Add current-version parameter to upload-terminology command.
This commit is contained in:
juan.marchionatto
parent
0a27b08aad
commit
e0e52c666c
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@ -22,6 +22,7 @@ package ca.uhn.fhir.cli;
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import ca.uhn.fhir.jpa.model.util.JpaConstants;
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import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
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import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
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import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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@ -38,6 +39,7 @@ import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.input.CountingInputStream;
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import org.apache.commons.lang3.StringUtils;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.hl7.fhir.instance.model.api.ICompositeType;
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import org.hl7.fhir.r4.model.CodeSystem;
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@ -58,6 +60,7 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UploadTerminologyCommand.class);
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private static final long DEFAULT_TRANSFER_SIZE_LIMIT = 10 * FileUtils.ONE_MB;
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private static long ourTransferSizeLimit = DEFAULT_TRANSFER_SIZE_LIMIT;
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private static final String CURRENT_VERSION = "current-version";
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@Override
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public String getCommandDescription() {
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@ -76,6 +79,8 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
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addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + ITermLoaderSvc.SCT_URI + ")");
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addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
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addOptionalOption(options, "m", "mode", true, "The upload mode: SNAPSHOT (default), ADD, REMOVE");
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addOptionalOption(options, null, CURRENT_VERSION, true, "For LOINC upload. If specified as 'false' the uploaded version will not become current. " +
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"Allowed values: true (default) or false");
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return options;
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}
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@ -102,6 +107,8 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
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throw new ParseException("No data file provided");
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}
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String makeCurrentVersionOption = theCommandLine.getOptionValue(CURRENT_VERSION);
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IGenericClient client = newClient(theCommandLine);
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if (theCommandLine.hasOption(VERBOSE_LOGGING_PARAM)) {
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@ -120,10 +127,11 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
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requestName = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE;
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break;
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}
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invokeOperation(termUrl, datafile, client, requestName);
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invokeOperation(termUrl, datafile, client, requestName, makeCurrentVersionOption);
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}
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private void invokeOperation(String theTermUrl, String[] theDatafile, IGenericClient theClient, String theOperationName) throws ParseException {
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private void invokeOperation(String theTermUrl, String[] theDatafile,
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IGenericClient theClient, String theOperationName, String makeCurrentVersionOption) throws ParseException {
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IBaseParameters inputParameters = ParametersUtil.newInstance(myFhirCtx);
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boolean isDeltaOperation =
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@ -132,6 +140,16 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
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ParametersUtil.addParameterToParametersUri(myFhirCtx, inputParameters, TerminologyUploaderProvider.PARAM_SYSTEM, theTermUrl);
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if (StringUtils.isNotBlank(makeCurrentVersionOption)) {
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boolean isMakeCurrentVersion = Boolean.parseBoolean(makeCurrentVersionOption);
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ParametersUtil.addParameterToParametersString(
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myFhirCtx, inputParameters, TermLoaderSvcImpl.MAKE_CURRENT_VERSION, String.valueOf(isMakeCurrentVersion));
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}
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//todo: is this the case?. Check with client
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// if (mode != ModeEnum.SNAPSHOT && ! isMakeCurrentVersion) {
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// throw new ParseException("Delta operations must use (or default to) " + CURRENT_VERSION + "=true parameter");
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// }
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ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
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ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
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int compressedSourceBytesCount = 0;
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@ -2,14 +2,17 @@ package ca.uhn.fhir.cli;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
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import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
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import ca.uhn.fhir.jpa.term.UploadStatistics;
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import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
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import ca.uhn.fhir.rest.server.RestfulServer;
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import ca.uhn.fhir.test.BaseTest;
