org.cqframework.cql.cql2elm.ModelManager Java Exaples

Source File: LibraryOperationsProvider.java From cqf-ruler with Apache License 2.0

8 votes

@Operation(name = "$refresh-generated-content", type = Library.class)
public MethodOutcome refreshGeneratedContent(HttpServletRequest theRequest, RequestDetails theRequestDetails,
        @IdParam IdType theId) {
    Library theResource = this.libraryResourceProvider.getDao().read(theId);
    //this.formatCql(theResource);

    ModelManager modelManager = this.getModelManager();
    LibraryManager libraryManager = this.getLibraryManager(modelManager);

    CqlTranslator translator = this.dataRequirementsProvider.getTranslator(theResource, libraryManager, modelManager);
    if (translator.getErrors().size() > 0) {
        throw new RuntimeException("Errors during library compilation.");
    }
    
    this.dataRequirementsProvider.ensureElm(theResource, translator);
    this.dataRequirementsProvider.ensureRelatedArtifacts(theResource, translator, this);
    this.dataRequirementsProvider.ensureDataRequirements(theResource, translator);

    Narrative n = this.narrativeProvider.getNarrative(this.libraryResourceProvider.getContext(), theResource);
    theResource.setText(n);

    return this.libraryResourceProvider.update(theRequest, theResource, theId,
            theRequestDetails.getConditionalUrl(RestOperationTypeEnum.UPDATE), theRequestDetails);
}

Source File: TranslatorHelper.java From cqf-ruler with Apache License 2.0

6 votes

public static CqlTranslator getTranslator(InputStream cqlStream, LibraryManager libraryManager, ModelManager modelManager) {
    ArrayList<CqlTranslator.Options> options = new ArrayList<>();
    options.add(CqlTranslator.Options.EnableAnnotations);
    options.add(CqlTranslator.Options.EnableLocators);
    options.add(CqlTranslator.Options.DisableListDemotion);
    options.add(CqlTranslator.Options.DisableListPromotion);
    options.add(CqlTranslator.Options.DisableMethodInvocation);
    CqlTranslator translator;
    try {
        translator = CqlTranslator.fromStream(cqlStream, modelManager, libraryManager,
                options.toArray(new CqlTranslator.Options[options.size()]));
    } catch (IOException e) {
        throw new IllegalArgumentException(String.format("Errors occurred translating library: %s", e.getMessage()));
    }
    
    return translator;
}

Source File: DataRequirementsProvider.java From cqf-ruler with Apache License 2.0

6 votes

public CqlTranslator getTranslator(org.hl7.fhir.r4.model.Library library, LibraryManager libraryManager, ModelManager modelManager) {
    Attachment cql = null;
    for (Attachment a : library.getContent()) {
        if (a.getContentType().equals("text/cql")) {
            cql = a;
            break;
        }
    }

    if (cql == null) {
        return null;
    }

    return TranslatorHelper.getTranslator(
            new ByteArrayInputStream(Base64.getDecoder().decode(cql.getDataElement().getValueAsString())),
            libraryManager, modelManager);
}

Source File: LibraryOperationsProvider.java From cqf-ruler with Apache License 2.0

6 votes

@Operation(name = "$get-elm", idempotent = true, type = Library.class)
public Parameters getElm(@IdParam IdType theId, @OptionalParam(name="format") String format) {
    Library theResource = this.libraryResourceProvider.getDao().read(theId);
    // this.formatCql(theResource);

    ModelManager modelManager = this.getModelManager();
    LibraryManager libraryManager = this.getLibraryManager(modelManager);

    String elm = "";
    CqlTranslator translator = this.dataRequirementsProvider.getTranslator(theResource, libraryManager, modelManager);
    if (translator != null) {
        if (format.equals("json")) {
            elm = translator.toJson();
        }
        else {
            elm = translator.toXml();
        }
    }
    Parameters p = new Parameters();
    p.addParameter().setValue(new StringType(elm));
    return p;
}

Source File: DataRequirementsProvider.java From cqf-ruler with Apache License 2.0

6 votes

public CqlTranslator getTranslator(org.hl7.fhir.dstu3.model.Library library, LibraryManager libraryManager, ModelManager modelManager) {
    Attachment cql = null;
    for (Attachment a : library.getContent()) {
        if (a.getContentType().equals("text/cql")) {
            cql = a;
            break;
        }
    }

    if (cql == null) {
        return null;
    }

    CqlTranslator translator = TranslatorHelper.getTranslator(
            new ByteArrayInputStream(Base64.getDecoder().decode(cql.getDataElement().getValueAsString())),
            libraryManager, modelManager);

    return translator;
}

Source File: LibraryOperationsProvider.java From cqf-ruler with Apache License 2.0

