jats-xml 1.0.5 → 1.0.7

package/dist/cli/parse.d.ts

@@ -1,7 +1,7 @@
 import { Command } from 'commander';
 import type { ISession } from '../types.js';
 import { Jats } from '../jats.js';
-import { type ResolutionOptions } from 'jats-download';
+import { type ResolutionOptions } from 'jats-fetch';
 export declare function parseJats(session: ISession, file: string, opts?: ResolutionOptions): Promise<Jats>;
 export declare function addDownloadCLI(program: Command): void;
 //# sourceMappingURL=parse.d.ts.map

package/dist/cli/parse.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../src/cli/parse.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAWpC,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAC5C,OAAO,EAAE,IAAI,EAAE,MAAM,YAAY,CAAC;AAClC,OAAO,EAA0C,KAAK,iBAAiB,EAAE,MAAM,eAAe,CAAC;AAgD/F,wBAAsB,SAAS,CAC7B,OAAO,EAAE,QAAQ,EACjB,IAAI,EAAE,MAAM,EACZ,IAAI,GAAE,iBAAoD,GACzD,OAAO,CAAC,IAAI,CAAC,CAef;AA2JD,wBAAgB,cAAc,CAAC,OAAO,EAAE,OAAO,QAI9C"}
+{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../src/cli/parse.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAWpC,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAC5C,OAAO,EAAE,IAAI,EAAE,MAAM,YAAY,CAAC;AAClC,OAAO,EAA0C,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAgD5F,wBAAsB,SAAS,CAC7B,OAAO,EAAE,QAAQ,EACjB,IAAI,EAAE,MAAM,EACZ,IAAI,GAAE,iBAAoD,GACzD,OAAO,CAAC,IAAI,CAAC,CAef;AA2JD,wBAAgB,cAAc,CAAC,OAAO,EAAE,OAAO,QAI9C"}

package/dist/cli/parse.js

@@ -10,7 +10,7 @@ import { toText } from 'myst-common';
 import { select, selectAll } from 'unist-util-select';
 import { getSession } from '../session.js';
 import { Jats } from '../jats.js';
-import { downloadJatsFromUrl, DEFAULT_RESOLVERS } from 'jats-download';
+import { downloadJatsFromUrl, DEFAULT_RESOLVERS } from 'jats-fetch';
 import { findArticleId, formatDate, toDate } from '../utils.js';
 function hasValidExtension(output) {
     return ['.xml', '.jats'].includes(extname(output).toLowerCase());

package/dist/index.d.ts

@@ -1,6 +1,7 @@
 export { default as version } from './version.js';
 export { Jats } from './jats.js';
-export { convertToUnist } from './utils.js';
+export { convertToUnist, convertToXml, escapeForXML } from './utils.js';
+export * from './serialize.js';
 export * from './session.js';
 export * from './types.js';
 export * from './validate/index.js';

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,cAAc,CAAC;AAClD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAC5C,cAAc,cAAc,CAAC;AAC7B,cAAc,YAAY,CAAC;AAC3B,cAAc,qBAAqB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,cAAc,CAAC;AAClD,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AACjC,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AACxE,cAAc,gBAAgB,CAAC;AAC/B,cAAc,cAAc,CAAC;AAC7B,cAAc,YAAY,CAAC;AAC3B,cAAc,qBAAqB,CAAC"}

package/dist/index.js

@@ -1,6 +1,7 @@
 export { default as version } from './version.js';
 export { Jats } from './jats.js';
-export { convertToUnist } from './utils.js';
+export { convertToUnist, convertToXml, escapeForXML } from './utils.js';
+export * from './serialize.js';
 export * from './session.js';
 export * from './types.js';
 export * from './validate/index.js';

