jats-xml 1.0.8 → 1.0.10

package/README.md

@@ -6,15 +6,6 @@
 
 Types and utilities for working with JATS XML documents in Node and Typescript.
 
-Read and write JATS XML from node or see summries from the command line.
-
-To use from the command line, use the `-g` to create a global install, which will provide a `jats` CLI:
-
-```
-npm install -g jats-xml
-jats -v
-```
-
 ## What is JATS?
 
 JATS is a NISO standard for Journal Article Tags Schema, which is a way to define the XML structure of a scientific article semantically. This includes the `front`-matter (authors, funding, title, abstract, etc.), the `body` of the article (sections, figures, equations, tables, etc.), and `back`-matter (references, footnotes, etc.). The JATS can also contain `sub-articles`.
@@ -23,58 +14,6 @@ The standard documents are hosted by the NIH <https://jats.nlm.nih.gov/>. There
 
 Note that most publishers do **not** provide the XML as a first class output - they should, it is an important part of open-science to have the content programatically accessible and interoperable. It is only [FAIR](https://www.go-fair.org/fair-principles/) 😉.
 
-## From the command line
-
-Commands available:
-
-`download`: attempt to find the JATS file and download it locally.
-
-```bash
-jats download https://elifesciences.org/articles/81952 article.jats
-```
-
-Note, currently this just downloads the XML, **not** the associated files.
-
-`summary`: summarize the contents of the JATS, given a URL, DOI, or local file
-
-```bash
-jats summary https://elifesciences.org/articles/81952
-jats summary 10.1371/journal.pclm.0000068
-jats summary /local/article.jats
-```
-
-This will provide a summary, including a list of what the JATS file contains.
-
-![Output of `jats summary`](/images/jats-output.png)
-
-`validate`: validate local file against JATS Archive DTD schema. By default, this uses JATS 1.3.
-
-```bash
-jats validate article.jats --jats 1.2 --mathmml 2
-```
-
-`test`: test a JATS file against a list of unit tests in YAML
-
-The test cases are useful for known exports and expecting specific pieces of information in the XML.
-
-```bash
-jats test article.jats --cases tests.yml
-```
-
-```yaml
-cases:
-  - title: Correct publisher ID (publisher-id)
-    select: 'front > journal-meta > journal-id[journal-id-type="publisher-id"] > *'
-    equals:
-      type: text
-      value: plos
-  - title: Every orcid is authenticated
-    selectAll: 'front > article-meta > contrib-group > contrib > contrib-id'
-    equals:
-      contrib-id-type: orcid
-      authenticated: 'true'
-```
-
 ## Working in Typescript
 
 All tags are accessible as types/enums. There is also documentation from each node-type
@@ -116,6 +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://curvenote.com" target="_blank" style="color: #aaa">
-    <img src="https://curvenote.dev/images/icon.png" style="height: 1em" /> Curvenote
+    <img src="https://cdn.curvenote.com/brand/logo-blue-icon.png" style="height: 1em" /> Curvenote
   </a>
 </p>

package/dist/index.d.ts

@@ -2,5 +2,6 @@ export { default as version } from './version.js';
 export { Jats } from './jats.js';
 export * from './session.js';
 export * from './types.js';
+export * from './utils.js';
 export * from './validate/index.js';
 //# sourceMappingURL=index.d.ts.map

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,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,cAAc,cAAc,CAAC;AAC7B,cAAc,YAAY,CAAC;AAC3B,cAAc,YAAY,CAAC;AAC3B,cAAc,qBAAqB,CAAC"}

package/dist/index.js

@@ -2,4 +2,5 @@ export { default as version } from './version.js';
 export { Jats } from './jats.js';
 export * from './session.js';
 export * from './types.js';
+export * from './utils.js';
 export * from './validate/index.js';

