Merge branch 'master' into dependabot/maven/org.apache.parquet-parquet-avro-1.16.0

Author: ndegwamartin

.github/PULL_REQUEST_TEMPLATE.md

@@ -40,9 +40,9 @@ automated e2e/unit tests.
       code that was well tested you do not have to add tests)
 - [ ] I ran `mvn clean package` right before creating this pull request and
       added all formatting changes to my commit.
-- [ ] If I made any Python code changes, I ran `black .` and `pylint .` right
-      before creating this pull request and added all formatting changes to my
-      commit.
+- [ ] If I made any Python code changes, I ran `black .`, `pylint .` and
+      `pyright` . right before creating this pull request and added all
+      formatting changes to my commit.
 - [ ] All new and existing **tests passed**.
 - [ ] My pull request is **based on the latest changes** of the master branch.
 

bunsen/bunsen-avro/src/main/java/com/cerner/bunsen/avro/AvroConverter.java

@@ -22,6 +22,7 @@
 import org.apache.avro.generic.IndexedRecord;
 import org.apache.commons.collections4.CollectionUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.jspecify.annotations.Nullable;
 
 /** Converter to change HAPI objects into Avro structures and vice versa. */
 public class AvroConverter {
@@ -74,6 +75,7 @@ private static AvroConverter visitResource(
     RuntimeResourceDefinition[] resources =
         new RuntimeResourceDefinition[1 + containedResourceTypeUrls.size()];
 
+    Preconditions.checkNotNull(converter.getElementType(), "Converter must have an element type");
     resources[0] = context.getResourceDefinition(converter.getElementType());
 
     for (int i = 0; i < containedResourceTypeUrls.size(); i++) {
@@ -210,6 +212,7 @@ public static AvroConverter forResource(
    * @param resource the FHIR resource
    * @return the record.
    */
+  @Nullable
   public IndexedRecord resourceToAvro(IBaseResource resource) {
 
     return (IndexedRecord) hapiToAvroConverter.fromHapi(resource);
@@ -221,6 +224,7 @@ public IndexedRecord resourceToAvro(IBaseResource resource) {
    * @param record the record
    * @return the FHIR resource.
    */
+  @Nullable
   public IBaseResource avroToResource(IndexedRecord record) {
 
     return (IBaseResource) avroToHapiConverter.toHapi(record);
@@ -241,6 +245,7 @@ public Schema getSchema() {
    *
    * @return the FHIR type of the resource being converted.
    */
+  @Nullable
   public String getResourceType() {
     return hapiToAvroConverter.getElementType();
   }

bunsen/bunsen-avro/src/main/java/com/cerner/bunsen/avro/converters/DefinitionToAvroVisitor.java

@@ -44,6 +44,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.jspecify.annotations.Nullable;
 
 public class DefinitionToAvroVisitor implements DefinitionVisitor<HapiConverter<Schema>> {
 
@@ -170,19 +171,19 @@ private static class CompositeToAvroConverter extends HapiCompositeConverter<Sch
     private final GenericData avroData = SpecificData.get();
 
     CompositeToAvroConverter(
-        String elementType,
+        @Nullable String elementType,
         List<StructureField<HapiConverter<Schema>>> children,
         Schema structType,
         FhirConversionSupport fhirSupport) {
       this(elementType, children, structType, fhirSupport, null);
     }
 
     CompositeToAvroConverter(
-        String elementType,
+        @Nullable String elementType,
         List<StructureField<HapiConverter<Schema>>> children,
         Schema structType,
         FhirConversionSupport fhirSupport,
-        String extensionUrl) {
+        @Nullable String extensionUrl) {
 
       super(elementType, children, structType, fhirSupport, extensionUrl);
     }
@@ -629,6 +630,7 @@ private static class NoOpFieldSetter implements HapiFieldSetter, HapiObjectConve
     public void setField(
         IBase parentObject, BaseRuntimeChildDefinition fieldToSet, Object sparkObject) {}
 