package/dist/jats.cjs

@@ -5741,7 +5741,7 @@ var require_js2xml = __commonJS({
 // ../../node_modules/xml-js/lib/json2xml.js
 var require_json2xml = __commonJS({
   "../../node_modules/xml-js/lib/json2xml.js"(exports, module2) {
-    var js2xml = require_js2xml();
+    var js2xml2 = require_js2xml();
     module2.exports = function(json2, options) {
       if (json2 instanceof Buffer) {
         json2 = json2.toString();
@@ -5756,7 +5756,7 @@ var require_json2xml = __commonJS({
       } else {
         js = json2;
       }
-      return js2xml(js, options);
+      return js2xml2(js, options);
     };
   }
 });
@@ -5766,12 +5766,12 @@ var require_lib2 = __commonJS({
   "../../node_modules/xml-js/lib/index.js"(exports, module2) {
     var xml2js2 = require_xml2js();
     var xml2json = require_xml2json();
-    var js2xml = require_js2xml();
+    var js2xml2 = require_js2xml();
     var json2xml = require_json2xml();
     module2.exports = {
       xml2js: xml2js2,
       xml2json,
-      js2xml,
+      js2xml: js2xml2,
       json2xml
     };
   }
@@ -13022,7 +13022,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.0.5";
+var version = "1.0.7";
 var version_default = version;
 
 // src/cli/parse.ts
@@ -15266,7 +15266,7 @@ function getSession(logger) {
 }
 
 // src/jats.ts
-var import_xml_js = __toESM(require_lib2(), 1);
+var import_xml_js2 = __toESM(require_lib2(), 1);
 
 // src/utils.ts
 function convertToUnist(node) {
@@ -15275,7 +15275,7 @@ function convertToUnist(node) {
       const { name: name2, attributes, elements } = node;
       const children = elements == null ? void 0 : elements.map(convertToUnist).filter((n) => !!n);
       const { type: type2, ...attrs } = attributes != null ? attributes : {};
-      if (type2)
+      if (type2 !== void 0)
         attrs._type = type2;
       const next = { type: name2 != null ? name2 : "unknown", ...attrs };
       if (name2 === "code") {
@@ -15289,7 +15289,7 @@ function convertToUnist(node) {
       return {
         type: "text",
         ...attributes,
-        value: String(text).replace(/\n(\s+)$/, "").replace("\n", " ")
+        value: String(text).replace(/\n(\s+)$/, "")
       };
     }
     case "cdata": {
@@ -15312,6 +15312,35 @@ function convertToUnist(node) {
       throw new Error(`found ${node.type} ${node.name}`);
   }
 }
+function convertToXml(node) {
+  const { type: type2, ...rest } = node;
+  switch (type2) {
+    case "text": {
+      const { value, ...attributes } = rest;
+      return { type: "text", attributes, text: value };
+    }
+    case "code": {
+      const { value, ...attributes } = rest;
+      return { type: "element", name: type2, attributes, elements: [{ type: "text", text: value }] };
+    }
+    case "comment": {
+      return { type: "comment", comment: rest.value };
+    }
+    case "cdata": {
+      const { cdata, ...attributes } = rest;
+      return { type: "cdata", attributes, cdata };
+    }
+    default: {
+      const { children, _type, ...attributes } = rest;
+      if (_type !== void 0)
+        attributes.type = _type;
+      return { type: "element", name: type2, attributes, elements: children == null ? void 0 : children.map(convertToXml) };
+    }
+  }
+}
+function escapeForXML(text) {
+  return text.replace(/&(?!amp;)/g, "&amp;").replace(/</g, "&lt;");
+}
 var MonthLookup = {
   jan: 0,
   january: 0,
@@ -15395,11 +15424,156 @@ function authorAndAffiliation(node, article) {
   return author;
 }
 