package/dist/jats.d.ts

@@ -1,7 +1,7 @@
 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, ArticleMeta } from 'jats-tags';
+import { type PageFrontmatter } from 'myst-frontmatter';
+import type { Front, Body, Back, SubArticle, RefList, Reference, TitleGroup, ArticleTitle, Subtitle, Permissions, PubDate, License, Abstract, ContribGroup, Contrib, Affiliation, KeywordGroup, Keyword, ArticleCategories, ArticleMeta } from 'jats-tags';
 import type { Logger } from 'myst-cli-utils';
 import { type SerializationOptions } from 'jats-utils';
 type Options = {
@@ -43,6 +43,7 @@ export declare class Jats {
     get contribGroup(): ContribGroup | undefined;
     get contribGroups(): ContribGroup[];
     get articleAuthors(): Contrib[];
+    get articleAffiliations(): Affiliation[];
     get body(): Body | undefined;
     get back(): Back | undefined;
     get subArticles(): SubArticle[];

package/dist/jats.d.ts.map

@@ -1 +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,KAAK,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AAIxD,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,YAAY,EACZ,OAAO,EACP,iBAAiB,EACjB,WAAW,EACZ,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;AASjD,KAAK,YAAY,GAAG,oBAAoB,GAAG;IACzC,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB,CAAC;AAEF,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;IAsBxC,IAAI,WAAW,IAAI,eAAe,CAmBjC;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,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,CAE9B;IAED,IAAI,IAAI,IAAI,IAAI,GAAG,SAAS,CAE3B;IAED,IAAI,IAAI,IAAI,IAAI,GAAG,SAAS,CAE3B;IAED,IAAI,WAAW,IAAI,UAAU,EAAE,CAE9B;IAED,IAAI,OAAO,IAAI,OAAO,GAAG,SAAS,CAEjC;IAED,IAAI,UAAU,IAAI,SAAS,EAAE,CAE5B;IAED,IAAI;IAUJ,SAAS,CAAC,IAAI,CAAC,EAAE,YAAY,GAAG,MAAM;CAoBvC"}
+{"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;AASjD,KAAK,YAAY,GAAG,oBAAoB,GAAG;IACzC,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB,CAAC;AAEF,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;IA0BxC,IAAI,WAAW,IAAI,eAAe,CAgEjC;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,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,IAAI,OAAO,IAAI,OAAO,GAAG,SAAS,CAEjC;IAED,IAAI,UAAU,IAAI,SAAS,EAAE,CAE5B;IAED,IAAI;IAeJ,SAAS,CAAC,IAAI,CAAC,EAAE,YAAY,GAAG,MAAM;CAoBvC"}

