How to customize pdf Annotation note formatting?

I see the Zotfile "extract annotations" action is now replaced with a native action. In Zotfile I could customize how the annotations were formatted in the note using the config editor. Can the same sort of customization be done with the new native note-making method?

Specifically, I'd like to precede the highlighted text with `> ` so that it is formatted as a block quote and to not surround it with quotation marks. This option is important for using my notes with a 3rd party program. I'd also like to have the note title default to plain text rather than a heading format, and to have a line break between the highlighted text and my comments.

I see a related question about customizing the note title was posed some months ago but was never answered, and I'm interested in doing this also: https://forums.zotero.org/discussion/92243/how-to-change-default-naming-format-of-annotation-notes/p1

Thanks!
  • Options to customize the format of both annotations added in notes and the exported Markdown are planned.
  • So, to make sure I understand, Zotero's native extract annotation feature does not yet have feature parity with Zotfile's extract annotation feature (in this case, it does not yet allow custom formatting). Yet you deprecated Zotfile's functionality at this time rather than waiting until it did have full feature parity. Based on comments in other threads, it seems that you did this to avoid user confusion, even though the Zotfile functionality was working fine from a technical perspective.

    This decision has not only disrupted my workflow, but actually will create a huge amount of pointless busy-work for me because I will now have to manually edit every note I move from Zotero into my 3rd party program.

    Question 1: is there any chance that you would consider adding back the option to use Zotfile's extract annotations feature until the native extract annotation feature actually has full feature parity? Your concern about user confusion is best addressed with additional documentation, not by removing working functionality that users rely on. I can help write the documentation if needed. I really hope that you are open to reconsidering this deprecation and that pride or inability to admit possible errors in judgment do not prevent you from even considering this option. We all make mistakes and in this case I am sure you didn't realize that this deprecation might be a very big deal for some users.

    Question 2: if you will not consider reactiving the Zotfile functionality, then how can I use a previous version of Zotero that allows that Zotfile functionality? I am using the Zotero beta and have been for many months, and my database is upgraded. Will installing the last stable version of Zotero work with my current database?

    Question 3: if you will not add back the option to use Zotfile, and I cannot use my upgraded database with an older version that does work with Zotfile, then I have been burdened with (honestly) hours of addition work based on this change, which was not mentioned in the changelog. Did you consider warning users about this lost functionality before having them upgrade? Or did you just assume that it was not a big deal? Or did you ask users about it on the forums and I just didn't see that thread?

    Question 4: Will you offer any timetable for adding customization of annotations in notes and exported Markdown? I assume based on previous threads on the forum that the Zotero devs will not offer any timeline for adding the formatting options that users previously relied on and which worked well with no technical problems, and I am also assuming (since you removed this functionality) that it is not a feature that is a personal priority for the devs, so adding these options back might take weeks, months, or years. Let me know if I am wrong about this.

    I'd really appreciate answers to all four questions.
  • Based on comments in other threads, it seems that you did this to avoid user confusion, even though the Zotfile functionality was working fine from a technical perspective.
    It was absolutely not working fine. It didn't extract Zotero-created annotations, which was causing a massive amount of confusion that wasn't going to be fixed by "documentation", and it contained a major data-loss bug where it would delete Zotero-created annotations if you used it on an attachment. There's no way we could launch Zotero 6 while those things were true, and we also didn't want to disable it entirely in Zotero 6, so we worked with the ZotFile developer to make these changes.

    Your tone here is not appropriate. No one forced you to use the beta, and if a possible temporary disruption in your workflow is a problem, you shouldn't use beta software.

    There's nothing stopping you from continuing to use Zotero 5, where ZotFile still works exactly the same as before. But if you're using the Zotero 6 beta — the major feature of which is a new PDF reader and note editor with deeply integrated annotation functionality — then annotation support is provided by Zotero.

    If your data is all online, you can downgrade by closing Zotero, reinstalling Zotero 5, moving zotero.sqlite from your Zotero data directory to a backup folder, and syncing Zotero 5 to pull down data from your online library.

    Beyond that, see my comment here. ZotFile could have been updated to extend Zotero 6's built-in annotation functionality, but the developer no longer has time to maintain it, and the only reason it works at all is that we've contributed patches to maintain it. Zotero 6 already supports the functionality that the vast majority of ZotFile users were using. We've implemented various other features to replace more advanced ZotFile/mdnotes workflows (e.g., Markdown export), and we intend to support more of ZotFile's advanced, hidden annotation features soon.
  • > > There's nothing stopping you from continuing to use Zotero 5, where ZotFile still works exactly the same as before. If your data is all online, you can downgrade by closing Zotero, reinstalling Zotero 5, moving zotero.sqlite from your Zotero data directory to a backup folder, and syncing Zotero 5 to pull down data from your online library.