+// src/order.ts
+var articleMetaOrder = [
+  "article-id",
+  "article-version",
+  "article-version-alternatives",
+  "article-categories",
+  "title-group",
+  "contrib-group",
+  "aff",
+  "aff-alternatives",
+  "x",
+  "author-notes",
+  "pub-date",
+  "pub-date-not-available",
+  "volume",
+  "volume-id",
+  "volume-series",
+  "issue",
+  "issue-id",
+  "issue-title",
+  "issue-title-group",
+  "issue-sponsor",
+  "issue-part",
+  "volume-issue-group",
+  "isbn",
+  "supplement",
+  "fpage",
+  "lpage",
+  "page-range",
+  "elocation-id",
+  "email",
+  "ext-link",
+  "uri",
+  "product",
+  "supplementary-material",
+  "history",
+  "pub-history",
+  "permissions",
+  "self-uri",
+  "related-article",
+  "related-object",
+  "abstract",
+  "trans-abstract",
+  "kwd-group",
+  "funding-group",
+  "support-group",
+  "conference",
+  "counts",
+  "custom-meta-group"
+];
+
+// src/serialize.ts
+var import_xml_js = __toESM(require_lib2(), 1);
+var both = [
+  "\\?xml",
+  "article",
+  "sub-article",
+  "front",
+  "front-stub",
+  "journal-meta",
+  "journal-title-group",
+  "publisher",
+  "article-meta",
+  "article-categories",
+  "title-group",
+  "contrib-group",
+  "contrib",
+  "institution-wrap",
+  "aff",
+  "permissions",
+  "license",
+  "kwd-group",
+  "history",
+  "self-uri",
+  "funding-group",
+  "award-group",
+  "principal-award-recipient",
+  "custom-meta-group",
+  "date",
+  "pub-date",
+  "abstract",
+  "counts",
+  "body",
+  "sec",
+  "fig",
+  "disp-formula",
+  "table-wrap",
+  "caption",
+  "table",
+  "thead",
+  "ref-list",
+  "ref",
+  "back"
+];
+var first = [
+  "journal-id",
+  "journal-title",
+  "issn",
+  "publisher-name",
+  "publisher-loc",
+  "article-id",
+  "article-title",
+  "alt-title",
+  "subtitle",
+  "kwd",
+  "name",
+  "email",
+  "contrib-id",
+  "role",
+  "institution",
+  "institution-id",
+  "award-id",
+  "meta-name",
+  "meta-value",
+  "title",
+  "p",
+  "tr",
+  "label",
+  "graphic",
+  "mixed-citation"
+];
+function indentXML(xml) {
+  return xml.replace(RegExp(`<(\\/)?(${both.join("|")})( [^>]*)?>`, "g"), "<$1$2$3>\n").replace(RegExp(`([^
+])<(\\/)?(${both.join("|")})( [^>]*)?>`, "g"), "$1\n<$2$3$4>").replace(RegExp(`([^
+])<(${first.join("|")})( [^>]*)?>`, "g"), "$1\n<$2$3>").replace(RegExp(`<\\/(${first.join("|")})(\\s*)>([^
+])`, "g"), "</$1>\n$3");
+}
+function serializeJatsXml(element, opts) {
+  const { format: format2 } = { format: "pretty", ...opts };
+  const xml = (0, import_xml_js.js2xml)(element, {
+    compact: false,
+    //  No way to write XML with new lines, but no indentation with js2xml.
+    // If you use 0 or '', you get a single line.
+    spaces: format2 === "flat" || format2 === "pretty" ? 0 : format2 || 1,
+    attributeValueFn: escapeForXML
+  });
+  if (format2 === 0) {
+    return xml.replace(/\n(\s*)</g, "\n<");
+  } else if (format2 === "pretty") {
+    return indentXML(xml);
+  }
+  return xml;
+}
+
 // src/jats.ts
 function select2(selector, node) {
   var _a;
   return (_a = select(selector, node)) != null ? _a : void 0;
 }
+var 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"';
 var Jats = class {
   constructor(data, opts) {
     var _a;
@@ -15408,7 +15582,7 @@ var Jats = class {
     if (opts == null ? void 0 : opts.source)
       this.source = opts.source;
     try {
-      this.raw = (0, import_xml_js.xml2js)(data, { compact: false });
+      this.raw = (0, import_xml_js2.xml2js)(data, { compact: false });
     } catch (error) {
       throw new Error("Problem parsing the JATS document, please ensure it is XML");
     }
@@ -15426,6 +15600,7 @@ var Jats = class {
     var _a, _b, _c, _d;
     const title = this.articleTitle;
     const subtitle = this.articleSubtitle;
+    const short_title = this.articleAltTitle;
     const date = this.publicationDate;
     const authors = this.articleAuthors;
     const firstSubject = select2(Tags.subject, (_a = this.articleCategories) != null ? _a : this.front);
@@ -15433,6 +15608,7 @@ var Jats = class {
     return {
       title: title ? toText(title) : void 0,
       subtitle: subtitle ? toText(subtitle) : void 0,
+      short_title: short_title ? toText(short_title) : void 0,
       doi: (_b = this.doi) != null ? _b : void 0,
       date: date ? (_c = toDate(date)) == null ? void 0 : _c.toISOString() : void 0,
       authors: authors == null ? void 0 : authors.map((a) => authorAndAffiliation(a, this.tree)),
@@ -15444,7 +15620,10 @@ var Jats = class {
   get front() {
     return select2(Tags.front, this.tree);
   }
-  get premissions() {
+  get articleMeta() {
+    return select2(Tags.articleMeta, this.tree);
+  }
+  get permissions() {
     return select2(Tags.permissions, this.front);
   }
   get doi() {
@@ -15465,7 +15644,7 @@ var Jats = class {
     return this.publicationDates.find((d) => !!select2(Tags.day, d));
   }
   get license() {
-    return select2(Tags.license, this.premissions);
+    return select2(Tags.license, this.permissions);
   }
   get keywordGroup() {
     return select2(Tags.kwdGroup, this.front);
@@ -15489,6 +15668,9 @@ var Jats = class {
   get articleSubtitle() {
     return select2(Tags.subtitle, this.titleGroup);
   }
+  get articleAltTitle() {
+    return select2(Tags.altTitle, this.titleGroup);
+  }
   get abstract() {
     return select2(Tags.abstract, this.front);
   }
@@ -15519,6 +15701,32 @@ var Jats = class {
   get references() {
     return selectAll(Tags.ref, this.refList);
   }
+  sort() {
+    var _a;
+    if (this.articleMeta) {
+      this.articleMeta.children = (_a = this.articleMeta) == null ? void 0 : _a.children.sort(
+        (a, b) => articleMetaOrder.findIndex((x2) => x2 === a.type) - articleMetaOrder.findIndex((x2) => x2 === b.type)
+      );
+    }
+  }
+  serialize(opts) {
+    var _a;
+    this.sort();
+    const body = convertToXml(this.tree);
+    const element = (opts == null ? void 0 : opts.bodyOnly) ? body : {
+      type: "element",
+      elements: [
+        {
+          type: "doctype",
+          doctype: this.doctype || DEFAULT_DOCTYPE
+        },
+        body
+      ],
+      declaration: { attributes: (_a = this.declaration) != null ? _a : { version: "1.0", encoding: "UTF-8" } }
+    };
+    const xml = serializeJatsXml(element, opts);
+    return xml;
+  }
 };
 function hasSingleArticle(element) {
   var _a;
@@ -16812,7 +17020,7 @@ function fixResponseChunkedTransferBadEnding(request, errorCallback) {
   });
 }
 
