978 cli tools for importing exporting terminology mappings need to be fixed (#988)
* Fixed export issue. * Fixed import issue. * Fixed tests. * Fixed tests.
This commit is contained in:
Diederik Muylwyk
GitHub
parent
b61a3cc10b
commit
903df68d2a
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@ -23,23 +23,23 @@ package ca.uhn.fhir.cli;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import org.apache.commons.cli.Options;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.csv.CSVFormat;
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import org.apache.commons.csv.CSVPrinter;
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import org.apache.commons.csv.QuoteMode;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.convertors.VersionConvertor_30_40;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.ConceptMap;
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import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
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import org.hl7.fhir.r4.model.ConceptMap.SourceElementComponent;
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.io.Writer;
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import java.nio.file.Files;
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import java.nio.file.Paths;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.concurrent.ExecutionException;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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@ -72,11 +72,11 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
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}
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@Override
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protected void process() throws ParseException {
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protected void process() throws ExecutionException {
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searchForConceptMapByUrl();
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}
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private void searchForConceptMapByUrl() {
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private void searchForConceptMapByUrl() throws ExecutionException {
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ourLog.info("Searching for ConceptMap with specified URL (i.e. ConceptMap.url): {}", conceptMapUrl);
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if (fhirVersion == FhirVersionEnum.DSTU3) {
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org.hl7.fhir.dstu3.model.Bundle response = client
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@ -111,61 +111,26 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
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}
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}
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private void convertConceptMapToCsv(org.hl7.fhir.dstu3.model.ConceptMap theConceptMap) {
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ourLog.info("Exporting ConceptMap to CSV...");
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BufferedWriter bufferedWriter = null;
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CSVPrinter csvPrinter = null;
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private void convertConceptMapToCsv(org.hl7.fhir.dstu3.model.ConceptMap theConceptMap) throws ExecutionException {
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try {
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bufferedWriter = Files.newBufferedWriter(Paths.get(file));
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csvPrinter = new CSVPrinter(
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bufferedWriter,
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CSVFormat
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.DEFAULT
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.withRecordSeparator("\n")
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.withHeader(Header.class));
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for (org.hl7.fhir.dstu3.model.ConceptMap.ConceptMapGroupComponent group : theConceptMap.getGroup()) {
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for (org.hl7.fhir.dstu3.model.ConceptMap.SourceElementComponent element : group.getElement()) {
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for (org.hl7.fhir.dstu3.model.ConceptMap.TargetElementComponent target : element.getTarget()) {
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List<String> columns = new ArrayList<>();
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columns.add(defaultString(group.getSource()));
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columns.add(defaultString(group.getSourceVersion()));
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columns.add(defaultString(group.getTarget()));
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columns.add(defaultString(group.getTargetVersion()));
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columns.add(defaultString(element.getCode()));
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columns.add(defaultString(element.getDisplay()));
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columns.add(defaultString(target.getCode()));
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columns.add(defaultString(target.getDisplay()));
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columns.add(defaultString(target.getEquivalence().toCode()));
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columns.add(defaultString(target.getComment()));
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csvPrinter.print(columns);
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}
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}
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}
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} catch (IOException ioe) {
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throw new InternalErrorException(ioe);
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} finally {
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IOUtils.closeQuietly(csvPrinter);
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IOUtils.closeQuietly(bufferedWriter);
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convertConceptMapToCsv(VersionConvertor_30_40.convertConceptMap(theConceptMap));
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} catch (FHIRException fe) {
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throw new ExecutionException(fe);
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}
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ourLog.info("Finished exporting to {}", file);
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}
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private void convertConceptMapToCsv(ConceptMap theConceptMap) {
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ourLog.info("Exporting ConceptMap to CSV...");
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Writer writer = null;
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CSVPrinter csvPrinter = null;
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try {
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writer = Files.newBufferedWriter(Paths.get(file));
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csvPrinter = new CSVPrinter(
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try (
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Writer writer = Files.newBufferedWriter(Paths.get(file));
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CSVPrinter csvPrinter = new CSVPrinter(
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writer,
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CSVFormat
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.DEFAULT
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.withRecordSeparator("\n")
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.withHeader(Header.class).withQuoteMode(QuoteMode.ALL));
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.withHeader(Header.class)
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.withQuoteMode(QuoteMode.ALL));
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) {
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for (ConceptMapGroupComponent group : theConceptMap.getGroup()) {
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for (SourceElementComponent element : group.getElement()) {
