jats-xml 0.0.17 → 0.1.0

package/dist/cjs/cli/parse.js

@@ -21,7 +21,7 @@ const doi_utils_1 = __importDefault(require("doi-utils"));
 const chalk_1 = __importDefault(require("chalk"));
 const fair_principles_1 = require("fair-principles");
 const session_1 = require("../session");
-const types_1 = require("../types");
+const jats_tags_1 = require("jats-tags");
 const jats_1 = require("../jats");
 const myst_common_1 = require("myst-common");
 const unist_util_select_1 = require("unist-util-select");
@@ -122,7 +122,7 @@ function jatsSummaryCLI(session, file) {
             Title: (_a = (0, myst_common_1.toText)(jats.articleTitle)) === null || _a === void 0 ? void 0 : _a.replace(/\n/g, ' '),
             Date: (0, utils_1.formatDate)((0, utils_1.toDate)(jats.publicationDate)),
             Authors: jats.articleAuthors
-                .map((a) => `${(0, myst_common_1.toText)((0, unist_util_select_1.select)(types_1.Tags.givenNames, a))} ${(0, myst_common_1.toText)((0, unist_util_select_1.select)(types_1.Tags.surname, a))}`)
+                .map((a) => `${(0, myst_common_1.toText)((0, unist_util_select_1.select)(jats_tags_1.Tags.givenNames, a))} ${(0, myst_common_1.toText)((0, unist_util_select_1.select)(jats_tags_1.Tags.surname, a))}`)
                 .join(', '),
             Abstract: (_b = (0, myst_common_1.toText)(jats.abstract)) === null || _b === void 0 ? void 0 : _b.replace(/\n/g, ' '),
             Keywords: jats.keywords.map((k) => (0, myst_common_1.toText)(k)).join(', '),
@@ -131,32 +131,32 @@ function jatsSummaryCLI(session, file) {
         if (jats.body) {
             summary.Figures = {
                 label: chalk_1.default.blue.bold,
-                value: String((0, unist_util_select_1.selectAll)(types_1.Tags.fig, jats.body).length),
+                value: String((0, unist_util_select_1.selectAll)(jats_tags_1.Tags.fig, jats.body).length),
             };
             summary.Equations = {
                 label: chalk_1.default.blue.bold,
-                value: String((0, unist_util_select_1.selectAll)(types_1.Tags.dispFormula, jats.body).length),
+                value: String((0, unist_util_select_1.selectAll)(jats_tags_1.Tags.dispFormula, jats.body).length),
             };
             summary.Tables = {
                 label: chalk_1.default.blue.bold,
-                value: String((0, unist_util_select_1.selectAll)(types_1.Tags.table, jats.body).length),
+                value: String((0, unist_util_select_1.selectAll)(jats_tags_1.Tags.table, jats.body).length),
             };
             summary.Code = {
                 label: chalk_1.default.blue.bold,
-                value: String((0, unist_util_select_1.selectAll)(types_1.Tags.code, jats.body).length),
+                value: String((0, unist_util_select_1.selectAll)(jats_tags_1.Tags.code, jats.body).length),
             };
             summary.Sections = {
                 label: chalk_1.default.blue.bold,
-                value: String((0, unist_util_select_1.selectAll)(types_1.Tags.sec, jats.body).length),
+                value: String((0, unist_util_select_1.selectAll)(jats_tags_1.Tags.sec, jats.body).length),
             };
             summary.Paragraphs = {
                 label: chalk_1.default.blue.bold,
-                value: String((0, unist_util_select_1.selectAll)(types_1.Tags.p, jats.body).length),
+                value: String((0, unist_util_select_1.selectAll)(jats_tags_1.Tags.p, jats.body).length),
             };
             summary.Citations = { label: chalk_1.default.blue.bold, value: String(jats.references.length) };
             summary['Cross-References'] = {
                 label: chalk_1.default.blue.bold,
-                value: String((0, unist_util_select_1.selectAll)(types_1.Tags.xref, jats.body).length),
+                value: String((0, unist_util_select_1.selectAll)(jats_tags_1.Tags.xref, jats.body).length),
             };
             summary['Sub Articles'] = { label: chalk_1.default.blue.bold, value: String(jats.subArticles.length) };
         }
@@ -172,9 +172,9 @@ function jatsReferencesCLI(session, file) {
         const sorted = jats.references
             .map((ref) => {
             const doiString = (0, utils_1.findArticleId)(ref, 'doi');
-            const title = (0, myst_common_1.toText)((0, unist_util_select_1.select)(types_1.Tags.articleTitle, ref));
-            const year = (0, myst_common_1.toText)((0, unist_util_select_1.select)(types_1.Tags.year, ref));
-            const surnames = (0, unist_util_select_1.selectAll)(types_1.Tags.surname, ref);
+            const title = (0, myst_common_1.toText)((0, unist_util_select_1.select)(jats_tags_1.Tags.articleTitle, ref));
+            const year = (0, myst_common_1.toText)((0, unist_util_select_1.select)(jats_tags_1.Tags.year, ref));
+            const surnames = (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.surname, ref);
             const short = surnames.length > 2
                 ? (0, myst_common_1.toText)(surnames[0]) + ' et al.'
                 : surnames.length === 2

