jats-xml 0.0.13 → 0.0.14

package/dist/cjs/{download.js → cli/download.js}

@@ -14,20 +14,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.downloadJatsFromUrl = exports.checkIfPubMedCentralHasJats = exports.convertPMID2PMCID = void 0;
 const doi_utils_1 = __importDefault(require("doi-utils"));
-const chalk_1 = __importDefault(require("chalk"));
 const node_fetch_1 = __importDefault(require("node-fetch"));
 const myst_cli_utils_1 = require("myst-cli-utils");
-const fair_principles_1 = require("fair-principles");
-const resolvers_1 = require("./resolvers");
-function logAboutJatsFailing(session, jatsUrls) {
-    session.log.warn('⛔️ JATS may not be Open Access 😭, you should petition your local representative 🪧');
-    session.log.info(`${chalk_1.default.green(`\nThe XML ${chalk_1.default.bold('should')} be here:\n\n${jatsUrls.join('\n')}`)}\n`);
-    const FAIR = (0, fair_principles_1.highlightFAIR)('A', { chalk: chalk_1.default });
-    session.log.info(`Some publishers aggressively block programmatic access, which isn't ${FAIR}.`);
-    session.log.debug((0, fair_principles_1.formatPrinciples)('A*', { chalk: chalk_1.default }));
-    session.log.info(`${chalk_1.default.blue('The link may work in a browser.')}\n`);
-}
-function dowloadFromUrl(session, jatsUrl, opts) {
+const resolvers_1 = require("../resolvers");
+function downloadFromUrl(session, jatsUrl, opts) {
     var _a, _b;
     return __awaiter(this, void 0, void 0, function* () {
         const toc = (0, myst_cli_utils_1.tic)();
@@ -41,7 +31,7 @@ function dowloadFromUrl(session, jatsUrl, opts) {
         if (!((contentType === null || contentType === void 0 ? void 0 : contentType.includes('application/xml')) ||
             (contentType === null || contentType === void 0 ? void 0 : contentType.includes('text/xml')) ||
             (contentType === null || contentType === void 0 ? void 0 : contentType.includes('text/plain')))) {
-            session.log.warn(`Expected content-type "application/xml" instead we got "${contentType}" for ${jatsUrl}\n${chalk_1.default.dim('Things may not work, but we are going to try our best...')}`);
+            session.log.warn(`Expected content-type "application/xml" instead we got "${contentType}" for ${jatsUrl}`);
         }
         const data = yield resp.text();
         session.log.debug(toc(`Fetched document with content-type "${contentType}" in %s`));
@@ -169,26 +159,26 @@ function downloadJatsFromUrl(session, urlOrDoi, opts = {}) {
             for (let index = 0; index < expectedUrls.length; index++) {
                 const url = expectedUrls[index];
                 try {
-                    const data = yield dowloadFromUrl(session, url, opts);
+                    const data = yield downloadFromUrl(session, url, opts);
                     if (data)
-                        return { source: url, data };
+                        return { success: true, source: url, data };
                 }
                 catch (error) {
                     session.log.debug(error.message);
                 }
             }
             // If there are expected URLs that don't work: see something, say something, etc.
-            logAboutJatsFailing(session, expectedUrls);
+            return { success: false, source: expectedUrls[0] };
         }
         if (doi_utils_1.default.validate(urlOrDoi)) {
             const jatsUrl = yield (0, resolvers_1.customResolveJatsUrlFromDoi)(session, urlOrDoi, opts);
-            const data = yield dowloadFromUrl(session, jatsUrl, opts);
-            return { source: jatsUrl, data };
+            const data = yield downloadFromUrl(session, jatsUrl, opts);
+            return { success: true, source: jatsUrl, data };
         }
         if ((0, myst_cli_utils_1.isUrl)(urlOrDoi)) {
             session.log.debug("No resolver matched, and the URL doesn't look like a DOI. We will attempt to download it directly.");
-            const data = yield dowloadFromUrl(session, urlOrDoi, opts);
-            return { source: urlOrDoi, data };
+            const data = yield downloadFromUrl(session, urlOrDoi, opts);
+            return { success: true, source: urlOrDoi, data };
         }
         throw new Error(`Could not find ${urlOrDoi} locally, and it doesn't look like a URL or DOI`);
     });

