Unable to Remove Notifications from Deleted (404) Repositories

[dcb9]

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I’ve received some notifications indicating that I was mentioned in certain repositories. However, these repositories have been removed by GitHub due to phishing activity. As a result, I’m left with notifications that I can no longer access or dismiss.

Could you please help resolve this issue or remove these inaccessible notifications from my account?

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• I have read the above statement and can confirm my post is relevant to the GitHub feature areas Issues and/or Projects.

[ettechh]

You might have to log in and out of ur account, or create an issue with GitHub support.

This is what I found somewhere else...

Use the GitHub API (Most Likely to Work)
This is the most reliable technical solution. You will create a temporary Personal Access Token (PAT) to tell the GitHub API to mark all your notifications as read, which almost always clears stuck ones.

Step 1: Create a Personal Access Token
Go to your GitHub Developer Settings: https://github.com/settings/tokens

Click "Personal access tokens" > "Tokens (classic)".

Click "Generate new token" > "Generate new token (classic)".

Give the token a Note (e.g., "Clear Stuck Notifications").

Set the Expiration to 7 days (you will delete this token right after you use it).

In the "Select scopes" section, check the box for notifications. This is the only permission needed.

Scroll to the bottom and click "Generate token".

Copy the token (it looks like ghp_...). Keep this somewhere safe for the next step. Do not close the page until you have copied it.

Step 2: Use the Token to Clear Notifications
You can use either the GitHub CLI (if you have it installed) or a simple curl command (available on most operating systems).

Method A: Using GitHub CLI (gh)

If you have the GitHub CLI installed, this is the easiest way.

Open your Terminal or Command Prompt.

Run the following command, pasting your copied token when prompted:

Bash

gh auth login --with-token
Once logged in, run this command to mark all notifications as read:

Bash

gh api -X PUT /notifications
This should immediately clear all notifications, including the stuck ones.

[dcb9]

Thank you for your reply — the notifications were successfully dismissed. However, the repositories themselves still appear in my notifications list.

I tried using the CLI to remove them, but it didn’t work. Here’s the command I ran and the response I received:

$ gh api -X PUT /repos/notify-hub/gitcoin/notifications
gh: Not Found (HTTP 404)
{
  "message": "Not Found",
  "documentation_url": "https://docs.github.com/rest",
  "status": "404"
}

I’ve created a support ticket with GitHub regarding this issue, so I’ll wait for their assistance.

[krakowski]

Did GitHub Support respond with a solution to this? I also have some scam repositories (Gitcoin-Developer/gitcoin.com and ycombinnator/-co) in my list and can't remove them.

[krakowski]

@dcb9, I found a solution based on @ettechh findings.

First you need to get all notifications (setting all=true is crucial here).

gh api \ 
  -H "Accept: application/vnd.github+json" \
  -H "X-GitHub-Api-Version: 2022-11-28" \
  "/notifications?all=true"

This will also include the phishing repos (full_name should match the repository name). Within the JSON object for the matched repository, you need to look inside the url property, which in my case looks like this.

"repository": {
  "full_name": "Gitcoin-Developer/gitcoin.com",

  "url": "https://api.github.com/notifications/threads/19103568493",
}

Using the thread id (19103568493 in my case), you can then mark the thread as Done, which will remove it from the list.

gh api \
  --method DELETE \
  -H "Accept: application/vnd.github+json" \
  -H "X-GitHub-Api-Version: 2022-11-28" \
  "/notifications/threads/19103568493"

[dcb9]

Thank you, it works!

Support team didn't give me the right answer, so I appended your answer to the support ticket so they can see the exact fix. Hopefully, it helps them improve their anti-scam feature.

[zerebos]

This saved me a massive headache, thanks!

[jwosty]

For the lazy, use jq to find the exact ID right away if you know the full repo name:

1. gh api -X GET /notifications | jq '.[] | select(.repository.full_name == "foundation-paradigm/paradigm") | {id:.id, title:.subject.title, url:.subject.url, repo:.repository.full_name}'
2. Copy the value of the id field of the returned JSON object
3. gh api -X PATCH /notifications/threads/PASTE_ID_HERE

[deltaidea]

Thank you so much!

I selected all unread notifications to avoid copy-pasting repo names:

gh api -X GET /notifications | jq ".[] | select(.unread == true) | {id:.id, repo:.repository.full_name, title:.subject.title}"

Use one of these, replace ID_HERE with the id from above:

• Mark as read: gh api -X PATCH /notifications/threads/ID_HERE
• Mark as done: gh api -X DELETE /notifications/threads/ID_HERE

P.S. Get gh from https://cli.github.com/ and jq from https://jqlang.org/download/