Copy constructors for settings classes (#564)

* clone() for EvaluationSettins, RetrieveSetttings, and TerminologySettings

* Clean up

* Add copy constructors

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/Measures.java

@@ -32,22 +32,16 @@ public class Measures {
     @Setup(Level.Trial)
     public void setupTrial() throws Exception {
         var evaluationOptions = MeasureEvaluationOptions.defaultOptions();
-
-        var retrieveSettings = evaluationOptions.getEvaluationSettings().getRetrieveSettings();
-        retrieveSettings
+        evaluationOptions.getEvaluationSettings().setLibraryCache(new HashMap<>());
+        evaluationOptions
+                .getEvaluationSettings()
+                .getRetrieveSettings()
                 .setSearchParameterMode(SEARCH_FILTER_MODE.FILTER_IN_MEMORY)
                 .setTerminologyParameterMode(TERMINOLOGY_FILTER_MODE.FILTER_IN_MEMORY);
-
-        var terminologySettings = evaluationOptions.getEvaluationSettings().getTerminologySettings();
-        terminologySettings.setValuesetExpansionMode(VALUESET_EXPANSION_MODE.PERFORM_NAIVE_EXPANSION);
-
-        var settingsBuilder = evaluationOptions.getEvaluationSettings().toBuilder();
-
-        settingsBuilder.libraryCache(new HashMap<>());
-        settingsBuilder.retrieveSettings(retrieveSettings);
-        settingsBuilder.terminologySettings(terminologySettings);
-
-        evaluationOptions.setEvaluationSettings(settingsBuilder.build());
+        evaluationOptions
+                .getEvaluationSettings()
+                .getTerminologySettings()
+                .setValuesetExpansionMode(VALUESET_EXPANSION_MODE.PERFORM_NAIVE_EXPANSION);
 
         this.when = Measure.given()
                 .repositoryFor("CaseRepresentation101")

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/MeasuresAdditionalData.java

@@ -34,22 +34,16 @@ public class MeasuresAdditionalData {
     @Setup(Level.Trial)
     public void setupTrial() throws Exception {
         var evaluationOptions = MeasureEvaluationOptions.defaultOptions();
-
-        var retrieveSettings = evaluationOptions.getEvaluationSettings().getRetrieveSettings();
-        retrieveSettings
+        evaluationOptions.getEvaluationSettings().setLibraryCache(new HashMap<>());
+        evaluationOptions
+                .getEvaluationSettings()
+                .getRetrieveSettings()
                 .setSearchParameterMode(SEARCH_FILTER_MODE.FILTER_IN_MEMORY)
                 .setTerminologyParameterMode(TERMINOLOGY_FILTER_MODE.FILTER_IN_MEMORY);
-
-        var terminologySettings = evaluationOptions.getEvaluationSettings().getTerminologySettings();
-        terminologySettings.setValuesetExpansionMode(VALUESET_EXPANSION_MODE.PERFORM_NAIVE_EXPANSION);
-
-        var settingsBuilder = evaluationOptions.getEvaluationSettings().toBuilder();
-
-        settingsBuilder.libraryCache(new HashMap<>());
-        settingsBuilder.retrieveSettings(retrieveSettings);
-        settingsBuilder.terminologySettings(terminologySettings);
-
-        evaluationOptions.setEvaluationSettings(settingsBuilder.build());
+        evaluationOptions
+                .getEvaluationSettings()
+                .getTerminologySettings()
+                .setValuesetExpansionMode(VALUESET_EXPANSION_MODE.PERFORM_NAIVE_EXPANSION);
 
         Bundle additionalData = (Bundle) FhirContext.forR4Cached()
                 .newJsonParser()

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/Engines.java

@@ -150,8 +150,7 @@ private static Map<String, DataProvider> buildDataProviders(
         var providers = new ArrayList<RetrieveProvider>();
         var modelResolver = FhirModelResolverCache.resolverForVersion(
                 repository.fhirContext().getVersion().getVersion());
-        // TODO: Make a federated repository here once that is ready for sure
-        // var fedRepo = new FederatedRepository(repository, bundleRepo);
+
         var retrieveProvider = new RepositoryRetrieveProvider(repository, terminologyProvider, retrieveSettings);
         providers.add(retrieveProvider);
         if (additionalData != null && modelResolver.resolvePath(additionalData, "entry") != null) {

