunWith;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Captor;
 import org.mockito.Mock;
-import org.mockito.runners.MockitoJUnitRunner;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.FileInputStream;
 import java.io.InputStream;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.TreeSet;
 import java.util.zip.ZipOutputStream;
 
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.CoreMatchers.containsString;
-import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.hasItem;
-import static org.mockito.Matchers.any;
+import static org.hamcrest.Matchers.not;
-import static org.mockito.Matchers.anyListOf;
+import static org.junit.Assert.assertThat;
-import static org.mockito.Mockito.mock;
+import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.*;
 import static org.mockito.Mockito.verify;
 
-@RunWith(MockitoJUnitRunner.class)
+public class TerminologyLoaderSvcSnomedCtTest extends BaseLoaderTest {
-public class TerminologyLoaderSvcSnomedCtTest {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcSnomedCtTest.class);
 	private TerminologyLoaderSvcImpl mySvc;
 
@@ -44,15 +41,12 @@ public class TerminologyLoaderSvcSnomedCtTest {
 	private IHapiTerminologySvc myTermSvc;
 	@Captor
 	private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
-	@Mock
-	private IHapiTerminologySvcDstu3 myTermSvcDstu3;
 	private ZipCollectionBuilder myFiles;
 
 	@Before
 	public void before() {
 		mySvc = new TerminologyLoaderSvcImpl();
 		mySvc.setTermSvcForUnitTests(myTermSvc);
-		mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
 
 		myFiles = new ZipCollectionBuilder();
 	}
@@ -84,17 +78,16 @@ public class TerminologyLoaderSvcSnomedCtTest {
 		myFiles.addFileZip("/sct/", "sct2_StatedRelationship_Full_INT_20160131.txt");
 		myFiles.addFileZip("/sct/", "sct2_TextDefinition_Full-en_INT_20160131.txt");
 
-		RequestDetails details = mock(RequestDetails.class);
+		mySvc.loadSnomedCt(myFiles.getFiles(), mySrd);
-		mySvc.loadSnomedCt(myFiles.getFiles(), details);
 
-		verify(myTermSvcDstu3).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyListOf(ValueSet.class), anyListOf(ConceptMap.class));
+		verify(myTermSvc).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyList(), anyListOf(ConceptMap.class));
 
 		TermCodeSystemVersion csv = myCsvCaptor.getValue();
 		TreeSet<String> allCodes = toCodes(csv, true);
 		ourLog.info(allCodes.toString());
 
-		assertThat(allCodes, containsInRelativeOrder("116680003"));
+		assertThat(allCodes, hasItem("116680003"));
-		assertThat(allCodes, not(containsInRelativeOrder("207527008")));
+		assertThat(allCodes, not(hasItem("207527008")));
 
 		allCodes = toCodes(csv, false);
 		ourLog.info(allCodes.toString());
@@ -110,8 +103,7 @@ public class TerminologyLoaderSvcSnomedCtTest {
 	public void testLoadSnomedCtAgainstRealFile() throws Exception {
 		byte[] bytes = IOUtils.toByteArray(new FileInputStream("/Users/james/Downloads/SnomedCT_Release_INT_20160131_Full.zip"));
 
-		RequestDetails details = mock(RequestDetails.class);
+		mySvc.loadSnomedCt(list(bytes), mySrd);
-		mySvc.loadSnomedCt(list(bytes), details);
 	}
 
 	@Test
@@ -123,9 +115,8 @@ public class TerminologyLoaderSvcSnomedCtTest {
 
 		ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
 
-		RequestDetails details = mock(RequestDetails.class);
 		try {
-			mySvc.loadSnomedCt(list(bos.toByteArray()), details);
+			mySvc.loadSnomedCt(list(bos.toByteArray()), mySrd);
 			fail();
 		} catch (UnprocessableEntityException e) {
 			assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input: "));

hapi-fhir-jpaserver-base/src/test/resources/custom_term/codesystem.json

@@ -0,0 +1,10 @@
+{
+	"resourceType": "CodeSystem",
+	"url": "http://example.com/labCodes",
+	"name": "Example Lab Codes",
+	"description": "A set of lab codes",
+	"status": "active",
+	"publisher": "Example Organization Corporation Worldwide",
+	"date": "2019-07-30",
+	"content": "not-present"
+}

hapi-fhir-jpaserver-base/src/test/resources/custom_term/concepts.csv

@@ -0,0 +1,8 @@
+CODE,DISPLAY
+
+CHEM,Chemistry
+HB,Hemoglobin
+NEUT,Neutrophils
+
+MICRO,Microbiology
+C&S,Culture and Sensitivity

hapi-fhir-jpaserver-base/src/test/resources/custom_term/hierarchy.csv

@@ -0,0 +1,6 @@
+PARENT,CHILD
+
+CHEM,HB
+CHEM,NEUT
+
+MICRO,C&S

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/CachingValidationSupport.java

