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Merge pull request #2116 from rwblair/feat/citationcff
feat: Validate CITATION.cff
2 parents e0ada04 + 0c1b20a commit 690a34a

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9 files changed

+129
-15
lines changed

9 files changed

+129
-15
lines changed

‎bids-validator/build.ts‎

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

‎bids-validator/deno.json‎

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@@ -27,20 +27,21 @@
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]
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},
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"imports": {
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"@ajv": "npm:[email protected]",
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"@bids/schema": "jsr:@bids/[email protected]+7f1f6737",
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"@cliffy/command": "jsr:@cliffy/[email protected]",
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"@cliffy/table": "jsr:@cliffy/[email protected]",
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"@hed/validator": "npm:[email protected]",
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"@ignore": "npm:[email protected]",
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"@libs/xml": "jsr:@libs/[email protected]",
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"@mango/nifti": "npm:[email protected]",
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"@std/assert": "jsr:@std/[email protected]",
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"@std/fmt": "jsr:@std/[email protected]",
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"@std/fs": "jsr:@std/[email protected]",
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"@std/io": "jsr:@std/[email protected]",
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"@std/log": "jsr:@std/[email protected]",
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"@std/path": "jsr:@std/[email protected]",
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"@ajv": "npm:[email protected]",
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"@bids/schema": "jsr:@bids/[email protected]+a73c1b06",
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"@cliffy/table": "jsr:@cliffy/[email protected]",
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"@cliffy/command": "jsr:@cliffy/[email protected]",
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"@hed/validator": "npm:[email protected]",
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"@ignore": "npm:[email protected]",
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"@mango/nifti": "npm:[email protected]",
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"@libs/xml": "jsr:@libs/[email protected]"
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"@std/yaml": "jsr:@std/yaml@^1.0.4"
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},
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"tasks": {
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"test": "deno test -A src/tests/"

‎bids-validator/src/issues/list.ts‎

Lines changed: 14 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -162,6 +162,20 @@ export const bidsIssues: IssueDefinitionRecord = {
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severity: 'error',
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reason: 'A json sidecar file was found without a corresponding data file',
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},
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BLACKLISTED_MODALITY: {
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severity: 'error',
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reason: 'The modality in this file is blacklisted through validator configuration.',
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},
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CITATION_CFF_VALIDATION_ERROR: {
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severity: 'error',
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reason:
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"The file does not pass validation using the citation.cff standard's schema." +
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'https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md'
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},
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FILE_READ: {
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severity: 'error',
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reason: 'We were unable to read this file.'
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}
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}
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const hedIssues: IssueDefinitionRecord = {
@@ -191,10 +205,6 @@ const hedIssues: IssueDefinitionRecord = {
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reason:
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"You should define 'HEDVersion' for this file. If you don't provide this information, the HED validation will use the latest version available.",
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},
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BLACKLISTED_MODALITY: {
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severity: 'error',
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reason: 'The modality in this file is blacklisted through validator configuration.',
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},
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}
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export const hedOldToNewLookup: Record<number, Partial<keyof IssueDefinitionRecord>> = {

‎bids-validator/src/setup/loadSchema.test.ts‎

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

‎bids-validator/src/validators/bids.ts‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -17,6 +17,7 @@ import { sidecarWithoutDatafile, unusedStimulus } from './internal/unusedFile.ts
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import { type BIDSContext, BIDSContextDataset } from '../schema/context.ts'
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import type { parseOptions } from '../setup/options.ts'
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import { hedValidate } from './hed.ts'
20+
import { citationValidate } from './citation.ts'
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/**
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* Ordering of checks to apply
@@ -32,6 +33,7 @@ const perContextChecks: ContextCheckFunction[] = [
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const perDSChecks: DSCheckFunction[] = [
3334
unusedStimulus,
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sidecarWithoutDatafile,
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citationValidate,
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]
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/**

