From 9d1882822bd7f0aa5ef4a32ee2537224c7d77927 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 14 Oct 2024 15:49:10 -0500 Subject: [PATCH 01/30] add further type checks to catching errors, and then immediately ts-ignore the issues.add because thats poorly typed. Update Deno.run to Deno.Command. Removes stubfile validators/isBidsy.ts. --- bids-validator/deno.json | 2 +- bids-validator/src/files/browser.test.ts | 2 +- bids-validator/src/files/deno.ts | 4 ++-- bids-validator/src/files/inheritance.test.ts | 5 ++++- bids-validator/src/schema/associations.ts | 3 ++- bids-validator/src/schema/context.ts | 3 ++- bids-validator/src/utils/errors.ts | 3 ++- bids-validator/src/validators/hed.ts | 2 +- bids-validator/src/validators/isBidsy.ts | 14 -------------- bids-validator/src/version.ts | 11 +++++------ 10 files changed, 20 insertions(+), 29 deletions(-) delete mode 100644 bids-validator/src/validators/isBidsy.ts diff --git a/bids-validator/deno.json b/bids-validator/deno.json index c1f9d14c4..3a5da9e39 100644 --- a/bids-validator/deno.json +++ b/bids-validator/deno.json @@ -31,7 +31,7 @@ "@bids/schema": "jsr:@bids/schema@0.11.4-dev.6+d9c23eb0", "@cliffy/command": "jsr:@cliffy/command@1.0.0-rc.5", "@cliffy/table": "jsr:@cliffy/table@1.0.0-rc.5", - "@hed/validator": "npm:hed-validator@3.15.4", + "@hed/validator": "npm:hed-validator@3.15.5", "@ignore": "npm:ignore@5.3.2", "@libs/xml": "jsr:@libs/xml@5.4.13", "@mango/nifti": "npm:nifti-reader-js@0.6.8", diff --git a/bids-validator/src/files/browser.test.ts b/bids-validator/src/files/browser.test.ts index 7486ff4a2..fca675b70 100644 --- a/bids-validator/src/files/browser.test.ts +++ b/bids-validator/src/files/browser.test.ts @@ -4,7 +4,7 @@ import { assertEquals, assertObjectMatch } from '@std/assert' import { BIDSFileBrowser, fileListToTree } from './browser.ts' class TestFile extends File { - webkitRelativePath: string + override webkitRelativePath: string constructor( fileBits: BlobPart[], fileName: string, diff --git a/bids-validator/src/files/deno.ts b/bids-validator/src/files/deno.ts index 44f3c052a..c58173b79 100644 --- a/bids-validator/src/files/deno.ts +++ b/bids-validator/src/files/deno.ts @@ -38,7 +38,7 @@ export class BIDSFileDeno implements BIDSFile { try { this.#fileInfo = Deno.statSync(this._getPath()) } catch (error) { - if (error.code === 'ENOENT') { + if (error && typeof error === 'object' && 'code' in error && error.code === 'ENOENT') { this.#fileInfo = Deno.lstatSync(this._getPath()) } } @@ -158,7 +158,7 @@ export async function readFileTree(rootPath: string): Promise { ) ignore.add(await readBidsIgnore(ignoreFile)) } catch (err) { - if (!Object.hasOwn(err, 'code') || err.code !== 'ENOENT') { + if (err && typeof err === 'object' && !('code' in err && err.code !== 'ENOENT')) { logger.error(`Failed to read '.bidsignore' file with the following error:\n${err}`) } } diff --git a/bids-validator/src/files/inheritance.test.ts b/bids-validator/src/files/inheritance.test.ts index 1d84c6a8b..9e73b7d29 100644 --- a/bids-validator/src/files/inheritance.test.ts +++ b/bids-validator/src/files/inheritance.test.ts @@ -1,4 +1,4 @@ -import { assertEquals, assertThrows } from '@std/assert' +import { assert, assertEquals, assertThrows } from '@std/assert' import { pathsToTree } from './filetree.ts' import { walkBack } from './inheritance.ts' @@ -17,6 +17,9 @@ Deno.test('walkback inheritance tests', async (t) => { continue } } catch (error) { + assert(error) + assert(typeof error === 'object') + assert('code' in error) assertEquals(error.code, 'MULTIPLE_INHERITABLE_FILES') throw error } diff --git a/bids-validator/src/schema/associations.ts b/bids-validator/src/schema/associations.ts index fea52a82e..ec1d17645 100644 --- a/bids-validator/src/schema/associations.ts +++ b/bids-validator/src/schema/associations.ts @@ -163,7 +163,8 @@ export async function buildAssociations( try { file = walkBack(source, inherit, extensions, suffix).next().value } catch (error) { - if (error.code === 'MULTIPLE_INHERITABLE_FILES') { + if (error && typeof error === 'object' && 'code' in error && error.code === 'MULTIPLE_INHERITABLE_FILES') { + // @ts-expect-error issues.add(error) break } else { diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts index 9adca5d41..e4b5c83e5 100644 --- a/bids-validator/src/schema/context.ts +++ b/bids-validator/src/schema/context.ts @@ -184,7 +184,8 @@ export class BIDSContext implements Context { try { sidecars = [...walkBack(this.file)] } catch (error) { - if (error.code === 'MULTIPLE_INHERITABLE_FILES') { + if (error && typeof error === 'object' && 'code' in error && error.code === 'MULTIPLE_INHERITABLE_FILES') { + // @ts-expect-error this.dataset.issues.add(error) } else { throw error diff --git a/bids-validator/src/utils/errors.ts b/bids-validator/src/utils/errors.ts index 66445113b..e5a99e934 100644 --- a/bids-validator/src/utils/errors.ts +++ b/bids-validator/src/utils/errors.ts @@ -1,5 +1,6 @@ export class SchemaStructureError extends Error { - constructor(schemaPath) { + schemaPath: string + constructor(schemaPath: string) { super(`Validator attempted to access ${schemaPath}, but it wasn't there.`) this.name = 'SchemaStructureError' this.schemaPath = schemaPath diff --git a/bids-validator/src/validators/hed.ts b/bids-validator/src/validators/hed.ts index cd832f960..fc34ec0df 100644 --- a/bids-validator/src/validators/hed.ts +++ b/bids-validator/src/validators/hed.ts @@ -80,7 +80,7 @@ export async function hedValidate( context.dataset.issues.add({ code: 'HED_ERROR', location: context.path, - issueMessage: error, + issueMessage: error as string, }) } diff --git a/bids-validator/src/validators/isBidsy.ts b/bids-validator/src/validators/isBidsy.ts deleted file mode 100644 index 73e02ff0c..000000000 --- a/bids-validator/src/validators/isBidsy.ts +++ /dev/null @@ -1,14 +0,0 @@ -/** - * Not sure if we want this yet. Would be to create issues for non standard - * derivatives to have the lowest common denomenator of bids like file names. - */ -// @ts-nocheck -import type { BIDSContext } from '../schema/context.ts' -import type { ContextCheckFunction } from '../../types/check.ts' -import type { BIDSFile } from '../types/filetree.ts' -import type { Schema } from '../types/schema.ts' - -export const isBidsyFilename: ContextCheckFunction = (schema, context) => { - // every '.', '-', '_' followed by an alnum - // only contains '.', '-', '_' and alnum -} diff --git a/bids-validator/src/version.ts b/bids-validator/src/version.ts index 10b25b372..c1739ea17 100644 --- a/bids-validator/src/version.ts +++ b/bids-validator/src/version.ts @@ -32,13 +32,12 @@ export async function getVersion(): Promise { } async function getLocalVersion(path: string): Promise { - const p = Deno.run({ - // safe.directory setting so we could still operate from another user - cmd: ['git', '-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'], - stdout: 'piped', + // safe.directory setting so we could still operate from another user + const command = new Deno.Command("git", { + args: ['git', '-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'], }) - const description = new TextDecoder().decode(await p.output()).trim() - p.close() + const { success, stdout } = await command.output(); + const description = new TextDecoder().decode(stdout).trim() return description } From cbe29a7816784c0d8371a938f37f409a4e9497c2 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 14 Oct 2024 16:01:54 -0500 Subject: [PATCH 02/30] bump github workflows to use deno v2 --- .github/workflows/deno_tests.yml | 6 +++--- .github/workflows/schema_web_build.yml | 4 ++-- .github/workflows/schema_web_deploy.yml | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index 0dc8eea91..a65ac7c38 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -22,9 +22,9 @@ jobs: - name: Save describe stamp id: describe run: echo version=$( git describe ) >> $GITHUB_OUTPUT - - uses: denoland/setup-deno@v1 + - uses: denoland/setup-deno@v2 with: - deno-version: v1.x + deno-version: v2.x - run: ./build.ts working-directory: ./bids-validator - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version @@ -52,7 +52,7 @@ jobs: submodules: true - uses: denoland/setup-deno@v1 with: - deno-version: v1.x + deno-version: v2.x - name: Set permissions with network access run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --allow-net' >> $GITHUB_ENV if: ${{ matrix.allow-net }} diff --git a/.github/workflows/schema_web_build.yml b/.github/workflows/schema_web_build.yml index 97f340216..07cd89275 100644 --- a/.github/workflows/schema_web_build.yml +++ b/.github/workflows/schema_web_build.yml @@ -17,9 +17,9 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: denoland/setup-deno@v1 + - uses: denoland/setup-deno@v2 with: - deno-version: v1.x + deno-version: v2.x - run: deno task build working-directory: ./web - uses: actions/upload-artifact@v4 diff --git a/.github/workflows/schema_web_deploy.yml b/.github/workflows/schema_web_deploy.yml index 2778bf4e5..82a5899b2 100644 --- a/.github/workflows/schema_web_deploy.yml +++ b/.github/workflows/schema_web_deploy.yml @@ -18,9 +18,9 @@ jobs: - uses: actions/setup-node@v4 with: node-version: 18 - - uses: denoland/setup-deno@v1 + - uses: denoland/setup-deno@v2 with: - deno-version: v1.x + deno-version: v2.x - run: deno task build working-directory: ./web - name: Install NPM deps From 0c4088eb66ff34c981a5a2d81723b486925bb9a5 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 14 Oct 2024 16:09:35 -0500 Subject: [PATCH 03/30] do we really need to specify --node-modules-dir=auto for these deno commands? --- .github/workflows/deno_tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index a65ac7c38..b0d6d2d87 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -25,7 +25,7 @@ jobs: - uses: denoland/setup-deno@v2 with: deno-version: v2.x - - run: ./build.ts + - run: deno --node-modules-dir=auto ./build.ts working-directory: ./bids-validator - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version - uses: actions/upload-artifact@v4 @@ -59,7 +59,7 @@ jobs: - name: Set permissions without network access run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --deny-net' >> $GITHUB_ENV if: ${{ ! matrix.allow-net }} - - run: deno test $PERMS --coverage=cov/ src/ + - run: deno test --node-modules-dir=auto $PERMS --coverage=cov/ src/ - name: Collect coverage run: deno coverage cov/ --lcov --output=coverage.lcov if: ${{ always() }} From ff37b3a9d6c4803e2ef093c4b9cac31932563f8e Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 14 Oct 2024 16:16:49 -0500 Subject: [PATCH 04/30] allow-env during build step. --- .github/workflows/deno_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index b0d6d2d87..c8ecc074d 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -25,7 +25,7 @@ jobs: - uses: denoland/setup-deno@v2 with: deno-version: v2.x - - run: deno --node-modules-dir=auto ./build.ts + - run: deno --node-modules-dir=auto --allow-env ./build.ts working-directory: ./bids-validator - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version - uses: actions/upload-artifact@v4 From 15ebfce537f74de9853bb02b87af9e0433d3cc7e Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 14 Oct 2024 16:23:09 -0500 Subject: [PATCH 05/30] why does installing std library require special permissions? --- .github/workflows/deno_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index c8ecc074d..4f411f9f5 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -25,7 +25,7 @@ jobs: - uses: denoland/setup-deno@v2 with: deno-version: v2.x - - run: deno --node-modules-dir=auto --allow-env ./build.ts + - run: deno --node-modules-dir=auto --allow-env --allow-read ./build.ts working-directory: ./bids-validator - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version - uses: actions/upload-artifact@v4 From 8877ba6734a8b8f82bafd8e8337e67d188f8c8bd Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 14 Oct 2024 16:27:45 -0500 Subject: [PATCH 06/30] build needs to run git, set --allow-run --- .github/workflows/deno_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index 4f411f9f5..f5ddfa7cf 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -25,7 +25,7 @@ jobs: - uses: denoland/setup-deno@v2 with: deno-version: v2.x - - run: deno --node-modules-dir=auto --allow-env --allow-read ./build.ts + - run: deno --node-modules-dir=auto --allow-env --allow-read --allow-run ./build.ts working-directory: ./bids-validator - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version - uses: actions/upload-artifact@v4 From e6aea460b7e746cb426ef561af0c9b74d196677f Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 14 Oct 2024 17:06:26 -0500 Subject: [PATCH 07/30] should of just -A'd it eh? --- .github/workflows/deno_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index f5ddfa7cf..0ad985512 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -25,7 +25,7 @@ jobs: - uses: denoland/setup-deno@v2 with: deno-version: v2.x - - run: deno --node-modules-dir=auto --allow-env --allow-read --allow-run ./build.ts + - run: deno --node-modules-dir=auto --allow-env --allow-read --allow-run --allow-net ./build.ts working-directory: ./bids-validator - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version - uses: actions/upload-artifact@v4 From 0af7d7e36c3cdc4bbc27909c822213bd39e78d0e Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Mon, 14 Oct 2024 20:40:24 -0400 Subject: [PATCH 08/30] Update .github/workflows/deno_tests.yml --- .github/workflows/deno_tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deno_tests.yml b/.github/workflows/deno_tests.yml index 0ad985512..8661556fa 100644 --- a/.github/workflows/deno_tests.yml +++ b/.github/workflows/deno_tests.yml @@ -25,7 +25,7 @@ jobs: - uses: denoland/setup-deno@v2 with: deno-version: v2.x - - run: deno --node-modules-dir=auto --allow-env --allow-read --allow-run --allow-net ./build.ts + - run: deno --node-modules-dir=auto -A ./build.ts working-directory: ./bids-validator - run: deno run -A ./bids-validator/dist/validator/bids-validator.js --version - uses: actions/upload-artifact@v4 From a174a768f15b44ed9b83cc9abf5ff2c316ae8a15 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 13:30:41 -0500 Subject: [PATCH 09/30] specify default import from ajv in validators/json.ts imports --- bids-validator/src/validators/json.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bids-validator/src/validators/json.ts b/bids-validator/src/validators/json.ts index af10f0dca..901c8e2f2 100644 --- a/bids-validator/src/validators/json.ts +++ b/bids-validator/src/validators/json.ts @@ -1,4 +1,4 @@ -import { Ajv, type JSONSchemaType, type ValidateFunction } from '@ajv' +import { default as Ajv, type JSONSchemaType, type ValidateFunction } from '@ajv' import type { Schema } from '../types/schema.ts' import { memoize } from '../utils/memoize.ts' import { logger } from '../utils/logger.ts' From b67e28febc0b34b51bf082215eb119d758ffb84d Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 13:44:33 -0500 Subject: [PATCH 10/30] revert ajv import bump version. Deno may be installing from package.json though... --- bids-validator/deno.json | 2 +- bids-validator/src/validators/json.ts | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bids-validator/deno.json b/bids-validator/deno.json index 3a5da9e39..3f24a1365 100644 --- a/bids-validator/deno.json +++ b/bids-validator/deno.json @@ -27,7 +27,7 @@ ] }, "imports": { - "@ajv": "npm:ajv@8.16.0", + "@ajv": "npm:ajv@8.17.1", "@bids/schema": "jsr:@bids/schema@0.11.4-dev.6+d9c23eb0", "@cliffy/command": "jsr:@cliffy/command@1.0.0-rc.5", "@cliffy/table": "jsr:@cliffy/table@1.0.0-rc.5", diff --git a/bids-validator/src/validators/json.ts b/bids-validator/src/validators/json.ts index 901c8e2f2..af10f0dca 100644 --- a/bids-validator/src/validators/json.ts +++ b/bids-validator/src/validators/json.ts @@ -1,4 +1,4 @@ -import { default as Ajv, type JSONSchemaType, type ValidateFunction } from '@ajv' +import { Ajv, type JSONSchemaType, type ValidateFunction } from '@ajv' import type { Schema } from '../types/schema.ts' import { memoize } from '../utils/memoize.ts' import { logger } from '../utils/logger.ts' From dde70074342cc78ca548639ce5b2100b4e3681c6 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 13:47:38 -0500 Subject: [PATCH 11/30] bump ajv in package.json. Will this break legacy? --- bids-validator/package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bids-validator/package.json b/bids-validator/package.json index 4b67bebcb..b1f8cfaaf 100644 --- a/bids-validator/package.json +++ b/bids-validator/package.json @@ -38,7 +38,7 @@ "homepage": "https://github.com/bids-standard/bids-validator", "dependencies": { "@aws-sdk/client-s3": "^3.637.0", - "ajv": "^6.5.2", + "ajv": "^8.17.1", "bytes": "^3.1.2", "colors": "^1.4.0", "cross-fetch": "^4.0.0", From 0b8890033d13729d8242c0016ce19ef863fa65dd Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 13:57:33 -0500 Subject: [PATCH 12/30] Revert "bump ajv in package.json. Will this break legacy?" This reverts commit dde70074342cc78ca548639ce5b2100b4e3681c6. --- bids-validator/package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bids-validator/package.json b/bids-validator/package.json index b1f8cfaaf..4b67bebcb 100644 --- a/bids-validator/package.json +++ b/bids-validator/package.json @@ -38,7 +38,7 @@ "homepage": "https://github.com/bids-standard/bids-validator", "dependencies": { "@aws-sdk/client-s3": "^3.637.0", - "ajv": "^8.17.1", + "ajv": "^6.5.2", "bytes": "^3.1.2", "colors": "^1.4.0", "cross-fetch": "^4.0.0", From fd86b31616aef580d46d51dbf96c86eda5141640 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 14:21:04 -0500 Subject: [PATCH 13/30] move legacy validator to its own directory. --- .github/workflows/node_tests.yml | 4 + .github/workflows/schema_web_deploy.yml | 4 +- .gitignore | 2 +- .gitmodules | 2 +- bids-validator/deno.lock | 398 ++++++++++++++++++ bids-validator/tests | 1 + Dockerfile => legacy/Dockerfile | 0 README.md => legacy/README.md | 0 babel.config.js => legacy/babel.config.js | 0 .../bids-validator-web}/.eslintrc | 0 .../bids-validator-web}/components/App.jsx | 0 .../components/ErrorLink.jsx | 0 .../bids-validator-web}/components/Issues.jsx | 0 .../bids-validator-web}/components/List.jsx | 0 .../components/Options.jsx | 0 .../components/Spinner.jsx | 0 .../components/Summary.jsx | 0 .../bids-validator-web}/components/Upload.jsx | 0 .../components/Validate.jsx | 0 .../components/results/Issue.jsx | 0 .../components/results/Issues.jsx | 0 .../components/results/Results.jsx | 0 .../bids-validator-web}/index.scss | 0 .../bids-validator-web}/next.config.js | 0 .../bids-validator-web}/package.json | 0 .../bids-validator-web}/pages/_app.js | 0 .../bids-validator-web}/pages/index.js | 0 .../bids-validator}/README.md | 0 .../rules/associated_data_rules.json | 0 .../rules/file_level_rules.json | 0 .../rules/phenotypic_rules.json | 0 .../rules/session_level_rules.json | 0 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rename {bids-validator => legacy/bids-validator}/validators/tsv/tsv.js (100%) rename {bids-validator => legacy/bids-validator}/validators/tsv/tsvParser.js (100%) rename {bids-validator => legacy/bids-validator}/validators/tsv/validate.js (100%) rename {bids-validator => legacy/bids-validator}/validators/tsv/validateContRecordings.js (100%) rename {bids-validator => legacy/bids-validator}/validators/tsv/validateTsvColumns.js (100%) rename lerna.json => legacy/lerna.json (100%) rename package-lock.json => legacy/package-lock.json (100%) rename package.json => legacy/package.json (100%) diff --git a/.github/workflows/node_tests.yml b/.github/workflows/node_tests.yml index 422a9dcd8..f5f86c802 100644 --- a/.github/workflows/node_tests.yml +++ b/.github/workflows/node_tests.yml @@ -35,6 +35,7 @@ jobs: git config --global user.email "bids.maintenance@gmail.com" git config --global user.name "bids-maintenance" - name: Set up Node + working-dir: ./legacy run: | npm install -g npm@^7 npm install @@ -44,11 +45,14 @@ jobs: run: git submodule update --init - name: Jest tests run: npm run coverage -- --maxWorkers=2 --testTimeout=10000 --colors + working-dir: ./legacy - name: Upload to codecov + working-dir: ./legacy uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} - name: Smoke tests + working-dir: ./legacy run: | bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders --json diff --git a/.github/workflows/schema_web_deploy.yml b/.github/workflows/schema_web_deploy.yml index 82a5899b2..f57e345dc 100644 --- a/.github/workflows/schema_web_deploy.yml +++ b/.github/workflows/schema_web_deploy.yml @@ -25,10 +25,12 @@ jobs: working-directory: ./web - name: Install NPM deps run: npm install + working-directory: ./legacy - name: Build legacy validator website run: npm run web-export + working-directory: ./legacy - name: Move legacy validator build into deno website - run: mv bids-validator-web/out web/dist/legacy + run: mv legacy/bids-validator-web/out web/dist/legacy - name: Upload GitHub Pages artifact uses: actions/upload-pages-artifact@v3 with: diff --git a/.gitignore b/.gitignore index b8dcdfd33..e0fa00f49 100644 --- a/.gitignore +++ b/.gitignore @@ -11,7 +11,7 @@ coverage/ __pycache__/ dist/ *.egg-info/ -bids-validator-web/out/ +legacy/bids-validator-web/out/ .next/ # Only use global yarn.lock diff --git a/.gitmodules b/.gitmodules index c1d12f480..bc251df05 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,3 @@ [submodule "bids-examples"] - path = bids-validator/tests/data/bids-examples + path = legacy/bids-validator/tests/data/bids-examples url = https://github.com/bids-standard/bids-examples.git diff --git a/bids-validator/deno.lock b/bids-validator/deno.lock new file mode 100644 index 000000000..023fb017e --- /dev/null +++ b/bids-validator/deno.lock @@ -0,0 +1,398 @@ +{ + "version": "4", 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a/bids-validator/validators/tsv/checkAcqTimeFormat.js b/legacy/bids-validator/validators/tsv/checkAcqTimeFormat.js similarity index 100% rename from bids-validator/validators/tsv/checkAcqTimeFormat.js rename to legacy/bids-validator/validators/tsv/checkAcqTimeFormat.js diff --git a/bids-validator/validators/tsv/checkAge89.js b/legacy/bids-validator/validators/tsv/checkAge89.js similarity index 100% rename from bids-validator/validators/tsv/checkAge89.js rename to legacy/bids-validator/validators/tsv/checkAge89.js diff --git a/bids-validator/validators/tsv/checkHeaders.js b/legacy/bids-validator/validators/tsv/checkHeaders.js similarity index 100% rename from bids-validator/validators/tsv/checkHeaders.js rename to legacy/bids-validator/validators/tsv/checkHeaders.js diff --git a/bids-validator/validators/tsv/checkMotionComponent.js b/legacy/bids-validator/validators/tsv/checkMotionComponent.js similarity index 100% rename from bids-validator/validators/tsv/checkMotionComponent.js rename to legacy/bids-validator/validators/tsv/checkMotionComponent.js diff --git a/bids-validator/validators/tsv/checkPhenotype.js b/legacy/bids-validator/validators/tsv/checkPhenotype.js similarity index 100% rename from bids-validator/validators/tsv/checkPhenotype.js rename to legacy/bids-validator/validators/tsv/checkPhenotype.js diff --git a/bids-validator/validators/tsv/checkStatusCol.js b/legacy/bids-validator/validators/tsv/checkStatusCol.js similarity index 100% rename from bids-validator/validators/tsv/checkStatusCol.js rename to legacy/bids-validator/validators/tsv/checkStatusCol.js diff --git a/bids-validator/validators/tsv/checkTypeCol.js b/legacy/bids-validator/validators/tsv/checkTypeCol.js similarity index 100% rename from bids-validator/validators/tsv/checkTypeCol.js rename to legacy/bids-validator/validators/tsv/checkTypeCol.js diff --git a/bids-validator/validators/tsv/index.js b/legacy/bids-validator/validators/tsv/index.js similarity index 100% rename from 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bids-validator/validators/tsv/validateContRecordings.js rename to legacy/bids-validator/validators/tsv/validateContRecordings.js diff --git a/bids-validator/validators/tsv/validateTsvColumns.js b/legacy/bids-validator/validators/tsv/validateTsvColumns.js similarity index 100% rename from bids-validator/validators/tsv/validateTsvColumns.js rename to legacy/bids-validator/validators/tsv/validateTsvColumns.js diff --git a/lerna.json b/legacy/lerna.json similarity index 100% rename from lerna.json rename to legacy/lerna.json diff --git a/package-lock.json b/legacy/package-lock.json similarity index 100% rename from package-lock.json rename to legacy/package-lock.json diff --git a/package.json b/legacy/package.json similarity index 100% rename from package.json rename to legacy/package.json From 3ac00ad1f99fdb939e96fa30c4300b9f5d0f9259 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 14:24:46 -0500 Subject: [PATCH 14/30] working-dir -> working-directory --- .github/workflows/node_tests.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/node_tests.yml b/.github/workflows/node_tests.yml index f5f86c802..78dd4010b 100644 --- a/.github/workflows/node_tests.yml +++ b/.github/workflows/node_tests.yml @@ -35,24 +35,26 @@ jobs: git config --global user.email "bids.maintenance@gmail.com" git config --global user.name "bids-maintenance" - name: Set up Node - working-dir: ./legacy + working-directory: ./legacy run: | npm install -g npm@^7 npm install - name: Eslint + working-directory: ./legacy run: npm run lint - name: Get bids-examples data + working-directory: ./legacy run: git submodule update --init - name: Jest tests + working-directory: ./legacy run: npm run coverage -- --maxWorkers=2 --testTimeout=10000 --colors - working-dir: ./legacy - name: Upload to codecov - working-dir: ./legacy + working-directory: ./legacy uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} - name: Smoke tests - working-dir: ./legacy + working-directory: ./legacy run: | bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders --json From 3331f805ebf498ad814f05e23c54cd67366ce5ce Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 14:30:06 -0500 Subject: [PATCH 15/30] more working-directory setting. fix sym link from legacy test to current tests --- .github/workflows/test-bids-examples.yml | 7 ++++++- bids-validator/tests | 2 +- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-bids-examples.yml b/.github/workflows/test-bids-examples.yml index 496a9d5aa..eb3d1cfbf 100644 --- a/.github/workflows/test-bids-examples.yml +++ b/.github/workflows/test-bids-examples.yml @@ -37,16 +37,19 @@ jobs: run: npm install --global npm - name: Install bids-validator + working-directory: ./legacy run: | npm install npm link ./bids-validator echo "./node_modules/.bin" >> $GITHUB_PATH - name: Get bids-examples data + working-directory: ./legacy run: | git clone --depth 1 https://github.com/bids-standard/bids-examples - name: Display versions and environment information + working-directory: ./legacy run: | echo $TZ export PATH="../node_modules/.bin:$PATH" @@ -58,15 +61,17 @@ jobs: ls -a $(which bids-validator) - name: Ignore examples not