add file read issues, have citation.ts report it when applicable.

Author: rwblair

bids-validator/src/issues/list.ts

@@ -162,6 +162,20 @@ export const bidsIssues: IssueDefinitionRecord = {
     severity: 'error',
     reason: 'A json sidecar file was found without a corresponding data file',
   },
+  BLACKLISTED_MODALITY: {
+    severity: 'error',
+    reason: 'The modality in this file is blacklisted through validator configuration.',
+  },
+  CITATION_CFF_VALIDATION_ERROR: {
+    severity: 'error',
+    reason: 
+      "The file does not pass validation using the citation.cff standard's schema." +
+      'https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md'
+  },
+  FILE_READ: {
+    severity: 'error',
+    reason: 'We were unable to read this file.'
+  }
 }
 
 const hedIssues: IssueDefinitionRecord = {
@@ -191,10 +205,6 @@ const hedIssues: IssueDefinitionRecord = {
     reason:
       "You should define 'HEDVersion' for this file. If you don't provide this information, the HED validation will use the latest version available.",
   },
-  BLACKLISTED_MODALITY: {
-    severity: 'error',
-    reason: 'The modality in this file is blacklisted through validator configuration.',
-  },
 }
 
 export const hedOldToNewLookup: Record<number, Partial<keyof IssueDefinitionRecord>> = {

bids-validator/src/validators/citation.test.ts

@@ -20,6 +20,6 @@ Deno.test('citation validation', async (t) => {
     const file = new BIDSFileDeno('tests/data/citation', 'bad.cff')
     tree.files[0].text = () => file.text()
     await citationValidate({} as GenericSchema, dsContext)
-    assert(dsContext.issues.size === 1)
+    assert(dsContext.issues.get({ code: 'CITATION_CFF_VALIDATION_ERROR' }).length === 1)
   })
 })

bids-validator/src/validators/citation.ts

@@ -18,7 +18,11 @@ export async function citationValidate(
   try {
     citation = parse(await citationFile.text())
   } catch (error) {
-    throw error
+    dsContext.issues.add({
+      code: 'FILE_READ',
+      issueMessage: `Error from attempted read of file:\n${error}`,
+      location: citationFilename,
+    })
     return
   }
   const validate = compile(citationSchema)