Merge pull request #3484 from jspsych/fix-build-citations-test

handle citation test edge case

.changeset/rich-fans-jump.md

@@ -0,0 +1,6 @@
+---
+"jspsych": patch
+"@jspsych/config": patch
+---
+
+Patches some edge cases for `getCitations` and the build process that reads CITATION.CFF files to include citation info

package-lock.json

@@ -16074,6 +16074,7 @@
         "@sucrase/jest-plugin": "3.0.0",
         "@types/gulp": "4.0.17",
         "@types/jest": "29.5.8",
+        "@types/node": "^22.10.10",
         "alias-hq": "6.2.4",
         "app-root-path": "^3.1.0",
         "canvas": "^2.11.2",
@@ -16095,13 +16096,20 @@
         "rollup-plugin-node-externals": "7.1.3",
         "sucrase": "3.34.0",
         "tslib": "2.6.2",
-        "typescript": "^5.2.2",
-        "yaml": "^2.5.1"
+        "typescript": "^5.2.2"
       },
       "engines": {
         "node": ">=18.0.0"
       }
     },
+    "packages/config/node_modules/@types/node": {
+      "version": "22.10.10",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-22.10.10.tgz",
+      "integrity": "sha512-X47y/mPNzxviAGY5TcYPtYL8JsY3kAq2n8fMmKoRCxq/c4v4pyGNCzM2R6+M5/umG4ZfHuT+sgqDYqWc9rJ6ww==",
+      "dependencies": {
+        "undici-types": "~6.20.0"
+      }
+    },
     "packages/config/node_modules/brace-expansion": {
       "version": "1.1.11",
       "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz",
@@ -16142,17 +16150,10 @@
         "node": "*"
       }
     },
-    "packages/config/node_modules/yaml": {
-      "version": "2.6.0",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.6.0.tgz",
-      "integrity": "sha512-a6ae//JvKDEra2kdi1qzCyrJW/WZCgFi8ydDV+eXExl95t+5R+ijnqHJbz9tmMh8FUjx3iv2fCQ4dclAQlO2UQ==",
-      "license": "ISC",
-      "bin": {
-        "yaml": "bin.mjs"
-      },
-      "engines": {
-        "node": ">= 14"
-      }
+    "packages/config/node_modules/undici-types": {
+      "version": "6.20.0",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.20.0.tgz",
+      "integrity": "sha512-Ny6QZ2Nju20vw1SRHe3d9jVu6gJ+4e3+MMpqu7pqE5HT6WsTSlce++GQmK5UXS8mzV8DSYHrQH+Xrf2jVcuKNg=="
     },
     "packages/extension-mouse-tracking": {
       "name": "@jspsych/extension-mouse-tracking",

packages/config/generateCitations.js

@@ -7,7 +7,6 @@ import path from "node:path";
 
 import { Cite } from "@citation-js/core";
 import appRootPath from "app-root-path";
-import yaml from "yaml";
 
 /**
  * Generate citation data from CITATION.cff file
@@ -23,11 +22,8 @@ export default function generateCitations() {
     let rawCff;
     const getCff = (path) => {
       rawCff = fs.readFileSync(path, "utf-8").toString();
-      const cffData = yaml.parse(rawCff);
-      if (cffData["preferred-citation"]) {
-        preferredCitation = true;
-      }
-      return yaml.stringify(rawCff);
+      preferredCitation = rawCff.includes("preferred-citation:");
+      return rawCff;
     };
 
     try {
@@ -80,7 +76,7 @@ export default function generateCitations() {
       return citationBibtex;
     } catch (error) {
       console.log(`Error converting CITATION.cff to BibTeX string: ${error.message}`);
-      return null;
+      return "";
     }
   })();
 

packages/config/jest.config.cjs

@@ -0,0 +1 @@
+module.exports = require("./jest.cjs").makePackageConfig(__dirname);