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import ca.uhn.fhir.test.utilities.JettyUtil;
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import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
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import ca.uhn.fhir.util.ParametersUtil;
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import com.google.common.base.Charsets;
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import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.DefaultParser;
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@ -22,6 +25,7 @@ import org.eclipse.jetty.servlet.ServletHolder;
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import org.hamcrest.Matchers;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Parameters;
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import org.hl7.fhir.r4.model.Patient;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeEach;
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@ -58,6 +62,8 @@ import static org.junit.jupiter.api.Assertions.fail;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.ArgumentMatchers.eq;
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import static org.mockito.Mockito.anyList;
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import static org.mockito.Mockito.doReturn;
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import static org.mockito.Mockito.spy;
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import static org.mockito.Mockito.times;
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import static org.mockito.Mockito.verify;
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import static org.mockito.Mockito.when;
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@ -346,139 +352,248 @@ public class UploadTerminologyCommandTest extends BaseTest {
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}
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@Nested
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public class HeaderPassthroughOptionTests {
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public class RestulServerExtensionTests {
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@RegisterExtension
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public final RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(myCtx);
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private final String headerKey1 = "test-header-key-1";
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private final String headerValue1 = "test header value-1";
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@Nested
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public class HeaderPassthroughOptionTests {
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private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
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private final UploadTerminologyCommand testedCommand =
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new RequestCapturingUploadTerminologyCommand(myCapturingInterceptor);
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private final String headerKey1 = "test-header-key-1";
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private final String headerValue1 = "test header value-1";
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@BeforeEach
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public void before() {
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when(myTermLoaderSvc.loadCustom(eq("http://foo"), anyList(), any()))
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.thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
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private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
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private final UploadTerminologyCommand testedCommand =
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new RequestCapturingUploadTerminologyCommand(myCapturingInterceptor);
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TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
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myRestfulServerExtension.registerProvider(provider);
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}
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@BeforeEach
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public void before() {
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when(myTermLoaderSvc.loadCustom(eq("http://foo"), anyList(), any()))
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.thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
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@Test
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public void oneHeader() throws Exception {
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String[] args = new String[] {
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"-v", "r4",
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"-m", "SNAPSHOT",
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"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
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"-u", "http://foo",
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"-d", myConceptsFileName,
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"-d", myHierarchyFileName,
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"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\""
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};
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writeConceptAndHierarchyFiles();
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final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
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testedCommand.run(commandLine);
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assertNotNull(myCapturingInterceptor.getLastRequest());
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Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
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assertFalse(allHeaders.isEmpty());
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assertTrue(allHeaders.containsKey(headerKey1));
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assertEquals(1, allHeaders.get(headerKey1).size());
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assertThat(allHeaders.get(headerKey1), hasItems(headerValue1));
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}
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@Test
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public void twoHeadersSameKey() throws Exception {
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final String headerValue2 = "test header value-2";
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String[] args = new String[] {
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"-v", "r4",
