[Bug] zk cannot query links of files in subdirectories

[B4rc1]

$ zk init
$ zk new --title one
$ zk new --title two
$ mkdir my_dir
$ zk new --title three my_dir

After this you end up with a folder looking something like this:

❯ tree
 .
├──  my_dir
│  └──  5r1k.md
├──  1zyl.md
└──  koxo.md

Now insert links to file on in file two and three.

You should end up with:

❯ zk list
one 1zyl.md (3 minutes ago)


three my_dir/5r1k.md (3 minutes ago)

  ‣ [[1zyl]]

two koxo.md (3 minutes ago)

  ‣ [[1zyl]]


Found 3 notes

as you can see two and three link to one. When asking zk which file links to one:

❯ zk list --link-to 1zyl.md
two koxo.md (5 minutes ago)

  ‣ [[1zyl]]


Found 1 note

When asking which file three links:

❯ zk list --linked-by "my_dir/5r1k.md"

Found 0 note

System Information
zk version: 0.9.0

❯ zk --version
zk dev

[mickael-menu]

Thank you for the detailed bug report, I can reproduce it.

[j-hui]

Probably related: zk also doesn't seem to count links from subdirectories when figuring out which notes are orphans.

$ zk init --no-input
$ zk new --title one # xu2y.md
$ mkdir my_dir && zk new --title two my_dir # he0x.md

Say I link these notes to each other:

$ zk list
one xu2y.md (3 minutes ago)

  ‣ [[my_dir/he0x]]

two my_dir/he0x.md (3 minutes ago)

  ‣ [[xu2y]]


Found 2 notes

Because these are linked circularly, neither should be considered an orphan. However:

$ zk list --orphan
one xu2y.md (4 minutes ago)

  ‣ [[my_dir/he0x]]


Found 1 note

one is still considered an orphan despite the link from two.

I post here because this seems like a different expression of the same issue, but I'm happy to open a new issue if that makes things easier to track.

[mickael-menu]

@j-hui It's fine here, I'll check if the issues are related after fixing the first one.

[waynezhang]

Coming from Logseq. I'm keeping journals in journals directory and other things in pages directory. But they can not refer to each others.

[dj8yfo]

Bump. Seeing this too.

[mickael-menu]

It should be fixed in main now, could someone confirm?

@j-hui Yes it was indeed the same issue.

[B4rc1]

still present for me on commit 7622d9e:

❯ ./zk list technical-tests/linking2.md
linking2 technical-tests/linking2.md (3 months ago)

  ‣ [[references/lua]]


Found 1 note

❯ ./zk list --linked-by technical-tests/linking2.md

Found 0 note

❯ ./zk list --link-to references/lua.md

Found 0 note

[mickael-menu]

@B4rc1 Your example works for me, make sure you are really using the latest version (check zk --version maybe).

Also forcing to reindex your notebook might help: zk index --force.

[B4rc1]

reindexing (zk index --force) fixed it. There should be a disclaimer somewhere to reindex your notebook on updates (or do that automatically)

[mickael-menu]

Yeah I think I'll add a reindexing step for the next release. Thanks for confirming the fix.