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/EvaluationSettings.java

@@ -14,162 +14,151 @@
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
 import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
 
-/**
- * This class contains settings used to set up CQL evaluation. This class is immutable once constructed.
- * Use the Builder to create and instance of this class, and the "toBuilder()" function to create a
- * new mutable builder to clone these settings if required.
- */
 public class EvaluationSettings {
 
-    private final Map<ModelIdentifier, Model> modelCache;
-    private final Map<VersionedIdentifier, CompiledLibrary> libraryCache;
-    private final Map<String, List<Code>> valueSetCache;
-    private final List<LibrarySourceProvider> librarySourceProviders;
-    private final CqlOptions cqlOptions;
-    private final RetrieveSettings retrieveSettings;
-    private final TerminologySettings terminologySettings;
-    private final NpmProcessor npmProcessor;
-
-    private EvaluationSettings(
-            Map<ModelIdentifier, Model> modelCache,
-            Map<VersionedIdentifier, CompiledLibrary> libraryCache,
-            Map<String, List<Code>> valueSetCache,
-            List<LibrarySourceProvider> librarySourceProviders,
-            CqlOptions cqlOptions,
-            RetrieveSettings retrieveSettings,
-            TerminologySettings terminologySettings,
-            NpmProcessor npmProcessor) {
-        this.modelCache = modelCache;
-        this.libraryCache = libraryCache;
-        this.valueSetCache = valueSetCache;
-        this.librarySourceProviders = librarySourceProviders;
-        this.cqlOptions = cqlOptions;
-        this.retrieveSettings = retrieveSettings;
-        this.terminologySettings = terminologySettings;
-        this.npmProcessor = npmProcessor;
-    }
+    private Map<ModelIdentifier, Model> modelCache;
+    private Map<VersionedIdentifier, CompiledLibrary> libraryCache;
+    private Map<String, List<Code>> valueSetCache;
+    private List<LibrarySourceProvider> librarySourceProviders;
+
+    private CqlOptions cqlOptions;
+
+    private RetrieveSettings retrieveSettings;
+    private TerminologySettings terminologySettings;
+    private NpmProcessor npmProcessor;
 
-    public static EvaluationSettings.Builder builder() {
-        return new Builder();
+    public static EvaluationSettings getDefault() {
+        return new EvaluationSettings();
     }
 
-    public EvaluationSettings.Builder toBuilder() {
-        return new EvaluationSettings.Builder()
-                .cqlOptions(this.cqlOptions)
-                .modelCache(this.modelCache)
-                .libraryCache(this.libraryCache)
-                .valueSetCache(this.valueSetCache)
-                .retrieveSettings(this.retrieveSettings)
-                .terminologySettings(this.terminologySettings)
-                .librarySourceProviders(new ArrayList<>(this.librarySourceProviders))
-                .npmProcessor(this.npmProcessor);
+    EvaluationSettings() {
+        this.modelCache = new ConcurrentHashMap<>();
+        this.libraryCache = new ConcurrentHashMap<>();
+        this.valueSetCache = new ConcurrentHashMap<>();
+        this.librarySourceProviders = new ArrayList<>();
+        this.cqlOptions = CqlOptions.defaultOptions();
+        this.retrieveSettings = new RetrieveSettings();
+        this.terminologySettings = new TerminologySettings();
+        this.npmProcessor = null;
     }
 
-    public static EvaluationSettings getDefault() {
-        var options = CqlOptions.defaultOptions();
-        var builder = new EvaluationSettings.Builder()
-                .cqlOptions(options)
-                .modelCache(new ConcurrentHashMap<>())
-                .libraryCache(new ConcurrentHashMap<>())
-                .valueSetCache(new ConcurrentHashMap<>())
-                .retrieveSettings(new RetrieveSettings())
-                .terminologySettings(new TerminologySettings())
-                .librarySourceProviders(new ArrayList<>());
-        return builder.build();
+    /**
+     * Copy constructor for EvaluationSettings
+     * @param settings
+     */
+    public EvaluationSettings(EvaluationSettings settings) {
+        this.modelCache = new ConcurrentHashMap<>(settings.modelCache);
+        this.libraryCache = new ConcurrentHashMap<>(settings.libraryCache);
+        this.valueSetCache = new ConcurrentHashMap<>(settings.valueSetCache);
+        this.cqlOptions = settings.cqlOptions;
+        this.retrieveSettings = new RetrieveSettings(settings.retrieveSettings);
+        this.terminologySettings = new TerminologySettings(settings.terminologySettings);
+        this.librarySourceProviders = new ArrayList<>(settings.librarySourceProviders);
+        this.npmProcessor =
+                settings.npmProcessor != null ? new NpmProcessor(settings.npmProcessor.getIgContext()) : null;
     }
 
