Merge remote-tracking branch 'remotes/origin/master' into livebundle-…

…support
hapifhir · Jun 3, 2019 · 3e63a76 · 3e63a76
2 parents 1e8b083 + aed5bb8
commit 3e63a76
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Showing 9 changed files with 247 additions and 64 deletions.
diff --git a/...-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/AbstractImportExportCsvConceptMapCommand.java b/...-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/AbstractImportExportCsvConceptMapCommand.java
@@ -27,10 +27,19 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.ByteOrderMark;
+import org.apache.commons.io.input.BOMInputStream;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 
-import java.util.*;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+import java.util.Arrays;
 import java.util.concurrent.ExecutionException;
 import java.util.stream.Collectors;
 
@@ -64,6 +73,29 @@ protected void addFhirVersionOption(Options theOptions) {
 		addRequiredOption(theOptions, FHIR_VERSION_PARAM, FHIR_VERSION_PARAM_LONGOPT, FHIR_VERSION_PARAM_NAME, FHIR_VERSION_PARAM_DESC + versions);
 	}
 
+	protected BufferedReader getBufferedReader() throws IOException {
+		return new BufferedReader(getInputStreamReader());
+	}
+
+	protected InputStreamReader getInputStreamReader() throws IOException {
+		return new InputStreamReader(getBOMInputStream());
+	}
+
+	protected BOMInputStream getBOMInputStream() throws IOException {
+		return new BOMInputStream(
+			getInputStream(),
+			false,
+			ByteOrderMark.UTF_8,
+			ByteOrderMark.UTF_16BE,
+			ByteOrderMark.UTF_16LE,
+			ByteOrderMark.UTF_32BE,
+			ByteOrderMark.UTF_32LE);
+	}
+
+	protected InputStream getInputStream() throws IOException {
+		return Files.newInputStream(Paths.get(file), StandardOpenOption.READ);
+	}
+
 	@Override
 	public void run(CommandLine theCommandLine) throws ParseException, ExecutionException {
 		parseFhirContext(theCommandLine);

diff --git a/...hir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommand.java b/...hir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommand.java
@@ -39,8 +39,6 @@
 
 import java.io.IOException;
 import java.io.Reader;
-import java.nio.file.Files;
-import java.nio.file.Paths;
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.Map;
@@ -166,7 +164,7 @@ private ConceptMap convertCsvToConceptMapR4() throws ExecutionException {
 		ourLog.info("Converting CSV to ConceptMap...");
 		ConceptMap retVal = new ConceptMap();
 		try (
-			Reader reader = Files.newBufferedReader(Paths.get(file));
+			Reader reader = getBufferedReader();
 			CSVParser csvParser = new CSVParser(
 				reader,
 				CSVFormat

diff --git a/...i/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandR4Test.java b/...i/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommandR4Test.java
@@ -369,4 +369,79 @@ public void testImportCsvToConceptMapCommand() throws FHIRException {
 
 		assertEquals("http://localhost:" + ourPort + "/ConceptMap/1/_history/2", conceptMap.getId());
 	}
+
+	@Test
+	public void testImportCsvToConceptMapCommandWithByteOrderMark() throws FHIRException {
+		ClassLoader classLoader = getClass().getClassLoader();
+		File fileToImport = new File(classLoader.getResource("loinc-to-phenx.csv").getFile());
+		ImportCsvToConceptMapCommandR4Test.file = fileToImport.getAbsolutePath();
+
+		App.main(new String[] {"import-csv-to-conceptmap",
+			"-v", ourVersion,
+			"-t", ourBase,
+			"-u", "http://loinc.org/cm/loinc-to-phenx",
+			"-i", "http://loinc.org",
+			"-o", "http://phenxtoolkit.org",
+			"-f", file,
+			"-l"});
+
+		Bundle response = ourClient
+			.search()
+			.forResource(ConceptMap.class)
+			.where(ConceptMap.URL.matches().value("http://loinc.org/cm/loinc-to-phenx"))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		ConceptMap conceptMap = (ConceptMap) response.getEntryFirstRep().getResource();
+
+		ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
+
+		assertEquals("http://localhost:" + ourPort + "/ConceptMap/1/_history/1", conceptMap.getId());
+
+		assertEquals("http://loinc.org/cm/loinc-to-phenx", conceptMap.getUrl());
+		assertEquals("http://loinc.org", conceptMap.getSourceUriType().getValueAsString());
+		assertEquals("http://phenxtoolkit.org", conceptMap.getTargetUriType().getValueAsString());
+
+		assertEquals(1, conceptMap.getGroup().size());
+
+		ConceptMapGroupComponent group = conceptMap.getGroup().get(0);
+		assertEquals("http://loinc.org", group.getSource());
+		assertNull(group.getSourceVersion());
+		assertEquals("http://phenxtoolkit.org", group.getTarget());
+		assertNull(group.getTargetVersion());
+
+		assertEquals(1, group.getElement().size());
+
+		SourceElementComponent source = group.getElement().get(0);
+		assertEquals("65191-9", source.getCode());
+		assertEquals("During the past 30 days, about how often did you feel restless or fidgety [Kessler 6 Distress]", source.getDisplay());
+
+		assertEquals(1, source.getTarget().size());
+
+		TargetElementComponent target = source.getTarget().get(0);
+		assertEquals("PX121301010300", target.getCode());
+		assertEquals("PX121301_Restless", target.getDisplay());
+		assertEquals(ConceptMapEquivalence.EQUIVALENT, target.getEquivalence());
+		assertNull(target.getComment());
+
+		App.main(new String[] {"import-csv-to-conceptmap",
+			"-v", ourVersion,
+			"-t", ourBase,
+			"-u", "http://loinc.org/cm/loinc-to-phenx",
+			"-i", "http://loinc.org",
+			"-o", "http://phenxtoolkit.org",
+			"-f", file,
+			"-l"});
+
+		response = ourClient
+			.search()
+			.forResource(ConceptMap.class)
+			.where(ConceptMap.URL.matches().value("http://loinc.org/cm/loinc-to-phenx"))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		conceptMap = (ConceptMap) response.getEntryFirstRep().getResource();
+
+		assertEquals("http://localhost:" + ourPort + "/ConceptMap/1/_history/2", conceptMap.getId());
+	}
 }
diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/loinc-to-phenx.csv b/hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/loinc-to-phenx.csv
@@ -0,0 +1,2 @@
+SOURCE_CODE_SYSTEM,SOURCE_CODE_SYSTEM_VERSION,TARGET_CODE_SYSTEM,TARGET_CODE_SYSTEM_VERSION,SOURCE_CODE,SOURCE_DISPLAY,TARGET_CODE,TARGET_DISPLAY,EQUIVALENCE,COMMENT
+http://loinc.org,,http://phenxtoolkit.org,,65191-9,"During the past 30 days, about how often did you feel restless or fidgety [Kessler 6 Distress]",PX121301010300,PX121301_Restless,equivalent,