org.fhir.ucum.UcumEssenceService Java Exaples

Source File: TestingUtilities.java From org.hl7.fhir.core with Apache License 2.0

6 votes

public static IWorkerContext context(String version) {
    String v = VersionUtilities.getMajMin(version);
    if (fcontexts == null) {
      fcontexts = new HashMap<>();
    }
    if (!fcontexts.containsKey(v)) {
      FilesystemPackageCacheManager pcm;
      try {
        pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
        IWorkerContext fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage(VersionUtilities.packageForVersion(version), version));
        fcontext.setUcumService(new UcumEssenceService(TestingUtilities.loadTestResourceStream("ucum", "ucum-essence.xml")));
        fcontext.setExpansionProfile(new Parameters());
//        ((SimpleWorkerContext) fcontext).connectToTSServer(new TerminologyClientR5("http://tx.fhir.org/r4"), null);
        fcontexts.put(v, fcontext);
      } catch (Exception e) {
        throw new Error(e);
      }
    }
    return fcontexts.get(v);
  }

Source File: TestingUtilitiesX.java From org.hl7.fhir.core with Apache License 2.0

6 votes

public static IWorkerContext context(String version) {
   if (fcontexts == null) {
     fcontexts = new HashMap<>();
   }
  if (!fcontexts.containsKey(version)) {
    FilesystemPackageCacheManager pcm;
    try {
      pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
      IWorkerContext fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage(VersionUtilities.packageForVersion(version), version), loaderForVersion(version));
      fcontext.setUcumService(new UcumEssenceService(TestingUtilitiesX.loadTestResourceStream("ucum", "ucum-essence.xml")));
      fcontext.setExpansionProfile(new Parameters());
      fcontexts.put(version, fcontext);
    } catch (Exception e) {
      throw new Error(e);
    }
  }
  return fcontexts.get(version);
}

Source File: Test.java From org.hl7.fhir.core with Apache License 2.0

6 votes

public static void main(String[] args) {
	try {
		CCDAConverter c = new CCDAConverter(new UcumEssenceService(UCUM_PATH), SimpleWorkerContext.fromPack(Utilities.path(SRC_PATH, "validation.zip")));
		Bundle a = c.convert(new FileInputStream(DEF_PATH + "ccda.xml"));
		String fx = DEF_PATH + "output.xml";
		IParser x = new XmlParser().setOutputStyle(OutputStyle.PRETTY);
		x.compose(new FileOutputStream(fx),  a);
		String fj = DEF_PATH + "output.json";
		IParser j = new JsonParser().setOutputStyle(OutputStyle.PRETTY);
		j.compose(new FileOutputStream(fj),  a);
		System.out.println("done. save as "+fx+" and "+fj);
	} catch (Exception e) {
		e.printStackTrace();
	}
	

}

Source File: TestingUtilities.java From org.hl7.fhir.core with Apache License 2.0

5 votes

public static IWorkerContext context() {
  if (fcontext == null) {
    FilesystemPackageCacheManager pcm;
    try {
      pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
      fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
      fcontext.setUcumService(new UcumEssenceService(TestingUtilities.resourceNameToFile("ucum", "ucum-essence.xml")));
      fcontext.setExpansionProfile(new Parameters());
    } catch (Exception e) {
      throw new Error(e);
    }

  }
  return fcontext;
}

Source File: ArgonautConverter.java From org.hl7.fhir.core with Apache License 2.0

