Add pandoc jats templates

since jats templates can’t be emitted from pandoc directly, convert this all to just download the source and get the templates from there.

Author: dragonstyle

package/src/common/update-pandoc.ts

@@ -20,6 +20,7 @@ import { archiveBinaryDependency } from "./archive-binary-dependencies.ts";
 
 import { execProcess } from "../../../src/core/process.ts";
 import { configureDependency } from "./dependencies/dependencies.ts";
+import { download, unzip } from "../util/utils.ts";
 
 export function updatePandoc() {
   return new Command()
@@ -54,69 +55,86 @@ export function updatePandoc() {
       // Call archive-bin-deps for this file
       await withWorkingDir(async (workingDir) => {
         await archiveBinaryDependency(pandocDependency, workingDir);
-      });
 
-      // Configure this version of pandoc
-      await configureDependency(pandocDependency, configuration);
+        // Configure this version of pandoc
+        await configureDependency(pandocDependency, configuration);
 
-      // Generate templates
-      await writePandocTemplates(configuration);
+        // Generate templates
+        await writePandocTemplates(configuration, version, workingDir);
+      });
     });
 }
 
-async function writePandocTemplates(config: Configuration) {
-  info("Reading latest pandoc templates...");
+async function writePandocTemplates(
+  config: Configuration,
+  version: string,
+  workingDir: string,
+) {
+  info("Reading pandoc templates...");
   const formatSrcDir = join(
     config.directoryInfo.src,
     "resources",
     "formats",
   );
-  const binPath = config.directoryInfo.bin;
-  const formatTemplates = [{
-    pandoc: "html",
-    output: join(
-      formatSrcDir,
-      "html",
-      "pandoc",
-      "html.template",
-    ),
-  }, {
-    pandoc: "revealjs",
-    output: join(formatSrcDir, "revealjs", "pandoc", "revealjs.template"),
-  }, {
-    pandoc: "latex",
-    output: join(formatSrcDir, "pdf", "pandoc", "latex.template"),
-  }];
-  for (const temp of formatTemplates) {
-    info(`> ${temp.pandoc}`);
-    const template = await readTemplate(temp.pandoc, binPath);
-    if (template) {
-      ensureDirSync(dirname(temp.output));
-      Deno.writeTextFileSync(temp.output, template);
-    } else {
-      throw new Error("Failed to read an expected template.");
+
+  const srcZipUrl =
+    `https://github.com/jgm/pandoc/archive/refs/tags/${version}.zip`;
+
+  const pandocDir = `pandoc-${version}`;
+  const zipFile = join(workingDir, "pandoc");
+  await download(srcZipUrl, zipFile);
+  await unzip(zipFile, workingDir);
+
+  // Jats templates are multi-part templates that
+  // are not properly emitted by pandoc itself, so download
+  // them from source instead
+  const templateDir = join(workingDir, pandocDir, "data", "templates");
+  const jatsOutDir = join(
+    formatSrcDir,
+    "jats",
+    "pandoc",
+    "default-templates",
+  );
+  const htmlOutdir = join(
+    formatSrcDir,
+    "html",
+    "pandoc",
+  );
+  const latexOutdir = join(formatSrcDir, "pdf", "pandoc");
+  const revealOutdir = join(formatSrcDir, "revealjs", "pandoc");
+
+  const templateDirFiles: Record<string, Array<{ from: string; to?: string }>> =
+    {
+      [jatsOutDir]: [
+        { from: "affiliations.jats" },
+        { from: "article.jats_publishing" },
+        { from: "default.jats_archiving" },
+        { from: "default.jats_articleauthoring" },
+        { from: "default.jats_publishing" },
+      ],
+      [htmlOutdir]: [
+        { from: "default.html5", to: "html.template" },
+      ],
+      [revealOutdir]: [
+        { from: "default.revealjs", to: "revealjs.template" },
+      ],
+      [latexOutdir]: [
+        { from: "default.latex", to: "latex.template" },
+      ],
+    };
+
+  // Move templates
+  for (const outDir of Object.keys(templateDirFiles)) {
+    ensureDirSync(outDir);
+    for (const file of templateDirFiles[outDir]) {
+      info(`> ${file.from}`);
+      Deno.copyFileSync(
+        join(templateDir, file.from),
+        join(outDir, file.to || file.from),
+      );
     }
   }
+
   info("done.");
   info("");
 }
-
-async function readTemplate(format: string, bin: string): Promise<string> {
-  const result = await execProcess({
-    cmd: [join(bin, "tools", "pandoc"), "--print-default-template", format],
-    stdout: "piped",
-    stderr: "piped",
-  });
-
-  if (result.success) {
-    if (result.stdout) {
-      return result.stdout;
-    } else {
-      return "";
-    }
-  } else {
-    throw new Error(
-      `Failed to read default template for ${format} from Pandoc`,
-    );
-  }
-}

src/resources/formats/jats/pandoc/default-templates/affiliations.jats

@@ -0,0 +1,36 @@
+$--
+$-- Affiliations
+$--
+<aff id="aff-$it.id$">
+$-- wrap affiliation if it has a known institution identifier
+$if(it.group)$
+<institution content-type="group">${it.group}</institution>
+$endif$
+$if(it.department)$
+<institution content-type="dept">${it.department}</institution>
+$endif$
+<institution-wrap>
+$if(it.organization)$
+<institution>${it.organization}</institution>
+$else$
+<institution>${it.name}</institution>
+$endif$
+$if(it.isni)$
+<institution-id institution-id-type="ISNI">${it.isni}</institution-id>
+$endif$
+$if(it.ringgold)$
+<institution-id institution-id-type="Ringgold">${it.ringgold}</institution-id>
+$endif$
+$if(it.ror)$
+<institution-id institution-id-type="ROR">${it.ror}</institution-id>
+$endif$
+$for(it.pid)$
+<institution-id institution-id-type="${it.type}">${it.id}</institution-id>
+$endfor$
+</institution-wrap>$if(it.street-address)$,
+$for(it.street-address)$
+<addr-line>${it}</addr-line>$sep$,
+$endfor$
+$else$$if(it.city)$, <city>$it.city$</city>$endif$$endif$$if(it.country)$,
+<country$if(it.country-code)$ country="$it.country-code$"$endif$>$it.country$</country>$endif$
+</aff>