package/dist/cjs/cli/parse.js

@@ -19,12 +19,13 @@ const path_1 = require("path");
 const myst_cli_utils_1 = require("myst-cli-utils");
 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_1 = require("../jats");
 const myst_common_1 = require("myst-common");
 const unist_util_select_1 = require("unist-util-select");
-const download_1 = require("../download");
+const download_1 = require("./download");
 const resolvers_1 = require("../resolvers");
 const utils_1 = require("../utils");
 function hasValidExtension(output) {
@@ -41,11 +42,23 @@ function downloadAndSaveJats(session, urlOrDoi, output, opts = { resolvers: reso
         if (!hasValidExtension(output)) {
             session.log.warn(`The extension ${(0, path_1.extname)(output)} is not a valid extension for JATS, try using ".xml" or ".jats"`);
         }
-        const { data } = yield (0, download_1.downloadJatsFromUrl)(session, urlOrDoi, opts);
+        const { success, data, source } = yield (0, download_1.downloadJatsFromUrl)(session, urlOrDoi, opts);
+        if (!success || !data) {
+            logAboutJatsFailing(session, [source]);
+            process.exit(1);
+        }
         (0, myst_cli_utils_1.writeFileToFolder)(output, data);
         return data;
     });
 }
+function logAboutJatsFailing(session, jatsUrls) {
+    session.log.warn('⛔️ JATS may not be Open Access 😭, you should petition your local representative 🪧');
+    session.log.info(`${chalk_1.default.green(`\nThe XML ${chalk_1.default.bold('should')} be here:\n\n${jatsUrls.join('\n')}`)}\n`);
+    const FAIR = (0, fair_principles_1.highlightFAIR)('A', { chalk: chalk_1.default });
+    session.log.info(`Some publishers aggressively block programmatic access, which isn't ${FAIR}.`);
+    session.log.debug((0, fair_principles_1.formatPrinciples)('A*', { chalk: chalk_1.default }));
+    session.log.info(`\n${chalk_1.default.blue('The link may work in a browser.')}\n`);
+}
 function parseJats(session, file, opts = { resolvers: resolvers_1.DEFAULT_RESOLVERS }) {
     return __awaiter(this, void 0, void 0, function* () {
         const toc = (0, myst_cli_utils_1.tic)();
@@ -54,7 +67,11 @@ function parseJats(session, file, opts = { resolvers: resolvers_1.DEFAULT_RESOLV
             const data = fs_1.default.readFileSync(file).toString();
             return new jats_1.Jats(data, { log: session.log });
         }
-        const { source, data } = yield (0, download_1.downloadJatsFromUrl)(session, file, opts);
+        const { success, source, data } = yield (0, download_1.downloadJatsFromUrl)(session, file, opts);
+        if (!success || !data) {
+            logAboutJatsFailing(session, [source]);
+            process.exit(1);
+        }
         const jats = new jats_1.Jats(data, { source, log: session.log });
         session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
         return jats;

package/dist/cjs/index.js

@@ -17,11 +17,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.downloadJatsFromUrl = exports.Jats = exports.version = void 0;
+exports.Jats = exports.version = void 0;
 var version_1 = require("./version");
 Object.defineProperty(exports, "version", { enumerable: true, get: function () { return __importDefault(version_1).default; } });
 var jats_1 = require("./jats");
 Object.defineProperty(exports, "Jats", { enumerable: true, get: function () { return jats_1.Jats; } });
-var download_1 = require("./download");
-Object.defineProperty(exports, "downloadJatsFromUrl", { enumerable: true, get: function () { return download_1.downloadJatsFromUrl; } });
 __exportStar(require("./types"), exports);

package/dist/esm/{download.js → cli/download.js}

@@ -8,20 +8,10 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
     });
 };
 import doi from 'doi-utils';
-import chalk from 'chalk';
 import fetch from 'node-fetch';
 import { isUrl, tic } from 'myst-cli-utils';
-import { formatPrinciples, highlightFAIR } from 'fair-principles';
-import { customResolveJatsUrlFromDoi } from './resolvers';
-function logAboutJatsFailing(session, jatsUrls) {
-    session.log.warn('⛔️ JATS may not be Open Access 😭, you should petition your local representative 🪧');
-    session.log.info(`${chalk.green(`\nThe XML ${chalk.bold('should')} be here:\n\n${jatsUrls.join('\n')}`)}\n`);
-    const FAIR = highlightFAIR('A', { chalk });
-    session.log.info(`Some publishers aggressively block programmatic access, which isn't ${FAIR}.`);
-    session.log.debug(formatPrinciples('A*', { chalk }));
-    session.log.info(`${chalk.blue('The link may work in a browser.')}\n`);
-}
-function dowloadFromUrl(session, jatsUrl, opts) {
+import { customResolveJatsUrlFromDoi } from '../resolvers';
+function downloadFromUrl(session, jatsUrl, opts) {
     var _a, _b;
     return __awaiter(this, void 0, void 0, function* () {
         const toc = tic();
@@ -35,7 +25,7 @@ function dowloadFromUrl(session, jatsUrl, opts) {
         if (!((contentType === null || contentType === void 0 ? void 0 : contentType.includes('application/xml')) ||
             (contentType === null || contentType === void 0 ? void 0 : contentType.includes('text/xml')) ||
             (contentType === null || contentType === void 0 ? void 0 : contentType.includes('text/plain')))) {
-            session.log.warn(`Expected content-type "application/xml" instead we got "${contentType}" for ${jatsUrl}\n${chalk.dim('Things may not work, but we are going to try our best...')}`);
+            session.log.warn(`Expected content-type "application/xml" instead we got "${contentType}" for ${jatsUrl}`);
         }
         const data = yield resp.text();
         session.log.debug(toc(`Fetched document with content-type "${contentType}" in %s`));
@@ -161,26 +151,26 @@ export function downloadJatsFromUrl(session, urlOrDoi, opts = {}) {
             for (let index = 0; index < expectedUrls.length; index++) {
                 const url = expectedUrls[index];
                 try {
-                    const data = yield dowloadFromUrl(session, url, opts);
+                    const data = yield downloadFromUrl(session, url, opts);
                     if (data)
-                        return { source: url, data };
+                        return { success: true, source: url, data };
                 }
                 catch (error) {
                     session.log.debug(error.message);
                 }
             }
             // If there are expected URLs that don't work: see something, say something, etc.
-            logAboutJatsFailing(session, expectedUrls);
+            return { success: false, source: expectedUrls[0] };
         }
         if (doi.validate(urlOrDoi)) {
             const jatsUrl = yield customResolveJatsUrlFromDoi(session, urlOrDoi, opts);
-            const data = yield dowloadFromUrl(session, jatsUrl, opts);
-            return { source: jatsUrl, data };
+            const data = yield downloadFromUrl(session, jatsUrl, opts);
+            return { success: true, source: jatsUrl, data };
         }
         if (isUrl(urlOrDoi)) {
             session.log.debug("No resolver matched, and the URL doesn't look like a DOI. We will attempt to download it directly.");
-            const data = yield dowloadFromUrl(session, urlOrDoi, opts);
-            return { source: urlOrDoi, data };
+            const data = yield downloadFromUrl(session, urlOrDoi, opts);
+            return { success: true, source: urlOrDoi, data };
         }
         throw new Error(`Could not find ${urlOrDoi} locally, and it doesn't look like a URL or DOI`);
     });

