LyZ: LyX plugin pro Zotero

LyZ je plugin pro bibliografický manažer Zotero (verze 2 a vyšší), jehož smyslem je zpříjemnit práci s vizuálním editorem pro LaTeX LyX. Bohužel jsem zatím neměl čas přeložit tuto stránku do češtiny. Zdrojový kód je zde: https://github.com/willsALMANJ/lyz.

Máte-li jakékoli dotazy, s radostí na ně odpovím. Pište na petr.simon@gmail.com.

190 comments to LyZ: LyX plugin pro Zotero

  • Mattia

    Hi,

    thanks for this plugin, it’s really useful and I’ve used it with great satisfaction. Just one question: any chance of seeing Lyz working with Zotero StandAlone? It would be really great for people that do not want to be bound to use Firefox.
    Cheers,

    Mattia

  • Jack Tanner

    LyZ 2.0.2 sometimes sends a signal that makes LyX crash. It has to do with changing the key of an entry, e.g.,
    1. use the cite key: author year title
    2. create a Zotero item without a year
    3. cite it in LyX via LyZ
    4. add the year to the Zotero item
    5. cite it in LyX again

    LyX shouldn’t crash, of course, but I wonder if LyZ is being as robust as it could. One thing that occurred to me is that LyZ writes a Zotero item key to the top of the .bib file, and then a separate author-year-title key to the Bibtex entry, and it also stores this info in the sqlite db. I think Bibtex is supposed to ignore fields that it doesn’t know about, so maybe LyZ could just write a Zotero key to the Bibtex entry directly, and not even have the keys table in sqlite.

  • Petr

    Thanks Jack,
    I am actually working on it right now and upon a suggestion I am changing that part a bit, so it should not happen in the next release. I will make the new release (lightly tested) probably tomorrow or during weekend.
    As for the keys in the database: I don’t want to have Zotero keys in the bibtex entry, because I want to let people decide on their one cite keys. I am keeping track of the keys to alert users that they need to run „Update Bibtex“ when their cite keys changed.
    But you rightly point out that Lyz is not robust in this respect.

  • Jack Tanner

    Petr, thanks for thinking about this. I think you missed my point a bit, though. I also like Bibtex keys to be nice, like author year title, but my point is that the Zotero key could go in a field other than the cite key.

    @book{milne1296winniethepooh,
    author = {Alan Alexander Milne},
    ..
    zotero = {0_2A2DPD9P}
    }

  • Petr

    Ah, OK. You are right that it could be written in the bibtex entry. I thought about this at the beginning, but it seemed to take quite a while to process that. Now I don’t need to look at the bibtex entries at all, just read the zotero keys from the first line of bibtex file. I don’t remember exactly, but when I was testing with large bibtex files, it seemed to take a lot of time to and freeze FF for too long… this seemed like a quick a easy solution. But tell me if you think I am missing something, that’s certainly quite possible :)

  • Jack Tanner

    Ah, so are the zotero keys at the top of the bib file written in the same order as the bibtex entries below them?

    Then how about this: write the zotero key both to the top of the bib file and to the zotero field in the bibtex entry. Whenever the entry is updated in Zotero, you can still quickly find it in the bib file using the information from the first line of the bib file. But before updating the actual bibtex entry, you can check that the zotero key matches. If it doesn’t match, then it’s the wrong entry, and the top line is screwed up. At this point LyZ would need to reindex the top line by the order of entries in the file.

    I’m still not clear – what’s the point of the keys table in sqlite?

  • Petr

    The second purpose for the keys table is to be able to have different cite keys for one zotero id. E.g. when you are collaborating with people that want to have different format of the keys. I find it more convenient (most likely faster) to read the table rather than to process text from bibtex file.
    Why would you rather have the zotero ids stored in bibtex entries?

  • Jack Tanner

    I would store the zotero ids both in bibtex entries and at the top of the bib file. If you only have the top line, you can’t be sure that, say, the third bibtex entry is the same as the third zotero id on the top line. It’s a validity check. The zotero id in the bibtex entry should be authoritative, and the top line just for speed of processing.