-// ../jats-download/dist/resolvers.js
+// ../jats-fetch/dist/resolvers.js
 var elife2 = {
   test(url) {
     return new URL(url).hostname === "elifesciences.org";
@@ -16857,7 +17065,7 @@ async function customResolveJatsUrlFromDoi(session, doiString, opts = { resolver
   return jatsUrl;
 }
 
-// ../jats-download/dist/download.js
+// ../jats-fetch/dist/download.js
 async function downloadFromUrl(session, jatsUrl, opts) {
   var _a, _b;
   const toc = tic();
@@ -19631,14 +19839,14 @@ function isPlainSafeLast(c) {
   return !isWhitespace(c) && c !== CHAR_COLON;
 }
 function codePointAt(string, pos) {
-  var first = string.charCodeAt(pos), second;
-  if (first >= 55296 && first <= 56319 && pos + 1 < string.length) {
+  var first2 = string.charCodeAt(pos), second;
+  if (first2 >= 55296 && first2 <= 56319 && pos + 1 < string.length) {
     second = string.charCodeAt(pos + 1);
     if (second >= 56320 && second <= 57343) {
-      return (first - 55296) * 1024 + second - 56320 + 65536;
+      return (first2 - 55296) * 1024 + second - 56320 + 65536;
     }
   }
-  return first;
+  return first2;
 }
 function needIndentIndicator(string) {
   var leadingSpaceRe = /^\n* /;