@@ -3,15 +3,17 @@ package org.hl7.fhir.r4.hapi.validation;
 import ca.uhn.fhir.context.FhirContext;
 import com.github.benmanes.caffeine.cache.Cache;
 import com.github.benmanes.caffeine.cache.Caffeine;
+import org.checkerframework.checker.nullness.qual.Nullable;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
 import org.hl7.fhir.r4.model.CodeSystem;
 import org.hl7.fhir.r4.model.StructureDefinition;
 import org.hl7.fhir.r4.model.ValueSet;
-import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.terminologies.ValueSetExpander;
 
 import java.util.List;
 import java.util.concurrent.TimeUnit;
+import java.util.function.Function;
 
 @SuppressWarnings("unchecked")
 public class CachingValidationSupport implements IValidationSupport {
@@ -21,7 +23,11 @@ public class CachingValidationSupport implements IValidationSupport {
 
 	public CachingValidationSupport(IValidationSupport theWrap) {
 		myWrap = theWrap;
-		myCache = Caffeine.newBuilder().expireAfterWrite(60, TimeUnit.SECONDS).build();
+		myCache = Caffeine
+			.newBuilder()
+			.expireAfterWrite(60, TimeUnit.SECONDS)
+			.maximumSize(5000)
+			.build();
 	}
 
 	@Override
@@ -31,14 +37,14 @@ public class CachingValidationSupport implements IValidationSupport {
 
 	@Override
 	public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
-		return (List<IBaseResource>) myCache.get("fetchAllConformanceResources",
+		String key = "fetchAllConformanceResources";
-			t -> myWrap.fetchAllConformanceResources(theContext));
+		return loadFromCache(key, t -> myWrap.fetchAllConformanceResources(theContext));
 	}
 
 	@Override
 	public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
-		return (List<StructureDefinition>) myCache.get("fetchAllStructureDefinitions",
+		String key = "fetchAllStructureDefinitions";
-			t -> myWrap.fetchAllStructureDefinitions(theContext));
+		return loadFromCache(key, t -> myWrap.fetchAllStructureDefinitions(theContext));
 	}
 
 	@Override
@@ -63,7 +69,8 @@ public class CachingValidationSupport implements IValidationSupport {
 
 	@Override
 	public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
-		return myWrap.isCodeSystemSupported(theContext, theSystem);
+		String key = "isCodeSystemSupported " + theSystem;
+		return loadFromCache(key, t -> myWrap.isCodeSystemSupported(theContext, theSystem));
 	}
 
 	@Override
@@ -73,11 +80,18 @@ public class CachingValidationSupport implements IValidationSupport {
 
 	@Override
 	public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
-		return myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay);
+		String key = "validateCode " + theCodeSystem + " " + theCode;
+		return loadFromCache(key, t -> myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay));
 	}
 
 	@Override
 	public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
-		return myWrap.lookupCode(theContext, theSystem, theCode);
+		String key = "lookupCode " + theSystem + " " + theCode;
+		return loadFromCache(key, t -> myWrap.lookupCode(theContext, theSystem, theCode));
+	}
+
+	@Nullable
+	private <T> T loadFromCache(String theKey, Function<String, T> theLoader) {
+		return (T) myCache.get(theKey, theLoader);
 	}
 }

src/changes/changes.xml

@@ -354,6 +354,11 @@
 				type for an operation declared on a plain provider without needing to use 
 				a specific version of the FHIR structures.
 			</action>
+			<action type="add">
+				The $upload-external-code-system operation and the corresponding HAPI FHIR CLI command
+				can now be used to upload custom vocabulary that has been converted into a standard file format
+				defined by HAPI FHIR. This is useful for uploading large organizational code systems.
+			</action>
 		</release>
 		<release version="3.8.0" date="2019-05-30" description="Hippo">
 			<action type="fix">