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"-m", "SNAPSHOT",
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"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
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"-u", "http://foo",
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"-d", myConceptsFileName,
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"-d", myHierarchyFileName,
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"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
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"-hp", "\"" + headerKey1 + ":" + headerValue2 + "\""
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};
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writeConceptAndHierarchyFiles();
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final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
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testedCommand.run(commandLine);
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assertNotNull(myCapturingInterceptor.getLastRequest());
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Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
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assertFalse(allHeaders.isEmpty());
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assertEquals(2, allHeaders.get(headerKey1).size());
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assertTrue(allHeaders.containsKey(headerKey1));
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assertEquals(2, allHeaders.get(headerKey1).size());
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assertEquals(headerValue1, allHeaders.get(headerKey1).get(0));
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assertEquals(headerValue2, allHeaders.get(headerKey1).get(1));
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}
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@Test
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public void twoHeadersDifferentKeys() throws Exception {
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final String headerKey2 = "test-header-key-2";
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final String headerValue2 = "test header value-2";
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String[] args = new String[] {
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"-v", "r4",
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"-m", "SNAPSHOT",
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"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
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"-u", "http://foo",
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"-d", myConceptsFileName,
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"-d", myHierarchyFileName,
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"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
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"-hp", "\"" + headerKey2 + ":" + headerValue2 + "\""
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};
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writeConceptAndHierarchyFiles();
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final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
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testedCommand.run(commandLine);
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assertNotNull(myCapturingInterceptor.getLastRequest());
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Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
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assertFalse(allHeaders.isEmpty());
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assertTrue(allHeaders.containsKey(headerKey1));
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assertEquals(1, allHeaders.get(headerKey1).size());
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assertThat(allHeaders.get(headerKey1), hasItems(headerValue1));
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assertTrue(allHeaders.containsKey(headerKey2));
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assertEquals(1, allHeaders.get(headerKey2).size());
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assertThat(allHeaders.get(headerKey2), hasItems(headerValue2));
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}
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private class RequestCapturingUploadTerminologyCommand extends UploadTerminologyCommand {
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private CapturingInterceptor myCapturingInterceptor;
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public RequestCapturingUploadTerminologyCommand(CapturingInterceptor theCapturingInterceptor) {
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myCapturingInterceptor = theCapturingInterceptor;
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TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
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myRestfulServerExtension.registerProvider(provider);
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}
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@Override
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protected IGenericClient newClient(CommandLine theCommandLine) throws ParseException {
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IGenericClient client = super.newClient(theCommandLine);
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client.getInterceptorService().registerInterceptor(myCapturingInterceptor);
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return client;
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@Test
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public void oneHeader() throws Exception {
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String[] args = new String[] {
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"-v", "r4",
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"-m", "SNAPSHOT",
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"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
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"-u", "http://foo",
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"-d", myConceptsFileName,
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"-d", myHierarchyFileName,
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"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\""
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};
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writeConceptAndHierarchyFiles();
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final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
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testedCommand.run(commandLine);
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assertNotNull(myCapturingInterceptor.getLastRequest());
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Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
