spotless and logs

cqf-fhir-cr-test/src/test/java/org/opencds/cqf/fhir/cr/visitor/dstu3/PackageVisitorTests.java

@@ -481,12 +481,13 @@ void fallback_to_tx_server_if_valueset_missing_locally() {
         final var authoritativeSource = "http://cts.nlm.nih.gov/fhir/";
         var bundle = (Bundle) jsonParser.parseResource(
                 ReleaseVisitorTests.class.getResourceAsStream("Bundle-ersd-small-active.json"));
-        Predicate<BundleEntryComponent> leafFinder = e -> e.getResource().getResourceType() == ResourceType.ValueSet && ((ValueSet) e.getResource()).getUrl().contains(leafOid);
+        Predicate<BundleEntryComponent> leafFinder = e -> e.getResource().getResourceType() == ResourceType.ValueSet
+                && ((ValueSet) e.getResource()).getUrl().contains(leafOid);
         // remove leaf from bundle
         var leafEntry = bundle.getEntry().stream().filter(leafFinder).findFirst();
-        var leafVset = leafEntry.map(e -> (ValueSet)e.getResource()).get();
+        var leafVset = leafEntry.map(e -> (ValueSet) e.getResource()).get();
         bundle.getEntry().remove(leafEntry.get());
-        
+
         repo.transaction(bundle);
         var library = repo.read(Library.class, new IdType("Library/SpecificationLibrary"))
                 .copy();
@@ -495,17 +496,18 @@ void fallback_to_tx_server_if_valueset_missing_locally() {
         var clientMock = mock(TerminologyServerClient.class, new ReturnsDeepStubs());
         when(clientMock.getResource(any(IEndpointAdapter.class), any(), any())).thenReturn(Optional.of(leafVset));
         doAnswer(new Answer<ValueSet>() {
-            @Override
-            public ValueSet answer(InvocationOnMock invocation) throws Throwable {
-                return new ValueSet(); // Return a new instance of ValueSet
-            }
-        }).when(clientMock).expand(any(IValueSetAdapter.class), any(IEndpointAdapter.class), any(IParametersAdapter.class));
+                    @Override
+                    public ValueSet answer(InvocationOnMock invocation) throws Throwable {
+                        return new ValueSet(); // Return a new instance of ValueSet
+                    }
+                })
+                .when(clientMock)
+                .expand(any(IValueSetAdapter.class), any(IEndpointAdapter.class), any(IParametersAdapter.class));
         var packageVisitor = new PackageVisitor(repo, clientMock);
         var libraryAdapter = new AdapterFactory().createLibrary(library);
-        var params = parameters(
-                part("terminologyEndpoint", (org.hl7.fhir.dstu3.model.Endpoint) endpoint.get()));
+        var params = parameters(part("terminologyEndpoint", (org.hl7.fhir.dstu3.model.Endpoint) endpoint.get()));
         // create package
-        var packagedBundle = (Bundle)libraryAdapter.accept(packageVisitor, params);
+        var packagedBundle = (Bundle) libraryAdapter.accept(packageVisitor, params);
         var containsVset = packagedBundle.getEntry().stream().anyMatch(leafFinder);
         // check for ValueSet
         assertTrue(containsVset);

cqf-fhir-cr-test/src/test/java/org/opencds/cqf/fhir/cr/visitor/r4/PackageVisitorTests.java

