refactor: ♻️ 🔏 🔊 🧑‍💻 Add Environment Variables and Convert Logging to Use Logwatch

.github/workflows/deploy-main.yml

@@ -26,6 +26,7 @@ jobs:
       KAMAL_SERVER_IP: ${{ secrets.KAMAL_SERVER_IP }}
       KAMAL_BOT_DOMAIN: ${{ secrets.KAMAL_BOT_DOMAIN }}
       DATABASE_URL: ${{ secrets.DATABASE_URL }}
+      BOT_LOGWATCH_URL: ${{ secrets.BOT_LOGWATCH_URL }}
       APP_ID: ${{ secrets.APP_ID }}
       GH_APP_ID: ${{ secrets.GH_APP_ID }}
       GH_APP_NAME: ${{ secrets.GH_APP_NAME }}
@@ -36,6 +37,7 @@ jobs:
       CODEFAIR_APP_DOMAIN: ${{ secrets.CODEFAIR_APP_DOMAIN }}
       ZENODO_API_ENDPOINT: ${{ secrets.ZENODO_API_ENDPOINT }}
       ZENODO_ENDPOINT: ${{ secrets.ZENODO_ENDPOINT }}
+      VALIDATOR_URL: ${{ secrets.VALIDATOR_URL }}
 
     steps:
       - uses: actions/checkout@v4
@@ -99,6 +101,7 @@ jobs:
       GH_OAUTH_APP_ID: ${{ secrets.GH_OAUTH_APP_ID }}
       GH_OAUTH_CLIENT_ID: ${{ secrets.GH_OAUTH_CLIENT_ID }}
       GH_OAUTH_CLIENT_SECRET: ${{ secrets.GH_OAUTH_CLIENT_SECRET }}
+      UI_LOGWATCH_URL: ${{ secrets.UI_LOGWATCH_URL }}
       ZENODO_API_ENDPOINT: ${{ secrets.ZENODO_API_ENDPOINT }}
       ZENODO_ENDPOINT: ${{ secrets.ZENODO_ENDPOINT }}
       ZENODO_CLIENT_ID: ${{ secrets.ZENODO_CLIENT_ID }}

.github/workflows/deploy-staging.yml

@@ -26,6 +26,7 @@ jobs:
       KAMAL_SERVER_IP: ${{ secrets.KAMAL_SERVER_IP }}
       KAMAL_BOT_DOMAIN: ${{ secrets.KAMAL_BOT_DOMAIN }}
       DATABASE_URL: ${{ secrets.DATABASE_URL }}
+      BOT_LOGWATCH_URL: ${{ secrets.BOT_LOGWATCH_URL }}
       APP_ID: ${{ secrets.APP_ID }}
       GH_APP_ID: ${{ secrets.GH_APP_ID }}
       GH_APP_NAME: ${{ secrets.GH_APP_NAME }}
@@ -36,6 +37,7 @@ jobs:
       CODEFAIR_APP_DOMAIN: ${{ secrets.CODEFAIR_APP_DOMAIN }}
       ZENODO_API_ENDPOINT: ${{ secrets.ZENODO_API_ENDPOINT }}
       ZENODO_ENDPOINT: ${{ secrets.ZENODO_ENDPOINT }}
+      VALIDATOR_URL: ${{ secrets.VALIDATOR_URL }}
 
     steps:
       - uses: actions/checkout@v4
@@ -99,6 +101,7 @@ jobs:
       GH_OAUTH_APP_ID: ${{ secrets.GH_OAUTH_APP_ID }}
       GH_OAUTH_CLIENT_ID: ${{ secrets.GH_OAUTH_CLIENT_ID }}
       GH_OAUTH_CLIENT_SECRET: ${{ secrets.GH_OAUTH_CLIENT_SECRET }}
+      UI_LOGWATCH_URL: ${{ secrets.UI_LOGWATCH_URL }}
       ZENODO_API_ENDPOINT: ${{ secrets.ZENODO_API_ENDPOINT }}
       ZENODO_ENDPOINT: ${{ secrets.ZENODO_ENDPOINT }}
       ZENODO_CLIENT_ID: ${{ secrets.ZENODO_CLIENT_ID }}

CHANGELOG.md

@@ -5,6 +5,17 @@ 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).
 