package/dist/jats.d.ts

@@ -1,12 +1,16 @@
 import type { GenericParent } from 'myst-common';
 import type { Element, DeclarationAttributes } from 'xml-js';
 import type { PageFrontmatter } from 'myst-frontmatter';
-import type { Front, Body, Back, SubArticle, RefList, Reference, TitleGroup, ArticleTitle, Subtitle, Permissions, PubDate, License, Abstract, ContribGroup, Contrib, KeywordGroup, Keyword, ArticleCategories } from 'jats-tags';
+import type { Front, Body, Back, SubArticle, RefList, Reference, TitleGroup, ArticleTitle, Subtitle, Permissions, PubDate, License, Abstract, ContribGroup, Contrib, KeywordGroup, Keyword, ArticleCategories, ArticleMeta } from 'jats-tags';
 import type { Logger } from 'myst-cli-utils';
+import { type SerializationOptions } from './serialize.js';
 type Options = {
     log?: Logger;
     source?: string;
 };
+type WriteOptions = SerializationOptions & {
+    bodyOnly?: boolean;
+};
 export declare class Jats {
     declaration?: DeclarationAttributes;
     doctype?: string;
@@ -17,7 +21,8 @@ export declare class Jats {
     constructor(data: string, opts?: Options);
     get frontmatter(): PageFrontmatter;
     get front(): Front | undefined;
-    get premissions(): Permissions | undefined;
+    get articleMeta(): ArticleMeta | undefined;
+    get permissions(): Permissions | undefined;
     get doi(): string | undefined;
     get pmc(): string | undefined;
     get pmid(): string | undefined;
@@ -32,6 +37,7 @@ export declare class Jats {
     get titleGroup(): TitleGroup | undefined;
     get articleTitle(): ArticleTitle | undefined;
     get articleSubtitle(): Subtitle | undefined;
+    get articleAltTitle(): Subtitle | undefined;
     get abstract(): Abstract | undefined;
     get abstracts(): Abstract[];
     get contribGroup(): ContribGroup | undefined;
@@ -42,6 +48,8 @@ export declare class Jats {
     get subArticles(): SubArticle[];
     get refList(): RefList | undefined;
     get references(): Reference[];
+    sort(): void;
+    serialize(opts?: WriteOptions): string;
 }
 export {};
 //# sourceMappingURL=jats.d.ts.map

package/dist/jats.d.ts.map

@@ -1 +1 @@
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package/dist/jats.js

