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Example 6 with TranslatingCqlLibraryProvider

use of com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.

the class SparkSchemaCreatorTest method setup.

@Before
public void setup() {
    cqlTranslator = new CqlToElmTranslator();
    cqlTranslator.registerModelInfo(new File("src/test/resources/output-validation/modelinfo/simple-all-types-model-info.xml"));
    CqlLibraryProvider backingProvider = new ClasspathCqlLibraryProvider("output-validation.cql");
    cqlLibraryProvider = new TranslatingCqlLibraryProvider(backingProvider, cqlTranslator);
    outputColumnNameFactory = new DefaultSparkOutputColumnEncoder(".");
}
Also used : TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) CqlToElmTranslator(com.ibm.cohort.cql.translation.CqlToElmTranslator) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) File(java.io.File) Before(org.junit.Before)

Example 7 with TranslatingCqlLibraryProvider

use of com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.

the class ColumnRuleCreatorTest method testGetFiltersForContextOnlyJoinColumns.

@Test
public void testGetFiltersForContextOnlyJoinColumns() throws Exception {
    CqlToElmTranslator cqlTranslator = new CqlToElmTranslator();
    cqlTranslator.registerModelInfo(new File("src/test/resources/alltypes/modelinfo/alltypes-modelinfo-1.0.0.xml"));
    ObjectMapper mapper = new ObjectMapper();
    CqlEvaluationRequests requests = mapper.readValue(new File("src/test/resources/alltypes/metadata/join-only.json"), CqlEvaluationRequests.class);
    CqlLibraryProvider backingProvider = new ClasspathCqlLibraryProvider("alltypes.cql");
    TranslatingCqlLibraryProvider cqlLibraryProvider = new TranslatingCqlLibraryProvider(backingProvider, cqlTranslator);
    ColumnRuleCreator columnRuleCreator = new ColumnRuleCreator(requests.getEvaluations(), cqlTranslator, cqlLibraryProvider);
    ContextDefinitions definitions = mapper.readValue(new File("src/test/resources/alltypes/metadata/context-definitions-related-column.json"), ContextDefinitions.class);
    ContextDefinition context = definitions.getContextDefinitionByName("Patient");
    Map<String, Set<StringMatcher>> actual = columnRuleCreator.getDataRequirementsForContext(context);
    Map<String, Set<StringMatcher>> expected = new HashMap<>();
    expected.put("A", new HashSet<>(Arrays.asList(new EqualsStringMatcher(ContextRetriever.SOURCE_FACT_IDX), new EqualsStringMatcher("id_col"), new EqualsStringMatcher("pat_id"))));
    expected.put("B", new HashSet<>(Arrays.asList(new EqualsStringMatcher(ContextRetriever.SOURCE_FACT_IDX), new EqualsStringMatcher("string"), new EqualsStringMatcher(ContextRetriever.JOIN_CONTEXT_VALUE_IDX))));
    expected.put("C", new HashSet<>(Arrays.asList(new EqualsStringMatcher(ContextRetriever.SOURCE_FACT_IDX), new EqualsStringMatcher("pat_id"), new EqualsStringMatcher(ContextRetriever.JOIN_CONTEXT_VALUE_IDX))));
    assertEquals(expected, actual);
}
Also used : Set(java.util.Set) HashSet(java.util.HashSet) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) HashMap(java.util.HashMap) CqlToElmTranslator(com.ibm.cohort.cql.translation.CqlToElmTranslator) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) EqualsStringMatcher(com.ibm.cohort.cql.util.EqualsStringMatcher) CqlEvaluationRequests(com.ibm.cohort.cql.evaluation.CqlEvaluationRequests) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) File(java.io.File) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) Test(org.junit.Test)

Example 8 with TranslatingCqlLibraryProvider

use of com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.

the class CohortCLI method runWithArgs.

