npm - jats-xml - Versions diffs - 1.1.0 → 1.1.2 - Mend

jats-xml 1.1.0 → 1.1.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (7) hide show

package/README.md CHANGED Viewed

@@ -55,6 +55,6 @@ As of v1.0.0 this package is [ESM only](https://gist.github.com/sindresorhus/a39
 <p style="text-align: center; color: #aaa; padding-top: 50px">
   Made with love by
   <a href="https://continuous.foundation" target="_blank" style="color: #aaa">
-    Continuous Science Foundation <img src="https://continuous.foundation/images/logo-small.svg" style="height: 1em" />
+    Continuous Science Foundation <img src="https://cdn.curvenote.com/static/site/csf/icon.svg" style="height: 1em" />
   </a>
 </p>

package/dist/jats.d.ts CHANGED Viewed

@@ -28,6 +28,20 @@ export declare class Jats {
     get pmid(): string | undefined;
     get publicationDates(): PubDate[];
     get publicationDate(): PubDate | undefined;
+    /**
+     * JATS `<history>` can include multiple `<date date-type="...">` nodes,
+     * often including an "accepted" date that is a better default for project/page `date`.
+     */
+    get historyDates(): GenericParent[];
+    get historyAcceptedDate(): GenericParent | undefined;
+    /**
+     * Some sources store important dates under:
+     * `<article-meta><pub-history><event><date date-type="...">...</date></event></pub-history>`.
+     */
+    get pubHistoryDates(): GenericParent[];
+    private findPubHistoryDateByType;
+    get pubHistoryPubDate(): GenericParent | undefined;
+    get pubHistoryAcceptedDate(): GenericParent | undefined;
     get license(): License | undefined;
     get keywordGroup(): KeywordGroup | undefined;
     /** The first keywords */
@@ -47,7 +61,11 @@ export declare class Jats {
     get body(): Body | undefined;
     get back(): Back | undefined;
     get subArticles(): SubArticle[];
+    /** First `ref-list` in back matter. */
     get refList(): RefList | undefined;
+    /** All `ref-list` elements under `back`, in document order. */
+    get refLists(): RefList[];
+    /** Every `ref` from every `ref-list` under `back`, in document order. */
     get references(): Reference[];
     sort(): void;
     serialize(opts?: WriteOptions): string;