supported by legacy validator + working-directory: ./legacy run: | for DS in bids-examples/mrs_*; do touch $DS/.SKIP_VALIDATION done - name: Validate all BIDS datasets using bids-validator + working-directory: ./legacy run: | export PATH="../node_modules/.bin:$PATH" cat ./run_tests.sh bash ./run_tests.sh shell: bash - working-directory: ./bids-examples + working-directory: /bids-examples diff --git a/bids-validator/tests b/bids-validator/tests index fade74556..0ea139f04 120000 --- a/bids-validator/tests +++ b/bids-validator/tests @@ -1 +1 @@ -../legacy/bids-validator-legacy/tests/ \ No newline at end of file +../legacy/bids-validator/tests/ \ No newline at end of file From d3258d2e582153a6291f8a90e6bb036677c1eee0 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 14:30:06 -0500 Subject: [PATCH 16/30] more working-directory setting. fix sym link from legacy test to current tests --- .github/workflows/test-bids-examples.yml | 7 ++++++- bids-validator/tests | 2 +- legacy/bids-validator/README.md | 2 +- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test-bids-examples.yml b/.github/workflows/test-bids-examples.yml index 496a9d5aa..eb3d1cfbf 100644 --- a/.github/workflows/test-bids-examples.yml +++ b/.github/workflows/test-bids-examples.yml @@ -37,16 +37,19 @@ jobs: run: npm install --global npm - name: Install bids-validator + working-directory: ./legacy run: | npm install npm link ./bids-validator echo "./node_modules/.bin" >> $GITHUB_PATH - name: Get bids-examples data + working-directory: ./legacy run: | git clone --depth 1 https://github.com/bids-standard/bids-examples - name: Display versions and environment information + working-directory: ./legacy run: | echo $TZ export PATH="../node_modules/.bin:$PATH" @@ -58,15 +61,17 @@ jobs: ls -a $(which bids-validator) - name: Ignore examples not supported by legacy validator + working-directory: ./legacy run: | for DS in bids-examples/mrs_*; do touch $DS/.SKIP_VALIDATION done - name: Validate all BIDS datasets using bids-validator + working-directory: ./legacy run: | export PATH="../node_modules/.bin:$PATH" cat ./run_tests.sh bash ./run_tests.sh shell: bash - working-directory: ./bids-examples + working-directory: /bids-examples diff --git a/bids-validator/tests b/bids-validator/tests index fade74556..0ea139f04 120000 --- a/bids-validator/tests +++ b/bids-validator/tests @@ -1 +1 @@ -../legacy/bids-validator-legacy/tests/ \ No newline at end of file +../legacy/bids-validator/tests/ \ No newline at end of file diff --git a/legacy/bids-validator/README.md b/legacy/bids-validator/README.md index 3ae513938..6dcc67ee3 100644 --- a/legacy/bids-validator/README.md +++ b/legacy/bids-validator/README.md @@ -439,5 +439,5 @@ funded projects/grants: - [BIDS Derivatives (NIMH: R24MH114705, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH114705-01) - [OpenNeuro (NIMH: R24MH117179, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH117179-01) -- [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](https://grantome.com/grant/NSF/IIS-1760950) +- [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](https://grantome.com/grant/NSF/ACI-1760950) - [ReproNim](http://repronim.org) [(NIH-NIBIB P41 EB019936, PI: Kennedy)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833) From c9ed50cbb714a89431adcdcd06860fdc2b76b7d7 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Tue, 15 Oct 2024 15:18:58 -0500 Subject: [PATCH 17/30] in progress README updates --- README.md | 438 +++++++++++++++++++++++++++++ bids-validator/{src => }/README.md | 4 +- 2 files changed, 439 insertions(+), 3 deletions(-) create mode 100644 README.md rename bids-validator/{src => }/README.md (86%) diff --git a/README.md b/README.md new file mode 100644 index 000000000..c769d7cf5 --- /dev/null +++ b/README.md @@ -0,0 +1,438 @@ +[![Node Tests](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/node_tests.yml) +[![bids-examples tests](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml/badge.svg)](https://github.com/bids-standard/bids-validator/actions/workflows/test-bids-examples.yml) +[![CircleCI](https://circleci.com/gh/bids-standard/bids-validator.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/bids-standard/bids-validator) +[![Codecov](https://codecov.io/gh/bids-standard/bids-validator/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-validator) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3688707.svg)](https://doi.org/10.5281/zenodo.3688707) + +# BIDS-Validator + +- [BIDS-Validator](#bids-validator) + - [Quickstart](#quickstart) + - [Support](#support) + - [Maintainers and Contributors](#maintainers-and-contributors) + - [Use](#use) + - [API](#api) + - [.bidsignore](#bidsignore) + - [Configuration](#configuration) + - [In the Browser](#in-the-browser) + - [On the Server](#on-the-server) + - [Through Command Line](#through-command-line) + - [Docker image](#docker-image) + - [Development](#development) + - [Running Locally in a Browser](#running-locally-in-a-browser) + - [Testing](#testing) + - [Publishing](#publishing) + - [Acknowledgments](#acknowledgments) + +## Quickstart + +This repository currently houses 4 packages: +1. [./bids-validator](./bids-validator)The current deno based bids-validator cli and library +2. [./web](./web)The current web based validator +3. [./legacy/bids-validator](legacy/bids-validator)The legacy node validator +4. [./legacy/bids-validator-web](legacy/bids-validator-web)The legacy web based validator + +1. Web version: + 1. Open [Google Chrome](https://www.google.com/chrome/) or + [Mozilla Firefox](https://mozilla.org/firefox) (currently the only + supported browsers) + 1. Go to https://bids-standard.github.io/bids-validator/ and select a folder + with your BIDS dataset. If the validator seems to be working longer than + couple of minutes please open [developer tools ](https://developer.chrome.com/devtools) + and report the error at [https://github.com/bids-standard/bids-validator/issues](https://github.com/bids-standard/bids-validator/issues). +1. Command line version: + 1. Install [Node.js](https://nodejs.org) (at least version 18.0.0) + 1. Update `npm` to be at least version 7 (`npm install --global npm@^7`) + 1. From a terminal run `npm install -g bids-validator` + 1. Run `bids-validator` to start validating datasets. +1. Docker + 1. Install Docker + 1. From a terminal run `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data` + but replace the `/path/to/data` part of the command with your own path on your machine. + +## Support + + +Please report any issues you experience while using these support targets via +the [GitHub issue tracker](https://github.com/bids-standard/bids-validator/issues). +If you experience issues outside of these supported environments and believe we +should extend our targeted support feel free to open a new issue describing the +issue, your support target and why you require extended support and we will +address these issues on a case by case basis. + +## Maintainers and Contributors + + + +[![All Contributors](https://img.shields.io/badge/all_contributors-43-orange.svg?style=flat-square)](#contributors-) + + + +This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. +Contributions of any kind are welcome! + +The project is maintained by [@rwblair](https://github.com/rwblair/) with the help of many contributors listed below. +(The [emoji key](https://allcontributors.org/docs/en/emoji-key) is indicating the kind of contribution) + +Please also see [Acknowledgments](#acknowledgments). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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+ + + + + + +## Use + +### API + +The BIDS Validator has one primary method that takes a directory as either a +path to the directory (node) or the object given by selecting a directory with a +file input (browser), an options object, and a callback. + +Available options include: + +- ignoreWarnings - (boolean - defaults to false) +- ignoreNiftiHeaders - (boolean - defaults to false) + +For example: + +`validate.BIDS(directory, {ignoreWarnings: true}, function (issues, summary) {console.log(issues.errors, issues.warnings);});` + +If you would like to test individual files you can use the file specific checks +that we expose. + +- validate.BIDS() +- validate.JSON() +- validate.TSV() +- validate.NIFTI() + +Additionally you can reformat stored errors against a new config using `validate.reformat()` + +### .bidsignore + +Optionally one can include a `.bidsignore` file in the root of the dataset. This +file lists patterns (compatible with the [.gitignore syntax](https://git-scm.com/docs/gitignore)) +defining files that should be ignored by the validator. This option is useful +when the validated dataset includes file types not yet supported by BIDS +specification. + +```Text +*_not_bids.txt +extra_data/ +``` + +### Configuration + +You can configure the severity of errors by passing a json configuration file +with a `-c` or `--config` flag to the command line interface or by defining a +config object on the options object passed during javascript usage. + +If no path is specified a default path of `.bids-validator-config.json` will be used. You can add this file to your dataset to share dataset specific validation configuration. To disable this behavior use `--no-config` and the default configuration will be used. + +The basic configuration format is outlined below. All configuration is optional. + +```JSON +{ + "ignore": [], + "warn": [], + "error": [], + "ignoredFiles": [] +} +``` + +`ignoredFiles` takes a list of file paths or glob patterns you'd like to ignore. +Lets say we want to ignore all files and sub-directory under `/derivatives/`. +**This is not the same syntax as used in the .bidsignore file** + +```JSON +{ + "ignoredFiles": ["/derivatives/**"] +} +``` + +Note that adding two stars `**` in path makes validator recognize all files and +sub-dir to be ignored. + +`ignore`, `warn`, and `error` take lists of issue codes or issue keys and change +the severity of those issues so they are either ignored or reported as warnings +or errors. You can find a list of all available issues at +[utils/issues/list](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/utils/issues/list.js). + +Some issues may be ignored by default, but can be elevated to warnings or errors. +These provide a way to check for common things that are more specific than BIDS +compatibility. An example is a check for the presence of a T1w modality. The +following would raise an error if no T1W image was found in a dataset. + +```JSON +{ + "error": ["NO_T1W"] +} +``` + +In addition to issue codes and keys these lists can also contain objects with +and "and" or "or" properties set to arrays of codes or keys. These allow some +level of conditional logic when configuring issues. For example: + +```JSON +{ + "ignore": [ + { + "and": [ + "ECHO_TIME_GREATER_THAN", + "ECHO_TIME_NOT_DEFINED" + ] + } + ] +} +``` + +In the above example the two issues will only be ignored if both of them are +triggered during validation. + +```JSON +{ + "ignore": [ + { + "and": [ + "ECHO_TIME_GREATER_THAN", + "ECHO_TIME_NOT_DEFINED" + { + "or": [ + "ECHO_TIME1-2_NOT_DEFINED", + "ECHO_TIME_MUST_DEFINE" + ] + } + ] + } + ] +} +``` + +And in this example the listed issues will only be ignored if +`ECHO_TIME_GREATER_THAN`, `ECHO_TIME_NOT_DEFINED` and either +`ECHO_TIME1-2_NOT_DEFINED` or `ECHO_TIME_MUST_DEFINE` are triggered during +validation. + +"or" arrays are not supported at the lowest level because it wouldn't add any +functionality. For example the following is not supported. + +```JSON +{ + "ignore": [ + { + "or": [ + "ECHO_TIME_GREATER_THAN", + "ECHO_TIME_NOT_DEFINED" + ] + } + ] +} +``` + +because it would be functionally the same as this: + +```JSON +{ + "ignore": [ + "ECHO_TIME_GREATER_THAN", + "ECHO_TIME_NOT_DEFINED" + ] +} +``` + +For passing a configuration while using the bids-validator on the command line, +you can use the following style to for example ignore empty +file errors (99) and files that cannot be read (44): + +``` +bids-validator --config.ignore=99 --config.ignore=44 path/to/bids/dir +``` + +This style of use puts limits on what configuration you can require, so for +complex scenarios, we advise users to create a dedicated configuration file with +contents as described above. + +### In the Browser + +The BIDS Validator currently works in the browser with [browserify](https://browserify.org/) +or [webpack](https://webpack.js.org/). You can add it to a project by cloning +the validator and requiring it with browserify syntax +`const validate = require('bids-validator');` or an ES2015 webpack import +`import validate from 'bids-validator'`. + +### On the Server + +The BIDS validator works like most npm packages. You can install it by running +`npm install bids-validator`. + +### Through Command Line + +If you install the bids validator globally by using `npm install -g bids-validator` +you will be able to use it as a command line tool. Once installed you should be +able to run `bids-validator /path/to/your/bids/directory` and see any validation +issues logged to the terminal. Run `bids-validator` without a directory path to +see available options. + +## Docker image + +[![Docker Image Version (latest by date)](https://img.shields.io/docker/v/bids/validator?label=docker)](https://hub.docker.com/r/bids/validator) + +To use bids validator with [docker](https://www.docker.com/), you simply need to +[install docker](https://docs.docker.com/install/) on your system. + +And then from a terminal run: + +- `docker run -ti --rm bids/validator --version` to print the version of the + docker image +- `docker run -ti --rm bids/validator --help` to print the help +- `docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data` + to validate the dataset `/path/to/data` on your host machine + +See here for a brief explanation of the commands: + +- `docker run` is the command to tell docker to run a certain docker image, + usually taking the form `docker run ` +- the `-ti` flag means the inputs are accepted and outputs are printed to the + terminal +- the `--rm` flag means that the state of the docker container is not saved + after it has run +- the `-v` flag is adding your local data to the docker container + ([bind-mounts](https://docs.docker.com/storage/bind-mounts/)). Importantly, + the input after the `-v` flag consists of three fields separated colons: `:` + - the first field is the path to the directory on the host machine: + `/path/to/data` + - the second field is the path where the directory is mounted in the + container + - the third field is optional. In our case, we use `ro` to specify that the + mounted data is _read only_ + +## Development + +To develop locally, clone the project and run `npm install` from the project +root. This will install external dependencies. If you wish to install +`bids-validator` globally (so that you can run it in other folders), use the +following command to install it globally: `cd bids-validator && npm install -g` (for windows users, if in a different drive add /d, e.g. `cd /d F:\bids-validator && npm install -g`) + +Please see the [CONTRIBUTING.md](../CONTRIBUTING.md) +for additional details. + +### Bundling + +bids-validator is bundled with esbuild. While developing, the script `bids-validator/bin/bids-validator` will automatically bundle the project each time it is run. To test a build without publishing it `npm -w bids-validator run build`. This will generate a bids-validator/dist directory containing the local build and `bids-validator/bin/bids-validator` will use this build. To return to automatic bundling on each run, remove the dist directory. + +### Running Locally in a Browser + +A note about OS X, the dependencies for the browser require a npm package called +node-gyp which needs xcode to be installed in order to be compiled. + +1. The browser version of `bids-validator` lives in the repo subdirectory + `/bids-validator-web`. It is a [React.js](https://reactjs.org/) application + that uses the [next.js](https://nextjs.org/) framework. +2. To develop `bids-validator` and see how it will act in the browser, simply run + `npm run web-dev` in the project root and navigate to `localhost:3000`. +3. In development mode, changes to the codebase will trigger rebuilds of the application + automatically. +4. Changes to the `/bids-validator` in the codebase will also be reflected in the + web application. +5. Tests use the [Jest](https://jestjs.io/index.html) testing library and should be developed in `/bids-validator-web/tests`. + We can always use more tests, so please feel free to contribute a test that reduces the chance + of any bugs you fix! +6. To ensure that the web application compiles successfully in production, run `npm run web-export` + +### Testing + +If it's your first time running tests, first use the command `git submodule update --init --depth 1` to pull the test example data. This repo contains the [bids-examples github repository](https://github.com/bids-standard/bids-examples) as a [submodule](https://git-scm.com/book/en/v2/Git-Tools-Submodules). + +To start the test suite run `npm run test` from the project root. `npm run test -- --watch` +is useful to run tests while making changes. A coverage report is available with +`npm run coverage`. + +To run the linter which checks code conventions run `npm run lint`. + +### Install globally from a development branch + +Global installs are not recommended for development because of the possibility of package conflicts with other Node.js projects. If you do need to test with a global install from a development tree, follow these steps to generate the NPM package without publishing it and install the package locally. + +1. `npm -w bids-validator run build` +2. `npm -w bids-validator pack` +3. `npm install -g bids-validator-*.tgz` + +### Publishing + + +## Acknowledgments + +Many contributions to the `bids-validator` were done by members of the +BIDS community. See the +[list of