jats-xml 1.0.0 → 1.0.2

package/dist/cli/download.d.ts

@@ -1,10 +1,10 @@
-import type { ISession, Options } from '../types.js';
+import type { ISession, ResolutionOptions } from '../types.js';
 /**
  * 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<{
+export declare function convertPMID2PMCID(session: ISession, PMID: string, opts: ResolutionOptions): Promise<string | undefined>;
+export declare function checkIfPubMedCentralHasJats(session: ISession, urlOrDoi: string, opts: ResolutionOptions): Promise<string | undefined>;
+export declare function downloadJatsFromUrl(session: ISession, urlOrDoi: string, opts?: ResolutionOptions): Promise<{
     success: boolean;
     source: string;
     data?: string;

package/dist/cli/parse.d.ts

@@ -1,5 +1,5 @@
 import { Command } from 'commander';
-import type { ISession, Options } from '../types.js';
+import type { ISession, ResolutionOptions } from '../types.js';
 import { Jats } from '../jats.js';
-export declare function parseJats(session: ISession, file: string, opts?: Options): Promise<Jats>;
+export declare function parseJats(session: ISession, file: string, opts?: ResolutionOptions): Promise<Jats>;
 export declare function addDownloadCLI(program: Command): void;

package/dist/jats.cjs

@@ -28100,7 +28100,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.0.0";
+var version = "1.0.2";
 var version_default = version;
 
 // src/cli/parse.ts
@@ -31951,9 +31951,9 @@ async function ensureDtdExists(session, opts) {
   }
 }
 function isXmllintAvailable() {
-  return (0, import_which.sync)("xmllint", { nothrow: true });
+  return import_which.default.sync("xmllint", { nothrow: true });
 }
-async function validateJatsAgainstDtd(session, file, opts) {
+async function xmllintValidate(session, file, dtd) {
   if (!isXmllintAvailable()) {
     session.log.error(
       `JATS validation against DTD requires xmllint
@@ -31964,20 +31964,24 @@ ${source_default.dim(
     );
     return;
   }
-  const inferredOpts = inferOptions(file);
-  const validatedOpts = validateOptions(session, opts != null ? opts : {}, inferredOpts);
-  await ensureDtdExists(session, validatedOpts);
-  session.log.debug(`Validating against: ${localDtdFile(validatedOpts)}`);
-  session.log.info(`\u{1F9D0} Validating against: ${dtdFolder(validatedOpts)}`);
   try {
     const dropDtdCommand = `xmllint --dropdtd`;
-    const validateCommand = `xmllint --noout --dtdvalid ${localDtdFile(validatedOpts)}`;
+    const validateCommand = `xmllint --noout --dtdvalid ${dtd}`;
     await makeExecutable(`${dropDtdCommand} ${file} | ${validateCommand} -`, session.log)();
   } catch {
     return false;
   }
   return true;
 }
+async function validateJatsAgainstDtd(session, file, opts) {
+  const inferredOpts = inferOptions(file);
+  const validatedOpts = validateOptions(session, opts != null ? opts : {}, inferredOpts);
+  await ensureDtdExists(session, validatedOpts);
+  session.log.debug(`Validating against: ${localDtdFile(validatedOpts)}`);
+  session.log.info(`\u{1F9D0} Validating against: ${dtdFolder(validatedOpts)}`);
+  const valid = await xmllintValidate(session, file, localDtdFile(validatedOpts));
+  return valid;
+}
 async function validateJatsAgainstDtdWrapper(session, file, opts) {
   const success = await validateJatsAgainstDtd(session, file, opts);
   if (success) {

package/dist/resolvers.d.ts

@@ -1,4 +1,4 @@
-import type { ISession, Options, Resolver } from './types.js';
+import type { ISession, ResolutionOptions, Resolver } from './types.js';
 export declare const elife: Resolver;
 export declare const plos: Resolver;
 export declare const joss: Resolver;
@@ -6,4 +6,4 @@ export declare const DEFAULT_RESOLVERS: Resolver[];
 /**
  * Use the known custom resolvers to pick where the JATS should be downloaded from.
  */
-export declare function customResolveJatsUrlFromDoi(session: ISession, doiString: string, opts?: Options): Promise<string>;
+export declare function customResolveJatsUrlFromDoi(session: ISession, doiString: string, opts?: ResolutionOptions): Promise<string>;

package/dist/types.d.ts

@@ -4,7 +4,7 @@ export interface Resolver {
     test: (url: string) => boolean;
     jatsUrl: (url: string) => string;
 }
-export type Options = {
+export type ResolutionOptions = {
     resolvers?: Resolver[];
     fetcher?: (url: string, contentType?: 'json' | 'xml') => Promise<Pick<Response, 'ok' | 'headers' | 'text' | 'json' | 'status' | 'statusText' | 'url'>>;
 };

