Merge branch 'main' of github.com:quarto-dev/quarto-cli into main

Author: jjallaire

news/changelog-1.1.md

@@ -15,6 +15,7 @@
 
 ## References
 
+- Write additional citation metadata for compatibility with Highwire/Zotero (#1609) 
 - Support for `nocite` within \_project.yml for book projects (#1660)
 
 ## Crossrefs

src/core/csl.ts

@@ -5,7 +5,18 @@
 *
 */
 
-import { parsePandocDate } from "./date.ts";
+import { formatDate, parsePandocDate } from "./date.ts";
+
+export const kPdfUrl = "pdf-url";
+export const kAbstractUrl = "abstract-url";
+export const kEIssn = "eissn";
+
+export interface CSLExtras {
+  [kPdfUrl]?: string;
+  [kAbstractUrl]?: string;
+  [kEIssn]?: string;
+  keywords?: string[];
+}
 
 export interface CSL extends Record<string, unknown> {
   // The id. This is technically required, but some providers (like crossref) don't provide
@@ -32,14 +43,16 @@ export interface CSL extends Record<string, unknown> {
   // Array of Contributors
   author?: CSLName[];
 
+  editor?: CSLName[];
+
   // Earliest of published-print and published-online
   issued?: CSLDate;
 
   // Full titles of the containing work (usually a book or journal)
   "container-title"?: string;
 
   // Short titles of the containing work (usually a book or journal)
-  "short-container-title"?: string;
+  "container-title-short"?: string;
 
   // Issue number of an article's journal
   issue?: string;
@@ -66,7 +79,9 @@ export interface CSL extends Record<string, unknown> {
   // primarily because they may need to be sanitized
   ISSN?: string;
   ISBN?: string;
+  PMID?: string;
   "original-title"?: string;
+  "collection-title"?: string;
   "short-title"?: string;
   subtitle?: string;
   subject?: string;
@@ -247,7 +262,8 @@ export function cslDate(dateRaw: unknown): CSLDate | undefined {
           date.getMonth() + 1,
           date.getDate(),
         ]],
-        raw: dateRaw,
+        literal: formatDate(date, "YYYY-MM-DD"),
+        raw: formatDate(date, "YYYY-MM-DD"),
       };
     }
     return undefined;

src/core/mapped-text.ts

@@ -40,8 +40,6 @@ export function mappedDiff(
   return withTiming("mapped-diff", () => {
     const sourceLineRanges = rangedLines(source.value).map((x) => x.range);
 
-    Deno.writeTextFileSync("/tmp/file1", source.value);
-    Deno.writeTextFileSync("/tmp/file2", target);
     let sourceCursor = 0;
 
     const resultChunks: (string | Range)[] = [];

src/format/html/format-html-appendix.ts

@@ -326,12 +326,12 @@ function creativeCommonsUrl(license: string, lang?: string) {
 }
 
 async function generateCite(input: string, format: Format, offset?: string) {
-  const entry = documentCSL(input, format, "webpage", offset);
-  if (entry) {
+  const { csl } = documentCSL(input, format, "webpage", offset);
+  if (csl) {
     // Render the HTML and BibTeX form of this document
     const cslPath = getCSLPath(input, format);
-    const html = await renderHtml(entry, cslPath);
-    const bibtex = await renderBibTex(entry);
+    const html = await renderHtml(csl, cslPath);
+    const bibtex = await renderBibTex(csl);
     return {
       html,
       bibtex,

src/format/html/format-html-meta.ts

@@ -8,7 +8,14 @@
 import { kHtmlEmptyPostProcessResult } from "../../command/render/constants.ts";
 import { Format, Metadata } from "../../config/types.ts";
 import { bibliographyCslJson } from "../../core/bibliography.ts";
-import { CSL, cslDateToEDTFDate } from "../../core/csl.ts";
+import {
+  CSL,
+  cslDateToEDTFDate,
+  CSLExtras,
+  kAbstractUrl,
+  kEIssn,
+  kPdfUrl,
+} from "../../core/csl.ts";
 import { Document } from "../../core/deno-dom.ts";
 import { encodeAttributeValue } from "../../core/html.ts";
 import { kWebsite } from "../../project/types/website/website-constants.ts";
@@ -24,8 +31,8 @@ export function metadataPostProcessor(
 ) {
   return async (doc: Document) => {
     if (googleScholarEnabled(format)) {
-      const csl = documentCSL(input, format, "webpage", offset);
-      const documentMetadata = googleScholarMeta(csl);
+      const { csl, extras } = documentCSL(input, format, "webpage", offset);
+      const documentMetadata = googleScholarMeta(csl, extras);
       const referenceMetadata = await googleScholarReferences(input, format);
       [...documentMetadata, ...referenceMetadata].forEach((meta) => {
         writeMetaTag(meta.name, meta.content, doc);
@@ -56,6 +63,7 @@ interface MetaTagData {
 
