Tuesday, October 15, 2024

Next.js, SWC, and citeproc-js

Last year I got a bug report that Citation.js was not working when built in a Next.js production environment for unclear reasons. Next.js is a popular server framework to make web applications with React, and by default transforms all JavaScript files and their dependencies into “chunks” to improve page load times. In production environments, Next.js uses the Rust-based “Speedy Web Compiler” SWC to optimize and minify JavaScript code.

I was able to figure out that somewhere, this process transformed an already difficult-to-grok function (makeRegExp) in the citeproc dependency into actually broken code. After some trial and error I found the following MCVE (Minimal Complete Verifiable Example):

function foo (bar) {
    var bar = bar.slice()
    return bar
}

foo(["bar"])

// equivalent to

function foo (bar) {
    var bar // a no-op in this case, apparently
    bar = bar.slice()
    return bar
}

foo(["bar"])

But then, in the chunks generated by Next.js, the argument bar gets optimized away from foo(), generating the following code (it also inlines the function).

var bar;
bar = bar.slice();

Now, this is a simple mistake to make. If you expect var bar to actually re-declare the bar argument, the argument is clearly unused and can be removed. Due to the quirks of JavaScript that is not the case though, and the incorrect assumption leads to incorrect code.

This is not a one-off thing though: last August I got another, similar bug report with the same cause: some slightly non-idiomatic code (CSL.parseXml) from citeproc got mis-compiled by SWC. I found another MCVE:

function foo (arg) {
    const a = { b: [] }
    const c = [a.b]
    c[0].push(arg)
    return a.b[0]
}

The compiler misses that c[0] refers to the same object as a.b and thinks that makes the function a no-op, though it does not optimize it away fully, instead producing the following:

function (n) {
    return [[]][0].push(n), [][0]
}

This was apparently already noticed and fixed last May though the SWC patch still has to land in a stable version of Next.js. Interestingly, the patch includes a test fixture that uses CSL.parseXml as example code; apparently citeproc is a good stress-test of JavaScript compilers.

This is all fine with me, I am not going to blame the maintainers of a complex open-source project like SWC for occasional bugs. However, I would like to see a popular framework like Next.js, with 6.5 million downloads per week and corporate backing, to do more testing for such essential parts of their infrastructure. I also do not see them among the sponsors of SWC.

Edited 2024-10-15 at 17:26: Actually, the creator for SWC is also a maintainer for Next.js, though I do not know in which order. Given that, it makes more sense that they switched away from the well-tested but slower BabelJS in version 12, and more confusing why they did not test it a bit more thoroughly.

Tuesday, March 5, 2024

Citation.js: BibLaTeX Data Annotations support

Version 0.7.9 of Citation.js comes with a new feature: plugin-bibtex now supports the import and export of Data Annotations in BibLaTeX files. This means ORCID identifiers from DOI, Wikidata, CFF, and other sources can now be exported to BibLaTeX. Combined with a BibLaTeX style that displays ORCID identifiers, you can now quickly improve your reference lists with ORCIDs.

const { Cite } = require('@citation-js/core')  
require('@citation-js/plugin-bibtex')  
require('@citation-js/plugin-doi')

Cite
  .async('10.1111/icad.12730')
  .then(cite => cite.format('biblatex'))

This produces the following BibLaTeX file (note the author+an:orcid field):

@article{Willighagen2024Mapping,  
  author = {Willighagen, Lars G. and Jongejans, Eelke},  
  author+an:orcid = {1="http://orcid.org/0000-0002-4751-4637"; 2="http://orcid.org/0000-0003-1148-7419"},  
  journaltitle = {Insect Conservation and Diversity},  
  shortjournal = {Insect Conserv Diversity},  
  doi = {10.1111/icad.12730},  
  issn = {1752-458X},  
  date = {2024-03-02},  
  language = {en},  
  publisher = {Wiley},  
  title = {Mapping wing morphs of \textit{{Tetrix} subulata} using citizen science data: Flightless groundhoppers are more prevalent in grasslands near water},  
  url = {http://dx.doi.org/10.1111/icad.12730},  
}

References

Saturday, March 2, 2024

Including ORCID identifiers in BibLaTeX (and using them)

On the Fediverse, @petrichor@digipres.club posited the question how to include identifiers for authors in Bib(La)TeX-based bibliographies:

Any Bib(La)TeX/biber users have a preferred way to include author identifiers like ORCID or ISNI in your .bib file? Ideally supported by a citation style that will include the identifiers and/or hyperlink the authors.

https://digipres.club/@petrichor/112020378570169913

I have wanted to try including ORCIDs in bibliographies for a while now, and while CSL-JSON makes it nearly trivial to encode, neither CSL styles nor CSL processors are at the point where those can actually be inserted in the formatted bibliography. However, BibLaTeX may grant more opportunities, so this piqued my interest.

