jats-xml 0.0.16 → 0.1.0

package/README.md

@@ -53,6 +53,28 @@ This will provide a summary, including a list of what the JATS file contains.
 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

package/dist/cjs/cli/index.js

@@ -8,9 +8,11 @@ const commander_1 = __importDefault(require("commander"));
 const version_1 = __importDefault(require("../version"));
 const parse_1 = require("./parse");
 const validate_1 = require("./validate");
+const jats_test_1 = require("./jats-test");
 const program = new commander_1.default.Command();
 (0, parse_1.addDownloadCLI)(program);
 (0, validate_1.addValidateCLI)(program);
+(0, jats_test_1.addTestCLI)(program);
 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/jats-test.js

@@ -0,0 +1,125 @@
+"use strict";
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.addTestCLI = exports.testJatsFile = void 0;
+const commander_1 = require("commander");
+const myst_cli_utils_1 = require("myst-cli-utils");
+const session_1 = require("../session");
+const js_yaml_1 = __importDefault(require("js-yaml"));
+const fs_1 = __importDefault(require("fs"));
+const parse_1 = require("./parse");
+const unist_util_select_1 = require("unist-util-select");
+const unist_util_is_1 = require("unist-util-is");
+const chalk_1 = __importDefault(require("chalk"));
+const INDENT = '       ';
+function printNodes(expected, received) {
+    return chalk_1.default.reset(`\n${INDENT}${chalk_1.default.greenBright('Expected node containing')}:\n${INDENT}  ${js_yaml_1.default
+        .dump(expected)
+        .replace(/\n/g, `\n${INDENT}  `)}\n${INDENT}${chalk_1.default.redBright('Received node')}:\n${INDENT}  ${js_yaml_1.default.dump(received).replace(/\n/g, `\n${INDENT}  `)}`);
+}
+function testJatsFile(session, file, opts) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const toc = (0, myst_cli_utils_1.tic)();
+        const jats = yield (0, parse_1.parseJats)(session, file);
+        const tests = js_yaml_1.default.load(fs_1.default.readFileSync(opts.cases).toString());
+        const results = tests.cases.map((testCase, index) => {
+            if (!testCase.title) {
+                return [`Test Case ${index}`, null, 'Test must include a title'];
+            }
+            if (testCase.equals === undefined) {
+                return [testCase.title, null, 'Test must have an equals statement'];
+            }
+            if (testCase.select) {
+                const node = (0, unist_util_select_1.select)(testCase.select, jats.tree);
+                const pass = (0, unist_util_is_1.is)(node, testCase.equals);
+                if (testCase.equals == null && node) {
+                    return [testCase.title, false, 'Expected no node to be present'];
+                }
+                if (!node && testCase.equals == null)
+                    return [testCase.title, true];
+                if (!node)
+                    return [testCase.title, false];
+                let failed = false;
+                const messages = [];
+                if (!pass) {
+                    failed = failed || true;
+                    messages.push(`Failed to validate node\n${printNodes(testCase.equals, node)}`);
+                }
+                return [testCase.title, !failed, messages.join('\n')];
+            }
+            else if (testCase.selectAll) {
+                const testNodes = (0, unist_util_select_1.selectAll)(testCase.selectAll, jats.tree);
+                if (!testNodes && testCase.equals == null)
+                    return [testCase.title, true];
+                if (!testNodes)
+                    return [testCase.title, false, 'Node not found'];
+                let equals = testCase.equals;
+                if (!Array.isArray(testCase.equals)) {
+                    equals = Array(testNodes.length).fill(testCase.equals);
+                }
+                let failed = false;
+                const messages = [];
+                if (equals.length !== testNodes.length) {
+                    failed = failed || true;
+                    messages.push(`Expected ${equals.length} nodes, got ${testNodes.length}\n${printNodes(equals, testNodes)}`);
+                }
+                else {
+                    equals.forEach((node, ii) => {
+                        const pass = (0, unist_util_is_1.is)(testNodes[ii], node);
+                        if (!pass) {
+                            failed = failed || true;
+                            messages.push(`Failed to validate node ${ii}\n${printNodes(node, testNodes[ii])}`);
+                        }
+                    });
+                }
+                return [testCase.title, !failed, messages.join('\n')];
+            }
+            else {
+                return [testCase.title, false, 'Test must have either `select` or `selectAll`'];
+            }
+        });
+        results.forEach((result) => {
+            const [title, pass, message] = result;
+            if (pass === null)
+                session.log.info(`${chalk_1.default.redBright.bold(`ERROR`)} - ${title}\n  ${chalk_1.default.blueBright(message)}`);
+            else if (pass)
+                session.log.info(`${chalk_1.default.green(`PASS`)} - ${title}`);
+            else
+                session.log.info(`${chalk_1.default.red(`FAIL`)} - ${title}\n\n${INDENT}${chalk_1.default.blueBright(message)}\n`);
+        }, true);
+        const passed = results.reduce((num, [, pass]) => num + (pass ? 1 : 0), 0);
+        const failed = results.length - passed;
+        if (failed > 0 && passed === 0) {
+            throw new Error(toc(`${chalk_1.default.red(`Failed ${failed} tests in %s`)} 👎`));
+        }
+        if (failed > 0) {
+            throw new Error(toc(`${chalk_1.default.green(`Passed ${passed}/${results.length} tests in %s`)}\n${chalk_1.default.red(`Failed ${failed} tests`)} 👎`));
+        }
+        session.log.info(chalk_1.default.green(toc(`Passed ${passed} tests in %s 🚀`)));
+        return true;
+    });
+}
+exports.testJatsFile = testJatsFile;
+function makeTestCLI(program) {
+    const command = new commander_1.Command('test')
+        .description('Test JATS file against a list of cases')
+        .argument('<file>', 'JATS file to test')
+        .addOption(new commander_1.Option('--cases <value>', 'The YAML file of unit tests to test against'))
+        .action((0, myst_cli_utils_1.clirun)(testJatsFile, { program, getSession: session_1.getSession }));
+    return command;
+}
+function addTestCLI(program) {
+    program.addCommand(makeTestCLI(program));
+}
+exports.addTestCLI = addTestCLI;