+    @Nullable
     @Override
     public IBase toHapi(Object input) {
       return null;
@@ -646,6 +648,7 @@ private static class RelativeValueConverter extends HapiConverter<Schema> {
       this.prefix = prefix;
     }
 
+    @Nullable
     @Override
     public Object fromHapi(Object input) {
       String uri = ((IPrimitiveType) input).getValueAsString();
@@ -763,11 +766,6 @@ public HapiConverter<Schema> visitParentExtension(
       String extensionUrl,
       List<StructureField<HapiConverter<Schema>>> children) {
 
-    // Ignore extension fields that don't have declared content for now.
-    if (children.isEmpty()) {
-      return null;
-    }
-
     String recordNamespace = DefinitionVisitorsUtil.namespaceFor(basePackage, extensionUrl);
 
     String localPart = extensionUrl.substring(extensionUrl.lastIndexOf('/') + 1);
@@ -850,13 +848,13 @@ public int getMaxDepth(String elementTypeUrl, String path) {
   }
 
   private static HapiCompositeConverter createCompositeConverter(
-      String elementType,
+      @Nullable String elementType,
       String recordName,
       String doc,
       String namespace,
       List<StructureField<HapiConverter<Schema>>> children,
       FhirConversionSupport fhirSupport,
-      String extensionUrl) {
+      @Nullable String extensionUrl) {
 
     List<Field> fields =
         children.stream()

bunsen/bunsen-avro/src/main/java/com/cerner/bunsen/avro/converters/NoOpConverter.java

@@ -8,9 +8,11 @@
 import org.apache.avro.Schema;
 import org.apache.avro.Schema.Type;
 import org.hl7.fhir.instance.model.api.IBase;
+import org.jspecify.annotations.Nullable;
 
 public class NoOpConverter extends HapiConverter<Schema> {
 
+  @Nullable
   @Override
   public Object fromHapi(Object input) {
     return null;
@@ -26,6 +28,7 @@ private static class FieldSetter implements HapiFieldSetter, HapiObjectConverter
     @Override
     public void setField(IBase parentObject, BaseRuntimeChildDefinition fieldToSet, Object value) {}
 
+    @Nullable
     @Override
     public IBase toHapi(Object input) {
       return null;

bunsen/bunsen-avro/src/main/java/com/cerner/bunsen/avro/tools/GenerateAggregatedSchemas.java

@@ -18,6 +18,7 @@
 import java.util.Map;
 import org.apache.avro.Schema;
 import org.apache.avro.SchemaFormatter;
+import org.jspecify.annotations.Nullable;
 
 /** This class can be used to generate aggregated avro schemas for the FHIR profile extensions. */
 public class GenerateAggregatedSchemas {
@@ -75,10 +76,10 @@ private static Map<String, String> convertArgsToPairs(String[] args) {
   }
 
   private static void generateAggregatedSchemas(
-      FhirVersionEnum fhirVersionEnum,
-      String structureDefinitionsPath,
-      List<String> resourceTypes,
-      String outputDir)
+      @Nullable FhirVersionEnum fhirVersionEnum,
+      @Nullable String structureDefinitionsPath,
+      @Nullable List<String> resourceTypes,
+      @Nullable String outputDir)
       throws ProfileException, IOException {
     Preconditions.checkNotNull(fhirVersionEnum, "%s cannot be empty", FHIR_VERSION);
     Preconditions.checkNotNull(
@@ -95,6 +96,15 @@ private static void generateAggregatedSchemas(
       List<String> resourceTypeURLs =
           ProfileMapperFhirContexts.getInstance()
               .getMappedProfilesForResource(FhirVersionEnum.R4, resourceType);
+      if (resourceTypeURLs == null || resourceTypeURLs.isEmpty()) {
+        System.out.printf(
+            "No profiles found for resourceType=%s, skipping schema generation for this"
+                + " resourceType%n",
+            resourceType);
+        continue; // TODO confirm if we need to throw a new ProfileException exception here instead
+        // of skipping
+      }
+
       AvroConverter aggregatedConverter =
           AvroConverter.forResources(fhirContext, resourceTypeURLs, 1);
       createOutputFile(resourceType, aggregatedConverter.getSchema(), outputDir);

bunsen/bunsen-avro/src/test/java/com/cerner/bunsen/avro/AvroConverterMergeTest.java

