Add DataRequrementsProcessor from cqframework elm

common/src/main/java/org/opencds/cqf/common/helpers/TranslatorHelper.java

@@ -5,11 +5,13 @@
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
+import java.util.List;
 
 import javax.xml.bind.JAXBException;
 
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.CqlTranslatorException;
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.LibraryManager;
 import org.cqframework.cql.cql2elm.ModelManager;
 import org.cqframework.cql.elm.execution.Library;
@@ -47,16 +49,22 @@ public static CqlTranslator getTranslator(String cql, LibraryManager libraryMana
                 modelManager);
     }
 
-    public static CqlTranslator getTranslator(InputStream cqlStream, LibraryManager libraryManager,
-            ModelManager modelManager) {
+    public static List<CqlTranslator.Options> generateDefaultTranslatorOptions() {
         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);
+        return options;
+    }
+
+    public static CqlTranslator getTranslator(InputStream cqlStream, LibraryManager libraryManager,
+            ModelManager modelManager) {
+
         CqlTranslator translator;
         try {
+            List<CqlTranslator.Options> options = generateDefaultTranslatorOptions();
             translator = CqlTranslator.fromStream(cqlStream, modelManager, libraryManager,
                     options.toArray(new CqlTranslator.Options[options.size()]));
         } catch (IOException e) {
@@ -81,4 +89,12 @@ public static Library translateLibrary(InputStream cqlStream, LibraryManager lib
     public static Library translateLibrary(CqlTranslator translator) {
         return readLibrary(new ByteArrayInputStream(translator.toXml().getBytes(StandardCharsets.UTF_8)));
     }
+
+    public static CqlTranslatorOptions getTranslatorOptions() {
+        CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
+        cqlTranslatorOptions.getOptions().addAll(generateDefaultTranslatorOptions());
+        cqlTranslatorOptions.setAnalyzeDataRequirements(true);
+        cqlTranslatorOptions.setCollapseDataRequirements(true);
+        return cqlTranslatorOptions;
+    }
 }

common/src/main/java/org/opencds/cqf/common/providers/CommonDataRequirementsProvider.java

