hardened OME metadata deserialization by ignoring unknown fields

brokkoli71 · brokkoli71 · commit 585690f014d1 · 2026-03-19T15:31:33.000+01:00
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/Acquisition.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/Acquisition.java
@@ -1,12 +1,14 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 
 /** An HCS acquisition entry within a plate. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class Acquisition {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/Axis.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/Axis.java
@@ -1,11 +1,13 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class Axis {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/CoordinateTransformation.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/CoordinateTransformation.java
@@ -1,12 +1,14 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 import java.util.List;
 
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class CoordinateTransformation {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/Dataset.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/Dataset.java
@@ -1,10 +1,12 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import java.util.List;
 
+@JsonIgnoreProperties(ignoreUnknown = true)
 public final class Dataset {
 
     public final String path;
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/NamedEntry.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/NamedEntry.java
@@ -1,10 +1,12 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 /** A named entry used for plate rows/columns. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class NamedEntry {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/OmeMetadata.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/OmeMetadata.java
@@ -1,13 +1,15 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 import java.util.List;
 
 /** OME-Zarr metadata stored under {@code attributes["ome"]} (v0.5). */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class OmeMetadata {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/OmeroMetadata.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/OmeroMetadata.java
@@ -1,6 +1,7 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
@@ -9,6 +10,7 @@
 import java.util.Map;
 
 /** Omero display metadata stored in OME-Zarr attributes. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class OmeroMetadata {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/PlateMetadata.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/PlateMetadata.java
@@ -1,13 +1,15 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 import java.util.List;
 
 /** OME-Zarr HCS plate metadata. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class PlateMetadata {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/WellImage.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/WellImage.java
@@ -1,12 +1,14 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 
 /** A reference to an image within a well. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class WellImage {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/WellMetadata.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/WellMetadata.java
@@ -1,13 +1,15 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 import java.util.List;
 
 /** OME-Zarr HCS well metadata. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class WellMetadata {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/metadata/WellRef.java b/src/main/java/dev/zarr/zarrjava/ome/metadata/WellRef.java
@@ -1,10 +1,12 @@
 package dev.zarr.zarrjava.ome.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 /** A reference to a well within a plate, identified by path and row/column indices. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class WellRef {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/v0_6/metadata/CoordinateTransformation.java b/src/main/java/dev/zarr/zarrjava/ome/v0_6/metadata/CoordinateTransformation.java
@@ -1,12 +1,14 @@
 package dev.zarr.zarrjava.ome.v0_6.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 import java.util.List;
 
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class CoordinateTransformation {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/v0_6/metadata/MultiscalesEntry.java b/src/main/java/dev/zarr/zarrjava/ome/v0_6/metadata/MultiscalesEntry.java
@@ -1,6 +1,7 @@
 package dev.zarr.zarrjava.ome.v0_6.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import dev.zarr.zarrjava.ome.metadata.Axis;
@@ -10,11 +11,13 @@
 import java.util.List;
 import java.util.Map;
 
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class MultiscalesEntry {
 
     @Nullable public final List<Axis> axes;
     public final List<Dataset> datasets;
+    @Nullable public final List<CoordinateTransformation> coordinateTransformations;
     @Nullable public final List<CoordinateSystem> coordinateSystems;
     @Nullable public final String name;
     @Nullable public final String type;
@@ -24,27 +27,29 @@ public final class MultiscalesEntry {
     public MultiscalesEntry(
             @Nullable @JsonProperty("axes") List<Axis> axes,
             @JsonProperty(value = "datasets", required = true) List<Dataset> datasets,
+            @Nullable @JsonProperty("coordinateTransformations") List<CoordinateTransformation> coordinateTransformations,
             @Nullable @JsonProperty("coordinateSystems") List<CoordinateSystem> coordinateSystems,
             @Nullable @JsonProperty("name") String name,
             @Nullable @JsonProperty("type") String type,
             @Nullable @JsonProperty("metadata") Map<String, Object> metadata
     ) {
         this.axes = axes;
         this.datasets = datasets;
+        this.coordinateTransformations = coordinateTransformations;
         this.coordinateSystems = coordinateSystems;
         this.name = name;
         this.type = type;
         this.metadata = metadata;
     }
 
     public MultiscalesEntry(List<Dataset> datasets, List<CoordinateSystem> coordinateSystems, String name) {
-        this(null, datasets, coordinateSystems, name, null, null);
+        this(null, datasets, null, coordinateSystems, name, null, null);
     }
 