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for (ConceptMap.TargetElementComponent target : element.getTarget()) {
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@ -188,10 +153,8 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
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}
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} catch (IOException ioe) {
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throw new InternalErrorException(ioe);
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} finally {
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IOUtils.closeQuietly(csvPrinter);
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IOUtils.closeQuietly(writer);
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}
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ourLog.info("Finished exporting to {}", file);
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}
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}
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@ -25,11 +25,9 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.Options;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.csv.CSVFormat;
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import org.apache.commons.csv.CSVParser;
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import org.apache.commons.csv.CSVRecord;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.convertors.VersionConvertor_30_40;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r4.model.ConceptMap;
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@ -43,7 +41,10 @@ import java.io.IOException;
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import java.io.Reader;
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import java.nio.file.Files;
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import java.nio.file.Paths;
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import java.util.*;
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import java.util.LinkedHashMap;
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import java.util.LinkedHashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.concurrent.ExecutionException;
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import static org.apache.commons.lang3.StringUtils.*;
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@ -96,7 +97,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
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}
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@Override
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protected void parseAdditionalParameters(CommandLine theCommandLine) throws ParseException {
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protected void parseAdditionalParameters(CommandLine theCommandLine) {
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sourceValueSet = theCommandLine.getOptionValue(SOURCE_VALUE_SET_PARAM);
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if (isBlank(sourceValueSet)) {
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ourLog.info("Source value set is not specified (i.e. ConceptMap.sourceUri).");
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@ -113,11 +114,11 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
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}
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@Override
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protected void process() throws ParseException, ExecutionException {
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protected void process() throws ExecutionException {
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searchForConceptMapByUrl();
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}
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private void searchForConceptMapByUrl() throws ParseException, ExecutionException {
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private void searchForConceptMapByUrl() throws ExecutionException {
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if (fhirVersion == FhirVersionEnum.DSTU3) {
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org.hl7.fhir.dstu3.model.ConceptMap conceptMap = convertCsvToConceptMapDstu3();
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@ -153,7 +154,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
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}
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}
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private org.hl7.fhir.dstu3.model.ConceptMap convertCsvToConceptMapDstu3() throws ParseException, ExecutionException {
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private org.hl7.fhir.dstu3.model.ConceptMap convertCsvToConceptMapDstu3() throws ExecutionException {
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try {
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return VersionConvertor_30_40.convertConceptMap(convertCsvToConceptMapR4());
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} catch (FHIRException fe) {
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@ -161,14 +162,12 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
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}
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}
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private ConceptMap convertCsvToConceptMapR4() throws ParseException, ExecutionException {
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private ConceptMap convertCsvToConceptMapR4() throws ExecutionException {
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ourLog.info("Converting CSV to ConceptMap...");
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ConceptMap retVal = new ConceptMap();
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Reader reader = null;
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CSVParser csvParser = null;
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try {
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reader = Files.newBufferedReader(Paths.get(file));
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csvParser = new CSVParser(
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try (
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Reader reader = Files.newBufferedReader(Paths.get(file));
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CSVParser csvParser = new CSVParser(
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reader,
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CSVFormat
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.DEFAULT
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@ -178,7 +177,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
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.withIgnoreHeaderCase()
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.withIgnoreEmptyLines()
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.withTrim());
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) {
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retVal.setUrl(conceptMapUrl);
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if (isNotBlank(sourceValueSet)) {
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@ -278,9 +277,6 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
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}
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} catch (IOException e) {
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throw new InternalErrorException(e);
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} finally {
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IOUtils.closeQuietly(csvParser);
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IOUtils.closeQuietly(reader);
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}
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ourLog.info("Finished converting CSV to ConceptMap.");
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@ -0,0 +1,283 @@
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package ca.uhn.fhir.cli;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.rest.server.RestfulServer;
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import ca.uhn.fhir.rest.server.interceptor.VerboseLoggingInterceptor;
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import ca.uhn.fhir.util.PortUtil;
