Closes #40. Tests won't pass until the OT PGx schema is updated, but here is a test run with validation commented out.
Git struggles with the expected test output diff, this is slightly better. Example evidence string from the test:
{
"datasourceId": "pharmgkb",
"datasourceVersion": "2023-03-23",
"datatypeId": "clinical_annotation",
"studyId": "1447979749",
"evidenceLevel": "1A",
"literature": ["29126871", "28606620", "27898234", "27898234", "25981758", "27805836", "27805836", "29327948", "29451946", "28325531", "27334259", "24973281", "24973281", "24973281", "27298017"],
"genotype": "CTT/del",
"genotypeAnnotationText": "Patients with cystic fibrosis and the rs113993960 CTT/del genotype (one copy of the CFTR F508del variant) may experience a limited benefit from treatment with the combination drug of ivacaftor/lumacaftor, as shown by improvement in sweat chloride concentrations CFQ-R questionnaire scores when compared to treatment with placebo. However, ppFEV1, BMI or body weight did not show a significant improvement following ivacaftor/lumacaftor treatment. This genotype is not an indication for use of the combination drug of ivacaftor/lumacaftor according to the FDA-approved drug label for this drug combination. Other genetic and clinical factors may also influence response to ivacaftor/lumacaftor.",
"drugsFromSource": [
"ivacaftor",
"lumacaftor"
],
"pgxCategory": "efficacy",
"phenotypeText": "Cystic Fibrosis",
"phenotypeFromSourceId": "MONDO_0009061",
"genotypeId": "21_5010011_CCTT_C,CCTT",
"variantRsId": "rs113993960"
}
Closes #40. Tests won't pass until the OT PGx schema is updated, but here is a test run with validation commented out.
Git struggles with the expected test output diff, this is slightly better. Example evidence string from the test:
FYI @DSuveges @ireneisdoomed