Bug fix to prevent an issue mapping a single FHIR resource from crash… #1398
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…ing the whole pipeline.
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| @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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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.
| 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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| log.error(errorMsg); | |
| log.error(errorMsg, e); |
| } | ||
| */ | ||
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| // Catch any RuntimeException and log the error instead of crashing the whole pipeline for an issue with one FHIR resource. |
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Please move this comment inside the function; this does not really document what the function does.
| return converterMap.get(resourceType); | ||
| } | ||
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| /* |
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Please remove this older version.
2 participants
Description of what I changed
Changed the convertToAvro() method in AvroConversionUtil.java to catch any RuntimeException errors while processing a given FHIR resource and logging the error instead of allowing a single mapping issue to crash the entire pipeline.
E2E test
TESTED:
I posted an eICR FHIR document (converted to a transaction Bundle) to my FHIR server and re-ran the pipeline. Before my change this crashed the pipeline. After my change it ran successfully and logged an error in a single FHIR resource that included dataAbsentReason extensions, which seem to not be mapped currently.
Checklist: I completed these to help reviewers :)
[X ] I have read and will follow the review process.
I am familiar with Google Style Guides for the language I have coded in.
No? Please take some time and review Java and Python style guides.
My IDE is configured to follow the Google code styles.
No? Unsure? -> configure your IDE.
I have added tests to cover my changes. (If you refactored existing code that was well tested you do not have to add tests)
I ran
mvn clean packageright before creating this pull request and added all formatting changes to my commit.All new and existing tests passed.
My pull request is based on the latest changes of the master branch.
No? Unsure? -> execute command
git pull --rebase upstream master