feat: ✨ validation status + trigger bot rerun full validation

bot/index.js

@@ -480,6 +480,8 @@ export default async (app, { getRouter }) => {
   app.on("issues.edited", async (context) => {
     const issueBody = context.payload.issue.body;
     const issueTitle = context.payload.issue.title;
+    const { repository } = context.payload;
+    const owner = context.payload.repository.owner.login;
 
     if (issueTitle === ISSUE_TITLE) {
       const installationCollection = db.collection("installation");
@@ -523,8 +525,6 @@ export default async (app, { getRouter }) => {
       issueTitle === ISSUE_TITLE
     ) {
       consola.start("Rerunning CWL Validation...");
-      const owner = context.payload.repository.owner.login;
-      const repository = context.payload.repository;
 
       const cwl = await getCWLFiles(context, owner, repository.name);
 
@@ -571,11 +571,55 @@ export default async (app, { getRouter }) => {
 
       consola.success("CWL Validation rerun successfully!");
     }
+
+    if (
+      issueBody.includes("<!-- @codefair-bot rerun-full-repo-validation -->") &&
+      issueTitle === ISSUE_TITLE
+    ) {
+      consola.start("Rerunning full repository validation...");
+
+      const license = await checkForLicense(context, owner, repository.name);
+      const citation = await checkForCitation(context, owner, repository.name);
+      const codemeta = await checkForCodeMeta(context, owner, repository.name);
+      const cwl = await getCWLFiles(context, owner, repository.name);
+
+      const cwlObject = {
+        contains_cwl: cwl.length > 0 || false,
+        files: cwl,
+        removed_files: [],
+      };
+
+      // If existing cwl validation exists, update the contains_cwl value
+      const cwlExists = await db.collection("cwlValidation").findOne({
+        repositoryId: repository.id,
+      });
+
+      if (cwlExists?.contains_cwl_files) {
+        cwlObject.contains_cwl = cwlExists.contains_cwl_files;
+      }
+
+      const subjects = {
+        citation,
+        codemeta,
+        cwl: cwlObject,
+        license,
+      };
+
+      const issueBody = await renderIssues(
+        context,
+        owner,
+        repository,
+        false,
+        subjects,
+      );
+
+      await createIssue(context, owner, repository, ISSUE_TITLE, issueBody);
+    }
   });
 
   // When an issue is deleted or closed
   app.on(["issues.deleted", "issues.closed"], async (context) => {
-    const repository = context.payload.repository;
+    const { repository } = context.payload;
     const issueTitle = context.payload.issue.title;
 
     if (issueTitle === ISSUE_TITLE) {
@@ -607,7 +651,7 @@ export default async (app, { getRouter }) => {
 
   // When an issue is reopened
   app.on("issues.reopened", async (context) => {
-    const repository = context.payload.repository;
+    const { repository } = context.payload;
     const owner = context.payload.repository.owner.login;
     const issueTitle = context.payload.issue.title;
 

bot/package.json

@@ -28,6 +28,7 @@
     "axios": "^1.6.8",
     "consola": "^3.2.3",
     "cwl-ts-auto": "^0.1.3",
+    "dayjs": "^1.11.11",
     "humanparser": "^2.7.0",
     "js-yaml": "^4.1.0",
     "mongodb": "^6.5.0",

bot/utils/license/index.js

@@ -173,100 +173,97 @@ export async function applyLicenseTemplate(
   owner,
   context,
 ) {
-  if (!subjects.license) {
-    const identifier = createId();
-    let url = `${CODEFAIR_DOMAIN}/add/license/${identifier}`;
-    const licenseCollection = dbInstance.getDb().collection("licenseRequests");
-    const existingLicense = await licenseCollection.findOne({
-      repositoryId: repository.id,
-    });
+  const licenseCollection = dbInstance.getDb().collection("licenseRequests");
+  const identifier = createId();
+  let badgeURL = `${CODEFAIR_DOMAIN}/add/license/${identifier}`;
+  const existingLicense = await licenseCollection.findOne({
+    repositoryId: repository.id,
+  });
+  let licenseId = null;
+  let licenseContent = null;
+  let licenseContentNotEmpty = null;
 
