anoopkcn / obsidian-reference-map Goto Github PK

Reference and citation map for literature review and discovery

License: GNU General Public License v3.0

JavaScript 0.19% TypeScript 98.28% CSS 1.53%

citation-mapping citations literature-review literature-search obsidian-plugin reference-maps references research literature-mining research-discover

obsidian-reference-map's Introduction

Hi there 👋

obsidian-reference-map's People

Contributors

Stargazers

Watchers

Forkers

blakenaccarato jimmylord

obsidian-reference-map's Issues

{{journal}} field should just be a journal title

I am using journal titles as links in my reference cards and I wanted to use the template [[{{journal}}]], but unfortunately, at the moment, this field includes not only the title, but also additional information such as volume number and pagination. I believe it would be beneficial to have separate fields for the title and this additional information.

Anyway, I appreciate the plugin as it automates many tasks that I previously had to do manually. Thanks!

Is there a way to know which citation (in the right panel) correspond to which "static reference list" (in the main text)

First of all, thank you so much for making this plug-in. This is definitely underrated and more people should be made aware of this awesome and useful plug-in, it transformed my workflow as a student who is doing a dissertation right now.

Currently, a list of citations appear in the right panel as long as you add a "static reference list" in the document. However, there is no way to know which citation correspond to which "static reference list" (unless you manually compare them). Is there a way, with a click of a button (e.g. clicking on the static reference list in the main body) can indicate which citation does it correspond to in the right panel? I think this will be especially useful when you have multiple citations in a document.

Thank you once again for creating this plug-in. I will recommend this to all of my friends and I wish that the number of users will grow exponentially.

Working on canvas?

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

Reference doesn't work in Canvas files

Describe the solution you'd like
A clear and concise description of what you want to happen.

If there is a reference in a note in the canvas, I'd like this app to show the relevant references.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Issue fetching references

Describe the bug

Starting today, I started getting an error when retrieving references. Nothing shows up on the panel even though there are several references on the active note.

To Reproduce

Open a note with @citekeys, nothing happens on the plugin board

Console output

Expected behavior

References showing on the plugin panel

Platform

OS: Ventura 13.2.1
Obsidian version: 1.1.15
Plugin version: 1.2.3

[FR] Pull bibliography from Zotero

Read data directly from Zotero library instead of using exported CSL file, just like plugins zotlit and pandoc reference list plugin, by using something like [@citekey]

Add the ability to specify `.bib` file on a per-note basis

Is your feature request related to a problem? Please describe.
I would like to keep my .bib files separated based by project rather than using one universal library. To use this plugin with this workflow I have switch the "library file path" depending on which project I'm working on.

Describe the solution you'd like
The relative path to the bibliography file can be listed in a bibliography frontmatter field, akin to Pandoc and by extension Quarto. This is used as the "library file path" for the note, so long as it is active.

Use Zotero Library as Semantic Scholar Fallback

Sometimes when using the application I reference a work not published as a traditional academic text, but are still meaningful to me (e.g. university lecture slides, internal company training, presentation, non-academic book, etc.). These are not counted as references by the plugin, yet they have entries and data in my Zotero library.

The feature I am proposing would be using the exported json or bib from a Zotero library as a fallback option if nothing is found on Semantic Scholar. Even if certain metrics are unavailable, such as cited works and citations, other information such as title, author, abstract, and BibTeX are still available. When using Zotero as a fallback, unavailable information is greyed out, but the reference is still counted as a reference and accessible via the reference map.

Templates?

Is it possible to modify the view via templates? I would love to add a Zotero link for example. The DOI or bibtex Link could be used to open the corresponding file via the url zotero://select/items/@[citekey]

Thanks :)

Finding citekey from links without prefix not working for Markdown links

I'd open a PR for this minor change, but I'm pointing out two potential changes and don't want to bundle them into one commit in case only one change or the other is necessary.

