test: fixed tests as config1 and config2 needed updating with the latest config format. Closes #32

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"
+
 

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"
 

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):