Add DataRequrementsProcessor from cqframework elm

pom.xml

@@ -53,7 +53,7 @@
         <cqf-tooling.version>1.3.1-SNAPSHOT</cqf-tooling.version>
         <cql-engine.version>1.5.2-SNAPSHOT</cql-engine.version>
         <cql-evaluator.version>1.2.1-SNAPSHOT</cql-evaluator.version>
-        <cqframework.version>1.5.3</cqframework.version>
+        <cqframework.version>1.5.4-SNAPSHOT</cqframework.version>
         <cds-hooks.version>1.3.1-SNAPSHOT</cds-hooks.version>
         <slf4j.version>1.7.30</slf4j.version>
 

r4/src/main/java/org/opencds/cqf/r4/providers/DataRequirementsProvider.java

@@ -8,11 +8,15 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
+import java.util.Date;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Objects;
+import  java.util.Set;
+import java.util.HashSet;
 import java.util.stream.Collectors;
 
 import javax.inject.Inject;
@@ -32,8 +36,10 @@
 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;
@@ -42,9 +48,11 @@
 import org.cqframework.cql.elm.execution.Library;
 import org.cqframework.cql.elm.execution.ValueSetDef;
 import org.cqframework.cql.elm.execution.VersionedIdentifier;
+import org.cqframework.cql.elm.requirements.fhir.DataRequirementsProcessor;
 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_40_50;
 import org.hl7.fhir.r4.model.Attachment;
 import org.hl7.fhir.r4.model.Base64BinaryType;
 import org.hl7.fhir.r4.model.CodeableConcept;
@@ -56,12 +64,17 @@
 import org.hl7.fhir.r4.model.ParameterDefinition;
 import org.hl7.fhir.r4.model.RelatedArtifact;
 import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r5.model.CanonicalType;
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.Meta;
 import org.opencds.cqf.common.helpers.TranslatorHelper;
 import org.opencds.cqf.cql.engine.execution.LibraryLoader;
 import org.opencds.cqf.tooling.measure.r4.CodeTerminologyRef;
 import org.opencds.cqf.tooling.measure.r4.CqfMeasure;
 import org.opencds.cqf.tooling.measure.r4.TerminologyRef;
 import org.opencds.cqf.tooling.measure.r4.TerminologyRef.TerminologyRefType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Component;
 
 import ca.uhn.fhir.cql.common.provider.LibraryResolutionProvider;
@@ -72,14 +85,128 @@
 
 @Component
 public class DataRequirementsProvider {
+    private static final Logger logger = LoggerFactory.getLogger(DataRequirementsProvider.class);
 
     private LibraryHelper libraryHelper;
 
     @Inject
     public DataRequirementsProvider(LibraryHelper libraryHelper) {
         this.libraryHelper = libraryHelper;
+    }
+
+    /*
+    public org.hl7.fhir.r5.model.Measure createMeasure(Measure r4Measure, LibraryManager libraryManager, TranslatedLibrary translatedLibrary, CqlTranslatorOptions options) {
+
+        org.hl7.fhir.r5.model.Measure measureToUse = (org.hl7.fhir.r5.model.Measure) VersionConvertor_40_50.convertResource(r4Measure);
+
+        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = getModuleDefinitionLibrary(measureToUse, libraryManager, translatedLibrary, options);
+        measureToUse.setDate(new Date());
+        setMeta(measureToUse, moduleDefinitionLibrary);
+        clearMeasureExtensions(measureToUse, "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter");
+        clearMeasureExtensions(measureToUse, "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement");
+        clearMeasureExtensions(measureToUse, "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode");
+        clearMeasureExtensions(measureToUse, "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition");
+        clearRelatedArtifacts(measureToUse);
+        setParameters(measureToUse, moduleDefinitionLibrary);
+        setDataRequirements(measureToUse, moduleDefinitionLibrary);
+        setDirectReferenceCode(measureToUse, moduleDefinitionLibrary);
+        setLogicDefinition(measureToUse, moduleDefinitionLibrary);
+        measureToUse.setRelatedArtifact(moduleDefinitionLibrary.getRelatedArtifact());
+
+        return measureToUse;
+    }
+*/
+    public org.hl7.fhir.r4.model.Library getModuleDefinitionLibrary(Measure r4Measure, LibraryManager libraryManager, TranslatedLibrary translatedLibrary, CqlTranslatorOptions options){
+
+        org.hl7.fhir.r5.model.Measure measureToUse = (org.hl7.fhir.r5.model.Measure) VersionConvertor_40_50.convertResource(r4Measure);
+
+        Set<String> expressionList = getExpressions(measureToUse);
+        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
+
+        org.hl7.fhir.r5.model.Library libraryR5 = dqReqTrans.gatherDataRequirements(libraryManager, translatedLibrary, options, expressionList, true);
+        org.hl7.fhir.r4.model.Library library = (org.hl7.fhir.r4.model.Library) VersionConvertor_40_50.convertResource(libraryR5);
+
+        return library;
+    }
+
+    private Set<String> getExpressions(org.hl7.fhir.r5.model.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(org.hl7.fhir.r5.model.Measure measure, String extensionUrl) {
+        List<Extension> extensionsToRemove = measure.getExtensionsByUrl(extensionUrl);
+        measure.getExtension().removeAll(extensionsToRemove);
+    }
+
+    private void clearRelatedArtifacts(org.hl7.fhir.r5.model.Measure measure) {
+        measure.getRelatedArtifact().removeIf(r -> r.getType() == org.hl7.fhir.r5.model.RelatedArtifact.RelatedArtifactType.DEPENDSON);
+    }
+
+    private void setLogicDefinition(org.hl7.fhir.r5.model.Measure measureToUse, org.hl7.fhir.r5.model.Library moduleDefinitionLibrary) {
+        moduleDefinitionLibrary.getExtension().forEach(extension -> {
+            if (extension.getUrl().equalsIgnoreCase("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition")) {
+                measureToUse.addExtension(extension);
+            }
+        });
+    }
+
+    private void setDirectReferenceCode(org.hl7.fhir.r5.model.Measure measureToUse, org.hl7.fhir.r5.model.Library moduleDefinitionLibrary) {
+        moduleDefinitionLibrary.getExtension().forEach(extension -> {
+            if(extension.getUrl().equalsIgnoreCase("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode")) {
+                measureToUse.addExtension(extension);
+            }
+        });
+    }
 