package/dist/esm/cli/parse.js

@@ -13,12 +13,13 @@ import { extname } from 'path';
 import { clirun, isUrl, tic, writeFileToFolder } from 'myst-cli-utils';
 import doi from 'doi-utils';
 import chalk from 'chalk';
+import { formatPrinciples, highlightFAIR } from 'fair-principles';
 import { getSession } from '../session';
 import { Tags } from '../types';
 import { Jats } from '../jats';
 import { toText } from 'myst-common';
 import { select, selectAll } from 'unist-util-select';
-import { downloadJatsFromUrl } from '../download';
+import { downloadJatsFromUrl } from './download';
 import { DEFAULT_RESOLVERS } from '../resolvers';
 import { findArticleId, formatDate, toDate } from '../utils';
 function hasValidExtension(output) {
@@ -35,11 +36,23 @@ function downloadAndSaveJats(session, urlOrDoi, output, opts = { resolvers: DEFA
         if (!hasValidExtension(output)) {
             session.log.warn(`The extension ${extname(output)} is not a valid extension for JATS, try using ".xml" or ".jats"`);
         }
-        const { data } = yield downloadJatsFromUrl(session, urlOrDoi, opts);
+        const { success, data, source } = yield downloadJatsFromUrl(session, urlOrDoi, opts);
+        if (!success || !data) {
+            logAboutJatsFailing(session, [source]);
+            process.exit(1);
+        }
         writeFileToFolder(output, data);
         return data;
     });
 }
+function logAboutJatsFailing(session, jatsUrls) {
+    session.log.warn('⛔️ JATS may not be Open Access 😭, you should petition your local representative 🪧');
+    session.log.info(`${chalk.green(`\nThe XML ${chalk.bold('should')} be here:\n\n${jatsUrls.join('\n')}`)}\n`);
+    const FAIR = highlightFAIR('A', { chalk });
+    session.log.info(`Some publishers aggressively block programmatic access, which isn't ${FAIR}.`);
+    session.log.debug(formatPrinciples('A*', { chalk }));
+    session.log.info(`\n${chalk.blue('The link may work in a browser.')}\n`);
+}
 function parseJats(session, file, opts = { resolvers: DEFAULT_RESOLVERS }) {
     return __awaiter(this, void 0, void 0, function* () {
         const toc = tic();
@@ -48,7 +61,11 @@ function parseJats(session, file, opts = { resolvers: DEFAULT_RESOLVERS }) {
             const data = fs.readFileSync(file).toString();
             return new Jats(data, { log: session.log });
         }
-        const { source, data } = yield downloadJatsFromUrl(session, file, opts);
+        const { success, source, data } = yield downloadJatsFromUrl(session, file, opts);
+        if (!success || !data) {
+            logAboutJatsFailing(session, [source]);
+            process.exit(1);
+        }
         const jats = new Jats(data, { source, log: session.log });
         session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
         return jats;

package/dist/esm/index.js

@@ -1,4 +1,3 @@
 export { default as version } from './version';
 export { Jats } from './jats';
-export { downloadJatsFromUrl } from './download';
 export * from './types';

package/dist/jats.js

@@ -2961,14 +2961,14 @@ var require_templates = __commonJS({
       }
       return results;
     }
-    function buildStyle(chalk4, styles) {
+    function buildStyle(chalk3, styles) {
       const enabled = {};
       for (const layer of styles) {
         for (const style of layer.styles) {
           enabled[style[0]] = layer.inverse ? null : style.slice(1);
         }
       }
-      let current = chalk4;
+      let current = chalk3;
       for (const [styleName, styles2] of Object.entries(enabled)) {
         if (!Array.isArray(styles2)) {
           continue;
@@ -2980,7 +2980,7 @@ var require_templates = __commonJS({
       }
       return current;
     }
-    module2.exports = (chalk4, temporary) => {
+    module2.exports = (chalk3, temporary) => {
       const styles = [];
       const chunks = [];
       let chunk = [];
@@ -2990,13 +2990,13 @@ var require_templates = __commonJS({
         } else if (style) {
           const string = chunk.join("");
           chunk = [];
-          chunks.push(styles.length === 0 ? string : buildStyle(chalk4, styles)(string));
+          chunks.push(styles.length === 0 ? string : buildStyle(chalk3, styles)(string));
           styles.push({ inverse, styles: parseStyle(style) });
         } else if (close) {
           if (styles.length === 0) {
             throw new Error("Found extraneous } in Chalk template literal");
           }
-          chunks.push(buildStyle(chalk4, styles)(chunk.join("")));
+          chunks.push(buildStyle(chalk3, styles)(chunk.join("")));
           chunk = [];
           styles.pop();
         } else {
@@ -3044,16 +3044,16 @@ var require_source = __commonJS({
       }
     };
     var chalkFactory = (options) => {
-      const chalk5 = {};
-      applyOptions(chalk5, options);
-      chalk5.template = (...arguments_) => chalkTag(chalk5.template, ...arguments_);
-      Object.setPrototypeOf(chalk5, Chalk.prototype);
-      Object.setPrototypeOf(chalk5.template, chalk5);
-      chalk5.template.constructor = () => {
+      const chalk4 = {};
+      applyOptions(chalk4, options);
+      chalk4.template = (...arguments_) => chalkTag(chalk4.template, ...arguments_);
+      Object.setPrototypeOf(chalk4, Chalk.prototype);
+      Object.setPrototypeOf(chalk4.template, chalk4);
+      chalk4.template.constructor = () => {
         throw new Error("`chalk.constructor()` is deprecated. Use `new chalk.Instance()` instead.");
       };
-      chalk5.template.Instance = ChalkClass;
-      return chalk5.template;
+      chalk4.template.Instance = ChalkClass;
+      return chalk4.template;
     };
     function Chalk(options) {
       return chalkFactory(options);
@@ -3164,7 +3164,7 @@ var require_source = __commonJS({
       return openAll + string + closeAll;
     };
     var template;
-    var chalkTag = (chalk5, ...strings) => {
+    var chalkTag = (chalk4, ...strings) => {
       const [firstString] = strings;
       if (!isArray(firstString) || !isArray(firstString.raw)) {
         return strings.join(" ");
@@ -3180,14 +3180,14 @@ var require_source = __commonJS({
       if (template === void 0) {
         template = require_templates();
       }
-      return template(chalk5, parts.join(""));
+      return template(chalk4, parts.join(""));
     };
     Object.defineProperties(Chalk.prototype, styles);
-    var chalk4 = Chalk();
-    chalk4.supportsColor = stdoutColor;
-    chalk4.stderr = Chalk({ level: stderrColor ? stderrColor.level : 0 });
-    chalk4.stderr.supportsColor = stderrColor;
-    module2.exports = chalk4;
+    var chalk3 = Chalk();
+    chalk3.supportsColor = stdoutColor;
+    chalk3.stderr = Chalk({ level: stderrColor ? stderrColor.level : 0 });
+    chalk3.stderr.supportsColor = stderrColor;
+    module2.exports = chalk3;
   }
 });
 
