#166

thanks , i know that but i am looking for a way to manage my files for a while now and I can’t find anything free and reliable remotely as good as zotero. do you know anything to complement zotero?
p.s. for movies I actually thinking about using obsidian and everything (search app) to do that

#167

I don’t, sadly! Might be worth starting a separate thread or asking in the Discord server!

1 Like
#169

@argentum, is it possible to replace the color´s name for the category that color represents? For instance, if all my blue highlights are concept definitions, I´d like to have “(concept)” showing up in the beginning of the quote, instead of “(Blue)”. I´ve tried changing extensions.zotfile.pdfExtraction.colorCategories, but the (Blue) label keeps showing up instead of (Concept).

#170

That’s done in the field extensions.zotfile.pdfExtraction.formatAnnotationHighlight, which defines how Zotfile outputs highlighted text when extracting highlights. In particular, you need to use the %(color_category) variable wherever you want your category name to show up. There’s some good examples in this workflow. As another example, I’ve set up the Admonitions plugin with custom admonitions for different highlight types, and then use this in the formatAnnotationHighlight field to produce admonition blocks matching what I’ve set up in the plugin:
<p>```ad-%(color_category)<br />title:&nbsp;<br />%(content) (%(cite))<br />```</p>

3 Likes
#171

Thank you very much for this great summary. Can you please elaborate more on bullet point 7. You are mentioning the “inbuilt printer of obsidian” but I haven’t found this feature yet. So far I use Marked2 with pandoc as pre-processor.

Regards,
Christian

#172

Is there a way to cretae a “Quick Copy” format in Zotero to export (in Obsidian, of course) both reference and item link? The result should look like that:

[Badiou, Alain. *Ethik: Versuch über das Bewusstsein des Bösen*. Translated by Jürgen Brankel. Wien Berlin: Verlag Turia + Kant, 2015.](zotero://select/library/items/INX5ZN8A)

In this way, you have a clickable reference, which would be for my purposes simply AMAZING.

2 Likes
#173

Hey all,
I was wondering if there is a way to skip the need to save the annotations to a dedicated file.
In my usual process I highlight/comment the PDF, then extract annotations, then export the same annotations to a .md file which I then have to open in order to copy and paste its contents to Obsidian (and then I have to manually delete the file).
If there was a way to send the annotations to the clipboard, this would save me a lot of time, given that this process is repeated for dozens of reference notes.
Maybe there’s a setting I’m not aware of somewhere…?
Thanks :slight_smile:

#174

@Sans why wouldn’t you save the file directly to your vault? Maybe I’m missing a bit of context

#175

You could also save the .md file directly in a folder in your vault (this is what I do)

#176

@y.h I didn’t think about it. This is possibly the solution I was looking for!

@argentum I am just stupid :stuck_out_tongue:

#177

In case anyone was looking for an (author, date) version of the plugin:

{
	"translatorID":"8dbf9b92-f796-4153-8f2e-ac6c157500dc",
	"translatorType":2,
	"label":"Markdown Item URI",
	"creator":"Silent",
	"target":"markdown",
	"minVersion":"2.0",
	"maxVersion":"",
	"priority":200,
	"inRepository":false,
	"lastUpdated":"2020-11-30"
	}
	 
	
	function doExport() {
		var item;
		while(item = Zotero.nextItem()) {
			var date = Zotero.Utilities.strToDate(item.date).year;

			var year = date && !isNaN(date) ? " " + date : (typeof item.date == 'undefined'?  "" : " " + item.date);
			var library_id = item.libraryID ? item.libraryID : "";
			var author_lastname = getValidAuthor(item);
			var title = item.title ? "*" + item.title + "*" : "";
			var key = item.key;
	
			Zotero.write(`[(${author_lastname},${year})](zotero://select/items/${library_id}_${key})`);
		}
	}

	function getValidAuthor(item){
		if(item.creators && item.creators[0] && item.creators[0].lastName){
			return item.creators[0].lastName + "";
		}else{
			return "";
		}

	}
1 Like
#178

Hi @argentum , this figure is exactly what I want! Particularly, I’m interested in the block IDs, I mean adams1979-78f7565. Do they come from zotfile/mdnotes? Are they fixed after each extraction from pdf to md files? Could you point me to a reference where I find instructions on setting up zotfile for these IDs?

#179

As @argentum commented on discord, this is a feature of mdnotes and it’s described at https://argentinaos.com/zotero-mdnotes/docs/next/advanced/hidden-prefs:

  • Setting extensions.mdnotes.obsidian.blocks to true will append a block ID to all non-header text blocks of exported Zotero notes, i.e. to each highlight and annotation extracted by Zotfile.
1 Like
Zotero -> zotfile -> mdnotes -> obsidian -> dataview Workflow
#180

In the latest beta version of Zotero and the new pdf-reader, you can export the annotations as md-files with working zotero-links. Just a head-up.

2 Likes
#181

@Kullenej Great news! Thanks for letting us know. The function is excellent and works well – it’s a little tucked away but in the expected place. [Select Annotation ] > Right Click> Export Item >Select Markdown option.

#182

Hi @Marc-A, could you tell me which version of zotero you use?

I just re-installed the latest zotero beta (5.0.97-beta.57+07df7d0de for Linux64) from dev builds. When I right-click on an annotation, unfortunately, it doesn’t display a markdown option. :frowning_face:

Screenshot_2021-12-18_10-28-00
Screenshot_2021-12-18_10-28-00699×1085 42.4 KB

#183

@janisc Using 5.0.97-beta58 on macOS. It looks like the function you’re missing was only added a few days ago. I’m sure it will be there in one of the next Linux updates.

Page 0001
Page 00011920×943 90.2 KB

Page 0001
Page 00011009×289 175 KB

1 Like
#184

Just in case someone has missed it:
With the new “Markdown export of notes” functionality of Zotero beta-pdf reader, it is not necessary to import your notes through an MD-file… You can also drag-and-drop them into a note in Obsidian (pressing Shift key during drag-and-drop will keep links back to Zotero items and individual annotations).

6 Likes
#185

can someone please explain it to me how this new system works step by step? I was using the old zotero zotfile mdnotes a while ago and then new pdf reader came and suddenly nothing was working and I waited for this workflow get fixed.
last i tried (which was like one or two weeks ago i think) i could not extract highlights added with new native zotero pdf reader via zotfile

#186

The Zotero beta reader does not store annotations in the PDF so Zotfile can’t see the annotations. You can force Zotero to write the annotations to the PDF (with a PDF open in the Zotero viewer, select File->Store annotations in file), at which point you can no longer edit them in Zotero. However, other changes to the Zotero beta have occasionally broken mdnotes so even with annotations stored in the PDF you may have to find other workarounds.

I believe the author of mdnotes has stated they’ll likely update once the new Zotero is out of beta. Zotfile’s maintainer has said they don’t really have time to work on it, and given that some of the main features of Zotfile are basically superseded by the new Zotero, I wouldn’t bet my workflow on Zotfile for the long-term.

The latest version of the Zotero beta does extract annotations and can then export them to Markdown. It’s pretty cumbersome (you have to select “Add Item Note from Annotations” from the Item Notes sidebar and then right-click export the note from your library), but it’s something.

2 Likes