package/dist/cjs/cli/parse.js

@@ -12,7 +12,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.addDownloadCLI = void 0;
+exports.addDownloadCLI = exports.parseJats = void 0;
 const commander_1 = require("commander");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = require("path");
@@ -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");
@@ -77,6 +77,7 @@ function parseJats(session, file, opts = { resolvers: resolvers_1.DEFAULT_RESOLV
         return jats;
     });
 }
+exports.parseJats = parseJats;
 function formatLongString(data, offset = 0, length = 88 - offset) {
     const out = [data.slice(0, length)];
     let left = data.slice(length);
@@ -121,7 +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(', '),
@@ -130,32 +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) };
         }
@@ -171,9 +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

@@ -7,24 +7,29 @@ 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': {
             const { name, attributes, elements } = node;
             const children = elements === null || elements === void 0 ? void 0 : elements.map(convertToUnist).filter((n) => !!n);
             const next = Object.assign({ type: name !== null && name !== void 0 ? name : 'unknown' }, attributes);
-            if (children)
+            if (name === 'code') {
+                next.value = elements === null || elements === void 0 ? void 0 : elements[0].text;
+            }
+            else if (children)
                 next.children = children;
             return next;
         }
         case 'text': {
             const { attributes, text } = node;
-            return Object.assign(Object.assign({ type: 'text' }, attributes), { value: String(text) });
+            return Object.assign(Object.assign({ type: 'text' }, attributes), { value: String(text)
+                    .replace(/\n(\s+)$/, '')
+                    .replace('\n', ' ') });
         }
         case 'cdata': {
             const { attributes, cdata } = node;
-            return Object.assign(Object.assign({ type: 'cdata' }, attributes), { cdata });
+            return Object.assign(Object.assign({ type: 'cdata' }, attributes), { cdata: String(cdata).trim() });
         }
         case 'comment': {
             const { comment } = node;
@@ -100,13 +105,13 @@ function findArticleId(node, pubIdType = 'doi') {
     const id = (0, unist_util_select_1.select)(`[pub-id-type=${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 = '0.0.16';
+const version = '0.1.0';
 exports.default = version;

package/dist/esm/cli/index.js

@@ -3,9 +3,11 @@ import commander from 'commander';
 import version from '../version';
 import { addDownloadCLI } from './parse';
 import { addValidateCLI } from './validate';
+import { addTestCLI } from './jats-test';
 const program = new commander.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);