This bug is related to the functionality introduced in #17. In the linked code below, it looks like the if (matches2) {...} clause is indented too shallowly, blocking the rest of the function from returning.

obsidian-reference-map/src/utils.ts

Lines 125 to 144 in 3163c99

 if (findCiteKeyFromLinksWithoutPrefix) { 

 const citekeyRegex2 = /\[\[([^\s].*)\]\]/ig // Wiki Link 

 const matches2 = content.matchAll(citekeyRegex2); 

 if (matches2) { 

 for (const match of matches2) { 

 const trial = match[1].trim().split(' ')[0] 

 output.push(sanitizeCiteKey(trial)); 

 } 

 } 

 const citekeyRegex3 = /\[^\^([^\s].*)\]\(/ig // Markdown Link 

 const matches3 = content.matchAll(citekeyRegex3); 

 if (matches3) { 

 for (const match of matches3) { 

 const trial = match[1].trim().split(' ')[0] 

 output.push(sanitizeCiteKey(trial)); 

 } 

 } 

 } 

 return new Set(output.sort());

Also, maybe citekeyRegex3 could be malformed? Per experimentation with https://regexr.com/, the ^ after the opening \[ seems to be operating as a "beginning" rather than a "negated set". Below I suggest an update to that regex which matches my cursory testing, but you could be trying to negate something related to carats or slashes that I'm not quite understanding at the beginning of your regex.

/\[^\^([^\s].*)\]\(/ig  # Current citekeyRegex3
/\[([^\s].*)\]\(/ig     # Suggested citekeyRegex3

Here is an example of one such Markdown link that is not being detected, but in fact all such links are undetected:

[aderaNonwettingDropletsHot2013](notes/aderaNonwettingDropletsHot2013.md)

Platform

OS: Windows 10 Pro 10.0.19045
Obsidian version v1.1.9
Plugin version v1.1.1

please add show or hide journal

Please add "show or hide journal", thanks!

Connect with latest Zotero

It was failed to connect with the latest Zotero.

Detect citekeys / pandoc citations followed by page numbers

Is your feature request related to a problem? Please describe.
The problem is that Reference Map does not detect pandoc citations with citekeys followed by a page number.

Example:
This is recognized [@Psillos1996ScientificRealismPessimistic] but not [@Psillos1996ScientificRealismPessimistic, p. 313].

Describe the solution you'd like
Since it is common to cite a specific page from a citation, it would be very useful (indeed essential, in my usecase) if Reference Map was able to detect citekeys that are followed by page numbers like so [@citekey, p. x].

Describe alternatives you've considered
The Pandoc Reference List plugin is capable of detecting citekeys despite page numbers without issue, so it should be doable, perhaps by borrowing some code from there.

Accents (éè öü) not showing in title

I have been using this plugin for a week now. It is wonderfully fast. The only problem (and a big one) is that accented letters vanish from paper titles.
As you probably know, when a European language uses accents to spell words, they are necessary, not optional.
Even in English this is necessary, as many author names or concepts may bear these accents.

French letters with accents: é, à, é, ê, ç, ê...
German letters with accents: ö, ä, ü, ß
Spanish letters: ñ, á, ó...

Process:

When using "Reference Map: Search online and insert", the accents in the title disappear (but not in the summary, if there is one).
try:

"mécanique" will show up as "mcanique"
"Schrödinger" as "Schrdinger"
"El Niño" as "El Nio"
"ça freudien" as "a freudien"
"Strauẞ" as "Strau"
"forêt" as "fort"

Using UTF-8 generally solves such encoding issues, but I don't know exactly how the plugin is programmed.

I have been able to reproduce the bug using a small vault without any other plugin activated, which means that it is not due to a conflict.

The debugging mode was not useful, as the console stays silent.

Platform

OS: Windows and Linux
Obsidian version: latest (1.5.3)
Plugin version: latest (1.8.1)

Provide the ability to deselect selected references in the `reference map graph` view

Is your feature request related to a problem? Please describe.
I cannot find a way to deselect and item I've selected in the reference map graph view. I would like to be able to do this so that I can clear the selected reference panel at the top of the graph when I am no longer interested in learning about that reference.

Describe the solution you'd like
Provide the ability to deselect selected references in the reference map graph view.

Provide the ability to set a background or text border beneath references in the `reference map graph` view.