 function googleScholarMeta(
   csl: CSL,
+  extras: CSLExtras,
 ): MetaTagData[] {
   // The scholar metadata that we'll generate into
   const scholarMeta: MetaTagData[] = [];
@@ -66,6 +74,14 @@ function googleScholarMeta(
     write("citation_title", csl.title);
   }
 
+  if (csl.abstract) {
+    write("citation_abstract", csl.abstract);
+  }
+
+  if (extras.keywords) {
+    write("citation_keywords", extras.keywords);
+  }
+
   // Authors
   if (csl.author) {
     csl.author.forEach((author) => {
@@ -76,6 +92,26 @@ function googleScholarMeta(
     });
   }
 
+  // Editors
+  if (csl.editor) {
+    csl.editor.forEach((editor) => {
+      write(
+        "citation_editor",
+        editor.literal || `${editor.given} ${editor.family}`,
+      );
+    });
+  }
+
+  if (csl.issued) {
+    const edtfIssued = cslDateToEDTFDate(csl.issued);
+    write("citation_publication_date", edtfIssued);
+    write("citation_cover_date", edtfIssued);
+    const parts = csl.issued["date-parts"];
+    if (parts) {
+      write("citation_year", parts[0][0]);
+    }
+  }
+
   if (csl["available-date"]) {
     write("citation_online_date", cslDateToEDTFDate(csl["available-date"]));
   }
@@ -87,14 +123,22 @@ function googleScholarMeta(
     );
   }
 
-  if (csl.issued) {
-    write("citation_publication_date", cslDateToEDTFDate(csl.issued));
+  if (extras[kPdfUrl]) {
+    write("citation_pdf_url", extras[kPdfUrl]);
+  }
+
+  if (extras[kAbstractUrl]) {
+    write("citation_abstract_html_url", extras[kAbstractUrl]);
   }
 
   if (csl.issue) {
     write("citation_issue", csl.issue);
   }
 
+  if (csl.DOI) {
+    write("citation_doi", csl.DOI);
+  }
+
   if (csl.ISBN) {
     write("citation_isbn", csl.ISBN);
   }
@@ -103,10 +147,22 @@ function googleScholarMeta(
     write("citation_issn", csl.ISSN);
   }
 
+  if (extras[kEIssn]) {
+    write("citation_eissn", extras[kEIssn]);
+  }
+
+  if (csl.PMID) {
+    write("citation_pmid", csl.PMID);
+  }
+
   if (csl.volume) {
     write("citation_volume", csl.volume);
   }
 
+  if (csl.language) {
+    write("citation_language", csl.language);
+  }
+
   if (csl["page-first"]) {
     write("citation_firstpage", csl["page-first"]);
   }
@@ -117,9 +173,17 @@ function googleScholarMeta(
 
   const type = csl.type;
   if (type === "paper-conference") {
-    write("citation_conference_title", csl["container-title"]);
+    if (csl["container-title"]) {
+      write("citation_conference_title", csl["container-title"]);
+    }
+
+    if (csl.publisher) {
+      write("citation_conference", csl.publisher);
+    }
   } else if (type === "thesis") {
-    write("citation_dissertation_institution", csl.publisher);
+    if (csl.publisher) {
+      write("citation_dissertation_institution", csl.publisher);
+    }
   } else if (type === "report") {
     if (csl.publisher) {
       write(
@@ -133,8 +197,28 @@ function googleScholarMeta(
         csl.number,
       );
     }
+  } else if (type === "book") {
+    if (csl["container-title"]) {
+      write("citation_book_title", csl["container-title"]);
+    }
+  } else if (type === "chapter") {
+    write("citation_inbook_title", csl["container-title"]);
   } else {
-    write("citation_journal_title", csl["container-title"]);
+    if (csl["container-title"]) {
+      write("citation_journal_title", csl["container-title"]);
+    }
+
+    if (csl["container-title-short"]) {
+      write("citation_journal_abbrev", csl["container-title-short"]);
+    }
+
+    if (csl.publisher) {
+      write("citation_publisher", csl.publisher);
+    }
+  }
+
+  if (csl["collection-title"]) {
+    write("citation_series_title", csl["collection-title"]);
   }
 