@@ -0,0 +1,140 @@
+package org.opencds.cqf.common.providers;
+
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
+import org.cqframework.cql.cql2elm.LibraryManager;
+import org.cqframework.cql.cql2elm.model.TranslatedLibrary;
+import org.cqframework.cql.elm.requirements.fhir.DataRequirementsProcessor;
+import org.hl7.fhir.r5.model.CanonicalType;
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.Library;
+import org.hl7.fhir.r5.model.Measure;
+import org.hl7.fhir.r5.model.Meta;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+@Component
+public class CommonDataRequirementsProvider {
+
+    private static final Logger logger = LoggerFactory.getLogger(CommonDataRequirementsProvider.class);
+
+    private static String EXTENSION_URL_PARAMETER = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter";
+    private static String EXTENSION_URL_DATA_REQUIREMENT = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement";
+    private static String EXTENSION_URL_REFERENCE_CODE = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode";
+    private static String EXTENSION_URL_LOGIC_DEFINITION = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition";
+    private static String EXTENSION_URL_COMPUTABLE_MEASURE = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/computable-measure-cqfm";
+
+
+    public Measure createMeasure(Measure measureToUse, LibraryManager libraryManager, TranslatedLibrary translatedLibrary, CqlTranslatorOptions options) {
+
+        Library moduleDefinitionLibrary = getModuleDefinitionLibrary(measureToUse, libraryManager, translatedLibrary, options);
+
+        measureToUse.setDate(new Date());
+        setMeta(measureToUse, moduleDefinitionLibrary);
+        clearMeasureExtensions(measureToUse, EXTENSION_URL_PARAMETER);
+        clearMeasureExtensions(measureToUse, EXTENSION_URL_DATA_REQUIREMENT);
+        clearMeasureExtensions(measureToUse, EXTENSION_URL_REFERENCE_CODE);
+        clearMeasureExtensions(measureToUse, EXTENSION_URL_LOGIC_DEFINITION);
+        clearRelatedArtifacts(measureToUse);
+        setParameters(measureToUse, moduleDefinitionLibrary);
+        setDataRequirements(measureToUse, moduleDefinitionLibrary);
+        setDirectReferenceCode(measureToUse, moduleDefinitionLibrary);
+        setLogicDefinition(measureToUse, moduleDefinitionLibrary);
+        measureToUse.setRelatedArtifact(moduleDefinitionLibrary.getRelatedArtifact());
+
+        return measureToUse;
+    }
+
+    public Library getModuleDefinitionLibrary(org.hl7.fhir.r5.model.Measure measureToUse, LibraryManager libraryManager, TranslatedLibrary translatedLibrary, CqlTranslatorOptions options) {
+
+        Set<String> expressionList = getExpressions(measureToUse);
+        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
+
+        Library library = dqReqTrans.gatherDataRequirements(libraryManager, translatedLibrary, options, expressionList, true);
+        return library;
+    }
+
+    private Set<String> getExpressions(Measure measureToUse) {
+        Set<String> expressionSet = new HashSet<>();
+        measureToUse.getSupplementalData().forEach(supData -> {
+            expressionSet.add(supData.getCriteria().getExpression());
+        });
+        measureToUse.getGroup().forEach(groupMember -> {
+            groupMember.getPopulation().forEach(population -> {
+                expressionSet.add(population.getCriteria().getExpression());
+            });
+            groupMember.getStratifier().forEach(stratifier -> {
+                expressionSet.add(stratifier.getCriteria().getExpression());
+            });
+        });
+        return expressionSet;
+    }
+
+    private void clearMeasureExtensions(Measure measure, String extensionUrl) {
+        List<Extension> extensionsToRemove = measure.getExtensionsByUrl(extensionUrl);
+        measure.getExtension().removeAll(extensionsToRemove);
+    }
+
+    private void clearRelatedArtifacts(Measure measure) {
+        measure.getRelatedArtifact().removeIf(r -> r.getType() == org.hl7.fhir.r5.model.RelatedArtifact.RelatedArtifactType.DEPENDSON);
+    }
+
+    private void setLogicDefinition(Measure measureToUse, org.hl7.fhir.r5.model.Library moduleDefinitionLibrary) {
+        moduleDefinitionLibrary.getExtension().forEach(extension -> {
+            if (extension.getUrl().equalsIgnoreCase(EXTENSION_URL_LOGIC_DEFINITION)) {
+                measureToUse.addExtension(extension);
+            }
+        });
+    }
+
+    private void setDirectReferenceCode(Measure measureToUse, org.hl7.fhir.r5.model.Library moduleDefinitionLibrary) {
+        moduleDefinitionLibrary.getExtension().forEach(extension -> {
+            if (extension.getUrl().equalsIgnoreCase(EXTENSION_URL_REFERENCE_CODE)) {
+                measureToUse.addExtension(extension);
+            }
+        });
+    }
+
+    private void setDataRequirements(Measure measureToUse, org.hl7.fhir.r5.model.Library moduleDefinitionLibrary) {
+        moduleDefinitionLibrary.getDataRequirement().forEach(dataRequirement -> {
+            Extension dataReqExtension = new Extension();
+            dataReqExtension.setUrl(EXTENSION_URL_DATA_REQUIREMENT);
+            dataReqExtension.setValue(dataRequirement);
+            measureToUse.addExtension(dataReqExtension);
+        });
+    }
+
+    private void setParameters(Measure measureToUse, org.hl7.fhir.r5.model.Library moduleDefinitionLibrary) {
+        Set<String> parameterName = new HashSet<>();
+        moduleDefinitionLibrary.getParameter().forEach(parameter -> {
+            if (!parameterName.contains(parameter.getName())) {
+                Extension parameterExtension = new Extension();
+                parameterExtension.setUrl(EXTENSION_URL_PARAMETER);
+                parameterExtension.setValue(parameter);
+                measureToUse.addExtension(parameterExtension);
+                parameterName.add(parameter.getName());
+            }
+        });
+    }
+
+    private void setMeta(Measure measureToUse, org.hl7.fhir.r5.model.Library moduleDefinitionLibrary) {
+        if (measureToUse.getMeta() == null) {
+            measureToUse.setMeta(new Meta());
+        }
+        boolean hasProfileMarker = false;
+        for (CanonicalType canonical : measureToUse.getMeta().getProfile()) {
+            if (EXTENSION_URL_COMPUTABLE_MEASURE.equals(canonical.getValue())) {
+                hasProfileMarker = true;
+            }
+        }
+        if (!hasProfileMarker) {
+            measureToUse.getMeta().addProfile(EXTENSION_URL_COMPUTABLE_MEASURE);
+        }
+    }
+
+}

dstu3/src/main/java/org/opencds/cqf/dstu3/helpers/LibraryHelper.java

@@ -1,5 +1,8 @@
 package org.opencds.cqf.dstu3.helpers;
 
