jats-cli 0.0.0 → 1.0.11

package/README.md

@@ -1,8 +1,8 @@
 # jats-cli
 
 [![jats-cli on npm](https://img.shields.io/npm/v/jats-cli.svg)](https://www.npmjs.com/package/jats-cli)
-[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/curvenote/jats-cli/blob/main/LICENSE)
-[![CI](https://github.com/curvenote/jats-cli/workflows/CI/badge.svg)](https://github.com/curvenote/jats-cli/actions)
+[![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/curvenote/jats/blob/main/LICENSE)
+[![CI](https://github.com/curvenote/jats/workflows/CI/badge.svg)](https://github.com/curvenote/jats-cli/actions)
 
 Node CLI for working with JATS XML documents.
 
@@ -11,7 +11,7 @@ Read, write, and convert JATS XML and log summaries 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
+npm install -g jats-cli
 jats -v
 ```
 
@@ -30,10 +30,20 @@ Commands available:
 `download`: attempt to find the JATS file and download it locally.
 
 ```bash
-jats download https://elifesciences.org/articles/81952 article.jats
+jats download https://elifesciences.org/articles/81952 -o article.jats
 ```
 
-Note, currently this just downloads the XML, **not** the associated files.
+For some Open Access PMC articles, you may download associated files with the `--data` option.
+
+```bash
+jats download PMC11025918 --data
+```
+
+`convert`: convert a JATS file to MyST-compatible JSON. The `--frontmatter project` option will write frontmatter to a `myst.yml` file.
+
+```bash
+jats convert article.jats --frontmatter project
+```
 
 `summary`: summarize the contents of the JATS, given a URL, DOI, or local file
 
@@ -84,6 +94,6 @@ As of v1.0.0 this package is [ESM only](https://gist.github.com/sindresorhus/a39
 <p style="text-align: center; color: #aaa; padding-top: 50px">
   Made with love by
   <a href="https://curvenote.com" target="_blank" style="color: #aaa">
-    <img src="https://curvenote.dev/images/icon.png" style="height: 1em" /> Curvenote
+    <img src="https://cdn.curvenote.com/brand/logo-blue-icon.png" style="height: 1em" /> Curvenote
   </a>
 </p>

package/dist/convert.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AAiB5C,wBAAgB,aAAa,CAAC,OAAO,EAAE,OAAO,QAE7C"}
+{"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../src/convert.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AA8B5C,wBAAgB,aAAa,CAAC,OAAO,EAAE,OAAO,QAE7C"}

package/dist/convert.js

@@ -1,11 +1,14 @@
 import { Command, Option } from 'commander';
 import { jatsConvert } from 'jats-convert';
+import { clirun, getSession } from 'myst-cli-utils';
 function makeConvertCLI(program) {
     const command = new Command('convert')
         .description('Convert JATS file to MyST mdast json')
         .argument('<input>', 'The JATS file')
         .addOption(new Option('--frontmatter <frontmatter>', 'Treat JATS frontmatter fields as page or project, or ignore if not specified').choices(['page', 'project']))
-        .action(jatsConvert);
+        .addOption(new Option('--no-doi, --no-dois', 'By default, DOIs are used for references when available, to be later resolved against doi.org. This option disables that behavior and creates bibtex entries for citations with DOIs.'))
+        .addOption(new Option('--no-bib, --no-bibtex', 'By default, a bibtex file will be written with referenced citations. This option prevents writing that file'))
+        .action(clirun(jatsConvert, { program, getSession }));
     return command;
 }
 export function addConvertCLI(program) {

package/dist/download.d.ts

@@ -0,0 +1,3 @@
+import { Command } from 'commander';
+export declare function addDownloadCLI(program: Command): void;
+//# sourceMappingURL=download.d.ts.map

package/dist/download.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"download.d.ts","sourceRoot":"","sources":["../src/download.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAU,MAAM,WAAW,CAAC;AAqB5C,wBAAgB,cAAc,CAAC,OAAO,EAAE,OAAO,QAE9C"}

package/dist/download.js

@@ -0,0 +1,17 @@
+import { Command, Option } from 'commander';
+import { jatsFetch } from 'jats-fetch';
+import { clirun, getSession } from 'myst-cli-utils';
+function makeDownloadCLI(program) {
+    const command = new Command('download')
+        .alias('fetch')
+        .description('Download JATS from URL or identifier')
+        .argument('<input>', 'URL or other article identifier')
+        .addOption(new Option('-o, --output <output>', 'Output filename or folder'))
+        .addOption(new Option('--data', 'Attempt to fetch all data associated with JATS XML'))
+        .addOption(new Option('--listing <listing>', 'Pointer to PMC listing file; if not provided, listing file will be downloaded and cached as needed'))
+        .action(clirun(jatsFetch, { program, getSession }));
+    return command;
+}
+export function addDownloadCLI(program) {
+    program.addCommand(makeDownloadCLI(program));
+}

package/dist/index.js

@@ -1,12 +1,14 @@
 #!/usr/bin/env node
 import { Command } from 'commander';
 import version from './version.js';
-import { addDownloadCLI } from './parse.js';
+import { addParseCLI } from './parse.js';
 import { addValidateCLI } from './validate.js';
 import { addTestCLI } from './jats-test.js';
 import { addConvertCLI } from './convert.js';
+import { addDownloadCLI } from './download.js';
 const program = new Command();
 addDownloadCLI(program);
+addParseCLI(program);
 addValidateCLI(program);
 addConvertCLI(program);
 addTestCLI(program);