@@ -3421,6 +3421,99 @@ var require_cjs = __commonJS({
   }
 });
 
+// node_modules/fair-principles/dist/cjs/index.js
+var require_cjs2 = __commonJS({
+  "node_modules/fair-principles/dist/cjs/index.js"(exports) {
+    "use strict";
+    Object.defineProperty(exports, "__esModule", { value: true });
+    exports.createPrincipleUrl = exports.formatPrinciples = exports.formatPrinciple = exports.principles = exports.principleNames = exports.highlightFAIR = void 0;
+    function format(text) {
+      return text;
+    }
+    var highlightFAIR2 = (letter, opts) => {
+      var _a, _b, _c;
+      const l = letter.toLowerCase();
+      const color = (_c = (_a = opts === null || opts === void 0 ? void 0 : opts.color) !== null && _a !== void 0 ? _a : (_b = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _b === void 0 ? void 0 : _b.red) !== null && _c !== void 0 ? _c : format;
+      return [
+        l.includes("f") ? color("F") : "F",
+        l.includes("a") ? color("A") : "A",
+        l.includes("i") ? color("I") : "I",
+        l.includes("r") ? color("R") : "R"
+      ].join("");
+    };
+    exports.highlightFAIR = highlightFAIR2;
+    exports.principleNames = {
+      F: "Findable",
+      A: "Accessible",
+      I: "Interoperable",
+      R: "Reusable"
+    };
+    exports.principles = {
+      F: "The first step in (re)using data is to find them. Metadata and data should be easy to find for both humans and computers. Machine-readable metadata are essential for automatic discovery of datasets and services, so this is an essential component of the FAIRification process.",
+      F1: "(Meta)data are assigned a globally unique and persistent identifier",
+      F2: "Data are described with rich metadata (defined by R1 below)",
+      F3: "Metadata clearly and explicitly include the identifier of the data they describe",
+      F4: "(Meta)data are registered or indexed in a searchable resource",
+      A: "Once the user finds the required data, she/he/they need to know how they can be accessed, possibly including authentication and authorisation.",
+      A1: "(Meta)data are retrievable by their identifier using a standardised communications protocol",
+      A1_1: "The protocol is open, free, and universally implementable",
+      A1_2: "The protocol allows for an authentication and authorisation procedure, where necessary",
+      A2: "Metadata are accessible, even when the data are no longer available",
+      I: "The data usually need to be integrated with other data. In addition, the data need to interoperate with applications or workflows for analysis, storage, and processing.",
+      I1: "(Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.",
+      I2: "(Meta)data use vocabularies that follow FAIR principles",
+      I3: "(Meta)data include qualified references to other (meta)data",
+      R: "The ultimate goal of FAIR is to optimise the reuse of data. To achieve this, metadata and data should be well-described so that they can be replicated and/or combined in different settings.",
+      R1: "(Meta)data are richly described with a plurality of accurate and relevant attributes",
+      R1_1: "(Meta)data are released with a clear and accessible data usage license",
+      R1_2: "(Meta)data are associated with detailed provenance",
+      R1_3: "(Meta)data meet domain-relevant community standards"
+    };
+    var principleKeys = Object.keys(exports.principles);
+    var mustExist = 'Principle does not exist, try "A1_1"';
+    function formatPrinciple(principle, opts) {
+      var _a, _b, _c, _d, _e, _f, _g, _h;
+      if (!(principle in exports.principles))
+        throw new Error(mustExist);
+      const key = principle.replace(/_/g, ".");
+      const header = exports.principleNames[principle];
+      const colorHeader = (_c = (_a = opts === null || opts === void 0 ? void 0 : opts.header) !== null && _a !== void 0 ? _a : (_b = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _b === void 0 ? void 0 : _b.bold.cyan) !== null && _c !== void 0 ? _c : format;
+      const underline = (_e = (_d = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _d === void 0 ? void 0 : _d.underline) !== null && _e !== void 0 ? _e : format;
+      const enumerator = (_h = (_f = opts === null || opts === void 0 ? void 0 : opts.enumerator) !== null && _f !== void 0 ? _f : (_g = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _g === void 0 ? void 0 : _g.bold.blue) !== null && _h !== void 0 ? _h : format;
+      if (header && (opts === null || opts === void 0 ? void 0 : opts.showHeader) !== false) {
+        return [
+          colorHeader(`${underline(header.slice(0, 1))}${header.slice(1)}`),
+          exports.principles[principle]
+        ].join("\n");
+      }
+      const indent = principle.includes("_") && (opts === null || opts === void 0 ? void 0 : opts.indent) !== false;
+      return `${indent ? "  " : ""}${enumerator(key)} ${exports.principles[principle]}`;
+    }
+    exports.formatPrinciple = formatPrinciple;
+    function formatPrinciples2(keys = "*", opts) {
+      var _a, _b, _c, _d, _e;
+      const input = typeof keys === "string" ? [keys] : keys;
+      const ordered = principleKeys.filter((key) => input.includes("*") || input.includes(key) || input.includes(key.slice(0, 1) + "*"));
+      const colorTitle = (_c = (_a = opts === null || opts === void 0 ? void 0 : opts.title) !== null && _a !== void 0 ? _a : (_b = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _b === void 0 ? void 0 : _b.bold.greenBright) !== null && _c !== void 0 ? _c : format;
+      const underline = (_e = (_d = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _d === void 0 ? void 0 : _d.underline) !== null && _e !== void 0 ? _e : format;
+      if ((opts === null || opts === void 0 ? void 0 : opts.showTitle) === false)
+        return ordered.map((k) => formatPrinciple(k, opts)).join("\n");
+      const header = `${colorTitle(`${(0, exports.highlightFAIR)(ordered.join(""), { color: underline })} Principle${ordered.length > 1 ? "s" : ""}`)}:`;
+      return [header, ...ordered.map((k) => formatPrinciple(k, opts))].join("\n");
+    }
+    exports.formatPrinciples = formatPrinciples2;
+    var baseUrl = "https://www.go-fair.org/fair-principles/";
+    function createPrincipleUrl(principle) {
+      if (!principle)
+        return baseUrl;
+      if (!(principle in exports.principles))
+        throw new Error(mustExist);
+      return `${baseUrl}${principle.toLowerCase().replace(/_/g, "-")}`;
+    }
+    exports.createPrincipleUrl = createPrincipleUrl;
+  }
+});
+
 // node_modules/unist-util-map/index.js
 var unist_util_map_exports = {};
 __export(unist_util_map_exports, {
@@ -5017,7 +5110,7 @@ var require_templates2 = __commonJS({
 });
 
