jats-xml 0.0.2 → 0.0.4

package/README.md

@@ -1,3 +1,76 @@
 # jats-xml
 
-Types and utilities for working with JATS XML documents.
+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`.
+
+The standard documents are hosted by the NIH <https://jats.nlm.nih.gov/>. There are three flavours, this library currently uses in most cases the most precriptive tag set (for article authoring). Another helpful resource is <https://jats4r.org/>, which provides other examples and recomendations for JATS.
+
+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://docs.python.org/3.7 article.jats
+```
+
+Note, currently this just downloads the XML, **not** the associated files.
+
+`sumamry`: 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`](/packages/jats-xml/images/jats-output.png)
+
+## Working in Typescript
+
+All tags are accessible as types/enums. There is also documentation from each node-type
+
+```typescript
+import { Tags } from 'jats-xml';
+
+Tags.journalId;
+```
+
+## Reading JATS in Node
+
+```typescript
+import 'fs' from 'fs';
+import { Inventory, toDate } from 'jats-xml';
+import { toText } from 'myst-common';
+import { select, selectAll } from 'unist-util-select';
+
+const data = fs.readFileSync('article.jats').toString();
+const jats = new JATS(data);
+// Easy access to properties
+jats.doi
+jats.body // A tree of the body (or front/back)
+toDate(jats.publicationDate) // as a Javascript Date object
+select('[id=fig1]', jats.body) // select a figure by an ID
+selectAll('fig', jats.body) // Or selectAll figures
+```
+
+## Write JATS in Node
+
+TODO!

package/dist/cjs/cli/index.js

@@ -9,6 +9,6 @@ const version_1 = __importDefault(require("../version"));
 const parse_1 = require("./parse");
 const program = new commander_1.default.Command();
 (0, parse_1.addDownloadCLI)(program);
-program.version(`v${version_1.default}`, '-v, --version', 'Print the current version of jtex');
+program.version(`v${version_1.default}`, '-v, --version', 'Print the current version of jats-xml');
 program.option('-d, --debug', 'Log out any errors to the console.');
 program.parse(process.argv);

package/dist/cjs/cli/parse.js

@@ -30,7 +30,7 @@ const utils_1 = require("../utils");
 function hasValidExtension(output) {
     return ['.xml', '.jats'].includes((0, path_1.extname)(output).toLowerCase());
 }
-function downloadJats(session, urlOrDoi, output) {
+function downloadAndSaveJats(session, urlOrDoi, output) {
     return __awaiter(this, void 0, void 0, function* () {
         if (fs_1.default.existsSync(urlOrDoi)) {
             throw new Error(`File "${urlOrDoi}" is local and cannot be downloaded!`);
@@ -55,12 +55,9 @@ function parseJats(session, file) {
             session.log.debug(toc(`Parsed JATS file from disk in %s`));
             return new jats_1.Jats(data);
         }
-        if (doi_utils_1.default.validate(file) || (0, myst_cli_utils_1.isUrl)(file)) {
-            const data = yield (0, download_1.downloadJatsFromUrl)(session, file, resolvers_1.DEFAULT_RESOLVERS);
-            session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
-            return new jats_1.Jats(data);
-        }
-        throw new Error(`Could not find ${file} locally, and it doesn't look like a URL or DOI`);
+        const data = yield (0, download_1.downloadJatsFromUrl)(session, file, resolvers_1.DEFAULT_RESOLVERS);
+        session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
+        return new jats_1.Jats(data);
     });
 }
 function formatLongString(data, offset = 0, length = 88 - offset) {
@@ -145,7 +142,7 @@ function jatsReferencesCLI(session, file) {
         const jats = yield parseJats(session, file);
         const sorted = jats.references
             .map((ref) => {
-            const doi = (0, utils_1.findDoi)(ref);
+            const doiString = (0, utils_1.findDoi)(ref);
             const title = (0, myst_common_1.toText)((0, unist_util_select_1.select)(types_1.Tags.articleTitle, ref));
             const year = (0, myst_common_1.toText)((0, unist_util_select_1.select)(types_1.Tags.year, ref));
             const surnames = (0, unist_util_select_1.selectAll)(types_1.Tags.surname, ref);
@@ -158,7 +155,7 @@ function jatsReferencesCLI(session, file) {
             return {
                 Citation: `${short} (${year})`,
                 Title: title,
-                DOI: doi ? doi_utils_1.default.buildUrl(doi) : null,
+                DOI: doiString ? doi_utils_1.default.buildUrl(doiString) : null,
                 Count: s.length,
             };
         })
@@ -188,7 +185,7 @@ function makeDownloadCLI(program) {
         .description('Parse a JATS file and provide a summary')
         .argument('<url>', 'The JATS url or a DOI')
         .argument('<output>', 'The JATS url or a DOI')
-        .action((0, myst_cli_utils_1.clirun)(downloadJats, { program, getSession: session_1.getSession }));
+        .action((0, myst_cli_utils_1.clirun)(downloadAndSaveJats, { program, getSession: session_1.getSession }));
     return command;
 }
 function addDownloadCLI(program) {

