BibNotes Formatter: New Plugin to Export and Format Annotations from Zotero into Obsidian

[TomcaT]

Wow I really love your progress! This plugin streamlines the Zotero native reader workflow so much already! Thank you!

I have got everything up and running except the images. In the notes I generated with bibnotes only comments to the images get displayed. Other things like text highlights and comments do work properly. I’m currently on Zotero 5.0.97-beta.63, bibnotes 9.02 on Win10.

Can the issue be in the fact that I have Zotero’s ‘data directory location’ set different than the default C:\Users… ? so that plugin can not find the image file?

This is what exported annotations in Zotero and generated file in Obsidian looks like :

Image without the comment does get only ‘double space’ as it is set in bibnotes settings. The image is also missing the page link, but that could be because of the issue with the image file.

[DummyME]

I think we have the same issue and its something related to Linux since it has been working for other people.

@stpag I had raised the issue, but please note that there might be something to do with linux. Some permission stuff, although obsidian does have all the permissions!

[stpag]

Yes, that is almost certainly the issue. Currently the plugin extracts the path of the Zotero data directory from the json file. The image import function will not work if the pdfs are exported in a different directory than the Zotero data directory. I have a couple of fixes in mind: 1) searching for the data directory in the default folder, and 2) adding a field in the setting where you can specify the path of the data directory.
Would you mind opening an issue on GitHub and sending a json file you are using extracting one source with pictures? this will help in coming up with an alternative.

[stpag]

Anna’s problem was fixed by the latest version I released this morning. Would you mind checking the version 0.9.03 ?

[DummyME]

I did.
Doesn’t work.

[Kabo]

fabulous plugin - pretty much all my dreams come true! I really can’t thank you enough!

I have a couple of questions. I thought I could append to each highlight the citation (author, year, page number) and a link to the Zotero file highlight (via setting “format annotations → in-text citations → end of highlight citation format” seems to only append the information (author, year, page number)), as well as add a custom text (eg #quote). But it doesn’t seem to work as expected.

only the very last extracted highlight gets the tag and the link to Zotero, but no page number in the expected format (Auhor, year, p.nr.)

The second picture is closer to what I expected, except that the tag and the link only seem to be appended to the last extract. Is this how it is meant to work? It would be great if all blocks would work like the last one

[Kabo]

and the other question I had (might be a feature request?) is, if it would be possible in the Metadata section to have a fully formatted reference? such as this:

Reference: Sheehan, Rebecca A. “Facebooking the Present: The Biopic and Cultural Instantaneity.” In The Biopic in Contemporary Film Culture, edited by Tom Brown and Belén Vidal, 35-51. London, UK: Taylor & Francis Group, 2013.

Ideally one could somewhere choose the output style (here it is Chicago 17th). Would that be possible? I often need to quickly grab the reference for lecture notes or some such, and it would be great not to have to go back to Zotero for this

[stpag]

This is odd. I would like to understand what is causing the issue. I have opened an issue on the GitHub repo of the plugin to troubleshoot that: Problem with exporting correct in-text citation · Issue #26 · stefanopagliari/bibnotes · GitHub
To help me, could I please ask you to:

• install version 0.9.04 (or later)
• at the bottom of the settings, activate the debugging mode
• export a single reference where the problem is occurring. You will be prompted to create a txt file
  share the file with me on that GitHub page (assuming there is no confidential/private information in the note and the settings), or through some other channel (email, discord, etc…)

[stpag]

Yes, creating a fully formatted reference that can be imported into the file is possible since the metadata information is already there. I have added it to my todo list but adding some “insert citation” command I will first clean up the remaining problems/bugs in exporting notes.

[Oblique]

Can we support you to register this as a proper community plug-in?

[TomcaT]

I created a brief GitHub issue. Thank you for looking into it.

But I keep thinking if:

1. My setup is correct. I have the Zotero data directory and Zotero-attachments set to my google drive. Idea was to have everything synchronized and on the platform which is storage unlimited for me.

2. Data directory location shouldn’t be defined in the library JSON file. Meaning, bringing this issue to the Zotero dev team.

[stpag]

Thank you for opening the issue on Github. I will look into it. I had written the workflow so that the script would specifically look for the images in the Zotero/storage/ subfolders. I need to change that to recognise and accommodate a different file path.

[DummyME]

@stpag I have raised an issue within a recently closed issue. I am not sure if you noticed it, so I am putting up a link here as well. It is related to images not being displayed (and copied into vault).

Unable to create literature note in Linux

Thanks!!

[stpag]

Thank you. I plan to submit this as a proper community plugin once I get to a stable version where the extraction of metadata/annotations/images work for most people across Mac/Windows/Linux.

[janisc]

Thanks very much for this excellent plugin. I have been using it for the last two days and am in love with it. It makes the zotero+obsidian workflow as natural as one would expect.

BTW, do you think it would be more convenient to add a ‘create/update literature note’ button to the sidebar?

[tim_hilde]

For some reason I am not able to import my annotations extracted with zotfile with you plugin. I both turned “extensions.zotfile.pdfExtraction.colorAnnotations” to true as well as defaulted “extensions.zotfile.pdfExtraction.colorCategories”. Neither adding “{{PDFNotes}}” nor “{{UserNotes}}” helps.

Do you have an idea what might be going on here?

[stpag]

A couple of quick things to check.

1. if so, when you click on the extracted note within Zotero, do you see the colour at the beginning of the note e.g. “(Yellow) Text Note”?
2. Is zotfile exporting the annotations grouped by colour? if this option is selected, the plugin is not currently able to extract the colour, although it may be something I can work with in the future

If you can see the name colour at the beginning of your notes within Zotero, could you please activate debug mode in the settings, save the file with the console logs, and open an issue on GitHub?

[stpag]

you could create a button in the sidebar for that command using this plugin: GitHub - phibr0/obsidian-customizable-sidebar: This Plugin allows you to add every Command to Obsidian's Sidebar Ribbon and add Custom Icons.
What probably would be more helpful is a different modal that recognise and update the open note (without re-opening the selector)

[tim_hilde]

Thank you for your fast reply! Indeed I am not seeing the color name in front of the highlight. Instead it looks like this:

[stpag]

Ok, it looks like Zotfile works differently on your machine than on mine (maybe a different version?). Could you maybe open an issue on GitHub and share the better bibtex json file from one reference? It looks like the highlight colour is retained (without the initial description) so maybe there is a trace of the highlight colour in the json file I can use