Merge pull request #234 from VisLab/revised-validator

Revised validator

.codeclimate.yml

@@ -0,0 +1,83 @@
+version: '2' # required to adjust maintainability checks
+
+checks:
+  argument-count:
+    enabled: true
+    config:
+      threshold: 4
+  complex-logic:
+    enabled: true
+    config:
+      threshold: 4
+  file-lines:
+    enabled: true
+    config:
+      threshold: 300
+  method-complexity:
+    enabled: true
+    config:
+      threshold: 5
+  method-count:
+    enabled: true
+    config:
+      threshold: 20
+  method-lines:
+    enabled: true
+    config:
+      threshold: 50
+  nested-control-flow:
+    enabled: true
+    config:
+      threshold: 4
+  return-statements:
+    enabled: true
+    config:
+      threshold: 4
+  similar-code:
+    enabled: true
+    config:
+      threshold: #language-specific defaults. overrides affect all languages.
+  identical-code:
+    enabled: true
+    config:
+      threshold: #language-specific defaults. overrides affect all languages.
+
+exclude_patterns:
+  - 'config/'
+  - 'db/'
+  - 'dist/'
+  - 'features/'
+  - '**/node_modules/'
+  - 'script/'
+  - '**/spec/'
+  - '**/test/'
+  - '**/tests/'
+  - '**/spec_tests/'
+  - '**/docs/'
+  - 'Tests/'
+  - '**/vendor/'
+  - '**/*_test.go'
+  - '**/*.d.ts'
+  - '**/*__init__.py'
+  - '**/*setup.py'
+  - '**/setup.cfg'
+  - '**/static/'
+  - '**/constants/'
+  - '**/deploy_hed/'
+  - '**/README*'
+  - '**/.gitignore'
+  - '**/LICENSE'
+  - '**/examples/'
+  - '**/*.yml'
+  - '**/*.yaml'
+  - '**/config_template.py'
+  - '**/*.txt'
+  - '**/*.html'
+  - '**/.coveragerc'
+  - '**/*.md'
+  - '**/*.rst'
+  - '**/templates/'
+  - '**/conf.py'
+  - '**/deprecated/'
+  - '**/versioneer.py'
+  - '**/_version.py'

.codespellrc

@@ -1,3 +1,3 @@
 [codespell]
 skip = datasets,.git,*.pdf,*.svg,deprecated,*.xml,*.mediawiki,*.omn,datasets
-ignore-words-list = covert,hed,recuse,afterAll
+ignore-words-list = covert,hed,recuse,afterAll,hertzs

.github/workflows/ci.yml

@@ -2,9 +2,9 @@ name: CI
 
 on:
   push:
-    branches: [master]
+    branches: [master, develop]
   pull_request:
-    branches: [master]
+    branches: [master, develop]
 
 jobs:
   Build:
@@ -43,8 +43,9 @@ jobs:
       - name: Download dependencies
         run: npm ci
       - name: Test & publish code coverage
-        uses: paambaati/codeclimate-action@v8.0.0
+        uses: paambaati/codeclimate-action@v9.0.0
         env:
           CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
         with:
+          config: .codeclimate.yml
           coverageCommand: ./node_modules/.bin/jest --coverage --testPathIgnorePatterns=spec_tests

.gitignore

@@ -7,6 +7,7 @@ dist/
 spec_tests/*.txt
 spec_tests/temp*.json
 spec_tests/temp.spec.js
+tests/temp.spec.js
 
 # Unit test / coverage reports
 htmlcov/

README.md

@@ -5,7 +5,7 @@
 
 # hed-validator
 
-This package contains a JavaScript validator for HED (hierarchical event descriptor) strings.
+This package contains a JavaScript validator for HED (Hierarchical Event Descriptor) strings.
 
 [HED](https://www.hedtags.org/) is a system for annotating events using comma-separated path strings.
 Any type of event can be annotated using HED-type syntax.
@@ -57,3 +57,8 @@ To use the `hed-validator`, you must install the npm `hed-validator` package and
 
 A sample of current `hed-validator` usage can be found in the BIDS validator in
 [`hed.js`](https://github.com/bids-standard/bids-validator/blob/5dfc3938ea8ce128c7db295e7bebc8eed2de1ce6/bids-validator/validators/hed.js).
+
+## Repository notes:
+
+The `develop` branch is now the default branch. All changes to the repository should
+be done as PRs (pull requests) to the `develop` branch.