package/dist/cjs/resolvers.js

@@ -33,22 +33,22 @@ exports.plos = {
 };
 exports.joss = {
     test(url) {
-        return new URL(url).hostname === 'joss.theoj.org';
+        return new URL(url).hostname === 'joss.theoj.org' && doi_utils_1.default.validate(url);
     },
     jatsUrl(url) {
         // Probably a better way to do this, the joss papers on on github!
-        const doi = new URL(url).pathname.replace('/papers/', '');
-        const [org, jossId] = doi.split('/');
+        const doiString = doi_utils_1.default.normalize(url);
+        const [org, jossId] = doiString.split('/');
         const id = jossId.split('.')[1];
         return `https://raw.githubusercontent.com/openjournals/joss-papers/master/joss.${id}/${org}.${jossId}.jats`;
     },
 };
 exports.DEFAULT_RESOLVERS = [exports.elife, exports.plos, exports.joss];
-function resolveJatsUrlFromDoi(session, doi, resolvers = exports.DEFAULT_RESOLVERS) {
+function resolveJatsUrlFromDoi(session, doiString, resolvers = exports.DEFAULT_RESOLVERS) {
     return __awaiter(this, void 0, void 0, function* () {
-        if (!doi_utils_1.default.validate(doi))
-            throw new Error(`The doi ${doi} is not valid`);
-        const doiUrl = doi_utils_1.default.buildUrl(doi);
+        if (!doi_utils_1.default.validate(doiString))
+            throw new Error(`The doi ${doiString} is not valid`);
+        const doiUrl = doi_utils_1.default.buildUrl(doiString);
         session.log.debug(`Resolving DOI ${doiUrl}`);
         const resp = yield (0, node_fetch_1.default)(doiUrl);
         const articleUrl = resp.url;

package/dist/cjs/session.js

@@ -5,7 +5,6 @@ const myst_cli_utils_1 = require("myst-cli-utils");
 class Session {
     constructor(opts) {
         var _a;
-        this.API_URL = 'https://api.myst.tools';
         this.log = (_a = opts === null || opts === void 0 ? void 0 : opts.logger) !== null && _a !== void 0 ? _a : (0, myst_cli_utils_1.chalkLogger)(myst_cli_utils_1.LogLevel.debug);
     }
 }

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const version = '0.0.2';
+const version = '0.0.4';
 exports.default = version;

package/dist/esm/cli/index.js

@@ -4,6 +4,6 @@ import version from '../version';
 import { addDownloadCLI } from './parse';
 const program = new commander.Command();
 addDownloadCLI(program);
-program.version(`v${version}`, '-v, --version', 'Print the current version of jtex');
+program.version(`v${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);

