Writing with Zotero and Obsidian
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- Опубліковано 6 лип 2024
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Timestamps:
0:00 Introduction
1:18 Zotero and Obsidian Setup
4:06 Example explanation
About:
Danny Hatcher is a researcher, filmmaker and journalist. He currently is based in Eastbourne, UK, reporting on interesting trends and stories domestically and around the globe. Danny's storytelling blends rigorous research with videography to create content that explains complex issues in relatable ways. He holds a BSc in Sports Coaching from Brighton University and an MSc in Strength and Conditioning from Brighton University.
#dannyhatcher
For anyone having the error "error: Received empty bibliography from Zotero. Ensure Zotero's quick copy settings are set and the selected citation style is installed":
settings -> Zotero Integration
In Import Formats / Bibliography Style, select a style which is installed in Zotero.
Hope this helps!
Thankyou 😁
I have this error and have set quick copy settings and citation style is the same - yet the I still get this error.
Very helpfull, thanks a alot.
Thank you very much! You opened up a whole new note taking workflow for me with PDF's. Finally a proper way to deal with PDF highlights in combination with Obsidian.
Danny thank you. You are so good at this!
really good video. useful, great tempo, no bullshit. great work!
Thank you! I like to avoid as much BS as I can 😁
I'm doing my masters degree on neurobiology, and you just helped me organize and structurize my knowledge and feel more confident and less stressed. Thank you very much my professional angel. Greetings from Mexico!!🥲😌☺😚
Happy to help
Hi Danny, I became your Patreon subscriber because of this video. Thank you for the tutorial and templates.
Always happy to help 😁
Thank you so much for the video, this is so good. Please make more Obsidian/zotero videos.
😊🧡
Thank you! I had been struggling to figure out what I was doing wrong and this video was so helpful. Subscribing. :)
Glad I could help!
For anyone struggling with the annotations not being imported at all: What fixed it for me was going into the Zotero settings -> Export and setting the Note Format to HTML (not "Markdown + Rich Rext"). I also checked the "Rich Text/HTML: Include Zotero Links" checkbox below. After restarting Zotero the annotation import with Bryan's template worked for me.
The "Zotero Integration: Data explorer" command helped me a lot in the process, it shows the available variables your template can use, you can also adjust the template file and the data explorer will apply the changes in real time
Thanks for this!
There are lots of little things that I don't encounter that others fix so I am glad you helped people out ehre 😁
Thanks a lot to both of you, it works like a charm!
Am having the same issue. Nothing is being imported from zotero at all. Tried your suggestions but no luck... very odd
@@abejoseph7699 the same to me. The notations won‘t appear
Hi Danny! Thanks for the super duper helpful video! Do you also use the pandoc export to docx feature just like you added in the CItations plugin video?
I don't use the plugin. I just use pandoc from the terminal 😁
very helpful, thanks!
The update function is a game changer! So much anxiety now gone❤😅
😁
This video was enough for me to subscribe your channel
That is great to hear 😁
@@DannyHatcherTech Actually, before that, I used 3 different plugins in zotero and obsidian (mdnotes, zotfile, and citation) but now I just use "zotero integratin". This work flow is more convenient. Thank you.
Thank you !
This is amazing!
Glad I could help 😁
What a timing, was precisely at this moment trying to figure out how to use Zotero Integration plugin :p
Awesome! 😁
Same! :D a big thanks to Danny!
Thank you so much for this! Really amazing tool. I'm falling hard for it. I have a question for you.
Is there a way to make the tags and authors that your template pulls from zotero their own individual #hashtages and MDnotes respectively? I couldn't even do this manually after the fact... I think because of the --- things blocking off the first section.
I would imagine it is possible as Obsidian is so flexible.
As I don't alter much from a basic import I can help unfortunately.
If you go to the Obsidian discord and ask in the Academia channel, people there should be able to help.
Thank you so much, great video! Is there a plug-in to enable feedback to Zotero notes? What I usually do is to quickly write notes to the paper inside of Zotero. To write a proper text, I would use Obsidian. It then would be nice to update my "quick&ugly" Zotero notes again with the new beautiful version, written in obsidian.
I keep the imported note in Obsidian the same from import so that if I do adjust my Zotero notes it won't interfere with the Obsidian file.
The imported file in Obsidian is treated as a source file for research projects.
Hope that helps.
Thanks!
I love this video.
Thank you 😊
Thank You
Thank you for the great video! Do you know, if it is possible to set the file path to the current folder im in when I execute the zotero integration command? I would like to have the note and image folder create there instead of the root location.
That might be in the plugin settings but I have never tried. Sorry.
Hi, Awsome video, I was wondering if there is a way to add something to the code that makes highlights and notes that you have taken on the highlights to be easily distinguished once they have been imported into obsidian? Love your videos!
You can customize the template in pretty much any way you want.
