fix mapping functions for surgeries in mapping template

CanDIG / clinical_ETL_code

A library to convert clinical data in csv format into json documents for CanDIG ingestion

GNU Lesser General Public License v3.0

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fix mapping functions for surgeries in mapping template #38

Closed mshadbolt closed 1 year ago

mshadbolt commented 1 year ago

We found that the mapping functions used for

DONOR.INDEX.primary_diagnoses.INDEX.treatments.INDEX.surgeries.INDEX.margin_types_involved.INDEX
DONOR.INDEX.primary_diagnoses.INDEX.treatments.INDEX.surgeries.INDEX.margin_types_not_involved.INDEX
DONOR.INDEX.primary_diagnoses.INDEX.treatments.INDEX.surgeries.INDEX.margin_types_not_assessed.INDEX

should be pipe_delim() rather than indexed_on()

this PR fixes the issue

daisieh commented 1 year ago

I went ahead and fixed the things that we talked about...can you tell me if the instructions for how to fix the failure (that I introduced on purpose) look to you?

(Ha, I just realized that the error message links to the main branch's readme: you'll want to read the instructions in the diff in this branch: https://github.com/CanDIG/clinical_ETL_code/pull/38/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5)

mshadbolt commented 1 year ago

Thanks! I think it makes sense and nice that you explain the errors if they come up.

mshadbolt commented 1 year ago

woo passing build