package/dist/esm/cli/parse.js

@@ -11,7 +11,7 @@ import { Command } from 'commander';
 import fs from 'fs';
 import { extname } from 'path';
 import { clirun, isUrl, tic, writeFileToFolder } from 'myst-cli-utils';
-import checkdoi from 'doi-utils';
+import doi from 'doi-utils';
 import chalk from 'chalk';
 import { getSession } from '../session';
 import { Tags } from '../types';
@@ -24,12 +24,12 @@ import { findDoi, formatDate, toDate } from '../utils';
 function hasValidExtension(output) {
     return ['.xml', '.jats'].includes(extname(output).toLowerCase());
 }
-function downloadJats(session, urlOrDoi, output) {
+function downloadAndSaveJats(session, urlOrDoi, output) {
     return __awaiter(this, void 0, void 0, function* () {
         if (fs.existsSync(urlOrDoi)) {
             throw new Error(`File "${urlOrDoi}" is local and cannot be downloaded!`);
         }
-        if (!(checkdoi.validate(urlOrDoi) || isUrl(urlOrDoi))) {
+        if (!(doi.validate(urlOrDoi) || isUrl(urlOrDoi))) {
             throw new Error(`Path must be a URL or DOI, not "${urlOrDoi}"`);
         }
         if (!hasValidExtension(output)) {
@@ -49,12 +49,9 @@ function parseJats(session, file) {
             session.log.debug(toc(`Parsed JATS file from disk in %s`));
             return new Jats(data);
         }
-        if (checkdoi.validate(file) || isUrl(file)) {
-            const data = yield downloadJatsFromUrl(session, file, DEFAULT_RESOLVERS);
-            session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
-            return new Jats(data);
-        }
-        throw new Error(`Could not find ${file} locally, and it doesn't look like a URL or DOI`);
+        const data = yield downloadJatsFromUrl(session, file, DEFAULT_RESOLVERS);
+        session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
+        return new Jats(data);
     });
 }
 function formatLongString(data, offset = 0, length = 88 - offset) {
@@ -94,7 +91,7 @@ function jatsSummaryCLI(session, file) {
     return __awaiter(this, void 0, void 0, function* () {
         const jats = yield parseJats(session, file);
         const summary = {
-            DOI: jats.doi ? checkdoi.buildUrl(jats.doi) : null,
+            DOI: jats.doi ? doi.buildUrl(jats.doi) : null,
             Title: (_a = toText(jats.articleTitle)) === null || _a === void 0 ? void 0 : _a.replace(/\n/g, ' '),
             Date: formatDate(toDate(jats.publicationDate)),
             Authors: jats.articleAuthors
@@ -139,7 +136,7 @@ function jatsReferencesCLI(session, file) {
         const jats = yield parseJats(session, file);
         const sorted = jats.references
             .map((ref) => {
-            const doi = findDoi(ref);
+            const doiString = findDoi(ref);
             const title = toText(select(Tags.articleTitle, ref));
             const year = toText(select(Tags.year, ref));
             const surnames = selectAll(Tags.surname, ref);
@@ -152,7 +149,7 @@ function jatsReferencesCLI(session, file) {
             return {
                 Citation: `${short} (${year})`,
                 Title: title,
-                DOI: doi ? checkdoi.buildUrl(doi) : null,
+                DOI: doiString ? doi.buildUrl(doiString) : null,
                 Count: s.length,
             };
         })
@@ -182,7 +179,7 @@ function makeDownloadCLI(program) {
         .description('Parse a JATS file and provide a summary')
         .argument('<url>', 'The JATS url or a DOI')
         .argument('<output>', 'The JATS url or a DOI')
-        .action(clirun(downloadJats, { program, getSession }));
+        .action(clirun(downloadAndSaveJats, { program, getSession }));
     return command;
 }
 export function addDownloadCLI(program) {

package/dist/esm/download.js

@@ -7,7 +7,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
-import checkdoi from 'doi-utils';
+import doi from 'doi-utils';
 import fetch from 'node-fetch';
 import { isUrl } from 'myst-cli-utils';
 import { resolveJatsUrlFromDoi } from './resolvers';
@@ -27,7 +27,7 @@ function dowloadFromUrl(session, jatsUrl) {
 }
 export function downloadJatsFromUrl(session, urlOrDoi, resolvers) {
     return __awaiter(this, void 0, void 0, function* () {
-        if (checkdoi.validate(urlOrDoi)) {
+        if (doi.validate(urlOrDoi)) {
             const jatsUrl = yield resolveJatsUrlFromDoi(session, urlOrDoi, resolvers);
             const data = yield dowloadFromUrl(session, jatsUrl);
             return data;