It would require some tinkering but yes it is doable.
You can treat the template file the same as your mark-down files with formating.
thanks so much for the great tutorial:) I have a question - how can I change the template so that the actual page numbers show up in obsidian, not the pdf page number? because zotero seems pretty good at spotting the actual page number of the work and I'd be glad to see them in Obsidian too. Any idea?
Thanks so much again, keep up the good work :)
I have another video about customizing the template which might help 😁
Hi this template is so great and simple! After many hours of failed template setup, this one worked quickly and great!! Thank you!
Question: How do I edit the template? For example, I would want to make the title bold, comments italicized and make the highlighted sections actually be highlighted in obsidian. And maybe add a couple of properties at the top. Is that possible?
It uses nunjunks which is a language I am not very familiar with. I just do the basics. I think the plugin github has a link to help you customize it.
Hi, I have a question about template
The indicated template in the documentation of GitHub has to be copied to make work it? ¿Doesn't need anything else?
I'm new in zotero too, but I really liked the workflow that offers.
For real, thanks to you for teaching and showing a way to solve so many questions about this.
Glad I could help 😁
Hi. Great Video!
If I have a string of tags in {{allTags}}, is it possible to separate them and then put them in [[tag_xy]] so that an entry is created or linked.
Best regards
Chris
I am not sure if you are referring to Zotero tags or Obsidian tags.
My assumption is Zotero tags in which case I am not sure as I don't import them into my vault. Sorry.
Would you mind linking directly to where this Template is in your Patreon files? It seems like a lot to traverse through what you've posted on Patreon, although I do look forward to signing up as a patron soon.
It is in the main mesaage file download. Down the bottom of the zip 😁
Hi great video as usual! Do you recommend to move to this workflow from the one you explained in your previous video "how I export my academic notes". Thanks for your work!
I have been uaing this for almost a year now. It works for me so I would say yes.
@@DannyHatcherTech Thnaks, I'll start using it right now!
@@DannyHatcherTech Thanks so much, it works perfectly, the only think I wasn't able to do is to make the paper notes be sabed in the specified folder...
Thank you again Danny - one of the best additions to my academic workflow since I stumbled upon this video a few months ago. I recently updated to a premium Zotero storage plan, and the import function struggles to pull up items that were added since I went over 300 MB. Or is it possibly related to the Zotero 7 update? Curious if others have run into this issue
Great question but one I dont have an answer for unfortunately.
@@DannyHatcherTech Turns out there was an issue with my backup process that removed some of the Better Bibtex Metadata, which made it hard for the Zotero Integration plugin to identify the files for import. It's now fixed!
Thank you for this video. I have a question: I use Zotero but I link the bibliographic records to PDF documents that are not saved in Zotero but on OneDrive. Can this approach work in my case, too?
If you have files saved in one drive or another cloud service the zoetero integration plugin wont work with them.
Bib information can be stored and used for pandoc export with manuscript writing.
It depends what workflow you are looking for.
Really useful Zotero videos you have going on. I have just started seting this up, and I got pretty confused looking at this one + you academic workflow (2022). Some doubts:
Are you still using the same pandoc setup you showed in your academic workflow (2022) video?
I see that here you are using a new template, so I assume that you no longer use the Citation plugin: Literature Note content template?
How would you add citations + pandoc export to this workflow? What things would you have to change? I see that here you automatically create the note, without having this two layer thing going on using both 'Example Note' and the actual link (Citations: Insert literature note link) to the note (using the citekey as the name of the note) . Here you just have the note with the citekey name. Is it necesarry to have the markdown citation (Citations: Insert Markdown Citation"') inserted for the pandoc export to work? Can the betterbibtex stuff
Do I have to change anything else or take something else into account to be able to export to pandoc?
Should I just copy this new template you have on this video to the Citation Literature Note content template?
Sorry for the convoluted and potential stupid questions, and for any obvious stuff which I am yet not aware of, I still have literally no idea what im doing, as is clearly apparent.
I rarely need pandoc now as I don't publish academic manuscripts.
The citation plugin is no longer my chosen plugin, it is zotero integration now.
Citations can be done either in Obsidian or with an export through pandoc. I would use [cite] in the text so citations are brought in when exporting using pandoc.
Always happy to help and answer questions - no question is to simple.
UA-cam doesn't notify me most the time so I would suggest joining the discord for further conversation if needed 😁
Great video and great template!! Very helpful!! But where can I find the name of Zotero fields and their definitions so I can include them in my template??
For example, I want to include the type of the item (e.g. book or journal article) and I also want to import the comments I have on Zotero item rather than only the highlights and comments inside the PDF.
If you look at the plugin help documentation it gives you instructuons.
¡Gracias!
Glad I could help 😁
Do you have a zeperate Zotero + Obsidian cource without alle the other organizing things in Obsidian? In that case I would buy the course imindently
A separate course no, but I am working on a template for my patreons that have the setup already done.
