Merge pull request #2116 from rwblair/feat/citationcff

feat: Validate CITATION.cff

Author: effigies

bids-validator/build.ts

@@ -27,7 +27,7 @@ const flags = parse(Deno.args, {
 
 const version = await getVersion()
 
-let versionPlugin = {
+const versionPlugin = {
   name: 'version',
   setup(build: esbuild.PluginBuild) {
     build.onResolve({ filter: /\.git-meta\.json/ }, (args) => ({
@@ -46,7 +46,7 @@ const result = await esbuild.build({
   format: 'esm',
   entryPoints: [MAIN_ENTRY, CLI_ENTRY],
   bundle: true,
-  outdir: path.join('dist','validator'),
+  outdir: path.join('dist', 'validator'),
   minify: flags.minify,
   target: ['chrome109', 'firefox109', 'safari16'],
   plugins: [

bids-validator/deno.json

@@ -27,20 +27,21 @@
     ]
   },
   "imports": {
+    "@ajv": "npm:ajv@8.16.0",
+    "@bids/schema": "jsr:@bids/schema@0.11.2-dev.2+7f1f6737",
+    "@cliffy/command": "jsr:@cliffy/command@1.0.0-rc.5",
+    "@cliffy/table": "jsr:@cliffy/table@1.0.0-rc.5",
+    "@hed/validator": "npm:hed-validator@3.15.4",
+    "@ignore": "npm:ignore@5.3.2",
+    "@libs/xml": "jsr:@libs/xml@5.4.13",
+    "@mango/nifti": "npm:nifti-reader-js@0.6.8",
     "@std/assert": "jsr:@std/assert@1.0.2",
     "@std/fmt": "jsr:@std/fmt@1.0.0",
     "@std/fs": "jsr:@std/fs@1.0.1",
     "@std/io": "jsr:@std/io@0.224.4",
     "@std/log": "jsr:@std/log@0.224.5",
     "@std/path": "jsr:@std/path@1.0.2",
-    "@ajv": "npm:ajv@8.16.0",
-    "@bids/schema": "jsr:@bids/schema@0.11.1-dev.4+a73c1b06",
-    "@cliffy/table": "jsr:@cliffy/table@1.0.0-rc.5",
-    "@cliffy/command": "jsr:@cliffy/command@1.0.0-rc.5",
-    "@hed/validator": "npm:hed-validator@3.15.4",
-    "@ignore": "npm:ignore@5.3.2",
-    "@mango/nifti": "npm:nifti-reader-js@0.6.8",
-    "@libs/xml": "jsr:@libs/xml@5.4.13"
+    "@std/yaml": "jsr:@std/yaml@^1.0.4"
   },
   "tasks": {
     "test": "deno test -A src/tests/"

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/setup/loadSchema.test.ts

@@ -1,7 +1,7 @@
 import { assert, assertObjectMatch } from '@std/assert'
 import { loadSchema } from './loadSchema.ts'
 
-Deno.test('schema yaml loader', async (t) => {
+Deno.test('schema loader', async (t) => {
   await t.step('reads in top level files document', async () => {
     const schemaDefs = await loadSchema()
     // Look for some stable fields in top level files

bids-validator/src/validators/bids.ts

@@ -17,6 +17,7 @@ import { sidecarWithoutDatafile, unusedStimulus } from './internal/unusedFile.ts
 import { type BIDSContext, BIDSContextDataset } from '../schema/context.ts'
 import type { parseOptions } from '../setup/options.ts'
 import { hedValidate } from './hed.ts'
+import { citationValidate } from './citation.ts'
 
 /**
  * Ordering of checks to apply
@@ -32,6 +33,7 @@ const perContextChecks: ContextCheckFunction[] = [
 const perDSChecks: DSCheckFunction[] = [
   unusedStimulus,
   sidecarWithoutDatafile,
+  citationValidate,
 ]
 
