Merge pull request #2231 from broadinstitute/jlc_ontology_colon_fix

Correctly allow colon separator in ontology IDs (SCP-5861)

Author: jlchang

app/javascript/lib/validation/validate-anndata.js

@@ -137,10 +137,16 @@ async function checkOntologyLabelsAndIds(key, ontologies, groups) {
   const rawUniques = Array.from(labelIdPairs)
 
   rawUniques.map(r => {
-    const [id, label] = r.split(' || ')
+    let [id, label] = r.split(' || ')
     const ontologyShortNameLc = id.split(/[_:]/)[0].toLowerCase()
     const ontology = ontologies[ontologyShortNameLc]
 
+    if (id.includes(':')) {
+      // Convert colon to underscore for ontology lookup
+      const idParts = id.split(':')
+      id = `${idParts[0]}_${idParts[1]}`
+    }
+
     if (!(id in ontology)) {
       // Register invalid ontology ID
       const msg = `Invalid ontology ID: ${id}`

test/js/lib/validate-anndata.test.js

@@ -56,6 +56,14 @@ describe('Client-side file validation for AnnData', () => {
     expect(issues).toHaveLength(0)
   })
 
+  /* TODO: Uncomment this after PR merge
+  it('Parses AnnData rows with colon ontology ID separator and detects no issues', async () => {
+    const url = `${BASE_URL}/valid_with_colon.h5ad`
+    const parseResults = await parseAnnDataFile(url)
+    expect(parseResults.issues).toHaveLength(0)
+  })
+  */
+
   it('Parses AnnData rows and reports invalid ontology IDs', async () => {
     const url = `${BASE_URL}/invalid_disease_id.h5ad`
     const parseResults = await parseAnnDataFile(url)