fairdataihub · slugb0t · Aug 27, 2024 · Jul 25, 2024 · Aug 2, 2024 · Aug 26, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,14 @@
+# Change Log
+
+All notable changes the Codefair App will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## v1.0.0 - 2024-08-26
+
+### Identifier
+https://doi.org/10.5281/zenodo.13376617
+
+### Added
+- First release with license file and metadata files generating features
diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,37 @@
+title: Codefair
+authors:
+  - given-names: Dorian
+    family-names: Portillo
+    email: dportillo@calmi2.org
+    affiliation: FAIR Data Innovations Hub, California Medical Innovations Institute
+  - given-names: Sanjay
+    family-names: Soundarajan
+    email: ssoundarajan@calmi2.org
+    affiliation: FAIR Data Innovations Hub, California Medical Innovations Institute
+  - given-names: Bhavesh
+    family-names: Patel
+    email: bpatel@calmi2.org
+    affiliation: FAIR Data Innovations Hub, California Medical Innovations Institute
+cff-version: 1.2.0
+message: If you use this software, please cite it using the metadata from this file.
+type: software
+identifiers:
+  - type: doi
+    value: https://doi.org/10.5281/zenodo.13376617
+abstract: "Codefair is a free and open source GitHub app that acts as your
+  personal assistant when it comes to making your research software reusable and
+  especially complying with the Findable, Accessible, Interoperable, Reusable
+  (FAIR) Principles for Research Software (FAIR4RS Principles). Whether you are
+  developing artificial intelligence (AI)/machine learning (ML) models with
+  Python, data visualization tools with Jupyter notebook, or data analysis code
+  with R, Codefair is here to assist you. "
+keywords:
+  - best-practices
+  - fair
+  - research
+  - reusable
+  - software
+license: MIT
+repository-code: https://github.com/fairdataihub/codefair-app
+version: 1.0.0
+date-released: 2024-08-26
diff --git a/README.md b/README.md
@@ -32,9 +32,13 @@ Your coding assistant to make research software reusable without breaking a swea
   <a href="https://github.com/fairdataihub/codefair-app/blob/main/LICENSE">
     <img src="https://img.shields.io/github/license/fairdataihub/codefair-app.svg?style=flat-square" alt="license" />
   </a>
-  <a href="https://fairdataihub.org/fairshare">
-    <img src="https://raw.githubusercontent.com/fairdataihub/FAIRshare/main/badge.svg" alt="Curated with FAIRshare" />
+  <a href="https://doi.org/10.5281/zenodo.13376617">
+    <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.13376617.svg" alt="Zenodo DOI" />
   </a>
+  <a href="https://archive.softwareheritage.org/browse/origin/https://github.com/fairdataihub/codefair-app/">
+    <img src="https://archive.softwareheritage.org/badge/origin/https://github.com/fairdataihub/codefair-app/" alt="Software Heritage archive" />
+  </a>
+
 </p>
 
 </div>
@@ -126,15 +130,8 @@ This work is licensed under
 If you are using this package or reusing the source code from this repository for any purpose, please cite:
 
 ```text
-    Coming soon...
+   Portillo, D., Soundarajan, S., & Patel, B., (2024). Codefair App. Zenodo. 10.5281/zenodo.13376617
 ```
-
-## Acknowledgements
-
-```text
-    Coming soon...
-```
-
 <br />
 
 ---

diff --git a/bot/index.js b/bot/index.js
@@ -1,7 +1,11 @@
 import { MongoClient } from "mongodb";
 import * as express from "express";
 import { renderIssues, createIssue } from "./utils/renderer/index.js";
-import { checkEnvVariable, isRepoEmpty, verifyRepoName } from "./utils/tools/index.js";
+import {
+  checkEnvVariable,
+  isRepoEmpty,
+  verifyRepoName,
+} from "./utils/tools/index.js";
 
 checkEnvVariable("MONGODB_URI");
 checkEnvVariable("MONGODB_DB_NAME");
@@ -93,7 +97,13 @@ export default async (app, { getRouter }) => {
         verifyRepoName(analytics.repo, repoName, owner, analyticsCollection);
       }
 
-      const issueBody = await renderIssues(context, owner, repository, db, emptyRepo);
+      const issueBody = await renderIssues(
+        context,
+        owner,
+        repository,
+        db,
+        emptyRepo,
+      );
 
       // Create an issue with the compliance issues
       await createIssue(context, owner, repoName, issueTitle, issueBody);
@@ -154,7 +164,13 @@ export default async (app, { getRouter }) => {
         verifyRepoName(analytics.repo, repoName, owner, analyticsCollection);
       }
 
-      const issueBody = await renderIssues(context, owner, repository, db, emptyRepo);
+      const issueBody = await renderIssues(
+        context,
+        owner,
+        repository,
+        db,
+        emptyRepo,
+      );
 