 // node_modules/myst-common/dist/cjs/index.js
-var require_cjs2 = __commonJS({
+var require_cjs3 = __commonJS({
   "node_modules/myst-common/dist/cjs/index.js"(exports) {
     "use strict";
     var __createBinding = exports && exports.__createBinding || (Object.create ? function(o, m, k, k2) {
@@ -10103,99 +10196,6 @@ var require_lib4 = __commonJS({
   }
 });
 
-// node_modules/fair-principles/dist/cjs/index.js
-var require_cjs3 = __commonJS({
-  "node_modules/fair-principles/dist/cjs/index.js"(exports) {
-    "use strict";
-    Object.defineProperty(exports, "__esModule", { value: true });
-    exports.createPrincipleUrl = exports.formatPrinciples = exports.formatPrinciple = exports.principles = exports.principleNames = exports.highlightFAIR = void 0;
-    function format(text) {
-      return text;
-    }
-    var highlightFAIR2 = (letter, opts) => {
-      var _a, _b, _c;
-      const l = letter.toLowerCase();
-      const color = (_c = (_a = opts === null || opts === void 0 ? void 0 : opts.color) !== null && _a !== void 0 ? _a : (_b = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _b === void 0 ? void 0 : _b.red) !== null && _c !== void 0 ? _c : format;
-      return [
-        l.includes("f") ? color("F") : "F",
-        l.includes("a") ? color("A") : "A",
-        l.includes("i") ? color("I") : "I",
-        l.includes("r") ? color("R") : "R"
-      ].join("");
-    };
-    exports.highlightFAIR = highlightFAIR2;
-    exports.principleNames = {
-      F: "Findable",
-      A: "Accessible",
-      I: "Interoperable",
-      R: "Reusable"
-    };
-    exports.principles = {
-      F: "The first step in (re)using data is to find them. Metadata and data should be easy to find for both humans and computers. Machine-readable metadata are essential for automatic discovery of datasets and services, so this is an essential component of the FAIRification process.",
-      F1: "(Meta)data are assigned a globally unique and persistent identifier",
-      F2: "Data are described with rich metadata (defined by R1 below)",
-      F3: "Metadata clearly and explicitly include the identifier of the data they describe",
-      F4: "(Meta)data are registered or indexed in a searchable resource",
-      A: "Once the user finds the required data, she/he/they need to know how they can be accessed, possibly including authentication and authorisation.",
-      A1: "(Meta)data are retrievable by their identifier using a standardised communications protocol",
-      A1_1: "The protocol is open, free, and universally implementable",
-      A1_2: "The protocol allows for an authentication and authorisation procedure, where necessary",
-      A2: "Metadata are accessible, even when the data are no longer available",
-      I: "The data usually need to be integrated with other data. In addition, the data need to interoperate with applications or workflows for analysis, storage, and processing.",
-      I1: "(Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.",
-      I2: "(Meta)data use vocabularies that follow FAIR principles",
-      I3: "(Meta)data include qualified references to other (meta)data",
-      R: "The ultimate goal of FAIR is to optimise the reuse of data. To achieve this, metadata and data should be well-described so that they can be replicated and/or combined in different settings.",
-      R1: "(Meta)data are richly described with a plurality of accurate and relevant attributes",
-      R1_1: "(Meta)data are released with a clear and accessible data usage license",
-      R1_2: "(Meta)data are associated with detailed provenance",
-      R1_3: "(Meta)data meet domain-relevant community standards"
-    };
-    var principleKeys = Object.keys(exports.principles);
-    var mustExist = 'Principle does not exist, try "A1_1"';
-    function formatPrinciple(principle, opts) {
-      var _a, _b, _c, _d, _e, _f, _g, _h;
-      if (!(principle in exports.principles))
-        throw new Error(mustExist);
-      const key = principle.replace(/_/g, ".");
-      const header = exports.principleNames[principle];
-      const colorHeader = (_c = (_a = opts === null || opts === void 0 ? void 0 : opts.header) !== null && _a !== void 0 ? _a : (_b = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _b === void 0 ? void 0 : _b.bold.cyan) !== null && _c !== void 0 ? _c : format;
-      const underline = (_e = (_d = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _d === void 0 ? void 0 : _d.underline) !== null && _e !== void 0 ? _e : format;
-      const enumerator = (_h = (_f = opts === null || opts === void 0 ? void 0 : opts.enumerator) !== null && _f !== void 0 ? _f : (_g = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _g === void 0 ? void 0 : _g.bold.blue) !== null && _h !== void 0 ? _h : format;
-      if (header && (opts === null || opts === void 0 ? void 0 : opts.showHeader) !== false) {
-        return [
-          colorHeader(`${underline(header.slice(0, 1))}${header.slice(1)}`),
-          exports.principles[principle]
-        ].join("\n");
-      }
-      const indent = principle.includes("_") && (opts === null || opts === void 0 ? void 0 : opts.indent) !== false;
-      return `${indent ? "  " : ""}${enumerator(key)} ${exports.principles[principle]}`;
-    }
-    exports.formatPrinciple = formatPrinciple;
-    function formatPrinciples2(keys = "*", opts) {
-      var _a, _b, _c, _d, _e;
-      const input = typeof keys === "string" ? [keys] : keys;
-      const ordered = principleKeys.filter((key) => input.includes("*") || input.includes(key) || input.includes(key.slice(0, 1) + "*"));
-      const colorTitle = (_c = (_a = opts === null || opts === void 0 ? void 0 : opts.title) !== null && _a !== void 0 ? _a : (_b = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _b === void 0 ? void 0 : _b.bold.greenBright) !== null && _c !== void 0 ? _c : format;
-      const underline = (_e = (_d = opts === null || opts === void 0 ? void 0 : opts.chalk) === null || _d === void 0 ? void 0 : _d.underline) !== null && _e !== void 0 ? _e : format;
-      if ((opts === null || opts === void 0 ? void 0 : opts.showTitle) === false)
-        return ordered.map((k) => formatPrinciple(k, opts)).join("\n");
-      const header = `${colorTitle(`${(0, exports.highlightFAIR)(ordered.join(""), { color: underline })} Principle${ordered.length > 1 ? "s" : ""}`)}:`;
-      return [header, ...ordered.map((k) => formatPrinciple(k, opts))].join("\n");
-    }
-    exports.formatPrinciples = formatPrinciples2;
-    var baseUrl = "https://www.go-fair.org/fair-principles/";
-    function createPrincipleUrl(principle) {
-      if (!principle)
-        return baseUrl;
-      if (!(principle in exports.principles))
-        throw new Error(mustExist);
-      return `${baseUrl}${principle.toLowerCase().replace(/_/g, "-")}`;
-    }
-    exports.createPrincipleUrl = createPrincipleUrl;
-  }
-});
-
 // src/cli/index.ts
 var import_commander2 = __toESM(require_commander());
 
@@ -10343,7 +10343,8 @@ function writeFileToFolder(filename, data, opts) {
 
 // src/cli/parse.ts
 var import_doi_utils5 = __toESM(require_cjs());
-var import_chalk3 = __toESM(require_source());
+var import_chalk2 = __toESM(require_source());
+var import_fair_principles = __toESM(require_cjs2());
 
 // src/session.ts
 var Session = class {
@@ -10357,12 +10358,12 @@ function getSession(logger) {
 }
 
 // src/jats.ts
-var import_myst_common2 = __toESM(require_cjs2());
+var import_myst_common2 = __toESM(require_cjs3());
 var import_xml_js = __toESM(require_lib2());
 var import_doi_utils2 = __toESM(require_cjs());
 
 // src/utils.ts
-var import_myst_common = __toESM(require_cjs2());
+var import_myst_common = __toESM(require_cjs3());
 var import_doi_utils = __toESM(require_cjs());
 init_unist_util_select();
 function convertToUnist(node) {
@@ -10615,14 +10616,12 @@ function hasSingleArticle(element) {
 }
 
 // src/cli/parse.ts
-var import_myst_common3 = __toESM(require_cjs2());
+var import_myst_common3 = __toESM(require_cjs3());
 init_unist_util_select();
 
