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GN Markdown Editor Integration

Notes

This is a to-do list to integrate the GN Markdown editor into GN2. To see the implementation, see:

https://git.genenetwork.org/gn-guile/

Tasks

[x] Implement APIs to fetch files for editing
[x] Add verification for the repository
[x] Implement API to edit and commit changes
[x] Replace JS with HTMX
[x] Support external links and image rendering
[x] Package dependencies
[x] show diff for files
[x] Handle errors
[ ] Review by users
[x] Integrate authentication into the system

API Documentation

This APi endpoints are implemented in guile See repo:

https://git.genenetwork.org/gn-guile/

The main endpoints are: `/edit` and `/commit`

Edit (GET)

This is a `GET` request to retrieve file content. Make sure you pass a valid `file_path` as `search_query` (the path should be relative to the repository).

**Edit Request Example:**

curl -G -d "file_path=test.md"  localhost:8091/edit

In case of a successful response, the expected result is:

{
"path": "<file_path>",
"content": "Test for new user\n test 2 for line\n test 3 for new line\n ## real markdown two test\n",
"hash": "<commit_sha>"
}

In case of an error, the expected response is:

{
"error": "<error_type>",
"msg": "<error_reason>"
}

Commit (POST)

**Endpoint:**

localhost:8091/commit

curl -X POST http://127.0.0.1:8091/commit \
-H 'Content-Type: application/json' \
-d '{
"content": "make test commit",
"filename": "test.md",
"email": "test@gmail.com",
"username": "test",
"commit_message": "init commit",
"prev_commit": "7cbfc40d98b49a64e98e7cd562f373053d0325bd"
}'

It expects the following data in JSON format:

`content` (the data you want to commit to the file, *valid markdown*)
`prev_commit` (required for integrity)
`filename` (file path to the file you are modifying)
`username` (identifier for the user, in our case from auth)
`email` (identifier email from the user, in our case from auth)
`commit_message`

If the request succeeds, the response should be:

{
"status": "201",
"message": "Committed file successfully",
"content": "Test for new user\n test 2 for line\n test 3 for new line\n ## real markdown two test\n",
"commit_sha": "47df3b7f13a935d50cc8b40e98ca9e513cba104c",
"commit_message": "commit by genetics"
}

If there are no changes to the file:

{
"status": "200",
"message": "Nothing to commit, working tree clean",
"commit_sha": "ecd96f27c45301279150fbda411544687db1aa45"
}

If the request fails, the expected results are:

{
"error": "<error_type>",
"msg": "Commits do not match. Please pull in the latest changes for the current commit *ecd96f27c45301279150fbda411544687db1aa45* and previous commits."
}

Related Issues

Notes on Gn-Editor UI

Here is the link to the PR for integrating the GN-Editor, including screenshots:

https://github.com/genenetwork/genenetwork2/pull/854

Genenetwork2 consumes the endpoint for the GN-Editor. Authentication is required to prevent access by malicious users and bots.

The main endpoint to fetch and edit a file is:

genenetwork.org/editor/edit?file-path=<relative file path>

This loads the editor with the content for editing.

Modifying Editor Settings

You can modify editor settings, such as font size and keyboard bindings. To do this, navigate to:

genenetwork.org/editor/settings

Be sure to save your changes for them to take effect.

Showing Diff for Editor

The editor also provides a diff functionality to show you the changes made to the file. Use the "Diff" button in the navigation to view these changes.

Committing Changes

To commit your changes, use the "Commit" button. A commit message is required in the text area for the commit to be processed.