Great video! I have one question, which is whether or not it’s possible to also include tags added to highlights in the import? I thought using another if statement with annotation.tag might work but it didn’t
I am sure there is a way to bring in tags. Weather they bring highlight specific tags I am not sure.
The academia channel on the Obsidian discord is where I would ask 😁
@@DannyHatcherTech Thank you! I will definitely check that out!
Great overview!
I tried annotating a couple of PDFs using that and the plugin was able to fetch the annotations from some PDFs and not others. I cannot figure out why. Have you encountered this issue?
I have found a couple of PDF's that couldn't be indexed but that is still a problem I am troubleshooting. I tdoesn't happen very often tho luckly for me.
@@DannyHatcherTech thanks for the feedback
Hi Danny. Thanks so much for the video, super helpful :)
Question - is there an easy way to remove/omit the colour of the highlight in the information exported to obsidian? eg just to have the page reference without the highlight colour (as all my highlights are in the same colour this is superfluous info that i would like to remove)
thanks again, Sam
I assume you are using my template.
You can customize the template in any way you like. By removing the if annotaiton.color stuff you should find that information is omitted on import.
@@DannyHatcherTech thanks so much. I have zero coding skills, but through trial and error i found the right bits of code. Thanks for getting back to me, and thanks again for your videos. I've been watching loads of obsidian tutorials and yours are the most helpful so far :)
what if citation key is not generated? I haven't used zotero before, but when i add any random pdf file into the Zotero library, it doesn't have citation key, which makes the import impossible.
When you add a PDF to Zotero it will be an 'attachment'. A citation key is added to a Zotero 'Item'.
If you use the clipper, items will be made automatically, and the same when using the identifier. Sometimes Zotero will do it with manually added PDF's but only if it can find appropriate information - otherwise you will need to add a new item to add the PDF to for a citation key.
I hope that helps.
Thanks Danny! Awesome stuff. Just one question. why the links in the template don't work for me? they just don't take me to zotero.... any advice
My best guess is that zotero better bibtex is eith not installed or configured in a way that confuses the item location.
The academia channel in the Obsidian discord erver might be able to help 😁
hello , danny please i am a medical student i used to use notion at the start it was amazing , helped me organise every part of the lecons and add comment and picture fluidy , but after time it became harder for me and take a lot of time to copy the lecons from pdf and past it in notion and reedit it cuz its doesnt conserve his format , and that consume a lot of time , is there an application as notion that i cant open a pdf file and comment it with note and change in it ? without having to copy and past every part and reedit it and giving it a new format
I use Obsidian and Zotero for that reason.
Thank you so much for the video! When I try to download the template, it says that the account can no longer have new subscribers so I cant access the template... is there another way to get access to it?
Try the related article 😁
Great video! Is it possible to sync zotero library and update periodically, say every 10 min.
Not sure what you mean by update?
The concatenation settings should work automatically via a trigger command which you can add to a hotkey.
You could make a script to do it for you but I don't need that so am not sure how to go about it.
Hey Danny! 🙌 Thanks for the stellar instructional video on the Zotero-Obsidian integration. It's genuinely upgraded my research workflow! 🚀 Quick question: do you have any tips on handling separate Appendix PDF documents? The Zotero plugin seems to manage one PDF per entry, so it looks like I'd need separate entries for exporting annotations to Obsidian. Would love some guidance on this. Cheers! 📚
Ooh that is a really good question.
Not something I have experienced. All appendix information is at the bottom of the research for me.
Yes, the plugin looks at one attachment file.
I would probably use different zotero items but honestly I am not sure.
Hey Danny, thanks so much for getting back to me! 🙌 From your videos, I've always gathered that you're a fan of smart and efficient solutions, so I was secretly hoping you had a magic trick up your sleeve for this one. 😅 In my research area, it's actually quite common to have the main paper and the supporting data in separate docs. But I'm with you on this - I think going with separate Zotero items might be the way to go. Thanks again for sharing your thoughts and keep up the amazing work with your videos! 👍📚
@@christophkral4021 i try and reply to all UA-cam comments but my discord server is the best place for questions normally.
fantastic overview. works as you demonstrate but i still get an error on import saying received empty bibliography (yet notes are working). Any other setting that's needed in Quick copy?
When you say bibliography are you referring to a citation import?
I don't use citation sytel files in my imports as I do my citations in the export through pandoc.
My problem is the other way around. It gets the bibliography data but can't grab the annotations. Still it says that it received an empty bibliopgraphy from Zotero. When I insert the annotations manually into the document it works. Makes it two more steps, extracting the annotations in Zotero and inserting them in a current document in Obsidian. At least I don't need Citations anymore. Have you found a fix for your problem yet?