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assertFalse(allHeaders.isEmpty());
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assertTrue(allHeaders.containsKey(headerKey1));
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assertEquals(1, allHeaders.get(headerKey1).size());
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assertThat(allHeaders.get(headerKey1), hasItems(headerValue1));
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}
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@Test
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public void twoHeadersSameKey() throws Exception {
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final String headerValue2 = "test header value-2";
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String[] args = new String[] {
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"-v", "r4",
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"-m", "SNAPSHOT",
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"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
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"-u", "http://foo",
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"-d", myConceptsFileName,
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"-d", myHierarchyFileName,
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"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
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"-hp", "\"" + headerKey1 + ":" + headerValue2 + "\""
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};
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writeConceptAndHierarchyFiles();
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final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
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testedCommand.run(commandLine);
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assertNotNull(myCapturingInterceptor.getLastRequest());
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Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
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assertFalse(allHeaders.isEmpty());
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assertEquals(2, allHeaders.get(headerKey1).size());
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assertTrue(allHeaders.containsKey(headerKey1));
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assertEquals(2, allHeaders.get(headerKey1).size());
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assertEquals(headerValue1, allHeaders.get(headerKey1).get(0));
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assertEquals(headerValue2, allHeaders.get(headerKey1).get(1));
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}
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@Test
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public void twoHeadersDifferentKeys() throws Exception {
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final String headerKey2 = "test-header-key-2";
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final String headerValue2 = "test header value-2";
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String[] args = new String[] {
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"-v", "r4",
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"-m", "SNAPSHOT",
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"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
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"-u", "http://foo",
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"-d", myConceptsFileName,
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"-d", myHierarchyFileName,
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"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
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"-hp", "\"" + headerKey2 + ":" + headerValue2 + "\""
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};
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writeConceptAndHierarchyFiles();
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final CommandLine commandLine = new DefaultParser().parse(testedCommand.getOptions(), args, true);
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testedCommand.run(commandLine);
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assertNotNull(myCapturingInterceptor.getLastRequest());
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Map<String, List<String>> allHeaders = myCapturingInterceptor.getLastRequest().getAllHeaders();
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assertFalse(allHeaders.isEmpty());
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assertTrue(allHeaders.containsKey(headerKey1));
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assertEquals(1, allHeaders.get(headerKey1).size());
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assertThat(allHeaders.get(headerKey1), hasItems(headerValue1));
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assertTrue(allHeaders.containsKey(headerKey2));
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assertEquals(1, allHeaders.get(headerKey2).size());
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assertThat(allHeaders.get(headerKey2), hasItems(headerValue2));
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}
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private class RequestCapturingUploadTerminologyCommand extends UploadTerminologyCommand {
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private CapturingInterceptor myCapturingInterceptor;
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public RequestCapturingUploadTerminologyCommand(CapturingInterceptor theCapturingInterceptor) {
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myCapturingInterceptor = theCapturingInterceptor;
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}
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@Override
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protected IGenericClient newClient(CommandLine theCommandLine) throws ParseException {
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IGenericClient client = super.newClient(theCommandLine);
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client.getInterceptorService().registerInterceptor(myCapturingInterceptor);
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return client;
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}
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}
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}
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@Nested
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public class CurrentVersionParameterTests {
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private TerminologyUploaderProvider terminologyUploaderProvider;
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private final UploadTerminologyCommand testedCommand = new UploadTerminologyCommand();
