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obsidian-zotero-integration's Introduction

Obsidian Zotero Integration

Insert and import citations, bibliographies, notes, and PDF annotations from Zotero into Obsidian. Requires the Better BibTeX for Zotero plugin.

You can find the documentation for this plugin here. The documentation is currently incomplete. Please reach out if you'd like to help.

Help, how do I install the plugin?

In Obsidian, open Settings, on the left under Options open Community Plugins, on Community Plugins select Browse and search for 'Zotero Integration'

Help, the plugin doesn't load!

Please insure your Obsidian installer version is at least v0.13.24. If not, try reinstalling obsidian.

Help, I get an error when creating a citation or bibliography!

Please ensure you have selected a quick copy style in Zotero:

A screenshot Zotero's quick copy settings

And that you can copy a citation in Zotero when and item is selected:

A screenshot Zotero's edit menu showing the copy citation option

Screenshots

A screenshot of this plugin's settings

A screenshot of available plugin commands

A screenshot of the Zotero search bar

A short gif demonstraiting importing notes form Zotero into the current file

obsidian-zotero-integration's People

Contributors

alpsencer avatar davidlandry93 avatar johan-mattias avatar lslightly avatar marcbenedi avatar mgmeyers avatar morekon avatar theotheo avatar vaudrain avatar volker-fr avatar

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obsidian-zotero-integration's Issues

Citation insert not including italics

I've got everything else working, but my citations (using Chicago Manual of Style 17th edition, full note) do not come with italicized titles. I'm on a Mac (Catalina 10.15.7) and the most updated version of Obsidian and the plugin as of today (April 7, 2022).

Failed to load plugin

I just download the new 1.1.3 ZDC main.js, manifest.json, and styles.css files to an obsidian-zotero-desktop-connector folder within the Obsidian plugins directory. The plug in is recognized in the settings, but when I try to enable the plugin, I get the error "Failed to load obsidian-zotero-desktop-connector." I uninstall the plugin and downloaded the file again, but continue to get the same error. FWIW: this is the same process I used for the previous releases and it worked perfectly.

image

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items on context dropdown list in zotero are incomplete

Hi there!
Thanks for this great plugin. It has already significantly enhanced integration between Obsidian and Zotero in my workflow. I find, however, that when I right-click on an Obsidian-Zotero synced item in Zotero and point to "Open ObsidianMD Note" or "Show Markdown File" I only get a list that seems limited to 16 Obsidian notes although I may have many more notes with the relevant Zotero itemkey. I cannot seem to find any button to scroll down to see other notes or some other means to see them.
Is this perhaps by design, or is it a bug? Or am I doing something wrong?

I could not find any thread on this issue and decided to submit it as a new one. I am sorry if I missed an already-existing thread on it.
Thanks for your help

how to output property of variable

Hi, mgmeyers
I need help outputing the property of a variable. Pardon me if I am using the wrong terms. What I want to do is format the Heading 1 title of my zotero export file like this: authorlastname - year - publication title.
I am able to get author - year - publication title using this template: {{authors}} - {{date}} - {{title}}. This renders, for instance, as "M. G. Meyers - 2014 - Philosophy in Pre-colonial Africa". What I want however is: "Meyers - 2014 - Philosophy in Pre-colonial Africa", i.e., without the initials M. G.

I see in the data explorer that the author's last name is an item under the "creators" variable, as shown in the screenshot below:
creators variable and items

My challenge is how to get the plugin to output the desired last name. I have tried {{creators.0.lastName}}, {{creators.creator.lastName}}, and {{creators.creator0.lastName}}. Nothing has worked.

I would appreciate your assistance. Thanks in advance.

Subset of CSL Styles Not Appearing for Import Settings

I'm in the legal world, and so rely on some citation conventions not common in other professions. I've been trying to get the desktop connector set up using Juris-M, the legal offshoot of Zotero, and am having trouble designating the desired citation & important styles.