contributors](https://bids-specification.readthedocs.io/en/stable/99-appendices/01-contributors.html). + +Development and contributions were supported through the following federally +funded projects/grants: + +- [BIDS Derivatives (NIMH: R24MH114705, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH114705-01) +- [OpenNeuro (NIMH: R24MH117179, PI: Poldrack)](https://grantome.com/grant/NIH/R24-MH117179-01) +- [Spokes: MEDIUM: WEST (NSF: 1760950, PI: Poldrack & Gorgolewski)](https://grantome.com/grant/NSF/ACI-1760950) +- [ReproNim](http://repronim.org) [(NIH-NIBIB P41 EB019936, PI: Kennedy)](https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833) diff --git a/bids-validator/src/README.md b/bids-validator/README.md similarity index 86% rename from bids-validator/src/README.md rename to bids-validator/README.md index b256d5a97..8a786bd6f 100644 --- a/bids-validator/src/README.md +++ b/bids-validator/README.md @@ -2,12 +2,10 @@ ## Intro -This is a partial rewrite of the bids-validator JavaScript implementation designed to read the [bids-specification schema](https://github.com/bids-standard/bids-specification/tree/master/src/schema) to apply the majority of validation rules. +This is a full rewrite of the bids-validator JavaScript implementation designed to use the [bids-specification schema](https://github.com/bids-standard/bids-specification/tree/master/src/schema) to apply the majority of validation rules. Deno is a JavaScript and TypeScript runtime that is used to run the schema based validator. Deno is simpler than Node.js and only requires one tool to use, the Deno executable itself. To install Deno, follow these [install instructions for your platform](https://deno.land/manual/getting_started/installation). -At the root of the repository there are two directories, `bids-validator` and `bids-validator-web`. These are separate npm packages, the Deno validator lives within the bids-validator package within the `src` directory. - ## Usage To use the latest validator hosted at https://deno.land/x/bids_validator, use the following command: From c87f70c95f34c5f38a70032e5f7e88e35b3bae81 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 17 Oct 2024 11:04:42 -0500 Subject: [PATCH 18/30] set working directory for circleci --- .circleci/config.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 22f52e701..03d18db33 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -4,6 +4,7 @@ jobs: test: docker: - image: node:18-alpine + working-directory: ~/project/legacy steps: - checkout - restore_cache: @@ -37,6 +38,7 @@ jobs: # Ubuntu 20.04, Docker v20.10.11, Docker Compose v1.29.2 # see: https://circleci.com/docs/2.0/configuration-reference/#available-machine-images image: ubuntu-2004:202111-02 + working-directory: ~/project/legacy steps: - checkout - run: docker build -t $IMAGE_NAME:latest . @@ -55,6 +57,7 @@ jobs: githubPagesTest: docker: - image: node:18-alpine + working-directory: ~/project/legacy steps: - run: npm install --global npm - run: apk --no-cache add ca-certificates git openssh-client rsync From 10044b7ab4b1a9546ea2c4c124afb08a86e751f9 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 17 Oct 2024 11:26:32 -0500 Subject: [PATCH 19/30] deno loader back to version 11 --- bids-validator/build.ts | 2 +- bids-validator/deno.lock | 33 ++++++++++++++++++++++++++++++++- 2 files changed, 33 insertions(+), 2 deletions(-) diff --git a/bids-validator/build.ts b/bids-validator/build.ts index 863ecd85b..ce581295f 100755 --- a/bids-validator/build.ts +++ b/bids-validator/build.ts @@ -6,7 +6,7 @@ */ import * as esbuild from 'https://deno.land/x/esbuild@v0.24.0/mod.js' import { parse } from 'https://deno.land/std@0.223.0/flags/mod.ts' -import { denoPlugins } from "jsr:@luca/esbuild-deno-loader@0.10.3" +import { denoPlugins } from "jsr:@luca/esbuild-deno-loader@0.11.0" import * as path from "https://deno.land/std@0.223.0/path/mod.ts" import { getVersion } from './src/version.ts' diff --git a/bids-validator/deno.lock b/bids-validator/deno.lock index 023fb017e..582bb6005 100644 --- a/bids-validator/deno.lock +++ b/bids-validator/deno.lock @@ -8,11 +8,14 @@ "jsr:@cliffy/table@1.0.0-rc.5": "1.0.0-rc.5", "jsr:@libs/typing@2": "2.9.0", "jsr:@libs/xml@5.4.13": "5.4.13", + "jsr:@luca/esbuild-deno-loader@0.10.3": "0.10.3", "jsr:@luca/esbuild-deno-loader@0.11.0": "0.11.0", "jsr:@std/assert@1.0.2": "1.0.2", + "jsr:@std/assert@~0.213.1": "0.213.1", "jsr:@std/bytes@^1.0.2": "1.0.2", "jsr:@std/bytes@^1.0.2-rc.3": "1.0.2", "jsr:@std/cli@1.0.0-rc.2": "1.0.0-rc.2", + "jsr:@std/encoding@0.213": "0.213.1", "jsr:@std/encoding@^1.0.5": "1.0.5", "jsr:@std/fmt@1.0.0": "1.0.0", "jsr:@std/fmt@^1.0.0-rc.1": "1.0.0", @@ -22,7 +25,9 @@ "jsr:@std/internal@^1.0.1": "1.0.4", "jsr:@std/io@0.224.4": "0.224.4", "jsr:@std/io@~0.224.3": "0.224.4", + "jsr:@std/jsonc@0.213": "0.213.1", "jsr:@std/log@0.224.5": "0.224.5", + "jsr:@std/path@0.213": "0.213.1", "jsr:@std/path@1.0.2": "1.0.2", "jsr:@std/path@^1.0.2": "1.0.2", "jsr:@std/path@^1.0.6": "1.0.6", @@ -72,14 +77,25 @@ "jsr:@libs/typing" ] }, + "@luca/esbuild-deno-loader@0.10.3": { + "integrity": "32fc93f7e7f78060234fd5929a740668aab1c742b808c6048b57f9aaea514921", + "dependencies": [ + "jsr:@std/encoding@0.213", + "jsr:@std/jsonc", + "jsr:@std/path@0.213" + ] + }, "@luca/esbuild-deno-loader@0.11.0": { "integrity": "c05a989aa7c4ee6992a27be5f15cfc5be12834cab7ff84cabb47313737c51a2c", "dependencies": [ "jsr:@std/bytes@^1.0.2", - "jsr:@std/encoding", + "jsr:@std/encoding@^1.0.5", "jsr:@std/path@^1.0.6" ] }, + "@std/assert@0.213.1": { + "integrity": "24c28178b30c8e0782c18e8e94ea72b16282207569cdd10ffb9d1d26f2edebfe" + }, "@std/assert@1.0.2": { "integrity": "ccacec332958126deaceb5c63ff8b4eaf9f5ed0eac9feccf124110435e59e49c", "dependencies": [ @@ -92,6 +108,9 @@ "@std/cli@1.0.0-rc.2": { "integrity": "97dfae82b9f0e189768ebfa7a5da53375955b94bad0a1804f8e3b73563b03787" }, + "@std/encoding@0.213.1": { + "integrity": "fcbb6928713dde941a18ca5db88ca1544d0755ec8fb20fe61e2dc8144b390c62" + }, "@std/encoding@1.0.5": { "integrity": "ecf363d4fc25bd85bd915ff6733a7e79b67e0e7806334af15f4645c569fefc04" }, @@ -116,6 +135,12 @@ "jsr:@std/bytes@^1.0.2-rc.3" ] }, + "@std/jsonc@0.213.1": { + "integrity": "5578f21aa583b7eb7317eed077ffcde47b294f1056bdbb9aacec407758637bfe", + "dependencies": [ + "jsr:@std/assert@~0.213.1" + ] + }, "@std/log@0.224.5": { "integrity": "4612a45189438441bbd923a4cad1cce5c44c6c4a039195a3e8d831ce38894eee", "dependencies": [ @@ -124,6 +149,12 @@ "jsr:@std/io@~0.224.3" ] }, + "@std/path@0.213.1": { + "integrity": "f187bf278a172752e02fcbacf6bd78a335ed320d080a7ed3a5a59c3e88abc673", + "dependencies": [ + "jsr:@std/assert@~0.213.1" + ] + }, "@std/path@1.0.2": { "integrity": "a452174603f8c620bd278a380c596437a9eef50c891c64b85812f735245d9ec7" }, From efbbc778733c1b081d3ee5a181a902dcce91df05 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 17 Oct 2024 11:28:50 -0500 Subject: [PATCH 20/30] amend circle cache paths, they may not respect working-directory --- .circleci/config.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 03d18db33..39450f83d 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -9,7 +9,7 @@ jobs: - checkout - restore_cache: keys: - - npm-deps-{{ checksum "package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 + - npm-deps-{{ checksum "./legacy/package.json" }}-{{ checksum "./legacy/bids-validator/package.json" }}-{{ checksum "./legacy/bids-validator-web/package.json" }}-v1 - run: apk --no-cache add git - run: npm install -g npm@^7 - run: npm install @@ -64,7 +64,7 @@ jobs: - checkout - restore_cache: keys: - - npm-deps-{{ checksum "package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 + - npm-deps-{{ checksum "./legacy/package.json" }}-{{ checksum "./legacy/bids-validator/package.json" }}-{{ checksum "./legacy/bids-validator-web/package.json" }}-v1 - run: name: Install bids-validator and bids-validator-web dependencies command: npm install @@ -72,7 +72,7 @@ jobs: name: Build and export web-validator command: npm run web-export && rsync -av ./bids-validator-web/out/ ~/web_version - save_cache: - key: npm-deps-{{ checksum "package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 + key: npm-deps-{{ checksum "./legacy/package.json" }}-{{ checksum "./legacy/bids-validator/package.json" }}-{{ checksum "./legacy/bids-validator-web/package.json" }}-v1 paths: - ./node_modules - ./.next/cache From bc6afbb376b1a20b26284ed09efd9fd573070567 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 17 Oct 2024 12:00:02 -0500 Subject: [PATCH 21/30] working-directory -> working_directory --- .circleci/config.