package/dist/jats.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"jats.d.ts","sourceRoot":"","sources":["../src/jats.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAI9D,OAAO,KAAK,EAAE,OAAO,EAAE,qBAAqB,EAAE,MAAM,QAAQ,CAAC;AAC7D,OAAO,EAA2B,KAAK,eAAe,EAAE,MAAM,kBAAkB,CAAC;AAIjF,OAAO,KAAK,EACV,KAAK,EACL,IAAI,EACJ,IAAI,EACJ,UAAU,EACV,OAAO,EACP,SAAS,EACT,UAAU,EACV,YAAY,EACZ,QAAQ,EACR,WAAW,EACX,OAAO,EACP,OAAO,EACP,QAAQ,EACR,YAAY,EACZ,OAAO,EACP,WAAW,EACX,YAAY,EACZ,OAAO,EACP,iBAAiB,EACjB,WAAW,EAEZ,MAAM,WAAW,CAAC;AACnB,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAG7C,OAAO,EAEL,KAAK,oBAAoB,EAI1B,MAAM,YAAY,CAAC;AAEpB,KAAK,OAAO,GAAG;IAAE,GAAG,CAAC,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAA;CAAE,CAAC;AAiBjD,KAAK,YAAY,GAAG,oBAAoB,GAAG;IACzC,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB,CAAC;AAiBF,qBAAa,IAAI;IACf,WAAW,CAAC,EAAE,qBAAqB,CAAC;IACpC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,GAAG,EAAE,OAAO,CAAC;IACb,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,aAAa,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;gBAEJ,IAAI,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,OAAO;IAoCxC,IAAI,WAAW,IAAI,eAAe,CA+EjC;IAED,IAAI,KAAK,IAAI,KAAK,GAAG,SAAS,CAE7B;IAED,IAAI,WAAW,IAAI,WAAW,GAAG,SAAS,CAEzC;IAED,IAAI,WAAW,IAAI,WAAW,GAAG,SAAS,CAEzC;IAED,IAAI,GAAG,IAAI,MAAM,GAAG,SAAS,CAE5B;IAED,IAAI,GAAG,IAAI,MAAM,GAAG,SAAS,CAE5B;IAED,IAAI,IAAI,IAAI,MAAM,GAAG,SAAS,CAE7B;IAED,IAAI,gBAAgB,IAAI,OAAO,EAAE,CAEhC;IAED,IAAI,eAAe,IAAI,OAAO,GAAG,SAAS,CAEzC;IAED;;;OAGG;IACH,IAAI,YAAY,IAAI,aAAa,EAAE,CAElC;IAED,IAAI,mBAAmB,IAAI,aAAa,GAAG,SAAS,CAOnD;IAED;;;OAGG;IACH,IAAI,eAAe,IAAI,aAAa,EAAE,CAErC;IAED,OAAO,CAAC,wBAAwB;IAUhC,IAAI,iBAAiB,IAAI,aAAa,GAAG,SAAS,CAEjD;IAED,IAAI,sBAAsB,IAAI,aAAa,GAAG,SAAS,CAEtD;IAED,IAAI,OAAO,IAAI,OAAO,GAAG,SAAS,CAEjC;IAED,IAAI,YAAY,IAAI,YAAY,GAAG,SAAS,CAE3C;IAED,yBAAyB;IACzB,IAAI,QAAQ,IAAI,OAAO,EAAE,CAExB;IAED,IAAI,aAAa,IAAI,YAAY,EAAE,CAElC;IAED,IAAI,iBAAiB,IAAI,iBAAiB,GAAG,SAAS,CAErD;IAED,IAAI,UAAU,IAAI,UAAU,GAAG,SAAS,CAEvC;IAED,IAAI,YAAY,IAAI,YAAY,GAAG,SAAS,CAE3C;IAED,IAAI,eAAe,IAAI,QAAQ,GAAG,SAAS,CAE1C;IAED,IAAI,eAAe,IAAI,QAAQ,GAAG,SAAS,CAE1C;IAED,IAAI,QAAQ,IAAI,QAAQ,GAAG,SAAS,CAEnC;IAED,IAAI,SAAS,IAAI,QAAQ,EAAE,CAE1B;IAED,IAAI,YAAY,IAAI,YAAY,GAAG,SAAS,CAE3C;IAED,IAAI,aAAa,IAAI,YAAY,EAAE,CAElC;IAED,IAAI,cAAc,IAAI,OAAO,EAAE,CAU9B;IAED,IAAI,mBAAmB,IAAI,WAAW,EAAE,CAEvC;IAED,IAAI,IAAI,IAAI,IAAI,GAAG,SAAS,CAE3B;IAED,IAAI,IAAI,IAAI,IAAI,GAAG,SAAS,CAE3B;IAED,IAAI,WAAW,IAAI,UAAU,EAAE,CAE9B;IAED,uCAAuC;IACvC,IAAI,OAAO,IAAI,OAAO,GAAG,SAAS,CAEjC;IAED,+DAA+D;IAC/D,IAAI,QAAQ,IAAI,OAAO,EAAE,CAGxB;IAED,yEAAyE;IACzE,IAAI,UAAU,IAAI,SAAS,EAAE,CAE5B;IAED,IAAI;IAeJ,SAAS,CAAC,IAAI,CAAC,EAAE,YAAY,GAAG,MAAM;CAoBvC"}