+    private void setDataRequirements(org.hl7.fhir.r5.model.Measure measureToUse, org.hl7.fhir.r5.model.Library moduleDefinitionLibrary) {
+        moduleDefinitionLibrary.getDataRequirement().forEach(dataRequirement -> {
+            Extension dataReqExtension = new Extension();
+            dataReqExtension.setUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement");
+            dataReqExtension.setValue(dataRequirement);
+            measureToUse.addExtension(dataReqExtension);
+        });
+    }
+
+    private void setParameters(org.hl7.fhir.r5.model.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("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter");
+                parameterExtension.setValue(parameter);
+                measureToUse.addExtension(parameterExtension);
+                parameterName.add(parameter.getName());
+            }
+        });
     }
+
+    private void setMeta(org.hl7.fhir.r5.model.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 ("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/computable-measure-cqfm".equals(canonical.getValue())) {
+                hasProfileMarker = true;
+            }
+        }
+        if (!hasProfileMarker) {
+            measureToUse.getMeta().addProfile("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/computable-measure-cqfm");
+        }
+    }
+
     // 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
@@ -96,6 +223,23 @@ public CqfMeasure createCqfMeasure(Measure measure,
         return this.createCqfMeasure(measure, libraryMap);
     }
 
+    public org.hl7.fhir.r4.model.Library getLibraryFromMeasure(Measure measure,
+               LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
+
+        org.hl7.fhir.r4.model.Library primaryLibrary = null;
+        Iterator var6 = measure.getLibrary().iterator();
+
+        String library= null;
+        while(var6.hasNext()) {
+            org.hl7.fhir.r4.model.CanonicalType ref = (org.hl7.fhir.r4.model.CanonicalType) var6.next();
+            library = (String) ref.getValue();
+
+        }
+        primaryLibrary = libraryHelper.resolveLibraryReference(libraryResourceProvider, library);
+
+        return primaryLibrary;
+    }
+
     private Map<VersionedIdentifier, Pair<Library, org.hl7.fhir.r4.model.Library>> createLibraryMap(Measure measure,
             LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResourceProvider) {
         LibraryLoader libraryLoader = this.libraryHelper.createLibraryLoader(libraryResourceProvider);

r4/src/main/java/org/opencds/cqf/r4/providers/MeasureOperationsProvider.java

@@ -1,7 +1,10 @@
 package org.opencds.cqf.r4.providers;
 
+import java.io.InputStream;
+import java.io.ByteArrayInputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Base64;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
@@ -13,14 +16,20 @@
 import javax.inject.Inject;
 import javax.servlet.http.HttpServletRequest;
 
+import ca.uhn.fhir.jpa.rp.r4.LibraryResourceProvider;
 import com.google.common.base.Strings;
 
