Adds ignoringUnrecognizedFields mode to Java JsonFormat and FhirPacka…

…ge classes. This allows parsing new versions of the spec using older versions of the spec, as long as the resource in question is normative (such as StructureDefinition).

PiperOrigin-RevId: 559911204

java/com/google/fhir/common/JsonFormat.java

@@ -596,10 +596,15 @@ public static Parser getParser() {
   public static final class Parser {
     private final ProtoGenTransformer protoGenTransformer;
     private final ZoneId defaultTimeZone;
+    private final boolean ignoreUnrecognizedFields;
 
-    private Parser(ZoneId defaultTimeZone, ProtoGenTransformer protoGenTransformer) {
+    private Parser(
+        ZoneId defaultTimeZone,
+        ProtoGenTransformer protoGenTransformer,
+        boolean ignoreUnrecognizedFields) {
       this.protoGenTransformer = protoGenTransformer;
       this.defaultTimeZone = defaultTimeZone;
+      this.ignoreUnrecognizedFields = ignoreUnrecognizedFields;
     }
 
     public static Parser withDefaultTimeZone(ZoneId defaultTimeZone) {
@@ -612,9 +617,10 @@ public static Builder newBuilder() {
     }
 
     /** Builder that can be used to obtain new instances of {@link Parser}. */
-    static final class Builder {
+    public static final class Builder {
       private ZoneId defaultTimeZone;
       private ProtoGenTransformer protoGenTransformer;
+      private boolean ignoreUnrecognizedFields = false;
 
       Builder(ZoneId defaultTimeZone) {
         this.defaultTimeZone = defaultTimeZone;
@@ -642,8 +648,14 @@ Builder withProtoGenTransformer(ProtoGenTransformer protoGenTransformer) {
         return this;
       }
 
-      Parser build() {
-        return new Parser(defaultTimeZone, protoGenTransformer);
+      @CanIgnoreReturnValue
+      public Builder ignoreUnrecognizedFields(boolean ignoreUnrecognizedFields) {
+        this.ignoreUnrecognizedFields = ignoreUnrecognizedFields;
+        return this;
+      }
+
+      public Parser build() {
+        return new Parser(defaultTimeZone, protoGenTransformer, ignoreUnrecognizedFields);
       }
     }
 
@@ -754,17 +766,22 @@ private void mergeMessage(JsonObject json, Message.Builder builder)
                     + descriptor.getFullName());
           }
         } else {
-          String names = "";
-          for (Map.Entry<String, FieldDescriptor> e : nameToDescriptorMap.entrySet()) {
-            names = names + " " + e.getKey();
+          if (ignoreUnrecognizedFields) {
+            continue;
+          } else {
+            String names = "";
+            for (Map.Entry<String, FieldDescriptor> e : nameToDescriptorMap.entrySet()) {
+              names = names + " " + e.getKey();
+            }
+
+            throw new InvalidFhirException(
+                "Unknown field "
+                    + fieldName
+                    + " in input of expected type "
+                    + builder.getDescriptorForType().getFullName()
+                    + ", known fields: "
+                    + names);
           }
-          throw new InvalidFhirException(
-              "Unknown field "
-                  + fieldName
-                  + " in input of expected type "
-                  + builder.getDescriptorForType().getFullName()
-                  + ", known fields: "
-                  + names);
         }
       }
       if (AnnotationUtils.isReference(builder.getDescriptorForType())) {

java/com/google/fhir/protogen/FhirPackage.java

@@ -151,6 +151,31 @@ public static FhirPackage load(String archiveFilePath) throws IOException, Inval
    */
   public static FhirPackage load(String archiveFilePath, PackageInfo packageInfo)
       throws IOException, InvalidFhirException {
+    return load(archiveFilePath, packageInfo, /* ignoreUnrecognizedFields= */ false);
+  }
+
+  /**
+   * Loads a package ZIP into a FhirPackage.
+   *
+   * <p>Parses all defining resources that are part of the spec.
+   *
+   * <p>To read PackageInfo out of the ZIP itself, use the version of this that does not accept a
+   * PackageProto argument.
+   *
+   * @param archiveFilePath The absolute path to the archive file (ZIP or TAR) that is loaded.
+   *     Expected to end with ".zip" "tar.gz" or ".tgz".
+   * @param packageInfo The package information to load. This package information is used,
+   *     irrespective of whether the ZIP contains one.
+   * @param ignoreUnrecognizedFields If true, will not fail if unrecognized fields are encountered
+   *     while parsing JSON. This allows for loading a FhirPackage of a new version of the Core FHIR
+   *     spec using a FhirPackage binary build with the older version of the spec. For instance, you
+   *     could parse an R5 StructureDefinition into an R4 StructureDefinition proto, since
+   *     StructureDefinition was made normative in R4, since normative implies that fields can be
+   *     added but not removed.
+   */
+  public static FhirPackage load(
+      String archiveFilePath, PackageInfo packageInfo, boolean ignoreUnrecognizedFields)
+      throws IOException, InvalidFhirException {
     PackageInfo extractedPackageInfo = null;
     try (ArchiveInputStream archiveEntries = getZipOrTarInputStream(archiveFilePath)) {
       List<JsonFile> jsonFiles = new ArrayList<>();
@@ -178,7 +203,9 @@ public static FhirPackage load(String archiveFilePath, PackageInfo packageInfo)
       }
 
