diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
index 6bca38ccd78..de2b5966e31 100644
--- a/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
+++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
@@ -38,6 +38,7 @@ import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.CountingInputStream;
+import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
@@ -242,10 +243,11 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
byte[] bytes = theBytes;
String fileName = theFileName;
+ String suffix = fileName.substring(fileName.lastIndexOf("."));
if (bytes.length > ourTransferSizeLimit) {
ourLog.info("File size is greater than {} - Going to use a local file reference instead of a direct HTTP transfer. Note that this will only work when executing this command on the same server as the FHIR server itself.", FileUtil.formatFileSize(ourTransferSizeLimit));
- String suffix = fileName.substring(fileName.lastIndexOf("."));
+
try {
File tempFile = File.createTempFile("hapi-fhir-cli", suffix);
tempFile.deleteOnExit();
@@ -260,6 +262,7 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
}
ICompositeType attachment = AttachmentUtil.newInstance(myFhirCtx);
+ AttachmentUtil.setContentType(myFhirCtx, attachment, getContentType(suffix));
AttachmentUtil.setUrl(myFhirCtx, attachment, fileName);
if (bytes != null) {
AttachmentUtil.setData(myFhirCtx, attachment, bytes);
@@ -267,6 +270,25 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_FILE, attachment);
}
+ /*
+ * Files may be included in the attachment as raw CSV/JSON/XML files, or may also be combined into a compressed ZIP file.
+ * Content Type reference: https://smilecdr.com/docs/terminology/uploading.html#delta-add-operation
+ */
+ private String getContentType(String theSuffix) {
+ String retVal = "";
+ if(StringUtils.isNotBlank(theSuffix)) {
+ switch (theSuffix.toLowerCase()) {
+ case "csv" : retVal = "text/csv"; break;
+ case "xml" : retVal = "application/xml"; break;
+ case "json" : retVal = "application/json"; break;
+ case "zip" : retVal = "application/zip"; break;
+ default: retVal = "text/plain";
+ }
+ }
+ ourLog.debug("File suffix given was {} and contentType is {}, defaulting to content type text/plain", theSuffix, retVal);
+ return retVal;
+ }
+
private enum ModeEnum {
SNAPSHOT, ADD, REMOVE
}
diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java b/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
index 85e4a28b604..71e96eeebf7 100644
--- a/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
+++ b/hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
@@ -1,19 +1,26 @@
package ca.uhn.fhir.cli;
import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
-import ca.uhn.fhir.test.utilities.TlsAuthenticationTestHelper;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.test.utilities.BaseRestServerHelper;
import ca.uhn.fhir.test.utilities.RestServerDstu3Helper;
import ca.uhn.fhir.test.utilities.RestServerR4Helper;
+import ca.uhn.fhir.test.utilities.TlsAuthenticationTestHelper;
+import ca.uhn.fhir.validation.FhirValidator;
import com.google.common.base.Charsets;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.hamcrest.Matchers;
+import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
+import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
+import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
+import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@@ -460,6 +467,19 @@ public class UploadTerminologyCommandTest {
@ParameterizedTest
@MethodSource("paramsProvider")
public void testUploadICD10UsingCompressedFile(String theFhirVersion, boolean theIncludeTls) throws IOException {
+ uploadICD10UsingCompressedFile(theFhirVersion, theIncludeTls);
+ }
+
+ @ParameterizedTest
+ @MethodSource("paramsProvider")
+ public void testUploadTerminologyWithEndpointValidation(String theFhirVersion, boolean theIncludeTls) throws IOException {
+ RequestValidatingInterceptor requestValidatingInterceptor = createRequestValidatingInterceptor();
+ myBaseRestServerHelper.registerInterceptor(requestValidatingInterceptor);
+
+ uploadICD10UsingCompressedFile(theFhirVersion, theIncludeTls);
+ }
+
+ private void uploadICD10UsingCompressedFile(String theFhirVersion, boolean theIncludeTls) throws IOException {
if (FHIR_VERSION_DSTU3.equals(theFhirVersion)) {
when(myTermLoaderSvc.loadIcd10cm(anyList(), any())).thenReturn(new UploadStatistics(100, new org.hl7.fhir.dstu3.model.IdType("CodeSystem/101")));
} else if (FHIR_VERSION_R4.equals(theFhirVersion)) {
@@ -486,6 +506,23 @@ public class UploadTerminologyCommandTest {
assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
}
+ private RequestValidatingInterceptor createRequestValidatingInterceptor(){
+ FhirInstanceValidator fhirInstanceValidator = new FhirInstanceValidator(myCtx);
+ ValidationSupportChain validationSupport = new ValidationSupportChain(
+ new DefaultProfileValidationSupport(myCtx),
+ new InMemoryTerminologyServerValidationSupport(myCtx),
+ new CommonCodeSystemsTerminologyService(myCtx)
+ );
+
+ fhirInstanceValidator.setValidationSupport(validationSupport);
+ FhirValidator fhirValidator = myCtx.newValidator();
+ fhirValidator.registerValidatorModule(fhirInstanceValidator);
+
+ RequestValidatingInterceptor requestValidatingInterceptor = new RequestValidatingInterceptor();
+ requestValidatingInterceptor.setValidatorModules(List.of(fhirInstanceValidator));
+ return requestValidatingInterceptor;
+ }
+
private synchronized void writeConceptAndHierarchyFiles() throws IOException {
if (!myConceptsFile.exists()) {
try (FileWriter w = new FileWriter(myConceptsFile, false)) {
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4035-upload-terminology-failure-with-endpoint-validation.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4035-upload-terminology-failure-with-endpoint-validation.yaml
new file mode 100644
index 00000000000..d4aa2d273e0
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4035-upload-terminology-failure-with-endpoint-validation.yaml
@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 4091
+jira: SMILE-3977
+title: "Previously, when the upload-terminology command was used to upload a terminology file with endpoint validation enabled, a validation error occurred due to a missing file content type.
+ This has been fixed by specifying the file content type of the uploaded file."