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@Captor private ArgumentCaptor<RequestDetails> myRequestDetailsCaptor;
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@BeforeEach
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public void before() throws IOException {
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writeConceptAndHierarchyFiles();
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terminologyUploaderProvider = spy(new TerminologyUploaderProvider(myCtx, myTermLoaderSvc));
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myRestfulServerExtension.registerProvider(terminologyUploaderProvider);
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}
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@Test
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public void noMakeCurrentVersionParam() throws ParseException {
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String[] args = new String[]{
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"-v", "r4",
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"-m", "SNAPSHOT",
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"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
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"-u", "http://loinc.org",
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"-d", myConceptsFileName,
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"-d", myHierarchyFileName
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};
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final CommandLine commandLine = new DefaultParser()
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.parse(testedCommand.getOptions(), args, true);
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doReturn(ParametersUtil.newInstance(myCtx)).when(terminologyUploaderProvider)
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.uploadSnapshot(any(), any(), any(), any(), myRequestDetailsCaptor.capture());
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testedCommand.run(commandLine);
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RequestDetails requestDetails = myRequestDetailsCaptor.getValue();
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Parameters params = (Parameters) requestDetails.getResource();
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assertFalse(params.hasParameter(TermLoaderSvcImpl.MAKE_CURRENT_VERSION));
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}
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@Test
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public void explicitMakeCurrentVersionTrueParam() throws ParseException {
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String[] args = new String[]{
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"-v", "r4",
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"-m", "SNAPSHOT",
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"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
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"-u", "http://loinc.org",
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"-d", myConceptsFileName,
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"-d", myHierarchyFileName,
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"--current-version", "true"
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};
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final CommandLine commandLine = new DefaultParser()
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.parse(testedCommand.getOptions(), args, true);
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|
||||
doReturn(ParametersUtil.newInstance(myCtx)).when(terminologyUploaderProvider)
|
||||
.uploadSnapshot(any(), any(), any(), any(), myRequestDetailsCaptor.capture());
|
||||
|
||||
testedCommand.run(commandLine);
|
||||
|
||||
RequestDetails requestDetails = myRequestDetailsCaptor.getValue();
|
||||
Parameters params = (Parameters) requestDetails.getResource();
|
||||
assertTrue(params.hasParameter(TermLoaderSvcImpl.MAKE_CURRENT_VERSION));
|
||||
assertEquals("true", params.getParameter(TermLoaderSvcImpl.MAKE_CURRENT_VERSION).toString());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void MakeCurrentVersionFalseParamReachesProvider() throws ParseException {
|
||||
String[] args = new String[]{
|
||||
"-v", "r4",
|
||||
"-m", "SNAPSHOT",
|
||||
"-t", "http://localhost:" + myRestfulServerExtension.getPort(),
|
||||
"-u", "http://loinc.org",
|
||||
"-d", myConceptsFileName,
|
||||
"-d", myHierarchyFileName,
|
||||
"--current-version", "false"
|
||||
};
|
||||
|
||||
final CommandLine commandLine = new DefaultParser()
|
||||
.parse(testedCommand.getOptions(), args, true);
|
||||
|
||||
doReturn(ParametersUtil.newInstance(myCtx)).when(terminologyUploaderProvider)
|
||||
.uploadSnapshot(any(), any(), any(), any(), myRequestDetailsCaptor.capture());
|
||||
|
||||
testedCommand.run(commandLine);
|
||||
|
||||
RequestDetails requestDetails = myRequestDetailsCaptor.getValue();
|
||||
Parameters params = (Parameters) requestDetails.getResource();
|
||||
List<String> values = ParametersUtil.getNamedParameterValuesAsString(
|
||||
myCtx, params, TermLoaderSvcImpl.MAKE_CURRENT_VERSION);
|
||||
assertEquals(1, values.size());
|
||||
assertEquals("false", values.get(0));
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
private void writeArchiveFile(File... theFiles) throws IOException {
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
private void writeArchiveFile(File... theFiles) throws IOException {
|
||||
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
|
||||
ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,5 @@
|
|||
---
|
||||
type: add
|
||||
issue: 2786
|
||||
title: "Add 'current-version' parameter to upload-terminology command to allow loading version
|
||||
without becoming current. Available for LOINC uploads".
|
||||
|
|
@ -102,6 +102,7 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
|
|||
public IBaseParameters uploadSnapshot(
|
||||
HttpServletRequest theServletRequest,
|
||||
@OperationParam(name = PARAM_SYSTEM, min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
|
||||
@OperationParam(name = TermLoaderSvcImpl.MAKE_CURRENT_VERSION, min = 0, max = 1) IPrimitiveType<String> isMakeCurrentVersion,
|
||||
@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles,
|
||||
RequestDetails theRequestDetails
|
||||
) {
|
||||
|
|
|
|||
|
|
@ -86,9 +86,6 @@ import java.util.UUID;
|
|||
import java.util.concurrent.atomic.AtomicInteger;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.defaultString;
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
||||
|
|
@ -381,7 +378,9 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
|
||||
@Override
|
||||
@Transactional
|
||||
public IIdType storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequest, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
