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Migrate staging changes into main #461

Merged
merged 10 commits into from
Mar 9, 2025
Merged

Migrate staging changes into main #461

merged 10 commits into from
Mar 9, 2025
+2,688 −1,160

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korikuzma
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@korikuzma
feat!: add support for transforming concepts that fail to normalize (#…
325b5ee 
…427)

close #417 

* This adds support for transforming concepts (such as gene, variant,
disease, and therapy) that fail to normalize.
* Since this work is mainly needed for ClinVar Submission work, this is
*only* focused on adding support in CDM files generated by the
Transformers. The database will NOT load statements that fail to
normalize concepts, and therefore the QueryHandler is unable to search
on these non-normalizable concepts.
* Concepts that fail to normalize will have the following `Extension`:
`{"name": "vicc_normalizer_failure", "value": True}`
* Since MOA does not have record IDs for some objects, the IDs used in
these cases will be `f"moa.{therapy|disease|gene}:{name}"`, where name
is the MOA label for the concept where whitespace characters are
replaced with underscores.
@korikuzma
fix!: resolve conflicts where moa therapies resolve to same concept (#…
6041697 
…429)

close #426

* If conflict occurs, the min label will be used as the primary label
for the mappable concept, and the other label will be added as an alias
in extensions
@korikuzma
feat!: moa disease conflict resolution should follow therapy conflict…
ac92bef 
… resolution (#430)
@korikuzma
build!: update vicc normalizers to pull in gks coding changes (#432)
4a89557 
close #423
@korikuzma
chore: add acceptance criteria to issue templates (#458)
ba2cc76 
close #453
@korikuzma
feat!: use system identifiers from source for normalization (#433)
18b8124 
close #431 

* Rather than returning the highest match for a list of queries, use
system identifiers for source
* Input is now a single query, rather than a list
@korikuzma
build!: update gks and normalizer versions (#434)
18b1087 
* Update to GKS Feb 2025 pre-release 
  * `label` -> `name`
  * Resolve places where we were adding extra attributes to models
@korikuzma
test: update test data (#435)
2f39406
@korikuzma
feat!: change civic classification.primaryCode to use clinvar enum (#…
add4368 
…455)

close #452

* Use ClinVar Submission `clinicalImpactClassificationDescription` enum
@korikuzma
fix: store variation aliases in aliases not extensions (#460)
c6ef41e 
close #459
@korikuzma korikuzma added the priority:low Low priority label Mar 9, 2025
@korikuzma korikuzma self-assigned this Mar 9, 2025
@korikuzma korikuzma merged commit 0247270 into main Mar 9, 2025
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