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import ca.uhn.fhir.util.TestUtil;
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import com.google.common.base.Charsets;
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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.eclipse.jetty.server.Server;
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import org.eclipse.jetty.servlet.ServletHandler;
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import org.eclipse.jetty.servlet.ServletHolder;
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import org.hl7.fhir.dstu3.model.ConceptMap;
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import org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence;
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import org.hl7.fhir.dstu3.model.UriType;
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import org.junit.AfterClass;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.IOException;
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import static org.junit.Assert.assertEquals;
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public class ExportConceptMapToCsvCommandDstu3Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExportConceptMapToCsvCommandDstu3Test.class);
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private static final String CM_URL = "http://example.com/conceptmap";
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private static final String VS_URL_1 = "http://example.com/valueset/1";
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private static final String VS_URL_2 = "http://example.com/valueset/2";
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private static final String CS_URL_1 = "http://example.com/codesystem/1";
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private static final String CS_URL_2 = "http://example.com/codesystem/2";
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private static final String CS_URL_3 = "http://example.com/codesystem/3";
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private static final String FILE = "./target/output.csv";
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private static String ourBase;
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private static IGenericClient ourClient;
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private static FhirContext ourCtx = FhirContext.forDstu3();
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private static int ourPort;
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private static Server ourServer;
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private static String ourVersion = "dstu3";
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static {
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System.setProperty("test", "true");
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}
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@AfterClass
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public static void afterClassClearContext() throws Exception {
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ourServer.stop();
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TestUtil.clearAllStaticFieldsForUnitTest();
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}
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@BeforeClass
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public static void beforeClass() throws Exception {
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ourPort = PortUtil.findFreePort();
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ourServer = new Server(ourPort);
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ServletHandler servletHandler = new ServletHandler();
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RestfulServer restfulServer = new RestfulServer(ourCtx);
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restfulServer.registerInterceptor(new VerboseLoggingInterceptor());
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restfulServer.setResourceProviders(new HashMapResourceProviderConceptMapDstu3(ourCtx));
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ServletHolder servletHolder = new ServletHolder(restfulServer);
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servletHandler.addServletWithMapping(servletHolder, "/*");
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ourServer.setHandler(servletHandler);
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ourServer.start();
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ourBase = "http://localhost:" + ourPort;
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ourClient = ourCtx.newRestfulGenericClient(ourBase);
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ourClient.create().resource(createConceptMap()).execute();
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}
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@Test
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public void testExportConceptMapToCsvCommand() throws IOException {
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ourLog.info("ConceptMap:\n" + ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createConceptMap()));
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App.main(new String[] {"export-conceptmap-to-csv",
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"-v", ourVersion,
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"-t", ourBase,
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"-u", CM_URL,
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"-f", FILE,
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"-l"});
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String expected = "\"SOURCE_CODE_SYSTEM\",\"SOURCE_CODE_SYSTEM_VERSION\",\"TARGET_CODE_SYSTEM\",\"TARGET_CODE_SYSTEM_VERSION\",\"SOURCE_CODE\",\"SOURCE_DISPLAY\",\"TARGET_CODE\",\"TARGET_DISPLAY\",\"EQUIVALENCE\",\"COMMENT\"\n" +
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"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1a\",\"Display 1a\",\"Code 2a\",\"Display 2a\",\"equal\",\"2a This is a comment.\"\n" +
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"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1b\",\"Display 1b\",\"Code 2b\",\"Display 2b\",\"equal\",\"2b This is a comment.\"\n" +
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"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1c\",\"Display 1c\",\"Code 2c\",\"Display 2c\",\"equal\",\"2c This is a comment.\"\n" +
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"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/2\",\"Version 2t\",\"Code 1d\",\"Display 1d\",\"Code 2d\",\"Display 2d\",\"equal\",\"2d This is a comment.\"\n" +
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"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1a\",\"Display 1a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
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"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1b\",\"Display 1b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
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"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1c\",\"Display 1c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
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"\"http://example.com/codesystem/1\",\"Version 1s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 1d\",\"Display 1d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n" +
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"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2a\",\"Display 2a\",\"Code 3a\",\"Display 3a\",\"equal\",\"3a This is a comment.\"\n" +
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"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2b\",\"Display 2b\",\"Code 3b\",\"Display 3b\",\"equal\",\"3b This is a comment.\"\n" +
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"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2c\",\"Display 2c\",\"Code 3c\",\"Display 3c\",\"equal\",\"3c This is a comment.\"\n" +
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"\"http://example.com/codesystem/2\",\"Version 2s\",\"http://example.com/codesystem/3\",\"Version 3t\",\"Code 2d\",\"Display 2d\",\"Code 3d\",\"Display 3d\",\"equal\",\"3d This is a comment.\"\n";
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String result = IOUtils.toString(new FileInputStream(FILE), Charsets.UTF_8);
