From 8fe19073cc045dce2ec76f1e1d323b00f829e848 Mon Sep 17 00:00:00 2001
From: Jakub Dylag <jjd1c23@soton.ac.uk>
Date: Fri, 28 Mar 2025 18:22:38 +0000
Subject: [PATCH] Allow multiple files per concept set - update yaml examples
---
examples/config1.yml | 10 ++++-----
examples/config2.yml | 18 ++++++++---------
examples/config3.yml | 48 ++++++++++++++++++++------------------------
3 files changed, 34 insertions(+), 42 deletions(-)
diff --git a/examples/config1.yml b/examples/config1.yml
index 2709d3f..12f0fd7 100644
--- a/examples/config1.yml
+++ b/examples/config1.yml
@@ -8,10 +8,8 @@ phenotype:
- "read2"
- "read3"
concept_sets:
- - name: "ABDO_PAIN"
- file:
- path: "clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv"
+ - name: ABDO_PAIN
+ files:
+ - path: clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv
columns:
- read2: "code"
- metadata: {}
-
+ read2: code
diff --git a/examples/config2.yml b/examples/config2.yml
index 4a9ad79..f7f3d03 100644
--- a/examples/config2.yml
+++ b/examples/config2.yml
@@ -8,15 +8,13 @@ phenotype:
- "read2"
- "read3"
concept_sets:
- - name: "CVD_EVENTS"
- file:
- path: "clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
+ - name: "CVD_EVENTS"
+ files:
+ - path: "clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
columns:
- icd10: "code"
- metadata: {}
- - name: "DID_NOT_ATTEND"
- file:
- path: "clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv"
+ icd10: "code"
+ - name: "DID_NOT_ATTEND"
+ files:
+ - path: "clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv"
columns:
- read2: "code"
- metadata: {}
\ No newline at end of file
+ read2: "code"
\ No newline at end of file
diff --git a/examples/config3.yml b/examples/config3.yml
index 2e07427..7cb84f0 100644
--- a/examples/config3.yml
+++ b/examples/config3.yml
@@ -10,33 +10,29 @@ phenotype:
- "snomed"
concept_sets:
- name: "CVD_EVENTS"
- file:
- path: "clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
- columns:
- icd10: "code"
- metadata: {}
+ files:
+ - path: "clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
+ columns:
+ icd10: "code"
- name: "DID_NOT_ATTEND"
- file:
- path: "clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv"
- columns:
- read2: "code"
- metadata: {}
+ files:
+ - path: "clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv"
+ columns:
+ read2: "code"
- name: "HYPERTENSION"
- file:
- path: "hanlon/Read_codes_for_diagnoses.csv"
- columns:
- read2: "Read Code"
- category: "2"
- actions:
- divide_col: "MMCode"
- metadata: {}
+ files:
+ - path: "hanlon/Read_codes_for_diagnoses.csv"
+ columns:
+ read2: "Read Code"
+ category: "2"
+ actions:
+ divide_col: "MMCode"
- name: "DEPRESSION"
- file:
- path: "hanlon/Read_codes_for_diagnoses.csv"
- columns:
- read2: "Read Code"
- category: "3"
- actions:
- divide_col: "MMCode"
- metadata: {}
+ files:
+ - path: "hanlon/Read_codes_for_diagnoses.csv"
+ columns:
+ read2: "Read Code"
+ category: "3"
+ actions:
+ divide_col: "MMCode"
--
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