5 votes

public static void main(String[] args) {
	try {
		ArgonautConverter c = new ArgonautConverter(new UcumEssenceService(UCUM_PATH), Utilities.path(SRC_PATH, "validation.xml.zip"));
		c.destFolder = "C:\\work\\com.healthintersections.fhir\\argonaut\\fhir";
		c.convert("C:\\work\\com.healthintersections.fhir\\argonaut\\cda\\file_emergency", new Coding().setSystem("http://hl7.org/fhir/v3/ActCode").setCode("EMER"));
		c.convert("C:\\work\\com.healthintersections.fhir\\argonaut\\cda\\file_ed", new Coding().setSystem("http://hl7.org/fhir/v3/ActCode").setCode("IMP"));
		c.convert("C:\\work\\com.healthintersections.fhir\\argonaut\\cda\\fileX", new Coding().setSystem("http://hl7.org/fhir/v3/ActCode").setCode("AMB"));
		c.printSectionSummaries();
		c.closeZips();
		System.out.println("All done. "+Integer.toString(c.getErrors())+" errors, "+Integer.toString(c.getWarnings())+" warnings");
	} catch (Exception e) {
		e.printStackTrace();
	}
}

Source File: CqlTestSuite.java From cql_engine with Apache License 2.0

5 votes

private Library translate(String file)  throws UcumException, JAXBException, IOException {
    ModelManager modelManager = new ModelManager();
    LibraryManager libraryManager = new LibraryManager(modelManager);
    UcumService ucumService = new UcumEssenceService(UcumEssenceService.class.getResourceAsStream("/ucum-essence.xml"));

    File cqlFile = new File(URLDecoder.decode(this.getClass().getResource(file).getFile(), "UTF-8"));

    CqlTranslator translator = CqlTranslator.fromFile(cqlFile, modelManager, libraryManager, ucumService);

    if (translator.getErrors().size() > 0) {
        System.err.println("Translation failed due to errors:");
        ArrayList<String> errors = new ArrayList<>();
        for (CqlTranslatorException error : translator.getErrors()) {
            TrackBack tb = error.getLocator();
            String lines = tb == null ? "[n/a]" : String.format("[%d:%d, %d:%d]",
                    tb.getStartLine(), tb.getStartChar(), tb.getEndLine(), tb.getEndChar());
            System.err.printf("%s %s%n", lines, error.getMessage());
            errors.add(lines + error.getMessage());
        }
        throw new IllegalArgumentException(errors.toString());
    }

    assertThat(translator.getErrors().size(), is(0));

    String xml = translator.toXml();

    return CqlLibraryReader.read(new StringReader(xml));
}

Source File: TestUtils.java From clinical_quality_language with Apache License 2.0

5 votes

private static void setup() {
    modelManager = new ModelManager();
    libraryManager = new LibraryManager(modelManager);
    libraryManager.getLibrarySourceLoader().registerProvider(new TestLibrarySourceProvider());
    libraryManager.getLibrarySourceLoader().registerProvider(new FhirLibrarySourceProvider());
    try {
        ucumService = new UcumEssenceService(UcumEssenceService.class.getResourceAsStream("/ucum-essence.xml"));
    }
    catch (UcumException e) {
        e.printStackTrace();
    }
}

Source File: FhirExecutionTestBase.java From cql_engine with Apache License 2.0

4 votes

@BeforeMethod
public void beforeEachTestMethod() throws JAXBException, IOException, UcumException {
    String fileName = this.getClass().getSimpleName();
    library = libraries.get(fileName);
    if (library == null) {
        ModelManager modelManager = new ModelManager();
        LibraryManager libraryManager = new LibraryManager(modelManager);
        UcumService ucumService = new UcumEssenceService(UcumEssenceService.class.getResourceAsStream("/ucum-essence.xml"));
        try {
            File cqlFile = new File(URLDecoder.decode(this.getClass().getResource(fileName + ".cql").getFile(), "UTF-8"));