-// src/download.ts
+// src/cli/download.ts
 var import_doi_utils4 = __toESM(require_cjs());
-var import_chalk2 = __toESM(require_source());
 var import_node_fetch2 = __toESM(require_lib4());
-var import_fair_principles = __toESM(require_cjs3());
 
 // src/resolvers.ts
 var import_doi_utils3 = __toESM(require_cjs());
@@ -10673,25 +10672,8 @@ function customResolveJatsUrlFromDoi(_0, _1) {
   });
 }
 
-// src/download.ts
-function logAboutJatsFailing(session, jatsUrls) {
-  session.log.warn(
-    "\u26D4\uFE0F JATS may not be Open Access \u{1F62D}, you should petition your local representative \u{1FAA7}"
-  );
-  session.log.info(
-    `${import_chalk2.default.green(`
-The XML ${import_chalk2.default.bold("should")} be here:
-
-${jatsUrls.join("\n")}`)}
-`
-  );
-  const FAIR = (0, import_fair_principles.highlightFAIR)("A", { chalk: import_chalk2.default });
-  session.log.info(`Some publishers aggressively block programmatic access, which isn't ${FAIR}.`);
-  session.log.debug((0, import_fair_principles.formatPrinciples)("A*", { chalk: import_chalk2.default }));
-  session.log.info(`${import_chalk2.default.blue("The link may work in a browser.")}
-`);
-}
-function dowloadFromUrl(session, jatsUrl, opts) {
+// src/cli/download.ts
+function downloadFromUrl(session, jatsUrl, opts) {
   return __async(this, null, function* () {
     var _a, _b;
     const toc = tic();
@@ -10704,10 +10686,7 @@ function dowloadFromUrl(session, jatsUrl, opts) {
     const contentType = (_b = resp.headers) == null ? void 0 : _b.get("content-type");
     if (!((contentType == null ? void 0 : contentType.includes("application/xml")) || (contentType == null ? void 0 : contentType.includes("text/xml")) || (contentType == null ? void 0 : contentType.includes("text/plain")))) {
       session.log.warn(
-        `Expected content-type "application/xml" instead we got "${contentType}" for ${jatsUrl}
-${import_chalk2.default.dim(
-          "Things may not work, but we are going to try our best..."
-        )}`
+        `Expected content-type "application/xml" instead we got "${contentType}" for ${jatsUrl}`
       );
     }
     const data = yield resp.text();
@@ -10837,26 +10816,26 @@ function downloadJatsFromUrl(_0, _1) {
       for (let index = 0; index < expectedUrls.length; index++) {
         const url = expectedUrls[index];
         try {
-          const data = yield dowloadFromUrl(session, url, opts);
+          const data = yield downloadFromUrl(session, url, opts);
           if (data)
-            return { source: url, data };
+            return { success: true, source: url, data };
         } catch (error) {
           session.log.debug(error.message);
         }
       }
-      logAboutJatsFailing(session, expectedUrls);
+      return { success: false, source: expectedUrls[0] };
     }
     if (import_doi_utils4.default.validate(urlOrDoi)) {
       const jatsUrl = yield customResolveJatsUrlFromDoi(session, urlOrDoi, opts);
-      const data = yield dowloadFromUrl(session, jatsUrl, opts);
-      return { source: jatsUrl, data };
+      const data = yield downloadFromUrl(session, jatsUrl, opts);
+      return { success: true, source: jatsUrl, data };
     }
     if (isUrl(urlOrDoi)) {
       session.log.debug(
         "No resolver matched, and the URL doesn't look like a DOI. We will attempt to download it directly."
       );
-      const data = yield dowloadFromUrl(session, urlOrDoi, opts);
-      return { source: urlOrDoi, data };
+      const data = yield downloadFromUrl(session, urlOrDoi, opts);
+      return { success: true, source: urlOrDoi, data };
     }
     throw new Error(`Could not find ${urlOrDoi} locally, and it doesn't look like a URL or DOI`);
   });
@@ -10881,11 +10860,33 @@ function downloadAndSaveJats(_0, _1, _2) {
         )} is not a valid extension for JATS, try using ".xml" or ".jats"`
       );
     }
-    const { data } = yield downloadJatsFromUrl(session, urlOrDoi, opts);
+    const { success, data, source } = yield downloadJatsFromUrl(session, urlOrDoi, opts);
+    if (!success || !data) {
+      logAboutJatsFailing(session, [source]);
