fix browser tool for citations

package-lock.json

@@ -9,6 +9,8 @@
       ],
       "dependencies": {
         "@citation-js/core": "^0.7.14",
+        "@citation-js/plugin-bibtex": "^0.7.14",
+        "@citation-js/plugin-csl": "^0.7.14",
         "@citation-js/plugin-software-formats": "^0.6.1",
         "symlink": "^2.1.0"
       },
@@ -1201,6 +1203,22 @@
         "node": ">=6"
       }
     },
+    "node_modules/@citation-js/plugin-bibtex": {
+      "version": "0.7.14",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-bibtex/-/plugin-bibtex-0.7.14.tgz",
+      "integrity": "sha512-xHOHqhF6dthLRv46N9U+mQgYLiiWQHLvQWK9+mcBKz+/3NWge62Xb1oBouNWwLEPd5FV/8gp9fp7SOp93T0dUg==",
+      "dependencies": {
+        "@citation-js/date": "^0.5.0",
+        "@citation-js/name": "^0.4.2",
+        "moo": "^0.5.1"
+      },
+      "engines": {
+        "node": ">=16.0.0"
+      },
+      "peerDependencies": {
+        "@citation-js/core": "^0.7.0"
+      }
+    },
     "node_modules/@citation-js/plugin-cff": {
       "version": "0.6.1",
       "resolved": "https://registry.npmjs.org/@citation-js/plugin-cff/-/plugin-cff-0.6.1.tgz",
@@ -1213,6 +1231,21 @@
         "node": ">=14.0.0"
       }
     },
+    "node_modules/@citation-js/plugin-csl": {
+      "version": "0.7.14",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-csl/-/plugin-csl-0.7.14.tgz",
+      "integrity": "sha512-7AKB8lMz1IqdtoE33NnWIpteLYMuSl3xqT+Cax7sQKwAIJEoq2HBmb43Ja8xQQ36nREAupQJv1V6XksIAmYnCg==",
+      "dependencies": {
+        "@citation-js/date": "^0.5.0",
+        "citeproc": "^2.4.6"
+      },
+      "engines": {
+        "node": ">=16.0.0"
+      },
+      "peerDependencies": {
+        "@citation-js/core": "^0.7.0"
+      }
+    },
     "node_modules/@citation-js/plugin-github": {
       "version": "0.6.1",
       "resolved": "https://registry.npmjs.org/@citation-js/plugin-github/-/plugin-github-0.6.1.tgz",
@@ -4820,6 +4853,11 @@
         "node": ">=8"
       }
     },
+    "node_modules/citeproc": {
+      "version": "2.4.63",
+      "resolved": "https://registry.npmjs.org/citeproc/-/citeproc-2.4.63.tgz",
+      "integrity": "sha512-68F95Bp4UbgZU/DBUGQn0qV3HDZLCdI9+Bb2ByrTaNJDL5VEm9LqaiNaxljsvoaExSLEXe1/r6n2Z06SCzW3/Q=="
+    },
     "node_modules/cjs-module-lexer": {
       "version": "1.4.1",
       "resolved": "https://registry.npmjs.org/cjs-module-lexer/-/cjs-module-lexer-1.4.1.tgz",
@@ -10380,6 +10418,11 @@
       "resolved": "https://registry.npmjs.org/module-alias/-/module-alias-2.2.3.tgz",
       "integrity": "sha512-23g5BFj4zdQL/b6tor7Ji+QY4pEfNH784BMslY9Qb0UnJWRAt+lQGLYmRaM0KDBwIG23ffEBELhZDP2rhi9f/Q=="
     },
+    "node_modules/moo": {
+      "version": "0.5.2",
+      "resolved": "https://registry.npmjs.org/moo/-/moo-0.5.2.tgz",
+      "integrity": "sha512-iSAJLHYKnX41mKcJKjqvnAN9sf0LMDTXDEvFv+ffuRR9a1MIuXLjMNL6EsnDHSkKLTWNqQQ5uo61P4EbU4NU+Q=="
+    },
     "node_modules/mri": {
       "version": "1.2.0",
       "resolved": "https://registry.npmjs.org/mri/-/mri-1.2.0.tgz",
@@ -14594,6 +14637,9 @@
         "tslib": "2.6.2",
         "typescript": "^5.2.2"
       },
+      "devDependencies": {
+        "yaml": "^2.5.1"
+      },
       "engines": {
         "node": ">=18.0.0"
       }
@@ -14631,6 +14677,18 @@
         "node": ">=14.17"
       }
     },
+    "packages/config/node_modules/yaml": {
+      "version": "2.5.1",
+      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.5.1.tgz",
+      "integrity": "sha512-bLQOjaX/ADgQ20isPJRvF0iRUHIxVhYvr53Of7wGcWlO2jvtUlH5m87DsmulFVxRpNLOnI4tB6p/oh8D7kpn9Q==",
+      "dev": true,
+      "bin": {
+        "yaml": "bin.mjs"
+      },
+      "engines": {
+        "node": ">= 14"
+      }
+    },
     "packages/extension-mouse-tracking": {
       "name": "@jspsych/extension-mouse-tracking",
       "version": "1.1.0",