+## v3.2.1 - 12-12-2024
+
+### Added
+
+- Convert logging from 'consola' to 'logwatch' for improved log management and consistency across the application.
+
+### Fixed
+
+- Update CI and deployment workflows to include new environment variables 'BOT_LOGWATCH_URL' and 'VALIDATOR_URL'.
+- Patch to Zenodo workflow that was causing the user to be notified of a failed Zenodo upload when the upload was successful.
+
 ## v3.2.0 - 12-10-2024
 
 ### Added

CITATION.cff

@@ -15,15 +15,15 @@ authors:
 cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
-doi: 10.5281/zenodo.14064362
-abstract:
+doi: 10.5281/zenodo.14400138
+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. 
+  with R, Codefair is here to assist you.
 keywords:
   - best-practices
   - fair
@@ -32,5 +32,5 @@ keywords:
   - software
 license: MIT
 repository-code: https://github.com/fairdataihub/codefair-app
-date-released: '2024-11-11'
-version: 3.1.1
+date-released: '2024-12-11'
+version: 3.2.0

bot/.kamal/secrets

@@ -15,6 +15,7 @@ KAMAL_SERVER_IP=$KAMAL_SERVER_IP
 # bot secrets
 APP_ID=$APP_ID
 DATABASE_URL=$DATABASE_URL
+BOT_LOGWATCH_URL=$BOT_LOGWATCH_URL
 GH_APP_ID=$GH_APP_ID
 GH_APP_NAME=$GH_APP_NAME
 GH_APP_CLIENT_ID=$GH_APP_CLIENT_ID
@@ -24,6 +25,7 @@ WEBHOOK_SECRET=$WEBHOOK_SECRET
 CODEFAIR_APP_DOMAIN=$CODEFAIR_APP_DOMAIN
 ZENODO_API_ENDPOINT=$ZENODO_API_ENDPOINT
 ZENODO_ENDPOINT=$ZENODO_ENDPOINT
+VALIDATOR_URL=$VALIDATOR_URL
 
 # Option 2: Read secrets via a command
 # RAILS_MASTER_KEY=$(cat config/master.key)

bot/archival/index.js

@@ -1,5 +1,6 @@
 import dbInstance from '../db.js';
 import { consola } from 'consola';
+import { logwatch } from '../utils/logwatch.js';
 import fs from 'fs';
 const licensesJson = JSON.parse(fs.readFileSync('./public/assets/data/licenses.json', 'utf8'));
 
@@ -20,7 +21,7 @@ export async function updateGitHubRelease(context, repositoryName, owner, releas
       release_id: releaseId,
       draft: false,
     });
-    consola.success("Updated release to not be a draft!");
+    logwatch.success("Updated release to not be a draft!");
   } catch (error) {
     throw new Error(`Error updating the GitHub release: ${error}`, { cause: error });
   }
@@ -33,7 +34,7 @@ export async function updateGitHubRelease(context, repositoryName, owner, releas
  */
 export async function publishZenodoDeposition(zenodoToken, depositionId) {
   try {
-    consola.start("Publishing the Zenodo deposition...", depositionId);
+    logwatch.start(`Publishing the Zenodo deposition: ${depositionId}`);
     const publishDeposition = await fetch(
       `${ZENODO_API_ENDPOINT}/deposit/depositions/${depositionId}/actions/publish`,
       {
@@ -50,7 +51,7 @@ export async function publishZenodoDeposition(zenodoToken, depositionId) {
     }
 
     const publishedDeposition = await publishDeposition.json();
-    consola.success("Zenodo deposition published successfully at:", publishedDeposition.links.latest_html);
+    logwatch.success(`Zenodo deposition published successfully at: ${publishedDeposition.links.latest_html}`);
   } catch (error) {
     throw new Error(`Error publishing the Zenodo deposition: ${error.message}`, { cause: error });
   }
@@ -251,7 +252,7 @@ export async function createNewVersionOfDeposition(zenodoToken, depositionId) {
       const errorText = await zenodoRecord.text();
       throw new Error(`Failed to create a new version of Zenodo deposition. Status: ${zenodoRecord.status}: ${zenodoRecord.statusText}.`, { cause: errorText});
     }
-    consola.success("New version of Zenodo deposition created successfully!");
+    logwatch.success("New version of Zenodo deposition created successfully!");
 
     const responseText = await zenodoRecord.json();
 
@@ -265,7 +266,7 @@ export async function createNewVersionOfDeposition(zenodoToken, depositionId) {
     });
 
     if (!draftZenodoRecord.ok) {
-      consola.error("Error fetching the latest draft of Zenodo deposition:", draftZenodoRecord);
+      logwatch.error({message: "Error fetching the latest draft of Zenodo deposition:", fetchReponse: draftZenodoRecord}, true);
       const errorText = await draftZenodoRecord.text();
       throw new Error(`Failed to fetch the latest draft of Zenodo deposition. Status: ${draftZenodoRecord.status}: ${draftZenodoRecord.statusText}. Error: ${errorText}`, { cause: errorText });
     }
@@ -295,7 +296,7 @@ export async function getZenodoDepositionInfo(
 
     if (zenodoDepositionInfo.submitted === false){
       // Delete the files in the draft
-      consola.start("Requested deposition is a draft. Deleting the files in the draft...");
+      logwatch.start("Requested deposition is a draft. Deleting the files in the draft...");
       for (const file of zenodoDepositionInfo.files) {
         await deleteFileFromZenodo(depositionId, zenodoToken, file.id);
       }
@@ -307,12 +308,12 @@ export async function getZenodoDepositionInfo(
 
     if (newZenodoVersion.files.length > 0) {
       for (const file of newZenodoVersion.files) {
-        consola.start("Deleting file from newly created draft:", file.links.download);
+        logwatch.start(`Deleting file from newly created draft: ${file.links.download}`);
         await deleteFileFromZenodo(newZenodoVersion.id, zenodoToken, file.id);
       }
     }
 