package/dist/jats.js

@@ -1,11 +1,12 @@
 import { toText } from 'myst-common';
 import { xml2js } from 'xml-js';
 import { doi } from 'doi-utils';
+import { validatePageFrontmatter } from 'myst-frontmatter';
 import { select as unistSelect, selectAll } from 'unist-util-select';
 import { Tags } from 'jats-tags';
-import { authorAndAffiliation, findArticleId } from './utils.js';
+import { findArticleId, processAffiliation, processContributor } from './utils.js';
 import { tic } from 'myst-cli-utils';
-import { articleMetaOrder } from './order.js';
+import { articleMetaOrder, tableWrapOrder } from './order.js';
 import { serializeJatsXml, convertToUnist, convertToXml, toDate, } from 'jats-utils';
 function select(selector, node) {
     var _a;
@@ -14,7 +15,7 @@ function select(selector, node) {
 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;
+        var _a, _b;
         const toc = tic();
         this.log = opts === null || opts === void 0 ? void 0 : opts.log;
         if (opts === null || opts === void 0 ? void 0 : opts.source)
@@ -27,34 +28,85 @@ export class Jats {
         }
         const { declaration, elements } = this.raw;
         this.declaration = declaration === null || declaration === void 0 ? void 0 : declaration.attributes;
+        if ((elements === null || elements === void 0 ? void 0 : elements.length) && elements[0].type !== 'doctype') {
+            (_a = this.log) === null || _a === void 0 ? void 0 : _a.warn('JATS is missing DOCTYPE declaration');
+            elements.unshift({ type: 'doctype' });
+        }
         if (!((elements === null || elements === void 0 ? void 0 : elements.length) === 2 && elements[0].type === 'doctype' && hasSingleArticle(elements[1]))) {
-            throw new Error('Element <article> is not the only element of the JATS');
+            throw new Error('JATS must be structured as <!DOCTYPE><article>...</article>');
         }
         this.doctype = elements[0].doctype;
         const converted = convertToUnist(elements[1]);
         this.tree = select('article', converted);
-        (_a = this.log) === null || _a === void 0 ? void 0 : _a.debug(toc('Parsed and converted JATS to unist tree in %s'));
+        (_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;
+        var _a, _b, _c, _d, _e, _f, _g, _h;
         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);
+        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');
+                date = `${year}-${month}-${day}`;
+            }
+        }
+        const authors = (_a = this.articleAuthors) === null || _a === void 0 ? void 0 : _a.map((auth) => {
+            return processContributor(auth);
+        });
+        const affiliations = (_b = this.articleAffiliations) === null || _b === void 0 ? void 0 : _b.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 journalTitle = select(Tags.journalTitle, this.front);
-        return {
+        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 (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;
+        }
+        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();
+        if (licenseType && ['openaccess', 'open-access'].includes(licenseType)) {
+            openAccess = true;
+        }
+        else if (licenseString === null || licenseString === void 0 ? void 0 : licenseString.match(/^\s*Open Access\s*This/)) {
+            licenseString = licenseString.replace(/^\s*Open Access\s*/, '');
+            openAccess = true;
+        }
+        else if (licenseString === null || licenseString === void 0 ? void 0 : licenseString.toLowerCase().startsWith('this is an open access article')) {
+            openAccess = true;
+        }
+        const frontmatter = validatePageFrontmatter({
             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)),
-            keywords: (_d = this.keywords) === null || _d === void 0 ? void 0 : _d.map((k) => toText(k)),
+            doi: (_h = this.doi) !== null && _h !== void 0 ? _h : undefined,
+            date,
+            authors: authors.length ? authors : undefined,
+            // editors,
+            affiliations: affiliations.length ? affiliations : undefined,
+            keywords: keywords.length ? keywords : undefined,
             venue: journalTitle ? { title: toText(journalTitle) } : undefined,
             subject: firstSubject ? toText(firstSubject) : undefined,
-        };
+            license: licenseString !== null && licenseString !== void 0 ? licenseString : undefined,
+            open_access: openAccess,
+        }, { property: 'frontmatter', messages: {} });
+        return frontmatter;
     }
     get front() {
         return select(Tags.front, this.tree);
@@ -123,7 +175,18 @@ export class Jats {
         return selectAll(Tags.contribGroup, this.front);
     }
     get articleAuthors() {
-        return selectAll(Tags.contrib, this.contribGroup);
+        const contribs = selectAll(Tags.contrib, {
+            type: 'contribGroups',
+            children: this.contribGroups,
+        });
+        const authors = contribs.filter((contrib) => {
+            const contribType = contrib['contrib-type'];
+            return !contribType || contribType === 'author';
+        });
+        return authors;
+    }
+    get articleAffiliations() {
+        return selectAll(`${Tags.aff}[id]`, this.front);
     }
     get body() {
         return select(Tags.body, this.tree);
@@ -146,6 +209,9 @@ export class Jats {
             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));
         }
+        selectAll('table-wrap', this.tree).forEach((tw) => {
+            tw.children = tw.children.sort((a, b) => { var _a, _b; return ((_a = tableWrapOrder[a.type]) !== null && _a !== void 0 ? _a : -1) - ((_b = tableWrapOrder[b.type]) !== null && _b !== void 0 ? _b : -1); });
+        });
     }
     serialize(opts) {
         var _a;

package/dist/order.d.ts

@@ -1,2 +1,3 @@
 export declare const articleMetaOrder: string[];
+export declare const tableWrapOrder: Record<string, number>;
 //# sourceMappingURL=order.d.ts.map