Is your feature request related to a problem? Please describe.
The text of references in reference map graph view is often blocked by nodes or otherwise difficult to see without a contrasting background for the text.

Describe the solution you'd like
Provide the ability to set a background or text border beneath references in the reference map graph view.

Support for BibTeX .bib database file

I am looking forward to use this plugin but my bibilography database is in a BibTeX .bib database file managed by BibDesk app.

Would it be possible to support this .bib file as well, as other reference plugins in the Obsidian, such as obsidian-pandoc-reference-list, do?

Thanks.

[FR] Add filtering function to Reference Map Graph

I hope to use the filtering function to exclude some nodes that I don't care about.

Provide the ability to autocomplete citation keys based on `.bib` file

Describe the solution you'd like
When typing in a markdown file in obsidian, typing @ triggers citation key auto completion based on the same .bib file that is being used by the plugin. This is in contrast to the current functionality that only works with citation keys when Zotero is connected.

Describe alternatives you've considered
mgmeyers's obsidian-pandoc-reference-list provides this functionality. While a wonderful plugin, I do not use many of it's other features and so would be grateful if this feature was implemented.

Feralflora proposed citation key autocomplete using Various Complements and QuickAdd here.

Filter redundent references

When the plugin searches for papers using semantic scholar, their database often seems inaccurate. an example is:
"AstronomicAL An interactive dashboard for visualisation integration and classification of data using Active Learning - G Stevens 2021" - the original paper references 17 items, Semantic Scholar references 29, some are obviously bugs on their end.

Top	bottom

Above demonstrates the issue

Semantic Scholar link

Appreciate you can't change Semantic Scholars side - Since broken links do not exist on Semantic Scholar, they have zero citations and zero references. Could you provide an option to filter these out from Batch results?

Long hangs

This plugin is causing long hangs on Obsidian. I presume it's because I have a large library. Obsidian will randomly hang for 30 seconds to minutes at a time while in use. This was fixed by disabling the plugin. Upon re-enabling the plugin, Obsidian hangs for a long time. Restarting obsidian with the plugin enabled adds a very long delay. I have an M2 nVME and plenty of unused DDR5 RAM so I doubt it's my hardware.

Support for citekeys in quotes

Citekeys in frontmatter, such as @brown2018application, are recognised by this plugin. They are not recognised if they are in quotes, "@brown2018application", as it is necessary in YAML.

Would it be possible for this plugin to process quoted references?

Support for bibtex citekeys

This is an amazing plugin for which I looked out for for a long time. However, most of my references are pandoc citekeys referring to a citation database (Zotero, bibtex,...). I think it is a typical situation, especially in academia. So, without being able to include those, 80% of my references would not be included and the value of the plug-in diminishes. Would it be very complicated to add and parse citation keys? Do you know the reference map that Zettlr creates in this fashion: https://docs.zettlr.com/en/academic/citations/ and https://docs.zettlr.com/en/core/sidebar/

Citekey references don't show up

First of all: great plugin, I already love it.

While DOI detection works fine, I have an issue using the cite keys, please see the screenshots:

The CSL JSON file is exported via Zotero:

I tried both, Better CSL JSON and BetterBibTex JSON, both files seem not to work. Am I doing something wrong?

Full.zip

Thanks!

Detection of citekeys in links without the @ prefix

This request comes from Discord user Cat (they/them)

Is your feature request related to a problem? Please describe.
Sometimes it is helpful to have citekey's without the @ symbol. One use case might be if you name your files using the citekey and reference those files in notes using the [[citekey]] link pattern.

Describe the solution you'd like
Show index cards for citekey wikilinks and citekey markdownlinks without the @ prefix

Describe alternatives you've considered
Changing the filename to put @ prefix for already existing libraries is difficult.

unable to add paper when using citekey

Hey, it's me again :)
Is it me or have I found a weird bug? From yesterday RefMap is unable to recognize papers using citekey, although it is in my Zotero library.
Let me show you an example (see attachment): when using doi.org/10.1016/j.arr.2022.101807 paper is recognized, when using [@raffinSedentaryBehaviorBiological2023] it is not.