       return makeFromJsonAndPackageInfo(
-          jsonFiles, packageInfo == null ? extractedPackageInfo : packageInfo);
+          jsonFiles,
+          packageInfo == null ? extractedPackageInfo : packageInfo,
+          ignoreUnrecognizedFields);
     }
   }
 
@@ -327,7 +354,7 @@ private static void buildResourceCollections(
   }
 
   private static FhirPackage makeFromJsonAndPackageInfo(
-      List<JsonFile> jsonFiles, PackageInfo packageInfo) {
+      List<JsonFile> jsonFiles, PackageInfo packageInfo, boolean ignoreUnrecognizedFields) {
     if (packageInfo != null) {
       if (packageInfo.getProtoPackage().isEmpty()) {
         throw new IllegalArgumentException(
@@ -338,8 +365,8 @@ private static FhirPackage makeFromJsonAndPackageInfo(
             "When PackageInfo is provided, must specify `fhir_version`.");
       }
     }
-
-    JsonFormat.Parser parser = JsonFormat.getParser();
+    JsonFormat.Parser parser =
+        JsonFormat.Parser.newBuilder().ignoreUnrecognizedFields(ignoreUnrecognizedFields).build();
 
     ResourceCollections resourceCollections = new ResourceCollections();
     resourceCollections.structureDefinitions =

javatests/com/google/fhir/protogen/FhirPackageTest.java

@@ -132,6 +132,44 @@ public void isCorePackage_withNonCorePackage() {
     assertThat(FhirPackage.isCorePackage(packageInfo)).isFalse();
   }
 
+  @Test
+  public void load_ignoringUnrecognizedFields() throws IOException, InvalidFhirException {
+    ImmutableList<PackageFile> files =
+        ImmutableList.of(
+            new PackageFile() {
+              {
+                fileName = "foo_package_info.prototxt";
+                fileContents =
+                    "proto_package: \"google.foo\""
+                        + "\njava_proto_package: \"com.google.foo\""
+                        + "\nfhir_version: R4"
+                        + "\nlicense: APACHE"
+                        + "\nlicense_date: \"2019\""
+                        + "\nlocal_contained_resource: true"
+                        + "\nfile_splitting_behavior: SPLIT_RESOURCES";
+              }
+            },
+            new PackageFile() {
+              {
+                fileName = "myStructDef.json";
+                fileContents =
+                    ""
+                        + "{ "
+                        + "  \"resourceType\": \"StructureDefinition\", "
+                        + "  \"id\": \"Patient\", "
+                        + "  \"url\": \"the-url.com\", "
+                        + "  \"garbage\": true"
+                        + "}";
+              }
+            });
+    String zipFile = createFhirPackageInfoZip("foo_package", files);
+    FhirPackage fhirPackage = FhirPackage.load(zipFile, null, /* ignoreUnrecognizedFields= */ true);
+
+    assertThat(fhirPackage.structureDefinitions()).hasSize(1);
+    assertThat(fhirPackage.structureDefinitions().iterator().next().getId().getValue())
+        .isEqualTo("Patient");
+  }
+
   @Test
   public void isCorePackage_withLoadedCorePackage() throws IOException, InvalidFhirException {
     ImmutableList<PackageFile> files =

