[Feature Request] Export the mixture of manual edits and extracted annotations

[XuShenLZ]

There was a very thorough discussion in #97 that the current export functionality only supports pure manual edits or pure extracted annotations in the same note:

Currently the code parses each note associated with an entry and it establishes if it is imported from the Zotero reader, Zotfile, or typed manually from the user. It is not possible to make this distinction line by line, at least not without a fundamental rewriting of the plugin.

I will write in the documentation that while it is possible to add user-generated notes, the plugin is not able to recognise when these are mixed with those extracted from Zotero.

One possible solution to import your data would be to create an empty note and paste into it the content of the mixed one. I don't know if that would work, but it could be worth a try

Originally posted by @stefanopagliari in https://github.com/stefanopagliari/bibnotes/issues/97#issuecomment-1162378894

There are definitely a lot of difficulties to rewrite the parser but I feel this would be a very helpful feature to consider in the future. It is now a super powerful feature of Zotero notes to let people write down their own ideas while directly dragging corresponding annotations from the PDF. However, this type of note is not supported by bibnotes now.

Personally I feel that it loses a lot of meaning to separate my personal ideas and extracted annotations into two Zotero notes and then two Obsidian sections ("Comments" and "Extracted Annotations"). It then becomes really hard to relate each extracted sentence back to my personal comments or summary.

Therefore I still would like to raise this feature request here to call for a future update of bibnotes that supports the mixture of two types in the same note.

Thanks again for your amazing work!

[FeralFlora]

I agree completely with the need to have manual comments and highlights exported together in their original context. This makes for a much more streamlined workflow.

[stefanopagliari]

@XuShenLZ and @MSBack, thank you. I will explore this and whether it is possible to move the determination of whether a piece of text is exported from the pdf or inputted manually from the note level to the sentence level

[FeralFlora]

@stefanopagliari Thanks for the quick response. I would like to specify that when I said "manual comments and highlights exported together in their original context", I was thinking of how any annotation comment added to a highlight in the native Zotero PDF reader would stay associated with that highlight, also when grouping by color using the color placeholders. This does not work for me currently with the following Zotero highlight template:

<p><blockquote>{{highlight quotes='true'}} {{citation}}{{if tags}}</br>#{{tags join=' #'}}{{endif}}</blockquote></p>{{if comment}}<p>{{comment}}</p>{{endif}}

Is this due to the line-break between the highlight and the comment?

[stefanopagliari]

@MSBack Could you provide an example of the expected behaviour and what you are getting instead?

[FeralFlora]

@MSBack Could you provide an example of the expected behaviour and what you are getting instead?

I believe my use-case is slightly different than that of @XuShenLZ, since I am mostly concerned with the comments/notes made in direct association with highlights.

I expected highlights and associated comments to be exported together when using color placeholders. So that {{Yellow}}, for example, would list any yellow highlights made within Zotero, and any comments associated with those.

In reality, only the highlights were being exported, and the comments did not show up in Obsidian.

When I tried the resetting to the default highlight template within the Zotero config editor, it works as expected.

So the issue for me seems to be that Bibnotes formatter expects comments of this kind to follow directly after the highlight, within the same paragraph. In my custom highlight template, comments were in a separate paragraph.

As such, there is the limitation that highlights and associated comments must currently be in the same paragraph.

[stefanopagliari]

@MSBack The processing of highlights and associated comments is done assuming that the standard Zotero template is used.

If you add a line break between the comments and the highlight in the template, these will be exported as two different elements and it will not be possible to recognition se that the comment was associated with the highlight of a given colour rather than being a standalone comment.

I would suggest that you use the default settings in Zotero and you adjust the line break between the highlight and the associated comment using the setting within BibNotes that I have added last week. You should be able to achieve the intended formatting by changing those settings. If not, please let me know how it should look like and I will try to find a solution from within Bibnotes.

[FeralFlora]

Okay, I see. Thanks for clarifying that, and thanks for the tip. Just to be clear, are you referring to the "Double spaced" toggle option? Or the "Custom text before all comments" option? In this case, what would you add? a <br>?

However, this got me thinking that standalone comments could perhaps be associated with certain colors by using certain words, tags or symbols as triggers for transformations / placement of notes - similar to how todo will transform comments into tasks, or how % will move the comment to before the highlight. For example, #yellow (or some other indicator) at the start of a comment would place it along with the rest of the yellow highlights when using the {{Yellow}} placeholder. Perhaps appended at the end after the last yellow highlight, or perhaps preferably after the nearest preceding yellow highlight?

[stefanopagliari]

@MSBack I'm referring to this setting: