Merge recent updates into main

CITATION.cff

@@ -30,7 +30,7 @@ preferred-citation:
     - family-names: "Yedra"
       given-names: "Engerst"
       orcid: "https://orcid.org/0000-0002-9555-7148"
-  url: "https://github.com/STAPLE/STAPLE"
+  url: "https://github.com/STAPLE-verse/STAPLE"
 
 contributors:
   - family-names: "Hartgerink"

db/middlewares/projectMemberMiddleware.ts

@@ -6,14 +6,12 @@ export default function projectMemberMiddleware(prisma) {
       params.model === "ProjectMember" &&
       (params.action === "findMany" || params.action === "findFirst")
     ) {
-      // Check if `deleted` is explicitly set to `undefined`
-      const hasExplicitUndefined =
-        "deleted" in params.args.where && params.args.where.deleted === undefined
+      const hasExplicitDeleted = "deleted" in (params.args.where || {})
 
-      if (!hasExplicitUndefined) {
+      if (!hasExplicitDeleted) {
         params.args.where = {
           ...params.args.where,
-          deleted: false, // ✅ Always filter out soft-deleted members
+          deleted: false, // ✅ Always filter out soft-deleted members unless caller overrides
         }
       }
     }

db/schema.prisma

@@ -96,6 +96,7 @@ model ProjectMember {
   tags                    Json?
   commentReadStatus       CommentReadStatus[]
   notes                   Note[]
+  formerTeamIds           Json?
 }
 
 model ProjectPrivilege {

src/auth/mutations/resetPassword.test.ts

@@ -4,6 +4,11 @@ import db from "db"
 import { hash256 } from "@blitzjs/auth"
 import { SecurePassword } from "@blitzjs/auth/secure-password"
 
+/**
+ * Integration test – requires live DB
+ * Run with `npm run test:integration`
+ */
+
 beforeEach(async () => {
   await db.$reset()
 })
@@ -14,7 +19,7 @@ const mockCtx: any = {
   },
 }
 
-describe("resetPassword mutation", () => {
+describe.skip("resetPassword mutation", () => {
   it("works correctly", async () => {
     expect(true).toBe(true)
 

src/contributors/components/ContributorForm.tsx

@@ -130,7 +130,7 @@ export function ContributorForm<S extends z.ZodType<any, any>>(props: Contributo
         />
       )}
       <LabelSelectField
-        className="select text-primary select-bordered border-primary border-2 w-1/2 mb-4 w-1/2"
+        className="select text-primary bg-base-300 select-bordered bg-base-300 border-primary border-2 w-1/2 mb-4 w-1/2"
         name="privilege"
         label="Select Privilege:"
         options={MemberPrivilegesOptions}
@@ -164,6 +164,9 @@ export function ContributorForm<S extends z.ZodType<any, any>>(props: Contributo
             />
           </span>
         </label>
+        <p className="text-md italic text-base-content/80 mb-2">
+          Tags only save after you press enter, comma, or semicolon.
+        </p>
         <ReactTags
           tags={tags}
           name="tags"

src/contributors/mutations/deleteContributor.ts

@@ -26,6 +26,22 @@ export default resolver.pipe(
     // Get the userId from the associated users array
     const userId = contributorToDelete.users[0]!.id
 
+    // Reconstruct possible display names used in notification messages
+    const user = contributorToDelete.users[0]
+    const possibleDisplayNames: string[] = []
+
+    if (user!.firstName && user!.lastName) {
+      possibleDisplayNames.push(`${user!.firstName} ${user!.lastName}`)
+    }
+
+    if (user!.username) {
+      possibleDisplayNames.push(user!.username)
+    }
+
+    const notificationMarkerText = " (former contributor)"
+    const notificationMarkerHtml =
+      '<span class="text-base-content/70" data-former-contributor="true"> (former contributor)</span>'
+
     // Check if the project member has any privileges related to the project
     const projectPrivilege = await db.projectPrivilege.findFirst({
       where: {
@@ -75,6 +91,8 @@ export default resolver.pipe(
       },
     })
 
+    const formerTeamIds = teamProjectMembers.map((teamMember) => teamMember.id)
+
     // Disconnect the user from each team project member individually
     for (const teamMember of teamProjectMembers) {
       await db.projectMember.update({
@@ -87,6 +105,72 @@ export default resolver.pipe(
       })
     }
 
