jats-cli 1.0.10 → 1.0.11

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;AA6B5C,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

@@ -1,13 +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']))
-        .addOption(new Option('--no-dois, --no-doi', '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-bibtex, --no-bib', 'By default, a bibtex file will be written with referenced citations. This option prevents writing that file'))
-        .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/jats.cjs

@@ -48999,7 +48999,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.0.10";
+var version = "1.0.11";
 var version_default = version;
 
 // src/parse.ts
@@ -57977,15 +57977,21 @@ async function downloadAndUnzipPMC(session, entry, outputDir, fetcher) {
     throw new Error(`Unable to download ${entry.url}`);
   }
   session.log.info(`Extracting PMC data from ${dest} to ${outputDir}`);
-  const unzip = makeExecutable(`tar -xf ${dest}`, session.log);
+  const unzip = makeExecutable(`tar -xf ${dest} -C ${outputDir}`, session.log);
   await unzip();
-  const zipContent = import_node_fs4.default.readdirSync(outputDir);
-  zipContent.filter((file) => file.toLowerCase().endsWith(".gif")).forEach((file) => {
-    const gifFile = import_node_path3.default.join(outputDir, file);
+  const zipDir = import_node_path3.default.join(outputDir, import_node_path3.default.basename(dest).replace(/\.(tar\.gz|tgz)$/, ""));
+  const zipContent = import_node_fs4.default.readdirSync(zipDir);
+  zipContent.map((file) => {
+    const oldPath = import_node_path3.default.join(zipDir, file);
+    const newPath = import_node_path3.default.join(outputDir, file);
+    import_node_fs4.default.renameSync(oldPath, newPath);
+    return newPath;
+  }).filter((file) => file.toLowerCase().endsWith(".gif")).forEach((gifFile) => {
     const jpgFile = gifFile.replace(/.gif$/, ".jpg");
     if (import_node_fs4.default.existsSync(jpgFile))
       import_node_fs4.default.rmSync(gifFile);
   });
+  import_node_fs4.default.rmdirSync(zipDir);
 }
 async function getDataFromPMC(session, pmcid, outputDir, listing, fetcher) {
   const listingFile = await getListingsFile(session, listing, fetcher);
@@ -58140,11 +58146,12 @@ async function jatsFetch(session, input, opts) {
     return;
   }
   let output = (_b = opts.output) !== null && _b !== void 0 ? _b : opts.data ? `${input}` : ".";
-  const filename = input.startsWith("PMC") ? `${input}.xml` : "jats.xml";
-  output = import_node_path4.default.join(output, filename);
+  if (!import_node_path4.default.extname(output)) {
+    const filename = input.startsWith("PMC") ? `${input}.xml` : "jats.xml";
+    output = import_node_path4.default.join(output, filename);
+  }
   if (import_node_path4.default.extname(output) && ![".xml", ".jats"].includes(import_node_path4.default.extname(output).toLowerCase())) {
-    session.log.error(`Output must be an XML file or a directory`);
-    process.exit(1);
+    throw new Error(`Output must be an XML file or a directory`);
   }
   let result;
   try {
@@ -58158,8 +58165,7 @@ async function jatsFetch(session, input, opts) {
     }
   }
   if (!(result === null || result === void 0 ? void 0 : result.data)) {
-    session.log.error(`Unable to resolve JATS XML content from ${input}`);
-    process.exit(1);
+    throw new Error(`Unable to resolve JATS XML content from ${input}`);
   }
   if (!import_node_path4.default.extname(output)) {
     import_node_fs5.default.mkdirSync(output, { recursive: true });
@@ -58573,11 +58579,14 @@ var Jats = class {
     } else if (licenseString === null || licenseString === void 0 ? void 0 : licenseString.toLowerCase().startsWith("this is an open access article")) {
       openAccess = true;
     }
+    const pmc = this.pmc;
+    const identifiers = pmc ? { pmcid: `PMC${pmc}` } : void 0;
     const frontmatter = validatePageFrontmatter({
       title: title ? toText(title) : void 0,
       subtitle: subtitle ? toText(subtitle) : void 0,
       short_title: short_title ? toText(short_title) : void 0,
       doi: (_h = this.doi) !== null && _h !== void 0 ? _h : void 0,
+      identifiers,
       date,
       authors: authors.length ? authors : void 0,
       // editors,
@@ -64778,6 +64787,35 @@ function toText2(node) {
 function copyNode2(node) {
   return copyNode(node);
 }
+function logMessagesFromVFile(session, file) {
+  if (!file)
+    return;
+  file.messages.forEach((message) => {
+    const kind = message.fatal === null ? "info" : message.fatal === false ? "warn" : "error";
+    const note = (message === null || message === void 0 ? void 0 : message.note) ? `
+   Note: ${message.note}` : "";
+    const url = (message === null || message === void 0 ? void 0 : message.url) ? `
+   See also: ${message.url}
+` : "";
+    const prefix = (message === null || message === void 0 ? void 0 : message.file) ? `${message === null || message === void 0 ? void 0 : message.file} ` : "";
+    const formatted = `${message.reason}${note}${url}`;
+    switch (kind) {
+      case "info":
+        session.log.info(`\u2139\uFE0F  ${prefix}${formatted}`);
+        break;
+      case "error":
+        session.log.error(`\u26D4\uFE0F ${prefix}${formatted}`);
+        break;
+      case "warn":
+        session.log.warn(`\u26A0\uFE0F  ${prefix}${formatted}`);
+        break;
+      default:
+        session.log.debug(`${prefix}${formatted}`);
+        break;
+    }
+  });
+  file.messages = [];
+}
 