            ArrayList<CqlTranslator.Options> options = new ArrayList<>();
            options.add(CqlTranslator.Options.EnableDateRangeOptimization);
            CqlTranslator translator = CqlTranslator.fromFile(cqlFile, modelManager, libraryManager, ucumService, options.toArray(new CqlTranslator.Options[options.size()]));

            if (translator.getErrors().size() > 0) {
                System.err.println("Translation failed due to errors:");
                ArrayList<String> errors = new ArrayList<>();
                for (CqlTranslatorException error : translator.getErrors()) {
                    TrackBack tb = error.getLocator();
                    String lines = tb == null ? "[n/a]" : String.format("[%d:%d, %d:%d]",
                            tb.getStartLine(), tb.getStartChar(), tb.getEndLine(), tb.getEndChar());
                    System.err.printf("%s %s%n", lines, error.getMessage());
                    errors.add(lines + error.getMessage());
                }
                throw new IllegalArgumentException(errors.toString());
            }

            assertThat(translator.getErrors().size(), is(0));

            xmlFile = new File(cqlFile.getParent(), fileName + ".xml");
            xmlFile.createNewFile();

            PrintWriter pw = new PrintWriter(xmlFile, "UTF-8");
            pw.println(translator.toXml());
            pw.println();
            pw.close();
        } catch (IOException e) {
            e.printStackTrace();
        }

        library = CqlLibraryReader.read(xmlFile);
        libraries.put(fileName, library);
    }
}

Source File: CqlExecutionTestBase.java From cql_engine with Apache License 2.0

4 votes

@BeforeMethod
public void beforeEachTestMethod() throws JAXBException, IOException, UcumException {
    String fileName = this.getClass().getSimpleName();
    library = libraries.get(fileName);
    if (library == null) {
        UcumService ucumService = new UcumEssenceService(UcumEssenceService.class.getResourceAsStream("/ucum-essence.xml"));
        try {
            File cqlFile = new File(URLDecoder.decode(this.getClass().getResource(fileName + ".cql").getFile(), "UTF-8"));

            ArrayList<CqlTranslator.Options> options = new ArrayList<>();
            options.add(CqlTranslator.Options.EnableDateRangeOptimization);
            options.add(CqlTranslator.Options.EnableAnnotations);
            options.add(CqlTranslator.Options.EnableLocators);
            CqlTranslator translator = CqlTranslator.fromFile(cqlFile, getModelManager(), getLibraryManager(), ucumService, options.toArray(new CqlTranslator.Options[options.size()]));

            if (translator.getErrors().size() > 0) {
                System.err.println("Translation failed due to errors:");
                ArrayList<String> errors = new ArrayList<>();
                for (CqlTranslatorException error : translator.getErrors()) {
                    TrackBack tb = error.getLocator();
                    String lines = tb == null ? "[n/a]" : String.format("[%d:%d, %d:%d]",
                            tb.getStartLine(), tb.getStartChar(), tb.getEndLine(), tb.getEndChar());
                    System.err.printf("%s %s%n", lines, error.getMessage());
                    errors.add(lines + error.getMessage());
                }
                throw new IllegalArgumentException(errors.toString());
            }

            assertThat(translator.getErrors().size(), is(0));

            xmlFile = new File(cqlFile.getParent(), fileName + ".xml");
            xmlFile.createNewFile();

            String xml = translator.toXml();

            PrintWriter pw = new PrintWriter(xmlFile, "UTF-8");
            pw.println(xml);
            pw.println();
            pw.close();
        } catch (IOException e) {
            e.printStackTrace();
        }

        library = CqlLibraryReader.read(xmlFile);
        libraries.put(fileName, library);
    }
}

Source File: IEEE11073Convertor.java From org.hl7.fhir.core with Apache License 2.0

3 votes

/**
 * argument 1: path to the rosetta csv file
 * argument 2: basePath to produce files to
 *  
 * @param args
 * @throws Exception
 */
public static void main(String[] args) throws Exception {
  UcumService ucum = new UcumEssenceService(UCUM_PATH);

  CodeSystem mdc = generateMDC(args[0], args[1], ucum);
  ConceptMap loinc = generateLoincMdcMap(mdc, args[1], args[2]);
}

org.fhir.ucum.UcumEssenceService Java Examples