Allow multiple files per concept set - update yaml examples

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

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

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"