 // ../jats-convert/dist/transforms/biorxiv.js
 function isBioRxiv(tree) {
@@ -65058,7 +65096,7 @@ function backToBodyTransform(jats) {
   });
   if (!((_b = jats.body) === null || _b === void 0 ? void 0 : _b.children) || backNodes.length === 0)
     return;
-  jats.body.children.push({ type: "thematicBreak" }, ...copyNode(backNodes));
+  jats.body.children.push({ type: "hr" }, ...copyNode(backNodes));
   backNodes.forEach((node) => {
     node.type = "__delete__";
   });
@@ -65424,7 +65462,7 @@ function journalTransforms(tree) {
 }
 
 // ../jats-convert/dist/version.js
-var version3 = "1.0.10";
+var version3 = "1.0.11";
 var version_default3 = version3;
 
 // ../jats-convert/dist/myst/inlineCitations.js
@@ -65580,6 +65618,25 @@ function inlineCitationsTransform(tree, referenceIds) {
   }
 }
 
+// ../jats-convert/dist/transforms/supplementary.js
+function floatToEndTransform(jats) {
+  var _a;
+  if (!jats.body)
+    return;
+  const floatSupplementaryMaterial = selectAll2("supplementary-material[position=float]", jats.body);
+  if (floatSupplementaryMaterial.length === 0)
+    return;
+  (_a = jats.body.children) === null || _a === void 0 ? void 0 : _a.push({ type: "hr" });
+  floatSupplementaryMaterial.forEach((node) => {
+    var _a2, _b;
+    const copy = copyNode2(node);
+    delete copy.position;
+    (_b = (_a2 = jats.body) === null || _a2 === void 0 ? void 0 : _a2.children) === null || _b === void 0 ? void 0 : _b.push(copy);
+    node.type = "__delete__";
+  });
+  remove(jats.body, "__delete__");
+}
+
 // ../jats-convert/dist/index.js
 function refTypeToReferenceKind(kind) {
   switch (kind) {
@@ -65677,9 +65734,6 @@ var handlers = {
   ["list-item"](node, state2) {
     state2.renderInline(node, "listItem");
   },
-  thematicBreak(node, state2) {
-    state2.addLeaf("thematicBreak");
-  },
   ["inline-formula"](node, state2) {
     const texMath = texMathFromNode(node);
     if (texMath) {
@@ -65877,81 +65931,21 @@ var handlers = {
       return;
     state2.addLeaf("thematicBreak");
   },
+  alternatives(node, state2) {
+    var _a;
+    const choice = (_a = node.children) === null || _a === void 0 ? void 0 : _a.find((child) => !!state2.handlers[child.type]);
+    if (!choice) {
+      state2.error(`No supported types in 'alternatives' node`);
+    } else {
+      state2.handlers[choice.type](choice, state2, node);
+    }
+  },
   break(node, state2) {
     state2.addLeaf("break");
   },
   ["named-content"](node, state2) {
     state2.renderChildren(node);
   },
-  // container(node, state) {
-  //   state.data.isInContainer = true;
-  //   switch (node.kind) {
-  //     case 'figure': {
-  //       state.renderInline(node, 'fig');
-  //       break;
-  //     }
-  //     case 'table': {
-  //       state.renderInline(node, 'table-wrap');
-  //       break;
-  //     }
-  //     case 'quote': {
-  //       // This is transformed in containers.ts
-  //       state.renderChildren(node);
-  //       break;
-  //     }
-  //     case 'code': {
-  //       // This is transformed in containers.ts
-  //       state.renderInline(node, 'boxed-text', { 'content-type': node.kind });
-  //       break;
-  //     }
-  //     default: {
-  //       state.error(`Unhandled container kind of ${node.kind}`, node, 'container');
-  //       state.renderChildren(node);
-  //     }
-  //   }
-  //   delete state.data.isInContainer;
-  // },
-  // caption(node, state) {
-  //   state.renderInline(node, 'caption');
-  // },
-  // captionNumber(node, state) {
-  //   state.renderInline(node, 'label');
-  // },
-  // crossReference(node, state) {
-  //   // Look up reference and add the text
-  //   const { identifier, kind } = node as CrossReference;
-  //   const attrs: Attributes = { 'ref-type': referenceKindToRefType(kind), rid: identifier };
-  //   if (attrs['ref-type'] === RefType.custom && kind) {
-  //     attrs['custom-type'] = kind;
-  //   }
-  //   state.renderInline(node, 'xref', attrs);
-  // },
-  // citeGroup(node, state) {
-  //   if (state.options.citestyle === 'numerical-only') {
-  //     state.write('\\cite{');
-  //   } else if (state.options.bibliography === 'biblatex') {
-  //     const command = node.kind === 'narrative' ? 'textcite' : 'parencite';
-  //     state.write(`\\${command}{`);
-  //   } else {
-  //     const tp = node.kind === 'narrative' ? 't' : 'p';
-  //     state.write(`\\cite${tp}{`);
-  //   }
-  //   state.renderChildren(node, true, ', ');
-  //   state.write('}');
-  // },
-  // cite(node, state, parent) {
-  //   if (!state.options.bibliography) {
-  //     state.usePackages('natbib');
-  //     // Don't include biblatex in the package list
-  //   }
-  //   if (parent.type === 'citeGroup') {
-  //     state.write(node.label);
-  //   } else if (state.options.bibliography === 'biblatex') {
-  //     state.write(`\\textcite{${node.label}}`);
-  //   } else {
-  //     state.write(`\\cite{${node.label}}`);
-  //   }
-  // },
   ["fn-group"](node, state2) {
     state2.renderChildren(node);
   },
@@ -65975,6 +65969,7 @@ var handlers = {
           kind: "narrative"
         });
         return;
+      case RefType.supplementaryMaterial:
       case RefType.sec:
       case RefType.fig:
       case RefType.dispFormula:
@@ -65990,17 +65985,28 @@ var handlers = {
       }
       default: {
         state2.renderInline(node, "crossReference", { identifier: node.rid });
-        state2.warn(`Unknown ref-type of ${refType}`, node);
+        state2.warn(`Unknown ref-type of ${refType}`);
         return;
       }
     }
   },
   ["supplementary-material"](node, state2) {
+    var _a;
+    if (node.id) {
+      const { label, identifier } = (_a = normalizeLabel(node.id)) !== null && _a !== void 0 ? _a : {};
+      state2.openNode("div", { label, identifier });
+    }
     state2.renderChildren(node);
+    if (node.id) {
+      state2.closeNode();
+    }
   },
   media(node, state2) {
     state2.renderInline(node, "link", { url: node["xlink:href"] });
   },
+  ["inline-supplementary-material"](node, state2) {
+    state2.renderInline(node, "link", { url: node["xlink:href"] });
+  },
   caption(node, state2) {
     state2.renderChildren(node);
   },
@@ -66033,18 +66039,16 @@ var JatsParser = class {
   top() {
     return this.stack[this.stack.length - 1];
   }
-  warn(message, node, source, opts) {
+  warn(message, source, opts) {
     fileError(this.file, message, {
       ...opts,
-      node,
       source: source ? `jats-convert:${source}` : "jats-convert",
       ruleId: RuleId.jatsParses
     });
   }
-  error(message, node, source, opts) {
+  error(message, source, opts) {
     fileError(this.file, message, {
       ...opts,
-      node,
       source: source ? `jats-convert:${source}` : "jats-convert",
       ruleId: RuleId.jatsParses
     });
@@ -66079,10 +66083,7 @@ var JatsParser = class {
         handler(child, this, node);
       } else {
         this.unhandled.push(child.type);
-        fileError(this.file, `Unhandled JATS conversion for node of "${child.type}"`, {
-          source: "jats-convert",
-          ruleId: RuleId.jatsParses
-        });
+        this.error(`Unhandled JATS conversion for node of "${child.type}"`);
       }
     });
   }
@@ -66177,7 +66178,7 @@ var jatsConvertPlugin = function(jats, opts) {
   };
 };
 async function jatsConvertTransform(data, opts) {
-  var _a, _b;
+  var _a, _b, _c;
   const jats = typeof data === "string" ? new Jats(data) : data;
   if (opts === null || opts === void 0 ? void 0 : opts.logInfo) {
     opts.logInfo.publisher = toText2(select3("publisher-name", jats.tree)) || null;
@@ -66200,13 +66201,14 @@ async function jatsConvertTransform(data, opts) {
     opts.logInfo.license = licenseString;
   }
   const { frontmatter } = jats;
-  const file = new VFile();
+  const file = (_b = opts === null || opts === void 0 ? void 0 : opts.vfile) !== null && _b !== void 0 ? _b : new VFile();
   const refLookup = await processJatsReferences(jats, opts);
+  floatToEndTransform(jats);
   backToBodyTransform(jats);
   const pipe = unified().use(jatsConvertPlugin, jats, opts);
-  const vfile2 = pipe.stringify((_b = jats.body) !== null && _b !== void 0 ? _b : { type: "body", children: [] }, file);
-  const references = vfile2.result.references;
-  const tree = vfile2.result.tree;
+  pipe.stringify((_c = jats.body) !== null && _c !== void 0 ? _c : { type: "body", children: [] }, file);
+  const references = file.result.references;
+  const tree = file.result.tree;
   resolveJatsCitations(tree, refLookup);
   inlineCitationsTransform(tree, [...Object.keys(references.data)]);
   abbreviationSectionTransform(tree, frontmatter);
@@ -66245,17 +66247,21 @@ async function jatsConvertTransform(data, opts) {
       myst: selectAll2("footnoteDefinition", tree).length
     };
   }
-  return { tree, jats, file, references, frontmatter };
+  return { tree, jats, references, frontmatter };
 }
-async function jatsConvert(input, opts) {
+async function jatsConvert(session, input, opts) {
   const logInfo = { jatsVersion: version_default3 };
   const dir = import_node_path6.default.dirname(input);
+  const vfile2 = new VFile();
+  vfile2.path = input;
   const { tree, frontmatter } = await jatsConvertTransform(import_node_fs7.default.readFileSync(input).toString(), {
+    vfile: vfile2,
     dir,
     logInfo,
     dois: opts === null || opts === void 0 ? void 0 : opts.dois,
     bibtex: opts === null || opts === void 0 ? void 0 : opts.bibtex
   });
+  logMessagesFromVFile(session, vfile2);
   const basename = import_node_path6.default.basename(input, import_node_path6.default.extname(input));
   const mystJson = import_node_path6.default.join(dir, `${basename}.myst.json`);
   const mystYml = import_node_path6.default.join(dir, "myst.yml");
@@ -66272,9 +66278,9 @@ async function jatsConvert(input, opts) {
     } else {
       import_node_fs7.default.writeFileSync(mystYml, js_yaml_default.dump({ version: 1, project: frontmatter, site: {} }));
     }
-    import_node_fs7.default.writeFileSync(mystJson, JSON.stringify({ mdast: tree }, null, 2));
+    import_node_fs7.default.writeFileSync(mystJson, JSON.stringify({ mdast: tree, frontmatter: { title: frontmatter.title } }, null, 2));
   } else {
-    import_node_fs7.default.writeFileSync(mystJson, JSON.stringify({ mdast: tree }, null, 2));
+    import_node_fs7.default.writeFileSync(mystJson, JSON.stringify({ mdast: tree, frontmatter: { title: frontmatter.title } }, null, 2));
   }
 }
 
