From e399138480fee841a7f0f1cae297074ff8828de6 Mon Sep 17 00:00:00 2001 From: Franklin Koch Date: Tue, 15 Apr 2025 01:21:20 -0600 Subject: [PATCH 1/2] =?UTF-8?q?=F0=9F=93=A6=20Update=20dependencies?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- package-lock.json | 1567 ++++++++++++++++++++++++++++++--------------- package.json | 12 +- 2 files changed, 1040 insertions(+), 539 deletions(-) diff --git a/package-lock.json b/package-lock.json index ddbf1ee..1912400 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,14 +14,14 @@ "chalk": "^5.3.0", "commander": "^11.1.0", "css-selector-parser": "^3.0.5", - "doi-utils": "^2.0.3", + "doi-utils": "^2.0.5", "inquirer": "^9.2.23", "js-yaml": "^4.1.0", - "myst-cli": "^1.3.12", - "myst-cli-utils": "^2.0.10", - "myst-common": "^1.7.1", - "myst-frontmatter": "^1.7.1", - "myst-to-jats": "^1.0.28", + "myst-cli": "^1.3.25", + "myst-cli-utils": "^2.0.11", + "myst-common": "^1.7.10", + "myst-frontmatter": "^1.7.10", + "myst-to-jats": "^1.0.33", "nanoid": "^5.0.5", "node-fetch": "^3.3.2", "unist-builder": "^4.0.0", @@ -529,9 +529,10 @@ } }, "node_modules/@citation-js/core": { - 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] + ], + "license": "MIT" }, "node_modules/micromark-util-html-tag-name": { "version": "1.2.0", @@ -9011,7 +9292,8 @@ "type": "OpenCollective", "url": "https://opencollective.com/unified" } - ] + ], + "license": "MIT" }, "node_modules/micromark-util-normalize-identifier": { "version": "1.1.0", @@ -9027,6 +9309,7 @@ "url": "https://opencollective.com/unified" } ], + "license": "MIT", "dependencies": { "micromark-util-symbol": "^1.0.0" } @@ -9045,6 +9328,7 @@ "url": "https://opencollective.com/unified" } ], + "license": "MIT", "dependencies": { "micromark-util-types": "^1.0.0" } @@ -9063,6 +9347,7 @@ "url": "https://opencollective.com/unified" } ], + "license": "MIT", "dependencies": { "micromark-util-character": "^1.0.0", "micromark-util-encode": "^1.0.0", @@ -9083,6 +9368,7 @@ "url": "https://opencollective.com/unified" } ], + "license": "MIT", "dependencies": { "micromark-util-chunked": "^1.0.0", "micromark-util-symbol": "^1.0.0", @@ -9103,7 +9389,8 @@ "type": "OpenCollective", "url": "https://opencollective.com/unified" } - 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"integrity": "sha512-huCv9IH9Tcf95zuYCsQraZtWnJvBtLVE0QHMOs8bWyZAFZNDcYjsPq1nEx8jKA9y+Beo9v+7OBPRisQTjinQMw==" + "integrity": "sha512-huCv9IH9Tcf95zuYCsQraZtWnJvBtLVE0QHMOs8bWyZAFZNDcYjsPq1nEx8jKA9y+Beo9v+7OBPRisQTjinQMw==", + "license": "MIT" }, "node_modules/xml-js": { "version": "1.6.11", @@ -15633,6 +16132,7 @@ "version": "1.0.6", "resolved": "https://registry.npmjs.org/y-protocols/-/y-protocols-1.0.6.tgz", "integrity": "sha512-vHRF2L6iT3rwj1jub/K5tYcTT/mEYDUppgNPXwp8fmLpui9f7Yeq3OEtTLVF012j39QnV+KEQpNqoN7CWU7Y9Q==", + "license": "MIT", "dependencies": { "lib0": "^0.2.85" }, @@ -15703,11 +16203,12 @@ } }, "node_modules/yjs": { - "version": "13.6.19", - "resolved": "https://registry.npmjs.org/yjs/-/yjs-13.6.19.tgz", - "integrity": "sha512-GNKw4mEUn5yWU2QPHRx8jppxmCm9KzbBhB4qJLUJFiiYD0g/tDVgXQ7aPkyh01YO28kbs2J/BEbWBagjuWyejw==", + "version": "13.6.24", + "resolved": "https://registry.npmjs.org/yjs/-/yjs-13.6.24.tgz", + "integrity": "sha512-xn/pYLTZa3uD1uDG8lpxfLRo5SR/rp0frdASOl2a71aYNvUXdWcLtVL91s2y7j+Q8ppmjZ9H3jsGVgoFMbT2VA==", + "license": "MIT", "dependencies": { - "lib0": "^0.2.86" + "lib0": "^0.2.99" }, "engines": { "node": ">=16.0.0", diff --git a/package.json b/package.json index cbb4fa3..76893ff 100644 --- a/package.json +++ b/package.json @@ -52,14 +52,14 @@ "chalk": "^5.3.0", "commander": "^11.1.0", "css-selector-parser": "^3.0.5", - "doi-utils": "^2.0.3", + "doi-utils": "^2.0.5", "inquirer": "^9.2.23", "js-yaml": "^4.1.0", - "myst-cli": "file:.yalc/myst-cli", - "myst-cli-utils": "^2.0.10", - "myst-common": "^1.7.1", - "myst-frontmatter": "^1.7.1", - "myst-to-jats": "^1.0.28", + "myst-cli": "^1.3.25", + "myst-cli-utils": "^2.0.11", + "myst-common": "^1.7.10", + "myst-frontmatter": "^1.7.10", + "myst-to-jats": "^1.0.33", "nanoid": "^5.0.5", "node-fetch": "^3.3.2", "unist-builder": "^4.0.0", From bfed5ab141553f1e8be25680cd1ccd20c42be290 Mon Sep 17 00:00:00 2001 From: Franklin Koch Date: Tue, 15 Apr 2025 01:22:21 -0600 Subject: [PATCH 2/2] =?UTF-8?q?=F0=9F=93=9D=20Remove=20newlines=20in=20jat?= =?UTF-8?q?s=20abstract?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .changeset/nervous-crabs-ring.md | 5 +++++ src/cli/deposit.ts | 2 ++ src/cli/utils.ts | 7 +++++++ 3 files changed, 14 insertions(+) create mode 100644 .changeset/nervous-crabs-ring.md diff --git a/.changeset/nervous-crabs-ring.md b/.changeset/nervous-crabs-ring.md new file mode 100644 index 0000000..6f61660 --- /dev/null +++ b/.changeset/nervous-crabs-ring.md @@ -0,0 +1,5 @@ +--- +"crossref-utils": patch +--- + +Remove newlines in jats abstract diff --git a/src/cli/deposit.ts b/src/cli/deposit.ts index c877e69..b9d04ad 100644 --- a/src/cli/deposit.ts +++ b/src/cli/deposit.ts @@ -30,6 +30,7 @@ import { addDoiToConfig, element2JatsUnist, transformCiteToText, + transformNewlineToSpace, transformXrefToLink, } from './utils.js'; import type { ProjectFrontmatter } from 'myst-frontmatter'; @@ -119,6 +120,7 @@ export async function depositArticleFromSource(session: ISession, depositSource: if (abstractPart) { transformXrefToLink(abstractPart); transformCiteToText(abstractPart); + transformNewlineToSpace(abstractPart); const serializer = new JatsSerializer(new VFile(), abstractPart as any); const jats = serializer.render(true).elements(); abstract = u( diff --git a/src/cli/utils.ts b/src/cli/utils.ts index e9c177c..105b07d 100644 --- a/src/cli/utils.ts +++ b/src/cli/utils.ts @@ -74,3 +74,10 @@ export function addDoiToConfig(configFile: string, doi: string) { ]; fs.writeFileSync(configFile, newLines.join('\n')); } + +export function transformNewlineToSpace(mdast: GenericParent) { + const text = selectAll('text', mdast) as GenericNode[]; + text.forEach((t) => { + t.value = t.value?.replaceAll(/\s*\n\s*/g, ' '); + }); +}