Merge: 🔀 merge main into staging

CHANGELOG.md

@@ -5,6 +5,28 @@ 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).
 
+
+## v.2.0.1 - 2024-09-03
+
+### Identifier
+
+https://doi.org/10.5281/zenodo.13651177
+
+### Added
+
+- Added a migration script to update the database for users who may try to access the dashboard before the v2.0.0 bot has ran on all their repositories.
+- Added badges to the CWL card on the dashboard to show the overall status of the CWL validations.
+
+### Fixed
+
+- Fixed a bug where the bot would updated the overall status of the CWL validation on the database.
+- Link generator for Codefair repository settings was fixed to correctly generate the link for a user or repository.
+
+### Removed
+
+- Removed references to the action key in the database as it was not being used.
+
+
 ## v.2.0.0 - 2024-08-29
 
 ### Identifier

CITATION.cff

@@ -17,7 +17,7 @@ message: If you use this software, please cite it using the metadata from this f
 type: software
 identifiers:
   - type: doi
-    value: https://doi.org/10.5281/zenodo.13544387
+    value: https://doi.org/10.5281/zenodo.13651177
 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
@@ -33,5 +33,5 @@ keywords:
   - software
 license: MIT
 repository-code: https://github.com/fairdataihub/codefair-app
-version: 2.0.0
-date-released: 2024-08-29
+version: 2.0.1
+date-released: 2024-09-03

bot/cwl/index.js

@@ -266,7 +266,7 @@ export async function applyCWLTemplate(
 
     // Check if the overall status is still valid
     for (const file of newFiles) {
-      if (file.overall_status === "invalid") {
+      if (file.validation_status === "invalid") {
         validOverall = false;
         break;
       }

bot/dev-migrate.ts

@@ -0,0 +1,115 @@
+import fs from "fs";
+import dotenv from "dotenv";
+import { MongoClient } from "mongodb";
+import { consola } from "consola";
+
+if (process.env.NODE_ENV !== "production") {
+  dotenv.config({
+    path: ".env",
+  });
+}
+
+if (!process.env.MONGODB_URI) {
+  throw new Error("Please define the MONGODB_URI environment variable");
+}
+
+if (!process.env.MONGODB_DB_NAME) {
+  throw new Error("Please define the MONGODB_DB_NAME environment variable");
+}
+
+const uri = process.env.MONGODB_URI;
+const dbName = process.env.MONGODB_DB_NAME;
+const devDbName = `${dbName}-migrations-test`;
+
+// Create a new MongoClient
+const client = new MongoClient(uri);
+
+await client.connect();
+
+const database = client.db(dbName);
+
+if (!database) {
+  throw new Error("Database not found");
+}
+
+const devDatabase = client.db(devDbName);
+
+// FOR DEV ONLY
+// Clone the original database
+// Get the list of collections in the original database
+consola.start("Cloning the original database...");
+
+const collections = await database.listCollections().toArray();
+
+for (const collection of collections) {
+  const collectionName = collection.name;
+
+  // Get the collection
+  const dbCollection = database.collection(collectionName);
+
+  // Get the documents in the collection
+  const documents = await dbCollection.find().toArray();
+
+  // Drop the collection in the new database if it exists
+  await devDatabase.dropCollection(collectionName).catch(() => {});
+
+  // Create a new collection in the new database
+  const newCollection = devDatabase.collection(collectionName);
+
+  // Insert the documents into the new collection
+  if (documents.length > 0) {
+    await newCollection.insertMany(documents);
+  }
+}
+
+consola.success("Database cloned!");
+
+// Get the list of files in the migrations folder
+const files = fs.readdirSync("./migrations");
+
+// Order the files by name
+files.sort();
+
+const migrationsCollection = devDatabase.collection("migrations");
+
+for (const file of files) {
+  // Get the file name without the extension
+  const migrationId = file.replace(".ts", "");
+
+  // Check if the migration has already been applied
+  const migration = await migrationsCollection.findOne({
+    migration_id: migrationId,
+  });
+
+  if (migration) {
+    consola.warn(`Migration ${migrationId} has already been applied`);
+    continue;
+  }
+
+  // Import the migration file
+  const { default: migrationFunction } = await import(
+    `./migrations/${migrationId}`
+  );
+
+  consola.start(`Applying migration ${migrationId}`);
+
+  try {
+    // Run the migration
+    await migrationFunction(uri, devDbName, migrationId);
+  } catch (error) {
+    consola.error(`Error applying migration ${migrationId}: ${error.message}`);
+    throw error;
+  }
+
+  consola.success(`Migration ${migrationId} has been applied!`);
+
+  // Insert the migration into the migrations collection
+  // await migrationsCollection.insertOne({
+  //   migration_id: migrationId,
+  //   created_at: new Date(),
+  // });
+}
+
+await client.close();
+
+process.exit();

bot/index.js

@@ -98,7 +98,6 @@ export default async (app, { getRouter }) => {
         await verifyInstallationAnalytics(
           context,
           repository,
-          applyActionLimit,
           actionCount,
           latestCommitInfo,
         );
@@ -259,7 +258,7 @@ export default async (app, { getRouter }) => {
         installationCollection,
       );
 