package/dist/order.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"order.d.ts","sourceRoot":"","sources":["../src/order.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,gBAAgB,UAgD5B,CAAC"}
+{"version":3,"file":"order.d.ts","sourceRoot":"","sources":["../src/order.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,gBAAgB,UAgD5B,CAAC;AAaF,eAAO,MAAM,cAAc,wBA0BzB,CAAC"}

package/dist/order.js

@@ -47,3 +47,39 @@ export const articleMetaOrder = [
     'counts',
     'custom-meta-group',
 ];
+function order(tags) {
+    return Object.fromEntries(tags
+        .map((tag, i) => {
+        if (typeof tag === 'string')
+            return [[tag, i]];
+        return tag.map((t) => [t, i]);
+    })
+        .flat());
+}
+export const tableWrapOrder = order([
+    'object-id',
+    'label',
+    'caption',
+    'abstract',
+    'kwd-group',
+    'subj-group',
+    ['alt-text', 'long-desc', 'email', 'ext-link', 'uri'],
+    [
+        'disp-quote',
+        'speech',
+        'statement',
+        'verse-group',
+        'def-list',
+        'list',
+        'alternatives',
+        'chem-struct-wrap',
+        'code',
+        'disp-formula',
+        'graphic',
+        'media',
+        'preformat',
+        'table',
+        'xref',
+    ],
+    ['table-wrap-foot', 'attrib', 'permissions'],
+]);

package/dist/session.d.ts

@@ -1,3 +1,4 @@
+import type { Response } from 'node-fetch';
 import type { Logger } from 'myst-cli-utils';
 import type { ISession } from './types.js';
 export declare class Session implements ISession {
@@ -5,6 +6,7 @@ export declare class Session implements ISession {
     constructor(opts?: {
         logger?: Logger;
     });
+    fetch(): Promise<Response>;
 }
 export declare function getSession(logger: Logger): Session;
 //# sourceMappingURL=session.d.ts.map

package/dist/session.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"session.d.ts","sourceRoot":"","sources":["../src/session.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAC7C,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAC;AAc3C,qBAAa,OAAQ,YAAW,QAAQ;IACtC,GAAG,EAAE,MAAM,CAAC;gBACA,IAAI,CAAC,EAAE;QAAE,MAAM,CAAC,EAAE,MAAM,CAAA;KAAE;CAGvC;AAED,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,WAExC"}
+{"version":3,"file":"session.d.ts","sourceRoot":"","sources":["../src/session.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAC;AAE3C,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAC7C,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAC;AAc3C,qBAAa,OAAQ,YAAW,QAAQ;IACtC,GAAG,EAAE,MAAM,CAAC;gBACA,IAAI,CAAC,EAAE;QAAE,MAAM,CAAC,EAAE,MAAM,CAAA;KAAE;IAGtC,KAAK,IAAI,OAAO,CAAC,QAAQ,CAAC;CAG3B;AAED,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,WAExC"}

package/dist/session.js

@@ -17,6 +17,9 @@ export class Session {
         var _a;
         this.log = xmllintLogWrapper((_a = opts === null || opts === void 0 ? void 0 : opts.logger) !== null && _a !== void 0 ? _a : chalkLogger(LogLevel.debug));
     }
+    fetch() {
+        throw new Error('fetch not implemented on session');
+    }
 }
 export function getSession(logger) {
     return new Session({ logger });

package/dist/utils.d.ts

@@ -1,6 +1,8 @@
 import type { GenericParent } from 'myst-common';
-import type { Contributor } from 'myst-frontmatter';
+import type { Affiliation, Contrib } from 'jats-tags';
+import type { Affiliation as AffiliationFM, Contributor as ContributorFM } from 'myst-frontmatter';
 export type PubIdTypes = 'doi' | 'pmc' | 'pmid' | 'publisher-id' | string;
 export declare function findArticleId(node: GenericParent | undefined, pubIdType?: PubIdTypes): string | undefined;
-export declare function authorAndAffiliation(node: GenericParent, article: GenericParent): Contributor;
+export declare function processContributor(contrib: Contrib): ContributorFM;
+export declare function processAffiliation(aff: Affiliation): AffiliationFM;
 //# sourceMappingURL=utils.d.ts.map

