logseq: Fix publishing graph

[LoveIsGrief]

Description of changes

Related to logseq/logseq#6880

Logseq publishes graphs by copying application assets into a folder and then the graph files (+/- some operations). In a normal linux distribution the application asset directories are rw but only by root. On nix, the directories are read-only, which leads to the copied directories also being ro and logseq failing
to copy the graph files into the target.

A fix from the logseq team isn't forthcoming (yet?), so we circumvent the entire ro issue by using
run-appimage, which extracts the appimage into a user-writeable directory.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 23.05 Release Notes (or backporting 22.11 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
  • (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes
• Fits CONTRIBUTING.md.

Fixes #199035

[LoveIsGrief]

Could you review this change please @weihua-lu?

[nixos-discourse]

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-ready-for-review/3032/1681

[SuperSandro2000]

Please rebase

[LoveIsGrief]

Rebased @SuperSandro2000

[nixos-discourse]

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/prs-ready-for-review/3032/1772

[LoveIsGrief]

Thanks for merging @SuperSandro2000 🙏

[necauqua]

It seems that this change broke Logseq Sync:
On start it asks for the password and then hangs (and sometimes unhangs and you can use logseq, but the sync is off - or you can cancel the password prompt).
The log shows

Error occurred in handler for 'main': [Error: Failed to create napi buffer] { code: 'Unknown' }
Error occurred in handler for 'main': [Error: Failed to create napi buffer] { code: 'Unknown' }
Error occurred in handler for 'main': [Error: cannot age decrypt: Header is invalid] { code: 'InvalidArg' }

Logseq version is 0.8.16 (b5b1a46)

And if I roll back to when it wasn't an appimage the version and commit are the same and everything works (except publishing I guess), although it still shows this one error line in logs

Error occurred in handler for 'main': [Error: cannot age decrypt: Header is invalid] { code: 'InvalidArg' }

Soo creating native nodejs buffers broke or something?.

[LoveIsGrief]

Looks  like Logseq Sync is a paid and limited feature. Unfortunately, I have no way of testing this. FYI they both use AppImage, the major difference is that prior to my PR the contents were extracted into the /nix/store (a read-only location) and now it's run with appimage-run which extracts the AppImage to a user's XDG folder (I think its the cache folder --> /home/user/.cache/...). Maybe appimage-run misses a step that mkDerivation does, I don't know 🫥  Have you tried opening the developer console? (Ctrl+shift+I) Maybe there's more information there?

[necauqua]

I'm not exactly sure what happened, but once again I've switched nixos to latest unstable, and now it asked me to do a full relogin and now it seems to work.
Also logseq asked for a full relogin on android, I'm thinking they actually might've fixed something on their backend 🤷