refactor to have individuals and cohorts, and enable variant interpretation on one individual or a cohort (PR on a PR) #5230
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…tation on one individual or a cohort
mswertz
commented
Jul 17, 2025
| @@ -0,0 +1,13 @@ | |||
| package org.molgenis.emx2.datamodels; | |||
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this is just a test runner, I suppose handy right if we want to quickly test run
mswertz
commented
Jul 17, 2025
| @@ -197,18 +197,22 @@ public TableMetadata getRefTable() { | |||
| } | |||
| } | |||
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| TableMetadata result = null; | |||
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these fixes are to capture null exceptions. Could be seperate PR
mswertz
commented
Jul 17, 2025
data/_models/shared/Analyses.csv
Outdated
| Variant intepretation analyses,Analyses,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C25391,Genome diagnostic variant interpretation analysis,Patient registry |
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renamed to Variant interpretation analyses. And then you can see that interpretation can be either on individual or cohort. Is that nice or crazy?
mswertz
commented
Jul 17, 2025
| @@ -2,7 +2,7 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,ref | |||
| Processes,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C29862,"An event (e.g., a sequencing run, a clinical observation) that belongs to an individual","Patient registry, FAIR Genomes" | |||
| Processes,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C29862,"An event (e.g., a sequencing run, a clinical observation) that belongs to an individual","Patient registry, FAIR Genomes" | |||
| Processes,,id,auto_id,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C25364,"One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing","Patient registry, FAIR Genomes" | |||
| Processes,,individuals,ref_array,,,,Individuals,,,,http://purl.obolibrary.org/obo/NCIT_C164337,A reference to one or more individuals associated to the process,"Patient registry, FAIR Genomes" | |||
| Processes,,individual,ref,,,,Individuals,,,,http://purl.obolibrary.org/obo/NCIT_C164337,A reference to one or more individuals associated to the process,"Patient registry, FAIR Genomes" | |||
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should discuss if we want to make this also work on cohorts. But then 'consent' is a bit weird to model as process??
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btw what is difference between Analysis and Process?
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mswertz
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Note, this is a PR on another PR not on master.