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assertEquals(expected, result);
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FileUtils.deleteQuietly(new File(FILE));
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}
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static ConceptMap createConceptMap() {
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ConceptMap conceptMap = new ConceptMap();
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conceptMap
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.setUrl(CM_URL)
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.setSource(new UriType(VS_URL_1))
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.setTarget(new UriType(VS_URL_2));
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ConceptMap.ConceptMapGroupComponent group = conceptMap.addGroup();
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group
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.setSource(CS_URL_1)
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.setSourceVersion("Version 1s")
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.setTarget(CS_URL_2)
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.setTargetVersion("Version 2t");
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ConceptMap.SourceElementComponent element = group.addElement();
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element
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.setCode("Code 1a")
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.setDisplay("Display 1a");
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ConceptMap.TargetElementComponent target = element.addTarget();
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target
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.setCode("Code 2a")
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.setDisplay("Display 2a")
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.setEquivalence(ConceptMapEquivalence.EQUAL)
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.setComment("2a This is a comment.");
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element = group.addElement();
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element
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.setCode("Code 1b")
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.setDisplay("Display 1b");
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target = element.addTarget();
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target
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.setCode("Code 2b")
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.setDisplay("Display 2b")
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.setEquivalence(ConceptMapEquivalence.EQUAL)
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.setComment("2b This is a comment.");
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element = group.addElement();
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element
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.setCode("Code 1c")
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.setDisplay("Display 1c");
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target = element.addTarget();
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target
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.setCode("Code 2c")
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.setDisplay("Display 2c")
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.setEquivalence(ConceptMapEquivalence.EQUAL)
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.setComment("2c This is a comment.");
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element = group.addElement();
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element
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.setCode("Code 1d")
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.setDisplay("Display 1d");
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target = element.addTarget();
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target
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.setCode("Code 2d")
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.setDisplay("Display 2d")
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.setEquivalence(ConceptMapEquivalence.EQUAL)
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.setComment("2d This is a comment.");
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group = conceptMap.addGroup();
|
||||
group
|
||||
.setSource(CS_URL_1)
|
||||
.setSourceVersion("Version 1s")
|
||||
.setTarget(CS_URL_3)
|
||||
.setTargetVersion("Version 3t");
|
||||
|
||||
element = group.addElement();
|
||||
element
|
||||
.setCode("Code 1a")
|
||||
.setDisplay("Display 1a");
|
||||
|
||||
target = element.addTarget();
|
||||
target
|
||||
.setCode("Code 3a")
|
||||
.setDisplay("Display 3a")
|
||||
.setEquivalence(ConceptMapEquivalence.EQUAL)
|
||||
.setComment("3a This is a comment.");
|
||||
|
||||
element = group.addElement();
|
||||
element
|
||||
.setCode("Code 1b")
|
||||
.setDisplay("Display 1b");
|
||||
|
||||
target = element.addTarget();
|
||||
target
|
||||
.setCode("Code 3b")
|
||||
.setDisplay("Display 3b")
|
||||
.setEquivalence(ConceptMapEquivalence.EQUAL)
|
||||
.setComment("3b This is a comment.");
|
||||
|
||||
element = group.addElement();
|
||||
element
|
||||
.setCode("Code 1c")
|
||||
.setDisplay("Display 1c");
|
||||
|
||||
target = element.addTarget();
|
||||
target
|
||||
.setCode("Code 3c")
|
||||
.setDisplay("Display 3c")
|
||||
.setEquivalence(ConceptMapEquivalence.EQUAL)
|
||||
.setComment("3c This is a comment.");
|
||||
|
||||
element = group.addElement();
|
||||
element
|
||||
.setCode("Code 1d")
|
||||
.setDisplay("Display 1d");
|
||||
|
||||
target = element.addTarget();
|
||||
target
|
||||
.setCode("Code 3d")
|
||||
.setDisplay("Display 3d")
|
||||
.setEquivalence(ConceptMapEquivalence.EQUAL)
|
||||
.setComment("3d This is a comment.");
|
||||
|
||||
group = conceptMap.addGroup();
|
||||
group
|
||||
.setSource(CS_URL_2)
|
||||
.setSourceVersion("Version 2s")
|
||||
.setTarget(CS_URL_3)
|
||||
.setTargetVersion("Version 3t");
|
||||
|
||||
element = group.addElement();
|
||||
element
|
||||
.setCode("Code 2a")
|
||||
.setDisplay("Display 2a");
|
||||
|
||||
target = element.addTarget();
|
||||
target
|
||||
.setCode("Code 3a")
|
||||
.setDisplay("Display 3a")
|
||||
.setEquivalence(ConceptMapEquivalence.EQUAL)
|
||||
.setComment("3a This is a comment.");
|
||||
|
||||
element = group.addElement();
|
||||
element
|
||||
.setCode("Code 2b")
|
||||
.setDisplay("Display 2b");
|
||||
|
||||
target = element.addTarget();
|
||||
target
|
||||
.setCode("Code 3b")
|
||||
.setDisplay("Display 3b")
|
||||
.setEquivalence(ConceptMapEquivalence.EQUAL)
|
||||
.setComment("3b This is a comment.");
|
||||
|
||||
element = group.addElement();
|
||||
element
|
||||
.setCode("Code 2c")
|
||||
.setDisplay("Display 2c");
|
||||
|
||||
target = element.addTarget();
|
||||
target
|
||||
.setCode("Code 3c")
|
||||
.setDisplay("Display 3c")
|
||||
.setEquivalence(ConceptMapEquivalence.EQUAL)
|
||||
.setComment("3c This is a comment.");
|
||||
|
||||
element = group.addElement();
|
||||
element
|
||||
.setCode("Code 2d")
|
||||
.setDisplay("Display 2d");
|
||||
|
||||
target = element.addTarget();
|
||||
target
|
||||
.setCode("Code 3d")
|
||||
.setDisplay("Display 3d")
|
||||
.setEquivalence(ConceptMapEquivalence.EQUAL)
|
||||
.setComment("3d This is a comment.");
|
||||
|
||||
return conceptMap;
|
||||
}
|
||||
}
|
||||
|
|
@ -25,8 +25,8 @@ import java.io.IOException;
|
|||
|
||||
import static org.junit.Assert.assertEquals;
|
||||
|
||||
public class ExportConceptMapToCsvCommandTest {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExportConceptMapToCsvCommandTest.class);
|
||||
public class ExportConceptMapToCsvCommandR4Test {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExportConceptMapToCsvCommandR4Test.class);
|
||||
private static final String CM_URL = "http://example.com/conceptmap";
|
||||
private static final String VS_URL_1 = "http://example.com/valueset/1";
|
||||
private static final String VS_URL_2 = "http://example.com/valueset/2";
|
||||
|
|
@ -40,6 +40,7 @@ public class ExportConceptMapToCsvCommandTest {
|
|||
private static FhirContext ourCtx = FhirContext.forR4();
|
||||
private static int ourPort;
|