package/dist/jats.js CHANGED Viewed

@@ -9,10 +9,34 @@ import { tic } from 'myst-cli-utils';
 import { articleMetaOrder, tableWrapOrder } from './order.js';
 import { serializeJatsXml, convertToUnist, convertToXml, toDate, } from 'jats-utils';
 function select(selector, node) {
-    var _a;
-    return ((_a = unistSelect(selector, node)) !== null && _a !== void 0 ? _a : undefined);
+    var _a, _b;
+    try {
+        return ((_a = unistSelect(selector, node)) !== null && _a !== void 0 ? _a : undefined);
+    }
+    catch (error) {
+        const nodeType = (_b = node === null || node === void 0 ? void 0 : node.type) !== null && _b !== void 0 ? _b : '(undefined)';
+        const msg = error instanceof Error ? error.message : String(error);
+        throw new Error(`[jats-xml/select] selector="${selector}" nodeType="${nodeType}" failed: ${msg}`);
+    }
 }
 const DEFAULT_DOCTYPE = 'article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with MathML3 v1.3 20210610//EN" "http://jats.nlm.nih.gov/publishing/1.3/JATS-archivearticle1-3-mathml3.dtd"';
+/**
+ * Drop comments and whitespace-only text nodes introduced by xml-js when
+ * `captureSpacesBetweenElements` is true (ignorable XML whitespace).
+ */
+function significantChildElements(elements) {
+    return elements === null || elements === void 0 ? void 0 : elements.filter((elem) => {
+        var _a;
+        if (elem.type === 'comment')
+            return false;
+        if (elem.type === 'text') {
+            const t = String((_a = elem.text) !== null && _a !== void 0 ? _a : '');
+            if (!t.trim())
+                return false;
+        }
+        return true;
+    });
+}
 export class Jats {
     constructor(data, opts) {
         var _a, _b;
@@ -21,14 +45,19 @@ export class Jats {
         if (opts === null || opts === void 0 ? void 0 : opts.source)
             this.source = opts.source;
         try {
-            this.raw = xml2js(data, { compact: false });
+            this.raw = xml2js(data, {
+                compact: false,
+                // Preserve whitespace-only text nodes between elements. This is usually unnecessary except inside <preformat>.
+                // convertToUnist drops these outside preformat so other content is processed independent of arbitrary xml whitespace.
+                captureSpacesBetweenElements: true,
+            });
         }
         catch (error) {
             throw new Error('Problem parsing the JATS document, please ensure it is XML');
         }
         const { declaration, elements } = this.raw;
         this.declaration = declaration === null || declaration === void 0 ? void 0 : declaration.attributes;
-        const filteredElements = elements === null || elements === void 0 ? void 0 : elements.filter((elem) => elem.type !== 'comment');
+        const filteredElements = significantChildElements(elements);
         if ((filteredElements === null || filteredElements === void 0 ? void 0 : filteredElements.length) && filteredElements[0].type !== 'doctype') {
             (_a = this.log) === null || _a === void 0 ? void 0 : _a.warn('JATS is missing DOCTYPE declaration');
             filteredElements.unshift({ type: 'doctype' });
@@ -44,46 +73,51 @@ export class Jats {
         (_b = this.log) === null || _b === void 0 ? void 0 : _b.debug(toc('Parsed and converted JATS to unist tree in %s'));
     }
     get frontmatter() {
-        var _a, _b, _c, _d, _e, _f, _g, _h;
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
         const title = this.articleTitle;
         const subtitle = this.articleSubtitle;
         const short_title = this.articleAltTitle;
         let date;
-        if (this.publicationDate) {
-            const pubDate = toDate(this.publicationDate);
-            if (pubDate) {
-                const year = pubDate.getFullYear();
-                const month = (pubDate.getMonth() + 1).toString().padStart(2, '0');
-                const day = pubDate.getDate().toString().padStart(2, '0');
+        // Prefer a fully-specified publication date (day/month/year).
+        // If publication date is incomplete (e.g. year-only), fall back to history accepted date.
+        const preferredDateNode = (_c = (_b = (_a = this.publicationDate) !== null && _a !== void 0 ? _a : this.pubHistoryPubDate) !== null && _b !== void 0 ? _b : this.pubHistoryAcceptedDate) !== null && _c !== void 0 ? _c : this.historyAcceptedDate;
+        if (preferredDateNode) {
+            const d = toDate(preferredDateNode);
+            if (d) {
+                const year = d.getUTCFullYear();
+                const month = (d.getUTCMonth() + 1).toString().padStart(2, '0');
+                const day = d.getUTCDate().toString().padStart(2, '0');
                 date = `${year}-${month}-${day}`;
             }
         }
-        const authors = (_a = this.articleAuthors) === null || _a === void 0 ? void 0 : _a.map((auth) => {
+        const authors = (_d = this.articleAuthors) === null || _d === void 0 ? void 0 : _d.map((auth) => {
             return processContributor(auth);
         });
-        const affiliations = (_b = this.articleAffiliations) === null || _b === void 0 ? void 0 : _b.map((aff) => {
+        const affiliations = (_e = this.articleAffiliations) === null || _e === void 0 ? void 0 : _e.map((aff) => {
             return processAffiliation(aff);
         });
-        const keywords = (_d = (_c = this.keywords) === null || _c === void 0 ? void 0 : _c.map((k) => toText(k))) !== null && _d !== void 0 ? _d : [];
-        const firstSubject = select(Tags.subject, (_e = this.articleCategories) !== null && _e !== void 0 ? _e : this.front);
+        const keywords = (_g = (_f = this.keywords) === null || _f === void 0 ? void 0 : _f.map((k) => toText(k))) !== null && _g !== void 0 ? _g : [];
+        const subjectScope = (_h = this.articleCategories) !== null && _h !== void 0 ? _h : this.front;
+        const journalCollSubject = select(`${Tags.subjGroup}[subj-group-type="hwp-journal-coll"] ${Tags.subject}`, subjectScope);
+        const articleSubject = journalCollSubject !== null && journalCollSubject !== void 0 ? journalCollSubject : select(Tags.subject, subjectScope);