@@engager6525 the custom import should work as shown in the video. Some issues have come from people importing a pdf rather than an item 🤷♂️
How can we add usual citation references like [1-5] associated with zotero in usual way, similar to what we have in Word?
I assume you are referring to the Zotero Word integration using a citation format that allows numbers.
In that case, Obsidian doesn't support that, as it they are markdown files.
Hi Danny, I wanted to ask if there is a way to keep updated the higlights. If I higlight something, import it into obsidian and afterwards I higlight another paragraph in Zotero it doesn't appear in Obsidian or I change the color of the higlight afterwards. What could I do?
Thanks.
As both apps are local, there is no automatic syncing. Files need to be integrated (imported) which at the moment is only manual.
The auto concatination setting int the plugin is what I use to help avoid duplicate imports.
Thank you for the great video! It helped me with my problem I described in your older video "How I export academic notes". It creates a new note with the template I have chosen and it also fills in the data from Zotero. However, it cannot extract annotations from any PDF. It always gives me the following error: Received empty bibliography from Zotero. Ensure Zotero's quick copy settings are set and the selected citation style is installed. Do you have an idea how to fix that?
An issue from another user was that they didn't have the PDF (attachment) in an item in Zotero. 🤷♂
@@DannyHatcherTech Thanks for your reply! Unfortunately, I have the PDFs in the tested items in Zotero. Anyway, by showing how to set up the Import Formats , I could actually get rid of Citations, which I basically just used for creating the note with bibliography information. Extracting annotations manually and insert them in Obsidian still works with Zotero Integrations, but I have to extract the annotations in Zotero and insert them in the current document by using the command "Insert Notes into current document".
I also added an @ before {{citekey}}.md in Zotero Integration since MarkDBConnect didn't recognize the notes anymore and didn't give me the tag in Zotero. I know it should be just a configuration thing, but I don't dare to touch the settings yet 😅
@@engager6525 There is something in the configuration that something isn't liking.
I would be happy to troubleshoot on discord if you want. UA-cam doesn't always tell me about messages.
@@DannyHatcherTech I see. I'll try to troubleshoot a little bit longer by myself because I don't want to bother you. At least I managed to fix the annotations problem, I think it was something wrong with my template. However, it still gives me the error, although everything is working fine now! (besides some flaws in the template I don't like). Therefore, the error wasn't about the annotations, but actually something with the bibliography, although it gives me the full bibliography information. So for now, I actually works, though it still gives me the error for something I don't even see in the end result. Thank you again for taking the time!
Hi Danny. Amazing Video. Thanks for recording this. Made me shift from Roam to Obsidian as this was a big bottleneck in the work flow. Cheers mate !!!
I am having one issue if you can help with that. I am getting the extractions fine but when I click on the end of the highlight where I have the Page number and the link, it is not opening the PDF and taking me to the highlight. If the PDF is open in Zotero, even then it doesnt take me there. What could be the reason ?
Without seeing the zotero and Obsidian setup I am not sure.
The academia channel in the Obsidian discord would be the best place to troubleshoot.
@@DannyHatcherTech I tried but couldn’t get much. Feeling stuck here. Can I take your help on this. Do you have any service around it ? Would be helpful to solve this with an expert’s help rather than figuring it out. Do let me know. Thanks :)
Thx Danny! Do you highlight in Zotero? I can't use zotero on android yet, can I highlight my papers in an android app and upload them into zotero? If my highlighting app writes to the pdf, it should work right?
Any better ideas until zotero is on android? Thx!
Yes I highlight in Zotero.
Zotero will read the pdf. If highlights are saved to it it will show, but as external highlights so cant be changed (i dont think anyway).
I assume you read on your phone, and highlight there.
Lots of other app options but I dont read in my phone so dont want ti recommend something i dont use, sorry 😁
Thank very much for this video, really helpful! Where can I find the template ? :)
In the starter pack in the description 😁
@@DannyHatcherTech Thank very much !
Hi Danny, thanks very much, it´s so helpful!! Is there any possibility to generate bibliography automatically like in word?
For example, when I use this plugin to insert a cite (Thomas, 2013), then at the end of this document, how can I get the bibliography of this citation? Should I do it manually by "insert a bibliography" again, or can it generate automatically, especially when there are maybe 30 citations in a document?
Thanks a lot!!!
I think you can do it automatically but I personally do that with the pandoc export to word
@@DannyHatcherTech many thanks! Do you have any tutorial about this (pandoc)?
@@lluvia3453 i have shown it but i dont remember what video it is.
Sorry, i think it is at the end of the other zotero/writing video
@@DannyHatcherTech Thanks!
Hi Danny! I am honestly so grateful for this video; and kinda surprised that there's a tool this effective. I wish this method existed back when I was studying as an undergraduate, but I'm very much excited to be using this for my Masters and even PhD studies someday 🤞!