javatests/com/google/fhir/r4/BUILD

@@ -15,7 +15,9 @@ java_test(
     test_class = "com.google.fhir.r4.JsonFormatTest",
     deps = [
         "//java/com/google/fhir/common:exceptions",
+        "//java/com/google/fhir/common:json_format",
         "//java/com/google/fhir/testing:json_format_test_base",
+        "//proto/google/fhir/proto/r4/core:datatypes_java_proto",
         "//proto/google/fhir/proto/r4/core/resources:account_java_proto",
         "//proto/google/fhir/proto/r4/core/resources:activity_definition_java_proto",
         "//proto/google/fhir/proto/r4/core/resources:adverse_event_java_proto",
@@ -140,6 +142,7 @@ java_test(
         "//proto/google/fhir/proto/r4/core/resources:slot_java_proto",
         "//proto/google/fhir/proto/r4/core/resources:specimen_definition_java_proto",
         "//proto/google/fhir/proto/r4/core/resources:specimen_java_proto",
+        "//proto/google/fhir/proto/r4/core/resources:structure_definition_java_proto",
         "//proto/google/fhir/proto/r4/core/resources:structure_map_java_proto",
         "//proto/google/fhir/proto/r4/core/resources:subscription_java_proto",
         "//proto/google/fhir/proto/r4/core/resources:substance_java_proto",
@@ -154,6 +157,7 @@ java_test(
         "//proto/google/fhir/proto/r4/core/resources:vision_prescription_java_proto",
         "@com_google_protobuf//:protobuf_java",
         "@maven//:com_google_guava_guava",
+        "@maven//:com_google_truth_extensions_truth_proto_extension",
         "@maven//:junit_junit",
     ],
 )

javatests/com/google/fhir/r4/JsonFormatTest.java

@@ -14,8 +14,12 @@
 
 package com.google.fhir.r4;
 
+import static com.google.common.truth.extensions.proto.ProtoTruth.assertThat;
+import static org.junit.Assert.assertThrows;
+
 import com.google.common.io.Files;
 import com.google.fhir.common.InvalidFhirException;
+import com.google.fhir.common.JsonFormat;
 import com.google.fhir.r4.core.Account;
 import com.google.fhir.r4.core.ActivityDefinition;
 import com.google.fhir.r4.core.AdverseEvent;
@@ -75,6 +79,7 @@
 import com.google.fhir.r4.core.Group;
 import com.google.fhir.r4.core.GuidanceResponse;
 import com.google.fhir.r4.core.HealthcareService;
+import com.google.fhir.r4.core.Id;
 import com.google.fhir.r4.core.ImagingStudy;
 import com.google.fhir.r4.core.Immunization;
 import com.google.fhir.r4.core.ImmunizationEvaluation;
@@ -140,6 +145,7 @@
 import com.google.fhir.r4.core.Slot;
 import com.google.fhir.r4.core.Specimen;
 import com.google.fhir.r4.core.SpecimenDefinition;
+import com.google.fhir.r4.core.StructureDefinition;
 import com.google.fhir.r4.core.StructureMap;
 import com.google.fhir.r4.core.Subscription;
 import com.google.fhir.r4.core.Substance;
@@ -202,6 +208,25 @@ private void testOrGenerate(String[] fileNames, Message.Builder type)
     }
   }
 
+  @Test
+  public void testIgnoringUnrecognizedFields_false_failsOnUnrecognizedField() throws Exception {
+    JsonFormat.Parser parser = JsonFormat.Parser.newBuilder().build();
+    StructureDefinition.Builder builder = StructureDefinition.newBuilder();
+    assertThrows(
+        InvalidFhirException.class,
+        () -> parser.merge("{ \"id\": \"123\", \"garbage\": true}", builder));
+  }
+
+  @Test
+  public void testIgnoringUnrecognizedFields_true_succeedsOnUnrecognizedField() throws Exception {
+    JsonFormat.Parser parser =
+        JsonFormat.Parser.newBuilder().ignoreUnrecognizedFields(true).build();
+    StructureDefinition.Builder builder = StructureDefinition.newBuilder();
+    parser.merge("{ \"id\": \"123\", \"garbage\": true}", builder);
+    assertThat(builder.build())
+        .isEqualTo(StructureDefinition.newBuilder().setId(Id.newBuilder().setValue("123")).build());
+  }
+
   /** Test the analytics output format. */
   @Test
   public void convertForAnalytics() throws Exception {
@@ -348,6 +373,7 @@ public void testBundlePt2() throws Exception {
   public void testBundlePt4() throws Exception {
     testOrGenerate(new String[] {"Bundle-conceptmaps", "Bundle-dataelements"}, Bundle.newBuilder());
   }
+
   //   TODO(b/244184211): These tests don't seem to ever finish for some reason - while other large
   //   files finish in at most a couple seconds, these time out even at 15 minutes.
   //   Seems to be a problem with the printer.  Figure out why, and reneable these tests.