    In an ideal world, there should be no bib file at all. LyZ would register with LyX as the citation database. When publishing (e.g., via pdflatex), LyX would call out to LyZ with a list of citation keys, LyZ would send their full zotero entries back, and LyX would generate the bib file as a side effect.

  • Petr

    Actually, the order of the entries in the bibtex file is not important, as far as I know. Thus I can simply truncate the file and fill it with updated entries. Much simpler and definitely faster then text processing.
    As for your ideal scenario: nothing is stopping you to hack that 😉 Actually before Lyz I have looked into connecting to Zotero directly from Lyx, because I don’t like switching windows, but there are (were) some rather annoying challenges to call FF api from the outside.

  • Jack Tanner

    Oh, I didn’t realize the bib was already a throw-away thing. You’re right, truncation is the way to go. But if my FF profile goes awa… The Zotero db will get populated by syncing to my Z account. But if I now run Update Bibtex, I’m screwed – the keys table was empty in the new LyZ install, and you just truncated my bib file.

    You’re right, it’d be nice to hack on that ideal scenario… some day :)

  • Petr

    There only one cure for this: BACKUP^2. Eg. I am syncing my important stuff to dropbox (versioned with mercurial) and sugarsync (their 1 version + my mercurial versioning) + evening external hdd (10 versions + mercurial). Now I feel quite safe 😉

  • Jack Tanner

    You’re right, but my point is that I’d never realized that the FF profile contained this information. Ideally, it’d be stored together with the LyX document / bib file.

    A workaround would be to check a bib file against a Zotero database to see if the cite keys match.

  • Jack Tanner

    I just ran an Update Bibtex that resulted in updating a bunch of entries. The list of updates in a pop-up window was so long that the window didn’t fit on my screen.

  • Petr

    Good point, I will remove that.

  • greg

    hi, does the new, forthcoming version of LyZ works with zotero as a tab? That would be great!

  • Chris

    Hi Petr!
    just discovered all your updates, thumbs up!

    I read above it is possible to unintentionally truncate/cleare the .bib file, maybe lyz could keep a couple of old versions of the .bib file aroung? (e.g. .bib-[1-5].bak) And refuse to write out empty files?

    Where you able to fix the cite keys in utf8 .bib files yet?:
    AUTHORfunctionendsithtringreturnthis.substrthis.length-endsithtring.lengthendsithtring;YEARtitle
    (Is that string „functionendsit…;“ between the AUTHOR and YEAR a thing of the past?)

    • Petr

      Hi Chris,
      good idea about several versions of backup files.
      I’ll think about the unintentional truncation a bit more. I didn’t see it as an issue, because I am a bit overcautious with regards to my creations and I regularly backup all my backups before I do something dangerous like „Update bibtex“ 😉
      Ad the utf8 keys: please give it a try and let me know if you still see some unexpected results. I kind of forgot what was that about… I tried it few times on mixture of Chinese and accented characters and it seemed to be working fine.
      Thanks

  • Chris

    Hi Petr,
    my lyx 2.0 just finished compiling and everything works fine with it. UTF8 gives nice umlauts, and the cite keys are clean.

    (There wasn’t even a hickup with updating the .bib, did you add special support for lyx documents under version control (rcs)?)

    Thank you, perfect!
    Chris

  • Petr

    Lets hope it will stay that way 😉

  • Russell J. Wilson

    The biggest problem I can see right off is that it is only compatible with Z 2.0, not the current 2.1.7

    or ahould that be 2.x?

  • Christoph

    hi petr, i tried your plugin and it seems very useful, so thank you!

    however, the bibtex keys that are generated are strange and not very useful. in the settings it says „author year title“.

    so for the book „an introduction to raytracing“ by andrew s. glassner from 1989 i would expect something like „glassner1989anintroduction“ … but i get „s.1989anintroduction“.

    can you give me a hint on how to fix this?

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