package/dist/cjs/jats.js

@@ -9,7 +9,7 @@ const xml_js_1 = require("xml-js");
 const doi_utils_1 = __importDefault(require("doi-utils"));
 const utils_1 = require("./utils");
 const unist_util_select_1 = require("unist-util-select");
-const types_1 = require("./types");
+const jats_tags_1 = require("jats-tags");
 const myst_cli_utils_1 = require("myst-cli-utils");
 function select(selector, node) {
     var _a;
@@ -44,8 +44,8 @@ class Jats {
         const subtitle = this.articleSubtitle;
         const date = this.publicationDate;
         const authors = this.articleAuthors;
-        const firstSubject = select(types_1.Tags.subject, (_a = this.articleCategories) !== null && _a !== void 0 ? _a : this.front);
-        const journalTitle = select(types_1.Tags.journalTitle, this.front);
+        const firstSubject = select(jats_tags_1.Tags.subject, (_a = this.articleCategories) !== null && _a !== void 0 ? _a : this.front);
+        const journalTitle = select(jats_tags_1.Tags.journalTitle, this.front);
         return {
             title: title ? (0, myst_common_1.toText)(title) : undefined,
             subtitle: subtitle ? (0, myst_common_1.toText)(subtitle) : undefined,
@@ -58,10 +58,10 @@ class Jats {
         };
     }
     get front() {
-        return select(types_1.Tags.front, this.tree);
+        return select(jats_tags_1.Tags.front, this.tree);
     }
     get premissions() {
-        return select(types_1.Tags.permissions, this.front);
+        return select(jats_tags_1.Tags.permissions, this.front);
     }
     get doi() {
         var _a;
@@ -75,65 +75,65 @@ class Jats {
         return (0, utils_1.findArticleId)(this.front, 'pmid');
     }
     get publicationDates() {
-        return (0, unist_util_select_1.selectAll)(types_1.Tags.pubDate, this.front);
+        return (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.pubDate, this.front);
     }
     get publicationDate() {
-        return this.publicationDates.find((d) => !!select(types_1.Tags.day, d));
+        return this.publicationDates.find((d) => !!select(jats_tags_1.Tags.day, d));
     }
     get license() {
-        return select(types_1.Tags.license, this.premissions);
+        return select(jats_tags_1.Tags.license, this.premissions);
     }
     get keywordGroup() {
-        return select(types_1.Tags.kwdGroup, this.front);
+        return select(jats_tags_1.Tags.kwdGroup, this.front);
     }
     /** The first keywords */
     get keywords() {
-        return (0, unist_util_select_1.selectAll)(types_1.Tags.kwd, this.keywordGroup);
+        return (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.kwd, this.keywordGroup);
     }
     get keywordGroups() {
-        return (0, unist_util_select_1.selectAll)(types_1.Tags.kwdGroup, this.front);
+        return (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.kwdGroup, this.front);
     }
     get articleCategories() {
-        return select(types_1.Tags.articleCategories, this.front);
+        return select(jats_tags_1.Tags.articleCategories, this.front);
     }
     get titleGroup() {
-        return select(types_1.Tags.titleGroup, this.front);
+        return select(jats_tags_1.Tags.titleGroup, this.front);
     }
     get articleTitle() {
-        return select(types_1.Tags.articleTitle, this.titleGroup);
+        return select(jats_tags_1.Tags.articleTitle, this.titleGroup);
     }
     get articleSubtitle() {
-        return select(types_1.Tags.subtitle, this.titleGroup);
+        return select(jats_tags_1.Tags.subtitle, this.titleGroup);
     }
     get abstract() {
-        return select(types_1.Tags.abstract, this.front);
+        return select(jats_tags_1.Tags.abstract, this.front);
     }
     get abstracts() {
-        return (0, unist_util_select_1.selectAll)(types_1.Tags.abstract, this.front);
+        return (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.abstract, this.front);
     }
     get contribGroup() {
-        return select(types_1.Tags.contribGroup, this.front);
+        return select(jats_tags_1.Tags.contribGroup, this.front);
     }
     get contribGroups() {
-        return (0, unist_util_select_1.selectAll)(types_1.Tags.contribGroup, this.front);
+        return (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.contribGroup, this.front);
     }
     get articleAuthors() {
-        return (0, unist_util_select_1.selectAll)(types_1.Tags.contrib, this.contribGroup);
+        return (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.contrib, this.contribGroup);
     }
     get body() {
-        return select(types_1.Tags.body, this.tree);
+        return select(jats_tags_1.Tags.body, this.tree);
     }
     get back() {
-        return select(types_1.Tags.back, this.tree);
+        return select(jats_tags_1.Tags.back, this.tree);
     }
     get subArticles() {
-        return (0, unist_util_select_1.selectAll)(types_1.Tags.subArticle, this.tree);
+        return (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.subArticle, this.tree);
     }
     get refList() {
-        return select(types_1.Tags.refList, this.back);
+        return select(jats_tags_1.Tags.refList, this.back);
     }
     get references() {
-        return (0, unist_util_select_1.selectAll)(types_1.Tags.ref, this.refList);
+        return (0, unist_util_select_1.selectAll)(jats_tags_1.Tags.ref, this.refList);
     }
 }
 exports.Jats = Jats;

