Merge pull request #1143 from nellh/git-hook-support

Add --filenames option to validate filenames from stdin

Author: nellh

bids-validator/bin/bids-validator

@@ -2,7 +2,7 @@
 
 process.title = 'bids-validator'
 
-var argv = require('yargs')
+const argv = require('yargs')
   .usage('Usage: $0 <dataset_directory> [options]')
   .help('help')
   .alias('help', 'h')
@@ -50,6 +50,13 @@ var argv = require('yargs')
       'Optional configuration file. See https://github.com/bids-standard/bids-validator for more info',
     default: '.bids-validator-config.json',
   })
+  .boolean('filenames')
+  .default('filenames', false)
+  .describe(
+    'filenames',
+    'A less accurate check that reads filenames one per line from stdin.',
+  )
+  .hide('filenames')
   .epilogue(
     'This tool checks if a dataset in a given directory is \
 compatible with the Brain Imaging Data Structure specification. To learn \

bids-validator/cli.js

@@ -5,7 +5,7 @@ import validate from './index.js'
 const format = validate.consoleFormat
 import colors from 'colors/safe'
 import fs from 'fs'
-import remoteFiles from './utils/files/remoteFiles'
+import { filenamesOnly } from './utils/filenamesOnly.js'
 
 const exitProcess = issues => {
   if (
@@ -51,6 +51,10 @@ export default function(dir, options) {
     process.exit(3)
   })
 
+  if (options.filenames) {
+    return filenamesOnly()
+  }
+
   if (fs.existsSync(dir)) {
     if (options.json) {
       validate.BIDS(dir, options, function(issues, summary) {

bids-validator/utils/__tests__/filenamesOnly.spec.js

@@ -0,0 +1,28 @@
+import { validateFilenames } from '../filenamesOnly.js'
+
+describe('test filenames mode', () => {
+  beforeEach(() => {
+    console.log = jest.fn()
+  })
+  it('throws an error when obviously non-BIDS input', async () => {
+    async function* badData() {
+      yield 'nope'
+      yield 'not-bids'
+      yield 'data'
+    }
+    const res = await validateFilenames(badData())
+    expect(res).toBe(false)
+  })
+  it('passes validation with a simple dataset', async () => {
+    async function* goodData() {
+      yield 'CHANGES'
+      yield 'dataset_description.json'
+      yield 'participants.tsv'
+      yield 'README'
+      yield 'sub-01/anat/sub-01_T1w.nii.gz'
+      yield 'T1w.json'
+    }
+    const res = await validateFilenames(goodData())
+    expect(res).toBe(true)
+  })
+})

bids-validator/utils/filenamesOnly.js

@@ -0,0 +1,73 @@
+/**
+ * Run validation against a list of input files from git pre-receive
+ */
+import readline from 'readline'
+import path from 'path'
+import { promisify } from 'util'
+import consoleFormat from './consoleFormat'
+import quickTest from '../validators/bids/quickTest'
+import fullTest from '../validators/bids/fullTest'
+
+// Disable most tests that might access files
+const defaultOptions = {
+  ignoreWarnings: true,
+  ignoreNiftiHeaders: true,
+  ignoreSymlinks: true,
+  ignoreSubjectConsistency: true,
+  verbose: false,
+  gitTreeMode: false,
+  remoteFiles: false,
+  gitRef: 'HEAD',
+  config: { ignore: [44], warn: [], error: [], ignoredFiles: [] },
+}
+
+async function generateFileObjects(stream) {
+  const inputFiles = {}
+  let index = 0
+  for await (const line of stream) {
+    const rootPath = `/${line}`
+    /**
+     * Simulated file object based on input
+     * File size is 1 to prevent 0 size errors but makes some checks inaccurate
+     */
+    const file = {
+      name: path.basename(line),
+      path: rootPath,
+      relativePath: rootPath,
+      size: 1,
+    }
+    inputFiles[index] = file
+    index++
+  }
+  return inputFiles
+}
+
+export async function validateFilenames(stream) {
+  const inputFiles = await generateFileObjects(stream)
+  const couldBeBIDS = quickTest(inputFiles)
+  if (couldBeBIDS) {
+    await new Promise(resolve => {
+      fullTest(inputFiles, defaultOptions, false, '/dev/null', function(
+        issues,
+        summary,
+      ) {
+        console.log(consoleFormat.issues(issues, defaultOptions) + '\n')
+        console.log(consoleFormat.summary(summary, defaultOptions))
+        resolve()
+      })
+    })
+    return true
+  } else {
+    console.log(
+      'This dataset failed a quick validation, please verify it is a BIDS dataset at the root of the git repository',
+    )
+    return false
+  }
+}
+
+export async function filenamesOnly() {
+  const rl = readline.createInterface({
+    input: process.stdin,
+  })
+  validateFilenames(rl)
+}