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.util.Base64;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
@@ -89,6 +92,21 @@ protected Boolean translatorOptionsMatch(Library library) {
         };
     }
 
+    public static InputStream extractContentStream(org.hl7.fhir.dstu3.model.Library library) {
+        org.hl7.fhir.dstu3.model.Attachment cql = null;
+        for (org.hl7.fhir.dstu3.model.Attachment a : library.getContent()) {
+            if (a.getContentType().equals("text/cql")) {
+                cql = a;
+                break;
+            }
+        }
+
+        if (cql == null) {
+            return null;
+        }
+        return new ByteArrayInputStream(Base64.getDecoder().decode(cql.getDataElement().getValueAsString()));
+    }
+
     // @Override
     // public org.opencds.cqf.cql.engine.execution.LibraryLoader createLibraryLoader(
     //         org.cqframework.cql.cql2elm.LibrarySourceProvider provider) {

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/DataRequirementsProvider.java

@@ -9,6 +9,7 @@
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -31,8 +32,10 @@
 import org.apache.commons.lang3.tuple.Pair;
 import org.apache.commons.lang3.tuple.Triple;
 import org.cqframework.cql.cql2elm.CqlTranslator;
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.cqframework.cql.cql2elm.LibraryManager;
 import org.cqframework.cql.cql2elm.ModelManager;
+import org.cqframework.cql.cql2elm.model.TranslatedLibrary;
 import org.cqframework.cql.elm.execution.CodeDef;
 import org.cqframework.cql.elm.execution.CodeSystemDef;
 import org.cqframework.cql.elm.execution.ExpressionDef;
@@ -44,6 +47,7 @@
 import org.cqframework.cql.tools.formatter.CqlFormatterVisitor;
 import org.cqframework.cql.tools.formatter.CqlFormatterVisitor.FormatResult;
 import org.hl7.elm.r1.ValueSetRef;
+import org.hl7.fhir.convertors.VersionConvertor_30_50;
 import org.hl7.fhir.dstu3.model.Attachment;
 import org.hl7.fhir.dstu3.model.Base64BinaryType;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -62,6 +66,7 @@
 import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.dstu3.model.Type;
 import org.opencds.cqf.common.helpers.TranslatorHelper;
+import org.opencds.cqf.common.providers.CommonDataRequirementsProvider;
 import org.opencds.cqf.cql.engine.execution.LibraryLoader;
 import org.opencds.cqf.tooling.measure.stu3.CodeTerminologyRef;
 import org.opencds.cqf.tooling.measure.stu3.CqfMeasure;
@@ -78,12 +83,43 @@
 public class DataRequirementsProvider {
 
     private LibraryHelper libraryHelper;
+    private CommonDataRequirementsProvider dataRequirementsProvider;
 
     @Inject
-    public DataRequirementsProvider(LibraryHelper libraryHelper) {
+    public DataRequirementsProvider(CommonDataRequirementsProvider dataRequirementsProvider,
+                                    LibraryHelper libraryHelper) {
+        this.dataRequirementsProvider = dataRequirementsProvider;
         this.libraryHelper = libraryHelper;
     }
 
+
+    public org.hl7.fhir.dstu3.model.Library getModuleDefinitionLibrary(org.hl7.fhir.dstu3.model.Measure measure, LibraryManager libraryManager, TranslatedLibrary translatedLibrary, CqlTranslatorOptions options) {
+        org.hl7.fhir.r5.model.Measure measureR5 = (org.hl7.fhir.r5.model.Measure) VersionConvertor_30_50.convertResource(measure);
+
+        org.hl7.fhir.r5.model.Library libraryR5 = dataRequirementsProvider.getModuleDefinitionLibrary(measureR5, libraryManager, translatedLibrary, options);
+        org.hl7.fhir.dstu3.model.Library libraryDstu3 = (org.hl7.fhir.dstu3.model.Library) VersionConvertor_30_50.convertResource(libraryR5);
+        return libraryDstu3;
+    }
+
+    public org.hl7.fhir.dstu3.model.Library getLibraryFromMeasure(org.hl7.fhir.dstu3.model.Measure measure,
+                                                               LibraryResolutionProvider<org.hl7.fhir.dstu3.model.Library> libraryResourceProvider) {
+        org.hl7.fhir.dstu3.model.Library primaryLibrary = null;
+        Iterator var6 = measure.getLibrary().iterator();
+
+        String id = null;
+        //use the first library
+        while (var6.hasNext() && id == null) {
+            Reference ref = (Reference)var6.next();
+            id = ref.getReferenceElement().getIdPart();
+            if (id.startsWith("#")) {
+                id = id.substring(1);
+            }
+        }
+        primaryLibrary = (org.hl7.fhir.dstu3.model.Library)libraryResourceProvider.resolveLibraryById(id);
+
+        return primaryLibrary;
+    }
+
     // For creating the CQF measure we need to:
     // 1. Find the Primary Library Resource
     // 2. Load the Primary Library as ELM. This will recursively load the dependent
@@ -498,13 +534,6 @@ private String markdownToHtml(Parser parser, HtmlRenderer renderer, String markd
         return renderer.render(document);
     }
 