package/dist/cjs/utils.js

@@ -7,7 +7,7 @@ exports.authorAndAffiliation = exports.findArticleId = exports.formatDate = expo
 const myst_common_1 = require("myst-common");
 const doi_utils_1 = __importDefault(require("doi-utils"));
 const unist_util_select_1 = require("unist-util-select");
-const types_1 = require("./types");
+const jats_tags_1 = require("jats-tags");
 function convertToUnist(node) {
     switch (node.type) {
         case 'element': {
@@ -29,7 +29,7 @@ function convertToUnist(node) {
         }
         case 'cdata': {
             const { attributes, cdata } = node;
-            return Object.assign(Object.assign({ type: 'cdata' }, attributes), { cdata });
+            return Object.assign(Object.assign({ type: 'cdata' }, attributes), { cdata: String(cdata).trim() });
         }
         case 'comment': {
             const { comment } = node;
@@ -105,13 +105,13 @@ function findArticleId(node, pubIdType = 'doi') {
     const id = (0, unist_util_select_1.select)(`[pub-id-type=${pubIdType}]`, node);
     if (id && (0, myst_common_1.toText)(id))
         return (0, myst_common_1.toText)(id);
-    const doiTag = (0, unist_util_select_1.selectAll)(`${types_1.Tags.articleId},${types_1.Tags.pubId}`, node).find((t) => doi_utils_1.default.validate((0, myst_common_1.toText)(t)));
+    const doiTag = (0, unist_util_select_1.selectAll)(`${jats_tags_1.Tags.articleId},${jats_tags_1.Tags.pubId}`, node).find((t) => doi_utils_1.default.validate((0, myst_common_1.toText)(t)));
     return (0, myst_common_1.toText)(doiTag) || undefined;
 }
 exports.findArticleId = findArticleId;
 function authorAndAffiliation(node, article) {
     const author = {
-        name: `${(0, myst_common_1.toText)((0, unist_util_select_1.select)(types_1.Tags.givenNames, node))} ${(0, myst_common_1.toText)((0, unist_util_select_1.select)(types_1.Tags.surname, node))}`,
+        name: `${(0, myst_common_1.toText)((0, unist_util_select_1.select)(jats_tags_1.Tags.givenNames, node))} ${(0, myst_common_1.toText)((0, unist_util_select_1.select)(jats_tags_1.Tags.surname, node))}`,
     };
     const orcid = (0, unist_util_select_1.select)('[contrib-id-type=orcid]', node);
     if (orcid) {

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const version = '0.0.17';
+const version = '0.1.0';
 exports.default = version;

package/dist/esm/cli/parse.js

@@ -15,7 +15,7 @@ import doi from 'doi-utils';
 import chalk from 'chalk';
 import { formatPrinciples, highlightFAIR } from 'fair-principles';
 import { getSession } from '../session';
-import { Tags } from '../types';
+import { Tags } from 'jats-tags';
 import { Jats } from '../jats';
 import { toText } from 'myst-common';
 import { select, selectAll } from 'unist-util-select';

package/dist/esm/jats.js

@@ -3,7 +3,7 @@ import { xml2js } from 'xml-js';
 import doi from 'doi-utils';
 import { authorAndAffiliation, convertToUnist, findArticleId, toDate } from './utils';
 import { select as unistSelect, selectAll } from 'unist-util-select';
-import { Tags } from './types';
+import { Tags } from 'jats-tags';
 import { tic } from 'myst-cli-utils';
 function select(selector, node) {
     var _a;

package/dist/esm/utils.js

@@ -1,7 +1,7 @@
 import { toText } from 'myst-common';
 import doi from 'doi-utils';
 import { select, selectAll } from 'unist-util-select';
-import { Tags } from './types';
+import { Tags } from 'jats-tags';
 export function convertToUnist(node) {
     switch (node.type) {
         case 'element': {
@@ -23,7 +23,7 @@ export function convertToUnist(node) {
         }
         case 'cdata': {
             const { attributes, cdata } = node;
-            return Object.assign(Object.assign({ type: 'cdata' }, attributes), { cdata });
+            return Object.assign(Object.assign({ type: 'cdata' }, attributes), { cdata: String(cdata).trim() });
         }
         case 'comment': {
             const { comment } = node;

package/dist/esm/version.js

@@ -1,2 +1,2 @@
-const version = '0.0.17';
+const version = '0.1.0';
 export default version;