I do have a problem: even after I have typed the correct folder name in the "Note Import Location" setting, the new files generated by "Zotero Integration: Import #1" command seem to just take place in the vault/root (not inserted to any folders whatsoever). This is a small problem, as I can just move them manually ofc. Still, are there any details that I seem to be missing?
For additional information, I tried also the command "Zotero Integration: Insert notes into current document" and it doesn't seem to be working as well (it just doesn't do anything). I tried disabling another Zotero-related plugin called "Citations" by Jon Gauthier in case it may have overlapped and cause problems. But that didn't solve the problem either. Would love to know if you have answers to this.
Nevertheless, this video is honestly kinda lifechanging for me, and I feel like I'm really stretching your generosity. Thank you so much!
It sounds like the import location with {{citekey}} is missing the folder path....
Folder/{{citekey}}
@@DannyHatcherTech Fixed now. Again, thank you!
Hey Danny,
thank you very much for the great video!
Your template is a very nice, but I have one problem with it:
For some reason, the images of the "selected area" are not imported from Zotero for some articles/items.
For some it works, for others it doesn't. This is despite the fact that they seem to be very similar (same item type, same options filled in and same way the PDF is attached).
Do you have any idea what the problem is and how to fix it?
I have not heard or seen that error before.
I suggest asking in the academia channel in the Obsidian discord.
@@DannyHatcherTech Thank you very much for the quick reply and again for the awesome video!
I will ask there and come back here if I find an answer.
In the meantime, I have found the answer to this behaviour:
I have 2 libraries: one Group Library for work, that is shared with the institution I'm working for, and one for personal use. Whenever I want to import an item from my personal library, that is already in the "work" library, the plugin selects the wrong one (even tough I select the item from "My Library"). It probably happens because both items have the same citation key.
I haven't found a real solution yet other than deleting the item from the Group Library, importing the annotations to Obsidian and then restoring the item again.
Thanks again for the great workflow!
@@jsoff9011 Ah, I see.
I have the same situation but don't get an error. That is interesting.
Hi Danny,
I still can't get the annotated picture synced to Obsidian.
Is there any missing step?
Do we need to export the Zotero libary? and what type of export that would need be?
Moreover, your Zotero template didn't showed up at the beginning of imported annotation (it created new node, only annotation without anything in the template).
Furthermore, I like the way that your imported annotation able to pick-up the annotation color in Zotero? unfortunately my trial didn't produce the same
I assume you are referring to the select area option.
Everything I show in the video is what I did in the example vault setup and the image export worked fine. I didn't do anything else in Zotero or Obsidian.
Apart from doing a restart, checking Zotero Integrations is up to date, and checking the settings I can't do much for here.
I am in discord if you want to continue the conversation - UA-cam doesn't always notify me of messages.
@@DannyHatcherTech after dozens of trials and errors, I finally managed to get the same output. Putting the reading notes in the root vault and using the right template is the key.
Thank you Danny !
I am glad you got there!
The concatenation feature is nifty, but using it implies that I should not manually edit that literature note in obsidian, because those edits will be overwritten by the re-export, right? But even if I leave the note alone, I suppose updating it with new highlights from Zotero will also break block links or transclusions using that note, or are such links somehow magically preserved?
To be honest I don't know as I only do one export sorry.
yeah, this seems to be the case.
In fact, you can protect parts of the literature note so that those will be preserved across multiple exports. This can include notes you might add manually as well as the exported annotations. So the problem is not at all as big as I thought, but I‘m still avoiding block level references to literature notes. Instead, I drag and drop the respective annotation directly from Zotero once again.
@@critical-chris oh how do you protect it?
@@critical-chris Yes, please share how this is done!
Hi Danny. Why did you decide to use Zotero instead of Readwise? Will be helpful to hear their comparison, pros, and cons.
Zotero has a better reader experience from my experience, zotero has easier searching and advanced search features, it is free, academic papers can be downloaded and stored, websites/pages can be locally stored.
Group libraries make collaboration easier. I can putt RSS feeds in zotero for easy capture and notification.
They are the first things that come to mind.
@@DannyHatcherTech thanks for the answer.
I really don't like readwise reader app for pdf reading. But I do like their functionalities like fast export to obsidian and UA-cam videos highlighting. UA-cam video has alternatives though.
And now I'm also thinking about dropping readwise for zotero because of price and vendor lock
@@DannyHatcherTech by the way it would be extremely interesting to listen to your thoughts about zotero VS readwise in a detailed video.
@@Trecoolerok I don't use readwise at all so a comparison would be very biased/unfair.
The main points for me is:
Zotero is free.
I can put EVERYTHING in there.
Works well with PDFs.
Search/tagging is really good.
Hey Danny for some reason whenever I try to add the template to Obsidian I get the following error 'failed to list templates. Folder "C:\Users\sbram\OneDrive\Desktop\Zotero Template" not found'. Today is my first day on both Zotero and Obsidian, so please bare that in mind when answering, thank you in advance :)
The path you are showing there doesn't look like the Obsidian template file "Zotero Template" is an Obsidian vault folder (where the plugin is) so the plugin can't find the file.
