jats-xml 0.0.2 → 0.0.3

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`](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/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const version = '0.0.2';
+const version = '0.0.3';
 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/version.js

@@ -1,2 +1,2 @@
-const version = '0.0.2';
+const version = '0.0.3';
 export default version;

package/dist/jats.js

@@ -9094,7 +9094,7 @@ var require_lib4 = __commonJS({
 var import_commander2 = __toESM(require_commander());
 
 // src/version.ts
-var version = "0.0.2";
+var version = "0.0.3";
 var version_default = version;
 
 // src/cli/parse.ts
@@ -10419,7 +10419,7 @@ 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/version.d.ts

@@ -1,3 +1,3 @@
-declare const version = "0.0.2";
+declare const version = "0.0.3";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-xml",
-  "version": "0.0.2",
+  "version": "0.0.3",
   "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",
@@ -38,7 +38,7 @@
     "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",
+    "test": "npm run copy:version && jest",
     "test:watch": "jest --watchAll",
     "lint": "eslint \"src/**/*.ts\" -c .eslintrc.js --max-warnings 1",
     "lint:format": "prettier --check src/*.ts src/**/*.ts",