update main with new features

.gitignore

@@ -62,7 +62,8 @@ STAPLE.Rproj
 db/migrations/local/
 db/migrations/
 tmp/*
-summary-viewer/docs/.nojekyll
-summary-viewer/docs/*
-viewer-builds/*
-summary-viewer/src/data/project_summary.json
+
+# ignore builds but keep the folder for folks
+viewer-builds/*.zip
+viewer-builds/Proj*
+viewer-builds/viewer*

CITATION.cff

@@ -0,0 +1,41 @@
+cff-version: 1.2.0
+message: "If you use STAPLE in your research, please cite it using the following information."
+title: "STAPLE: Science Tracking Across the Project Lifespan"
+doi: "10.5281/zenodo.13916969"
+authors:
+  - family-names: "Buchanan"
+    given-names: "Erin M."
+    orcid: "https://orcid.org/0000-0002-9689-4189"
+  - family-names: "Kovacs"
+    given-names: "Marton"
+    orcid: "https://orcid.org/0000-0002-8142-8492"
+  - family-names: "Yedra"
+    given-names: "Engerst"
+    orcid: "https://orcid.org/0000-0002-9555-7148"
+  # Add more authors here, e.g.:
+  # - family-names: "Doe"
+  #   given-names: "Jane"
+  #   orcid: "https://orcid.org/XXXX-XXXX-XXXX-XXXX"
+
+preferred-citation:
+  type: software
+  title: "STAPLE: Science Tracking Across the Project Lifespan"
+  authors:
+    - family-names: "Buchanan"
+      given-names: "Erin M."
+      orcid: "https://orcid.org/0000-0002-9689-4189"
+    - family-names: "Kovacs"
+      given-names: "Marton"
+      orcid: "https://orcid.org/0000-0002-8142-8492"
+    - family-names: "Yedra"
+      given-names: "Engerst"
+      orcid: "https://orcid.org/0000-0002-9555-7148"
+  url: "https://github.com/STAPLE/STAPLE"
+
+contributors:
+  - family-names: "Hartgerink"
+    given-names: "Chris"
+    orcid: "https://orcid.org/0000-0003-1050-6809"
+  - family-names: "Sunami"
+    given-names: "Nami"
+    orcid: "https://orcid.org/0000-0001-5482-8370"

cron/cronJobDaily.sh

@@ -3,4 +3,4 @@ SCRIPT_DIR="/var/www/html/STAPLE/cron"
 # Change to the script's directory
 cd "$SCRIPT_DIR" || exit
 # Run the Node.js scriptnode cronJob.mjs
-node cronJobMailer.mjs
+node cronJobDailyMailer.mjs

cron/cronJobMailer.mjs → cron/cronJobDailyMailer.mjs

@@ -1,7 +1,7 @@
 import dotenv from "dotenv"
 dotenv.config({ path: "../.env.local" })
 import moment from "moment"
-import { PrismaClient } from "@prisma/client"
+import { PrismaClient, EmailFrequency } from "@prisma/client"
 import fetch from "node-fetch"
 import { resolver } from "@blitzjs/rpc"
 
@@ -26,6 +26,7 @@ function createDailyNotification(email, notificationContent, overdueContent) {
         <p>
           This email is to notify you about overdue tasks and recent updates to your project(s).
           You can view all notifications on the <a href="https://app.staple.science/auth/login?next=%2Fnotifications">Notifications page</a>.
+          You change the frequency of these emails on your <a href="https://app.staple.science/auth/login?next=%2Fprofile">Profile page</a>.
           </p>
 
         <h3>⏰ Overdue Tasks</h3>
@@ -191,43 +192,93 @@ const checkRateLimit = async () => {
     }
   }
 }
-// Function to send grouped notifications
+// Function to send grouped notifications (daily), respecting user email preferences
 export async function sendGroupedNotifications(groupedNotifications, groupedOverdues) {
-  const delayTime = 500 // Delay time between each email in milliseconds (e.g., 1 second)
+  const delayTime = 500 // Delay time between each email in milliseconds
 
   const allEmails = new Set([
     ...Object.keys(groupedNotifications || {}),
     ...Object.keys(groupedOverdues || {}),
   ])
 
   for (const email of allEmails) {
-    const projects = groupedNotifications?.[email] || {}
+    // Look up the user to read their email frequency preferences
+    const user = await db.user.findUnique({
+      where: { email },
+      select: {
+        id: true,
+        emailProjectActivityFrequency: true,
+        emailOverdueTaskFrequency: true,
+      },
+    })
+
+    if (!user) {
+      console.log(`[Mailer] No user found for email ${email}, skipping.`)
+      continue
+    }
+
+    // This is the DAILY mailer, so only honor DAILY preferences here
+    const wantsProjectDaily = user.emailProjectActivityFrequency === EmailFrequency.DAILY
+    const wantsOverdueDaily = user.emailOverdueTaskFrequency === EmailFrequency.DAILY
 