package/dist/utils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../src/utils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAMjD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAEpD,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"}
+{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../src/utils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAe,aAAa,EAAE,MAAM,aAAa,CAAC;AAK9D,OAAO,KAAK,EAAE,WAAW,EAAa,OAAO,EAAmB,MAAM,WAAW,CAAC;AAElF,OAAO,KAAK,EAAE,WAAW,IAAI,aAAa,EAAE,WAAW,IAAI,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAGnG,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,kBAAkB,CAAC,OAAO,EAAE,OAAO,GAAG,aAAa,CAmBlE;AAmBD,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,WAAW,GAAG,aAAa,CAqElE"}

package/dist/utils.js

@@ -2,6 +2,7 @@ import { toText } from 'myst-common';
 import { doi } from 'doi-utils';
 import { select, selectAll } from 'unist-util-select';
 import { Tags } from 'jats-tags';
+import { remove } from 'unist-util-remove';
 export function findArticleId(node, pubIdType = 'doi') {
     if (!node)
         return undefined;
@@ -11,43 +12,107 @@ export function findArticleId(node, pubIdType = 'doi') {
     const doiTag = selectAll(`${Tags.articleId},${Tags.pubId}`, node).find((t) => doi.validate(toText(t)));
     return toText(doiTag) || undefined;
 }
-export function authorAndAffiliation(node, article) {
+export function processContributor(contrib) {
     const author = {
-        name: `${toText(select(Tags.givenNames, node))} ${toText(select(Tags.surname, node))}`,
+        name: `${toText(select(Tags.givenNames, contrib))} ${toText(select(Tags.surname, contrib))}`,
     };
-    const orcid = select('[contrib-id-type=orcid]', node);
+    const orcid = select('[contrib-id-type=orcid]', contrib);
     if (orcid) {
         author.orcid = toText(orcid).replace(/(https?:\/\/)?orcid\.org\//, '');
     }
-    //
-    /**
-     * For example:
-     *
-     * ```xml
-     * <aff id="aff2">
-     * <label>2</label>
-     * <institution-wrap>
-     * <institution-id institution-id-type="ror">https://ror.org/00t9vx427</institution-id>
-     * <institution>Department of Biochemistry, University of Texas Southwestern Medical Center</institution>
-     * </institution-wrap>
-     * <addr-line>
-     * <named-content content-type="city">Dallas</named-content>
-     * </addr-line>
-     * <country>United States</country>
-     * </aff>
-     * ```
-     */
-    const affiliationRefs = selectAll('xref[ref-type=aff]', node);
-    const affiliations = affiliationRefs.map((xref) => select(`[id=${xref.rid}]`, article));
-    const affiliationText = affiliations
-        .map((aff) => {
-        // TODO: handle rors!
-        const ror = select(`[institution-id-type=ror]`, aff);
-        return toText(select('institution', aff));
-    })
-        .filter((t) => !!t);
-    if (affiliationText.length > 0) {
-        author.affiliations = affiliationText;
+    const affiliationRefs = selectAll('xref[ref-type=aff]', contrib);
+    const affiliationIds = affiliationRefs.map((xref) => xref.rid);
+    if (affiliationIds.length > 0) {
+        author.affiliations = affiliationIds;
     }
+    const uri = select('uri', contrib);
+    if (uri === null || uri === void 0 ? void 0 : uri['xlink:href']) {
+        author.url = uri['xlink:href'];
+    }
+    // If there are no aff xrefs AND contrib is in a contrib group with affs AND those affs do not have IDs, add them as affiliations...
     return author;
 }
+/**
+ * Perform standard toText, trim, remove trailing comma and semicolon
+ *
+ * Additionally, this returns undefined instead of empty string if node is undefined
+ */
+function toTextAndTrim(content) {
+    const text = toText(content);
+    if (!text)