Invalid regular expression

The problem

I guess this could be the problem but I'm not able to 'read' (understand) what's the problem and how to solve it, could you help?
Thanks a lot, the plugin looks very promising!

`findZoteroCiteKeyFromID` is unexpectedly case-sensitive

Describe the bug

findZoteroCiteKeyFromID is unexpectedly case-sensitive. If the case of the DOI does not match exactly (incl. case) in the Zotero record, then the citekey is not picked up.

It is possible that this affects other features, but I've only noticed it in this particular feature flag. This crops up because Semantic Scholar often has all-caps DOIs, and citations generated from journal sources e.g. using Zotero's browser plugin often generate lower- or mixed-case DOIs.

To Reproduce

Enable the specified feature, have an appropriately-updated/synced CSL-JSON from Zotero, and have one of your notes with doi:{{doi}} where {{doi}} may differ in its case relative to the DOI field in the Zotero library/interface.

Expected behavior

The citekey chould be picked up regardless of differences in case between the Zotero item and the DOI specified in the Obsidian note.

Platform

OS: Windows 10
Obsidian v1.1.9
Plugin version v0.9.1

Additional context

I'm not very familiar with TypeScript/JavaScript, but I believe I've found the relevant parts of the codebase where changes would be made. This is probably related to the doi-regex dependency matching "case insensitive for ASCII chars (but capitalised in the registry)".

It seems setCiteKeyID is called when findZoteroCiteKeyFromID is enabled, and at least the code path in setCiteKeyID corresponding to the csl-json adapter results in the match happening in a case-sensitive way.

obsidian-reference-map/src/components/ReferenceMapList.tsx

Lines 30 to 43 in 3ed6033

 const processPapers = async (currentView: MarkdownView) => { 

 const rootPapers: IndexPaper[] = []; 

 const fileContent = await app.vault.cachedRead(currentView.file); 

 const paperIds = getPaperIds(fileContent); 

 paperIds.forEach(async (paperId) => { 

 const paper = await props.viewManager.getIndexPaper(paperId); 

 let paperCiteId = paperId 

 if (props.settings.searchCiteKey && props.citeKeyData && props.settings.findZoteroCiteKeyFromID) { 

 paperCiteId = setCiteKeyId(paperId, props.citeKeyData, props.adapter) 

 } 

 if (paper !== null) rootPapers.push({ id: paperCiteId, paper: paper }); 

 if (rootPapers.length > 0) setPapers(removeNullReferences(rootPapers)); 

 });

obsidian-reference-map/src/utils.ts

Lines 225 to 240 in 3ed6033

 export const setCiteKeyId = (paperId: string, citeKeyData: citeKeyLibrary[], adapter = ''): string => { 

 if (adapter === 'csl-json') { 

 const citeKey = citeKeyData.find((item) => 

 item?.DOI === paperId || item?.DOI === `https://doi.org/${paperId}` 

 )?.id; 

 return citeKey ? '@' + citeKey : paperId; 

 } else if (adapter === 'bibtex') { 

 const citeKey = citeKeyData.find((item) => 

 item.fields?.doi?.[0] === paperId || item.fields?.doi?.[0] === `https://doi.org/${paperId}` 

 )?.key; 

 return citeKey ? '@' + citeKey : paperId; 

 } else { 

 return paperId 

 } 

 }

Support DOI search in Search Reference

Is your feature request related to a problem? Please describe.
Support DOI search in Search Reference

Describe the solution you'd like
It would be great to support retrieving doi, like 10.1111/1475-6765.12529, or doi:10.1111/1475-6765.12529 or https://doi.org/10.3390/e20110814

[FR] Eliminating duplicate references

When a file contains both citekey and doi, it may result in duplicate bibliographic information. Eliminating duplicate references is not necessary, but it would be better if it could be achieved.

Port of zotero is not available in settings

First, thank you so much for this plugin.

I can't integrate zotero and I can't try to change my zotero port which seems to be 23119.

