Open alisman opened 3 days ago
We get the sampleId
for Clinical Data from clinical_data_derived
,
and we get the sampleId
for clinical_data_derived
from sample_derived
.
In the sample_derived
we construct the sample unique id
by adding the study id in front of the sample stable id
Legacy implementation, on the other hand, just uses stable ids when generating the clinical data.
This is why we end up with sample ids like skcm_mskcc_2014_CR04885
in the clickhouse implementation instead of CR04885
.
Modifying the getSampleClinicalDataFromStudyViewFilter mapper to use the stable id instead of the unique id should fix this discrepancy, but we need to make sure that it doesn't break something else.
@onursumer just adding what i think you already know that the problem is in convertPatientClinicalDataToSampleClinicalData where we lose data presumably because of overlapping ids or something.
@onursumer i'm seeing a discrepancy in the sample ids in the response. Looks like counts are matching.
Clickhouse:
Legacy