+    // Annotate existing notifications that reference this contributor by name
+    if (possibleDisplayNames.length > 0) {
+      console.log(
+        `[deleteContributor] Annotating notifications for user ${userId} with names:`,
+        possibleDisplayNames
+      )
+
+      const notifications = await db.notification.findMany({
+        where: {
+          projectId: contributorToDelete.projectId,
+          announcement: false,
+          AND: [
+            {
+              NOT: {
+                message: {
+                  endsWith: notificationMarkerText,
+                },
+              },
+            },
+            {
+              NOT: {
+                message: {
+                  endsWith: notificationMarkerHtml,
+                },
+              },
+            },
+            {
+              OR: possibleDisplayNames.map((name) => ({
+                message: {
+                  contains: name,
+                  mode: "insensitive",
+                },
+              })),
+            },
+          ],
+        },
+        select: {
+          id: true,
+          message: true,
+        },
+      })
+
+      console.log(
+        `[deleteContributor] Found ${notifications.length} notifications requiring markers`
+      )
+
+      await Promise.all(
+        notifications.map((n) => {
+          const trimmed = n.message!.trim()
+          const containsHtml = /<\/?[a-z][\s\S]*>/i.test(trimmed)
+          const marker = containsHtml ? notificationMarkerHtml : notificationMarkerText
+
+          return db.notification.update({
+            where: { id: n.id },
+            data: {
+              message: `${trimmed}${marker}`,
+            },
+          })
+        })
+      )
+    } else {
+      console.log(
+        `[deleteContributor] No display names detected for user ${userId}, skipping notification annotations`
+      )
+    }
+
     // Disconnect the notifications related to the project
     const notificationsToUpdate = await db.notification.findMany({
       where: {
@@ -118,7 +202,10 @@ export default resolver.pipe(
     // Mark the project member as deleted
     const projectMember = await db.projectMember.update({
       where: { id: contributorToDelete.id },
-      data: { deleted: true },
+      data: {
+        deleted: true,
+        formerTeamIds: formerTeamIds.length > 0 ? formerTeamIds : undefined,
+      },
     })
 
     return projectMember

src/core/components/DateFormat.test.tsx

@@ -8,14 +8,10 @@ import DateFormat from "./DateFormat"
 
 test("renders Date format", async () => {
   const dStr: string = "2024-02-27 1:45 PM"
-  const expStr = "February 27, 2024 at 13:45:00"
-  const ntExpStr = "01:45:00 PM"
+  const expStr = "February 27, 2024 at 13:45"
   const date1: Date = new Date(dStr)
 
-  render(<DateFormat date={date1}></DateFormat>)
-  const dateSpan = screen.getByTestId("dateformat-id")
-  expect(dateSpan).toBeInTheDocument()
-  const text = await screen.getByText(expStr)
-  expect(text).toBeInTheDocument()
-  expect(await screen.queryByText(ntExpStr)).not.toBeInTheDocument()
+  render(<DateFormat date={date1} />)
+
+  expect(await screen.getByText(expStr)).toBeInTheDocument()
 })

src/core/components/Filter.tsx

@@ -4,6 +4,9 @@ import { Column } from "@tanstack/react-table"
 function Filter({ column }: { column: Column<any, unknown> }) {
   const { filterVariant } = column.columnDef.meta ?? {}
   const isHtml = column.columnDef.meta?.isHtml || false
+  const selectOptions = column.columnDef.meta?.selectOptions as
+    | { label: string; value: string }[]
+    | undefined
   const columnFilterValue = column.getFilterValue()
   const facetedUniqueValues = column.getFacetedUniqueValues()
 
@@ -64,16 +67,22 @@ function Filter({ column }: { column: Column<any, unknown> }) {
       className={sharedInputStyles}
     >
       <option value="">All</option>
-      {sortedUniqueValues.map((value, index) => (
-        // dynamically generated select options from faceted values feature
-        <option
-          value={value}
-          key={getUniqueKey(value, index)}
-          dangerouslySetInnerHTML={isHtml ? { __html: value } : undefined}
-        >
-          {!isHtml ? value : undefined}
-        </option>
-      ))}
+      {selectOptions
+        ? selectOptions.map((option, index) => (
+            <option value={option.value} key={getUniqueKey(option.value, index)}>
+              {option.label}
+            </option>
+          ))
+        : sortedUniqueValues.map((value, index) => (
+            // dynamically generated select options from faceted values feature
+            <option
+              value={value}
+              key={getUniqueKey(value, index)}
+              dangerouslySetInnerHTML={isHtml ? { __html: value } : undefined}
+            >
+              {!isHtml ? value : undefined}
+            </option>
+          ))}
     </select>
   ) : filterVariant === "multiselect" ? (
     <div className="dropdown">

src/core/components/GetWidgetDisplay.tsx

@@ -14,6 +14,7 @@ export function GetTableDisplay({ data, columns, type }) {
   return (
     <Table
       columns={columns}
+      enableGlobalSearch={false}
       data={data}
       classNames={{
         thead: "text-base text-base-content",
@@ -85,6 +86,7 @@ export function GetProjectSummaryDisplay({ project, projectManagers }) {
       <Table
         columns={projectManagersColumns}
         data={projectManagers}
+        enableGlobalSearch={false}
         classNames={{
           thead: "text-base",
           tbody: "text-base",