Merge pull request #307 from nellh/quicktest-error-code

Introduce quick test error code to replace 'Invalid' string

Author: chrisgorgo

cli.js

@@ -12,7 +12,7 @@ module.exports = function (dir, options) {
         validate.BIDS(dir, options, function (issues, summary) {
             var errors = issues.errors;
             var warnings = issues.warnings;
-            if (issues === 'Invalid') {
+            if (issues.errors.length === 1 && issues.errors[0].code === '61') {
                 console.log(colors.red("The directory " + dir + " failed an initial Quick Test. This means the basic names and structure of the files and directories do not comply with BIDS specification. For more info go to http://bids.neuroimaging.io/"));
             } else if (issues.config && issues.config.length >= 1) {
                 console.log(colors.red('Invalid Config File'));

package.json

@@ -1,6 +1,6 @@
 {
   "name": "bids-validator",
-  "version": "0.22.4",
+  "version": "0.23.0",
   "description": "",
   "main": "index.js",
   "repository": {
@@ -22,6 +22,7 @@
   },
   "homepage": "https://github.com/INCF/bids-validator",
   "dependencies": {
+    "ajv": "^4.9.0",
     "async": "^2.1.5",
     "bytes": "^2.3.0",
     "cliff": "^0.1.10",
@@ -30,9 +31,9 @@
     "minimatch": "3.0.3",
     "nifti-js": "^1.0.0",
     "pako": "^1.0.4",
+    "path": "^0.12.7",
     "pluralize": "^3.1.0",
-    "yargs": "^6.6.0",
-    "ajv": "^4.9.0"
+    "yargs": "^6.6.0"
   },
   "devDependencies": {
     "adm-zip": "",

tests/utils/files.spec.js

@@ -0,0 +1,44 @@
+const assert = require('assert');
+const after = require('mocha').after;
+const utils = require('../../utils');
+
+const setupMocks = () => {
+    // Mock version of the File API for tests
+    global.File = function MockFile(data, fileName, options) {
+        assert(data.hasOwnProperty('length'));
+        assert.equal(typeof data[0], 'string');
+        this._data = data;
+        this._options = options;
+        this.name = fileName;
+    };
+};
+const cleanupMocks = () => {
+    delete global.File;
+};
+
+describe('files utils in nodejs', () => {
+    describe('FileAPI', () => {
+        it('should return a mock implementation', () => {
+            let File = utils.files.FileAPI();
+            assert(typeof File !== 'undefined');
+            assert(File.name === 'NodeFile');
+        });
+    });
+    describe('newFile', () => {
+        it('creates a new File API object', () => {
+            let file = utils.files.newFile('test-file');
+            assert.equal(file.name, 'test-file');
+        });
+    });
+});
+
+describe('files utils in browsers', () => {
+    before(setupMocks);
+    after(cleanupMocks);
+    describe('newFile', () => {
+        it('creates a new File API object', () => {
+            const test_file = utils.files.newFile('test-file');
+            assert(File.prototype.isPrototypeOf(test_file));
+        });
+    });
+});

utils/files.js

@@ -17,6 +17,8 @@ if (typeof window === 'undefined') {
 // public API ---------------------------------------------------------------------
 
 var fileUtils = {
+    FileAPI: FileAPI,
+    newFile: newFile,
     readFile: readFile,
     readDir: readDir,
     readNiftiHeader: readNiftiHeader,
@@ -273,4 +275,43 @@ function testFile (file, callback) {
     });
 }
 
+/**
+ * Simulates some of the browser File API interface.
+ * https://developer.mozilla.org/en-US/docs/Web/API/File
+ * 
+ * @param {string[]} parts - file contents as bytes
+ * @param {string} filename - filename without path info
+ * @param {Object} properties - unused Blob properties
+ */
+function NodeFile(parts, filename, properties) {
+    this.parts = parts;
+    this.name = filename;
+    this.properties = properties;
+    this.size = parts.reduce(function (a, val) {
+        return a + val.length;
+    }, 0);
+    // Unknown defacto mime-type
+    this.type = 'application/octet-stream';
+    this.lastModified = 0;
+}
+
+/**
+ * Return a either a mock or real FileAPI if one is available
+ */
+function FileAPI() {
+    return typeof File === 'undefined' ? NodeFile: File;
+}
+
+/**
+ * New File
+ *
+ * Creates an empty File object
+ * 
+ * @param {string} filename - the filename without path info
+ */
+function newFile(filename) {
+    var File = FileAPI();
+    return new File([''], filename);
+}
+
 module.exports = fileUtils;

utils/issues/list.js

@@ -302,4 +302,9 @@ module.exports = {
         severity: 'error',
         reason: 'sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.'
     },
+    61: {
+        key: 'QUICK_VALIDATION_FAILED',
+        severity: 'error',
+        reason: 'Quick validation failed - the general folder structure does not resamble a BIDS dataset. Have you chosen the right folder (with "sub-*/" subfolders)? Check for structural/naming issues and presence of at least one subject.',
+    }
 };

validators/bids.js

@@ -1,5 +1,6 @@
 var async  = require('async');
 var fs     = require('fs');
+var path   = require('path');
 var utils  = require('../utils');
 var Issue  = utils.issues.Issue;
 
@@ -41,7 +42,20 @@ BIDS = {
                         if (couldBeBIDS) {
                             self.fullTest(files, callback);
                         } else {
-                            callback('Invalid');
+                            // Return an error immediately if quickTest fails
+                            var issue = new Issue({
+                                code: 61,
+                                file: utils.files.newFile(path.basename(dir))
+                            });
+                            var summary = {
+                                sessions: [],
+                                subjects: [],
+                                tasks: [],
+                                modalities: [],
+                                totalFiles: Object.keys(files).length,
+                                size: 0
+                            };
+                            callback(utils.issues.format([issue], summary, options));
                         }
                     });
                 });