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 39450f83d..124087a0e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -4,12 +4,12 @@ jobs: test: docker: - image: node:18-alpine - working-directory: ~/project/legacy + working_directory: ~/project/legacy steps: - checkout - restore_cache: keys: - - npm-deps-{{ checksum "./legacy/package.json" }}-{{ checksum "./legacy/bids-validator/package.json" }}-{{ checksum "./legacy/bids-validator-web/package.json" }}-v1 + - npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 - run: apk --no-cache add git - run: npm install -g npm@^7 - run: npm install @@ -38,7 +38,7 @@ jobs: # Ubuntu 20.04, Docker v20.10.11, Docker Compose v1.29.2 # see: https://circleci.com/docs/2.0/configuration-reference/#available-machine-images image: ubuntu-2004:202111-02 - working-directory: ~/project/legacy + working_directory: ~/project/legacy steps: - checkout - run: docker build -t $IMAGE_NAME:latest . @@ -57,14 +57,14 @@ jobs: githubPagesTest: docker: - image: node:18-alpine - working-directory: ~/project/legacy + working_directory: ~/project/legacy steps: - run: npm install --global npm - run: apk --no-cache add ca-certificates git openssh-client rsync - checkout - restore_cache: keys: - - npm-deps-{{ checksum "./legacy/package.json" }}-{{ checksum "./legacy/bids-validator/package.json" }}-{{ checksum "./legacy/bids-validator-web/package.json" }}-v1 + - npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 - run: name: Install bids-validator and bids-validator-web dependencies command: npm install @@ -72,7 +72,7 @@ jobs: name: Build and export web-validator command: npm run web-export && rsync -av ./bids-validator-web/out/ ~/web_version - save_cache: - key: npm-deps-{{ checksum "./legacy/package.json" }}-{{ checksum "./legacy/bids-validator/package.json" }}-{{ checksum "./legacy/bids-validator-web/package.json" }}-v1 + key: npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 paths: - ./node_modules - ./.next/cache From 8f4fd8f7608c0a62e79a98b4adde4c65fbbe97dd Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 17 Oct 2024 16:28:50 -0500 Subject: [PATCH 22/30] fix call to get local version --- bids-validator/src/version.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bids-validator/src/version.ts b/bids-validator/src/version.ts index c1739ea17..a54acf381 100644 --- a/bids-validator/src/version.ts +++ b/bids-validator/src/version.ts @@ -34,7 +34,7 @@ export async function getVersion(): Promise { async function getLocalVersion(path: string): Promise { // safe.directory setting so we could still operate from another user const command = new Deno.Command("git", { - args: ['git', '-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'], + args: ['-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'], }) const { success, stdout } = await command.output(); const description = new TextDecoder().decode(stdout).trim() From 25c4bb3bd20d9813b1a5c8fe509cbb981129380c Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 17 Oct 2024 16:29:20 -0500 Subject: [PATCH 23/30] remove circleci config --- .circleci/config.yml | 102 ------------------------------------------- 1 file changed, 102 deletions(-) delete mode 100644 .circleci/config.yml diff --git a/.circleci/config.yml b/.circleci/config.yml deleted file mode 100644 index 124087a0e..000000000 --- a/.circleci/config.yml +++ /dev/null @@ -1,102 +0,0 @@ -version: 2 - -jobs: - test: - docker: - - image: node:18-alpine - working_directory: ~/project/legacy - steps: - - checkout - - restore_cache: - keys: - - npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 - - run: apk --no-cache add git - - run: npm install -g npm@^7 - - run: npm install - - run: - name: Eslint - command: npm run lint - - run: - name: Get bids-examples data - command: git submodule update --init - - run: - # must include separating --, see https://stackoverflow.com/a/14404223/5201771 - name: Jest tests - command: npm run coverage -- --maxWorkers=2 --testTimeout=10000 - - run: - name: Upload to codecov - command: npm run codecov - - run: - name: Smoke tests - command: | - bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders - bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders --json - test_docker: - environment: - IMAGE_NAME: bids/validator - machine: - # Ubuntu 20.04, Docker v20.10.11, Docker Compose v1.29.2 - # see: https://circleci.com/docs/2.0/configuration-reference/#available-machine-images - image: ubuntu-2004:202111-02 - working_directory: ~/project/legacy - steps: - - checkout - - run: docker build -t $IMAGE_NAME:latest . - - run: - name: Smoke tests - command: | - docker run --rm -it -v $PWD/bids-validator/tests/data/valid_headers:/data bids/validator:latest /data --ignoreNiftiHeaders - docker run --rm -it -v $PWD/bids-validator/tests/data/valid_headers:/data bids/validator:latest /data --ignoreNiftiHeaders --json - - run: - name: Archive Docker image - command: docker save -o image.tar $IMAGE_NAME - - persist_to_workspace: - root: . - paths: - - ./image.tar - githubPagesTest: - docker: - - image: node:18-alpine - working_directory: ~/project/legacy - steps: - - run: npm install --global npm - - run: apk --no-cache add ca-certificates git openssh-client rsync - - checkout - - restore_cache: - keys: - - npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 - - run: - name: Install bids-validator and bids-validator-web dependencies - command: npm install - - run: - name: Build and export web-validator - command: npm run web-export && rsync -av ./bids-validator-web/out/ ~/web_version - - save_cache: - key: npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 - paths: - - ./node_modules - - ./.next/cache - - store_artifacts: - path: ~/web_version -workflows: - version: 2 - build-deploy: - jobs: - - test: - filters: - branches: - only: /.*/ - tags: - only: /.*/ - - test_docker: - filters: - tags: - only: /.*/ - - githubPagesTest: - requires: - - test - filters: - branches: - only: /.*/ - tags: - only: /.*/ From 0c3f8a816372087a85912b6d236de6a65c78c2d7 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 21 Oct 2024 13:12:54 -0500 Subject: [PATCH 24/30] first pass at deno dockerfile. Update docker github workflow accordingly. --- .github/workflows/docker-build-push.yml | 62 +++---------------------- bids-validator/Dockerfile | 20 ++++++++ 2 files changed, 26 insertions(+), 56 deletions(-) create mode 100644 bids-validator/Dockerfile diff --git a/.github/workflows/docker-build-push.yml b/.github/workflows/docker-build-push.yml index 911dbddc0..b6430dcec 100644 --- a/.github/workflows/docker-build-push.yml +++ b/.github/workflows/docker-build-push.yml @@ -1,6 +1,8 @@ name: Build & publish containers on: + pull_request: + branches: [master] push: tags: - 'v[0-9]+.[0-9]+.[0-9]+' @@ -9,6 +11,7 @@ jobs: push_docker_to_registry: name: Push Docker image to Docker Hub runs-on: ubuntu-latest + working-directory: bids-validator steps: - name: Check out the repo uses: actions/checkout@v4 @@ -29,61 +32,8 @@ jobs: uses: docker/build-push-action@v6 with: context: . - push: true + push: false + target: base tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} - - push_singularity_to_registry: - runs-on: ubuntu-latest - needs: - - push_docker_to_registry - steps: - - name: Set up Go 1.13 - uses: actions/setup-go@v5 - with: - go-version: 1.13 - id: go - - name: Install Dependencies - run: | - sudo apt-get update && sudo apt-get install -y \ - build-essential \ - libssl-dev \ - uuid-dev \ - libgpgme11-dev \ - squashfs-tools \ - libseccomp-dev \ - pkg-config - - name: Install Singularity - env: - SINGULARITY_VERSION: 3.8.0 - GOPATH: /tmp/go - run: | - mkdir -p $GOPATH - sudo mkdir -p /usr/local/var/singularity/mnt && \ - mkdir -p $GOPATH/src/github.com/sylabs && \ - cd $GOPATH/src/github.com/sylabs && \ - wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \ - tar xzv && \ - cd singularity-ce-${SINGULARITY_VERSION} && \ - ./mconfig -p /usr/local && \ - make -C builddir && \ - sudo make -C builddir install - - name: Check out code for the container build - uses: actions/checkout@v4 - - name: Extract metadata (tags, labels) for Docker - id: meta - uses: docker/metadata-action@v5 - with: - images: bids/validator - - name: Build Container - run: | - tags=${{ steps.meta.outputs.tags }} - echo $tags - singularity pull container.sif docker://${tags%,*} - - name: Login and Deploy Container - if: (github.event_name != 'pull_request') - run: | - tags=${{ steps.meta.outputs.tags }} - echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io - for tag in $(echo $tags | sed "s/,/ /g" | sed "s/bids\/validator/bids-standard\/bids-validator/g"); - do echo $tag; singularity push container.sif oras://ghcr.io/$tag; done + outputs: type=cacheonly diff --git a/bids-validator/Dockerfile b/bids-validator/Dockerfile new file mode 100644 index 000000000..1fde2e02b --- /dev/null +++ b/bids-validator/Dockerfile @@ -0,0 +1,20 @@ +ARG BASE_IMAGE=denoland/deno:2.0.1 +FROM ${BASE_IMAGE} AS base +WORKDIR /src + +RUN apt-get update && \ + apt-get install -y git && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + +COPY . . +RUN deno cache ./bids-validator-deno +RUN ./build.ts + +ENTRYPOINT ["./bids-validator-deno"] + +FROM ${BASE_IMAGE} AS min +WORKDIR /src +COPY --from=base /src/dist/validator/* . + +ENTRYPOINT ["deno", "-A", "./bids-validator.js"] From 5f75b1eb6da3a59ea379b2121be05a9b36914256 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Mon, 21 Oct 2024 14:03:55 -0500 