     /** Returns a new MultiscalesEntry with the given dataset appended. */
     public MultiscalesEntry withDataset(Dataset dataset) {
         List<Dataset> updated = new ArrayList<>(this.datasets);
         updated.add(dataset);
-        return new MultiscalesEntry(axes, updated, coordinateSystems, name, type, metadata);
+        return new MultiscalesEntry(axes, updated, coordinateTransformations, coordinateSystems, name, type, metadata);
     }
 }
diff --git a/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/CollectionMetadata.java b/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/CollectionMetadata.java
@@ -1,13 +1,15 @@
 package dev.zarr.zarrjava.ome.v1_0.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 import java.util.List;
 
 /** OME-Zarr v1.0 collection metadata stored under {@code attributes["ome"]["collection"]}. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class CollectionMetadata {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/Level.java b/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/Level.java
@@ -1,13 +1,15 @@
 package dev.zarr.zarrjava.ome.v1_0.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import dev.zarr.zarrjava.ome.v0_6.metadata.CoordinateTransformation;
 
 import java.util.List;
 
 /** A single resolution level within a v1.0 multiscale image (replaces v0.6 Dataset). */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class Level {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/MultiscaleMetadata.java b/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/MultiscaleMetadata.java
@@ -1,6 +1,7 @@
 package dev.zarr.zarrjava.ome.v1_0.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import dev.zarr.zarrjava.ome.metadata.Axis;
@@ -11,6 +12,7 @@
 import java.util.List;
 
 /** OME-Zarr v1.0 multiscale metadata stored under {@code attributes["ome"]["multiscale"]} (singular). */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class MultiscaleMetadata {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/NodeRef.java b/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/NodeRef.java
@@ -1,12 +1,14 @@
 package dev.zarr.zarrjava.ome.v1_0.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 
 /** A reference to a child node within a v1.0 collection. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class NodeRef {
 
diff --git a/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/OmeMetadata.java b/src/main/java/dev/zarr/zarrjava/ome/v1_0/metadata/OmeMetadata.java
@@ -1,12 +1,14 @@
 package dev.zarr.zarrjava.ome.v1_0.metadata;
 
 import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import javax.annotation.Nullable;
 
 /** OME-Zarr v1.0 top-level wrapper stored under {@code attributes["ome"]}. */
+@JsonIgnoreProperties(ignoreUnknown = true)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class OmeMetadata {
 
diff --git a/src/test/java/dev/zarr/zarrjava/ome/OmeZarrV06Test.java b/src/test/java/dev/zarr/zarrjava/ome/OmeZarrV06Test.java
@@ -16,6 +16,8 @@ public class OmeZarrV06Test extends OmeZarrBaseTest {
             TESTDATA.resolve("ome/v0.6/examples/2d/basic/scale_multiscale.zarr");
     private static final java.nio.file.Path V06_3D =
             TESTDATA.resolve("ome/v0.6/examples/3d/basic/scale_multiscale.zarr");
+    private static final java.nio.file.Path V06_HUMAN_ORGAN_ATLAS_OVERVIEW =
+            TESTDATA.resolve("ome/v0.6/examples/user_stories/human_organ_atlas.zarr/overview.ome.zarr");
 
     @Override
     StoreHandle imageStoreHandle() throws Exception {
@@ -124,4 +126,27 @@ void read3dUnifiedAxisNames() throws Exception {
         List<String> axisNames = image.getAxisNames();
         assertEquals(Arrays.asList("z", "y", "x"), axisNames);
     }
+
+    @Test
+    void readHumanOrganAtlasOverview() throws Exception {
+        MultiscaleImage image = MultiscaleImage.open(storeHandle(V06_HUMAN_ORGAN_ATLAS_OVERVIEW));
+        assertInstanceOf(dev.zarr.zarrjava.ome.v0_6.MultiscaleImage.class, image);
+
+        assertEquals(2, image.getScaleLevelCount());
+        assertEquals(Arrays.asList("x", "y", "z"), image.getAxisNames());
+        assertEquals(Arrays.asList("0", "1"), Arrays.asList(
+                image.getMultiscaleNode(0).datasets.get(0).path,
+                image.getMultiscaleNode(0).datasets.get(1).path));
+
+        dev.zarr.zarrjava.core.Array level0 = image.openScaleLevel(0);
+        assertArrayEquals(new long[]{8308, 8308, 9564}, level0.metadata().shape);
+
+        dev.zarr.zarrjava.ome.v0_6.MultiscaleImage typed = (dev.zarr.zarrjava.ome.v0_6.MultiscaleImage) image;
+        dev.zarr.zarrjava.ome.v0_6.metadata.MultiscalesEntry entry = typed.getMultiscalesEntry(0);
+        assertNotNull(entry.coordinateSystems);
+        assertEquals(2, entry.coordinateSystems.size());
+        assertEquals("physical", entry.coordinateSystems.get(0).name);
+        assertEquals("anatomical", entry.coordinateSystems.get(1).name);
+        assertEquals("sequence", entry.datasets.get(0).coordinateTransformations.get(0).type);
+    }
 }