Hi Danny, how are you?
I wanted to ask something:
When I import a document and add in the obsidian properties, and later I update the file because I added new higlights, the tags that I added disappear.
And also, Obsidian is not showing the tags that I select in Zotero previously.
Thanks.
If you have concatenation on, the new import will overwrite the original file edits.
I don't think Zotero tags are brought into Obsidian unless you bring it in with the template NunJunks which I don't do.
Thanks, I don't know this template, could you share it?@@DannyHatcherTech
If you add some text to the note created with the plugin in Obsidian, and then re-load the note from Zotero, would it delete your text?
That is a great question and I am not sure I would need to test it.
I don't add notes to the source in Obsidian. I write things up in a working note and reference the page.
Grazie.
Glad I could help 😁
Thanks for your instructions.
I see it wors great.
But I wonder how to export my drawings (with my ipad).
The only one thing i can do is export pdf with my drawings inside it.
I am not a tablet user so am not sure unfortunately.
Danny, Your speech pace is okay. I just sped up my thinking. LOL I downloaded the basic template but get an error parsing template "Templates/Basic import with properties.md: (unknown path) line 5, Column 23 parseAggregate: expected colon after dict key Authors: {{Authors}} {{Directors}} Any ideas?
Sorry UA-cam put this comment for review so am only just seeing this.
parsing errors are normally due to setting issues - discord would be the best place to troubleshoot if you are still struggling.
Can you please elaborate on how you use Zotero as a replacement for Readwise??
I clip blogs, podcasts, videos, tweets etc all to Zotero.
Do highlights of point on written content in there.
Tag for priority and export highlights to Obsidian.
Hi Danny, I followed your procedure. But when I want to link back to pdf in zotero, it shows: failed to open URI. Do you know how to solve it? I think it's an issue in zotero.
From Obsidian to Zotero the issue is likely citekey related.
From Zotero to Obsidian the issue is likely filename related.
Discord would be the best place to troubleshoot. Academia channel in Obsidian discord.
Whaaaaat!!??😂 this is what I’ve been waiting for!❤❤ thanks. What is your logic for creating citekeys? I have been trying to get it closest to APA citing conventions… for my Masters …what is the reason for using’@‘?
The @ citekey in Obisidan allows for a zotero plugin to find the citekey and add a tag inside zotero so I know what I have in Obsidian by looking at zotero.
@@DannyHatcherTech oooh ok, that's fancy, and very useful! thanks for the explanation:)
Is there a way to make the template import both annotations AND notes?
As this imports only annotations, but if you have extracted notes, they will not be imported to the note.
I am sure there is a way to do it with the template script - might be worth going into the Academia channel in the discord serer.
@@DannyHatcherTech Thanks Danny. So I assume you do not incorporate notes in your Zotero workflow? Since you export PDF annotations only?
@@TheJoshtheboss correct.
All notes are in Obsidian.
@@DannyHatcherTech Thanks for the clarification.
Thanks Danny. I still can't decide if I prefer this or BibNotes Formatter.
I am not as familiar with BibNotes but I have not found any issues with this plugin yet 🤷♂
@@DannyHatcherTech The dev isn't going to release it on the community plugins until he can extract annotations directly from the PDF as well as Zotero. I install it using BRAT as I like to live on the bleeding edge and my productivity is always zero. Have a great weekend.
I’ve been logseq’ing for the past year, but this integration of Zotero annotations and images might bring me back to Obsidian. That, plus I’m really tired of managing my own git sync between iPad and desktop, and not having plugins or even PDFs on iPad 😢
I have been using this plugins for months seamlessly.
I have a video on Obsidian Git if you want to still use it automatically.
I tried to use the zotero template, but I got an error message saying "unexpected end of JSON input" : what should I do ?
I have not seen that error before. The Obsidian disco4d academic tools channel may have people that have seen thar before
OK, nevermind, I'll find another template, thanks for the reactivity anyway
I wonder if Zotero Obsidian Integration can export area highlights. If yes, how?
They are exported just like the others
I am encountering an issue when trying to import papers from Zotero. have done as you said for the setup, except for the Template part which I left blank (is this the cause of the issue?). When trying to import a paper, Obsidian gives me the error "Error: Received empty bibliography from Zotero. Ensure Zotero's quick copy settings are set and the selected citation style is installed."
The bibliography error is normally for a citation import format rather than an import format.
A template would be needed for a custom format so it know what to import otherwise you can use the default option of brining in the notes in zotero.
@@DannyHatcherTech Then I am not sure what causes the error, would you have any idea what kind of citation import format issue could be the cause?
@@OnlyOnePlaylist If you are using the citation format without a bibliography format that would be it.