||||
private static Server ourServer;
|
||||
private static String ourVersion = "r4";
|
||||
|
||||
static {
|
||||
System.setProperty("test", "true");
|
||||
|
|
@ -80,7 +81,7 @@ public class ExportConceptMapToCsvCommandTest {
|
|||
ourLog.info("ConceptMap:\n" + ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createConceptMap()));
|
||||
|
||||
App.main(new String[] {"export-conceptmap-to-csv",
|
||||
"-v", "r4",
|
||||
"-v", ourVersion,
|
||||
"-t", ourBase,
|
||||
"-u", CM_URL,
|
||||
"-f", FILE,
|
||||
|
|
@ -0,0 +1,127 @@
|
|||
package ca.uhn.fhir.cli;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Server Framework
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2018 University Health Network
|
||||
* %%
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.rest.annotation.*;
|
||||
import ca.uhn.fhir.rest.api.MethodOutcome;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.provider.AbstractHashMapResourceProvider;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.http.NameValuePair;
|
||||
import org.apache.http.client.utils.URLEncodedUtils;
|
||||
import org.hl7.fhir.dstu3.model.ConceptMap;
|
||||
import org.hl7.fhir.dstu3.model.IdType;
|
||||
|
||||
import java.net.URI;
|
||||
import java.net.URISyntaxException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.TreeMap;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
/**
|
||||
* This is a subclass to implement FHIR operations specific to DSTU3 ConceptMap
|
||||
* resources. Its superclass, {@link AbstractHashMapResourceProvider}, is a simple
|
||||
* implementation of the resource provider interface that uses a HashMap to
|
||||
* store all resources in memory.
|
||||
* <p>
|
||||
* This subclass currently supports the following FHIR operations:
|
||||
* </p>
|
||||
* <ul>
|
||||
* <li>Search for DSTU3 ConceptMap resources by ConceptMap.url</li>
|
||||
* <li>Conditional update for DSTU3 ConceptMap resources by ConceptMap.url</li>
|
||||
* </ul>
|
||||
*/
|
||||
public class HashMapResourceProviderConceptMapDstu3 extends AbstractHashMapResourceProvider<ConceptMap> {
|
||||
@SuppressWarnings("unchecked")
|
||||
public HashMapResourceProviderConceptMapDstu3(FhirContext theFhirContext) {
|
||||
super(theFhirContext, ConceptMap.class);
|
||||
|
||||
FhirVersionEnum fhirVersion = theFhirContext.getVersion().getVersion();
|
||||
if (fhirVersion != FhirVersionEnum.DSTU3) {
|
||||
throw new IllegalStateException("Requires FHIR version DSTU3. Unsupported FHIR version provided: " + fhirVersion);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Search
|
||||
public List<ConceptMap> searchByUrl(
|
||||
@RequiredParam(name=ConceptMap.SP_URL) String theConceptMapUrl) {
|
||||
|
||||
List<ConceptMap> retVal = new ArrayList<>();
|
||||
|
||||
for (TreeMap<Long, ConceptMap> next : myIdToVersionToResourceMap.values()) {
|
||||
if (!next.isEmpty()) {
|
||||
ConceptMap conceptMap = next.lastEntry().getValue();
|
||||
if (theConceptMapUrl.equals(conceptMap.getUrl()))
|
||||
retVal.add(conceptMap);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Update
|
||||
public MethodOutcome updateConceptMapConditional(
|
||||
@ResourceParam ConceptMap theConceptMap,
|
||||
@IdParam IdType theId,
|
||||
@ConditionalUrlParam String theConditional) {
|
||||
|
||||
MethodOutcome methodOutcome = new MethodOutcome();
|
||||
|
||||
if (theConditional != null) {
|
||||
|
||||
String url = null;
|
||||
|
||||
try {
|
||||
List<NameValuePair> params = URLEncodedUtils.parse(new URI(theConditional), Charsets.UTF_8);
|
||||
for (NameValuePair param : params) {
|
||||
if (param.getName().equalsIgnoreCase("url")) {
|
||||
url = param.getValue();
|
||||
break;
|
||||
}
|
||||
}
|
||||
} catch (URISyntaxException urise) {
|
||||
throw new InvalidRequestException(urise);
|
||||
}
|
||||
|
||||
if (isNotBlank(url)) {
|
||||
List<ConceptMap> conceptMaps = searchByUrl(url);
|
||||
|
||||
if (!conceptMaps.isEmpty()) {
|
||||
methodOutcome = update(conceptMaps.get(0));
|
||||
} else {
|
||||
methodOutcome = create(theConceptMap);
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
methodOutcome = update(theConceptMap);
|
||||
}
|
||||
|
||||
return methodOutcome;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,367 @@
|
|||
package ca.uhn.fhir.cli;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.rest.api.MethodOutcome;
|
||||
import ca.uhn.fhir.rest.client.api.IGenericClient;
|
||||
import ca.uhn.fhir.rest.server.RestfulServer;
|
||||
import ca.uhn.fhir.rest.server.interceptor.VerboseLoggingInterceptor;
|
||||
import ca.uhn.fhir.util.PortUtil;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import org.eclipse.jetty.server.Server;
|
||||
import org.eclipse.jetty.servlet.ServletHandler;
|
||||
import org.eclipse.jetty.servlet.ServletHolder;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.dstu3.model.Bundle;
|
||||
import org.hl7.fhir.dstu3.model.ConceptMap;
|
||||
import org.hl7.fhir.dstu3.model.ConceptMap.ConceptMapGroupComponent;
|
||||
import org.hl7.fhir.dstu3.model.ConceptMap.SourceElementComponent;
|
||||
import org.hl7.fhir.dstu3.model.ConceptMap.TargetElementComponent;
|
||||
import org.hl7.fhir.dstu3.model.Enumerations.ConceptMapEquivalence;
|
||||
import org.junit.After;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
|
||||
import java.io.File;
|
||||
|
||||
import static org.junit.Assert.*;
|
||||
|
||||
public class ImportCsvToConceptMapCommandDstu3Test {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ImportCsvToConceptMapCommandDstu3Test.class);
|
||||
private static final String CM_URL = "http://example.com/conceptmap";
|
||||
private static final String VS_URL_1 = "http://example.com/valueset/1";
|
||||
private static final String VS_URL_2 = "http://example.com/valueset/2";
|
||||
private static final String CS_URL_1 = "http://example.com/codesystem/1";
|
||||
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 String file;
|
||||
private static String ourBase;
|
||||
private static IGenericClient ourClient;
|
||||
private static FhirContext ourCtx = FhirContext.forDstu3();
|
||||
private static int ourPort;
|
||||
private static Server ourServer;
|
||||
private static String ourVersion = "dstu3";
|
||||
|
||||
private static RestfulServer restfulServer;
|
||||
|
||||
private static HashMapResourceProviderConceptMapDstu3 hashMapResourceProviderConceptMapDstu3;
|
||||
|
||||
static {
|
||||
System.setProperty("test", "true");
|
||||
}
|
||||
|
||||
@After
|
||||
public void afterClearResourceProvider() {
|
||||
HashMapResourceProviderConceptMapDstu3 resourceProvider = (HashMapResourceProviderConceptMapDstu3) restfulServer.getResourceProviders().iterator().next();
|
||||
resourceProvider.clear();
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() throws Exception {
|
||||
ourServer.stop();
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
}
|
||||
|
||||
@BeforeClass
|
||||
public static void beforeClass() throws Exception {
|
||||
ourPort = PortUtil.findFreePort();
|
||||
ourServer = new Server(ourPort);
|
||||
|
||||
ServletHandler servletHandler = new ServletHandler();
|
||||
|
||||
restfulServer = new RestfulServer(ourCtx);
|
||||
restfulServer.registerInterceptor(new VerboseLoggingInterceptor());
|
||||
restfulServer.setResourceProviders(new HashMapResourceProviderConceptMapDstu3(ourCtx));
|
||||
|
||||
ServletHolder servletHolder = new ServletHolder(restfulServer);
|
||||
servletHandler.addServletWithMapping(servletHolder, "/*");
|
||||
ourServer.setHandler(servletHandler);
|
||||
|
||||
ourServer.start();
|
||||
|
||||
ourBase = "http://localhost:" + ourPort;
|
||||
|
||||
ourClient = ourCtx.newRestfulGenericClient(ourBase);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testConditionalUpdateResultsInCreate() {
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandDstu3Test.createConceptMap();
|
||||
String conceptMapUrl = conceptMap.getUrl();
|
||||
|
||||
ourLog.info("Searching for existing ConceptMap with specified URL (i.e. ConceptMap.url): {}", conceptMapUrl);
|
||||
MethodOutcome methodOutcome = ourClient
|
||||
.update()
|
||||
.resource(conceptMap)
|
||||
.conditional()
|
||||
.where(ConceptMap.URL.matches().value(conceptMapUrl))
|
||||
.execute();
|
||||
|
||||
assertEquals(Boolean.TRUE, methodOutcome.getCreated());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testConditionalUpdateResultsInUpdate() {
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandDstu3Test.createConceptMap();
