Add validation check for CT/1 having a CL ID

hubmapconsortium · Sep 6, 2023 · 70a9c17 · 70a9c17
1 parent a44835c
commit 70a9c17
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Showing 3 changed files with 11 additions and 3 deletions.
diff --git a/asctb-api/scripts/generate-draft-validation-reports.js b/asctb-api/scripts/generate-draft-validation-reports.js
@@ -43,6 +43,7 @@ async function getData(draftItems) {
       "Missing Uberon or CL IDs?",
       "Unmapped Data found?",
       "Bad Column found?",
+      "CT/1 has CL ID?"
     ],
   ];
   const workbook = XLSX.utils.book_new();
@@ -65,7 +66,7 @@ async function getData(draftItems) {
         title,
         ...data
           .split("\n")
-          .slice(0, 8)
+          .slice(0, rows[0].length - 1)
           .map((d) => {
             const status = d.slice(-6);
             return status === "passed" ? checkmark : crossmark;
@@ -85,6 +86,7 @@ async function getData(draftItems) {
         crossmark,
         crossmark,
         crossmark,
+        crossmark,
       ]);
       console.log(
         "Invalid CSV!",

diff --git a/asctb-api/src/functions/api.functions.ts b/asctb-api/src/functions/api.functions.ts
@@ -208,6 +208,10 @@ function checkMissingIds(column: string[], index: number, row: Row, value: strin
         const colName = columnIndexToName(index-1);
         warnings.add(`WARNING: Missing RDFS Label for ID ${idValue} at Column: ${colName}, Row: ${row.rowNumber+1} (Code ${WarningCode.MissingCTorAnatomy})`);
       }
+      if (column.join('/') == 'CT/1/ID' && (!idValue || !idValue.startsWith('CL:'))) {
+        const colName = columnIndexToName(index);
+        warnings.add(`WARNING: CT/1/ID is not a CL ID (required) at Column: ${colName}, Row: ${row.rowNumber+1} (Code ${WarningCode.NoIdInCT1})`);
+      }
     }
   }
 }

diff --git a/asctb-api/src/utils/warnings.ts b/asctb-api/src/utils/warnings.ts
@@ -8,7 +8,8 @@ export enum WarningCode {
   InvalidCharacter = 5,
   MissingCTorAnatomy = 6,
   UnmappedData = 7,
-  BadColumn = 8
+  BadColumn = 8,
+  NoIdInCT1 = 9
 }
 
 export const WarningLabels = {
@@ -19,5 +20,6 @@ export const WarningLabels = {
   [WarningCode.InvalidCharacter]: 'Invalid Character found?',
   [WarningCode.MissingCTorAnatomy]: 'Missing Uberon or CL IDs?',
   [WarningCode.UnmappedData]: 'Unmapped Data found?',
-  [WarningCode.BadColumn]: 'Bad Column found?'
+  [WarningCode.BadColumn]: 'Bad Column found?',
+  [WarningCode.NoIdInCT1]: 'CT/1 has CL ID?',
 };