From d42cf541691af9aef06b5eaff54027825bf01927 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Mon, 24 Feb 2025 14:49:41 +0000
Subject: [PATCH] test: fixed tests as config1 and config2 needed updating with
the latest config format. Closes #32
---
examples/config1.yaml | 4 ++--
examples/config2.yaml | 6 ++----
tests/test_acmc.py | 1 +
3 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/examples/config1.yaml b/examples/config1.yaml
index 964f15c..f8c21bc 100644
--- a/examples/config1.yaml
+++ b/examples/config1.yaml
@@ -6,7 +6,6 @@ concept_sets:
vocabulary_reference: "https://git.soton.ac.uk/meldb/concepts-processing/-/tree/main/examples"
concept_set:
- concept_set_name: "ABDO_PAIN"
- concept_set_status: "AGREED"
metadata: {}
codes:
@@ -19,5 +18,6 @@ codes:
metadata:
- "description"
concept_set:
- - "ABDO_PAIN"
+ - name: "ABDO_PAIN"
+
diff --git a/examples/config2.yaml b/examples/config2.yaml
index ee36425..ccf2839 100644
--- a/examples/config2.yaml
+++ b/examples/config2.yaml
@@ -6,10 +6,8 @@ concept_sets:
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:
@@ -21,11 +19,11 @@ codes:
icd10: "code"
metadata: []
concept_set:
- - "CVD_EVENTS"
+ - name: "CVD_EVENTS"
- file: "Non-attendance codes/res201-did-not-attend-appointment.csv"
columns:
read2: "code"
metadata: []
concept_set:
- - "DID_NOT_ATTEND"
+ - name: "DID_NOT_ATTEND"
diff --git a/tests/test_acmc.py b/tests/test_acmc.py
index 3548a1d..e70fc0a 100644
--- a/tests/test_acmc.py
+++ b/tests/test_acmc.py
@@ -51,6 +51,7 @@ def test_phen_init_local_specified(tmp_dir, monkeypatch, caplog):
[
("config1.yaml"), # config.yaml test case
("config2.yaml"), # config.yaml test case
+ ("config3.yaml"), # config.yaml test case
],
)
def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
--
GitLab