3962 import csv to conceptmap needs status element (#3963)

* wip

* test

* refactor

* doc change and changelog

* add test cases

* edit msg.code

* fix msg code

Co-authored-by: Justin_Dar <justin.dar@smilecdr.com>

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

@@ -138,7 +138,7 @@ public abstract class AbstractImportExportCsvConceptMapCommand extends BaseReque
 		process();
 	}
 
-	protected void parseAdditionalParameters(CommandLine theCommandLine) {}
+	protected void parseAdditionalParameters(CommandLine theCommandLine) throws ParseException {}
 
 	protected abstract void process() throws ParseException, ExecutionException;
 

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVParser;
 import org.apache.commons.csv.CSVRecord;
@@ -64,10 +65,15 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 	protected static final String TARGET_VALUE_SET_PARAM_LONGOPT = "output";
 	protected static final String TARGET_VALUE_SET_PARAM_NAME = "output";
 	protected static final String TARGET_VALUE_SET_PARAM_DESC = "The target value set of the ConceptMap to be imported (i.e. ConceptMap.targetUri).";
+	protected static final String CONCEPTMAP_STATUS_PARAM = "s";
+	protected static final String CONCEPTMAP_STATUS_PARAM_LONGOPT = "status";
+	protected static final String CONCEPTMAP_STATUS_PARAM_NAME = "status";
+	protected static final String CONCEPTMAP_STATUS_PARAM_DESC = "The status of the ConceptMap resource to be imported/exported (i.e. ConceptMap.status).";
 
 	protected String sourceValueSet;
 	protected String targetValueSet;
 
+	private String status;
 	private boolean hasElements;
 	private boolean hasTargets;
 
@@ -86,6 +92,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 		Options options = super.getOptions();
 
 		addRequiredOption(options, CONCEPTMAP_URL_PARAM, CONCEPTMAP_URL_PARAM_LONGOPT, CONCEPTMAP_URL_PARAM_NAME, CONCEPTMAP_URL_PARAM_DESC);
+		addRequiredOption(options, CONCEPTMAP_STATUS_PARAM, CONCEPTMAP_STATUS_PARAM_LONGOPT, CONCEPTMAP_STATUS_PARAM_NAME, CONCEPTMAP_STATUS_PARAM_DESC);
 		// </editor-fold desc="Additional parameters.">
 		addOptionalOption(options, SOURCE_VALUE_SET_PARAM, SOURCE_VALUE_SET_PARAM_LONGOPT, SOURCE_VALUE_SET_PARAM_NAME, SOURCE_VALUE_SET_PARAM_DESC);
 		addOptionalOption(options, TARGET_VALUE_SET_PARAM, TARGET_VALUE_SET_PARAM_LONGOPT, TARGET_VALUE_SET_PARAM_NAME, TARGET_VALUE_SET_PARAM_DESC);
@@ -96,7 +103,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 	}
 
 	@Override
-	protected void parseAdditionalParameters(CommandLine theCommandLine) {
+	protected void parseAdditionalParameters(CommandLine theCommandLine) throws ParseException {
 		sourceValueSet = theCommandLine.getOptionValue(SOURCE_VALUE_SET_PARAM);
 		if (isBlank(sourceValueSet)) {
 			ourLog.info("Source value set is not specified (i.e. ConceptMap.sourceUri).");
@@ -110,6 +117,11 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 		} else {
 			ourLog.info("Specified target value set (i.e. ConceptMap.targetUri): {}", targetValueSet);
 		}
+
+		status = theCommandLine.getOptionValue(CONCEPTMAP_STATUS_PARAM);
+		if (isBlank(status)) {
+			throw new ParseException(Msg.code(2132) + "No status (" + CONCEPTMAP_STATUS_PARAM + ") specified.");
+		}
 	}
 
 	@Override
@@ -178,6 +190,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
 					.withTrim())
 		) {
 			retVal.setUrl(conceptMapUrl);
+			retVal.setStatus(Enumerations.PublicationStatus.fromCode(status));
 
 			if (isNotBlank(sourceValueSet)) {
 				retVal.setSource(new UriType(sourceValueSet));

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandR4Test.java

@@ -2,8 +2,8 @@ package ca.uhn.fhir.cli;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.api.MethodOutcome;
-import ca.uhn.fhir.test.utilities.TlsAuthenticationTestHelper;
 import ca.uhn.fhir.test.utilities.RestServerR4Helper;
+import ca.uhn.fhir.test.utilities.TlsAuthenticationTestHelper;
 import ca.uhn.fhir.util.TestUtil;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.model.Bundle;
@@ -11,6 +11,7 @@ import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
 import org.hl7.fhir.r4.model.ConceptMap.SourceElementComponent;
 import org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent;
+import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
@@ -24,6 +25,7 @@ import java.io.File;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
 
 public class ImportCsvToConceptMapCommandR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ImportCsvToConceptMapCommandR4Test.class);
@@ -34,6 +36,7 @@ public class ImportCsvToConceptMapCommandR4Test {
 	private static final String CS_URL_2 = "http://example.com/codesystem/2";
 	private static final String CS_URL_3 = "http://example.com/codesystem/3";
 	private static final String FILENAME = "import-csv-to-conceptmap-command-test-input.csv";
+	private static final String STATUS = "Active";
 
 	static {
 		System.setProperty("test", "true");
@@ -42,6 +45,8 @@ public class ImportCsvToConceptMapCommandR4Test {
 	private final FhirContext myFhirContext = FhirContext.forR4();
 	private final String myVersion = "r4";
 	private String myFilePath;
+	private final String myStatus = Enumerations.PublicationStatus.ACTIVE.toCode();
+
 