package/dist/esm/resolvers.js

@@ -7,7 +7,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
-import checkdoi from 'doi-utils';
+import doi from 'doi-utils';
 import fetch from 'node-fetch';
 export const elife = {
     test(url) {
@@ -27,22 +27,22 @@ export const plos = {
 };
 export const joss = {
     test(url) {
-        return new URL(url).hostname === 'joss.theoj.org';
+        return new URL(url).hostname === 'joss.theoj.org' && doi.validate(url);
     },
     jatsUrl(url) {
         // Probably a better way to do this, the joss papers on on github!
-        const doi = new URL(url).pathname.replace('/papers/', '');
-        const [org, jossId] = doi.split('/');
+        const doiString = doi.normalize(url);
+        const [org, jossId] = doiString.split('/');
         const id = jossId.split('.')[1];
         return `https://raw.githubusercontent.com/openjournals/joss-papers/master/joss.${id}/${org}.${jossId}.jats`;
     },
 };
 export const DEFAULT_RESOLVERS = [elife, plos, joss];
-export function resolveJatsUrlFromDoi(session, doi, resolvers = DEFAULT_RESOLVERS) {
+export function resolveJatsUrlFromDoi(session, doiString, resolvers = DEFAULT_RESOLVERS) {
     return __awaiter(this, void 0, void 0, function* () {
-        if (!checkdoi.validate(doi))
-            throw new Error(`The doi ${doi} is not valid`);
-        const doiUrl = checkdoi.buildUrl(doi);
+        if (!doi.validate(doiString))
+            throw new Error(`The doi ${doiString} is not valid`);
+        const doiUrl = doi.buildUrl(doiString);
         session.log.debug(`Resolving DOI ${doiUrl}`);
         const resp = yield fetch(doiUrl);
         const articleUrl = resp.url;

package/dist/esm/session.js

@@ -2,7 +2,6 @@ import { chalkLogger, LogLevel } from 'myst-cli-utils';
 export class Session {
     constructor(opts) {
         var _a;
-        this.API_URL = 'https://api.myst.tools';
         this.log = (_a = opts === null || opts === void 0 ? void 0 : opts.logger) !== null && _a !== void 0 ? _a : chalkLogger(LogLevel.debug);
     }
 }

package/dist/esm/utils.js

@@ -1,5 +1,5 @@
 import { toText } from 'myst-common';
-import checkdoi from 'doi-utils';
+import doi from 'doi-utils';
 import { select, selectAll } from 'unist-util-select';
 import { Tags } from './types';
 export function convertToUnist(node) {
@@ -83,6 +83,6 @@ export function findDoi(node) {
     const id = select('[pub-id-type=doi]', node);
     if (id && toText(id))
         return toText(id);
-    const doiTag = selectAll(`${Tags.articleId},${Tags.pubId}`, node).find((t) => checkdoi.validate(toText(t)));
+    const doiTag = selectAll(`${Tags.articleId},${Tags.pubId}`, node).find((t) => doi.validate(toText(t)));
     return toText(doiTag) || null;
 }

package/dist/esm/version.js

@@ -1,2 +1,2 @@
-const version = '0.0.2';
+const version = '0.0.4';
 export default version;