-    public org.hl7.fhir.dstu3.model.Library getDataRequirements(Measure measure,
-            LibraryResolutionProvider<org.hl7.fhir.dstu3.model.Library> libraryResourceProvider) {
-        Map<VersionedIdentifier, Pair<Library, org.hl7.fhir.dstu3.model.Library>> libraryMap = this
-                .createLibraryMap(measure, libraryResourceProvider);
-        return this.getDataRequirements(measure, libraryMap.values().stream().map(x -> x.getRight())
-                .filter(x -> x != null).collect(Collectors.toList()));
-    }
 
     private org.hl7.fhir.dstu3.model.Library getDataRequirements(Measure measure,
             Collection<org.hl7.fhir.dstu3.model.Library> libraries) {

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/MeasureOperationsProvider.java

@@ -12,6 +12,9 @@
 import javax.inject.Inject;
 import javax.servlet.http.HttpServletRequest;
 
+import org.cqframework.cql.cql2elm.CqlTranslator;
+import org.cqframework.cql.cql2elm.LibraryManager;
+import org.cqframework.cql.cql2elm.ModelManager;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
@@ -40,6 +43,7 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.opencds.cqf.common.config.HapiProperties;
 import org.opencds.cqf.common.evaluation.EvaluationProviderFactory;
+import org.opencds.cqf.common.helpers.TranslatorHelper;
 import org.opencds.cqf.cql.engine.data.DataProvider;
 import org.opencds.cqf.cql.engine.execution.LibraryLoader;
 import org.opencds.cqf.dstu3.evaluation.MeasureEvaluation;
@@ -634,7 +638,23 @@ public org.hl7.fhir.dstu3.model.Library dataRequirements(@IdParam IdType theId,
             @OperationParam(name = "endPeriod") String endPeriod) throws InternalErrorException, FHIRException {
 
         Measure measure = this.measureResourceProvider.getDao().read(theId);
-        return this.dataRequirementsProvider.getDataRequirements(measure, this.libraryResolutionProvider);
+
+        ModelManager modelManager = libraryHelper.getModelManager();
+        LibraryManager libraryManager = libraryHelper.getLibraryManager(libraryResolutionProvider);
+
+        Library library = this.dataRequirementsProvider.getLibraryFromMeasure(measure, libraryResolutionProvider);
+        if (library == null) {
+            throw new RuntimeException("Could not load measure library.");
+        }
+
+        CqlTranslator translator = TranslatorHelper.getTranslator(
+                LibraryHelper.extractContentStream(library), libraryManager, modelManager);
+        if (translator.getErrors().size() > 0) {
+            throw new RuntimeException("Errors during library compilation.");
+        }
+
+        return this.dataRequirementsProvider.getModuleDefinitionLibrary(measure, libraryManager,
+                translator.getTranslatedLibrary(), TranslatorHelper.getTranslatorOptions());
     }
 
     @SuppressWarnings("unchecked")

r4/src/main/java/org/opencds/cqf/r4/helpers/LibraryHelper.java

@@ -1,5 +1,8 @@
 package org.opencds.cqf.r4.helpers;
 
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.util.Base64;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
@@ -74,4 +77,19 @@ public org.opencds.cqf.cql.engine.execution.LibraryLoader createLibraryLoader(
 
         return new CacheAwareLibraryLoaderDecorator(translatingLibraryLoader, libraryCache);
     }
+
+    public static InputStream extractContentStream(org.hl7.fhir.r4.model.Library library) {
+        Attachment cql = null;
+        for (Attachment a : library.getContent()) {
+            if (a.getContentType().equals("text/cql")) {
+                cql = a;
+                break;
+            }
+        }
+
+        if (cql == null) {
+            return null;
+        }
+        return new ByteArrayInputStream(Base64.getDecoder().decode(cql.getDataElement().getValueAsString()));
+    }
 }