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Bug fix to prevent an issue mapping a single FHIR resource from crash… #1398

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Bug fix to prevent an issue mapping a single FHIR resource from crash… #1398

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Bug fix to prevent an issue mapping a single FHIR resource from crash…
rgeimer Jun 25, 2025
d291647
Merge branch 'google:master' into master
rgeimer Jul 11, 2025
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17 changes: 17 additions & 0 deletions pipelines/common/src/main/java/com/google/fhir/analytics/AvroConversionUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -151,12 +151,29 @@ synchronized AvroConverter getConverter(String resourceType) throws ProfileExcep
return converterMap.get(resourceType);
}

/*
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@bashir2 bashir2 Jul 17, 2025

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Please remove this older version.

@VisibleForTesting
@Nullable GenericRecord convertToAvro(Resource resource) throws ProfileException {
AvroConverter converter = getConverter(resource.getResourceType().name());
// TODO: Check why Bunsen returns IndexedRecord instead of GenericRecord.
return (GenericRecord) converter.resourceToAvro(resource);
}
*/

// Catch any RuntimeException and log the error instead of crashing the whole pipeline for an issue with one FHIR resource.
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@bashir2 bashir2 Jul 17, 2025

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Please move this comment inside the function; this does not really document what the function does.

@VisibleForTesting
@Nullable GenericRecord convertToAvro(Resource resource) throws ProfileException {
AvroConverter converter = getConverter(resource.getResourceType().name());
// TODO: Check why Bunsen returns IndexedRecord instead of GenericRecord.
GenericRecord gr = null;
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@bashir2 bashir2 Jul 17, 2025

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Please make sure that you run mvn clean package and include the formatting changes after that in the PR. There are some style issues in these lines which should be fixed by that.

try {
gr = (GenericRecord) converter.resourceToAvro(resource);
} catch (RuntimeException e) {
String errorMsg = "Unable to process resource " + resource.getResourceType().name() + "/" + resource.getId() + ": " + e.toString();
log.error(errorMsg);
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@bashir2 bashir2 Jul 17, 2025

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Suggested change
log.error(errorMsg);
log.error(errorMsg, e);

}
return gr;
}

@VisibleForTesting
Resource convertToHapi(GenericRecord record, String resourceType) throws ProfileException {
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