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

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,27 @@
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import { assert } from '@std/assert'
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import { pathsToTree } from '../files/filetree.ts'
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import { BIDSFileDeno } from '../files/deno.ts'
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import { citationValidate } from './citation.ts'
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import { BIDSContextDataset } from '../schema/context.ts'
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import { GenericSchema } from '../types/schema.ts'
7+
import { loadSchema } from '../setup/loadSchema.ts'
8+
9+
Deno.test('citation validation', async (t) => {
10+
const schema = await loadSchema()
11+
await t.step('no errors on the good citation.cff', async () => {
12+
const tree = pathsToTree(['CITATION.cff'])
13+
const dsContext = new BIDSContextDataset({ tree })
14+
const file = new BIDSFileDeno('tests/data/citation', 'good.cff')
15+
tree.files[0].text = () => file.text()
16+
await citationValidate({} as GenericSchema, dsContext)
17+
assert(dsContext.issues.size === 0)
18+
})
19+
await t.step('An error on the bad citation.cff', async () => {
20+
const tree = pathsToTree(['CITATION.cff'])
21+
const dsContext = new BIDSContextDataset({ tree })
22+
const file = new BIDSFileDeno('tests/data/citation', 'bad.cff')
23+
tree.files[0].text = () => file.text()
24+
await citationValidate({} as GenericSchema, dsContext)
25+
assert(dsContext.issues.get({ code: 'CITATION_CFF_VALIDATION_ERROR' }).length === 1)
26+
})
27+
})

‎bids-validator/src/validators/citation.ts‎

Lines changed: 39 additions & 0 deletions
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@@ -0,0 +1,39 @@
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import type { GenericSchema } from '../types/schema.ts'
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import type { BIDSFile, FileTree } from '../types/filetree.ts'
3+
import type { BIDSContextDataset } from '../schema/context.ts'
4+
import { schema as citationSchema } from '@bids/schema/citation'
5+
import { compile } from './json.ts'
6+
import type { DefinedError } from '@ajv'
7+
import { parse } from '@std/yaml'
8+
9+
const citationFilename = 'CITATION.cff'
10+
11+
export async function citationValidate(
12+
schema: GenericSchema,
13+
dsContext: BIDSContextDataset,
14+
) {
15+
const citationFile = dsContext.tree.get(citationFilename)
16+
if (!citationFile || 'directories' in citationFile) return
17+
let citation: unknown = {}
18+
try {
19+
citation = parse(await citationFile.text())
20+
} catch (error) {
21+
dsContext.issues.add({
22+
code: 'FILE_READ',
23+
issueMessage: `Error from attempted read of file:\n${error}`,
24+
location: citationFilename,
25+
})
26+
return
27+
}
28+
const validate = compile(citationSchema)
29+
if (!validate(citation)) {
30+
for (const err of validate.errors as DefinedError[]) {
31+
dsContext.issues.add({
32+
code: 'CITATION_CFF_VALIDATION_ERROR',
33+
subCode: err['instancePath'],
34+
issueMessage: err['message'],
35+
location: citationFilename,
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})
37+
}
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}
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}

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

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@@ -0,0 +1,15 @@
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cff-version: 1.2.0
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message: If you use this software, please cite it using these metadata.
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title: My Research Software
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abstract: This is my awesome research software. It does many things.
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version: 0.11.2
6+
date-released: "2021-07-18"
7+
identifiers:
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- description: This is the collection of archived snapshots of all versions of My Research Software
9+
type: doi
10+
value: "10.5281/zenodo.123456"
11+
- description: This is the archived snapshot of version 0.11.2 of My Research Software
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type: doi
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value: "10.5281/zenodo.123457"
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license: Apache-2.0
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repository-code: "https://github.com/citation-file-format/my-research-software"

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

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@@ -0,0 +1,20 @@
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cff-version: 1.2.0
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message: If you use this software, please cite it using these metadata.
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title: My Research Software
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abstract: This is my awesome research software. It does many things.
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authors:
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- family-names: Druskat
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given-names: Stephan
8+
orcid: "https://orcid.org/1234-5678-9101-1121"
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- name: "The Research Software project"
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version: 0.11.2
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date-released: "2021-07-18"
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identifiers:
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- description: This is the collection of archived snapshots of all versions of My Research Software
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type: doi
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value: "10.5281/zenodo.123456"
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- description: This is the archived snapshot of version 0.11.2 of My Research Software
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type: doi
18+
value: "10.5281/zenodo.123457"
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license: Apache-2.0
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repository-code: "https://github.com/citation-file-format/my-research-software"

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