-      if (installation?.action && installation?.action_count > 0) {
+      if (installation?.action_count > 0) {
         consola.warn(
           "Action limit count down:",
           installation.action_count,
@@ -288,7 +287,6 @@ export default async (app, { getRouter }) => {
           { repositoryId: repository.id },
           {
             $set: {
-              action: false,
               action_count: 0,
               latestCommitDate: latestCommitInfo.latestCommitDate,
               latestCommitMessage: latestCommitInfo.latestCommitMessage,
@@ -452,7 +450,7 @@ export default async (app, { getRouter }) => {
     const installation = await installationCollection.findOne({
       repositoryId: repository.id,
     });
-    if (installation?.action && installation?.action_count > 0) {
+    if (installation?.action_count > 0) {
       installationCollection.updateOne(
         { repositoryId: repository.id },
         {
@@ -470,7 +468,6 @@ export default async (app, { getRouter }) => {
         { repositoryId: repository.id },
         {
           $set: {
-            action: false,
             action_count: 0,
           },
         },
@@ -543,7 +540,7 @@ export default async (app, { getRouter }) => {
           installationCollection,
         );
 
-        if (installation?.action && installation?.action_count > 0) {
+        if (installation?.action_count > 0) {
           installationCollection.updateOne(
             { repositoryId: context.payload.repository.id },
             { $set: { action_count: installation.action_count - 1 } },
@@ -557,7 +554,6 @@ export default async (app, { getRouter }) => {
             { repositoryId: context.payload.repository.id },
             {
               $set: {
-                action: false,
                 action_count: 0,
               },
             },
@@ -749,7 +745,6 @@ export default async (app, { getRouter }) => {
       await verifyInstallationAnalytics(
         context,
         repository,
-        false,
         0,
         latestCommitInfo,
       );

bot/migrate.ts

@@ -1,8 +1,7 @@
+import fs from "fs";
 import dotenv from "dotenv";
 import { MongoClient } from "mongodb";
-import fs from "fs";
 import { consola } from "consola";
-import { nanoid } from "nanoid";
 
 if (process.env.NODE_ENV !== "production") {
   dotenv.config({
@@ -20,7 +19,6 @@ if (!process.env.MONGODB_DB_NAME) {
 
 const uri = process.env.MONGODB_URI;
 const dbName = process.env.MONGODB_DB_NAME;
-const devDbName = `${dbName}-migrations-test`;
 
 // Create a new MongoClient
 const client = new MongoClient(uri);
@@ -33,45 +31,13 @@ if (!database) {
   throw new Error("Database not found");
 }
 
-const devDatabase = client.db(devDbName);
-
-// FOR DEV ONLY
-// Clone the original database
-// Get the list of collections in the original database
-consola.start("Cloning the original database...");
-
-const collections = await database.listCollections().toArray();
-
-for (const collection of collections) {
-  const collectionName = collection.name;
-
-  // Get the collection
-  const dbCollection = database.collection(collectionName);
-
-  // Get the documents in the collection
-  const documents = await dbCollection.find().toArray();
-
-  // Drop the collection in the new database if it exists
-  await devDatabase.dropCollection(collectionName).catch(() => {});
-
-  // Create a new collection in the new database
-  const newCollection = devDatabase.collection(collectionName);
-
-  // Insert the documents into the new collection
-  if (documents.length > 0) {
-    await newCollection.insertMany(documents);
-  }
-}
-
-consola.success("Database cloned!");
-
 // Get the list of files in the migrations folder
 const files = fs.readdirSync("./migrations");
 
 // Order the files by name
 files.sort();
 
-const migrationsCollection = devDatabase.collection("migrations");
+const migrationsCollection = database.collection("migrations");
 
 for (const file of files) {
   // Get the file name without the extension
@@ -96,19 +62,20 @@ for (const file of files) {
 
   try {
     // Run the migration
-    await migrationFunction(uri, devDbName, migrationId);
+    const entriesUpdated = await migrationFunction(uri, dbName, migrationId);
+
+    consola.success(`Migration ${migrationId} has been applied!`);
+
+    // Insert the migration into the migrations collection
+    await migrationsCollection.insertOne({
+      created_at: new Date(),
+      entries_updated: entriesUpdated,
+      migration_id: migrationId,
+    });
   } catch (error) {
     consola.error(`Error applying migration ${migrationId}: ${error.message}`);
     throw error;
   }
-
-  consola.success(`Migration ${migrationId} has been applied!`);
-
-  // Insert the migration into the migrations collection
-  // await migrationsCollection.insertOne({
-  //   migration_id: migrationId,
-  //   created_at: new Date(),
-  // });
 }
 
 await client.close();