-    const notificationContent =
-      Object.entries(projects)
-        .map(([projectName, messages]) => {
-          const projectHeader = `<h4>Project: ${projectName}</h4>`
-          const messagesList = messages.map((message) => `<li>${message}</li>`).join("")
-          return projectHeader + `<ul>${messagesList}</ul>`
-        })
-        .join("") || "<p>No new updates in the last 24 hours.</p>"
+    // If the user doesn't want any daily emails, skip them entirely
+    if (!wantsProjectDaily && !wantsOverdueDaily) {
+      console.log(`[Mailer] User ${email} has no DAILY email prefs, skipping in daily job.`)
+      continue
+    }
 
-    // Build overdue content for this recipient (if any)
+    const projects = groupedNotifications?.[email] || {}
     const overdueProjects = groupedOverdues?.[email] || {}
-    const overdueContent =
-      Object.entries(overdueProjects)
-        .map(([projectName, rows]) => {
-          const projectHeader = `<h4>Project: ${projectName}</h4>`
-          const items = rows.map((row) => `<li>${row}</li>`).join("")
-          return projectHeader + `<ul>${items}</ul>`
-        })
-        .join("") || "<p>No overdue tasks 🎉</p>"
+
+    const hasProjectData = Object.keys(projects).length > 0
+    const hasOverdueData = Object.keys(overdueProjects).length > 0
+
+    const willHaveProjectSection = wantsProjectDaily && hasProjectData
+    const willHaveOverdueSection = wantsOverdueDaily && hasOverdueData
+
+    console.log(
+      `[Mailer][Daily] ${email} prefs: project=${user.emailProjectActivityFrequency}, overdue=${user.emailOverdueTaskFrequency}; ` +
+        `wantsProjectDaily=${wantsProjectDaily}, wantsOverdueDaily=${wantsOverdueDaily}; ` +
+        `hasProjectData=${hasProjectData}, hasOverdueData=${hasOverdueData}, ` +
+        `willHaveProjectSection=${willHaveProjectSection}, willHaveOverdueSection=${willHaveOverdueSection}`
+    )
+
+    // If there is nothing relevant to send for this cadence, skip
+    if (!willHaveProjectSection && !willHaveOverdueSection) {
+      console.log(`[Mailer] No relevant daily content for ${email} (prefs or data), skipping.`)
+      continue
+    }
+
+    // Build project updates section
+    const notificationContent = !wantsProjectDaily
+      ? "<p>You are not subscribed to daily project update emails.</p>"
+      : hasProjectData
+      ? Object.entries(projects)
+          .map(([projectName, messages]) => {
+            const projectHeader = `<h4>Project: ${projectName}</h4>`
+            const messagesList = messages.map((message) => `<li>${message}</li>`).join("")
+            return projectHeader + `<ul>${messagesList}</ul>`
+          })
+          .join("")
+      : "<p>No new updates in the last 24 hours.</p>"
+
+    // Build overdue tasks section
+    const overdueContent = !wantsOverdueDaily
+      ? "<p>You are not subscribed to daily overdue task emails.</p>"
+      : hasOverdueData
+      ? Object.entries(overdueProjects)
+          .map(([projectName, rows]) => {
+            const projectHeader = `<h4>Project: ${projectName}</h4>`
+            const items = rows.map((row) => `<li>${row}</li>`).join("")
+            return projectHeader + `<ul>${items}</ul>`
+          })
+          .join("")
+      : "<p>No overdue tasks 🎉</p>"
 
     const emailContent = createDailyNotification(email, notificationContent, overdueContent)
 
     console.log(
-      `[Mailer] Prepared email for ${email}: hasOverdues=${!!Object.keys(overdueProjects)
-        .length}, hasUpdates=${!!Object.keys(projects).length}`
+      `[Mailer] Prepared daily email for ${email}: hasOverdues=${willHaveOverdueSection}, hasUpdates=${willHaveProjectSection}`
     )
 
     // Check rate limit before sending email

cron/cronJobDeleteTmp.mjs

@@ -1,8 +1,12 @@
 import fs from "fs"
 import path from "path"
+import { fileURLToPath } from "url"
+
+const __filename = fileURLToPath(import.meta.url)
+const __dirname = path.dirname(__filename)
 
 function cleanUpViewerZips() {
-  const zipDir = path.join(process.cwd(), "viewer-builds")
+  const zipDir = path.join(__dirname, "..", "viewer-builds")
   if (!fs.existsSync(zipDir)) return
 
   const files = fs.readdirSync(zipDir)

cron/cronJobFolderSize.mjs

@@ -1,8 +1,12 @@
 import fs from "fs"
 import path from "path"
+import { fileURLToPath } from "url"
+
+const __filename = fileURLToPath(import.meta.url)
+const __dirname = path.dirname(__filename)
 
 function checkViewerBuildsSize() {
-  const zipDir = path.join(process.cwd(), "viewer-builds")
+  const zipDir = path.join(__dirname, "..", "viewer-builds")
   if (!fs.existsSync(zipDir)) return
 
   const files = fs.readdirSync(zipDir)

cron/cronJobWeekly.sh

@@ -0,0 +1,6 @@
+# Absolute path to the directory where your cronJob.mjs is located
+SCRIPT_DIR="/var/www/html/STAPLE/cron"
+# Change to the script's directory
+cd "$SCRIPT_DIR" || exit
+# Run the Node.js scriptnode cronJob.mjs
+node cronJobWeeklyMailer.mjs