@@ -3,12 +3,15 @@ import { xml2js } from 'xml-js';
 import { doi } from 'doi-utils';
 import { select as unistSelect, selectAll } from 'unist-util-select';
 import { Tags } from 'jats-tags';
-import { authorAndAffiliation, convertToUnist, findArticleId, toDate } from './utils.js';
+import { authorAndAffiliation, convertToUnist, convertToXml, findArticleId, toDate, } from './utils.js';
 import { tic } from 'myst-cli-utils';
+import { articleMetaOrder } from './order.js';
+import { serializeJatsXml } from './serialize.js';
 function select(selector, node) {
     var _a;
     return ((_a = unistSelect(selector, node)) !== null && _a !== void 0 ? _a : undefined);
 }
+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"';
 export class Jats {
     constructor(data, opts) {
         var _a;
@@ -36,6 +39,7 @@ export class Jats {
         var _a, _b, _c, _d;
         const title = this.articleTitle;
         const subtitle = this.articleSubtitle;
+        const short_title = this.articleAltTitle;
         const date = this.publicationDate;
         const authors = this.articleAuthors;
         const firstSubject = select(Tags.subject, (_a = this.articleCategories) !== null && _a !== void 0 ? _a : this.front);
@@ -43,6 +47,7 @@ export class Jats {
         return {
             title: title ? toText(title) : undefined,
             subtitle: subtitle ? toText(subtitle) : undefined,
+            short_title: short_title ? toText(short_title) : undefined,
             doi: (_b = this.doi) !== null && _b !== void 0 ? _b : undefined,
             date: date ? (_c = toDate(date)) === null || _c === void 0 ? void 0 : _c.toISOString() : undefined,
             authors: authors === null || authors === void 0 ? void 0 : authors.map((a) => authorAndAffiliation(a, this.tree)),
@@ -54,7 +59,10 @@ export class Jats {
     get front() {
         return select(Tags.front, this.tree);
     }
-    get premissions() {
+    get articleMeta() {
+        return select(Tags.articleMeta, this.tree);
+    }
+    get permissions() {
         return select(Tags.permissions, this.front);
     }
     get doi() {
@@ -75,7 +83,7 @@ export class Jats {
         return this.publicationDates.find((d) => !!select(Tags.day, d));
     }
     get license() {
-        return select(Tags.license, this.premissions);
+        return select(Tags.license, this.permissions);
     }
     get keywordGroup() {
         return select(Tags.kwdGroup, this.front);
@@ -99,6 +107,9 @@ export class Jats {
     get articleSubtitle() {
         return select(Tags.subtitle, this.titleGroup);
     }
+    get articleAltTitle() {
+        return select(Tags.altTitle, this.titleGroup);
+    }
     get abstract() {
         return select(Tags.abstract, this.front);
     }
@@ -129,6 +140,33 @@ export class Jats {
     get references() {
         return selectAll(Tags.ref, this.refList);
     }
+    sort() {
+        var _a;
+        if (this.articleMeta) {
+            this.articleMeta.children = (_a = this.articleMeta) === null || _a === void 0 ? void 0 : _a.children.sort((a, b) => articleMetaOrder.findIndex((x) => x === a.type) -
+                articleMetaOrder.findIndex((x) => x === b.type));
+        }
+    }
+    serialize(opts) {
+        var _a;
+        this.sort();
+        const body = convertToXml(this.tree);
+        const element = (opts === null || opts === void 0 ? void 0 : opts.bodyOnly)
+            ? body
+            : {
+                type: 'element',
+                elements: [
+                    {
+                        type: 'doctype',
+                        doctype: this.doctype || DEFAULT_DOCTYPE,
+                    },
+                    body,
+                ],
+                declaration: { attributes: (_a = this.declaration) !== null && _a !== void 0 ? _a : { version: '1.0', encoding: 'UTF-8' } },
+            };
+        const xml = serializeJatsXml(element, opts);
+        return xml;
+    }
 }
 function hasSingleArticle(element) {
     var _a;

package/dist/order.d.ts

@@ -0,0 +1,2 @@
+export declare const articleMetaOrder: string[];
+//# sourceMappingURL=order.d.ts.map

package/dist/order.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"order.d.ts","sourceRoot":"","sources":["../src/order.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,gBAAgB,UAgD5B,CAAC"}

package/dist/order.js

@@ -0,0 +1,49 @@
+export const articleMetaOrder = [
+    'article-id',
+    'article-version',
+    'article-version-alternatives',
+    'article-categories',
+    'title-group',
+    'contrib-group',
+    'aff',
+    'aff-alternatives',
+    'x',
+    'author-notes',
+    'pub-date',
+    'pub-date-not-available',
+    'volume',
+    'volume-id',
+    'volume-series',
+    'issue',
+    'issue-id',
+    'issue-title',
+    'issue-title-group',
+    'issue-sponsor',
+    'issue-part',
+    'volume-issue-group',
+    'isbn',
+    'supplement',
+    'fpage',
+    'lpage',
+    'page-range',
+    'elocation-id',
+    'email',
+    'ext-link',
+    'uri',
+    'product',
+    'supplementary-material',
+    'history',
+    'pub-history',
+    'permissions',
+    'self-uri',
+    'related-article',
+    'related-object',
+    'abstract',
+    'trans-abstract',
+    'kwd-group',
+    'funding-group',
+    'support-group',
+    'conference',
+    'counts',
+    'custom-meta-group',
+];

package/dist/serialize.d.ts

@@ -0,0 +1,12 @@
+import { type Element } from 'xml-js';
+export type SerializationOptions = {
+    /**
+     * When 'pretty', the default, the xml be formatted in a custom, opinionated way
+     * When 'flat', the xml will be on a single line
+     * When `0`, the XML will be on different lines with 0 spaces.
+     * When any other value (e.g. `2` or `\t`) the XML will be indented at the start of the line by that amount.
+     */
+    format?: number | 'flat' | 'pretty' | '\t';
+};
+export declare function serializeJatsXml(element: Element, opts?: SerializationOptions): string;
+//# sourceMappingURL=serialize.d.ts.map