@@DannyHatcherTech I haven't added a citation format (as you don't do it in your video), so I am not quite sure what to do there. Should I press Add Citation Format and add some bibliography format? Can't I just use the plugin without?
@@OnlyOnePlaylist Did you ever find a fix Jeremy?
Hi Danny! I'm a patreon supporter and I've downloaded this template. For some reason, the template is not bringing the pictures and annotations I've made into obsidian. I haven't changed your code at all... help!
Hi 👋 I have a discord for longer conversations if that is needed.
If you are importing an item from zotero and a file is being created but no information is in it you might be using the citation import instead of the normal import. Have a look in the settings
Sorry, not a coder. But I did download your template. I would like to understand with the different components mean. What programming language is used in your template? I love your channel!
I think I have a link in my website article but this page should help: mozilla.github.io/nunjucks/
@@DannyHatcherTech thanks!
How can I add the abstract to the template using this integration?
In the template documentation there are options to add the abstract. My guess would be {{abstract}} but worth checking the documntation.
Somehow it shows "error in retrieve the data: Unexpected end of json input." Not sure if others have the some issue.
This sounds like a specific error worth troubleshooting in the guthub repo
12 seconds in you say "you can add an image around any of the blocks". I try but don't see any way to do that. Can you tell me how to do it or point me to documentation (I haven't succeeded in finding it by searching). Thanks.
Adding images theough the zotero integration should be in the settings of the plugin.
Tesseract might be needed, i cant remeber of the top of my head 😁
Where is the link to the templat, bro?
It is on my patreon.
The blog version has a section about the template which directs you to patreon. 😁
Is there a way to keep the obsidian version of zotero notes updated automatically?
Unfortunately as both tools are local first, no.
Unless there is a script or plugin I am unaware off.
@@DannyHatcherTech Ok, thanks for responding. I figured something that accesses zotero notes and exports them to the obsidian vault would be nice. I'm tempted to develop it. I haven't really developed a real app yet so any pointers would be appreciated! Maybe a zotero plugin, since it sounds like zotero files aren't system accessible, or at least not when zotero isn't running.
Wow this helped so much! Just a simple question you might help with:
In your for loop for the annotations, is there a way to target specific colours ? E.g. only extract annotations in the colour Yellow.
I tried to look through the zotero integration documentation and the nunjucks documentation but i dont know how to target the specific colour or colourCategory of the metadata
i thought it might be something like {%- if annotation.annotatedText and annotation.colorCategory(Yellow)(i dont know the notation that's the problem)-%} or state that in the for part
Thank you in advance to anybody who might help me
Yes there is a way but I am not sure how.
The academia channel in the Obsidian discord server would be the best place to ask.
Hi Danny, Great video! I meet a problem when using this plugins. No matter what I enter in the input box(namely Note Import Location), it puts the newly generated file in the initial root directory when I enter it. Do you know where the problem is?
The location of the import is decided in the import path.
My guess is that you don't have a folder in the path location.
@@DannyHatcherTech Wow, thanks for the quick reply. The folder name I specified is "readingnotes", and the input box on the right side of Note Import Location is also written "readingnotes". Unfortunately, the generated file still appears under the root directory.
@@user-iq1ng9ou4m If you are that import it should put the file in that path.
I have seen some people trigger the default import rather than the custom one. Make sure you are using the correct import.
If it still doesn't work I would suggest putting in a bug report to the developer.
@@DannyHatcherTechok thanks for your help🧡
Hmm... I followed your instructions but get this error:
Error processing PDF: Command failed with
exit code 1:
...
Tvpe3 fonts are not currently supported
(feature not currently supported)
Anyone got some suggestions for me?
I am guessing you have either a different font in Obsidian or Zotero that the plugin doesn't like.
I would suggest contacting the plugin developer
@@DannyHatcherTech I looked into it more and it seems type 3 fonts are something associated to the PDF and are a pain in the ass to correct. Thanks for the response.
@@AdventuresThroughTheMind interesting. I have never come across that before. Thanks for sharing!
@@DannyHatcherTech Turns out it was either because of a watermark left over from a "free service" pdf editor, or from the pre-printer marks left on the edges page). Once those were cropped away, the issue was totally gone.
how to set annotation.imageRelativePath, it shows couldn't be found
Without more info I cant help much. Try message on discord - yourube isnt great with comments.
are you able to have the full functionality you had with the earlier process of exporting a markdown that you showed in the "how the zotero 6 update changed my workflow" video?
Yes.
The Zotero 6 update made this Obsidian plugin even better 😁
@@DannyHatcherTech sweet thank you. The hardest part about getting set up with research linking Sotero with obsidian is that things are changing it such breakneck speed that it’s hard to know what to use and what to discount.
So if I understand correctly. I can just do everything with Zotero, better bibtex, the integration plugin, obsidian, and dataview. Now to figure out how to integrate it with Excalibur draw.