package/dist/validate/dtd.d.ts

@@ -1,5 +1,5 @@
 import type { ISession } from '../types.js';
-type Options = {
+export type JatsOptions = {
     jats: string;
     mathml: '2' | '3';
     oasis: boolean;
@@ -11,17 +11,24 @@ type Options = {
  *
  * This looks at DTD file name in DOCTYPE as well as dtd-version in article element
  */
-export declare function inferOptions(file: string): Partial<Options>;
+export declare function inferOptions(file: string): Partial<JatsOptions>;
+/**
+ * Test if xmllint is available as a cli command
+ */
+export declare function isXmllintAvailable(): string | null;
+/**
+ * Run xmllint validation
+ */
+export declare function xmllintValidate(session: ISession, file: string, dtd: string): Promise<boolean | undefined>;
 /**
  * Check if JATS file is valid based on JATS version/library/etc.
  *
  * Returns true if valid and false if invalid.
  */
-export declare function validateJatsAgainstDtd(session: ISession, file: string, opts?: Partial<Options>): Promise<boolean | undefined>;
+export declare function validateJatsAgainstDtd(session: ISession, file: string, opts?: Partial<JatsOptions>): Promise<boolean | undefined>;
 /**
  * Check if JATS file is valid based on JATS version/library/etc.
  *
  * Logs confirmation message if valid and throws an error if invalid.
  */
-export declare function validateJatsAgainstDtdWrapper(session: ISession, file: string, opts?: Partial<Options>): Promise<void>;
-export {};
+export declare function validateJatsAgainstDtdWrapper(session: ISession, file: string, opts?: Partial<JatsOptions>): Promise<void>;

package/dist/validate/dtd.js

@@ -2,7 +2,7 @@ import fs, { createReadStream } from 'fs';
 import path from 'path';
 import fetch from 'node-fetch';
 import unzipper from 'unzipper';
-import { sync as which } from 'which';
+import which from 'which';
 import { makeExecutable, writeFileToFolder } from 'myst-cli-utils';
 import chalk from 'chalk';
 const JATS_VERSIONS = [
@@ -224,28 +224,21 @@ async function ensureDtdExists(session, opts) {
 /**
  * Test if xmllint is available as a cli command
  */
-function isXmllintAvailable() {
-    return which('xmllint', { nothrow: true });
+export function isXmllintAvailable() {
+    return which.sync('xmllint', { nothrow: true });
 }
 /**
- * Check if JATS file is valid based on JATS version/library/etc.
- *
- * Returns true if valid and false if invalid.
+ * Run xmllint validation
  */
-export async function validateJatsAgainstDtd(session, file, opts) {
+export async function xmllintValidate(session, file, dtd) {
     if (!isXmllintAvailable()) {
         session.log.error(`JATS validation against DTD requires xmllint\n\n${chalk.dim('To install:\n  mac:    brew install xmlstarlet\n  debian: apt install libxml2-utils')}`);
         return;
     }
-    const inferredOpts = inferOptions(file);
-    const validatedOpts = validateOptions(session, opts !== null && opts !== void 0 ? opts : {}, inferredOpts);
-    await ensureDtdExists(session, validatedOpts);
-    session.log.debug(`Validating against: ${localDtdFile(validatedOpts)}`);
-    session.log.info(`🧐 Validating against: ${dtdFolder(validatedOpts)}`);
     try {
         // First drop DOCTYPE with DTD in it - we have already fetched the DTD
         const dropDtdCommand = `xmllint --dropdtd`;
-        const validateCommand = `xmllint --noout --dtdvalid ${localDtdFile(validatedOpts)}`;
+        const validateCommand = `xmllint --noout --dtdvalid ${dtd}`;
         await makeExecutable(`${dropDtdCommand} ${file} | ${validateCommand} -`, session.log)();
     }
     catch {
@@ -253,6 +246,20 @@ export async function validateJatsAgainstDtd(session, file, opts) {
     }
     return true;
 }
+/**
+ * Check if JATS file is valid based on JATS version/library/etc.
+ *
+ * Returns true if valid and false if invalid.
+ */
+export async function validateJatsAgainstDtd(session, file, opts) {
+    const inferredOpts = inferOptions(file);
+    const validatedOpts = validateOptions(session, opts !== null && opts !== void 0 ? opts : {}, inferredOpts);
+    await ensureDtdExists(session, validatedOpts);
+    session.log.debug(`Validating against: ${localDtdFile(validatedOpts)}`);
+    session.log.info(`🧐 Validating against: ${dtdFolder(validatedOpts)}`);
+    const valid = await xmllintValidate(session, file, localDtdFile(validatedOpts));
+    return valid;
+}
 /**
  * Check if JATS file is valid based on JATS version/library/etc.
  *

package/dist/version.d.ts

@@ -1,2 +1,2 @@
-declare const version = "1.0.0";
+declare const version = "1.0.2";
 export default version;

package/dist/version.js

@@ -1,2 +1,2 @@
-const version = '1.0.0';
+const version = '1.0.2';
 export default version;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-xml",
-  "version": "1.0.0",
+  "version": "1.0.2",
   "description": "Types and utilities for working with JATS in Typescript",
   "author": "Rowan Cockett <rowan@curvenote.com>",
   "homepage": "https://github.com/curvenote/jats-xml",
@@ -47,7 +47,7 @@
   "dependencies": {
     "doi-utils": "^2.0.0",
     "fair-principles": "^2.0.0",
-    "jats-tags": "^1.0.0",
+    "jats-tags": "^1.0.2",
     "js-yaml": "^4.1.0",
     "node-fetch": "^3.3.1",
     "unist-util-is": "^5.2.1",