Mx Linux
Obsidian version 1.4.16
Plugin version 1.5.5

FR: Search the citation/references

I think being able to search through the list of references/citations would make a lot of sense for this plugin?

minor FR: label citations/reference count

especially now with the label removed (which was good for space-saving!) I now cannot tell which of the two numbers is citations, and which is references.

as a solution, you could label then (number + r, number + c) or add a tooltip to it maybe?

FR: Add support to DOIs that are part of links

I import papers via Zotero Integration which bring DOIs as links so that I can quickly refer to the web version of each paper. However, your plugin does not take a DOI that is part of a markdown link a-la [DOI#](link-to-DOI). It would be great to have this feature which will save those of us using this workflow having to reformat hundreds of files. Thanks!

Feat: Find reference via title of the note

Hi there! My literature notes have the note's title as the paper's title. Is it possible with the Semantic Scholar API to find the reference via the note's title (as an option)? Or does the API not support full-text search/matching?

Error when use citekey on macOS

Hello,

Many thanks for your excellent plugin!

I try to use citekey to build the reference map. However, it has an issue with the output.

It can only works with some citations.

Here is the setting of the plugin:

I am sure that cited citekeys are included in the reference file.

May I know how to solve this problem?

Many thanks!

Account for doi ending with a point

Some bibliography style put a "." at the end of doi. Those doi are not see by reference-map plugin.

e.g.

https://doi.org/10.1371/journal.pone.0131069. -> not worknig

https://doi.org/10.1371/journal.pone.0131069 -> work

Thanks for your work!

[FR] Add literature in Reference Map Graph directly

For example, add literature A、B in Reference Map Graph directly. The connection between A B will show in Reference Map Graph.

Then, when activate a file with reference C, the connection between A B C will show in Reference Map Graph.

Detect citekeys in double brackets `[[]]`

Is your feature request related to a problem? Please describe.
My workflow is to import relevant literature from Zotero to markdown files in Obsidian and naming the MD file identical as the bibtex citekey, e.g. @author.shorttitle.year. Linking to that document using double brackets, like [[@author.shorttile.year]] gets not detected as valid citekey and thus does not show up in the reference map. [@author.shorttile.year]

Describe the solution you'd like
It would be great to see [[@author.shorttile.year]] in the ref map.

Edit: got the problem, it was part of this sentence: (see [[@tu.ARMABasedDigitalTwin.2021]]). The last ) breaks the detection. So it's not about the brackets, but what character follows.

FR: Make sidebar more space efficient

Thank you for the plugin, it seems incredibly useful!

Given the nature of the plugin, there is often a lot of content added in its sidebar tab, not only requiring you to scroll through it, but even requiring you to scroll a lot sometimes.

Therefore, I think it might make sense to make this the sidebar more space efficient, for example by removing padding and reducing font size.

Also, here are some ui changes which could save even more space:

Show all the references in the Zotero library at once?

Is there a way to show all the references at once in the map without showing the connections to other references that I do not have (in Zotero)?
I want to be able to visualize the connections among only the references I own.

export references to clipboard

A lot of the papers I read have a lot of overlap in the references they use. It would be useful to copy the list of references generated to the clipboard (ideally in a customisable format i.e [[title - Author Year]] , as that's how my notes are titled for papers). That way it would be easy to see which notes I already have created as well as see which papers have the most overlap.

Could you see this being a useful addition?

Cheers,
Grant

When clicking a button on the index card in the `reference map`, highlight / zoom in on the reference in the `reference map graph` view

Is your feature request related to a problem? Please describe.
I would like to be able to quickly zoom in or focus on a specific reference in the reference map graph view via selecting a card (or clicking a button on a card) rather than panning across the graph in search of the reference.

Describe the solution you'd like
When clicking a button on the index card in the reference map, highlight / zoom in on the reference in the reference map graph view. Maybe:

2nd+ degree references fade out,
2nd+ degree references are hidden, or
the view zooms in on the reference and its direct connections.