packages/config/package.json

@@ -3,6 +3,10 @@
   "version": "3.2.1",
   "description": "Shared (build) configuration for jsPsych packages",
   "type": "module",
+  "scripts": {
+    "test": "jest",
+    "test:watch": "npm test -- --watch"
+  },
   "exports": {
     "./gulp": {
       "import": "./gulp.js",
@@ -45,6 +49,7 @@
     "@sucrase/jest-plugin": "3.0.0",
     "@types/gulp": "4.0.17",
     "@types/jest": "29.5.8",
+    "@types/node": "^22.10.10",
     "alias-hq": "6.2.4",
     "app-root-path": "^3.1.0",
     "canvas": "^2.11.2",
@@ -66,7 +71,6 @@
     "rollup-plugin-node-externals": "7.1.3",
     "sucrase": "3.34.0",
     "tslib": "2.6.2",
-    "typescript": "^5.2.2",
-    "yaml": "^2.5.1"
+    "typescript": "^5.2.2"
   }
 }

packages/config/tests/generateCitations.test.js

@@ -0,0 +1,94 @@
+import fs from "node:fs";
+
+import generateCitations from "../generateCitations";
+
+// Mock filesystem
+jest.mock("node:fs");
+jest.mock("app-root-path", () => ({
+  path: "/mock/root/path",
+}));
+
+describe("generateCitations", () => {
+  beforeEach(() => {
+    jest.clearAllMocks();
+  });
+
+  const validCitationCff = `
+cff-version: 1.2.0
+message: Please cite this software using these metadata
+title: Test Software
+authors:
+  - family-names: Doe
+    given-names: John
+version: 1.0.0
+date-released: 2023-01-01
+  `;
+
+  const citationCffWithPreferred = `
+cff-version: 1.2.0
+message: Please cite this software using these metadata
+title: Test Software
+authors:
+  - family-names: Doe
+    given-names: John
+preferred-citation:
+  title: Preferred Citation
+  authors:
+    - family-names: Smith
+      given-names: Jane
+  `;
+
+  test("should generate citations when CITATION.cff exists in current directory", () => {
+    fs.readFileSync.mockReturnValue(validCitationCff);
+
+    const result = generateCitations();
+
+    expect(result).toHaveProperty("apa");
+    expect(result).toHaveProperty("bibtex");
+    expect(result.apa).not.toBe("");
+    expect(result.bibtex).not.toBe("");
+  });
+
+  test("should handle preferred-citation when present", () => {
+    fs.readFileSync.mockReturnValue(citationCffWithPreferred);
+
+    const result = generateCitations();
+
+    expect(result).toHaveProperty("apa");
+    expect(result).toHaveProperty("bibtex");
+    expect(result.apa.includes("Smith")).toBeTruthy();
+  });
+
+  test("should return empty strings when CITATION.cff is not found", () => {
+    fs.readFileSync.mockImplementation(() => {
+      throw new Error("File not found");
+    });
+
+    const result = generateCitations();
+
+    expect(result).toEqual({
+      apa: "",
+      bibtex: "",
+    });
+  });
+
+  test("should handle malformed CITATION.cff", () => {
+    fs.readFileSync.mockReturnValue("invalid: yaml: content:");
+
+    const result = generateCitations();
+
+    expect(result).toEqual({
+      apa: "",
+      bibtex: "",
+    });
+  });
+
+  test("should remove newlines from citations", () => {
+    fs.readFileSync.mockReturnValue(validCitationCff);
+
+    const result = generateCitations();
+
+    expect(result.apa).not.toMatch(/\n/);
+    expect(result.bibtex).not.toMatch(/\n/);
+  });
+});

packages/jspsych/src/JsPsych.ts

@@ -36,6 +36,9 @@ export class JsPsych {
     return version;
   }
 
+  // prettier-ignore
+  private citation: any = '__CITATIONS__';
+
   /** Options */
   private options: any = {};
 