|
||||
ourClient.create().resource(conceptMap).execute();
|
||||
String conceptMapUrl = conceptMap.getUrl();
|
||||
|
||||
ourLog.info("Searching for existing ConceptMap with specified URL (i.e. ConceptMap.url): {}", conceptMapUrl);
|
||||
MethodOutcome methodOutcome = ourClient
|
||||
.update()
|
||||
.resource(conceptMap)
|
||||
.conditional()
|
||||
.where(ConceptMap.URL.matches().value(conceptMapUrl))
|
||||
.execute();
|
||||
|
||||
assertNull(methodOutcome.getCreated());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testNonConditionalUpdate() {
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandDstu3Test.createConceptMap();
|
||||
ourClient.create().resource(conceptMap).execute();
|
||||
|
||||
Bundle response = ourClient
|
||||
.search()
|
||||
.forResource(ConceptMap.class)
|
||||
.where(ConceptMap.URL.matches().value(CM_URL))
|
||||
.returnBundle(Bundle.class)
|
||||
.execute();
|
||||
|
||||
ConceptMap resultConceptMap = (ConceptMap) response.getEntryFirstRep().getResource();
|
||||
|
||||
MethodOutcome methodOutcome = ourClient
|
||||
.update()
|
||||
.resource(resultConceptMap)
|
||||
.withId(resultConceptMap.getIdElement())
|
||||
.execute();
|
||||
|
||||
assertNull(methodOutcome.getCreated());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testImportCsvToConceptMapCommand() throws FHIRException {
|
||||
ClassLoader classLoader = getClass().getClassLoader();
|
||||
File fileToImport = new File(classLoader.getResource(FILENAME).getFile());
|
||||
ImportCsvToConceptMapCommandDstu3Test.file = fileToImport.getAbsolutePath();
|
||||
|
||||
App.main(new String[] {"import-csv-to-conceptmap",
|
||||
"-v", ourVersion,
|
||||
"-t", ourBase,
|
||||
"-u", CM_URL,
|
||||
"-i", VS_URL_1,
|
||||
"-o", VS_URL_2,
|
||||
"-f", file,
|
||||
"-l"});
|
||||
|
||||
Bundle response = ourClient
|
||||
.search()
|
||||
.forResource(ConceptMap.class)
|
||||
.where(ConceptMap.URL.matches().value(CM_URL))
|
||||
.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(CM_URL, conceptMap.getUrl());
|
||||
assertEquals(VS_URL_1, conceptMap.getSourceUriType().getValueAsString());
|
||||
assertEquals(VS_URL_2, conceptMap.getTargetUriType().getValueAsString());
|
||||
|
||||
assertEquals(3, conceptMap.getGroup().size());
|
||||
|
||||
ConceptMapGroupComponent group = conceptMap.getGroup().get(0);
|
||||
assertEquals(CS_URL_1, group.getSource());
|
||||
assertEquals("Version 1s", group.getSourceVersion());
|
||||
assertEquals(CS_URL_2, group.getTarget());
|
||||
assertEquals("Version 2t", group.getTargetVersion());
|
||||
|
||||
assertEquals(4, group.getElement().size());
|
||||
|
||||
SourceElementComponent source = group.getElement().get(0);
|
||||
assertEquals("Code 1a", source.getCode());
|
||||
assertEquals("Display 1a", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
TargetElementComponent target = source.getTarget().get(0);
|
||||
assertEquals("Code 2a", target.getCode());
|
||||
assertEquals("Display 2a", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("2a This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(1);
|
||||
assertEquals("Code 1b", source.getCode());
|
||||
assertEquals("Display 1b", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 2b", target.getCode());
|
||||
assertEquals("Display 2b", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("2b This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(2);
|
||||
assertEquals("Code 1c", source.getCode());
|
||||
assertEquals("Display 1c", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 2c", target.getCode());
|
||||
assertEquals("Display 2c", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("2c This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(3);
|
||||
assertEquals("Code 1d", source.getCode());
|
||||
assertEquals("Display 1d", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 2d", target.getCode());
|
||||
assertEquals("Display 2d", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("2d This is a comment.", target.getComment());
|
||||
|
||||
group = conceptMap.getGroup().get(1);
|
||||
assertEquals(CS_URL_1, group.getSource());
|
||||
assertEquals("Version 1s", group.getSourceVersion());
|
||||
assertEquals(CS_URL_3, group.getTarget());
|
||||
assertEquals("Version 3t", group.getTargetVersion());
|
||||
|
||||
assertEquals(4, group.getElement().size());
|
||||
|
||||
source = group.getElement().get(0);
|
||||
assertEquals("Code 1a", source.getCode());
|
||||
assertEquals("Display 1a", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 3a", target.getCode());
|
||||
assertEquals("Display 3a", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("3a This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(1);
|
||||
assertEquals("Code 1b", source.getCode());
|
||||
assertEquals("Display 1b", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 3b", target.getCode());
|
||||
assertEquals("Display 3b", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("3b This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(2);
|
||||
assertEquals("Code 1c", source.getCode());
|
||||
assertEquals("Display 1c", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 3c", target.getCode());
|
||||
assertEquals("Display 3c", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("3c This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(3);
|
||||
assertEquals("Code 1d", source.getCode());
|
||||
assertEquals("Display 1d", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 3d", target.getCode());
|
||||
assertEquals("Display 3d", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("3d This is a comment.", target.getComment());
|
||||
|
||||
group = conceptMap.getGroup().get(2);
|
||||
assertEquals(CS_URL_2, group.getSource());
|
||||
assertEquals("Version 2s", group.getSourceVersion());
|
||||
assertEquals(CS_URL_3, group.getTarget());
|
||||
assertEquals("Version 3t", group.getTargetVersion());
|
||||
|
||||
assertEquals(4, group.getElement().size());
|
||||
|
||||
source = group.getElement().get(0);
|
||||
assertEquals("Code 2a", source.getCode());
|
||||
assertEquals("Display 2a", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 3a", target.getCode());
|
||||
assertEquals("Display 3a", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("3a This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(1);
|
||||
assertEquals("Code 2b", source.getCode());
|
||||
assertEquals("Display 2b", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 3b", target.getCode());
|
||||
assertEquals("Display 3b", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("3b This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(2);
|
||||
assertEquals("Code 2c", source.getCode());
|
||||
assertEquals("Display 2c", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 3c", target.getCode());
|
||||
assertEquals("Display 3c", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("3c This is a comment.", target.getComment());
|
||||
|
||||
source = group.getElement().get(3);
|
||||
assertEquals("Code 2d", source.getCode());
|
||||
assertEquals("Display 2d", source.getDisplay());
|
||||
|
||||
assertEquals(1, source.getTarget().size());
|
||||
|
||||
target = source.getTarget().get(0);
|
||||
assertEquals("Code 3d", target.getCode());
|
||||
assertEquals("Display 3d", target.getDisplay());
|
||||
assertEquals(ConceptMapEquivalence.EQUAL, target.getEquivalence());
|
||||
assertEquals("3d This is a comment.", target.getComment());
|
||||
|
||||
App.main(new String[] {"import-csv-to-conceptmap",
|
||||
"-v", ourVersion,
|
||||
"-t", ourBase,
|
||||
"-u", CM_URL,
|
||||
"-i", VS_URL_1,
|
||||
"-o", VS_URL_2,
|
||||
"-f", file,
|
||||
"-l"});
|
||||
|
||||
response = ourClient
|
||||
.search()
|
||||
.forResource(ConceptMap.class)
|
||||
.where(ConceptMap.URL.matches().value(CM_URL))
|
||||
.returnBundle(Bundle.class)
|
||||
.execute();
|
||||
|
||||
conceptMap = (ConceptMap) response.getEntryFirstRep().getResource();
|
||||
|
||||
assertEquals("http://localhost:" + ourPort + "/ConceptMap/1/_history/2", conceptMap.getId());
|
||||
}
|
||||
}
|
||||
|
|
@ -10,13 +10,13 @@ import ca.uhn.fhir.util.TestUtil;
|
|||
import org.eclipse.jetty.server.Server;
|
||||
import org.eclipse.jetty.servlet.ServletHandler;
|
||||
import org.eclipse.jetty.servlet.ServletHolder;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