 	@RegisterExtension
 	public final RestServerR4Helper myRestServerR4Helper = new RestServerR4Helper(true);
@@ -134,6 +139,7 @@ public class ImportCsvToConceptMapCommandR4Test {
 				"-i", VS_URL_1,
 				"-o", VS_URL_2,
 				"-f", myFilePath,
+				"-s", myStatus,
 				"-l"
 			},
 			"-t", theIncludeTls, myRestServerR4Helper
@@ -153,6 +159,7 @@ public class ImportCsvToConceptMapCommandR4Test {
 		assertEquals(myRestServerR4Helper.getBase() + "/ConceptMap/1/_history/1", conceptMap.getId());
 
 		assertEquals(CM_URL, conceptMap.getUrl());
+		assertEquals(STATUS, conceptMap.getStatus().getDisplay());
 		assertEquals(VS_URL_1, conceptMap.getSourceUriType().getValueAsString());
 		assertEquals(VS_URL_2, conceptMap.getTargetUriType().getValueAsString());
 
@@ -334,6 +341,7 @@ public class ImportCsvToConceptMapCommandR4Test {
 				"-i", VS_URL_1,
 				"-o", VS_URL_2,
 				"-f", myFilePath,
+				"-s", myStatus,
 				"-l"
 			},
 			"-t", theIncludeTls, myRestServerR4Helper
@@ -366,6 +374,7 @@ public class ImportCsvToConceptMapCommandR4Test {
 				"-i", "http://loinc.org",
 				"-o", "http://phenxtoolkit.org",
 				"-f", myFilePath,
+				"-s", myStatus,
 				"-l"
 			},
 			"-t", theIncludeTls, myRestServerR4Helper
@@ -385,6 +394,7 @@ public class ImportCsvToConceptMapCommandR4Test {
 		assertEquals(myRestServerR4Helper.getBase() + "/ConceptMap/1/_history/1", conceptMap.getId());
 
 		assertEquals("http://loinc.org/cm/loinc-to-phenx", conceptMap.getUrl());
+		assertEquals(STATUS, conceptMap.getStatus().getDisplay());
 		assertEquals("http://loinc.org", conceptMap.getSourceUriType().getValueAsString());
 		assertEquals("http://phenxtoolkit.org", conceptMap.getTargetUriType().getValueAsString());
 
@@ -418,6 +428,7 @@ public class ImportCsvToConceptMapCommandR4Test {
 				"-i", "http://loinc.org",
 				"-o", "http://phenxtoolkit.org",
 				"-f", myFilePath,
+				"-s", myStatus,
 				"-l"
 			},
 			"-t", theIncludeTls, myRestServerR4Helper
@@ -434,4 +445,29 @@ public class ImportCsvToConceptMapCommandR4Test {
 
 		assertEquals(myRestServerR4Helper.getBase() + "/ConceptMap/1/_history/2", conceptMap.getId());
 	}
+
+	@Test
+	public void testImportCsvToConceptMapCommand_withNoStatus_Fails() throws FHIRException {
+		ClassLoader classLoader = getClass().getClassLoader();
+		File fileToImport = new File(classLoader.getResource("loinc-to-phenx.csv").getFile());
+		myFilePath = fileToImport.getAbsolutePath();
+
+		try {
+			App.main(myTlsAuthenticationTestHelper.createBaseRequestGeneratingCommandArgs(
+				new String[]{
+					ImportCsvToConceptMapCommand.COMMAND,
+					"-v", myVersion,
+					"-u", "http://loinc.org/cm/loinc-to-phenx",
+					"-i", "http://loinc.org",
+					"-o", "http://phenxtoolkit.org",
+					"-f", myFilePath,
+					"-l"
+				},
+				"-t", true, myRestServerR4Helper
+			));
+			fail();
+		} catch (Error e) {
+			assertTrue(e.getMessage().contains("Missing required option: s"));
+		}
+	}
 }

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3962-import-csv-to-conceptmap-needs-status-element.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 3962
+jira: SMILE-4516
+title: "Previously, using the `import-csv-to-conceptmap` command in the CLI successfully created ConceptMap resources 
+without a `ConceptMap.status` element, which is against the FHIR specification. This has been fixed by adding a required
+option for status for the command."