         const journalTitle = select(Tags.journalTitle, this.front);
         const license = this.license;
         let licenseString = null;
         if (license === null || license === void 0 ? void 0 : license['xlink:href']) {
             licenseString = license['xlink:href'];
         }
-        else if (select('[type=ali:license_ref]', license)) {
-            licenseString = toText(select('[type=ali:license_ref]', license));
+        else if (license && select('[type=ali\\:license_ref]', license)) {
+            licenseString = toText(select('[type=ali\\:license_ref]', license));
         }
         else if (selectAll('ext-link', license).length === 1) {
             // this should only happen if there is only one ext-link
-            licenseString = (_f = select('ext-link', license)['xlink:href']) !== null && _f !== void 0 ? _f : null;
+            licenseString = (_j = select('ext-link', license)['xlink:href']) !== null && _j !== void 0 ? _j : null;
         }
         else if (license) {
             licenseString = toText(license);
         }
         let openAccess;
-        const licenseType = (_g = license === null || license === void 0 ? void 0 : license['license-type']) === null || _g === void 0 ? void 0 : _g.toLowerCase();
+        const licenseType = (_k = license === null || license === void 0 ? void 0 : license['license-type']) === null || _k === void 0 ? void 0 : _k.toLowerCase();
         if (licenseType && ['openaccess', 'open-access'].includes(licenseType)) {
             openAccess = true;
         }
@@ -100,7 +134,7 @@ export class Jats {
             title: title ? toText(title) : undefined,
             subtitle: subtitle ? toText(subtitle) : undefined,
             short_title: short_title ? toText(short_title) : undefined,
-            doi: (_h = this.doi) !== null && _h !== void 0 ? _h : undefined,
+            doi: (_l = this.doi) !== null && _l !== void 0 ? _l : undefined,
             identifiers,
             date,
             authors: authors.length ? authors : undefined,
@@ -108,7 +142,7 @@ export class Jats {
             affiliations: affiliations.length ? affiliations : undefined,
             keywords: keywords.length ? keywords : undefined,
             venue: journalTitle ? { title: toText(journalTitle) } : undefined,
-            subject: firstSubject ? toText(firstSubject) : undefined,
+            subject: articleSubject ? toText(articleSubject) : undefined,
             license: licenseString !== null && licenseString !== void 0 ? licenseString : undefined,
             open_access: openAccess,
         }, { property: 'frontmatter', messages: {} });
@@ -140,6 +174,49 @@ export class Jats {
     get publicationDate() {
         return this.publicationDates.find((d) => !!select(Tags.day, d));
     }
+    /**
+     * JATS `<history>` can include multiple `<date date-type="...">` nodes,
+     * often including an "accepted" date that is a better default for project/page `date`.
+     */
+    get historyDates() {
+        var _a;
+        return selectAll('history date', (_a = this.articleMeta) !== null && _a !== void 0 ? _a : this.front);
+    }
+    get historyAcceptedDate() {
+        const accepted = this.historyDates.find((d) => {
+            var _a;
+            const dt = String((_a = d['date-type']) !== null && _a !== void 0 ? _a : '').toLowerCase();
+            return dt === 'accepted' || dt === 'accept';
+        });
+        if (accepted && select(Tags.day, accepted))
+            return accepted;
+        return undefined;
+    }
+    /**
+     * Some sources store important dates under:
+     * `<article-meta><pub-history><event><date date-type="...">...</date></event></pub-history>`.
+     */
+    get pubHistoryDates() {
+        var _a;
+        return selectAll('pub-history event date', (_a = this.articleMeta) !== null && _a !== void 0 ? _a : this.front);
+    }
+    findPubHistoryDateByType(types) {
+        const wanted = new Set(types.map((t) => t.toLowerCase()));
+        const found = this.pubHistoryDates.find((d) => {
+            var _a;
+            const dt = String((_a = d['date-type']) !== null && _a !== void 0 ? _a : '').toLowerCase();
+            return wanted.has(dt);
+        });
+        if (found && select(Tags.day, found))
+            return found;
+        return undefined;
+    }
+    get pubHistoryPubDate() {
+        return this.findPubHistoryDateByType(['pub', 'published', 'publication']);
+    }
+    get pubHistoryAcceptedDate() {
+        return this.findPubHistoryDateByType(['accepted', 'accept']);
+    }
     get license() {
         return select(Tags.license, this.permissions);
     }
@@ -203,11 +280,19 @@ export class Jats {
     get subArticles() {
         return selectAll(Tags.subArticle, this.tree);
     }
+    /** First `ref-list` in back matter. */
     get refList() {
-        return select(Tags.refList, this.back);
+        return this.refLists[0];
     }
+    /** All `ref-list` elements under `back`, in document order. */
+    get refLists() {
+        if (!this.back)
+            return [];
+        return selectAll(Tags.refList, this.back);
+    }
+    /** Every `ref` from every `ref-list` under `back`, in document order. */
     get references() {
-        return selectAll(Tags.ref, this.refList);
+        return this.refLists.flatMap((list) => selectAll(Tags.ref, list));
     }
     sort() {
         var _a;
@@ -241,14 +326,12 @@ export class Jats {
     }
 }
 function hasSingleArticle(element) {
-    var _a;
     if (element.name === 'article') {
         return true;
     }
-    if (element.name === 'pmc-articleset' &&
-        ((_a = element.elements) === null || _a === void 0 ? void 0 : _a.length) === 1 &&
-        element.elements[0].name === 'article') {
-        return true;
+    if (element.name === 'pmc-articleset') {
+        const children = significantChildElements(element.elements);
+        return (children === null || children === void 0 ? void 0 : children.length) === 1 && children[0].name === 'article';
     }
     return false;
 }