@@Sagitarria That is what I do.
I dont use excalidraw so would suggest asking in the discord for that one 😁
@@DannyHatcherTech definitely ty for your excellent video. If I start here will I need to go to your other zotero 6 for set up specifics ?
Error converting formatted bibliography to markdown:Error:mode must be bibliograpy, not export. How can i fix this?
I dont use a bibliography file. You can add one or ignore the missing info error.
When I try to import my notes it says "Erorr converting formatted bibliography to markdown: TypeError: style.getCiteProc is not a function" :(
That is something to do with your bib file if you are using one.
I don't use a bib file for my imports. Sometimes an error may appear but the import still work.
In the Obsidian discord, academia channel, the developer tends to update and answer questions about the plugin.
I cannot find your template - otherwise great video!
If you are looking for the zotero template it is on my patreon 😁
How to delete the color highlight from the template?
I assume this is my template.
Remove the annotation.color bit
No matter what I choose as the import folder, the imported annotations note go to root folder? Anyone else experiencing this?
You might be using the default import option rather than the one you have created.
If anybody is still around... this is really annoying me. For some reason the abstract won't copy over to the template. Any ideas? I'm using {{abstract}}. Just noticed that Authors or year etc. isn't transferring also. Yelp.
I suppose I might ask also whilst I am here: Why does the template have criteria in the --- --- field and then alternative criteria below it?
I don't know the intricacies of the plugin integration as the Nunjunks langauge goes beyond me.
In the Obsidian discord academia channel there is a thread that has the developer and other people much more equipt to answer you questions.
hope that helps.
@@DannyHatcherTech Appreciate it!
Why does it deccribe the highlight colour, instead of highlighting in that colour...
That is my preference with the import.
You can add that into the template script but that is not for me.
It would be worth going into the Academia channel in the Obsidian discord for help on that.
@@DannyHatcherTech Thanks Danny.
Hi great video, I was hoping to be able to adapt that, but it just doesn't work... I repeated the installation process three times and it still doesn't work.
I can select literature from zotero with the shortcut in obsidian but when I click enter, nothing happens. Not even an error message. Did anyone else have that problem and knows how to fix it?
My guess is that either you are using the citation format rather than import format, or there is something in the settings that isn't quite right.
Happy to help in discord.
I also tried what @woxta mentioned who seemed to have the same problem. Didn't fix it.
Hey, I know that its old, but have you fixed this? I am getting the same issue
Sadly there seems tot be an issue with the link to the template. it says:
Something's come undone.
Sorry, this page can't be reached because of a database connection issue.
I don't seem to be having any issues with the link. The template link should take you to my website.
@@DannyHatcherTech I confirm it is now working! Many thanks for your work Sir Hatcher!
I Have One problem!!
I don't Have ""tools"" in the bar; File, Edit, ecc...
On mac it might be in the edit menu.
@@DannyHatcherTech and on Windows?
@@Scorpion-gp1wg I use windows and see the tools option. Not sure why you are not seeing it
really good video. using zotero within obsidian is still a bit rough around the edges, but getting there. I wonder what will change when obsidian has its own pdf annotation tool - native I mean - that extends the base obsidian to something like logseq and remnote are doing. great work.
I am keeping my eye on it but I dont see Zotero being beat anytime soon
can you open zotero inside canvas ?
If you mean, embed the library view, I don't think so.
But I don't know how that would be helpful. I am either reading in Zotero, or writing in Obsidian.
@@DannyHatcherTech So that you can directly extract the content from Zotero to obsidian canvas.
@@Cawnnak the Zotero integration plugin brings in the information as files. You might be able to make a script to have it automatically go into the canvas but I would just drag and drop it from the recent files plugin in my sidebar.
@@DannyHatcherTech make sense. May be I'm over thinking this. we programmer trying to find automate everything is a problem. lol
Thank you for quick response.
Nothing works
Could you be more specific so I can help?
Can you install the plugin?
Can you add a template?
Can you open Zotero?
Does any import work?
etc....
Unfortunately, I have no luck and cannot make your template work. I get a blank note as a result. Otherwise great video as always
When you say blank, if the file is completely empty make sure you use the custom format not the defualt other wise the template isn't actually being tirggered.
If you get the yaml at the top but no highlights, make sure the PDF attachment is in the item in Zotero.
Assuming both those are done, there are some PDF files that are 'protected' so Zotero can't get the highlights. That currently has no work around.
@@DannyHatcherTech It worked! Thank you so much!
Danny, Just a suggestion, in future videos, slow down the pace of your presentation.
I have done - thank you
Do you know that if you go a bit slower, you can target wider audience? Absolutely wonderful video, no crap but it's too fast to follow
Yes I am aware. Changing my natural speaking speed takes constant mental reminders, I am working on it 😁