@@ -30,12 +30,10 @@
 import java.util.Optional;
 import java.util.concurrent.ThreadLocalRandom;
 import java.util.function.Predicate;
-import java.util.stream.Collectors;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.hl7.fhir.r4.model.CanonicalType;
-import org.hl7.fhir.r4.model.CodeType;
 import org.hl7.fhir.r4.model.Endpoint;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.IntegerType;
@@ -58,7 +56,6 @@
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cr.visitor.IValueSetExpansionCache;
 import org.opencds.cqf.fhir.cr.visitor.PackageVisitor;
-import org.opencds.cqf.fhir.utility.Canonicals;
 import org.opencds.cqf.fhir.utility.Constants;
 import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
 import org.opencds.cqf.fhir.utility.adapter.IEndpointAdapter;
@@ -443,12 +440,13 @@ void fallback_to_tx_server_if_valueset_missing_locally() {
         final var authoritativeSource = "http://cts.nlm.nih.gov/fhir/";
         var bundle = (Bundle) jsonParser.parseResource(
                 ReleaseVisitorTests.class.getResourceAsStream("Bundle-ersd-small-active.json"));
-        Predicate<BundleEntryComponent> leafFinder = e -> e.getResource().getResourceType() == ResourceType.ValueSet && ((ValueSet) e.getResource()).getUrl().contains(leafOid);
+        Predicate<BundleEntryComponent> leafFinder = e -> e.getResource().getResourceType() == ResourceType.ValueSet
+                && ((ValueSet) e.getResource()).getUrl().contains(leafOid);
         // remove leaf from bundle
         var leafEntry = bundle.getEntry().stream().filter(leafFinder).findFirst();
-        var leafVset = leafEntry.map(e -> (ValueSet)e.getResource()).get();
+        var leafVset = leafEntry.map(e -> (ValueSet) e.getResource()).get();
         bundle.getEntry().remove(leafEntry.get());
-        
+
         repo.transaction(bundle);
         var library = repo.read(Library.class, new IdType("Library/SpecificationLibrary"))
                 .copy();
@@ -457,17 +455,18 @@ void fallback_to_tx_server_if_valueset_missing_locally() {
         var clientMock = mock(TerminologyServerClient.class, new ReturnsDeepStubs());
         when(clientMock.getResource(any(IEndpointAdapter.class), any(), any())).thenReturn(Optional.of(leafVset));
         doAnswer(new Answer<ValueSet>() {
-            @Override
-            public ValueSet answer(InvocationOnMock invocation) throws Throwable {
-                return new ValueSet(); // Return a new instance of ValueSet
-            }
-        }).when(clientMock).expand(any(IValueSetAdapter.class), any(IEndpointAdapter.class), any(IParametersAdapter.class));
+                    @Override
+                    public ValueSet answer(InvocationOnMock invocation) throws Throwable {
+                        return new ValueSet(); // Return a new instance of ValueSet
+                    }
+                })
+                .when(clientMock)
+                .expand(any(IValueSetAdapter.class), any(IEndpointAdapter.class), any(IParametersAdapter.class));
         var packageVisitor = new PackageVisitor(repo, clientMock);
         var libraryAdapter = new AdapterFactory().createLibrary(library);
-        var params = parameters(
-                part("terminologyEndpoint", (org.hl7.fhir.r4.model.Endpoint) endpoint.get()));
+        var params = parameters(part("terminologyEndpoint", (org.hl7.fhir.r4.model.Endpoint) endpoint.get()));
         // create package
-        var packagedBundle = (Bundle)libraryAdapter.accept(packageVisitor, params);
+        var packagedBundle = (Bundle) libraryAdapter.accept(packageVisitor, params);
         var containsVset = packagedBundle.getEntry().stream().anyMatch(leafFinder);
         // check for ValueSet
         assertTrue(containsVset);

cqf-fhir-cr-test/src/test/java/org/opencds/cqf/fhir/cr/visitor/r5/PackageVisitorTests.java

