feat: extend OncoTree metadata in database and models (#11993)#11997
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Annu881 wants to merge 2 commits intocBioPortal:masterfrom
Open
feat: extend OncoTree metadata in database and models (#11993)#11997Annu881 wants to merge 2 commits intocBioPortal:masterfrom
Annu881 wants to merge 2 commits intocBioPortal:masterfrom
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Fix #11993
Describe changes proposed in this pull request:
This PR extends the OncoTree metadata support in the
type_of_cancertable by adding additional fields to store versioning and status information. This enables better handling of deprecated or historical OncoTree codes.Changes include:
type_of_cancertable to include the following columns:VERSIONSTATUSHISTORYURIImplemented for both MySQL and ClickHouse schemas.
TypeOfCancer(legacy domain model)CancerType(application model)StudyMapper.xmlCancerStudyMapper.xmlCancerStudyMetadataMapper.xmlClickhouseCancerStudyMapper.xmlAdded a MySQL migration script:
Updated test seed data with sample OncoTree metadata:
seed_mini.sqlclickhouse_data_legacy.sqlThis allows storing structured OncoTree metadata such as version history and status information, which can help support deprecated OncoTree codes and improve data traceability.
Checks
Verified with:
CancerTypeMyBatisRepositoryTestCancerTypeServiceImplTestCancerStudyMetadataExporterTestsTested using Java 21
Yes — OncoTree metadata fields (
VERSION,STATUS,HISTORY,URI) are clinical classification metadata.Recommended label: feature
Any screenshots or GIFs?
N/A (Backend change)
Notify reviewers
@inodb @sheridancbio @YashhCanCode