P.S. Thanks for the amazing plugin!

bibtex output different to SematicScholar cite (causing bib error)

As an example

GAN Paper gives:
@inproceedings{Goodfellow2014GenerativeAN,
title={Generative Adversarial Nets},
author={Ian J. Goodfellow and Jean Pouget-Abadie and Mehdi Mirza and Bing Xu and David Warde-Farley and Sherjil Ozair and Aaron C. Courville and Yoshua Bengio},
booktitle={NIPS},
year={2014}
}

whereas your output is:
@['JournalArticle', 'Conference']{Goodfellow2014GenerativeAN,
author = {Ian J. Goodfellow and Jean Pouget-Abadie and Mehdi Mirza and Bing Xu and David Warde-Farley and Sherjil Ozair and Aaron C. Courville and Yoshua Bengio},
booktitle = {NIPS},
pages = {2672-2680},
title = {Generative Adversarial Nets},
year = {2014}
}

seem like all of the @#### are not coming out correct.

Not sure if thats an API issue but currently they're not usable in bib files

Thanks again for the great plugin.

Unable to find a paper when there is no whitespace after a citekey

hey!

I was using a citekey at the end of the sentence like that: [@interestingPaper_Year]. And for some reason, this plugin was unable to parse a citekey. I added a whitespace like that [@interestingPaper_Year] . and then the paper was parsed into Reference Map automatically.
The same behaviour was noticed when creating metadata template {{author}}, {{year}} %%[{{id}}] %%, I was forced to add that whitespace in order for paper to parse into the system.

It would also be great help for me if you can explicitly add {{citekey}} to allowed metadata fields

p.s. I was looking for something to manage my zotero lib from obsidian and accidentally bumped up into your plugin. I love it, great work!

[FR] Insert the metadata into the corresponding entry in the note's YAML area

Is your feature request related to a problem? Please describe.
Sometimes, I create literature notes in Obsidian and add literature information in the YAML section.

Describe the solution you'd like
I hope that the search insert and search create functions will provide the ability to insert metadata into the corresponding entry in the note's YAML section.

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	if (findCiteKeyFromLinksWithoutPrefix) {
	const citekeyRegex2 = /\[\[([^\s].*)\]\]/ig // Wiki Link
	const matches2 = content.matchAll(citekeyRegex2);
	if (matches2) {
	for (const match of matches2) {
	const trial = match[1].trim().split(' ')[0]
	output.push(sanitizeCiteKey(trial));
	}
	}

	const citekeyRegex3 = /\[^\^([^\s].*)\]\(/ig // Markdown Link
	const matches3 = content.matchAll(citekeyRegex3);
	if (matches3) {
	for (const match of matches3) {
	const trial = match[1].trim().split(' ')[0]
	output.push(sanitizeCiteKey(trial));
	}
	}
	}
	return new Set(output.sort());

	const processPapers = async (currentView: MarkdownView) => {
	const rootPapers: IndexPaper[] = [];
	const fileContent = await app.vault.cachedRead(currentView.file);
	const paperIds = getPaperIds(fileContent);
	paperIds.forEach(async (paperId) => {
	const paper = await props.viewManager.getIndexPaper(paperId);
	let paperCiteId = paperId
	if (props.settings.searchCiteKey && props.citeKeyData && props.settings.findZoteroCiteKeyFromID) {
	paperCiteId = setCiteKeyId(paperId, props.citeKeyData, props.adapter)

	}
	if (paper !== null) rootPapers.push({ id: paperCiteId, paper: paper });
	if (rootPapers.length > 0) setPapers(removeNullReferences(rootPapers));
	});

	export const setCiteKeyId = (paperId: string, citeKeyData: citeKeyLibrary[], adapter = ''): string => {
	if (adapter === 'csl-json') {
	const citeKey = citeKeyData.find((item) =>
	item?.DOI === paperId \|\| item?.DOI === `https://doi.org/${paperId}`
	)?.id;
	return citeKey ? '@' + citeKey : paperId;
	} else if (adapter === 'bibtex') {
	const citeKey = citeKeyData.find((item) =>
	item.fields?.doi?.[0] === paperId \|\| item.fields?.doi?.[0] === `https://doi.org/${paperId}`
	)?.key;
	return citeKey ? '@' + citeKey : paperId;
	} else {
	return paperId
	}

	}