 /**

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

@@ -0,0 +1,27 @@
+import { assert } from '@std/assert'
+import { pathsToTree } from '../files/filetree.ts'
+import { BIDSFileDeno } from '../files/deno.ts'
+import { citationValidate } from './citation.ts'
+import { BIDSContextDataset } from '../schema/context.ts'
+import { GenericSchema } from '../types/schema.ts'
+import { loadSchema } from '../setup/loadSchema.ts'
+
+Deno.test('citation validation', async (t) => {
+  const schema = await loadSchema()
+  await t.step('no errors on the good citation.cff', async () => {
+    const tree = pathsToTree(['CITATION.cff'])
+    const dsContext = new BIDSContextDataset({ tree })
+    const file = new BIDSFileDeno('tests/data/citation', 'good.cff')
+    tree.files[0].text = () => file.text()
+    await citationValidate({} as GenericSchema, dsContext)
+    assert(dsContext.issues.size === 0)
+  })
+  await t.step('An error on the bad citation.cff', async () => {
+    const tree = pathsToTree(['CITATION.cff'])
+    const dsContext = new BIDSContextDataset({ tree })
+    const file = new BIDSFileDeno('tests/data/citation', 'bad.cff')
+    tree.files[0].text = () => file.text()
+    await citationValidate({} as GenericSchema, dsContext)
+    assert(dsContext.issues.get({ code: 'CITATION_CFF_VALIDATION_ERROR' }).length === 1)
+  })
+})

bids-validator/src/validators/citation.ts

@@ -0,0 +1,39 @@
+import type { GenericSchema } from '../types/schema.ts'
+import type { BIDSFile, FileTree } from '../types/filetree.ts'
+import type { BIDSContextDataset } from '../schema/context.ts'
+import { schema as citationSchema } from '@bids/schema/citation'
+import { compile } from './json.ts'
+import type { DefinedError } from '@ajv'
+import { parse } from '@std/yaml'
+
+const citationFilename = 'CITATION.cff'
+
+export async function citationValidate(
+  schema: GenericSchema,
+  dsContext: BIDSContextDataset,
+) {
+  const citationFile = dsContext.tree.get(citationFilename)
+  if (!citationFile || 'directories' in citationFile) return
+  let citation: unknown = {}
+  try {
+    citation = parse(await citationFile.text())
+  } catch (error) {
+    dsContext.issues.add({
+      code: 'FILE_READ',
+      issueMessage: `Error from attempted read of file:\n${error}`,
+      location: citationFilename,
+    })
+    return
+  }
+  const validate = compile(citationSchema)
+  if (!validate(citation)) {
+    for (const err of validate.errors as DefinedError[]) {
+      dsContext.issues.add({
+        code: 'CITATION_CFF_VALIDATION_ERROR',
+        subCode: err['instancePath'],
+        issueMessage: err['message'],
+        location: citationFilename,
+      })
+    }
+  }
+}

bids-validator/tests/data/citation/bad.cff

@@ -0,0 +1,15 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+title: My Research Software
+abstract: This is my awesome research software. It does many things.
+version: 0.11.2
+date-released: "2021-07-18"
+identifiers:
+  - description: This is the collection of archived snapshots of all versions of My Research Software
+    type: doi
+    value: "10.5281/zenodo.123456"
+  - description: This is the archived snapshot of version 0.11.2 of My Research Software
+    type: doi
+    value: "10.5281/zenodo.123457"
+license: Apache-2.0
+repository-code: "https://github.com/citation-file-format/my-research-software"

bids-validator/tests/data/citation/good.cff

@@ -0,0 +1,20 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+title: My Research Software
+abstract: This is my awesome research software. It does many things.
+authors:
+  - family-names: Druskat
+    given-names: Stephan
+    orcid: "https://orcid.org/1234-5678-9101-1121"
+  - name: "The Research Software project"
+version: 0.11.2
+date-released: "2021-07-18"
+identifiers:
+  - description: This is the collection of archived snapshots of all versions of My Research Software
+    type: doi
+    value: "10.5281/zenodo.123456"
+  - description: This is the archived snapshot of version 0.11.2 of My Research Software
+    type: doi
+    value: "10.5281/zenodo.123457"
+license: Apache-2.0
+repository-code: "https://github.com/citation-file-format/my-research-software"