@@ -66287,15 +66293,15 @@ function makeConvertCLI(program3) {
     ).choices(["page", "project"])
   ).addOption(
     new Option(
-      "--no-dois, --no-doi",
+      "--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-bibtex, --no-bib",
+      "--no-bib, --no-bibtex",
       "By default, a bibtex file will be written with referenced citations. This option prevents writing that file"
     )
-  ).action(jatsConvert);
+  ).action(clirun(jatsConvert, { program: program3, getSession }));
   return command;
 }
 function addConvertCLI(program3) {

package/dist/version.d.ts

@@ -1,3 +1,3 @@
-declare const version = "1.0.10";
+declare const version = "1.0.11";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/dist/version.js

@@ -1,2 +1,2 @@
-const version = '1.0.10';
+const version = '1.0.11';
 export default version;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-cli",
-  "version": "1.0.10",
+  "version": "1.0.11",
   "description": "Typescript CLI for with JATS",
   "author": "Rowan Cockett <rowan@curvenote.com>",
   "homepage": "https://github.com/curvenote/jats",
@@ -45,11 +45,11 @@
   "dependencies": {
     "doi-utils": "^2.0.0",
     "fair-principles": "^2.0.0",
-    "jats-convert": "^1.0.10",
-    "jats-fetch": "^1.0.10",
-    "jats-tags": "^1.0.10",
-    "jats-utils": "^1.0.10",
-    "jats-xml": "^1.0.10",
+    "jats-convert": "^1.0.11",
+    "jats-fetch": "^1.0.11",
+    "jats-tags": "^1.0.11",
+    "jats-utils": "^1.0.11",
+    "jats-xml": "^1.0.11",
     "js-yaml": "^4.1.0",
     "unist-util-is": "^5.2.1",
     "unist-util-select": "^4.0.0"