fix: update civic test fixtures + re-run make all #243
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| relation: exactMatch | ||
| primaryCode: IA | ||
| hasEvidenceLines: | ||
| - directionOfEvidenceProvided: supports |
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@ahwagner This is a required property. I think for CIViC, it would always be supports?
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Yes, for AMP/ASCO/CAP
| systemVersion: "2017" | ||
| relation: exactMatch | ||
| primaryCode: IA | ||
| hasEvidenceLines: |
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@ahwagner I only included hasEvidenceItems and directionOfEvidenceProvided for CIViC. Wasn't sure if you wanted to include any of the following fields that an Evidence Line has: targetProposition, strengthOfEvidenceProvided, scoreOfEvidenceProvided, or evidenceOutcome.
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I'm also realizing that I only created a single evidence line for ALL evidence items. But maybe I was supposed to do 1:1 for evidence line to evidence item?
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I'm also realizing that I only created a single evidence line for ALL evidence items. But maybe I was supposed to do 1:1 for evidence line to evidence item?
Ended up doing 1:1
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@ahwagner This is a nested example. I'm not sure how you would want to do an inline example using iriReferences
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Also we're missing Date last evaluated for ClinVar submission
Required, if available: date the classification of the variant was last evaluated by the submitter (not the date the patient was evaluated in the clinic). If not available, leave blank. If only month/year is provided we will convert it to the first day of the month. If only year is provided it will be converted to the first day of the first month of the year. Please use the format yyyy-mm-dd.
It's optional, but not sure if civicpy captures this information
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AW: We should add this support in civicpy
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For now, we can just have civicpy query civic graphql api for now rather than adding this in the cache.pkl
| @@ -557,7 +557,6 @@ $defs: | |||
| ordered: false | |||
| items: | |||
| anyOf: | |||
| - $ref: "#/$defs/StudyResult" | |||
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@ga4gh/va-admin I removed this. I was getting jsonschema.exceptions._WrappedReferencingError: Unresolvable: /ga4gh/schema/va-spec/1.0.0-ballot.2024-11.2/base/json/StudyResult since this seems to be an abstract class.
tests/fixtures/civic_fusion.yaml
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Example of how we will represent molecular profiles that cannot be normalized
Keeping this as a draft for now. This is how we will be transforming CIViC evidence and assertion records to GKS compatible objects in MetaKB.