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Upload Terminology with Endpoint Validation (#4035)

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* add failing test

* Fix doc upload issue

* Add change log yaml file

* update due to review from Nathan

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: weiping202209 <weiping.yang@smilecdr.com>
This commit is contained in:
Nathan Doef 2022-09-28 11:17:01 -04:00 committed by GitHub
parent e4a2285f30
commit 31e13e6adb
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3 changed files with 67 additions and 2 deletions
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24
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
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@ -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
}

39
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
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@ -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)) {

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/4035-upload-terminology-failure-with-endpoint-validation.yaml Normal file
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@ -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."