@@ -115,8 +115,10 @@ public void validateR4UsCoreResourceWithExtension() throws ProfileException, IOE
     Patient patient =
         (Patient)
             loadResource(fhirContext, "/r4-us-core-resources/patient_us_core.json", Patient.class);
-    IndexedRecord avroRecord = patientConverter.resourceToAvro(patient);
-    Patient patientDecoded = (Patient) patientConverter.avroToResource(avroRecord);
+    IndexedRecord patientRecord = patientConverter.resourceToAvro(patient);
+    Assert.assertNotNull(patientRecord);
+    Patient patientDecoded = (Patient) patientConverter.avroToResource(patientRecord);
+    Assert.assertNotNull(patientDecoded);
     Assert.assertTrue(
         patient.equalsDeep(
             (Base) TestUtil.encodeThenParse(patientDecoded, Patient.class, fhirContext)));
@@ -137,9 +139,11 @@ public void validateMergedStu3UsCoreResourceWithExtensions()
                 fhirContext,
                 "/stu3-us-core-resources/patient_us_core.json",
                 org.hl7.fhir.dstu3.model.Patient.class);
-    IndexedRecord avroRecord = patientConverter.resourceToAvro(patient);
+    IndexedRecord patientRecord = patientConverter.resourceToAvro(patient);
+    Assert.assertNotNull(patientRecord);
     org.hl7.fhir.dstu3.model.Patient patientDecoded =
-        (org.hl7.fhir.dstu3.model.Patient) patientConverter.avroToResource(avroRecord);
+        (org.hl7.fhir.dstu3.model.Patient) patientConverter.avroToResource(patientRecord);
+    Assert.assertNotNull(patientDecoded);
     patientDecoded.setId(patient.getId());
     // TODO : The text field is not properly copied to the decoded object back, hence manually
     // copying it, check here for details https://github.com/google/fhir-data-pipes/issues/1014

bunsen/bunsen-avro/src/test/java/com/cerner/bunsen/avro/R4AvroConverterCustomProfileTest.java

@@ -24,6 +24,9 @@
  * This class tests the user-defined structure definitions which should also follow the HL7 FHIR
  * specifications. These are additional test cases beyond the regular US Core Profiles tests.
  */
+
+// Suppressing NullAway warnings for test code
+@SuppressWarnings("NullAway")
 public class R4AvroConverterCustomProfileTest {
 
   private static final Patient testBunsenTestProfilePatient =

bunsen/bunsen-avro/src/test/java/com/cerner/bunsen/avro/R4AvroConverterUsCoreTest.java

@@ -46,6 +46,8 @@
 import org.junit.Test;
 
 // TODO refactor the shared code with `Stu3AvroConverterUsCoreTest`.
+// Suppressing NullAway warnings for test code
+@SuppressWarnings("NullAway")
 public class R4AvroConverterUsCoreTest {
 
   private static final Observation testObservation = TestData.newObservation();

bunsen/bunsen-avro/src/test/java/com/cerner/bunsen/avro/Stu3AvroConverterCustomProfileTest.java

@@ -24,6 +24,8 @@
  * <p>TODO: Refactor this and the R43AvroConverterCustomProfileTest.java to move the duplicate code
  * into a common class and add only relevant cases here
  */
+// Suppressing NullAway warnings for test code
+@SuppressWarnings("NullAway")
 public class Stu3AvroConverterCustomProfileTest {
 
   private static final Patient testBunsenTestProfilePatient =

bunsen/bunsen-avro/src/test/java/com/cerner/bunsen/avro/Stu3AvroConverterUsCoreTest.java

@@ -42,6 +42,8 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+// Suppressing NullAway warnings for test code
+@SuppressWarnings("NullAway")
 public class Stu3AvroConverterUsCoreTest {
 
   private static final Observation testObservation = TestData.newObservation();