+        return undefined;
+    return text.replace(/^[\s;,]+/, '').replace(/[\s;,]+$/, '');
+}
+function markForDeletion(nodes) {
+    nodes.forEach((node) => {
+        if (node)
+            node.type = '__delete__';
+    });
+}
+export function processAffiliation(aff) {
+    var _a, _b;
+    const id = aff.id;
+    let ror;
+    let isni;
+    const rorNode = select(`institution-id[institution-id-type=ror]`, aff);
+    if (rorNode) {
+        ror = toTextAndTrim(rorNode);
+    }
+    const isniNode = select(`institution-id[institution-id-type=ISNI]`, aff);
+    if (isniNode) {
+        isni = toTextAndTrim(isniNode);
+    }
+    markForDeletion(selectAll('institution-id', aff));
+    remove(aff, '__delete__');
+    const institutions = selectAll('institution', aff);
+    const textAddress = selectAll('addr-line > text', aff);
+    const namedContent = selectAll('named-content', aff);
+    const departmentNode = (_a = institutions.find((inst) => inst['content-type'] === 'dept')) !== null && _a !== void 0 ? _a : namedContent.find((content) => content['content-type'] === 'organisation-division');
+    const addressNode = namedContent.find((content) => content['content-type'] === 'street');
+    const cityNode = namedContent.find((content) => content['content-type'] === 'city');
+    const stateNode = namedContent.find((content) => content['content-type'] === 'country-part');
+    const postalCodeNode = namedContent.find((content) => content['content-type'] === 'post-code');
+    const countryNode = (_b = select('country', aff)) !== null && _b !== void 0 ? _b : namedContent.find((content) => content['content-type'] === 'country');
+    markForDeletion([
+        ...textAddress,
+        ...namedContent,
+        departmentNode,
+        addressNode,
+        cityNode,
+        stateNode,
+        postalCodeNode,
+        countryNode,
+    ]);
+    remove(aff, '__delete__');
+    const affChildren = aff.children.filter((child) => child.type !== 'label');
+    let institution;
+    if (affChildren.filter((child) => ['text', 'institution-wrap', 'institution'].includes(child.type))
+        .length === affChildren.length) {
+        institution = toTextAndTrim(affChildren);
+    }
+    else {
+        institution = toTextAndTrim(institutions.find((inst) => inst['content-type'] !== 'dept'));
+    }
+    const addressLines = textAddress
+        .map((line) => toTextAndTrim(line))
+        .filter((line) => !!line);
+    let department = departmentNode
+        ? toTextAndTrim(departmentNode)
+        : addressLines.find((line) => line.toLowerCase().includes('department'));
+    let address = addressNode
+        ? toTextAndTrim(addressNode)
+        : addressLines.find((line) => !line.toLowerCase().includes('department'));
+    if (address && !institution) {
+        institution = address;
+        address = undefined;
+    }
+    if (department && !institution) {
+        institution = department;
+        department = undefined;
+    }
+    const city = toTextAndTrim(cityNode);
+    const state = toTextAndTrim(stateNode);
+    const postal_code = toTextAndTrim(postalCodeNode);
+    const country = toTextAndTrim(countryNode);
+    return { id, ror, isni, department, institution, address, city, state, postal_code, country };
+}

package/dist/version.d.ts

@@ -1,3 +1,3 @@
-declare const version = "1.0.8";
+declare const version = "1.0.10";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/dist/version.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"version.d.ts","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,QAAA,MAAM,OAAO,UAAU,CAAC;AACxB,eAAe,OAAO,CAAC"}
+{"version":3,"file":"version.d.ts","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,QAAA,MAAM,OAAO,WAAW,CAAC;AACzB,eAAe,OAAO,CAAC"}