The preferred CSL style is "JM Indigo Book", which closely mirrors the Bluebook citation style most often used by legal academics. But in working with the dropdown search boxes under "Citation Style" and "Bibliography Style," the Desktop Connector seems not to detect the "JM Indigo Book" style.

Is there any way to make this option selectable? I have the JM Indigo Book style installed on both Juris-M & Zotero, so I know it's not an issue of needing to install the target style.

Zotero picker bar

The Zotero citation picker bar thingy stays in the background. Is there a way of forcing it to the surface - always on top, kind thing?

Fearture request: include Zotero links in notes

Would it be possible to include the Zotero file links in the Import Notes function?

As I'm sure you know, the Annotations file generated by Zotero includes a link to the location of the note in the PDF and clicking on it Obsidian takes the user directly to that spot in the document. (Side note: it appears that in Zotero v6.x, this link will only take you to the annotation location when using Zotero to open/read PDFs. If that is not the Zotero setting, the link will open the document in the selected PDF reader. I believe this is a different behavior than Zotero v5.x.)

Sanitize {{title}} if used in filename - case of slash `/`

Great plugin! :)

For template {citekey}} - {{title}}.md and paper named

Large-Scale Topographical Analysis of Electrophysiological 1/f and Oscillations Reveals Patterns of Spatial Variation the / is interpreted as folder path and the result is
the file f and Oscillations Reveals Patterns of Spatial Variation in a folder donoghue2019 Large-Scale Topographical Analysis of Electrophysiological 1

Unfortunately, reference to 1/f distribution is quite often in titles in my library ;)

pdf extract fail, go runtime issue?

panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x0 pc=0x446c23b]

goroutine 91 [running]:
main.getTextByAnnotBounds(0x0?, 0x0?, 0x4060d5c28f5c28f6?, {{0x4072f0a3d70a3d71?, 0xc007b46000?}, {0xe88?, 0x43d83df?}})
github.com/mgmeyers/pdf-annots2json/helpers.go:95 +0x3b
main.processAnnotations.func1()
github.com/mgmeyers/pdf-annots2json/main.go:279 +0xa1a
golang.org/x/sync/errgroup.(*Group).Go.func1()
golang.org/x/[email protected]/errgroup/errgroup.go:57 +0x67
created by golang.org/x/sync/errgroup.(*Group).Go
golang.org/x/[email protected]/errgroup/errgroup.go:54 +0x8d

Add {{collections}} to fetch the collection(s) of the item in Zotero

Hi, bro!

This is a very nice plugin, and I very like it! However, I find that there is no field data to fetch the information about the collection(s) of the item in Zotero

If possible, it could not be better that there would be a such placeholder!

I will appreciate it if you could cnsider this possible enhancement!

image

Feature request: insert currently selected Zotero item

I'm migrating from emacs/orgmode, and there the Zotero connector has a nice feature to insert the item that is currently selected in Zotero. This is extremely convenient: after you add a paper to Zotero using the webclipper, it's automatically selected there, so that you can insert a reference to the new paper in a note without needing to search for it...

I can't open data explorer

I can insert notes from a Zotero entry into the current file. But I'm having no luck using Data Explorer, it throws an error in the obsidian console after I select a Zotero entry, and I get no output:
image

The Brackets are still showing

First of all, thanks a lot for making this amazing plugin.

I have an issue with the Pandoc citation. Even though I have not checked Include Brackets but the brackets are still showing.

image

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Installer Version

0.13.31

Which editor are you using?

  • New Editor
  • Legacy Editor

In which mode(s) does the problem occur? (if applicable)

  • Source (Edit)
  • Reading (Preview)
  • Live Preview

Which operating system?