-    if (!existingLicense) {
-      // Entry does not exist in db, create a new one
-      const newDate = Date.now();
-      await licenseCollection.insertOne({
-        contains_license: false,
-        created_at: newDate,
-        identifier,
-        open: true,
-        owner,
-        repo: repository.name,
-        repositoryId: repository.id,
-        updated_at: newDate,
-      });
-    } else {
-      // Get the identifier of the existing license request
-      // Update the database
-      await licenseCollection.updateOne(
-        { repositoryId: repository.id },
-        { $set: { contains_license: false, updated_at: Date.now() } },
-      );
-      url = `${CODEFAIR_DOMAIN}/add/license/${existingLicense.identifier}`;
-    }
-    // No license file found text
-    const licenseBadge = `[![License](https://img.shields.io/badge/Add_License-dc2626.svg)](${url})`;
-    baseTemplate += `## 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). If you would like Codefair to add a license file, click the "Add license" button below to go to our interface for selecting and adding a license. You can also add a license file yourself and Codefair will update the the dashboard when it detects it on the main branch.\n\n${licenseBadge}`;
-  } else {
+  if (subjects.license) {
     // Get the license identifier
     const licenseRequest = await context.octokit.rest.licenses.getForRepo({
       owner,
       repo: repository.name,
     });
 
-    let licenseId = licenseRequest.data.license.spdx_id;
-    let licenseContent = Buffer.from(
+    licenseId = licenseRequest.data.license.spdx_id;
+    licenseContent = Buffer.from(
       licenseRequest.data.content,
       "base64",
     ).toString("utf-8");
+
     if (
       licenseRequest.data.license.spdx_id === "no-license" ||
       licenseRequest.data.license.spdx_id === "NOASSERTION"
     ) {
+      consola.info("Resetting license id and content back to null");
       licenseId = null;
       licenseContent = null;
     }
 
-    // License file found text
-    const identifier = createId();
-    let url = `${CODEFAIR_DOMAIN}/add/license/${identifier}`;
-    const licenseCollection = dbInstance.getDb().collection("licenseRequests");
-    const existingLicense = await licenseCollection.findOne({
+    licenseContentNotEmpty = licenseContent && licenseContent.trim().length > 0;
+  }
+
+  if (existingLicense) {
+    // Determine if the existing license is still valid
+    const isExistingLicenseValid =
+      existingLicense?.licenseContent && existingLicense.licenseId;
+
+    // Use the new license data if the existing license is invalid or the license has changed
+    const finalLicenseId =
+      isExistingLicenseValid && licenseId === null && !subjects.license
+        ? existingLicense?.licenseId
+        : licenseId;
+    const finalLicenseContent =
+      isExistingLicenseValid && licenseContent === null && !subjects.license
+        ? existingLicense?.licenseContent
+        : licenseContent;
+
+    badgeURL = `${CODEFAIR_DOMAIN}/add/license/${existingLicense.identifier}`;
+    await licenseCollection.updateOne(
+      { repositoryId: repository.id },
+      {
+        $set: {
+          contains_license: subjects.license,
+          updated_at: Date.now(),
+          license_status:
+            finalLicenseContent &&
+            finalLicenseContent.trim().length > 0 &&
+            subjects.license
+              ? "valid"
+              : "invalid",
+          licenseId: finalLicenseId,
+          licenseContent: finalLicenseContent,
+        },
+      },
+    );
+  } else {
+    const newDate = Date.now();
+    await licenseCollection.insertOne({
+      contains_license: subjects.license,
+      license_status: licenseContentNotEmpty ? "valid" : "invalid",
+      created_at: newDate,
+      licenseId,
+      licenseContent,
+      identifier,
+      open: true,
+      owner,
+      repo: repository.name,
       repositoryId: repository.id,
+      updated_at: newDate,
     });
+  }
 