   return scholarMeta;
@@ -149,7 +233,7 @@ async function googleScholarReferences(input: string, format: Format) {
 
   if (references) {
     references.forEach((reference) => {
-      const refMetas = googleScholarMeta(reference);
+      const refMetas = googleScholarMeta(reference, {});
       const metaStrs = refMetas.map((refMeta) => {
         return `${refMeta.name}=${refMeta.content};`;
       });

src/quarto-core/attribution/document.ts

@@ -20,9 +20,13 @@ import { pathWithForwardSlashes } from "../../core/path.ts";
 import {
   CSL,
   cslDate,
+  CSLExtras,
   cslNames,
   CSLType,
   cslType,
+  kAbstractUrl,
+  kEIssn,
+  kPdfUrl,
   suggestId,
 } from "../../core/csl.ts";
 import {
@@ -35,6 +39,7 @@ const kCitation = "citation";
 const kURL = "URL";
 const kId = "id";
 const kCitationKey = "citation-key";
+const kEditor = "editor";
 
 const kType = "type";
 const kCategories = "categories";
@@ -81,7 +86,7 @@ export function documentCSL(
   format: Format,
   defaultType: CSLType,
   offset?: string,
-) {
+): { csl: CSL; extras: CSLExtras } {
   const citationMetadata = citationMeta(format);
 
   // The type
@@ -104,12 +109,20 @@ export function documentCSL(
 
   // Author
   const authors = parseAuthor(
-    format.metadata[kAuthor] || citationMetadata[kAuthor],
+    citationMetadata[kAuthor] || format.metadata[kAuthor],
   );
   csl.author = cslNames(
     authors?.filter((auth) => auth !== undefined).map((auth) => auth?.name),
   );
 
+  // Editors
+  const editors = parseAuthor(citationMetadata[kEditor]);
+  csl.editor = cslNames(
+    editors?.filter((editor) => editor !== undefined).map((editor) =>
+      editor?.name
+    ),
+  );
+
   // Categories
   const categories =
     (citationMetadata[kCategories] || format.metadata[kCategories]);
@@ -371,7 +384,29 @@ export function documentCSL(
     csl[kCustom] = custom;
   }
 
-  return csl;
+  // Process anything extra
+  const extras: CSLExtras = {};
+  if (format.metadata.keywords) {
+    const kw = format.metadata.keywords;
+    extras.keywords = Array.isArray(kw) ? kw : [kw];
+  }
+
+  // Process extra URLS
+  if (citationMetadata[kPdfUrl]) {
+    extras[kPdfUrl] = citationMetadata[kPdfUrl] as string;
+  }
+  if (citationMetadata[kAbstractUrl]) {
+    extras[kAbstractUrl] = citationMetadata[kAbstractUrl] as string;
+  }
+
+  if (citationMetadata[kEIssn]) {
+    extras[kEIssn] = citationMetadata[kEIssn] as string;
+  }
+
+  return {
+    csl,
+    extras,
+  };
 }
 
 interface PageRange {
@@ -400,10 +435,14 @@ function synthesizeCitationUrl(
   if (baseUrl && outputFile && offset) {
     const rootDir = Deno.realPathSync(join(dirname(input), offset));
     if (outputFile === "index.html") {
-      return `${baseUrl}/${pathWithForwardSlashes(relative(rootDir, dirname(input)))}`;
+      return `${baseUrl}/${
+        pathWithForwardSlashes(relative(rootDir, dirname(input)))
+      }`;
     } else {
-      return `${baseUrl}/${pathWithForwardSlashes(
-        relative(rootDir, join(dirname(input), outputFile)))
+      return `${baseUrl}/${
+        pathWithForwardSlashes(
+          relative(rootDir, join(dirname(input), outputFile)),
+        )
       }`;
     }
   } else {