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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>
This commit is contained in:
jdar8 2022-09-02 10:58:57 -07:00 committed by GitHub
parent 9fd0addec6
commit 21cce44524
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4 changed files with 59 additions and 3 deletions
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2
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/AbstractImportExportCsvConceptMapCommand.java
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@ -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;

15
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommand.java
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@ -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));

38
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandR4Test.java
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@ -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"));
}
}
}

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_0/3962-import-csv-to-conceptmap-needs-status-element.yaml Normal file
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@ -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."