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config2.yaml
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mjbonifa authored
refactor: converted all examples to yaml and added test for config2. Updated readme. Fixed but in diff that assumed all csv files in map directory where map files when some where error files if no codes exists, moved error files to errors directory in the map directory to avoid this.
mjbonifa authoredrefactor: converted all examples to yaml and added test for config2. Updated readme. Fixed but in diff that assumed all csv files in map directory where map files when some where error files if no codes exists, moved error files to errors directory in the map directory to avoid this.
config2.yaml 906 B
concept_sets:
version: "v1.0.4"
omop:
vocabulary_id: "ACMC_Example"
vocabulary_name: "ACMC example phenotype"
vocabulary_reference: "https://www.it-innovation.soton.ac.uk/projects/meldb/concept-processing/example"
concept_set:
- concept_set_name: "CVD_EVENTS"
concept_set_status: "AGREED"
metadata: {}
- concept_set_name: "DID_NOT_ATTEND"
concept_set_status: "AGREED"
metadata: {}
codes:
- folder: "clinical-codes-org"
description: "Downloaded 16/11/23"
files:
- file: "Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
columns:
icd10: "code"
metadata: []
concept_set:
- "CVD_EVENTS"
- file: "Non-attendance codes/res201-did-not-attend-appointment.csv"
columns:
read2: "code"
metadata: []
concept_set:
- "DID_NOT_ATTEND"