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Make logging of unknown fields in OME metadata less severe #75

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Merged
normanrz merged 8 commits into from
Sep 8, 2026
Merged

Make logging of unknown fields in OME metadata less severe #75

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3d5f95f
Make logging of unknown fields in OME metadata less severe
stefanhahmann May 7, 2026
98ac961
Merge branch 'main' into stefanhahmann-patch-1
normanrz Jul 28, 2026
ee9ec2f
Merge branch 'main' into stefanhahmann-patch-1
normanrz Jul 29, 2026
796e5cd
Merge branch 'main' into stefanhahmann-patch-1
normanrz Sep 8, 2026
252b9d9
Apply suggestion from @normanrz
normanrz Sep 8, 2026
577c63a
Apply suggestion from @normanrz
normanrz Sep 8, 2026
ecf63f5
Log unknown OME fields at INFO instead of FINE
normanrz Sep 8, 2026
bc1314e
Keep unknown OME field logging at FINE
normanrz Sep 8, 2026
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14 changes: 7 additions & 7 deletions src/main/java/dev/zarr/zarrjava/experimental/ome/OmeObjectMappers.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,20 +19,20 @@ private OmeObjectMappers() {
static ObjectMapper makeV2Mapper() {
ObjectMapper mapper = dev.zarr.zarrjava.v2.Node.makeObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true);
mapper.addHandler(new UnknownOmePropertyWarningHandler());
mapper.addHandler(new UnknownOmePropertyLoggingHandler());
return mapper;
}

static ObjectMapper makeV3Mapper() {
ObjectMapper mapper = dev.zarr.zarrjava.v3.Node.makeObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true);
mapper.addHandler(new UnknownOmePropertyWarningHandler());
mapper.addHandler(new UnknownOmePropertyLoggingHandler());
return mapper;
}

private static final class UnknownOmePropertyWarningHandler extends DeserializationProblemHandler {
private static final Logger LOGGER = Logger.getLogger(UnknownOmePropertyWarningHandler.class.getName());
private static final Set<String> WARNED_FIELDS = ConcurrentHashMap.newKeySet();
private static final class UnknownOmePropertyLoggingHandler extends DeserializationProblemHandler {
private static final Logger LOGGER = Logger.getLogger(UnknownOmePropertyLoggingHandler.class.getName());
private static final Set<String> UNKNOWN_FIELDS = ConcurrentHashMap.newKeySet();

@Override
public boolean handleUnknownProperty(
Expand All @@ -46,8 +46,8 @@ public boolean handleUnknownProperty(
? ((Class<?>) beanOrClass).getName()
: beanOrClass.getClass().getName();
String key = target + "#" + propertyName;
if (WARNED_FIELDS.add(key)) {
LOGGER.warning(
if (UNKNOWN_FIELDS.add(key)) {
LOGGER.fine(
"Ignoring unknown OME metadata field '" + propertyName + "' for " + target);
}
p.skipChildren();
Expand Down
36 changes: 21 additions & 15 deletions src/test/java/dev/zarr/zarrjava/experimental/ome/OmeObjectMappersTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,11 @@

class OmeObjectMappersTest {

private static final String WARNING_LOGGER_NAME =
"dev.zarr.zarrjava.experimental.ome.OmeObjectMappers$UnknownOmePropertyWarningHandler";
private static final String HANDLER_LOGGER_NAME =
"dev.zarr.zarrjava.experimental.ome.OmeObjectMappers$UnknownOmePropertyLoggingHandler";

@Test
void v3MapperWarnsAndContinuesOnUnknownOmeFields() {
void v3MapperLogsAndContinuesOnUnknownOmeFields() {
String unknownTop = "unknown_top_" + UUID.randomUUID();
String unknownAxis = "unknown_axis_" + UUID.randomUUID();

Expand All @@ -54,9 +54,11 @@ void v3MapperWarnsAndContinuesOnUnknownOmeFields() {
omeRaw.put("multiscales", Arrays.asList(multiscale));
omeRaw.put(unknownTop, "surprise");

Logger logger = Logger.getLogger(WARNING_LOGGER_NAME);
Logger logger = Logger.getLogger(HANDLER_LOGGER_NAME);
CapturingHandler handler = new CapturingHandler();
Level previousLevel = logger.getLevel();
logger.addHandler(handler);
logger.setLevel(Level.FINE);
try {
ObjectMapper mapper = OmeObjectMappers.makeV3Mapper();
OmeMetadata parsed = mapper.convertValue(omeRaw, OmeMetadata.class);
Expand All @@ -66,15 +68,16 @@ void v3MapperWarnsAndContinuesOnUnknownOmeFields() {
assertNotNull(parsed.multiscales);
assertEquals(1, parsed.multiscales.size());
assertEquals("x", parsed.multiscales.get(0).axes.get(0).name);
assertTrue(handler.containsWarningWith(unknownTop));
assertTrue(handler.containsWarningWith(unknownAxis));
assertTrue(handler.containsMessageWith(unknownTop));
assertTrue(handler.containsMessageWith(unknownAxis));
} finally {
logger.removeHandler(handler);
logger.setLevel(previousLevel);
}
}

@Test
void v2MapperWarnsAndContinuesOnUnknownFields() {
void v2MapperLogsAndContinuesOnUnknownFields() {
String unknownEntryField = "unknown_entry_" + UUID.randomUUID();

Map<String, Object> axis = new HashMap<>();
Expand All @@ -94,9 +97,11 @@ void v2MapperWarnsAndContinuesOnUnknownFields() {
entryRaw.put("datasets", Arrays.asList(dataset));
entryRaw.put(unknownEntryField, 123);

Logger logger = Logger.getLogger(WARNING_LOGGER_NAME);
Logger logger = Logger.getLogger(HANDLER_LOGGER_NAME);
CapturingHandler handler = new CapturingHandler();
Level previousLevel = logger.getLevel();
logger.addHandler(handler);
logger.setLevel(Level.FINE);
try {
ObjectMapper mapper = OmeObjectMappers.makeV2Mapper();
MultiscalesEntry entry = mapper.convertValue(entryRaw, MultiscalesEntry.class);
Expand All @@ -105,9 +110,10 @@ void v2MapperWarnsAndContinuesOnUnknownFields() {
assertEquals(1, entry.axes.size());
assertEquals(1, entry.datasets.size());
assertFalse(entry.datasets.get(0).coordinateTransformations.isEmpty());
assertTrue(handler.containsWarningWith(unknownEntryField));
assertTrue(handler.containsMessageWith(unknownEntryField));
} finally {
logger.removeHandler(handler);
logger.setLevel(previousLevel);
}
}

Expand Down Expand Up @@ -346,12 +352,12 @@ void v3MapperParsesV06SceneMetadataRefsAndNestedTransforms() {
}

private static final class CapturingHandler extends Handler {
private final List<String> warnings = new ArrayList<>();
private final List<String> messages = new ArrayList<>();

@Override
public void publish(LogRecord record) {
if (record.getLevel().intValue() >= Level.WARNING.intValue()) {
warnings.add(record.getMessage());
if (record.getLevel().intValue() >= Level.FINE.intValue()) {
messages.add(record.getMessage());
}
}

Expand All @@ -363,9 +369,9 @@ public void flush() {
public void close() {
}

boolean containsWarningWith(String token) {
for (String warning : warnings) {
if (warning != null && warning.contains(token)) {
boolean containsMessageWith(String token) {
for (String message : messages) {
if (message != null && message.contains(token)) {
return true;
}
}
Expand Down
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