|
||||
public IIdType storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion,
|
||||
RequestDetails theRequest, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, boolean theIsMakeItCurrentVersion) {
|
||||
|
||||
assert TransactionSynchronizationManager.isActualTransactionActive();
|
||||
|
||||
Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
|
||||
|
|
@ -396,7 +395,8 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
|
||||
populateCodeSystemVersionProperties(theCodeSystemVersion, theCodeSystemResource, resource);
|
||||
|
||||
storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemResource.getName(), theCodeSystemResource.getVersion(), theCodeSystemVersion, resource);
|
||||
storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemResource.getName(),
|
||||
theCodeSystemResource.getVersion(), theCodeSystemVersion, resource, theIsMakeItCurrentVersion);
|
||||
|
||||
myDeferredStorageSvc.addConceptMapsToStorageQueue(theConceptMaps);
|
||||
myDeferredStorageSvc.addValueSetsToStorageQueue(theValueSets);
|
||||
|
|
@ -406,7 +406,10 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
|
||||
@Override
|
||||
@Transactional
|
||||
public void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theCodeSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
|
||||
public void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri,
|
||||
String theSystemName, String theCodeSystemVersionId, TermCodeSystemVersion theCodeSystemVersion,
|
||||
ResourceTable theCodeSystemResourceTable, boolean theIsMakeItCurrentVersion) {
|
||||
|
||||
assert TransactionSynchronizationManager.isActualTransactionActive();
|
||||
|
||||
ourLog.debug("Storing code system");
|
||||
|
|
@ -470,32 +473,39 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
|
|||
|
||||
ourLog.debug("Saving code system");
|
||||
|
||||
codeSystem.setCurrentVersion(codeSystemToStore);
|
||||
if (codeSystem.getPid() == null) {
|
||||
codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
|
||||
}
|
||||
|
||||
ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
|
||||
|
||||
for (TermConcept next : conceptsToSave) {
|
||||
populateVersion(next, codeSystemToStore);
|
||||
}
|
||||
|
||||
ourLog.debug("Saving {} concepts...", totalCodeCount);
|
||||
|
||||
IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
|
||||
for (TermConcept next : conceptsToSave) {
|
||||
persistChildren(next, codeSystemToStore, conceptsStack2, totalCodeCount);
|
||||
}
|
||||
|
||||
ourLog.debug("Done saving concepts, flushing to database");
|
||||
|
||||
if (myDeferredStorageSvc.isStorageQueueEmpty() == false) {
|
||||
ourLog.info("Note that some concept saving has been deferred");
|
||||
if (theIsMakeItCurrentVersion) {
|
||||
makeCodeSystemCurrentVersion(codeSystem, codeSystemToStore, conceptsToSave, totalCodeCount);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
private void makeCodeSystemCurrentVersion(TermCodeSystem theCodeSystem, TermCodeSystemVersion theCodeSystemToStore,
|
||||
Collection<TermConcept> theConceptsToSave, int theTotalCodeCount) {
|
||||
|
||||
theCodeSystem.setCurrentVersion(theCodeSystemToStore);
|
||||
if (theCodeSystem.getPid() == null) {
|
||||
theCodeSystem = myCodeSystemDao.saveAndFlush(theCodeSystem);
|
||||
}
|
||||
|
||||
ourLog.debug("Setting CodeSystemVersion[{}] on {} concepts...", theCodeSystem.getPid(), theTotalCodeCount);
|
||||
for (TermConcept next : theConceptsToSave) {
|
||||
populateVersion(next, theCodeSystemToStore);
|
||||
}
|
||||
|
||||
ourLog.debug("Saving {} concepts...", theTotalCodeCount);
|
||||
IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
|
||||
for (TermConcept next : theConceptsToSave) {
|
||||
persistChildren(next, theCodeSystemToStore, conceptsStack2, theTotalCodeCount);
|
||||
}
|
||||
|
||||
ourLog.debug("Done saving concepts, flushing to database");
|
||||
if (! myDeferredStorageSvc.isStorageQueueEmpty()) {
|
||||
ourLog.info("Note that some concept saving has been deferred");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private TermCodeSystemVersion getExistingTermCodeSystemVersion(Long theCodeSystemVersionPid, String theCodeSystemVersion) {
|
||||
TermCodeSystemVersion existing;
|
||||
if (theCodeSystemVersion == null) {
|
||||
|
|
|
|||
|
|
@ -38,9 +38,11 @@ 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.util.ClasspathUtil;
|
||||
import ca.uhn.fhir.util.ParametersUtil;
|
||||
import ca.uhn.fhir.util.ValidateUtil;
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.collections4.CollectionUtils;
|
||||
import org.apache.commons.csv.CSVFormat;
|
||||
import org.apache.commons.csv.CSVParser;
|
||||
import org.apache.commons.csv.CSVRecord;
|
||||
|
|
@ -49,10 +51,12 @@ import org.apache.commons.io.IOUtils;
|
|||
import org.apache.commons.lang3.ObjectUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.ConceptMap;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.springframework.aop.support.AopUtils;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
|
@ -148,6 +152,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
|
||||
public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
|
||||
public static final String CUSTOM_PROPERTIES_FILE = "properties.csv";
|
||||
public static final String MAKE_CURRENT_VERSION = "isMakeCurrentVersion";
|
||||
static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
|
||||
static final String IMGTHLA_HLA_XML = "hla.xml";
|
||||
static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
|
||||
|
|
@ -188,7 +193,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
|
||||
@Override
|
||||
public UploadStatistics loadImgthla(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
|
||||
try (LoadedFileDescriptors descriptors = getLoadedFileDescriptors(theFiles)) {
|
||||
List<String> mandatoryFilenameFragments = Arrays.asList(
|
||||
IMGTHLA_HLA_NOM_TXT,
|
||||
IMGTHLA_HLA_XML
|
||||
|
|
@ -201,11 +206,23 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
}
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
LoadedFileDescriptors getLoadedFileDescriptors(List<FileDescriptor> theFiles) {
|
||||
return new LoadedFileDescriptors(theFiles);
|
||||
}
|
||||
|
||||
@Override
|
||||
public UploadStatistics loadLoinc(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
|
||||
try (LoadedFileDescriptors descriptors = getLoadedFileDescriptors(theFiles)) {
|
||||
Properties uploadProperties = getProperties(descriptors, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
|
||||
|
||||
String codeSystemVersionId = uploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
|
||||
boolean isMakeCurrentVersion = getIsMakeCurrentVersion(theRequestDetails);
|
||||
if (StringUtils.isBlank(codeSystemVersionId) && ! isMakeCurrentVersion) {
|
||||
throw new InvalidRequestException("'" + LOINC_CODESYSTEM_VERSION.getCode() +
|
||||
"' property is required when 'current-version' parameter is 'false'");
|
||||
}
|
||||
|
||||
