Zotero 6.0 annotation extraction problem

Lizackery

Hi, when exporting highlighting to markdown format, can Zotero distinguish what is highlighted or underlined like Zotfile?


I would like to know that if the exported text could be hierarchical. For example in Zotfile, the underlined content is exported as a markdown tertiary heading (###) by default.

In general, I think it would be nice to have three levels of separation. For example, underlined markdown exports as a first level heading (#), wavy lines as a second level (##), and highlighting as the body (###).

I know I'm probably being vague, and the fact that I'm not a native English speaker doesn't help at all.

Thank you very much.

dstillman

This is with the hidden .pdfExtraction.UnderlineHtmlTagStart option in ZotFile?

Zotero's own PDF reader doesn't support underline annotations, and Zotero doesn't currently do anything with underlined annotations from external readers.

Could you say a bit more about the use case here?

Lizackery

Yes, it's in the hidden options of zotfile.
When reading a PDF, the reader marks different content, which itself has different layers.
One case is to distinguish between major and minor headings and body text, for example I would underline the headings and the body text is highlighted.

The other is to distinguish between different content, such as concepts, definitions with underlining, the other with highlighting.

It would be much less difficult for me to follow up if I could distinguish between these contents when exporting the highlighting, like zotfile does. Thanks.

dstillman

Sorry, I was actually wrong about this — we do import underline annotations, but we just import them as highlights. We're not currently planning to treat them any differently, nor are we planning to support creating underline annotations in Zotero.

You can of course just use a different color for those annotations and differentiate them that way.

Lizackery

Thanks for your reply!
Then how can I display different colors in the exported text? There doesn't seem to be any information about colors in the markdown file, and I can't find it in the export settings.

dstillman

Sorry, I forgot this was about the Markdown output, not just the note in Zotero. Colors aren't currently included in Markdown output, but there's a discussion here: https://forums.zotero.org/discussion/94335/markdown-export-colors-and-tags-in-output

Lizackery

Thanks!
The problem I am having is that I have a lot of PDFs with underlined markup and I need to deal with them. I have to open the zotero database with a version that supports the full functionality of zotfile. Can you please tell me where I can download a beta that works?
I will consider changing to a different color later, but for now I need to deal with this issue, thank you very much.

Lizackery

Zotero-5.0.97-beta.38 f27432347 is not working...
No error is reported when opening the database with it, but only the folder directory is visible, and no literature information can be displayed.

dstillman

You can install ZotFile 5.0.16 from GitHub, extract any last annotations, and then upgrade again to ZotFile 5.1.0. [Edit: See my next comment as well.]

Lizackery

Thanks for your reply!
I did, but:
The plugin "ZotFile" could not be installed. It may not be compatible with this version of Zotero.
(zotero 6.0)

dstillman

Actually, if you've updated to the latest Zotero beta you'll also need the last version before we bumped the version number:

Mac Windows Linux

But this is an unfinished beta and you obviously won't want to stay on this version. The older ZotFile build also contains a major data loss bug when using the Zotero PDF reader.

Lizackery

Thank you so much! It works!

dstillman

I may need some time to deal with these PDFs. Would like to ask if I need to use this version of Zotero beta for a while, will there be any problems?

We can't really provide any guarantees about old beta versions.

Is there anything easy Zotero could do when importing underline annotations that would make things tolerable for you in the meantime? E.g., an optional tag that could be added to such annotations? (Annotation tags aren't currently added to notes, but they will be soon.)

Lizackery

Oh, I realize I may not have expressed myself clearly. I'm sorry about that.
It's not that I need the exported text to show the underline as well. If it （the underlined text in PDF ) can just be marked as a markdown heading at some level (e.g. automatically with a '##' symbol).The form does not need to be consistent with the PDF, as long as different markup can be distinguished from each other, so that the user can immediately know the nature of the markup.

I guess most people need this effect: in the export at the same time, but also completed the initial highlighting of the work of finishing . That is, when users read PDF, they encounter different types of content that they want to mark up (large and small headings and body text, or concepts, examples, methods), will be marked up in different ways, and the exported text is also distinguished, regardless of whether the form is consistent with the PDF.
Thanks for your asking!

dstillman

We haven't seen any evidence that underlining, separate from highlighting in multiple colors, is a thing most people care about. The Zotero PDF reader has been out for almost a year and we've gotten very few requests for it.

But we'll see if there's anything we can do for existing users of underline annotations in external tools.

Lizackery

I can see your concern, but here is some evidence (second half of the article and comments):

https://forum.obsidian.md/t/zotero-zotfile-mdnotes-obsidian-dataview-workflow/15536

Thanks! Looking forward to the new version of Zotero!

dstillman

We've added note templates that can be used to set a particular highlight color as a heading. There's an example in the docs.

Lizackery

Thanks!!! I will definitely try it!