@@ -482,12 +482,13 @@ void fallback_to_tx_server_if_valueset_missing_locally() {
         final var authoritativeSource = "http://cts.nlm.nih.gov/fhir/";
         var bundle = (Bundle) jsonParser.parseResource(
                 ReleaseVisitorTests.class.getResourceAsStream("Bundle-ersd-small-active.json"));
-        Predicate<BundleEntryComponent> leafFinder = e -> e.getResource().getResourceType() == ResourceType.ValueSet && ((ValueSet) e.getResource()).getUrl().contains(leafOid);
+        Predicate<BundleEntryComponent> leafFinder = e -> e.getResource().getResourceType() == ResourceType.ValueSet
+                && ((ValueSet) e.getResource()).getUrl().contains(leafOid);
         // remove leaf from bundle
         var leafEntry = bundle.getEntry().stream().filter(leafFinder).findFirst();
-        var leafVset = leafEntry.map(e -> (ValueSet)e.getResource()).get();
+        var leafVset = leafEntry.map(e -> (ValueSet) e.getResource()).get();
         bundle.getEntry().remove(leafEntry.get());
-        
+
         repo.transaction(bundle);
         var library = repo.read(Library.class, new IdType("Library/SpecificationLibrary"))
                 .copy();
@@ -496,17 +497,18 @@ void fallback_to_tx_server_if_valueset_missing_locally() {
         var clientMock = mock(TerminologyServerClient.class, new ReturnsDeepStubs());
         when(clientMock.getResource(any(IEndpointAdapter.class), any(), any())).thenReturn(Optional.of(leafVset));
         doAnswer(new Answer<ValueSet>() {
-            @Override
-            public ValueSet answer(InvocationOnMock invocation) throws Throwable {
-                return new ValueSet(); // Return a new instance of ValueSet
-            }
-        }).when(clientMock).expand(any(IValueSetAdapter.class), any(IEndpointAdapter.class), any(IParametersAdapter.class));
+                    @Override
+                    public ValueSet answer(InvocationOnMock invocation) throws Throwable {
+                        return new ValueSet(); // Return a new instance of ValueSet
+                    }
+                })
+                .when(clientMock)
+                .expand(any(IValueSetAdapter.class), any(IEndpointAdapter.class), any(IParametersAdapter.class));
         var packageVisitor = new PackageVisitor(repo, clientMock);
         var libraryAdapter = new AdapterFactory().createLibrary(library);
-        var params = parameters(
-                part("terminologyEndpoint", (org.hl7.fhir.r5.model.Endpoint) endpoint.get()));
+        var params = parameters(part("terminologyEndpoint", (org.hl7.fhir.r5.model.Endpoint) endpoint.get()));
         // create package
-        var packagedBundle = (Bundle)libraryAdapter.accept(packageVisitor, params);
+        var packagedBundle = (Bundle) libraryAdapter.accept(packageVisitor, params);
         var containsVset = packagedBundle.getEntry().stream().anyMatch(leafFinder);
         // check for ValueSet
         assertTrue(containsVset);

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/visitor/BaseKnowledgeArtifactVisitor.java

@@ -131,8 +131,6 @@ protected void recursiveGather(
         if (adapter == null) {
             return;
         }
-        myLogger.info(gatheredResources.keySet().stream().collect(Collectors.joining(",")));
-        myLogger.info(adapter.getCanonical());
         if (!gatheredResources.keySet().contains(adapter.getCanonical())) {
             gatheredResources.put(adapter.getCanonical(), adapter);
             findUnsupportedCapability(adapter, capability);

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/visitor/ExpandHelper.java

@@ -84,8 +84,6 @@ public void expandValueSet(
                         || authoritativeSourceUrl.equals(
                                 terminologyEndpoint.get().getAddress()))) {
             try {
-                myLogger.info("Expanding using Tx Server: "
-                        + terminologyEndpoint.get().getAddress());
                 var expandedValueSet = (IValueSetAdapter) createAdapterForResource(
                         terminologyServerClient.expand(valueSet, terminologyEndpoint.get(), expansionParameters));
                 // expansions are only valid for a particular version
@@ -233,7 +231,6 @@ private IValueSetAdapter getIncludedValueSet(
                                 .map(r -> (IValueSetAdapter) createAdapterForResource(r))
                                 .orElse(null);
                     } else {
-                        myLogger.info("pulled VS from repo: " + reference);
                         return VisitorHelper.tryGetLatestVersion(reference, repository)
                                 .map(a -> (IValueSetAdapter) a)
                                 .orElse(null);

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/visitor/PackageVisitor.java