       // Create an issue with the compliance issues
       // console.log("CREATING ISSUE");
@@ -227,13 +243,7 @@ export default async (app, { getRouter }) => {
     console.log("Empty Repo: ", emptyRepo);
 
     if (!installation) {
-      await installationCollection.insertOne({
-        installationId: context.payload.installation.id,
-        owner,
-        repo: repoName,
-        repositoryId: repoId,
-        timestamp: Date.now(),
-      })
+      return;
     } else {
       await verifyRepoName(
         installation.repo,
@@ -243,7 +253,6 @@ export default async (app, { getRouter }) => {
       );
     }
 
-
     // Grab the commits being pushed
     const { commits } = context.payload;
 
@@ -336,7 +345,7 @@ export default async (app, { getRouter }) => {
         repo: repoName,
         repositoryId: repoId,
         timestamp: Date.now(),
-      })
+      });
     } else {
       await verifyRepoName(
         installation.repo,

diff --git a/bot/utils/renderer/index.js b/bot/utils/renderer/index.js
@@ -63,7 +63,7 @@ export async function applyMetadataTemplate(
       url = `${CODEFAIR_DOMAIN}/add/code-metadata/${existingMetadata.identifier}`;
     }
     const metadataBadge = `[![Metadata](https://img.shields.io/badge/Add_Metadata-dc2626.svg)](${url})`;
-    baseTemplate += `\n\n## Metadata ❌\n\nTo make your software FAIR, a CITATION.cff and codemetada.json are expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org/docs/guidelines). These files are not found in the repository. If you would like Codefair to add these files, click the "Add metadata" button below to go to our interface for providing metadata and generating these files.\n\n${metadataBadge}`;
+    baseTemplate += `\n\n## Metadata ❌\n\nTo make your software FAIR, a CITATION.cff and codemeta.json are expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org/docs/guidelines). These files are not found in the repository. If you would like Codefair to add these files, click the "Add metadata" button below to go to our interface for providing metadata and generating these files.\n\n${metadataBadge}`;
   }
 
   if (subjects.codemeta && subjects.citation && subjects.license) {
@@ -125,7 +125,7 @@ export async function applyMetadataTemplate(
   if (!subjects.license) {
     // License was not found
     const metadataBadge = `![Metadata](https://img.shields.io/badge/Metadata_Not_Checked-fbbf24)`;
-    baseTemplate += `\n\n## Metadata\n\nTo make your software FAIR a CITATION.cff and codemetada.json metadata files are expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org/docs/guidelines). Codefair will check for these files after a license file is detected.\n\n${metadataBadge}`;
+    baseTemplate += `\n\n## Metadata\n\nTo make your software FAIR a CITATION.cff and codemeta.json metadata files are expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org/docs/guidelines). Codefair will check for these files after a license file is detected.\n\n${metadataBadge}`;
   }
 
   return baseTemplate;
@@ -155,7 +155,7 @@ export async function applyCodemetaTemplate(
 
     let url = `${CODEFAIR_DOMAIN}/add/codemeta/${identifier}`;
 
-    const codemetaCollection = db.collection("codemetaRequests");
+    const codemetaCollection = db.collection("codeMetadata");
     // console.log(repository);
     const existingCodemeta = await codemetaCollection.findOne({
       repositoryId: repository.id,
@@ -183,7 +183,7 @@ export async function applyCodemetaTemplate(
     }
 
     const codemetaBadge = `[![Citation](https://img.shields.io/badge/Add_Codemeta-dc2626.svg)](${url})`;
-    baseTemplate += `\n\n## codemeta.json\n\nA codemeta.json file was not found in the repository. To make your software reusable a codemetada.json is expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org).\n\n${codemetaBadge}`;
+    baseTemplate += `\n\n## codemeta.json\n\nA codemeta.json file was not found in the repository. To make your software reusable a codemeta.json is expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org).\n\n${codemetaBadge}`;
   } else if (subjects.codemeta && subjects.license) {
     // License was found and codemetata.json also exists
     // Then add codemeta section mentioning it will be checked after license is added
@@ -214,7 +214,7 @@ export async function applyCodemetaTemplate(
   } else {
     // codemeta and license does not exist
     const codemetaBadge = `![CodeMeta](https://img.shields.io/badge/Codemeta_Not_Checked-fbbf24)`;
-    baseTemplate += `\n\n## codemeta.json\n\nA codemeta.json file will be checked after a license file is added. To make your software reusable a codemetada.json is expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org).\n\n${codemetaBadge}`;
+    baseTemplate += `\n\n## codemeta.json\n\nA codemeta.json file will be checked after a license file is added. To make your software reusable a codemeta.json is expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org).\n\n${codemetaBadge}`;
   }
 