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.ConceptMapEquivalence;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.junit.After;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.BeforeClass;
|
||||
|
|
@ -26,8 +26,8 @@ import java.io.File;
|
|||
|
||||
import static org.junit.Assert.*;
|
||||
|
||||
public class ImportCsvToConceptMapCommandTest {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ImportCsvToConceptMapCommandTest.class);
|
||||
public class ImportCsvToConceptMapCommandR4Test {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ImportCsvToConceptMapCommandR4Test.class);
|
||||
private static final String CM_URL = "http://example.com/conceptmap";
|
||||
private static final String VS_URL_1 = "http://example.com/valueset/1";
|
||||
private static final String VS_URL_2 = "http://example.com/valueset/2";
|
||||
|
|
@ -42,6 +42,7 @@ public class ImportCsvToConceptMapCommandTest {
|
|||
private static FhirContext ourCtx = FhirContext.forR4();
|
||||
private static int ourPort;
|
||||
private static Server ourServer;
|
||||
private static String ourVersion = "r4";
|
||||
|
||||
private static RestfulServer restfulServer;
|
||||
|
||||
|
|
@ -87,7 +88,7 @@ public class ImportCsvToConceptMapCommandTest {
|
|||
|
||||
@Test
|
||||
public void testConditionalUpdateResultsInCreate() {
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandTest.createConceptMap();
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandR4Test.createConceptMap();
|
||||
String conceptMapUrl = conceptMap.getUrl();
|
||||
|
||||
ourLog.info("Searching for existing ConceptMap with specified URL (i.e. ConceptMap.url): {}", conceptMapUrl);
|
||||
|
|
@ -104,7 +105,7 @@ public class ImportCsvToConceptMapCommandTest {
|
|||
|
||||
@Test
|
||||
public void testConditionalUpdateResultsInUpdate() {
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandTest.createConceptMap();
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandR4Test.createConceptMap();
|
||||
ourClient.create().resource(conceptMap).execute();
|
||||
String conceptMapUrl = conceptMap.getUrl();
|
||||
|
||||
|
|
@ -122,7 +123,7 @@ public class ImportCsvToConceptMapCommandTest {
|
|||
|
||||
@Test
|
||||
public void testNonConditionalUpdate() {
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandTest.createConceptMap();
|
||||
ConceptMap conceptMap = ExportConceptMapToCsvCommandR4Test.createConceptMap();
|
||||
ourClient.create().resource(conceptMap).execute();
|
||||
|
||||
Bundle response = ourClient
|
||||
|
|
@ -150,10 +151,10 @@ public class ImportCsvToConceptMapCommandTest {
|
|||
public void testImportCsvToConceptMapCommand() throws FHIRException {
|
||||
ClassLoader classLoader = getClass().getClassLoader();
|
||||
File fileToImport = new File(classLoader.getResource(FILENAME).getFile());
|
||||
ImportCsvToConceptMapCommandTest.file = fileToImport.getAbsolutePath();
|
||||
ImportCsvToConceptMapCommandR4Test.file = fileToImport.getAbsolutePath();
|
||||
|
||||
App.main(new String[] {"import-csv-to-conceptmap",
|
||||
"-v", "r4",
|
||||
"-v", ourVersion,
|
||||
"-t", ourBase,
|
||||
"-u", CM_URL,
|
||||
"-i", VS_URL_1,
|
||||
|
|
@ -349,7 +350,7 @@ public class ImportCsvToConceptMapCommandTest {
|
|||
assertEquals("3d This is a comment.", target.getComment());
|
||||
|
||||
App.main(new String[] {"import-csv-to-conceptmap",
|
||||
"-v", "r4",
|
||||
"-v", ourVersion,
|
||||
"-t", ourBase,
|
||||
"-u", CM_URL,
|
||||
"-i", VS_URL_1,
|
||||
|
|
@ -27,7 +27,7 @@ import org.springframework.data.repository.query.Param;
|
|||
*/
|
||||
|
||||
public interface ITermConceptMapGroupDao extends JpaRepository<TermConceptMapGroup, Long> {
|
||||
@Query("DELETE FROM TermConceptMapGroup g WHERE g.myConceptMap.myId = :pid")
|
||||
@Query("DELETE FROM TermConceptMapGroup g WHERE g.myId = :pid")
|
||||
@Modifying
|
||||
void deleteTermConceptMapGroupById(@Param("pid") Long theId);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ import org.springframework.data.repository.query.Param;
|
|||
*/
|
||||
|
||||
public interface ITermConceptMapGroupElementDao extends JpaRepository<TermConceptMapGroupElement, Long> {
|
||||
@Query("DELETE FROM TermConceptMapGroupElement e WHERE e.myConceptMapGroup.myConceptMap.myId = :pid")
|
||||
@Query("DELETE FROM TermConceptMapGroupElement e WHERE e.myId = :pid")
|
||||
@Modifying
|
||||
void deleteTermConceptMapGroupElementById(@Param("pid") Long theId);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ import org.springframework.data.repository.query.Param;
|
|||
*/
|
||||
|
||||
public interface ITermConceptMapGroupElementTargetDao extends JpaRepository<TermConceptMapGroupElementTarget, Long> {
|
||||
@Query("DELETE FROM TermConceptMapGroupElementTarget t WHERE t.myConceptMapGroupElement.myConceptMapGroup.myConceptMap.myId = :pid")
|
||||
@Query("DELETE FROM TermConceptMapGroupElementTarget t WHERE t.myId = :pid")
|
||||
@Modifying
|
||||
void deleteTermConceptMapGroupElementTargetById(@Param("pid") Long theId);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -115,11 +115,12 @@ public class TermConceptMap implements Serializable {
|
|||
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
|
||||
.append("myId", myId)
|
||||
.append("myResource", myResource.toString())
|
||||
.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
|
||||
.append("myResourcePid", myResourcePid)
|
||||
.append("mySource", mySource)
|
||||
.append("myTarget", myTarget)
|
||||
.append("myUrl", myUrl)
|
||||
.append("myConceptMapGroups - size", myConceptMapGroups.size())
|
||||
.append(myConceptMapGroups != null ? ("myConceptMapGroups - size=" + myConceptMapGroups.size()) : ("myConceptMapGroups=(null)"))
|
||||
.toString();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -137,12 +137,12 @@ public class TermConceptMapGroup implements Serializable {
|
|||
public String toString() {
|
||||
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
|
||||
.append("myId", myId)
|
||||
.append("myConceptMap - id", myConceptMap.getId())
|
||||
.append(myConceptMap != null ? ("myConceptMap - id=" + myConceptMap.getId()) : ("myConceptMap=(null)"))
|
||||
.append("mySource", mySource)
|
||||
.append("mySourceVersion", mySourceVersion)
|
||||
.append("myTarget", myTarget)
|
||||
.append("myTargetVersion", myTargetVersion)
|
||||
.append("myConceptMapGroupElements - size", myConceptMapGroupElements.size())
|
||||
.append(myConceptMapGroupElements != null ? ("myConceptMapGroupElements - size=" + myConceptMapGroupElements.size()) : ("myConceptMapGroupElements=(null)"))
|
||||
.append("myConceptMapUrl", this.getConceptMapUrl())
|
||||
.append("mySourceValueSet", this.getSourceValueSet())
|
||||
.append("myTargetValueSet", this.getTargetValueSet())
|
||||
|
|
|
|||
|
|
@ -151,10 +151,10 @@ public class TermConceptMapGroupElement implements Serializable {
|
|||
public String toString() {
|
||||
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
|
||||
.append("myId", myId)
|
||||
.append("myConceptMapGroup - id", myConceptMapGroup.getId())
|
||||
.append(myConceptMapGroup != null ? ("myConceptMapGroup - id=" + myConceptMapGroup.getId()) : ("myConceptMapGroup=(null)"))
|
||||
.append("myCode", myCode)
|
||||
.append("myDisplay", myDisplay)
|
||||
.append("myConceptMapGroupElementTargets - size", myConceptMapGroupElementTargets.size())
|
||||
.append(myConceptMapGroupElementTargets != null ? ("myConceptMapGroupElementTargets - size=" + myConceptMapGroupElementTargets.size()) : ("myConceptMapGroupElementTargets=(null)"))
|
||||
.append("myConceptMapUrl", this.getConceptMapUrl())
|
||||
.append("mySystem", this.getSystem())
|
||||
.append("mySystemVersion", this.getSystemVersion())
|
||||
|
|
|
|||
|
|
@ -153,7 +153,7 @@ public class TermConceptMapGroupElementTarget implements Serializable {
|
|||
public String toString() {
|
||||
return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE)
|
||||
.append("myId", myId)
|
||||
.append("myConceptMapGroupElement - id", myConceptMapGroupElement.getId())
|
||||
.append(myConceptMapGroupElement != null ? ("myConceptMapGroupElement - id=" + myConceptMapGroupElement.getId()) : ("myConceptMapGroupElement=(null)"))
|
||||
.append("myCode", myCode)
|
||||
.append("myDisplay", myDisplay)
|
||||
.append("myEquivalence", myEquivalence.toCode())
|
||||
|
|
|
|||
|
|
@ -964,20 +964,33 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
termConceptMap.setUrl(theConceptMap.getUrl());
|
||||
|
||||
// Get existing entity so it can be deleted.
