Merge pull request #2131 from rwblair/feat/output_to_file

Add option to write validation results to file.

bids-validator/src/files/nifti.ts

@@ -1,6 +1,6 @@
 import { isCompressed, readHeader } from '@mango/nifti'
 import type { BIDSFile } from '../types/filetree.ts'
-import type { logger } from '../utils/logger.ts'
+import { logger } from '../utils/logger.ts'
 import type { NiftiHeader } from '@bids/schema/context'
 
 async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array> {
@@ -29,9 +29,12 @@ async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array>
 
 function readHeaderQuiet(buf: ArrayBuffer) {
   const console_error = console.error
-  console.error = () => {}
+  const console_log = console.log
+  console.error = (msg: string) => { logger.info(msg)}
+  console.log = (msg: string) => { logger.info(msg)}
   const header = readHeader(buf)
   console.error = console_error
+  console.log = console_log
   return header
 }
 

bids-validator/src/main.ts

@@ -5,7 +5,7 @@ import { readFileTree } from './files/deno.ts'
 import { fileListToTree } from './files/browser.ts'
 import { resolve } from '@std/path'
 import { validate } from './validators/bids.ts'
-import { consoleFormat } from './utils/output.ts'
+import { consoleFormat, resultToJSONStr } from './utils/output.ts'
 import { setupLogging } from './utils/logger.ts'
 import type { ValidationResult } from './types/validation-result.ts'
 
@@ -27,26 +27,24 @@ export async function main(): Promise<ValidationResult> {
   // Run the schema based validator
   const schemaResult = await validate(tree, options, config)
 
+  let output_string = ""
   if (options.json) {
-    console.log(
-      JSON.stringify(schemaResult, (key, value) => {
-        if (value?.parent) {
-          // Remove parent reference to avoid circular references
-          value.parent = undefined
-        }
-        if (value instanceof Map) {
-          return Object.fromEntries(value)
-        } else {
-          return value
-        }
-      }),
-    )
+      output_string = resultToJSONStr(schemaResult)
   } else {
-    console.log(
-      consoleFormat(schemaResult, {
-        verbose: options.verbose ? options.verbose : false,
-      }),
-    )
+    output_string = consoleFormat(schemaResult, {
+      verbose: options.verbose ? options.verbose : false,
+    })
+  }
+
+  if (options.outfile) {
+    if (globalThis.Deno) {
+      Deno.writeTextFileSync(options.outfile, output_string)
+    } else {
+      console.error("Output to file only supported in Deno runtime")
+      console.log(output_string)
+    }
+  } else {
+    console.log(output_string)
   }
 
   return schemaResult

bids-validator/src/setup/options.ts

@@ -26,6 +26,7 @@ export type ValidatorOptions = {
   debug: LevelName
   color?: boolean
   recursive?: boolean
+  outfile?: string
   blacklistModalities: string[]
 }
 
@@ -34,7 +35,7 @@ const modalityType = new EnumType<string>(
 )
 
 /** Extendable Cliffy Command with built in BIDS validator options */
-export const validateCommand: Command<void, void, any, string[]> = new Command()
+export const validateCommand: Command<void, void, any, string[], void> = new Command()
   .name('bids-validator')
   .type('debugLevel', new EnumType(LogLevelNames))
   .description(
@@ -70,6 +71,10 @@ export const validateCommand: Command<void, void, any, string[]> = new Command()
     '-r, --recursive',
     'Validate datasets found in derivatives directories in addition to root dataset',
   )
+  .option(
+    '-o, --outfile <file:string>',
+    'File to write validation results to.',
+  )
 
 // Disabling color output is only available in Deno
 if (typeof Deno !== 'undefined') {

bids-validator/src/utils/output.ts

@@ -170,3 +170,17 @@ function helpUrl(code: string): string {
   // Provide a link to NeuroStars
   return `https://neurostars.org/search?q=${code}`
 }
+
+export function resultToJSONStr(result: ValidationResult) {
+  return JSON.stringify(result, (key, value) => {
+    if (value?.parent) {
+      // Remove parent reference to avoid circular references
+      value.parent = undefined
+    }
+    if (value instanceof Map) {
+      return Object.fromEntries(value)
+    } else {
+      return value
+    }
+  })
+}