  • macOS
  • Linux
  • Windows
  • iOS
  • Android

Theme

Shimmering Focus

The problem that the literature selection box is not at the top

Dear author, hello!
Thank you very much for the plugin you developed, it saved me a lot of time. However, here is a small problem to reflect to you. When I open this plugin and pop up the literature selection box, the selection box is sometimes not at the top level, but at the next level of obsidian. There is also a small problem, when I insert a document, the line break between the insertion sequence number and the content of the citation, instead of immediately following the sequence number.
Thanks again for the plugin. Excellent!
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Defined ‘header’ template does not work

I defined one ‘header’ template makedown file like your example in Readme file.
But it can't work, the result just have note and annotation content ,

## {{title}}

### Formatted Bibliography

{{bibliography}}
{% if abstractNote %}

### Abstract

{{abstractNote}}
{% endif %}

The header template code does not work also.

{{title}}
{{abstractNote}}

Problem with command that insert notes from into obsidian note

I have tried other commands like data explorer and if I want to cite something, they all work but when it comes to inserting the annotations and notes that I made in one document it fails and does nothing when I run that one. After selecting the document, the note page is still empty although when using the data explorer the annotations and other things all are there and you see them but it doesn't work in that one command and I cant import them into notes automatically. If someone could help me I'd be appreciated.

1
2

Changing Citation Style?

Thank you so much for making this! I couldn't get the other citation plugin to work for me, so this is great!

However, is there a way to change the citation style that governs the in-text citations the plugin adds?

The default seems to be (Author, Year) but since I'm using MLA I only need (Author Page#).

Is there a way to change this?

Thanks!!

Reference inserted is blank

When I try the command to insert the citation, I can select the paper, but then the citation just reads '[1]'.

I'm using the IEEE format:

image

That format is available in Zotero:

image

Using only Zotero, when right-clicking on an entry and choosing 'Generate bibliography from item', it puts the reference to the clipboard without problems (but without the URI of course)

Show ODF Scan Code in Data Explorer

Hi,
Thanks again for this plugin.
Is it possible to get the Data Explorer to show the ODF scan code (pardon me if that is not the right term) of a Zotero item? It is in this format: { | Author, YYYY | | |zu:UserID:ItemKey}. With my Quickcopy item format set to "Scannable Cite" in Zotero, I access the code by right-clicking the desired item and selecting the Zutilo command "Quickcopy items to clipboard." Having it in the Data Explorer would enable me to integrate it into the automated templates I am trying to develop for my note-making process in Obsidian.

Thanks for your response.

Refreshing same note unexpected behaviour

I am using

Header
Annotations
Footer

  • and using ZDC to refresh the same note over and over again

not sure if this is expected behaviour but when I do this but this is the result

  • the header remains the same (which is correct)
  • the footer gets nuked completely - never to return (I would expect this to remain just as the header does)
  • ...and the middle file (annotations) keeps getting duplicated over and over again (appended again with each iteration of refresh)

I would expect the annotations (middle part) to get wiped and replaced with the new data per the template

[Bug] Citation autocomplete fail completely

I have a bibliography in bib, auto linked with my opened zotero. The plugin works well through plugin command.

I use pandoc bracket format.

When I type [@ I don't have any complete, same if i start to type.
Same for [@ cascella

When typing @c :
image
image

Output {{title}} is pdf not metadata

when I generate the output file using {{title}}.md the note is titled using the attachment (pdf) file name.

The expected behaviour would be to use the metadata of the title {{title}} which works as expected in the body of the note, just not for naming the file itself

version 1.1.3. fails to load

Hi there,

after the update to the most recent version (1.1.3), the plugin fails to load in Obsidian (v0.14.2 on macOS 12.3).

Clarification of goal and functions of this plugin

Hi mgmeyers!
I was looking at your github profile to see what you had been working on lately (because I was encountering a small bug with kanban and card links #486 ).
I stumbled upon this plugin that looks just amazing :) I love that you are able to trigger the search using Zotero connector to integrate citations into obsidian.