     public Map<ModelIdentifier, Model> getModelCache() {
         return this.modelCache;
     }
 
+    public void setModelCache(Map<ModelIdentifier, Model> modelCache) {
+        this.modelCache = modelCache;
+    }
+
+    public EvaluationSettings withModelCache(Map<ModelIdentifier, Model> modelCache) {
+        setModelCache(modelCache);
+        return this;
+    }
+
     public Map<VersionedIdentifier, CompiledLibrary> getLibraryCache() {
         return this.libraryCache;
     }
 
+    public void setLibraryCache(Map<VersionedIdentifier, CompiledLibrary> libraryCache) {
+        this.libraryCache = libraryCache;
+    }
+
+    public EvaluationSettings withLibraryCache(Map<VersionedIdentifier, CompiledLibrary> libraryCache) {
+        setLibraryCache(libraryCache);
+        return this;
+    }
+
     public Map<String, List<Code>> getValueSetCache() {
         return this.valueSetCache;
     }
 
+    public void setValueSetCache(Map<String, List<Code>> valueSetCache) {
+        this.valueSetCache = valueSetCache;
+    }
+
+    public EvaluationSettings withValueSetCache(Map<String, List<Code>> valueSetCache) {
+        setValueSetCache(valueSetCache);
+        return this;
+    }
+
     public CqlOptions getCqlOptions() {
         return this.cqlOptions;
     }
 
+    public EvaluationSettings withCqlOptions(CqlOptions cqlOptions) {
+        setCqlOptions(cqlOptions);
+        return this;
+    }
+
+    public void setCqlOptions(CqlOptions cqlOptions) {
+        this.cqlOptions = cqlOptions;
+    }
+
     public RetrieveSettings getRetrieveSettings() {
         return this.retrieveSettings;
     }
 
+    public EvaluationSettings withRetrieveSettings(RetrieveSettings retrieveSettings) {
+        setRetrieveSettings(retrieveSettings);
+        return this;
+    }
+
+    public void setRetrieveSettings(RetrieveSettings retrieveSettings) {
+        this.retrieveSettings = retrieveSettings;
+    }
+
     public TerminologySettings getTerminologySettings() {
         return this.terminologySettings;
     }
 
+    public EvaluationSettings withTerminologySettings(TerminologySettings terminologySettings) {
+        setTerminologySettings(terminologySettings);
+        return this;
+    }
+
+    public void setTerminologySettings(TerminologySettings terminologySettings) {
+        this.terminologySettings = terminologySettings;
+    }
+
     public List<LibrarySourceProvider> getLibrarySourceProviders() {
         return librarySourceProviders;
     }
 