package/dist/jats.js

@@ -3279,7 +3279,7 @@ var require_resolvers = __commonJS({
     Object.defineProperty(exports, "__esModule", {
       value: true
     });
-    exports.DEFAULT_RESOLVERS = void 0;
+    exports.DEFAULT_RESOLVERS = exports.STRICT_RESOLVERS = void 0;
     var _validatePart = require_validatePart();
     var doiOrg = {
       test(url) {
@@ -3329,6 +3329,10 @@ var require_resolvers = __commonJS({
         return clumpParts(url).find(_validatePart.validatePart);
       }
     };
+    var STRICT_RESOLVERS = [
+      doiOrg
+    ];
+    exports.STRICT_RESOLVERS = STRICT_RESOLVERS;
     var DEFAULT_RESOLVERS2 = [
       doiOrg,
       doiSubdomain,
@@ -3347,53 +3351,57 @@ var require_cjs = __commonJS({
     Object.defineProperty(exports, "__esModule", {
       value: true
     });
-    Object.defineProperty(exports, "validatePart", {
+    Object.defineProperty(exports, "DEFAULT_RESOLVERS", {
+      enumerable: true,
+      get: function() {
+        return _resolvers.DEFAULT_RESOLVERS;
+      }
+    });
+    Object.defineProperty(exports, "STRICT_RESOLVERS", {
       enumerable: true,
       get: function() {
-        return _validatePart.validatePart;
+        return _resolvers.STRICT_RESOLVERS;
       }
     });
-    exports.validate = validate;
-    exports.normalize = normalize;
-    exports.buildUrl = buildUrl;
     exports.default = void 0;
     var _resolvers = require_resolvers();
     var _validatePart = require_validatePart();
-    function validate(possibleDOI) {
+    function validate(possibleDOI, opts) {
       if (!possibleDOI)
         return false;
-      return !!normalize(possibleDOI);
+      return !!normalize(possibleDOI, opts);
     }
-    function normalize(possibleDOI) {
-      let doi = void 0;
+    function normalize(possibleDOI, opts) {
+      let doi5 = void 0;
       if (!possibleDOI)
         return void 0;
       if ((0, _validatePart).validatePart(possibleDOI))
         return possibleDOI;
       if (possibleDOI.startsWith("doi:")) {
-        doi = possibleDOI.slice(4);
-        if ((0, _validatePart).validatePart(doi))
-          return doi;
+        doi5 = possibleDOI.slice(4);
+        if ((0, _validatePart).validatePart(doi5))
+          return doi5;
       }
       try {
         const url = new URL(possibleDOI.startsWith("http") ? possibleDOI : `http://${possibleDOI}`);
-        const resolver = _resolvers.DEFAULT_RESOLVERS.find(
+        const resolvers = (opts === null || opts === void 0 ? void 0 : opts.strict) ? _resolvers.STRICT_RESOLVERS : _resolvers.DEFAULT_RESOLVERS;
+        const resolver = resolvers.find(
           (r) => r.test(url)
         );
         if (!resolver)
           return void 0;
-        doi = resolver.parse(url);
+        doi5 = resolver.parse(url);
       } catch (error) {
       }
-      if ((0, _validatePart).validatePart(doi))
-        return doi;
+      if ((0, _validatePart).validatePart(doi5))
+        return doi5;
       return void 0;
     }
-    function buildUrl(possibleDOI) {
-      const doi = normalize(possibleDOI);
-      if (!doi)
+    function buildUrl(possibleDOI, opts) {
+      const doi5 = normalize(possibleDOI, opts);
+      if (!doi5)
         return void 0;
-      return `https://doi.org/${doi}`;
+      return `https://doi.org/${doi5}`;
     }
     var _default = {
       validatePart: _validatePart.validatePart,
@@ -9094,7 +9102,7 @@ var require_lib4 = __commonJS({
 var import_commander2 = __toESM(require_commander());
 
 // src/version.ts
-var version = "0.0.2";
+var version = "0.0.4";
 var version_default = version;
 