List<String> mandatoryFilenameFragments = Arrays.asList(
|
||||
uploadProperties.getProperty(LOINC_ANSWERLIST_FILE.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode()),
|
||||
uploadProperties.getProperty(LOINC_ANSWERLIST_LINK_FILE.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode()),
|
||||
|
|
@ -238,21 +255,47 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
|
||||
ourLog.info("Beginning LOINC processing");
|
||||
|
||||
if (isMakeCurrentVersion) {
|
||||
if (codeSystemVersionId != null) {
|
||||
processLoincFiles(descriptors, theRequestDetails, uploadProperties, false, isMakeCurrentVersion);
|
||||
uploadProperties.remove(LOINC_CODESYSTEM_VERSION.getCode());
|
||||
}
|
||||
ourLog.info("Uploading CodeSystem and making it current version");
|
||||
|
||||
String codeSystemVersionId = uploadProperties.getProperty(LOINC_CODESYSTEM_VERSION.getCode());
|
||||
if (codeSystemVersionId != null) {
|
||||
// Load the code system with version and then remove the version property.
|
||||
processLoincFiles(descriptors, theRequestDetails, uploadProperties, false);
|
||||
uploadProperties.remove(LOINC_CODESYSTEM_VERSION.getCode());
|
||||
} else {
|
||||
ourLog.info("Uploading CodeSystem without updating current version");
|
||||
}
|
||||
// Load the same code system with null version. This will become the default version.
|
||||
return processLoincFiles(descriptors, theRequestDetails, uploadProperties, true);
|
||||
return processLoincFiles(descriptors, theRequestDetails, uploadProperties, true, isMakeCurrentVersion);
|
||||
}
|
||||
}
|
||||
|
||||
private boolean getIsMakeCurrentVersion(RequestDetails theRequestDetails) throws InvalidRequestException{
|
||||
boolean defaultResponse = true;
|
||||
|
||||
IBaseResource requestResource = theRequestDetails.getResource();
|
||||
if (requestResource == null) return defaultResponse;
|
||||
|
||||
if (! (requestResource instanceof Parameters)) return defaultResponse;
|
||||
Parameters parameters = (Parameters) theRequestDetails.getResource();
|
||||
|
||||
List<String> values = ParametersUtil.getNamedParameterValuesAsString(FhirContext.forR4(), parameters, MAKE_CURRENT_VERSION);
|
||||
if (CollectionUtils.isEmpty(values)) return true;
|
||||
|
||||
if (values.size() > 1) {
|
||||
throw new InvalidRequestException("Parameter '" + MAKE_CURRENT_VERSION + "' was specified more than once.");
|
||||
}
|
||||
|
||||
if (! values.get(0).equalsIgnoreCase("false") && ! values.get(0).equalsIgnoreCase("true")) {
|
||||
throw new InvalidRequestException("Parameter " + MAKE_CURRENT_VERSION + " only accepts values: ['true' or 'false']");
|
||||
}
|
||||
|
||||
return Boolean.parseBoolean(values.get(0));
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
|
||||
try (LoadedFileDescriptors descriptors = getLoadedFileDescriptors(theFiles)) {
|
||||
|
||||
List<String> expectedFilenameFragments = Arrays.asList(
|
||||
SCT_FILE_DESCRIPTION,
|
||||
|
|
@ -279,7 +322,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
|
||||
int count = 0;
|
||||
|
||||
try (LoadedFileDescriptors compressedDescriptors = new LoadedFileDescriptors(theFiles)) {
|
||||
try (LoadedFileDescriptors compressedDescriptors = getLoadedFileDescriptors(theFiles)) {
|
||||
for (FileDescriptor nextDescriptor : compressedDescriptors.getUncompressedFileDescriptors()) {
|
||||
if (nextDescriptor.getFilename().toLowerCase(Locale.US).endsWith(".xml")) {
|
||||
try (InputStream inputStream = nextDescriptor.getInputStream();
|
||||
|
|
@ -296,13 +339,13 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
|
||||
cs.setVersion(codeSystemVersion.getCodeSystemVersionId());
|
||||
|
||||
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null, null);
|
||||
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null, null, true);
|
||||
return new UploadStatistics(count, target);
|
||||
}
|
||||
|
||||
@Override
|
||||
public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
|
||||
try (LoadedFileDescriptors descriptors = getLoadedFileDescriptors(theFiles)) {
|
||||
Optional<String> codeSystemContent = loadFile(descriptors, CUSTOM_CODESYSTEM_JSON, CUSTOM_CODESYSTEM_XML);
|
||||
CodeSystem codeSystem;
|
||||
if (codeSystemContent.isPresent()) {
|
||||
|
|
@ -321,7 +364,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, false);
|
||||
TermCodeSystemVersion csv = terminologySet.toCodeSystemVersion();
|
||||
|
||||
IIdType target = storeCodeSystem(theRequestDetails, csv, codeSystem, null, null);
|
||||
IIdType target = storeCodeSystem(theRequestDetails, csv, codeSystem, null, null, true);
|
||||
return new UploadStatistics(terminologySet.getSize(), target);
|
||||
}
|
||||
}
|
||||
|
|
@ -330,7 +373,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
@Override
|
||||
public UploadStatistics loadDeltaAdd(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
ourLog.info("Processing terminology delta ADD for system[{}] with files: {}", theSystem, theFiles.stream().map(t -> t.getFilename()).collect(Collectors.toList()));
|
||||
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
|
||||
try (LoadedFileDescriptors descriptors = getLoadedFileDescriptors(theFiles)) {
|
||||
CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, false);
|
||||
return myCodeSystemStorageSvc.applyDeltaCodeSystemsAdd(theSystem, terminologySet);
|
||||
}
|
||||
|
|
@ -339,7 +382,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
@Override
|
||||
public UploadStatistics loadDeltaRemove(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
|
||||
ourLog.info("Processing terminology delta REMOVE for system[{}] with files: {}", theSystem, theFiles.stream().map(t -> t.getFilename()).collect(Collectors.toList()));
|
||||
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
|
||||
try (LoadedFileDescriptors descriptors = getLoadedFileDescriptors(theFiles)) {
|
||||
CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, true);
|
||||
return myCodeSystemStorageSvc.applyDeltaCodeSystemsRemove(theSystem, terminologySet);
|
||||
}
|
||||
|
|
@ -378,8 +421,9 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
@NotNull
|
||||
private Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
|
||||
Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
|
||||
Properties retVal = new Properties();
|
||||
|
||||
try (InputStream propertyStream = TermLoaderSvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loincupload.properties")) {
|
||||
|
|
@ -515,7 +559,9 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
// return new UploadStatistics(conceptCount, target);
|
||||
}
|
||||
|
||||
UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails, Properties theUploadProperties, Boolean theCloseFiles) {
|
||||
UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails,
|
||||
Properties theUploadProperties, Boolean theCloseFiles, boolean isMakeCurrentVersion) {
|
||||
|
||||
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
|
||||
final Map<String, TermConcept> code2concept = new HashMap<>();