package/dist/version.d.ts CHANGED Viewed

@@ -1,3 +1,3 @@
-declare const version = "1.1.0";
+declare const version = "1.1.2";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/dist/version.js CHANGED Viewed

@@ -1,2 +1,2 @@
-const version = '1.1.0';
+const version = '1.1.2';
 export default version;

package/package.json CHANGED Viewed

@@ -1,8 +1,8 @@
 {
   "name": "jats-xml",
-  "version": "1.1.0",
+  "version": "1.1.2",
   "description": "Types and utilities for working with JATS in Typescript",
-  "author": "Rowan Cockett <rowan@continuous.foundation>",
+  "author": "Rowan Cockett <rowan@continuousfoundation.org>",
   "homepage": "https://github.com/continuous-foundation/jats",
   "license": "MIT",
   "sideEffects": false,
@@ -40,8 +40,8 @@
   "dependencies": {
     "adm-zip": "^0.5.10",
     "doi-utils": "^2.0.6",
-    "jats-tags": "^1.1.0",
-    "jats-utils": "^1.1.0",
+    "jats-tags": "^1.1.2",
+    "jats-utils": "^1.1.2",
     "myst-cli-utils": "^2.0.11",
     "myst-common": "^1.7.5",
     "myst-frontmatter": "^1.7.5",