@@ -274,8 +277,6 @@ export class JsPsych {
     format: "apa" | "bibtex" = "apa"
   ) {
     const formatOptions = ["apa", "bibtex"];
-    // prettier-ignore
-    const jsPsychCitations: any = '__CITATIONS__';
     format = format.toLowerCase() as "apa" | "bibtex";
     // Check if plugins is an array
     if (!Array.isArray(plugins)) {
@@ -287,7 +288,7 @@ export class JsPsych {
     }
     // Print citations
     else {
-      const jsPsychCitation = jsPsychCitations[format];
+      const jsPsychCitation = this.citation[format];
       const citationSet = new Set([jsPsychCitation]);
 
       for (const plugin of plugins) {

packages/jspsych/tests/citations/citations.test.ts

@@ -1,94 +1,76 @@
+import { initJsPsych } from "../../src";
 import { TestExtension } from "../extensions/TestExtension";
 import TestPlugin from "../TestPlugin";
 
-const jsPsychApaCitation =
-  "de Leeuw, J. R., Gilbert, R. A., & Luchterhandt, B. (2023). jsPsych: Enabling an Open-Source Collaborative Ecosystem of Behavioral Experiments. Journal of Open Source Software, 8(85), 5351. https://doi.org/10.21105/joss.05351 ";
-const jsPsychBibtexCitation =
-  '@article{Leeuw2023jsPsych, 	author = {de Leeuw, Joshua R. and Gilbert, Rebecca A. and Luchterhandt, Bj{\\" o}rn}, 	journal = {Journal of Open Source Software}, 	doi = {10.21105/joss.05351}, 	issn = {2475-9066}, 	number = {85}, 	year = {2023}, 	month = {may 11}, 	pages = {5351}, 	publisher = {Open Journals}, 	title = {jsPsych: Enabling an {Open}-{Source} {Collaborative} {Ecosystem} of {Behavioral} {Experiments}}, 	url = {https://joss.theoj.org/papers/10.21105/joss.05351}, 	volume = {8}, }  ';
+const jsPsychApaCitation = "Test base APA citation";
+const jsPsychBibtexCitation = "Test base BibTeX citation";
 const testPluginApaCitation = "Test plugin APA citation";
 const testPluginBibtexCitation = "Test plugin BibTeX citation";
 const testExtensionApaCitation = "Test extension APA citation";
 
-let JsPsych;
+let jspsych;
 
-/**
- * These tests are skipped if the built version of JsPsych is not found.
- * This is because the citation functionality is only available in the built version
- * due to code injections that run during the build.
- */
+beforeEach(() => {
+  jspsych = initJsPsych();
+  (jspsych as any).citation = {
+    apa: "Test base APA citation",
+    bibtex: "Test base BibTeX citation",
+  };
+});
 
-try {
-  // Try to import built version
-  JsPsych = require("../../dist/index").JsPsych;
-  let jspsych: typeof JsPsych;
-
-  beforeEach(() => {
-    jspsych = new JsPsych();
+describe("citing not using an array", () => {
+  test("citing without input", () => {
+    expect(jspsych.getCitations()).toBe(jsPsychApaCitation);
   });
+  test("citing null", () => {
+    expect(() => jspsych.getCitations(null)).toThrow("Expected array of plugins/extensions");
+  });
+  test("citing without input and with invalid format", () => {
+    expect(() => jspsych.getCitations(null, "apa")).toThrow("Expected array of plugins/extensions");
+  });
+});
 
-  describe("citing not using an array", () => {
-    test("citing without input", () => {
-      expect(jspsych.getCitations()).toBe(jsPsychApaCitation);
-    });
-    test("citing null", () => {
-      expect(() => jspsych.getCitations(null)).toThrow("Expected array of plugins/extensions");
-    });
-    test("citing without input and with invalid format", () => {
-      expect(() => jspsych.getCitations(null, "apa")).toThrow(
-        "Expected array of plugins/extensions"
-      );
-    });
+describe("citing using an array in different formats", () => {
+  test("citing empty array with APA format", () => {
+    expect(jspsych.getCitations([], "apa")).toBe(jsPsychApaCitation);
   });
+  test("citing empty array with BibTeX format", () => {
+    expect(jspsych.getCitations([], "bibtex")).toBe(jsPsychBibtexCitation);
+  });
+  test("citing empty array without format", () => {
+    expect(jspsych.getCitations([])).toBe(jsPsychApaCitation);
+  });
+  test("citing one plugin with valid format in all caps", () => {
+    expect(jspsych.getCitations([TestPlugin], "APA")).toBe(
+      jsPsychApaCitation + "\n" + testPluginApaCitation
+    );
+  });
+  test("citing with unsupported format", () => {
+    expect(() => jspsych.getCitations([TestPlugin], "DummyTex")).toThrow(
+      "Unsupported citation format"
+    );
+  });
+});
 