+      process.exit(1);
+    }
     writeFileToFolder(output, data);
     return data;
   });
 }
+function logAboutJatsFailing(session, jatsUrls) {
+  session.log.warn(
+    "\u26D4\uFE0F JATS may not be Open Access \u{1F62D}, you should petition your local representative \u{1FAA7}"
+  );
+  session.log.info(
+    `${import_chalk2.default.green(`
+The XML ${import_chalk2.default.bold("should")} be here:
+
+${jatsUrls.join("\n")}`)}
+`
+  );
+  const FAIR = (0, import_fair_principles.highlightFAIR)("A", { chalk: import_chalk2.default });
+  session.log.info(`Some publishers aggressively block programmatic access, which isn't ${FAIR}.`);
+  session.log.debug((0, import_fair_principles.formatPrinciples)("A*", { chalk: import_chalk2.default }));
+  session.log.info(`
+${import_chalk2.default.blue("The link may work in a browser.")}
+`);
+}
 function parseJats(_0, _1) {
   return __async(this, arguments, function* (session, file, opts = { resolvers: DEFAULT_RESOLVERS }) {
     const toc = tic();
@@ -10894,7 +10895,11 @@ function parseJats(_0, _1) {
       const data2 = import_fs2.default.readFileSync(file).toString();
       return new Jats(data2, { log: session.log });
     }
-    const { source, data } = yield downloadJatsFromUrl(session, file, opts);
+    const { success, source, data } = yield downloadJatsFromUrl(session, file, opts);
+    if (!success || !data) {
+      logAboutJatsFailing(session, [source]);
+      process.exit(1);
+    }
     const jats = new Jats(data, { source, log: session.log });
     session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
     return jats;
@@ -10920,7 +10925,7 @@ function formatDictionary(dict, opts) {
       return null;
     let wrap = typeof (opts == null ? void 0 : opts.wrap) === "boolean" ? opts.wrap : true;
     let value = t;
-    let color = import_chalk3.default.yellow.bold;
+    let color = import_chalk2.default.yellow.bold;
     if (t && typeof t === "object") {
       if (!t.value)
         return null;
@@ -10948,35 +10953,35 @@ function jatsSummaryCLI(session, file) {
     };
     if (jats.body) {
       summary.Figures = {
-        label: import_chalk3.default.blue.bold,
+        label: import_chalk2.default.blue.bold,
         value: String(selectAll("fig" /* fig */, jats.body).length)
       };
       summary.Equations = {
-        label: import_chalk3.default.blue.bold,
+        label: import_chalk2.default.blue.bold,
         value: String(selectAll("disp-formula" /* dispFormula */, jats.body).length)
       };
       summary.Tables = {
-        label: import_chalk3.default.blue.bold,
+        label: import_chalk2.default.blue.bold,
         value: String(selectAll("table" /* table */, jats.body).length)
       };
       summary.Code = {
-        label: import_chalk3.default.blue.bold,
+        label: import_chalk2.default.blue.bold,
         value: String(selectAll("code" /* code */, jats.body).length)
       };
       summary.Sections = {
-        label: import_chalk3.default.blue.bold,
+        label: import_chalk2.default.blue.bold,
         value: String(selectAll("sec" /* sec */, jats.body).length)
       };
       summary.Paragraphs = {
-        label: import_chalk3.default.blue.bold,
+        label: import_chalk2.default.blue.bold,
         value: String(selectAll("p" /* p */, jats.body).length)
       };
-      summary.Citations = { label: import_chalk3.default.blue.bold, value: String(jats.references.length) };
+      summary.Citations = { label: import_chalk2.default.blue.bold, value: String(jats.references.length) };
       summary["Cross-References"] = {
-        label: import_chalk3.default.blue.bold,
+        label: import_chalk2.default.blue.bold,
         value: String(selectAll("xref" /* xref */, jats.body).length)
       };
-      summary["Sub Articles"] = { label: import_chalk3.default.blue.bold, value: String(jats.subArticles.length) };
+      summary["Sub Articles"] = { label: import_chalk2.default.blue.bold, value: String(jats.subArticles.length) };
     }
     session.log.info(formatDictionary(summary));
     if (!jats.body) {