6 votes

@Operation(name = "$get-elm", idempotent = true, type = Library.class)
public Parameters getElm(@IdParam IdType theId, @OptionalParam(name="format") String format) {
    Library theResource = this.libraryResourceProvider.getDao().read(theId);
    // this.formatCql(theResource);

    ModelManager modelManager = this.getModelManager();
    LibraryManager libraryManager = this.getLibraryManager(modelManager);


    String elm = "";
    CqlTranslator translator = this.dataRequirementsProvider.getTranslator(theResource, libraryManager, modelManager);
    if (translator != null) {
        if (format.equals("json")) {
            elm = translator.toJson();
        }
        else {
            elm = translator.toXml();
        }
    }
    Parameters p = new Parameters();
    p.addParameter().setValue(new StringType(elm));
    return p;
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(QueryTest.class.getResourceAsStream("../OperatorTests/Query.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(CqlIntervalOperatorsTest.class.getResourceAsStream("../OperatorTests/CqlIntervalOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    if (library.getStatements() != null) {
        for (ExpressionDef def : library.getStatements().getDef()) {
            defs.put(def.getName(), def);
        }
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(TimeOperatorsTest.class.getResourceAsStream("../OperatorTests/TimeOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(ArithmeticOperatorsTest.class.getResourceAsStream("../OperatorTests/ArithmeticOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(QueryTest.class.getResourceAsStream("../OperatorTests/Sorting.cql"), modelManager, new LibraryManager(modelManager));
    
    // The alias test creates an error
    assertThat(translator.getErrors().size(), is(1));

    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(ListOperatorsTest.class.getResourceAsStream("../OperatorTests/ListOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(TypeOperatorsTest.class.getResourceAsStream("../OperatorTests/TypeOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(CqlListOperatorsTest.class.getResourceAsStream("../OperatorTests/CqlListOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    if (library.getStatements() != null) {
        for (ExpressionDef def : library.getStatements().getDef()) {
            defs.put(def.getName(), def);
        }
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(AggregateOperatorsTest.class.getResourceAsStream("../OperatorTests/AggregateOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    if (library.getStatements() != null) {
        for (ExpressionDef def : library.getStatements().getDef()) {
            defs.put(def.getName(), def);
        }
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(AgeOperatorsTest.class.getResourceAsStream("../OperatorTests/AgeOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    if (library.getStatements() != null) {
        for (ExpressionDef def : library.getStatements().getDef()) {
            defs.put(def.getName(), def);
        }
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(StringOperatorsTest.class.getResourceAsStream("../OperatorTests/StringOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(NullologicalOperatorsTest.class.getResourceAsStream("../OperatorTests/NullologicalOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(CqlComparisonOperatorsTest.class.getResourceAsStream("../OperatorTests/CqlComparisonOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    if (library.getStatements() != null) {
        for (ExpressionDef def : library.getStatements().getDef()) {
            defs.put(def.getName(), def);
        }
    }
}

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

5 votes

@BeforeTest
public void setup() throws IOException {
    ModelManager modelManager = new ModelManager();
    CqlTranslator translator = CqlTranslator.fromStream(DateTimeOperatorsTest.class.getResourceAsStream("../OperatorTests/DateTimeOperators.cql"), modelManager, new LibraryManager(modelManager));
    assertThat(translator.getErrors().size(), is(0));
    Library library = translator.toELM();
    defs = new HashMap<>();
    for (ExpressionDef def: library.getStatements().getDef()) {
        defs.put(def.getName(), def);
    }
}

Source File: TestDstu3ModelResolver.java From cql_engine with Apache License 2.0

5 votes

@Test
// This tests all the types that are present in the modelinfo
public void resolveModelInfoTests() {
    ModelResolver resolver = new Dstu3FhirModelResolver();
    ModelManager mm = new ModelManager();
    Model m = mm.resolveModel(new VersionedIdentifier().withId("FHIR").withVersion("3.0.0"));

    List<TypeInfo> typeInfos = m.getModelInfo().getTypeInfo();

    for (TypeInfo ti : typeInfos) {
        ClassInfo ci = (ClassInfo)ti;
        if (ci != null) {
            switch (ci.getBaseType()) {
                // Astract classes
                case "FHIR.BackboneElement":
                case "FHIR.Element": continue;
            }

            switch (ci.getName()) {
                // TODO: HAPI Doesn't have a ResourceContainer type for Dstu3
                case "ResourceContainer": continue;
            }

            resolver.resolveType(ci.getName());
        }
    }
}

Source File: TestR4ModelResolver.java From cql_engine with Apache License 2.0

5 votes

@Test
public void resolveModelInfoTests() {
    ModelResolver resolver = new R4FhirModelResolver();
    ModelManager mm = new ModelManager();
    Model m = mm.resolveModel(new VersionedIdentifier().withId("FHIR").withVersion("4.0.0"));