 // src/cli/parse.ts
@@ -9243,7 +9251,6 @@ var import_chalk2 = __toESM(require_source());
 // src/session.ts
 var Session2 = class {
   constructor(opts) {
-    this.API_URL = "https://api.myst.tools";
     var _a;
     this.log = (_a = opts == null ? void 0 : opts.logger) != null ? _a : chalkLogger(LogLevel.debug);
   }
@@ -10205,21 +10212,21 @@ var plos = {
 };
 var joss = {
   test(url) {
-    return new URL(url).hostname === "joss.theoj.org";
+    return new URL(url).hostname === "joss.theoj.org" && import_doi_utils2.default.validate(url);
   },
   jatsUrl(url) {
-    const doi = new URL(url).pathname.replace("/papers/", "");
-    const [org, jossId] = doi.split("/");
+    const doiString = import_doi_utils2.default.normalize(url);
+    const [org, jossId] = doiString.split("/");
     const id = jossId.split(".")[1];
     return `https://raw.githubusercontent.com/openjournals/joss-papers/master/joss.${id}/${org}.${jossId}.jats`;
   }
 };
 var DEFAULT_RESOLVERS = [elife, plos, joss];
 function resolveJatsUrlFromDoi(_0, _1) {
-  return __async(this, arguments, function* (session, doi, resolvers = DEFAULT_RESOLVERS) {
-    if (!import_doi_utils2.default.validate(doi))
-      throw new Error(`The doi ${doi} is not valid`);
-    const doiUrl = import_doi_utils2.default.buildUrl(doi);
+  return __async(this, arguments, function* (session, doiString, resolvers = DEFAULT_RESOLVERS) {
+    if (!import_doi_utils2.default.validate(doiString))
+      throw new Error(`The doi ${doiString} is not valid`);
+    const doiUrl = import_doi_utils2.default.buildUrl(doiString);
     session.log.debug(`Resolving DOI ${doiUrl}`);
     const resp = yield (0, import_node_fetch.default)(doiUrl);
     const articleUrl = resp.url;
@@ -10268,7 +10275,7 @@ function downloadJatsFromUrl(session, urlOrDoi, resolvers) {
 function hasValidExtension(output) {
   return [".xml", ".jats"].includes((0, import_path2.extname)(output).toLowerCase());
 }
-function downloadJats(session, urlOrDoi, output) {
+function downloadAndSaveJats(session, urlOrDoi, output) {
   return __async(this, null, function* () {
     if (import_fs2.default.existsSync(urlOrDoi)) {
       throw new Error(`File "${urlOrDoi}" is local and cannot be downloaded!`);
@@ -10293,16 +10300,13 @@ function parseJats(session, file) {
     const toc = tic();
     if (import_fs2.default.existsSync(file)) {
       session.log.debug(`Found ${file} locally, parsing`);
-      const data = import_fs2.default.readFileSync(file).toString();
+      const data2 = import_fs2.default.readFileSync(file).toString();
       session.log.debug(toc(`Parsed JATS file from disk in %s`));
-      return new Jats(data);
-    }
-    if (import_doi_utils4.default.validate(file) || isUrl(file)) {
-      const data = yield downloadJatsFromUrl(session, file, DEFAULT_RESOLVERS);
-      session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
-      return new Jats(data);
+      return new Jats(data2);
     }
-    throw new Error(`Could not find ${file} locally, and it doesn't look like a URL or DOI`);
+    const data = yield downloadJatsFromUrl(session, file, DEFAULT_RESOLVERS);
+    session.log.debug(toc(`Downloaded and parsed JATS file in %s`));
+    return new Jats(data);
   });
 }
 function formatLongString(data, offset = 0, length = 88 - offset) {
@@ -10380,7 +10384,7 @@ function jatsReferencesCLI(session, file) {
   return __async(this, null, function* () {
     const jats = yield parseJats(session, file);
     const sorted = jats.references.map((ref) => {
-      const doi = findDoi(ref);
+      const doiString = findDoi(ref);
       const title = toText(select("article-title" /* articleTitle */, ref));
       const year = toText(select("year" /* year */, ref));
       const surnames = selectAll("surname" /* surname */, ref);
@@ -10389,7 +10393,7 @@ function jatsReferencesCLI(session, file) {
       return {
         Citation: `${short} (${year})`,
         Title: title,
-        DOI: doi ? import_doi_utils4.default.buildUrl(doi) : null,
+        DOI: doiString ? import_doi_utils4.default.buildUrl(doiString) : null,
         Count: s.length
       };
     }).sort((a, b) => b.Count - a.Count);
@@ -10407,7 +10411,7 @@ function makeReferencesCLI(program2) {
   return command;
 }
 function makeDownloadCLI(program2) {
-  const command = new import_commander.Command("download").description("Parse a JATS file and provide a summary").argument("<url>", "The JATS url or a DOI").argument("<output>", "The JATS url or a DOI").action(clirun(downloadJats, { program: program2, getSession: getSession2 }));
+  const command = new import_commander.Command("download").description("Parse a JATS file and provide a summary").argument("<url>", "The JATS url or a DOI").argument("<output>", "The JATS url or a DOI").action(clirun(downloadAndSaveJats, { program: program2, getSession: getSession2 }));
   return command;
 }
 function addDownloadCLI(program2) {
@@ -10419,7 +10423,7 @@ function addDownloadCLI(program2) {
 // src/cli/index.ts
 var program = new import_commander2.default.Command();
 addDownloadCLI(program);
-program.version(`v${version_default}`, "-v, --version", "Print the current version of jtex");
+program.version(`v${version_default}`, "-v, --version", "Print the current version of jats-xml");
 program.option("-d, --debug", "Log out any errors to the console.");
 program.parse(process.argv);
 /*! http://mths.be/fromcodepoint v0.1.0 by @mathias */

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;AAoMpC,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;AAqMpC,wBAAgB,cAAc,CAAC,OAAO,EAAE,OAAO,QAI9C"}