I noticed you have a feature to import notes into a document. I wonder whether your aim is to come up with similar functionalities as the bibnotes plugin? It would be great to have a fusion of your two plugins, but I admit I don't know how realistic or feasible this would be as the two plugins can coexist.

But perhaps, you want this plugin to be very specific in its use and do what it is currently doing: citations, bibliography, and simple note inserts in any document.

template for export filename not rendering completely

Hi, mgmeyers
Thanks for this extremely useful and promising plugin for Obsidian. I find, though, that the template for the export filename only renders partially. Forgive me if my statement is unclear: I am new to templating. What I mean is this: I have a template for the export filename thus: {{authors}} - {{date | format("YYYY")}} - {{title}}

However, the filename of the export renders without the author's name; e.g., "- 2014 - Philosophy in Pre-colonial Africa" instead of "Meyers - 2014 - Philosophy in Pre-colonial Africa".

The same template works correctly as Header 1 in the document but not in its filename. I cannot understand why. Perhaps I am missing something?

This issue seems related to another raised by someone else regarding the template for the export filename rendering as the filename for the item's PDF. But it also seems significantly different; moreover that issue has been closed.

Thanks in advance for your help.

after the update, the date explorer can have data ,but import note is nothing.

the 2.1.8 version

TP

{{title}}

Formatted Bibliography

{{bibliography}}
{% if abstractNote %}

Abstract

{{abstractNote}}
{% endif %}

{% for annotation in annotations %}
{% if annotation.annotatedText %}

{{annotation.annotatedText}}
{% endif %}
{% if annotation.comment %}
{{annotation.comment}}
{% endif %}
{% endfor %}


and this is output form data explorer

Foaming of PLA Composites by Supercritical Fluid-Assisted Processes: A Review

Formatted Bibliography

(1)

Villamil Jiménez, J. A.; Le Moigne, N.; Bénézet, J.-C.; Sauceau, M.; Sescousse, R.; Fages, J. Foaming of PLA Composites by Supercritical Fluid-Assisted Processes: A Review. Molecules 2020, 25 (15), 3408. https://doi.org/10.3390/molecules25153408.

Abstract

Polylactic acid (PLA) is a well-known and commercially available biopolymer that can be produced from different sources. Its different characteristics generated a great deal of interest in various industrial fields. Besides, its use as a polymer matrix for foam production has increased in recent years. With the rise of technologies that seek to reduce the negative environmental impact of processes, chemical foaming agents are being substituted by physical agents, primarily supercritical fluids (SCFs). Currently, the mass production of low-density PLA foams with a uniform cell morphology using SCFs as blowing agents is a challenge. This is mainly due to the low melt strength of PLA and its slow crystallization kinetics. Among the different options to improve the PLA characteristics, compounding it with different types of fillers has great potential. This strategy does not only have foaming advantages, but can also improve the performances of the final composites, regardless of the implemented foaming process, i.e., batch, injection molding, and extrusion. In addition, the operating conditions and the characteristics of the fillers, such as their size, shape factor, and surface chemistry, play an important role in the final foam morphology. This article proposes a critical review on the different SCF-assisted processes and effects of operating conditions and fillers on foaming of PLA composites.

【摘要翻译】聚乳酸(PLA)是一种广为人知的商用生物聚合物,可从不同来源生产。其不同的特性在各个工业领域引起了极大的兴趣。此外,近年来,其作为泡沫生产的聚合物基质的用途有所增加。随着寻求减少工艺对环境的负面影响的技术的兴起,化学发泡剂正被物理剂取代,主要是超临界流体(SCF)。目前,使用单细胞纤维作为发泡剂大规模生产具有均匀泡孔形态的低密度PLA泡沫是一个挑战。这主要是由于PLA的低熔体强度和缓慢的结晶动力学。在改善聚乳酸特性的各种选择中,将其与不同类型的填料复合具有很大的潜力。该策略不仅具有发泡优势,而且可以改善最终复合材料的性能,无论采用何种发泡工艺,即分批、注射成型和挤出。此外,填料的操作条件和特性,如尺寸、形状因子和表面化学,对最终泡沫形态起着重要作用。本文对不同的SCF辅助工艺以及操作条件和填料对PLA复合材料发泡的影响进行了综述。