-    consola.success("New draft version of Zenodo deposition created successfully!");
+    logwatch.success("New draft version of Zenodo deposition created successfully!");
     return newZenodoVersion;
   }
 }
@@ -354,8 +355,8 @@ export async function createZenodoMetadata(codemetadata, repository) {
     });
     if (!codeMetaContent.license) {
       // fetch from the db
-      consola.warn(`No license found in the codemeta.json file. Fetching from the database...`);
-      consola.info(`License found in the database: ${existingLicense?.license_id}`);
+      logwatch.warn(`No license found in the codemeta.json file. Fetching from the database...`);
+      logwatch.info(`License found in the database: ${existingLicense?.license_id}`);
       codeMetaContent.license = `https://spdx.org/licenses/${existingLicense?.license_id}`;
     }
     const license = licensesJson.find((license) => license.detailsUrl === `${codeMetaContent.license}.json`);
@@ -372,7 +373,7 @@ export async function createZenodoMetadata(codemetadata, repository) {
     })
 
     if (!zenodoMetadata) {
-      consola.error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
+      logwatch.error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
       throw new Error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
     }
 
@@ -440,7 +441,7 @@ export async function updateZenodoMetadata(depositionId, zenodoToken, metadata)
     );
 
     const updatedMetadataInfo = await updatedMetadata.json();
-    consola.success("Zenodo deposition metadata updated successfully!");
+    logwatch.success("Zenodo deposition metadata updated successfully!");
     return updatedMetadataInfo;
   } catch (error) {
     throw new Error(`Error updating Zenodo metadata: ${error}`, { cause: error });
@@ -480,7 +481,7 @@ export async function uploadReleaseAssetsToZenodo(
             accept: 'application/octet-stream'
           }
         });
-        consola.success(`Asset data fetched for ${asset.name}, for the release ${tagVersion}, from the GitHub repository: ${repository.name}`);
+        logwatch.success(`Asset data fetched for ${asset.name}, for the release ${tagVersion}, from the GitHub repository: ${repository.name}`);
 
         // Upload the file to Zenodo
         const uploadAsset = await fetch(`${bucket_url}/${asset.name}`,
@@ -493,9 +494,9 @@ export async function uploadReleaseAssetsToZenodo(
         });
 
         if (!uploadAsset.ok) {
-          consola.error(`Failed to upload ${asset.name}. Status: ${uploadAsset.statusText}. Error: ${uploadAsset}`);
+          logwatch.error(`Failed to upload ${asset.name}. Status: ${uploadAsset.statusText}. Error: ${uploadAsset}`);
         } else {
-          consola.success(`${asset.name} successfully uploaded to Zenodo!`);
+          logwatch.success(`${asset.name} successfully uploaded to Zenodo!`);
         }
       } catch (error) {
         throw new Error(`Error uploading assets to Zenodo: ${error}`, { cause: error });
@@ -516,13 +517,13 @@ export async function uploadReleaseAssetsToZenodo(
   );
 
   if (!uploadZip.ok) {
-    consola.error(`Failed to upload zip file. Status: ${uploadZip.statusText}`);
+    logwatch.error(`Failed to upload zip file. Status: ${uploadZip.statusText}`);
     throw new Error(`Failed to upload zip file. Status: ${uploadZip.statusText}`);
   }
 
   const endTime = performance.now();
-  consola.info(`Total duration to upload assets and zip to Zenodo deposition: ${(endTime - startTime) / 1000} seconds`);
-  consola.success("Zip file successfully uploaded to Zenodo!");
+  logwatch.info(`Total duration to upload assets and zip to Zenodo deposition: ${(endTime - startTime) / 1000} seconds`);
+  logwatch.success("Zip file successfully uploaded to Zenodo!");
 }
 
 /**
@@ -543,12 +544,11 @@ export async function deleteFileFromZenodo(depositionId, zenodoToken, fileId) {
     );
 
     if (!deleteFile.ok) {
-      consola.error(deleteFile);
       const errorText = await deleteFile.text();
       throw new Error(`Failed to delete file from Zenodo. Status: ${deleteFile.status}: ${deleteFile.statusText}. Error: ${errorText}`);
     }
 
-    consola.success("File successfully deleted from Zenodo!");
+    logwatch.success("File successfully deleted from Zenodo!");
   } catch (error) {
     throw new Error(`Error deleting file from Zenodo: ${error}`, { cause: error });
   }

bot/config/deploy.yml

@@ -54,6 +54,8 @@ env:
     - CODEFAIR_APP_DOMAIN
     - ZENODO_API_ENDPOINT
     - ZENODO_ENDPOINT
+    - VALIDATOR_URL
+    - BOT_LOGWATCH_URL
   clear:
     NODE_ENV: production