package/dist/version.js

@@ -1,2 +1,2 @@
-const version = '1.0.8';
+const version = '1.0.10';
 export default version;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-xml",
-  "version": "1.0.8",
+  "version": "1.0.10",
   "description": "Types and utilities for working with JATS in Typescript",
   "author": "Rowan Cockett <rowan@curvenote.com>",
   "homepage": "https://github.com/curvenote/jats",
@@ -24,53 +24,41 @@
     "type": "git",
     "url": "git+https://github.com/curvenote/jats.git"
   },
-  "bin": {
-    "jats": "./dist/jats.cjs"
-  },
   "scripts": {
     "copy:version": "echo \"const version = '\"$npm_package_version\"';\nexport default version;\" > src/version.ts",
     "clean": "rm -rf dist",
-    "unlink": "npm uninstall -g jats-xml;",
-    "link": "npm run unlink; npm link;",
-    "dev": "npm run copy:version && npm run link && esbuild src/cli/index.ts --bundle --outfile=dist/jats.cjs --platform=node --watch",
     "test": "npm run copy:version && vitest run",
     "test:watch": "npm run copy:version && vitest watch",
     "lint": "eslint \"src/**/*.ts*\" -c ./.eslintrc.cjs",
     "lint:format": "prettier --check \"src/**/*.{ts,tsx,md}\"",
     "build:esm": "tsc",
-    "build:cli": "esbuild src/cli/index.ts --bundle --outfile=dist/jats.cjs --platform=node",
-    "build": "npm-run-all -l clean copy:version -p build:esm build:cli"
+    "build": "npm-run-all -l clean copy:version -p build:esm"
   },
   "bugs": {
     "url": "https://github.com/curvenote/jats/issues"
   },
   "dependencies": {
     "adm-zip": "^0.5.10",
-    "doi-utils": "^2.0.0",
-    "fair-principles": "^2.0.0",
-    "jats-fetch": "^1.0.8",
-    "jats-tags": "^1.0.8",
-    "jats-utils": "^1.0.8",
-    "js-yaml": "^4.1.0",
+    "doi-utils": "^2.0.3",
+    "jats-tags": "^1.0.10",
+    "jats-utils": "^1.0.10",
+    "myst-cli-utils": "^2.0.11",
+    "myst-common": "^1.7.5",
+    "myst-frontmatter": "^1.7.5",
     "node-fetch": "^3.3.1",
-    "unist-util-is": "^5.2.1",
-    "unist-util-remove": "^3.1.0",
     "unist-util-select": "^4.0.0",
+    "unist-util-remove": "4.0.0",
     "which": "^3.0.1",
     "xml-js": "^1.6.11"
   },
   "peerDependencies": {
-    "chalk": "^5.2.0",
-    "commander": "^10.0.1"
+    "chalk": "^5.2.0"
   },
   "devDependencies": {
     "@types/adm-zip": "^0.5.0",
     "@types/js-yaml": "^4.0.5",
     "@types/which": "^3.0.0",
     "chalk": "^5.2.0",
-    "commander": "^10.0.1",
-    "myst-cli-utils": "^2.0.0",
-    "myst-common": "^1.0.0",
-    "myst-frontmatter": "^1.0.0"
+    "js-yaml": "^4.1.0"
   }
 }

package/dist/cli/index.d.ts

@@ -1,3 +0,0 @@
-#!/usr/bin/env node
-export {};
-//# sourceMappingURL=index.d.ts.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cli/index.ts"],"names":[],"mappings":""}

package/dist/cli/index.js

@@ -1,13 +0,0 @@
-#!/usr/bin/env node
-import { Command } from 'commander';
-import version from '../version.js';
-import { addDownloadCLI } from './parse.js';
-import { addValidateCLI } from './validate.js';
-import { addTestCLI } from './jats-test.js';
-const program = new Command();
-addDownloadCLI(program);
-addValidateCLI(program);
-addTestCLI(program);
-program.version(`v${version}`, '-v, --version', 'Print the current version of jats-xml');
-program.option('-d, --debug', 'Log out any errors to the console.');
-program.parse(process.argv);