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Bug fix: validationReport interpretation fix (#85)
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Stack trace:

```
com.fasterxml.jackson.databind.exc.MismatchedInputException: Cannot construct instance of `java.util.LinkedHashMap` (although at least one Creator exists): no String-argument constructor/factory method to deserialize from String value ('{"fastQs":"missing","igoComplete":"false"}')
 at [Source: REDACTED (`StreamReadFeature.INCLUDE_SOURCE_IN_LOCATION` disabled); line: 1, column: 1]
	at com.fasterxml.jackson.databind.exc.MismatchedInputException.from(MismatchedInputException.java:63) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.DeserializationContext.reportInputMismatch(DeserializationContext.java:1754) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.DeserializationContext.handleMissingInstantiator(DeserializationContext.java:1379) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.deser.std.StdDeserializer._deserializeFromString(StdDeserializer.java:311) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:454) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:32) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.deser.DefaultDeserializationContext.readRootValue(DefaultDeserializationContext.java:342) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4905) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3848) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3816) ~[jackson-databind-2.17.2.jar!/:2.17.2]
	at org.mskcc.smile.service.impl.CmoLabelGeneratorServiceImpl.generateValidationReport(CmoLabelGeneratorServiceImpl.java:630) ~[!/:0.1.0]
	at org.mskcc.smile.service.impl.LabelGenMessageHandlingServiceImpl$CmoLabelGeneratorHandler.run(LabelGenMessageHandlingServiceImpl.java:319) ~[!/:0.1.0]
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) ~[na:na]
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) ~[na:na]
	at java.base/java.lang.Thread.run(Thread.java:1583) ~[na:na]
```

Signed-off-by: Angelica Ochoa <[email protected]>
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ao508 authored Dec 2, 2024
1 parent e73de9f commit 51c91be
Showing 1 changed file with 2 additions and 2 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -623,8 +623,8 @@ public String generateValidationReport(String originalJson, String filteredJson,
Map.class);
Map<String, String> sampleValidationReport = new HashMap<>();
if (!sampleStatusMap.get("validationReport").toString().equals("{}")) {
sampleValidationReport =
mapper.convertValue(sampleStatusMap.get("validationReport"), Map.class);
sampleValidationReport = mapper.readValue(
sampleStatusMap.get("validationReport").toString(), Map.class);
}

try {
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