/**
 * Simulate main method behavior in a non-static context for use in testing
 * tools. This method is intended to be called only once. Multiple calls for the
 * same library path will attempt duplicate library loading.
 *
 * @param args parameter values
 * @param out  location where contents that would normally go to stdout should
 *             be written
 * @return CQLEvaluator
 * @throws IOException IOException
 */
public CqlEvaluator runWithArgs(String[] args, PrintStream out) throws IOException {
    Arguments arguments = new Arguments();
    Console console = new DefaultConsole(out);
    JCommander jc = JCommander.newBuilder().programName("cql-engine").console(console).addObject(arguments).build();
    jc.parse(args);
    CqlEvaluator wrapper = null;
    if (arguments.isDisplayHelp) {
        jc.usage();
    } else {
        FhirClientBuilderFactory factory = FhirClientBuilderFactory.newInstance();
        FhirClientBuilder fhirClientBuilder = factory.newFhirClientBuilder();
        readConnectionConfiguration(arguments);
        MapCqlLibraryProviderFactory libraryProviderFactory = new MapCqlLibraryProviderFactory();
        String[] filters = null;
        if (arguments.filters != null) {
            filters = arguments.filters.toArray(new String[arguments.filters.size()]);
        }
        CqlLibraryProvider backingLibraryProvider;
        Path libraryFolder = Paths.get(arguments.libraryPath);
        if (libraryFolder.toFile().isDirectory()) {
            out.println(String.format("Loading libraries from folder '%s'", libraryFolder.toString()));
            backingLibraryProvider = libraryProviderFactory.fromDirectory(libraryFolder, filters);
        } else if (FileHelpers.isZip(libraryFolder.toFile())) {
            out.println(String.format("Loading libraries from ZIP '%s'", libraryFolder.toString()));
            backingLibraryProvider = libraryProviderFactory.fromZipFile(libraryFolder, filters);
        } else {
            out.println(String.format("Loading libraries from FHIR Library '%s'", libraryFolder.toString()));
            IGenericClient measureClient = fhirClientBuilder.createFhirClient(measureServerConfig);
            FhirResourceResolver<Library> libraryResolver = R4FhirServerResourceResolverFactory.createLibraryResolver(measureClient);
            R4LibraryDependencyGatherer dependencyGatherer = new R4LibraryDependencyGatherer(libraryResolver);
            List<Library> cqlLibraries = dependencyGatherer.gatherForLibraryId(arguments.libraryPath);
            Map<CqlLibraryDescriptor, CqlLibrary> cqlLibraryMap = toCqlLibraryMap(cqlLibraries);
            backingLibraryProvider = new MapCqlLibraryProvider(cqlLibraryMap);
        }
        CqlLibraryProvider fhirClasspathProvider = new ClasspathCqlLibraryProvider();
        backingLibraryProvider = new PriorityCqlLibraryProvider(backingLibraryProvider, fhirClasspathProvider);
        CqlToElmTranslator translator = new CqlToElmTranslator();
        if (arguments.modelInfoFile != null && arguments.modelInfoFile.exists()) {
            translator.registerModelInfo(arguments.modelInfoFile);
        }
        boolean isForceTranslation = arguments.sourceFormat == Format.CQL;
        CqlLibraryProvider libraryProvider = new TranslatingCqlLibraryProvider(backingLibraryProvider, translator, isForceTranslation);
        IGenericClient dataClient = fhirClientBuilder.createFhirClient(dataServerConfig);
        IGenericClient termClient = fhirClientBuilder.createFhirClient(terminologyServerConfig);
        CqlTerminologyProvider termProvider = new R4RestFhirTerminologyProvider(termClient);
        Map<String, com.ibm.cohort.cql.evaluation.parameters.Parameter> parameters = null;
        if (arguments.parameters != null) {
            parameters = parseParameterArguments(arguments.parameters);
        }
        CqlVersionedIdentifier libraryIdentifier = new CqlVersionedIdentifier(arguments.libraryName, arguments.libraryVersion);
        List<Pair<String, String>> contexts;
        if (arguments.contextIds == null || arguments.contextIds.isEmpty()) {
            // If no context ids are provided, perform one run using a null context
            contexts = Collections.singletonList(null);
        } else {
            contexts = arguments.contextIds.stream().map(x -> new ImmutablePair<>(arguments.contextName, x)).collect(Collectors.toList());
        }
        try (RetrieveCacheContext cacheContext = new DefaultRetrieveCacheContext()) {
            CqlDataProvider dataProvider = R4DataProviderFactory.createDataProvider(dataClient, termProvider, cacheContext, R4FhirModelResolverFactory.createCachingResolver(), !arguments.enableTerminologyOptimization, arguments.searchPageSize);
            wrapper = new CqlEvaluator().setLibraryProvider(libraryProvider).setDataProvider(dataProvider).setTerminologyProvider(termProvider);
            ZonedDateTime evaluationDateTime = ZonedDateTime.now();
            for (Pair<String, String> context : contexts) {
                String contextLabel = context == null ? "null" : context.getRight();
                out.println("Context: " + contextLabel);
                CqlEvaluationResult result = wrapper.evaluate(libraryIdentifier, parameters, context, arguments.expressions, arguments.loggingLevel, evaluationDateTime);
                out.print(prettyPrintResult(result));
                out.println("---");
            }
        }
    }
    return wrapper;
}
Also used : FhirResourceResolver(com.ibm.cohort.cql.fhir.resolver.FhirResourceResolver) DefaultConsole(com.beust.jcommander.internal.DefaultConsole) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) R4RestFhirTerminologyProvider(com.ibm.cohort.engine.terminology.R4RestFhirTerminologyProvider) DefaultRetrieveCacheContext(com.ibm.cohort.engine.measure.cache.DefaultRetrieveCacheContext) RetrieveCacheContext(com.ibm.cohort.engine.measure.cache.RetrieveCacheContext) CqlToElmTranslator(com.ibm.cohort.cql.translation.CqlToElmTranslator) MapCqlLibraryProvider(com.ibm.cohort.cql.library.MapCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) PriorityCqlLibraryProvider(com.ibm.cohort.cql.library.PriorityCqlLibraryProvider) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) ZonedDateTime(java.time.ZonedDateTime) JCommander(com.beust.jcommander.JCommander) Console(com.beust.jcommander.internal.Console) DefaultConsole(com.beust.jcommander.internal.DefaultConsole) R4LibraryDependencyGatherer(com.ibm.cohort.cql.hapi.R4LibraryDependencyGatherer) List(java.util.List) MapCqlLibraryProviderFactory(com.ibm.cohort.cql.library.MapCqlLibraryProviderFactory) CqlTerminologyProvider(com.ibm.cohort.cql.terminology.CqlTerminologyProvider) CqlDataProvider(com.ibm.cohort.cql.data.CqlDataProvider) Pair(org.apache.commons.lang3.tuple.Pair) ImmutablePair(org.apache.commons.lang3.tuple.ImmutablePair) Path(java.nio.file.Path) FhirClientBuilder(com.ibm.cohort.fhir.client.config.FhirClientBuilder) ParameterHelper.parseParameterArguments(com.ibm.cohort.cli.ParameterHelper.parseParameterArguments) MapCqlLibraryProvider(com.ibm.cohort.cql.library.MapCqlLibraryProvider) CqlEvaluationResult(com.ibm.cohort.cql.evaluation.CqlEvaluationResult) DefaultRetrieveCacheContext(com.ibm.cohort.engine.measure.cache.DefaultRetrieveCacheContext) PriorityCqlLibraryProvider(com.ibm.cohort.cql.library.PriorityCqlLibraryProvider) FhirClientBuilderFactory(com.ibm.cohort.fhir.client.config.FhirClientBuilderFactory) Parameter(com.beust.jcommander.Parameter) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) Map(java.util.Map) HashMap(java.util.HashMap) CqlEvaluator(com.ibm.cohort.cql.evaluation.CqlEvaluator) CqlVersionedIdentifier(com.ibm.cohort.cql.library.CqlVersionedIdentifier)