|
||||
final List<ValueSet> valueSets = new ArrayList<>();
|
||||
|
|
@ -646,7 +692,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
int conceptCount = code2concept.size();
|
||||
ourLog.info("Have {} total concepts, {} root concepts, {} ValueSets", conceptCount, rootConceptCount, valueSetCount);
|
||||
|
||||
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, loincCs, valueSets, conceptMaps);
|
||||
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, loincCs, valueSets, conceptMaps, isMakeCurrentVersion);
|
||||
|
||||
return new UploadStatistics(conceptCount, target);
|
||||
}
|
||||
|
|
@ -720,12 +766,14 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
cs.setName("SNOMED CT");
|
||||
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null, null);
|
||||
IIdType target = storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null, null, true);
|
||||
|
||||
return new UploadStatistics(code2concept.size(), target);
|
||||
}
|
||||
|
||||
private IIdType storeCodeSystem(RequestDetails theRequestDetails, final TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystem, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
|
||||
private IIdType storeCodeSystem(RequestDetails theRequestDetails, final TermCodeSystemVersion theCodeSystemVersion,
|
||||
CodeSystem theCodeSystem, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, boolean isMakeCurrentVersion) {
|
||||
|
||||
Validate.isTrue(theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
|
||||
List<ValueSet> valueSets = ObjectUtils.defaultIfNull(theValueSets, Collections.emptyList());
|
||||
|
|
@ -733,7 +781,8 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
|||
|
||||
IIdType retVal;
|
||||
myDeferredStorageSvc.setProcessDeferred(false);
|
||||
retVal = myCodeSystemStorageSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
|
||||
retVal = myCodeSystemStorageSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion,
|
||||
theRequestDetails, valueSets, conceptMaps, isMakeCurrentVersion);
|
||||
myDeferredStorageSvc.setProcessDeferred(true);
|
||||
|
||||
return retVal;
|
||||
|
|
|
|||
|
|
@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.term.api;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
|
|
@ -28,10 +27,12 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
|||
import ca.uhn.fhir.jpa.term.UploadStatistics;
|
||||
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.ValueSet;
|
||||
|
||||
import javax.transaction.Transactional;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
|
|
@ -43,12 +44,44 @@ public interface ITermCodeSystemStorageSvc {
|
|||
|
||||
void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);
|
||||
|
||||
void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
|
||||
|
||||
/**
|
||||
* Default implementation supports previous signature of method which was added theIsMakeItCurrentVersion parameter
|
||||
*/
|
||||
@Transactional
|
||||
default void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName,
|
||||
String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
|
||||
|
||||
storeNewCodeSystemVersion(theCodeSystemResourcePid, theSystemUri, theSystemName, theSystemVersionId,
|
||||
theCodeSystemVersion, theCodeSystemResourceTable, true);
|
||||
}
|
||||
|
||||
void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName,
|
||||
String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable,
|
||||
boolean theIsMakeItCurrentVersion);
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Default implementation supports previous signature of method which was added theIsMakeItCurrentVersion parameter
|
||||
* @return Returns the ID of the created/updated code system
|
||||
*/
|
||||
@Transactional
|
||||
default IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource,
|
||||
TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets,
|
||||
List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps) {
|
||||
|
||||
return storeNewCodeSystemVersion(theCodeSystemResource, theCodeSystemVersion,
|
||||
theRequestDetails, theValueSets, theConceptMaps, true);
|
||||
}
|
||||
|
||||
/**
|
||||
* @return Returns the ID of the created/updated code system
|
||||
*/
|
||||
IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
|
||||
IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource,
|
||||
TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets,
|
||||
List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps, boolean theIsMakeItCurrentVersion);
|
||||
|
||||
|
||||
void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity);
|
||||
|
||||
|
|
|
|||
|
|
@ -52,7 +52,9 @@ public class TerminologyLoaderSvcCustomTest extends BaseLoaderTest {
|
|||
// Actually do the load
|
||||
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
|
||||
|
||||
verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
|
||||
verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(
|
||||
mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(),
|
||||
myConceptMapCaptor.capture(), eq(true));
|
||||
Map<String, TermConcept> concepts = extractConcepts();
|
||||
|
||||
// Verify codesystem
|
||||
|
|
@ -82,7 +84,9 @@ public class TerminologyLoaderSvcCustomTest extends BaseLoaderTest {
|
|||
// Actually do the load
|
||||
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
|
||||
|
||||
verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
|
||||
verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(
|
||||
mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class),
|
||||
myValueSetsCaptor.capture(), myConceptMapCaptor.capture(), eq(true));
|
||||
Map<String, TermConcept> concepts = extractConcepts();
|
||||
|
||||
// Verify codesystem
|
||||
|
|
@ -101,7 +105,9 @@ public class TerminologyLoaderSvcCustomTest extends BaseLoaderTest {
|
|||
// Actually do the load
|
||||
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
|
||||
|
||||
verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
|
||||
verify(myTermCodeSystemStorageSvc, times(1)).storeNewCodeSystemVersion(
|
||||
mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class),
|
||||
myValueSetsCaptor.capture(), myConceptMapCaptor.capture(), eq(true));
|
||||
Map<String, TermConcept> concepts = extractConcepts();
|
||||
|
||||
TermConcept code;
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -82,7 +82,8 @@ public class TerminologyLoaderSvcSnomedCtTest extends BaseLoaderTest {
|
|||
|
||||
mySvc.loadSnomedCt(myFiles.getFiles(), mySrd);
|
||||
|
||||
verify(myTermCodeSystemStorageSvc).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyList(), anyListOf(ConceptMap.class));
|
||||
verify(myTermCodeSystemStorageSvc).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(),
|
||||
any(RequestDetails.class), anyList(), anyListOf(ConceptMap.class), eq(true));
|
||||
|
||||
TermCodeSystemVersion csv = myCsvCaptor.getValue();
|
||||
TreeSet<String> allCodes = toCodes(csv, true);
|
||||
|
|
|
|||
Loading…
Reference in New Issue