+    public void setLibrarySourceProviders(List<LibrarySourceProvider> librarySourceProviders) {
+        this.librarySourceProviders = librarySourceProviders;
+    }
+
+    public EvaluationSettings withLibrarySourceProviders(List<LibrarySourceProvider> librarySourceProviders) {
+        setLibrarySourceProviders(librarySourceProviders);
+        return this;
+    }
+
     public NpmProcessor getNpmProcessor() {
-        return this.npmProcessor;
-    }
-
-    public static class Builder {
-        private Map<ModelIdentifier, Model> modelCache;
-        private Map<VersionedIdentifier, CompiledLibrary> libraryCache;
-        private Map<String, List<Code>> valueSetCache;
-        private List<LibrarySourceProvider> librarySourceProviders;
-        private CqlOptions cqlOptions;
-        private RetrieveSettings retrieveSettings;
-        private TerminologySettings terminologySettings;
-        private NpmProcessor npmProcessor;
-
-        public Builder modelCache(Map<ModelIdentifier, Model> modelCache) {
-            this.modelCache = modelCache;
-            return this;
-        }
-
-        public Builder libraryCache(Map<VersionedIdentifier, CompiledLibrary> libraryCache) {
-            this.libraryCache = libraryCache;
-            return this;
-        }
-
-        public Builder valueSetCache(Map<String, List<Code>> valueSetCache) {
-            this.valueSetCache = valueSetCache;
-            return this;
-        }
-
-        public Builder librarySourceProviders(List<LibrarySourceProvider> librarySourceProviders) {
-            this.librarySourceProviders = librarySourceProviders;
-            return this;
-        }
-
-        public Builder cqlOptions(CqlOptions cqlOptions) {
-            this.cqlOptions = cqlOptions;
-            return this;
-        }
-
-        public Builder retrieveSettings(RetrieveSettings retrieveSettings) {
-            this.retrieveSettings = retrieveSettings;
-            return this;
-        }
-
-        public Builder terminologySettings(TerminologySettings terminologySettings) {
-            this.terminologySettings = terminologySettings;
-            return this;
-        }
-
-        public Builder npmProcessor(NpmProcessor npmProcessor) {
-            this.npmProcessor = npmProcessor;
-            return this;
-        }
-
-        public EvaluationSettings build() {
-            return new EvaluationSettings(
-                    this.modelCache,
-                    this.libraryCache,
-                    this.valueSetCache,
-                    this.librarySourceProviders,
-                    this.cqlOptions,
-                    this.retrieveSettings,
-                    this.terminologySettings,
-                    this.npmProcessor);
-        }
+        return npmProcessor;
+    }
+
+    public void setNpmProcessor(NpmProcessor npmProcessor) {
+        this.npmProcessor = npmProcessor;
+    }
+
+    public EvaluationSettings withNpmProcessor(NpmProcessor npmProcessor) {
+        setNpmProcessor(npmProcessor);
+        return this;
     }
 }

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/LibraryEngine.java

@@ -15,7 +15,6 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
-import org.cqframework.cql.cql2elm.LibrarySourceProvider;
 import org.cqframework.cql.cql2elm.StringLibrarySourceProvider;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -129,16 +128,12 @@ public IBaseParameters evaluateExpression(
         Set<String> expressions = new HashSet<>();
         expressions.add("return");
 
-        List<LibrarySourceProvider> librarySourceProviders = new ArrayList<>();
-        librarySourceProviders.add(new StringLibrarySourceProvider(Lists.newArrayList(cql)));
+        var requestSettings = new EvaluationSettings(settings);
 
-        var requestSettings = settings.toBuilder().libraryCache(null).build();
+        requestSettings.getLibrarySourceProviders().add(new StringLibrarySourceProvider(Lists.newArrayList(cql)));
 
         var engine = Engines.forRepository(repository, requestSettings, bundle);
-        var providers = engine.getEnvironment().getLibraryManager().getLibrarySourceLoader();
-        for (var source : librarySourceProviders) {
-            providers.registerProvider(source);
-        }
+
         var evaluationParameters = cqlFhirParametersConverter.toCqlParameters(parameters);
         if (contextParameter != null) {
             evaluationParameters.put("%fhirpathcontext", contextParameter);

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/retrieve/RetrieveSettings.java

@@ -6,6 +6,23 @@ public class RetrieveSettings {
     private PROFILE_MODE profileMode = PROFILE_MODE.OFF;
     private TERMINOLOGY_FILTER_MODE terminologyParameterMode = TERMINOLOGY_FILTER_MODE.AUTO;
 
+    /**
+     * Default constructor for RetrieveSettings
+     */
+    public RetrieveSettings() {
+        // intentionally empty
+    }
+
+    /**
+     * Copy constructor for RetrieveSettings
+     * @param retrieveSettings
+     */
+    public RetrieveSettings(RetrieveSettings retrieveSettings) {
+        this.searchParameterMode = retrieveSettings.searchParameterMode;
+        this.profileMode = retrieveSettings.profileMode;
+        this.terminologyParameterMode = retrieveSettings.terminologyParameterMode;
+    }
+
     // Decreasing order of performance
     // Applies to all search parameters
     // EXCEPT terminology search parameters, which are controlled by the terminology settings.