diff --git a/examples/config1.yaml b/examples/config1.yaml index 964f15c55846fccdb63a2487408021e7603279b2..f8c21bc050f5bd28970751d59a456b0815f16550 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 ee36425dfd69776fd450857132169c11f9f3dae4..ccf2839a3fde7362c213fa0022895a872c60e0ee 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 3548a1d14362295d5a41d88e6181051a2c52ea06..e70fc0aef14e000f8570c7f91a0a3fb2feb695b8 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):