package/dist/types/{download.d.ts → cli/download.d.ts}

@@ -1,11 +1,12 @@
-import type { ISession, Options } from './types';
+import type { ISession, Options } from '../types';
 /**
  * https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
  */
 export declare function convertPMID2PMCID(session: ISession, PMID: string, opts: Options): Promise<string | undefined>;
 export declare function checkIfPubMedCentralHasJats(session: ISession, urlOrDoi: string, opts: Options): Promise<string | undefined>;
 export declare function downloadJatsFromUrl(session: ISession, urlOrDoi: string, opts?: Options): Promise<{
+    success: boolean;
     source: string;
-    data: string;
+    data?: string;
 }>;
 //# sourceMappingURL=download.d.ts.map

package/dist/types/cli/download.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"download.d.ts","sourceRoot":"","sources":["../../../src/cli/download.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,UAAU,CAAC;AA+FlD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,OAAO,EAAE,QAAQ,EACjB,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,OAAO,GACZ,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAqB7B;AAOD,wBAAsB,2BAA2B,CAC/C,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,OAAO,GACZ,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAgC7B;AAED,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,MAAM,EAChB,IAAI,GAAE,OAAY,GACjB,OAAO,CAAC;IAAE,OAAO,EAAE,OAAO,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,CAAC,CAkC9D"}

package/dist/types/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;AAsNpC,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;AA4OpC,wBAAgB,cAAc,CAAC,OAAO,EAAE,OAAO,QAI9C"}

package/dist/types/index.d.ts

@@ -1,5 +1,4 @@
 export { default as version } from './version';
 export { Jats } from './jats';
-export { downloadJatsFromUrl } from './download';
 export * from './types';
 //# sourceMappingURL=index.d.ts.map

package/dist/types/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,WAAW,CAAC;AAC/C,OAAO,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAC;AAC9B,OAAO,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAC;AACjD,cAAc,SAAS,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,WAAW,CAAC;AAC/C,OAAO,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAC;AAC9B,cAAc,SAAS,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-xml",
-  "version": "0.0.13",
+  "version": "0.0.14",
   "description": "Types and utilities for working with JATS in Typescript",
   "author": "Rowan Cockett <rowan@curvenote.com>",
   "homepage": "https://github.com/curvenote/jats-xml",

package/dist/types/download.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"download.d.ts","sourceRoot":"","sources":["../../src/download.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AA8GjD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,OAAO,EAAE,QAAQ,EACjB,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,OAAO,GACZ,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAqB7B;AAOD,wBAAsB,2BAA2B,CAC/C,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,OAAO,GACZ,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAgC7B;AAED,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,MAAM,EAChB,IAAI,GAAE,OAAY,GACjB,OAAO,CAAC;IAAE,MAAM,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,CAkC3C"}