package/dist/types/resolvers.d.ts

@@ -7,5 +7,5 @@ export declare const elife: Resolver;
 export declare const plos: Resolver;
 export declare const joss: Resolver;
 export declare const DEFAULT_RESOLVERS: Resolver[];
-export declare function resolveJatsUrlFromDoi(session: ISession, doi: string, resolvers?: Resolver[]): Promise<string>;
+export declare function resolveJatsUrlFromDoi(session: ISession, doiString: string, resolvers?: Resolver[]): Promise<string>;
 //# sourceMappingURL=resolvers.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"resolvers.d.ts","sourceRoot":"","sources":["../../src/resolvers.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AAExC,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC;IAC/B,OAAO,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAAC;CAClC;AAED,eAAO,MAAM,KAAK,EAAE,QAOnB,CAAC;AAEF,eAAO,MAAM,IAAI,EAAE,QAOlB,CAAC;AAEF,eAAO,MAAM,IAAI,EAAE,QAWlB,CAAC;AAEF,eAAO,MAAM,iBAAiB,EAAE,QAAQ,EAAwB,CAAC;AAEjE,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,QAAQ,EACjB,GAAG,EAAE,MAAM,EACX,SAAS,aAAoB,GAC5B,OAAO,CAAC,MAAM,CAAC,CAWjB"}
+{"version":3,"file":"resolvers.d.ts","sourceRoot":"","sources":["../../src/resolvers.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AAExC,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC;IAC/B,OAAO,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,CAAC;CAClC;AAED,eAAO,MAAM,KAAK,EAAE,QAOnB,CAAC;AAEF,eAAO,MAAM,IAAI,EAAE,QAOlB,CAAC;AAEF,eAAO,MAAM,IAAI,EAAE,QAWlB,CAAC;AAEF,eAAO,MAAM,iBAAiB,EAAE,QAAQ,EAAwB,CAAC;AAEjE,wBAAsB,qBAAqB,CACzC,OAAO,EAAE,QAAQ,EACjB,SAAS,EAAE,MAAM,EACjB,SAAS,aAAoB,GAC5B,OAAO,CAAC,MAAM,CAAC,CAWjB"}

package/dist/types/session.d.ts

@@ -1,7 +1,6 @@
 import type { Logger } from 'myst-cli-utils';
 import type { ISession } from './types';
 export declare class Session implements ISession {
-    API_URL: string;
     log: Logger;
     constructor(opts?: {
         logger?: Logger;

package/dist/types/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,SAAS,CAAC;AAExC,qBAAa,OAAQ,YAAW,QAAQ;IACtC,OAAO,SAA4B;IACnC,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":"AACA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAC7C,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AAExC,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"}

package/dist/types/version.d.ts

@@ -1,3 +1,3 @@
-declare const version = "0.0.2";
+declare const version = "0.0.4";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-xml",
-  "version": "0.0.2",
+  "version": "0.0.4",
   "description": "Types and utilities for working with JATS in Typescript",
   "author": "Rowan Cockett <rowan@curvenote.com>",
   "homepage": "https://github.com/executablebooks/mystjs/tree/main/packages/jats-xml",
@@ -34,25 +34,25 @@
   "scripts": {
     "copy:version": "echo \"const version = '\"$npm_package_version\"';\nexport default version;\" > src/version.ts",
     "clean": "rm -rf dist",
-    "prepublishOnly": "npm run build;",
+    "prepublishOnly": "npm run copy:version && npm run build;",
     "unlink": "npm uninstall -g jats-xml;",
     "link": "npm run unlink; npm link;",
-    "dev": "npm run link && esbuild src/cli/index.ts --bundle --outfile=dist/jats.js --platform=node --watch",
-    "test": "copy:version && jest",
+    "dev": "npm run copy:version && npm run link && esbuild src/cli/index.ts --bundle --outfile=dist/jats.js --platform=node --watch",
+    "test": "npm run copy:version && jest",
     "test:watch": "jest --watchAll",
-    "lint": "eslint \"src/**/*.ts\" -c .eslintrc.js --max-warnings 1",
+    "lint": "npm run copy:version && eslint \"src/**/*.ts\" -c .eslintrc.js --max-warnings 1",
     "lint:format": "prettier --check src/*.ts src/**/*.ts",
     "build:esm": "tsc --module es2015   --outDir dist/esm",
     "build:cjs": "tsc --module commonjs --outDir dist/cjs",
     "build:cli": "esbuild src/cli/index.ts --bundle --outfile=dist/jats.js --platform=node",
     "declarations": "tsc --declaration --emitDeclarationOnly --declarationMap --outDir dist/types",
-    "build": "npm-run-all -l clean -p copy:version build:cjs build:esm declarations build:cli"
+    "build": "npm-run-all -l clean copy:version -p build:cjs build:esm declarations build:cli"
   },
   "bugs": {
     "url": "https://github.com/executablebooks/mystjs/issues"
   },
   "dependencies": {
-    "myst-common": "^0.0.6"
+    "myst-common": "^0.0.7"
   },
   "devDependencies": {
     "npm-run-all": "^4.1.5",