Backport gh-2054

metaschema: Require additional_columns field for tables
schema: Define missing additional columns
fix: Add initial_columns to blood.tsv rule to match spec

Author: effigies

src/metaschema.json

@@ -634,15 +634,16 @@
               "additionalProperties": false
             },
             "additional_columns": {
-              "type": "string"
+              "type": "string",
+              "enum": ["allowed", "allowed_if_defined", "not_allowed", "n/a"]
             },
             "index_columns": { "type": "array", "items": { "type": "string" } },
             "initial_columns": {
               "type": "array",
               "items": { "type": "string" }
             }
           },
-          "required": ["selectors", "columns"],
+          "required": ["selectors", "columns", "additional_columns"],
           "additionalProperties": false
         }
       }

src/schema/rules/tabular_data/derivatives/common_derivatives.yaml

@@ -10,6 +10,7 @@ SegmentationLookup:
     color: optional
     mapping: optional
   index_columns: [index]
+  additional_columns: allowed
 
 Descriptions:
   selectors:

src/schema/rules/tabular_data/pet.yaml

@@ -4,6 +4,7 @@ Blood:
     - datatype == "pet"
     - suffix == "blood"
     - extension == ".tsv"
+  initial_columns: [time]
   columns:
     time: required
     plasma_radioactivity:
@@ -21,6 +22,7 @@ Blood:
     whole_blood_radioactivity:
       level: optional
       level_addendum: required if `WholeBloodAvail` is `true`
+  additional_columns: allowed
 
 BloodPlasma:
   selectors:
@@ -30,6 +32,7 @@ BloodPlasma:
     - sidecar.PlasmaAvail == true
   columns:
     plasma_radioactivity: required
+  additional_columns: n/a
 
 BloodMetabolite:
   selectors:
@@ -40,6 +43,7 @@ BloodMetabolite:
   columns:
     metabolite_parent_fraction: required
     metabolite_polar_fraction: recommended
+  additional_columns: n/a
 
 BloodMetaboliteCorrection:
   selectors:
@@ -49,6 +53,7 @@ BloodMetaboliteCorrection:
     - sidecar.MetaboliteRecoveryCorrectionApplied == true
   columns:
     hplc_recovery_fractions: required
+  additional_columns: n/a
 
 BloodWholeBlood:
   selectors:
@@ -58,3 +63,4 @@ BloodWholeBlood:
     - sidecar.WholeBloodAvail == true
   columns:
     whole_blood_radioactivity: required
+  additional_columns: n/a