bids/index.js

@@ -1,16 +1,15 @@
 import buildBidsSchemas from './schema'
 import validateBidsDataset from './validate'
 import { BidsJsonFile, BidsSidecar } from './types/json'
-import { BidsEventFile, BidsTabularFile, BidsTsvFile } from './types/tsv'
+import { BidsTabularFile, BidsTsvFile } from './types/tsv'
 import BidsDataset from './types/dataset'
 import { BidsHedIssue, BidsIssue } from './types/issues'
-import BidsHedSidecarValidator from './validator/bidsHedSidecarValidator'
-import BidsHedTsvValidator from './validator/bidsHedTsvValidator'
+import BidsHedSidecarValidator from './validator/sidecarValidator'
+import BidsHedTsvValidator from './validator/tsvValidator'
 
 export {
   BidsDataset,
   BidsTsvFile,
-  BidsEventFile,
   BidsTabularFile,
   BidsJsonFile,
   BidsSidecar,
@@ -25,7 +24,6 @@ export {
 export default {
   BidsDataset,
   BidsTsvFile,
-  BidsEventFile,
   BidsTabularFile,
   BidsJsonFile,
   BidsSidecar,

bids/schema.js

@@ -1,9 +1,9 @@
 import castArray from 'lodash/castArray'
 import semver from 'semver'
 
-import { buildSchemas } from '../validator/schema/init'
-import { generateIssue, IssueError } from '../common/issues/issues'
-import { SchemaSpec, SchemasSpec } from '../common/schema/types'
+import { buildSchemas } from '../schema/init'
+import { IssueError } from '../common/issues/issues'
+import { SchemaSpec, SchemasSpec } from '../schema/specs'
 
 const alphabeticRegExp = new RegExp('^[a-zA-Z]+$')
 
@@ -31,7 +31,7 @@ export async function buildBidsSchemas(datasetDescription, schemaDefinition) {
  * @returns {SchemasSpec|null} The schema specification to be used to build the schemas, or null if the specification is missing.
  * @throws {IssueError} If the schema specification is invalid.
  */
-function buildSchemasSpec(datasetDescription, schemaDefinition) {
+export function buildSchemasSpec(datasetDescription, schemaDefinition) {
   if (schemaDefinition) {
     return validateSchemasSpec(schemaDefinition)
   } else if (datasetDescription.jsonData?.HEDVersion) {
@@ -104,4 +104,4 @@ function splitLibraryAndVersion(schemaVersion, originalVersion) {
   return [library, version]
 }
 
-export default buildBidsSchemas
+//export default buildBidsSchemas

bids/types/basic.js

@@ -1,4 +1,5 @@
 import { BidsHedIssue } from './issues'
+import { generateIssue } from '../../common/issues/issues'
 
 /**
  * A BIDS file.
@@ -36,15 +37,27 @@ export class BidsFile {
     return false
   }
 
-  validate(hedSchemas) {
+  /**
+   * Validate this validator's tsv file
+   *
+   * @param {Schemas} schemas
+   * @returns {BidsIssue[]} Any issues found during validation of this TSV file.
+   */
+  validate(schemas) {
     if (!this.hasHedData()) {
       return []
-    } else if (hedSchemas === null) {
-      return null
+    }
+    if (!schemas) {
+      BidsHedIssue.fromHedIssue(
+        generateIssue('genericError', {
+          message: 'BIDS file HED validation requires a HED schema, but the schema received was null.',
+        }),
+        { path: this.file.file, relativePath: this.file.file },
+      )
     }
 
     try {
-      const validator = new this.validatorClass(this, hedSchemas)
+      const validator = new this.validatorClass(this, schemas)
       return validator.validate()
     } catch (internalError) {
       return BidsHedIssue.fromHedIssues(internalError, this.file)

bids/types/dataset.js

@@ -1,5 +1,3 @@
-import { fallbackDatasetDescription } from './json'
-
 export class BidsDataset {
   /**
    * The dataset's event file data.
@@ -22,7 +20,7 @@ export class BidsDataset {
    */
   datasetRootDirectory
 
-  constructor(eventData, sidecarData, datasetDescription = fallbackDatasetDescription, datasetRootDirectory = null) {
+  constructor(eventData, sidecarData, datasetDescription, datasetRootDirectory = null) {
     this.eventData = eventData
     this.sidecarData = sidecarData
     this.datasetDescription = datasetDescription

bids/types/issues.js

@@ -38,7 +38,7 @@ export class BidsIssue {
    * Determine if any of the passed issues are errors.
    *
    * @param {BidsIssue[]} issues A list of issues.
-   * @return {boolean} Whether any of the passed issues are errors (rather than warnings).
+   * @returns {boolean} Whether any of the passed issues are errors (rather than warnings).
    */
   static anyAreErrors(issues) {
     return issues.some((issue) => issue.isError())