Example 9 with TranslatingCqlLibraryProvider

use of com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.

the class SparkCqlEvaluator method createLibraryProvider.

/**
 * Initialize a library provider that will load resources from the configured path
 * in local storage or from the well-known classpath locations. The library provider
 * comes configured with CQL translation enabled and will use custom modelinfo
 * definitions if provided in the configuration.
 *
 * @return configured library provider
 * @throws IOException when model info cannot be read
 * @throws FileNotFoundException when a specified model info file cannot be found
 */
protected CqlLibraryProvider createLibraryProvider() throws IOException, FileNotFoundException {
    CqlLibraryProvider hadoopBasedLp = new HadoopBasedCqlLibraryProvider(new Path(args.cqlPath), this.hadoopConfiguration.value());
    // we are excluding the pre-compiled FHIRHelpers libraries because they were not compiled
    // with the EnableResultTypes option that is required for some of the features of this program.
    ClasspathCqlLibraryProvider cpBasedLp = new ClasspathCqlLibraryProvider();
    cpBasedLp.setSupportedFormats(Format.CQL);
    CqlLibraryProvider priorityLp = new PriorityCqlLibraryProvider(hadoopBasedLp, cpBasedLp);
    return new TranslatingCqlLibraryProvider(priorityLp, getCqlTranslator());
}
Also used : Path(org.apache.hadoop.fs.Path) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) HadoopBasedCqlLibraryProvider(com.ibm.cohort.cql.library.HadoopBasedCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) PriorityCqlLibraryProvider(com.ibm.cohort.cql.library.PriorityCqlLibraryProvider) HadoopBasedCqlLibraryProvider(com.ibm.cohort.cql.library.HadoopBasedCqlLibraryProvider) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) PriorityCqlLibraryProvider(com.ibm.cohort.cql.library.PriorityCqlLibraryProvider)

Example 10 with TranslatingCqlLibraryProvider

use of com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.

the class ColumnRuleCreatorTest method testGetFiltersForContext.