@@ -116,9 +116,11 @@ public IBase visit(IKnowledgeArtifactAdapter adapter, IBaseParameters packagePar
 
         Optional<String> artifactRoute = VisitorHelper.getStringParameter("artifactRoute", packageParameters);
         Optional<String> endpointUri = VisitorHelper.getStringParameter("endpointUri", packageParameters);
-        Optional<IEndpointAdapter> endpoint = VisitorHelper.getResourceParameter("endpoint", packageParameters).map(ep -> (IEndpointAdapter)createAdapterForResource(ep));
-        Optional<IEndpointAdapter> terminologyEndpoint =
-                VisitorHelper.getResourceParameter("terminologyEndpoint", packageParameters).map(ep -> (IEndpointAdapter)createAdapterForResource(ep));
+        Optional<IEndpointAdapter> endpoint = VisitorHelper.getResourceParameter("endpoint", packageParameters)
+                .map(ep -> (IEndpointAdapter) createAdapterForResource(ep));
+        Optional<IEndpointAdapter> terminologyEndpoint = VisitorHelper.getResourceParameter(
+                        "terminologyEndpoint", packageParameters)
+                .map(ep -> (IEndpointAdapter) createAdapterForResource(ep));
         Optional<Boolean> packageOnly = VisitorHelper.getBooleanParameter("packageOnly", packageParameters);
         Optional<Integer> count = VisitorHelper.getIntegerParameter("count", packageParameters);
         Optional<Integer> offset = VisitorHelper.getIntegerParameter("offset", packageParameters);
@@ -165,11 +167,17 @@ public IBase visit(IKnowledgeArtifactAdapter adapter, IBaseParameters packagePar
             BundleHelper.addEntry(packagedBundle, entry);
         } else {
             var packagedResources = new HashMap<String, IKnowledgeArtifactAdapter>();
-            recursiveGather(adapter, packagedResources, capability, include, versionTuple, terminologyEndpoint.orElse(null), terminologyServerClient);
+            recursiveGather(
+                    adapter,
+                    packagedResources,
+                    capability,
+                    include,
+                    versionTuple,
+                    terminologyEndpoint.orElse(null),
+                    terminologyServerClient);
             packagedResources.values().stream()
                     .filter(r -> !r.getCanonical().equals(adapter.getCanonical()))
                     .forEach(r -> addBundleEntry(packagedBundle, isPut, r));
-            myLogger.info(String.valueOf(packagedResources.size()));
             var included = findUnsupportedInclude(BundleHelper.getEntry(packagedBundle), include, adapter);
             BundleHelper.setEntry(packagedBundle, included);
         }
@@ -226,13 +234,7 @@ protected void handleValueSets(IBaseBundle packagedBundle, Optional<IEndpointAda
         missingInCache.forEach(valueSet -> {
             var url = valueSet.getUrl();
             var expansionStartTime = new Date().getTime();
-            expandHelper.expandValueSet(
-                    valueSet,
-                    params,
-                    terminologyEndpoint,
-                    valueSets,
-                    expandedList,
-                    new Date());
+            expandHelper.expandValueSet(valueSet, params, terminologyEndpoint, valueSets, expandedList, new Date());
             var elapsed = String.valueOf(((new Date()).getTime() - expansionStartTime) / 1000);
             myLogger.info("Expanded {} in {}s", url, elapsed);
             if (expansionCache.isPresent()) {

cqf-fhir-utility/src/main/java/org/opencds/cqf/fhir/utility/client/TerminologyServerClient.java

@@ -79,7 +79,6 @@ public IBaseResource expand(
         if (parameters.getParameter(versionParamName) == null && valueSetVersion != null) {
             parameters.addParameter(Parameters.newStringPart(ctx, versionParamName, valueSetVersion));
         }
-        myLogger.info("Expanding with Parameters: " + ctx.newJsonParser().encodeResourceToString(parameters.get()));
         // Invoke on the type using the url parameter
         return fhirClient
                 .operation()