+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.hibernate.cfg.NotYetImplementedException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Attachment;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.CanonicalType;
@@ -32,6 +41,7 @@
 import org.hl7.fhir.r4.model.Group;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Identifier;
+import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.ListResource;
 import org.hl7.fhir.r4.model.Measure;
 import org.hl7.fhir.r4.model.MeasureReport;
@@ -49,6 +59,8 @@
 import org.opencds.cqf.common.config.HapiProperties;
 import org.opencds.cqf.common.evaluation.EvaluationProviderFactory;
 import org.opencds.cqf.common.helpers.DateHelper;
+import org.opencds.cqf.common.helpers.TranslatorHelper;
+import org.opencds.cqf.common.providers.LibraryContentProvider;
 import org.opencds.cqf.cql.engine.execution.LibraryLoader;
 import org.opencds.cqf.r4.evaluation.MeasureEvaluation;
 import org.opencds.cqf.r4.evaluation.MeasureEvaluationSeed;
@@ -95,7 +107,7 @@ public class MeasureOperationsProvider {
     private static final Logger logger = LoggerFactory.getLogger(MeasureOperationsProvider.class);
 
     @Inject
-    public MeasureOperationsProvider(DaoRegistry registry, EvaluationProviderFactory factory,
+    public MeasureOperationsProvider(DaoRegistry registry, EvaluationProviderFactory factory, LibraryResourceProvider libraryResourceProvider,
             NarrativeProvider narrativeProvider, HQMFProvider hqmfProvider,
             LibraryResolutionProvider<org.hl7.fhir.r4.model.Library> libraryResolutionProvider,
             MeasureResourceProvider measureResourceProvider, DataRequirementsProvider dataRequirementsProvider, LibraryHelper libraryHelper) {
@@ -110,6 +122,28 @@ public MeasureOperationsProvider(DaoRegistry registry, EvaluationProviderFactory
         this.libraryHelper = libraryHelper;
     }
 
+    private ModelManager getModelManager() {
+        return new ModelManager();
+    }
+
+    private LibraryManager getLibraryManager(ModelManager modelManager) {
+        LibraryManager libraryManager = new LibraryManager(modelManager);
+        libraryManager.getLibrarySourceLoader().clearProviders();
+        libraryManager.getLibrarySourceLoader().registerProvider(getLibrarySourceProvider());
+
+        return libraryManager;
+    }
+
+    private LibraryContentProvider<org.hl7.fhir.r4.model.Library, org.hl7.fhir.r4.model.Attachment> librarySourceProvider;
+
+    private LibraryContentProvider<Library, Attachment> getLibrarySourceProvider() {
+        if (librarySourceProvider == null) {
+            librarySourceProvider = new LibraryContentProvider<org.hl7.fhir.r4.model.Library, org.hl7.fhir.r4.model.Attachment>(
+                    this.libraryResolutionProvider, x -> x.getContent(), x -> x.getContentType(), x -> x.getData());
+        }
+        return librarySourceProvider;
+    }
+
     @Operation(name = "$hqmf", idempotent = true, type = Measure.class)
     public Parameters hqmf(@IdParam IdType theId) {
         Measure theResource = this.measureResourceProvider.getDao().read(theId);
@@ -880,7 +914,49 @@ public org.hl7.fhir.r4.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 = this.getModelManager();
+        LibraryManager libraryManager = this.getLibraryManager(modelManager);
+
+        Library library = dataRequirementsProvider.getLibraryFromMeasure(measure, libraryResolutionProvider);
+
+        if (library == null) {
+            throw new RuntimeException("Could not load measure library.");
+        }
+
+        CqlTranslator translator = TranslatorHelper.getTranslator(getContentStream(library), libraryManager, modelManager);
+
+        if (translator.getErrors().size() > 0) {
+            throw new RuntimeException("Errors during library compilation.");
+        }
+
+        return this.dataRequirementsProvider.getModuleDefinitionLibrary(measure, libraryManager, translator.getTranslatedLibrary(), getTranslatorOptions());
+    }
+
+
+    private CqlTranslatorOptions getTranslatorOptions() {
+        CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
+        cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
+        cqlTranslatorOptions.getOptions().add(CqlTranslator.Options.EnableAnnotations);
+        cqlTranslatorOptions.setAnalyzeDataRequirements(true);
+        cqlTranslatorOptions.setCollapseDataRequirements(true);
+        return cqlTranslatorOptions;
+    }
+
+    private InputStream getContentStream(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()));
     }
 
     @SuppressWarnings("unchecked")