    Given that I have over 50GB of files both locally and in Zotero online storage, is there a way to do this without re-downloading all of those files, while retaining database links to those documents?

    And, will doing this break citation links in my existing writings that are linked to my Zotero database?
  • is there a way to do this without re-downloading all of those files, while retaining database links to those documents?
    Yes, by doing exactly what I said.

    But I'd encourage you to just wait a short while if possible. Your use case would be addressed by the most basic template functionality, and we'll likely have something for that soon.
  • Thanks. Can you explain why you said my tone was inappropriate? I didn't attribute bad motive to anyone. Is the idea that since no one forced me to use the beta, I shouldn't question any decisions made about the beta development, or request any changes to beta functionality, or want to be warned about removal of features that have existed unchanged for years? I took care to word my post politely and I honestly don't see why you were offended.
  • Let's not waste time. You were obviously annoyed, and you accused us of making a thoughtless mistake without concern for users, when we've gone to significant lengths over the years to ensure that an unmaintained third-party plugin remains available to users, works with current features, and doesn't start wiping out data after they upgrade. If we hadn't submitted a patch, ZotFile would have disappeared completely yesterday when we bumped the Zotero version number.

    And yes, unless you're studying GitHub commit logs, you absolutely should not expect to be warned about changes in the beta. You shouldn't use the beta if that's a requirement.
  • What on earth are you talking about? I questioned one specific decision you made about Zotfile, and you interpreted that as an accusation that you don't care about Zotfile at all or users in general? I guess that's why you started talking about all of the hard work you have done to support Zotfile, which is totally irrelevant to the specific issue I was asking about. And I suppose that you thought I was somehow questioning your decisionmaking or motivations in general, which would be inappropriate, if it were true, but I did nothing of the sort.

    I suggested that maybe you didn't fully realize the impact of this particular decision on others and should reconsider it, and you got offended. Does the fact that you have done work to maintain Zotfile in the past somehow mean that every plugin decision you make is self-evidently correct and that questioning it is "not appropriate"?

    You also never actually said whether you realized the impact of this decision or not. Did you not consider that this could have large effects on users, or did you realize that and not care enough to let people know? Instead of wagging your finger at me for daring to ask this question, how about responding to a user like me who has been negatively impacted by saying something like, "We didn't think that removal of custom formatting would be an issue for most users, and sorry that removing it is causing you problems. We had good reasons for doing it, but we probably should have included a warning about this in the changelog."
  • I have been burdened with (honestly) hours of addition work based on this change, which was not mentioned in the changelog
    will create a huge amount of pointless busy-work for me
    I really hope that […] pride or inability to admit possible errors in judgment
    We all make mistakes
    Did you consider warning users about this lost functionality before having them upgrade? Or did you just assume that it was not a big deal?
    If you can't acknowledge that your post had a tone of condescension, annoyance, and entitlement, and that that's not appropriate here, particularly regarding beta software you made a decision to use, I'm not going to bother engaging with you.
    Did you not consider that this could have large effects on users
    It does not have a large impact on users. You are mistaking your own use, as an advanced user of a feature configurable solely through a hidden preference in the Config Editor in the Advanced pane of the Zotero preferences, with the way the vast majority of people use Zotero and ZotFile. Same with your previous comments about our decision to build a PDF reader at all, which are just so completely ignorant of constant feedback over many years and the overwhelmingly positive feedback to the beta as to be absurd.

    Feedback is fine — that's what beta software is for, and that's what these forums are for. But please bear in mind when posting here that your experience is not universal, and maybe there were good reasons for changes you don't like.
    We had good reasons for doing it, but we probably should have included a warning about this in the changelog.
    You keep referring to a "changelog". There is no changelog. The only relevant changelog would be the ZotFile release tag on GitHub, which we have nothing to do with. And the fact that you've repeatedly mentioned a changelog that you didn't actually read — since it doesn't exist — perhaps suggests you haven't engaged entirely in good faith here.

    Anyway, there's really no need to keep arguing about this. You were using a hidden, advanced feature in an unmaintained third-party plugin, and we're going to do what we can to support it in Zotero soon.
This discussion has been closed.