|
||||
Optional<TermConceptMap> optionalExistingTermConceptMapById = myConceptMapDao.findTermConceptMapByResourcePid(termConceptMap.getResourcePid());
|
||||
Optional<TermConceptMap> optionalExistingTermConceptMapById = myConceptMapDao.findTermConceptMapByResourcePid(theResourceTable.getId());
|
||||
|
||||
/*
|
||||
* For now we always delete old versions. At some point, it would be nice to allow configuration to keep old versions.
|
||||
*/
|
||||
|
||||
if (optionalExistingTermConceptMapById.isPresent()) {
|
||||
Long id = optionalExistingTermConceptMapById.get().getId();
|
||||
ourLog.info("Deleting existing TermConceptMap {} and its children...", id);
|
||||
myConceptMapGroupElementTargetDao.deleteTermConceptMapGroupElementTargetById(id);
|
||||
myConceptMapGroupElementDao.deleteTermConceptMapGroupElementById(id);
|
||||
myConceptMapGroupDao.deleteTermConceptMapGroupById(id);
|
||||
myConceptMapDao.deleteTermConceptMapById(id);
|
||||
ourLog.info("Done deleting existing TermConceptMap {} and its children.", id);
|
||||
TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapById.get();
|
||||
|
||||
ourLog.info("Deleting existing TermConceptMap {} and its children...", existingTermConceptMap.getId());
|
||||
for (TermConceptMapGroup group : existingTermConceptMap.getConceptMapGroups()) {
|
||||
|
||||
for (TermConceptMapGroupElement element : group.getConceptMapGroupElements()) {
|
||||
|
||||
for (TermConceptMapGroupElementTarget target : element.getConceptMapGroupElementTargets()) {
|
||||
|
||||
myConceptMapGroupElementTargetDao.deleteTermConceptMapGroupElementTargetById(target.getId());
|
||||
}
|
||||
|
||||
myConceptMapGroupElementDao.deleteTermConceptMapGroupElementById(element.getId());
|
||||
}
|
||||
|
||||
myConceptMapGroupDao.deleteTermConceptMapGroupById(group.getId());
|
||||
}
|
||||
|
||||
myConceptMapDao.deleteTermConceptMapById(existingTermConceptMap.getId());
|
||||
ourLog.info("Done deleting existing TermConceptMap {} and its children.", existingTermConceptMap.getId());
|
||||
|
||||
ourLog.info("Flushing...");
|
||||
myConceptMapGroupElementTargetDao.flush();
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
package ca.uhn.fhir.jpa.provider.dstu3;
|
||||
|
||||
import ca.uhn.fhir.rest.api.MethodOutcome;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import org.hl7.fhir.dstu3.model.*;
|
||||
import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
|
||||
|
|
@ -29,6 +30,37 @@ public class ResourceProviderDstu3ConceptMapTest extends BaseResourceProviderDst
|
|||
myConceptMapId = myConceptMapDao.create(createConceptMap(), mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testStoreExistingTermConceptMapAndChildren() {
|
||||
ConceptMap conceptMap = createConceptMap();
|
||||
|
||||
MethodOutcome methodOutcome = ourClient
|
||||
.update()
|
||||
.resource(conceptMap)
|
||||
.conditional()
|
||||
.where(ConceptMap.URL.matches().value(conceptMap.getUrl()))
|
||||
.execute();
|
||||
|
||||
assertNull(methodOutcome.getCreated());
|
||||
assertEquals("1", methodOutcome.getId().getVersionIdPart());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testStoreUpdatedTermConceptMapAndChildren() {
|
||||
ConceptMap conceptMap = createConceptMap();
|
||||
conceptMap.getGroupFirstRep().getElementFirstRep().setCode("UPDATED_CODE");
|
||||
|
||||
MethodOutcome methodOutcome = ourClient
|
||||
.update()
|
||||
.resource(conceptMap)
|
||||
.conditional()
|
||||
.where(ConceptMap.URL.matches().value(conceptMap.getUrl()))
|
||||
.execute();
|
||||
|
||||
assertNull(methodOutcome.getCreated());
|
||||
assertEquals("2", methodOutcome.getId().getVersionIdPart());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
package ca.uhn.fhir.jpa.provider.r4;
|
||||
|
||||
import ca.uhn.fhir.rest.api.MethodOutcome;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
|
|
@ -29,6 +30,37 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
myConceptMapId = myConceptMapDao.create(createConceptMap(), mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testStoreExistingTermConceptMapAndChildren() {
|
||||
ConceptMap conceptMap = createConceptMap();
|
||||
|
||||
MethodOutcome methodOutcome = myClient
|
||||
.update()
|
||||
.resource(conceptMap)
|
||||
.conditional()
|
||||
.where(ConceptMap.URL.matches().value(conceptMap.getUrl()))
|
||||
.execute();
|
||||
|
||||
assertNull(methodOutcome.getCreated());
|
||||
assertEquals("1", methodOutcome.getId().getVersionIdPart());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testStoreUpdatedTermConceptMapAndChildren() {
|
||||
ConceptMap conceptMap = createConceptMap();
|
||||
conceptMap.getGroupFirstRep().getElementFirstRep().setCode("UPDATED_CODE");
|
||||
|
||||
MethodOutcome methodOutcome = myClient
|
||||
.update()
|
||||
.resource(conceptMap)
|
||||
.conditional()
|
||||
.where(ConceptMap.URL.matches().value(conceptMap.getUrl()))
|
||||
.execute();
|
||||
|
||||
assertNull(methodOutcome.getCreated());
|
||||
assertEquals("2", methodOutcome.getId().getVersionIdPart());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
|
|||
Loading…
Reference in New Issue