package/dist/serialize.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"serialize.d.ts","sourceRoot":"","sources":["../src/serialize.ts"],"names":[],"mappings":"AAAA,OAAO,EAAU,KAAK,OAAO,EAAE,MAAM,QAAQ,CAAC;AAG9C,MAAM,MAAM,oBAAoB,GAAG;IACjC;;;;;OAKG;IACH,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,QAAQ,GAAG,IAAI,CAAC;CAC5C,CAAC;AA+EF,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,IAAI,CAAC,EAAE,oBAAoB,UAgB7E"}

package/dist/serialize.js

@@ -0,0 +1,95 @@
+import { js2xml } from 'xml-js';
+import { escapeForXML } from './utils.js';
+const both = [
+    '\\?xml',
+    'article',
+    'sub-article',
+    'front',
+    'front-stub',
+    'journal-meta',
+    'journal-title-group',
+    'publisher',
+    'article-meta',
+    'article-categories',
+    'title-group',
+    'contrib-group',
+    'contrib',
+    'institution-wrap',
+    'aff',
+    'permissions',
+    'license',
+    'kwd-group',
+    'history',
+    'self-uri',
+    'funding-group',
+    'award-group',
+    'principal-award-recipient',
+    'custom-meta-group',
+    'date',
+    'pub-date',
+    'abstract',
+    'counts',
+    'body',
+    'sec',
+    'fig',
+    'disp-formula',
+    'table-wrap',
+    'caption',
+    'table',
+    'thead',
+    'ref-list',
+    'ref',
+    'back',
+];
+const first = [
+    'journal-id',
+    'journal-title',
+    'issn',
+    'publisher-name',
+    'publisher-loc',
+    'article-id',
+    'article-title',
+    'alt-title',
+    'subtitle',
+    'kwd',
+    'name',
+    'email',
+    'contrib-id',
+    'role',
+    'institution',
+    'institution-id',
+    'award-id',
+    'meta-name',
+    'meta-value',
+    'title',
+    'p',
+    'tr',
+    'label',
+    'graphic',
+    'mixed-citation',
+];
+function indentXML(xml) {
+    return xml
+        .replace(RegExp(`<(\\/)?(${both.join('|')})( [^>]*)?>`, 'g'), '<$1$2$3>\n')
+        .replace(RegExp(`([^\n])<(\\/)?(${both.join('|')})( [^>]*)?>`, 'g'), '$1\n<$2$3$4>')
+        .replace(RegExp(`([^\n])<(${first.join('|')})( [^>]*)?>`, 'g'), '$1\n<$2$3>')
+        .replace(RegExp(`<\\/(${first.join('|')})(\\s*)>([^\n])`, 'g'), '</$1>\n$3');
+}
+export function serializeJatsXml(element, opts) {
+    const { format } = { format: 'pretty', ...opts };
+    const xml = js2xml(element, {
+        compact: false,
+        //  No way to write XML with new lines, but no indentation with js2xml.
+        // If you use 0 or '', you get a single line.
+        spaces: format === 'flat' || format === 'pretty' ? 0 : format || 1,
+        attributeValueFn: escapeForXML,
+    });
+    if (format === 0) {
+        // either `0` or `''`
+        return xml.replace(/\n(\s*)</g, '\n<');
+    }
+    else if (format === 'pretty') {
+        return indentXML(xml);
+    }
+    return xml;
+}

package/dist/utils.d.ts

@@ -2,6 +2,8 @@ import type { GenericNode, GenericParent } from 'myst-common';
 import type { Element } from 'xml-js';
 import type { Contributor } from 'myst-frontmatter';
 export declare function convertToUnist(node: Element): GenericNode | GenericParent | undefined;
+export declare function convertToXml(node: GenericNode): Element;
+export declare function escapeForXML(text: string): string;
 export declare function toDate(date?: GenericParent): Date | undefined;
 export declare function formatDate(date?: Date): string | undefined;
 export type PubIdTypes = 'doi' | 'pmc' | 'pmid' | 'publisher-id' | string;

