JabRef: build from source

[linsui]

Motivation for this change

JabRef 5.5 crashes

Things done

1. Build JabRef from source
2. Fix problem that files can't be opened

• 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/)
• 22.05 Release Notes (or backporting 21.11 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.

@Artturin @zoedsoupe @wamserma @Coda-Coda

Closes #130717
Closes #134516

[Artturin]

@ofborg build jabref

[linsui]

@ofborg build jabref

[linsui]

@ofborg build jabref

[linsui]

@Artturin Could you please review again?

[linsui]

@ofborg build jabref

[linsui]

@ofborg build jabref

[wamserma]

Built on aarch64-linux and x86_64-linux.

[rbtmcl]

Hi,

i tried your patch and it works like charm. Thanks so much for tackling this build-jabref-from-source thing. I have also tried this before, but gave up very quickly.

In the past I used the derivation from 21.11 with a small modification to make the Firefox plugin work. Glad to see, that you already fixed this.

Unfortunately, $out/opt/jabref/lib/jabrefHost.py and $out/bin/.Jabref-wrapped don't work together out of the box - at least at my machine (nixos 22.05, x86_64-linux). I got some weird error message in the Browser Console. Something like

JabRef: Got success response from JabRef with details  
b"/nix/store/vkrhnpbqy7iyzciyjr4wzjfvcxf8n0gh-jabref-5.6/bin/.JabRef-wrapped: line 238: @techreport{wesselkamp_misleading_2022,: command not found\n/nix/store/vkrhnpbqy7iyzciyjr4wzjfvcxf8n0gh-jabref-5.6/bin/.JabRef-wrapped: line 239: title: command not found\n/nix/store/vkrhnpbqy7iyzciyjr4wzjfvcxf8n0gh-jabref-5.6/bin/.JabRef-wrapped: line 240: url: command not found\n/nix/store/vkrhnpbqy7iyzciyjr4wzjfvcxf8n0gh-jabref-5.6/bin/.JabRef-wrapped: line 241: doi: command not found\n/nix/store/vkrhnpbqy7iyzciyjr4wzjfvcxf8n0gh-jabref-5.6/bin/.JabRef-wrapped: eval: line 242: syntax error near unexpected token `('\n/nix/store/vkrhnpbqy7iyzciyjr4wzjfvcxf8n0gh-jabref-5.6/bin/.JabRef-wrapped: eval: line 242: `\tabstract = {Generative adversarial networks (GANs) have made remarkable progress in synthesizing realistic-looking images that effectively outsmart even humans. Although several detection methods can recognize these deep fakes by checking for image artifacts from the generation process, multi…

To make it work again I applied the following change to jabrefHost.py

77c77
<     cmd = str(JABREF_PATH).split() + ["--importBibtex", r"{}".format(data)]
---
>     cmd = str(JABREF_PATH).split() + ["--importBibtex", r"'{}'".format(data)]

by adding the following line to the installPhase.

sed -i "s/r\"{}\"/r\"'{}'\"/g" $out/opt/jabref/lib/jabrefHost.py

At the moment I am not sure which of the two files is the root cause. Unfortunately, I don't have time to investigate this further in the next few days. Nevertheless, I did not want to withhold this from you.

Cheers

[linsui]

I build it again and the hash changed again even with gradle.lockfile. I guess the problem is that snapshot deps are used which are not locked.

[linsui]

@koschtschei Thanks! I have been confused about why the extension doesn't work for a long time! I implement your fix and it work now!

[linsui]

@ofborg build jabref

[linsui]

I removed those test deps including some snapshot. Now there is only one snapshot which has been inactive since 2019.

[wamserma]

Result of nixpkgs-review pr 162593 run on aarch64-linux 1

1 package built:

• jabref

[nixos-discourse]

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

https://discourse.nixos.org/t/prs-already-reviewed/2617/553

[SuperSandro2000]

@ofborg build jabref

[linsui]

Thanks!

[fleimgruber]

@SuperSandro2000 could you please try backporting this via label backport release-22.05 as you did after #165182 (comment)? If auto backporting fails here as well, I will open a manual backport PR.

Edit: opened a manual backport PR in any case.

[SuperSandro2000]

If you are a maintainer you can add the label yourself.

[fleimgruber]

Thanks for notifying. I am not a maintainer, but I will notify maintainers with such requests in the future.

[github-actions]

Backport failed for release-22.05, because it was unable to cherry-pick the commit(s).

Please cherry-pick the changes locally.

git fetch origin release-22.05
git worktree add -d .worktree/backport-162593-to-release-22.05 origin/release-22.05
cd .worktree/backport-162593-to-release-22.05
git checkout -b backport-162593-to-release-22.05
ancref=$(git merge-base 0b683abff06fe55755ea992ba47f2e787081a30f 2df7e1869949e771d7b989fafdc02e1690053f1b)
git cherry-pick -x $ancref..2df7e1869949e771d7b989fafdc02e1690053f1b