-    if (!existingLicense) {
-      // Entry does not exist in db, create a new one
-      const newDate = Date.now();
-      await licenseCollection.insertOne({
-        contains_license: true,
-        created_at: newDate,
-        identifier,
-        licenseContent,
-        licenseId,
-        open: true,
-        owner,
-        repo: repository.name,
-        repositoryId: repository.id,
-        updated_at: newDate,
-      });
-    } else {
-      // Get the identifier of the existing license request
-      // Update the database
-      await licenseCollection.updateOne(
-        { repositoryId: repository.id },
-        {
-          $set: {
-            contains_license: true,
-            licenseContent,
-            licenseId,
-            updated_at: Date.now(),
-          },
-        },
-      );
-      url = `${CODEFAIR_DOMAIN}/add/license/${existingLicense.identifier}`;
-    }
-    const licenseBadge = `[![License](https://img.shields.io/badge/Edit_License-0ea5e9.svg)](${url})`;
+  const licenseBadge = `[![License](https://img.shields.io/badge/${subjects.license ? "Edit_License-0ea5e9" : "Add_License-dc2626"}.svg)](${badgeURL})`;
+
+  if (subjects.license) {
     baseTemplate += `## LICENSE ✔️\n\nA LICENSE file is found at the root level of the repository.\n\n${licenseBadge}`;
+  } else {
+    baseTemplate += `## LICENSE ❌\n\nTo make your software reusable a license file is expected at the root level of your repository, as recommended in the [FAIR-BioRS Guidelines](https://fair-biors.org). If you would like Codefair to add a license file, click the "Add license" button below to go to our interface for selecting and adding a license. You can also add a license file yourself and Codefair will update the the dashboard when it detects it on the main branch.\n\n${licenseBadge}`;
   }
 
   return baseTemplate;

bot/utils/metadata/index.js

@@ -322,11 +322,35 @@ export async function applyMetadataTemplate(
 
   if (subjects.codemeta && subjects.citation && subjects.license) {
     // Download the codemeta.json file from the repo
-    const codemetaFile = await context.octokit.repos.getContent({
-      owner,
-      path: "codemeta.json",
-      repo: repository.name,
-    });
+    let validCodemeta = false;
+    let validCitation = false;
+
+    try {
+      const codemetaFile = await context.octokit.repos.getContent({
+        owner,
+        path: "codemeta.json",
+        repo: repository.name,
+      });
+
+      JSON.parse(Buffer.from(codemetaFile.data.content, "base64").toString());
+
+      validCodemeta = true;
+    } catch (error) {
+      consola.error("Error getting codemeta.json file", error);
+    }
+
+    try {
+      const citationFile = await context.octokit.repos.getContent({
+        owner,
+        path: "CITATION.cff",
+        repo: repository.name,
+      });
+
+      yaml.load(Buffer.from(citationFile.data.content, "base64").toString());
+      validCitation = true;
+    } catch (error) {
+      consola.error("Error getting CITATION.cff file", error);
+    }
 
     // Convert the content to a json object
     const codemetaContent = JSON.parse(
@@ -351,6 +375,8 @@ export async function applyMetadataTemplate(
       const newDate = Date.now();
       // const gatheredMetadata = await gatherMetadata(context, owner, repository);
       await metadataCollection.insertOne({
+        citation_status: validCitation ? "valid" : "invalid",
+        codemeta_status: validCodemeta ? "valid" : "invalid",
         contains_citation: subjects.citation,
         contains_codemeta: subjects.codemeta,
         contains_metadata: subjects.codemeta && subjects.citation,
@@ -369,6 +395,8 @@ export async function applyMetadataTemplate(
         { repositoryId: repository.id },
         {
           $set: {
+            citation_status: validCitation ? "valid" : "invalid",
+            codemeta_status: validCodemeta ? "valid" : "invalid",
             contains_citation: subjects.citation,
             contains_codemeta: subjects.codemeta,
             contains_metadata: subjects.codemeta && subjects.citation,