   return baseTemplate;
@@ -422,7 +422,7 @@ export async function renderIssues(
 ) {
   if (emptyRepo) {
     console.log("emtpy repo and returning base");
-    return `# Check the FAIRness of your software\n\nTThis issue is your repository's dashboard for all things FAIR. Keep it open as making and keeping software FAIR is a continuous process that evolves along with the software. You can read the [documentation](https://docs.codefair.io/docs/dashboard.html) to learn more.\n\n> [!WARNING]\n> Currently your repository is empty and will not be checked until content is detected within your repository.\n\n## LICENSE\n\nTo make your software reusable a license file is expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org). Codefair will check for a license file after you add content to your repository.\n\n![License](https://img.shields.io/badge/License_Not_Checked-fbbf24)\n\n## Metadata\n\nTo make your software FAIR a CITATION.cff and codemetada.json metadata files are expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org/docs/guidelines). Codefair will check for these files after a license file is detected.\n\n![Metadata](https://img.shields.io/badge/Metadata_Not_Checked-fbbf24)`;
+    return `# Check the FAIRness of your software\n\nTThis issue is your repository's dashboard for all things FAIR. Keep it open as making and keeping software FAIR is a continuous process that evolves along with the software. You can read the [documentation](https://docs.codefair.io/docs/dashboard.html) to learn more.\n\n> [!WARNING]\n> Currently your repository is empty and will not be checked until content is detected within your repository.\n\n## LICENSE\n\nTo make your software reusable a license file is expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org). Codefair will check for a license file after you add content to your repository.\n\n![License](https://img.shields.io/badge/License_Not_Checked-fbbf24)\n\n## Metadata\n\nTo make your software FAIR a CITATION.cff and codemeta.json metadata files are expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org/docs/guidelines). Codefair will check for these files after a license file is detected.\n\n![Metadata](https://img.shields.io/badge/Metadata_Not_Checked-fbbf24)`;
   }
 
   let license = await checkForLicense(context, owner, repository.name);
@@ -514,8 +514,11 @@ export async function createIssue(context, owner, repo, title, body) {
     let noIssue = false;
     let issueNumber;
     for (let i = 0; i < issue.data.length; i++) {
-      console.log(issue.data[i].title);
-      if (issue.data[i].title === title) {
+      if (issue.data[i]?.pull_request) {
+        continue;
+      }
+
+      if (issue.data[i].title === title && issue.data[i].state === "open") {
         noIssue = true;
         issueNumber = issue.data[i].number;
         break;

diff --git a/codemeta.json b/codemeta.json
@@ -0,0 +1,72 @@
+{
+  "name": "Codefair",
+  "@context": "https://w3id.org/codemeta/3.0",
+  "applicationCategory": "Content management software",
+  "author": [
+    {
+      "affiliation": {
+        "name": "FAIR Data Innovations Hub, California Medical Innovations Institute",
+        "type": "Organization"
+      },
+      "email": "dportillo@calmi2.org",
+      "familyName": "Portillo",
+      "id": "_:author_1",
+      "givenName": "Dorian",
+      "type": "Person"
+    },
+    {
+      "affiliation": {
+        "name": "FAIR Data Innovations Hub, California Medical Innovations Institute",
+        "type": "Organization"
+      },
+      "email": "ssoundarajan@calmi2.org",
+      "familyName": "Soundarajan",
+      "id": "_:author_2",
+      "givenName": "Sanjay",
+      "type": "Person"
+    },
+    {
+      "affiliation": {
+        "name": "FAIR Data Innovations Hub, California Medical Innovations Institute",
+        "type": "Organization"
+      },
+      "email": "bpatel@calmi2.org",
+      "familyName": "Patel",
+      "id": "_:author_3",
+      "givenName": "Bhavesh",
+      "type": "Person"
+    }
+  ],
+  "codeRepository": "https://github.com/fairdataihub/codefair-app",
+  "dateCreated": "2024-03-27",
+  "dateModified": "2024-08-26",
+  "datePublished": "2024-08-26",
+  "description": "Codefair is a free and open source GitHub app that acts as your personal assistant when it comes to making your research software reusable and especially complying with the Findable, Accessible, Interoperable, Reusable (FAIR) Principles for Research Software (FAIR4RS Principles). Whether you are developing artificial intelligence (AI)/machine learning (ML) models with Python, data visualization tools with Jupyter notebook, or data analysis code with R, Codefair is here to assist you. ",
+  "developmentStatus": "active",
+  "downloadUrl": "https://github.com/marketplace/codefair-app",
+  "identifier": "https://doi.org/10.5281/zenodo.13376617",
+  "issueTracker": "https://github.com/fairdataihub/codefair-app/issues",
+  "keywords": [
+    "best-practices",
+    "fair",
+    "research",
+    "reusable",
+    "software"
+  ],
+  "license": "https://spdx.org/licenses/MIT",
+  "operatingSystem": [],
+  "programmingLanguage": [
+    "Vue",
+    "JavaScript",
+    "HTML",
+    "TypeScript",
+    "CSS",
+    "Dockerfile"
+  ],
+  "relatedLink": [],
+  "runtimePlatform": [],
+  "schema:releaseNotes": "First release",
+  "softwareRequirements": [],
+  "version": "1.0.0",
+  "type": "SoftwareSourceCode"
+}
diff --git a/ui/server/api/codeMetadata/[identifier]/index.post.ts b/ui/server/api/codeMetadata/[identifier]/index.post.ts
@@ -133,7 +133,7 @@ export default defineEventHandler(async (event) => {
 
   const codeMeta = {
     name: codeMetadataRecord.name,
-    "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+    "@context": "https://w3id.org/codemeta/3.0",
     ...(codeMetadataRecord.applicationCategory && {
       applicationCategory: codeMetadataRecord.applicationCategory,
     }),