package.json

@@ -55,6 +55,8 @@
   "dependencies": {
     "@citation-js/core": "^0.7.14",
     "@citation-js/plugin-software-formats": "^0.6.1",
+    "@citation-js/plugin-bibtex": "^0.7.14",
+    "@citation-js/plugin-csl": "^0.7.14",
     "symlink": "^2.1.0"
   }
 }

packages/config/package.json

@@ -66,5 +66,8 @@
       "jscodeshift": "0.16.1",
       "inquirer": "10.1.6"
     }
+  },
+  "devDependencies": {
+    "yaml": "^2.5.1"
   }
 }

packages/config/rollup-plugin-build-citation.js

@@ -1,4 +1,6 @@
+import "@citation-js/plugin-bibtex";
 import "@citation-js/plugin-software-formats";
+import "@citation-js/plugin-csl";
 
 import fs from "node:fs";
 import { extname } from "path";
@@ -6,6 +8,7 @@ import { extname } from "path";
 import { Cite } from "@citation-js/core";
 import { createFilter } from "@rollup/pluginutils";
 import MagicString from "magic-string";
+import yaml from "yaml";
 
 export default function cffToJsonPlugin() {
   const options = { include: ["**/index*"], exclude: [], sourcemap: false };
@@ -17,39 +20,37 @@ export default function cffToJsonPlugin() {
     transform: function (code, id) {
       if (!filter(id) || (extname(id) !== ".js" && extname(id) !== ".ts")) return;
       const magicString = new MagicString(code);
+      let preferredCitation = false;
 
-      // Try to find CITATION.cff file
+      // Try to find CITATION.cff file and look for preferred-citation
       const citationCff = (() => {
         try {
-          return fs.readFileSync("./CITATION.cff", "utf-8").toString();
+          const rawCff = fs.readFileSync("./CITATION.cff", "utf-8").toString();
+          const cffData = yaml.parse(rawCff);
+          if (cffData["preferred-citation"]) {
+            console.log("Found 'preferred-citation' in CITATION.cff");
+            preferredCitation = true;
+          } else {
+            console.log("No 'preferred-citation' found in CITATION.cff");
+          }
+          return yaml.stringify(rawCff);
         } catch (error) {
           console.log(`Error finding CITATION.cff: ${error.message}`);
           return null;
         }
       })();
 
-      // Try to convert CITATION.cff to JSON
-      const citationJson = (() => {
-        if (!citationCff) return null;
-        try {
-          return Cite(citationCff).format("data", {
-            format: "object",
-            lang: "en-us",
-          });
-        } catch (error) {
-          console.log(`Error converting CITATION.cff to JSON: ${error.message}`);
-          return null;
-        }
-      })();
-
       // Try to convert CITATION.cff to APA string
       const citationApa = (() => {
         try {
-          return Cite(citationJson).format("data", {
+          const apaCite = new Cite(citationCff);
-            format: "html",
+          apaCite["data"] = preferredCitation ? apaCite["data"].slice(1) : apaCite["data"];
-            template: "citation-apa",
+          const citationApa = apaCite.format("bibliography", {
+            format: "text",
+            template: "apa",
             lang: "en-us",
           });
+          return citationApa;
         } catch (error) {
           console.log(`Error converting CITATION.cff to APA string: ${error.message}`);
           return null;
@@ -58,14 +59,15 @@ export default function cffToJsonPlugin() {
 
       // Try to convert CITATION.cff to bibtex string
       const citationBibtex = (() => {
-        if (!citationJson) return null;
         try {
-          let bibtexCitation = Cite(citationJson).format("data", {
+          const bibtexCite = new Cite(citationCff);
-            format: "html",
+          bibtexCite["data"] = preferredCitation ? bibtexCite["data"].slice(1) : bibtexCite["data"];
-            template: "citation-bibtex",
+          const citationBibtex = bibtexCite.format("bibtex", {
+            format: "text",
+            template: "bibtex",
             lang: "en-us",
           });
-          return bibtexCitation;
+          return citationBibtex;
         } catch (error) {
           console.log(`Error converting CITATION.cff to bibtex string: ${error.message}`);
           return null;
@@ -76,11 +78,15 @@ export default function cffToJsonPlugin() {
       if (!citationApa && !citationBibtex) {
         return { code: code };
       }
-      const citationString = `citation: { "apa": "${citationApa}", "bibtex": "${citationBibtex}" }`;
+      //console.log(`citation: {\napa: "${citationApa.replace(/\n/g, ' ')}", \nbibtex: "${citationBibtex.replace(/\n/g, ' ')}"\n}`);
+      const citationString = `citation:\n { apa: "${citationApa.replace(
+        /\n/g,
+        " "
+      )}",\n bibtex: "${citationBibtex.replace(/\n/g, " ")}"\n }`;
+      console.log(citationString);
       const targetString = "citation: []";
       const startIndex = code.indexOf(targetString);
       if (startIndex !== -1) {
-        console.log(citationApa);
         magicString.overwrite(startIndex, startIndex + targetString.length, citationString);
         return { code: magicString.toString() };
       } else {