-  describe("citing using an array in different formats", () => {
-    test("citing empty array with APA format", () => {
-      expect(jspsych.getCitations([], "apa")).toBe(jsPsychApaCitation);
-    });
-    test("citing empty array with BibTeX format", () => {
-      expect(jspsych.getCitations([], "bibtex")).toBe(jsPsychBibtexCitation);
-    });
-    test("citing empty array without format", () => {
-      expect(jspsych.getCitations([])).toBe(jsPsychApaCitation);
-    });
-    test("citing one plugin with valid format in all caps", () => {
-      expect(jspsych.getCitations([TestPlugin], "APA")).toBe(
-        jsPsychApaCitation + "\n" + testPluginApaCitation
-      );
-    });
-    test("citing with unsupported format", () => {
-      expect(() => jspsych.getCitations([TestPlugin], "DummyTex")).toThrow(
-        "Unsupported citation format"
-      );
-    });
+describe("citing mix of valid plugins/extensions", () => {
+  test("citing a plugin", () => {
+    expect(jspsych.getCitations([TestPlugin])).toBe(
+      jsPsychApaCitation + "\n" + testPluginApaCitation
+    );
   });
-
-  describe("citing mix of valid plugins/extensions", () => {
-    test("citing a plugin", () => {
-      expect(jspsych.getCitations([TestPlugin])).toBe(
-        jsPsychApaCitation + "\n" + testPluginApaCitation
-      );
-    });
-    test("citing a plugin in BibTeX", () => {
-      expect(jspsych.getCitations([TestPlugin], "bibtex")).toBe(
-        jsPsychBibtexCitation + "\n" + testPluginBibtexCitation
-      );
-    });
-    test("citing multiple plugins", () => {
-      expect(jspsych.getCitations([TestPlugin, TestPlugin])).toBe(
-        jsPsychApaCitation + "\n" + testPluginApaCitation
-      );
-    });
-    test("citing mix of plugins and extensions", () => {
-      expect(jspsych.getCitations([TestPlugin, TestExtension])).toBe(
-        jsPsychApaCitation + "\n" + testPluginApaCitation + "\n" + testExtensionApaCitation
-      );
-    });
+  test("citing a plugin in BibTeX", () => {
+    expect(jspsych.getCitations([TestPlugin], "bibtex")).toBe(
+      jsPsychBibtexCitation + "\n" + testPluginBibtexCitation
+    );
   });
-} catch (e) {
-  // Fall back to development version if built version not found
-  describe("skipping citation tests because of missing built version", () => {
-    test.skip("skip", () => {
-      expect(true).toBe(true);
-    });
+  test("citing multiple plugins", () => {
+    expect(jspsych.getCitations([TestPlugin, TestPlugin])).toBe(
+      jsPsychApaCitation + "\n" + testPluginApaCitation
+    );
   });
-}
+  test("citing mix of plugins and extensions", () => {
+    expect(jspsych.getCitations([TestPlugin, TestExtension])).toBe(
+      jsPsychApaCitation + "\n" + testPluginApaCitation + "\n" + testExtensionApaCitation
+    );
+  });
+});

packages/jspsych/tests/core/simulation-mode.test.ts

@@ -542,8 +542,6 @@ describe("data simulation mode", () => {
 
     const data = getData().values()[1];
 
-    console.log(data);
-
     expect(data.rt).toBeGreaterThan(0);
     expect(data.response).toBeDefined();
   });

packages/plugin-instructions/src/index.spec.ts

@@ -155,8 +155,6 @@ describe("instructions plugin simulation", () => {
 
     const data = getData().values()[0];
 
-    console.log(data.view_history);
-
     expect(data.rt).toBe(4000);
 
     let sum_view_history_rt = 0;