@Test
public void testGetFiltersForContext() throws Exception {
    CqlToElmTranslator cqlTranslator = new CqlToElmTranslator();
    cqlTranslator.registerModelInfo(new File("src/test/resources/alltypes/modelinfo/alltypes-modelinfo-1.0.0.xml"));
    ObjectMapper mapper = new ObjectMapper();
    CqlEvaluationRequests requests = mapper.readValue(new File("src/test/resources/alltypes/metadata/parent-child-jobs.json"), CqlEvaluationRequests.class);
    CqlLibraryProvider backingProvider = new ClasspathCqlLibraryProvider("alltypes.cql");
    TranslatingCqlLibraryProvider cqlLibraryProvider = new TranslatingCqlLibraryProvider(backingProvider, cqlTranslator);
    ColumnRuleCreator columnRuleCreator = new ColumnRuleCreator(requests.getEvaluations(), cqlTranslator, cqlLibraryProvider);
    ContextDefinitions definitions = mapper.readValue(new File("src/test/resources/alltypes/metadata/context-definitions.json"), ContextDefinitions.class);
    ContextDefinition context = definitions.getContextDefinitionByName("Patient");
    Map<String, Set<StringMatcher>> actual = columnRuleCreator.getDataRequirementsForContext(context);
    Map<String, Set<StringMatcher>> expected = new HashMap<>();
    expected.put("A", new HashSet<>(Arrays.asList(new EqualsStringMatcher(ContextRetriever.SOURCE_FACT_IDX), new EqualsStringMatcher("pat_id"), new EqualsStringMatcher("code_col"), new EqualsStringMatcher("boolean_col"))));
    assertEquals(expected, actual);
}
Also used : Set(java.util.Set) HashSet(java.util.HashSet) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) HashMap(java.util.HashMap) CqlToElmTranslator(com.ibm.cohort.cql.translation.CqlToElmTranslator) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) EqualsStringMatcher(com.ibm.cohort.cql.util.EqualsStringMatcher) CqlEvaluationRequests(com.ibm.cohort.cql.evaluation.CqlEvaluationRequests) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) File(java.io.File) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) Test(org.junit.Test)

Aggregations

TranslatingCqlLibraryProvider (com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider)17 CqlToElmTranslator (com.ibm.cohort.cql.translation.CqlToElmTranslator)15 CqlLibraryProvider (com.ibm.cohort.cql.library.CqlLibraryProvider)12 ClasspathCqlLibraryProvider (com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider)11 Test (org.junit.Test)11 CqlTerminologyProvider (com.ibm.cohort.cql.terminology.CqlTerminologyProvider)8 HashMap (java.util.HashMap)8 CqlDataProvider (com.ibm.cohort.cql.data.CqlDataProvider)7 PriorityCqlLibraryProvider (com.ibm.cohort.cql.library.PriorityCqlLibraryProvider)5 File (java.io.File)5 ObjectMapper (com.fasterxml.jackson.databind.ObjectMapper)4 IGenericClient (ca.uhn.fhir.rest.client.api.IGenericClient)3 CqlEvaluationRequests (com.ibm.cohort.cql.evaluation.CqlEvaluationRequests)3 CqlEvaluator (com.ibm.cohort.cql.evaluation.CqlEvaluator)3 IntegerParameter (com.ibm.cohort.cql.evaluation.parameters.IntegerParameter)3 Parameter (com.ibm.cohort.cql.evaluation.parameters.Parameter)3 CqlLibrary (com.ibm.cohort.cql.library.CqlLibrary)3 CqlLibraryDescriptor (com.ibm.cohort.cql.library.CqlLibraryDescriptor)3 CqlVersionedIdentifier (com.ibm.cohort.cql.library.CqlVersionedIdentifier)3 MapCqlLibraryProviderFactory (com.ibm.cohort.cql.library.MapCqlLibraryProviderFactory)3