package/dist/utils.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../src/utils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAE9D,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAC;AAKtC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAEpD,wBAAgB,cAAc,CAAC,IAAI,EAAE,OAAO,GAAG,WAAW,GAAG,aAAa,GAAG,SAAS,CA2CrF;AAED,wBAAgB,YAAY,CAAC,IAAI,EAAE,WAAW,GAAG,OAAO,CAwBvD;AAED,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,UAExC;AA6BD,wBAAgB,MAAM,CAAC,IAAI,CAAC,EAAE,aAAa,GAAG,IAAI,GAAG,SAAS,CAa7D;AAED,wBAAgB,UAAU,CAAC,IAAI,CAAC,EAAE,IAAI,sBAGrC;AAED,MAAM,MAAM,UAAU,GAAG,KAAK,GAAG,KAAK,GAAG,MAAM,GAAG,cAAc,GAAG,MAAM,CAAC;AAE1E,wBAAgB,aAAa,CAC3B,IAAI,EAAE,aAAa,GAAG,SAAS,EAC/B,SAAS,GAAE,UAAkB,GAC5B,MAAM,GAAG,SAAS,CAQpB;AAED,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,aAAa,EAAE,OAAO,EAAE,aAAa,GAAG,WAAW,CAyC7F"}

package/dist/utils.js

@@ -8,7 +8,7 @@ export function convertToUnist(node) {
             const { name, attributes, elements } = node;
             const children = elements === null || elements === void 0 ? void 0 : elements.map(convertToUnist).filter((n) => !!n);
             const { type, ...attrs } = attributes !== null && attributes !== void 0 ? attributes : {};
-            if (type)
+            if (type !== undefined)
                 attrs._type = type;
             const next = { type: name !== null && name !== void 0 ? name : 'unknown', ...attrs };
             if (name === 'code') {
@@ -23,9 +23,7 @@ export function convertToUnist(node) {
             return {
                 type: 'text',
                 ...attributes,
-                value: String(text)
-                    .replace(/\n(\s+)$/, '')
-                    .replace('\n', ' '),
+                value: String(text).replace(/\n(\s+)$/, ''),
             };
         }
         case 'cdata': {
@@ -51,6 +49,35 @@ export function convertToUnist(node) {
             throw new Error(`found ${node.type} ${node.name}`);
     }
 }
+export function convertToXml(node) {
+    const { type, ...rest } = node;
+    switch (type) {
+        case 'text': {
+            const { value, ...attributes } = rest;
+            return { type: 'text', attributes, text: value };
+        }
+        case 'code': {
+            const { value, ...attributes } = rest;
+            return { type: 'element', name: type, attributes, elements: [{ type: 'text', text: value }] };
+        }
+        case 'comment': {
+            return { type: 'comment', comment: rest.value };
+        }
+        case 'cdata': {
+            const { cdata, ...attributes } = rest;
+            return { type: 'cdata', attributes, cdata };
+        }
+        default: {
+            const { children, _type, ...attributes } = rest;
+            if (_type !== undefined)
+                attributes.type = _type;
+            return { type: 'element', name: type, attributes, elements: children === null || children === void 0 ? void 0 : children.map(convertToXml) };
+        }
+    }
+}
+export function escapeForXML(text) {
+    return text.replace(/&(?!amp;)/g, '&amp;').replace(/</g, '&lt;');
+}
 const MonthLookup = {
     jan: 0,
     january: 0,

package/dist/version.d.ts

@@ -1,3 +1,3 @@
-declare const version = "1.0.5";
+declare const version = "1.0.7";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/dist/version.js

@@ -1,2 +1,2 @@
-const version = '1.0.5';
+const version = '1.0.7';
 export default version;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-xml",
-  "version": "1.0.5",
+  "version": "1.0.7",
   "description": "Types and utilities for working with JATS in Typescript",
   "author": "Rowan Cockett <rowan@curvenote.com>",
   "homepage": "https://github.com/curvenote/jats",
@@ -48,8 +48,8 @@
     "adm-zip": "^0.5.10",
     "doi-utils": "^2.0.0",
     "fair-principles": "^2.0.0",
-    "jats-download": "^1.0.5",
-    "jats-tags": "^1.0.5",
+    "jats-fetch": "^1.0.7",
+    "jats-tags": "^1.0.7",
     "js-yaml": "^4.1.0",
     "node-fetch": "^3.3.1",
     "unist-util-is": "^5.2.1",