Subject: [PATCH 25/30] Revert "remove circleci config" This reverts commit 25c4bb3bd20d9813b1a5c8fe509cbb981129380c. --- .circleci/config.yml | 102 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 .circleci/config.yml diff --git a/.circleci/config.yml b/.circleci/config.yml new file mode 100644 index 000000000..124087a0e --- /dev/null +++ b/.circleci/config.yml @@ -0,0 +1,102 @@ +version: 2 + +jobs: + test: + docker: + - image: node:18-alpine + working_directory: ~/project/legacy + steps: + - checkout + - restore_cache: + keys: + - npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 + - run: apk --no-cache add git + - run: npm install -g npm@^7 + - run: npm install + - run: + name: Eslint + command: npm run lint + - run: + name: Get bids-examples data + command: git submodule update --init + - run: + # must include separating --, see https://stackoverflow.com/a/14404223/5201771 + name: Jest tests + command: npm run coverage -- --maxWorkers=2 --testTimeout=10000 + - run: + name: Upload to codecov + command: npm run codecov + - run: + name: Smoke tests + command: | + bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders + bids-validator/bin/bids-validator bids-validator/tests/data/valid_headers/ --ignoreNiftiHeaders --json + test_docker: + environment: + IMAGE_NAME: bids/validator + machine: + # Ubuntu 20.04, Docker v20.10.11, Docker Compose v1.29.2 + # see: https://circleci.com/docs/2.0/configuration-reference/#available-machine-images + image: ubuntu-2004:202111-02 + working_directory: ~/project/legacy + steps: + - checkout + - run: docker build -t $IMAGE_NAME:latest . + - run: + name: Smoke tests + command: | + docker run --rm -it -v $PWD/bids-validator/tests/data/valid_headers:/data bids/validator:latest /data --ignoreNiftiHeaders + docker run --rm -it -v $PWD/bids-validator/tests/data/valid_headers:/data bids/validator:latest /data --ignoreNiftiHeaders --json + - run: + name: Archive Docker image + command: docker save -o image.tar $IMAGE_NAME + - persist_to_workspace: + root: . + paths: + - ./image.tar + githubPagesTest: + docker: + - image: node:18-alpine + working_directory: ~/project/legacy + steps: + - run: npm install --global npm + - run: apk --no-cache add ca-certificates git openssh-client rsync + - checkout + - restore_cache: + keys: + - npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 + - run: + name: Install bids-validator and bids-validator-web dependencies + command: npm install + - run: + name: Build and export web-validator + command: npm run web-export && rsync -av ./bids-validator-web/out/ ~/web_version + - save_cache: + key: npm-deps-{{ checksum "./package.json" }}-{{ checksum "./bids-validator/package.json" }}-{{ checksum "./bids-validator-web/package.json" }}-v1 + paths: + - ./node_modules + - ./.next/cache + - store_artifacts: + path: ~/web_version +workflows: + version: 2 + build-deploy: + jobs: + - test: + filters: + branches: + only: /.*/ + tags: + only: /.*/ + - test_docker: + filters: + tags: + only: /.*/ + - githubPagesTest: + requires: + - test + filters: + branches: + only: /.*/ + tags: + only: /.*/ From 6923b6ff2244fa0b8e8d8bcd40d61deb2786dead Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 24 Oct 2024 15:07:33 -0500 Subject: [PATCH 26/30] Move dockerfile to base. Deno cli now handles git not existing. --- .dockerignore | 1 - Dockerfile | 30 ++++++++++++++++++++++++++++++ README.md | 2 +- bids-validator/Dockerfile | 20 -------------------- bids-validator/src/version.ts | 17 +++++++++++------ 5 files changed, 42 insertions(+), 28 deletions(-) create mode 100644 Dockerfile delete mode 100644 bids-validator/Dockerfile diff --git a/.dockerignore b/.dockerignore index 3c67b0a1b..80e59ef52 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,3 +1,2 @@ tests -.git node_modules diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 000000000..68f9fc032 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,30 @@ +ARG BASE_IMAGE=denoland/deno:2.0.1 +FROM ${BASE_IMAGE} AS build +WORKDIR /src + +RUN apt-get update && \ + apt-get install -y git jq && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + +ADD . . +RUN export VERSION=`git -C . -c safe.directory=* describe --tags --always` && \ + jq -r ".version|=\"$VERSION\"" bids-validator/deno.json > ._deno.json + +WORKDIR /src/bids-validator +RUN deno cache ./bids-validator-deno +RUN ./build.ts + +FROM ${BASE_IMAGE} AS base +WORKDIR /src +COPY . . +COPY --from=build /src/._deno.json /src/bids-validator/deno.json +WORKDIR /src/bids-validator +RUN deno cache ./bids-validator-deno +ENTRYPOINT ["./bids-validator-deno"] + +FROM ${BASE_IMAGE} AS min +WORKDIR /src +COPY --from=build /src/bids-validator/dist/validator/* . + +ENTRYPOINT ["deno", "-A", "./bids-validator.js"] diff --git a/README.md b/README.md index c769d7cf5..e4b1b1590 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ ## Quickstart -This repository currently houses 4 packages: +This repository houses 4 packages: 1. [./bids-validator](./bids-validator)The current deno based bids-validator cli and library 2. [./web](./web)The current web based validator 3. [./legacy/bids-validator](legacy/bids-validator)The legacy node validator diff --git a/bids-validator/Dockerfile b/bids-validator/Dockerfile deleted file mode 100644 index 1fde2e02b..000000000 --- a/bids-validator/Dockerfile +++ /dev/null @@ -1,20 +0,0 @@ -ARG BASE_IMAGE=denoland/deno:2.0.1 -FROM ${BASE_IMAGE} AS base -WORKDIR /src - -RUN apt-get update && \ - apt-get install -y git && \ - apt-get clean && \ - rm -rf /var/lib/apt/lists/* - -COPY . . -RUN deno cache ./bids-validator-deno -RUN ./build.ts - -ENTRYPOINT ["./bids-validator-deno"] - -FROM ${BASE_IMAGE} AS min -WORKDIR /src -COPY --from=base /src/dist/validator/* . - -ENTRYPOINT ["deno", "-A", "./bids-validator.js"] diff --git a/bids-validator/src/version.ts b/bids-validator/src/version.ts index a54acf381..7c65b06ec 100644 --- a/bids-validator/src/version.ts +++ b/bids-validator/src/version.ts @@ -33,12 +33,17 @@ export async function getVersion(): Promise { async function getLocalVersion(path: string): Promise { // safe.directory setting so we could still operate from another user - const command = new Deno.Command("git", { - args: ['-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'], - }) - const { success, stdout } = await command.output(); - const description = new TextDecoder().decode(stdout).trim() - return description + try { + const command = new Deno.Command("git", { + args: ['-C', path, '-c', 'safe.directory=*', 'describe', '--tags', '--always'], + }) + const { success, stdout } = await command.output(); + console.log(success) + const description = new TextDecoder().decode(stdout).trim() + return description + } catch(err) { + return "" + } } function getArchiveVersion(): string | undefined { From ddb0e2583c862f0d53bb140fb976f8139ef8897a Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 24 Oct 2024 15:19:15 -0500 Subject: [PATCH 27/30] empty circle jobs array --- .circleci/config.yml | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 124087a0e..e4640e7e1 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -82,21 +82,3 @@ workflows: version: 2 build-deploy: jobs: - - test: - filters: - branches: - only: /.*/ - tags: - only: /.*/ - - test_docker: - filters: - tags: - only: /.*/ - - githubPagesTest: - requires: - - test - filters: - branches: - only: /.*/ - tags: - only: /.*/ From a77945a1fa10b896dab3656f75aed5f5364d728a Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 24 Oct 2024 15:21:20 -0500 Subject: [PATCH 28/30] empty out circle workflows entirely --- .circleci/config.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index e4640e7e1..cb60c48c6 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -79,6 +79,3 @@ jobs: - store_artifacts: path: ~/web_version workflows: - version: 2 - build-deploy: - jobs: From 40dbd625181195d5f41835f2350329b802c85288 Mon Sep 17 00:00:00 2001 From: Ross Blair Date: Thu, 24 Oct 2024 15:34:57 -0500 Subject: [PATCH 29/30] dont think working directory directive needed for docker build action now that dockerfile in root. --- .github/workflows/docker-build-push.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/docker-build-push.yml b/.github/workflows/docker-build-push.yml index b6430dcec..5edf171b9 100644 --- a/.github/workflows/docker-build-push.yml +++ b/.github/workflows/docker-build-push.yml @@ -11,7 +11,6 @@ jobs: push_docker_to_registry: name: Push Docker image to Docker Hub runs-on: ubuntu-latest - working-directory: bids-validator steps: - name: Check out the repo uses: actions/checkout@v4 From 7e40d43a448469efceb22db8a32cf7f49bfc740f Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 24 Oct 2024 16:37:50 -0400 Subject: [PATCH 30/30] Update .circleci/config.yml --- .circleci/config.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index cb60c48c6..1cee4c816 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -79,3 +79,6 @@ jobs: - store_artifacts: path: ~/web_version workflows: + version: 2 + build-deploy: + jobs: []