package/dist/esm/cli/jats-test.js

@@ -0,0 +1,117 @@
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+import { Command, Option } from 'commander';
+import { clirun, tic } from 'myst-cli-utils';
+import { getSession } from '../session';
+import yaml from 'js-yaml';
+import fs from 'fs';
+import { parseJats } from './parse';
+import { select, selectAll } from 'unist-util-select';
+import { is } from 'unist-util-is';
+import chalk from 'chalk';
+const INDENT = '       ';
+function printNodes(expected, received) {
+    return chalk.reset(`\n${INDENT}${chalk.greenBright('Expected node containing')}:\n${INDENT}  ${yaml
+        .dump(expected)
+        .replace(/\n/g, `\n${INDENT}  `)}\n${INDENT}${chalk.redBright('Received node')}:\n${INDENT}  ${yaml.dump(received).replace(/\n/g, `\n${INDENT}  `)}`);
+}
+export function testJatsFile(session, file, opts) {
+    return __awaiter(this, void 0, void 0, function* () {
+        const toc = tic();
+        const jats = yield parseJats(session, file);
+        const tests = yaml.load(fs.readFileSync(opts.cases).toString());
+        const results = tests.cases.map((testCase, index) => {
+            if (!testCase.title) {
+                return [`Test Case ${index}`, null, 'Test must include a title'];
+            }
+            if (testCase.equals === undefined) {
+                return [testCase.title, null, 'Test must have an equals statement'];
+            }
+            if (testCase.select) {
+                const node = select(testCase.select, jats.tree);
+                const pass = is(node, testCase.equals);
+                if (testCase.equals == null && node) {
+                    return [testCase.title, false, 'Expected no node to be present'];
+                }
+                if (!node && testCase.equals == null)
+                    return [testCase.title, true];
+                if (!node)
+                    return [testCase.title, false];
+                let failed = false;
+                const messages = [];
+                if (!pass) {
+                    failed = failed || true;
+                    messages.push(`Failed to validate node\n${printNodes(testCase.equals, node)}`);
+                }
+                return [testCase.title, !failed, messages.join('\n')];
+            }
+            else if (testCase.selectAll) {
+                const testNodes = selectAll(testCase.selectAll, jats.tree);
+                if (!testNodes && testCase.equals == null)
+                    return [testCase.title, true];
+                if (!testNodes)
+                    return [testCase.title, false, 'Node not found'];
+                let equals = testCase.equals;
+                if (!Array.isArray(testCase.equals)) {
+                    equals = Array(testNodes.length).fill(testCase.equals);
+                }
+                let failed = false;
+                const messages = [];
+                if (equals.length !== testNodes.length) {
+                    failed = failed || true;
+                    messages.push(`Expected ${equals.length} nodes, got ${testNodes.length}\n${printNodes(equals, testNodes)}`);
+                }
+                else {
+                    equals.forEach((node, ii) => {
+                        const pass = is(testNodes[ii], node);
+                        if (!pass) {
+                            failed = failed || true;
+                            messages.push(`Failed to validate node ${ii}\n${printNodes(node, testNodes[ii])}`);
+                        }
+                    });
+                }
+                return [testCase.title, !failed, messages.join('\n')];
+            }
+            else {
+                return [testCase.title, false, 'Test must have either `select` or `selectAll`'];
+            }
+        });
+        results.forEach((result) => {
+            const [title, pass, message] = result;
+            if (pass === null)
+                session.log.info(`${chalk.redBright.bold(`ERROR`)} - ${title}\n  ${chalk.blueBright(message)}`);
+            else if (pass)
+                session.log.info(`${chalk.green(`PASS`)} - ${title}`);
+            else
+                session.log.info(`${chalk.red(`FAIL`)} - ${title}\n\n${INDENT}${chalk.blueBright(message)}\n`);
+        }, true);
+        const passed = results.reduce((num, [, pass]) => num + (pass ? 1 : 0), 0);
+        const failed = results.length - passed;
+        if (failed > 0 && passed === 0) {
+            throw new Error(toc(`${chalk.red(`Failed ${failed} tests in %s`)} 👎`));
+        }
+        if (failed > 0) {
+            throw new Error(toc(`${chalk.green(`Passed ${passed}/${results.length} tests in %s`)}\n${chalk.red(`Failed ${failed} tests`)} 👎`));
+        }
+        session.log.info(chalk.green(toc(`Passed ${passed} tests in %s 🚀`)));
+        return true;
+    });
+}
+function makeTestCLI(program) {
+    const command = new Command('test')
+        .description('Test JATS file against a list of cases')
+        .argument('<file>', 'JATS file to test')
+        .addOption(new Option('--cases <value>', 'The YAML file of unit tests to test against'))
+        .action(clirun(testJatsFile, { program, getSession }));
+    return command;
+}
+export function addTestCLI(program) {
+    program.addCommand(makeTestCLI(program));
+}

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';
@@ -53,7 +53,7 @@ function logAboutJatsFailing(session, jatsUrls) {
     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 }) {
+export function parseJats(session, file, opts = { resolvers: DEFAULT_RESOLVERS }) {
     return __awaiter(this, void 0, void 0, function* () {
         const toc = tic();
         if (fs.existsSync(file)) {

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

@@ -1,24 +1,29 @@
 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': {
             const { name, attributes, elements } = node;
             const children = elements === null || elements === void 0 ? void 0 : elements.map(convertToUnist).filter((n) => !!n);
             const next = Object.assign({ type: name !== null && name !== void 0 ? name : 'unknown' }, attributes);
-            if (children)
+            if (name === 'code') {
+                next.value = elements === null || elements === void 0 ? void 0 : elements[0].text;
+            }
+            else if (children)
                 next.children = children;
             return next;
         }
         case 'text': {
             const { attributes, text } = node;
-            return Object.assign(Object.assign({ type: 'text' }, attributes), { value: String(text) });
+            return Object.assign(Object.assign({ type: 'text' }, attributes), { value: String(text)
+                    .replace(/\n(\s+)$/, '')
+                    .replace('\n', ' ') });
         }
         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 = '0.0.16';
+const version = '0.1.0';
 export default version;