    List<TypeInfo> typeInfos = m.getModelInfo().getTypeInfo();

    for (TypeInfo ti : typeInfos) {
        ClassInfo ci = (ClassInfo)ti;
        if (ci != null) {
            switch (ci.getBaseType()) {
                // Astract classes
                case "FHIR.BackboneElement":
                case "FHIR.Element": continue;
            }

            switch (ci.getName()) {
                // TODO: HAPI Doesn't have a ResourceContainer type
                case "ResourceContainer": continue;
            }


            // TODO: The cause of failure for this is unknown.
            // Need to figure out if it's a gap in happy,
            // or if a manual mapping is required, or what.
            switch(ci.getName()) {
                case "ItemInstance" : continue;
            }

            resolver.resolveType(ci.getName());
        }
    }
}

Source File: LibraryOperationsProvider.java From cqf-ruler with Apache License 2.0

5 votes

@Operation(name = "$refresh-generated-content", type = Library.class)
  public MethodOutcome refreshGeneratedContent(HttpServletRequest theRequest, RequestDetails theRequestDetails,
          @IdParam IdType theId) {
      Library theResource = this.libraryResourceProvider.getDao().read(theId);
      //this.formatCql(theResource);

      ModelManager modelManager = this.getModelManager();
      LibraryManager libraryManager = this.getLibraryManager(modelManager);

      CqlTranslator translator = this.dataRequirementsProvider.getTranslator(theResource, libraryManager, modelManager);
      if (translator.getErrors().size() > 0) {
          throw new RuntimeException("Errors during library compilation.");
      }
      
      this.dataRequirementsProvider.ensureElm(theResource, translator);
      this.dataRequirementsProvider.ensureRelatedArtifacts(theResource, translator, this);
      this.dataRequirementsProvider.ensureDataRequirements(theResource, translator);

try {
	Narrative n = this.narrativeProvider.getNarrative(this.libraryResourceProvider.getContext(), theResource);
	theResource.setText(n);
} catch (Exception e) {
	//Ignore the exception so the resource still gets updated
}

      return this.libraryResourceProvider.update(theRequest, theResource, theId,
              theRequestDetails.getConditionalUrl(RestOperationTypeEnum.UPDATE), theRequestDetails);
  }

Source File: LibraryOperationsProvider.java From cqf-ruler with Apache License 2.0

5 votes

private LibraryManager getLibraryManager(ModelManager modelManager)
{
    LibraryManager libraryManager = new LibraryManager(modelManager);
    libraryManager.getLibrarySourceLoader().clearProviders();
    libraryManager.getLibrarySourceLoader().registerProvider(getLibrarySourceProvider());

    return libraryManager;
}

Source File: LibraryHelper.java From cqf-ruler with Apache License 2.0

5 votes

public static LibraryLoader createLibraryLoader(LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> provider) {
    ModelManager modelManager = new ModelManager();
    LibraryManager libraryManager = new LibraryManager(modelManager);
    libraryManager.getLibrarySourceLoader().clearProviders();
    
    libraryManager.getLibrarySourceLoader().registerProvider(
        new LibrarySourceProvider<org.hl7.fhir.r4.model.Library, org.hl7.fhir.r4.model.Attachment>(
            provider, 
            x -> x.getContent(),
            x -> x.getContentType(),
            x -> x.getData()));

    return new LibraryLoader(libraryManager, modelManager);
}

Source File: LibraryOperationsProvider.java From cqf-ruler with Apache License 2.0

5 votes

private LibraryManager getLibraryManager(ModelManager modelManager)
{
    LibraryManager libraryManager = new LibraryManager(modelManager);
    libraryManager.getLibrarySourceLoader().clearProviders();
    libraryManager.getLibrarySourceLoader().registerProvider(getLibrarySourceProvider());

    return libraryManager;
}

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: LibraryHelper.java From cqf-ruler with Apache License 2.0

5 votes

public static LibraryLoader createLibraryLoader(LibraryResolutionProvider<org.hl7.fhir.dstu3.model.Library> provider) {
    ModelManager modelManager = new ModelManager();
    LibraryManager libraryManager = new LibraryManager(modelManager);
    libraryManager.getLibrarySourceLoader().clearProviders();
    
    libraryManager.getLibrarySourceLoader().registerProvider(
        new LibrarySourceProvider<org.hl7.fhir.dstu3.model.Library, org.hl7.fhir.dstu3.model.Attachment>(
            provider, 
            x -> x.getContent(),
            x -> x.getContentType(),
            x -> x.getData()));

    return new LibraryLoader(libraryManager, modelManager);
}

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: TranslatorHelper.java From cqf-ruler with Apache License 2.0

4 votes

public static Library translateLibrary(String cql, LibraryManager libraryManager, ModelManager modelManager) {
    return translateLibrary(new ByteArrayInputStream(cql.getBytes(StandardCharsets.UTF_8)), libraryManager, modelManager);
}

org.cqframework.cql.cql2elm.ModelManager Java Examples