LA Composites by f PLA Compos sted Processes:

ǍN4uLmAOSRz[PLAYTgPevllċ

mposite; nanocomposite; super

聚乳酸;生物复合材料;纳米复合材料;超临界流体;泡沫

%% Import Date: 2022-04-30T20:26:20.685Z %%

Keep zotero Markdown links in notes

This plugin works perfectly for me with Zotero 6, but it would be really nice if it could preserve the Markdown links when copying them over.

Can't open data explorer

I can sort of get the plugin working -- for example, I can insert notes from a Zotero entry into the current file. But I'm having no luck using an export template; just fails quietly to do anything. When I try to use Data Explorer, it throws an error in the obsidian console after I select a Zotero entry, and I get no output:
VM243:61 Uncaught (in promise) TypeError: Cannot read properties of undefined (reading 'annotations')
at eval (eval at (app.js:formatted:67493), :61:10301)
at Array.forEach ()
at eval (eval at (app.js:formatted:67493), :61:10201)
at Generator.next ()
at i (eval at (app.js:formatted:67493), :6:1251)

annotations aren't being extracted

I'm running Obsidian 0.14.6, with Zotero 6.0.5 beta 5, and I've checked to be sure that ZDC is up to date. The settings say that the PDF utility is also up to date. I've set up an import format called "Literature note," and I've created a header template and an annotations template for it, and included them in the settings. However, when I attempt to create a literature note, the header renders fine but no annotations are extracted. I've used the data explorer and see no annotations in the raw data.

BUG: Insert notes into current document not working

here's my zotero:

image

but when I try to insert my notes into the current document using the Zotero Desktop Connector, it throws an error that says "no notes found for selected items."

I didn't see any errors in devtools. I'm on Zotero 6 and ZDC 1.0.2

PDF annotation extraction and literature note creation

For the sake of flexibility, I'd like to support a robust templating engine of some sort for annotations and literature notes, but I also want to be mindful of non-technical users.

The consensus was that:

  • templater is a bit much.
  • nunjucks is pretty user-friendly.
  • jinja is used by readwise but is python not javascript; nunjucks is the typescript alternative recommended by argentum & mgmeyers; there's also one obsidian plugin using nunjucks already.
  • mdnotes {{ }} style is nice but probably harder to implement.

See also: my request for templating on the zotero forums & the extract pdf annotations plugin.

Additionally, here's @argenos's wishlist in Discord, mostly surrounding templating options.

an imported note from zotero "select area" misses link back to pdf

I use Zotero annotation function and then use ZDC to import via "make note from annotations" in Zotero. Zotero's own markdown export from "select area" annotations doesn't export images, but it does include a link back to the pdf selected area. But when I import via ZDC, the link is missing. Any chance this could be fixed? Thanks!

Formatting Dates

Is there currently a way to format moment dates with templates? {{date}} currently renders as seconds since the epoch.

Error: Header template not found PathToTemplate

Can't get the basic template from the docs to work.

Problem

Error: Header template not found PathToTemplate
Error: No templates found for export Export 1

The Zotero data explorer seems to work correctly though, I can see all template data for a selected paper.

What I've tried:

  • Dumbing down the basic template as I thought maybe its not working because bibliography might not work or something ...
  • Paths tried:
    • Nested in templates folder in vault VaultName/Templates/basicexample.md
    • Nested in templates folder Templates/basicexample.md
    • VaultName/basicexample.md
    • basicexample.md

Am I making a dumb mistake somewhere?

Thanks in advance!

Basic template for reference:

{{title}}

Formatted Bibliography

{{bibliography}}
{% if abstractNote %}

Abstract

{{abstractNote}}
{% endif %}

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