I first thought of the Extended Name Format (Kime et al., 2023, §3.4), which allows breaking names up in key-value pairs. Normally, those are reserved for name parts (family, given, etc.), but I believed I had seen a way to define additional “name parts”, one of which could be used for specifying the ORCID. However, in the process of figuring that out, I found the actual, intended, proper solution.

BibLaTeX has, exactly for things like this, Data Annotations (Kime et al., 2023, §3.7). For every field, or every item of every field in the case of list fields, additional annotations can be provided. (There are some additional features and nuances; for a full explanation see the manual.) For ORCIDs, data annotations could look like this:

@software{willighagen_2022_7017208,
  author          = {Willighagen, Lars and
                     Willighagen, Egon},
  author+an:orcid = {1="0000-0002-4751-4637"; 2="0000-0001-7542-0286"},
  title           = {ISAAC Chrome Extension},
  month           = aug,
  year            = 2022,
  publisher       = {Zenodo},
  version         = {v1.4.0},
  doi             = {10.5281/zenodo.7017208}
}

Now, implementing it in a BibLaTeX style proved more difficult than I hoped, but that might have been due to my inexperience with argument expansion and Biber internals. I started with the authoryear style and looked for the default name format that it uses in bibliographies; this turned out to be family-given/given-family. I copied that definition, and amended it to include the ORCID icon after each name (when available). To insert the icon, I used the orcidlink package. This part was tricky, as \getitemannotation does not work in an argument to \orcidlink or \href, but I ended up with the following.

\DeclareNameFormat{family-given/given-family}{%
  % ...
  \hasitemannotation[\currentname][orcid]
    {~\orcidlink{\expandafter\csname abx@annotation@literal@item@\currentname @orcid@\the\value{listcount}\endcsname}}
    {}%
  % ...
  }

References. Willighagen, Lars [ORCID icon with cyan outline] and Egon Willighagen [ORCID icon with cyan outline] (Aug. 2022). ISAAC Chrome Extension. Version v1.4.0. DOI: 10.5281/zenodo.7017208

You could repeat the same with ISNI links, or Wikidata, VIAF, you get the idea. Then you could put the \DeclareNameFormat in a new authoryear-orcid.bbx file so that the changes do not show up in the in-text citations, and set the bibliography style like so:

\usepackage[bibstyle=authoryear-orcid]{biblatex}

This can all be seen in action on Overleaf: https://www.overleaf.com/read/gvxqmrqmwswh#f156b5

References

Friday, February 2, 2024

Three new userscripts for Wikidata

Today I worked on three user scripts for Wikidata. Together, these tools hopefully make the data in Wikidata more accessible and make it easier to navigate between items. To enable these, include one or more of the following lines in your common.js (depending on which script(s) you want):

mw.loader.load('//www.wikidata.org/w/index.php?title=User:Lagewi/properties.js&oldid=2039401177&action=raw&ctype=text/javascript');
mw.loader.load('//www.wikidata.org/w/index.php?title=User:Lagewi/references.js&oldid=2039248554&action=raw&ctype=text/javascript');
mw.loader.load('//www.wikidata.org/w/index.php?title=User:Lagewi/bibliography.js&oldid=2039245516&action=raw&ctype=text/javascript');

User:Lagewi/properties.js

Note: It turns out there is a Gadget, EasyQuery, that does something similar to this user script.

Inspired by the interface for observation fields on iNaturalist, I wanted to easily find entities that also used a certain property, or that had a specific property-value combination. This script adds two types of links:

  • For each property, a link to query results listing entities that have that property.
  • For each statement, a link to query results listing entities that have that claim, e.g. this property-value combination. (This does not account for qualifiers.)

These queries are certainly not useful for all properties: listing instance of (P31) human (Q5) is not particularly meaningful in the context of a specific person. However, sometimes it just helps to find other items that use a property, and listing other compounds found in taxon (P703) Pinus sylvestris (Q133128) is interesting.

https://www.wikidata.org/wiki/User:Lagewi/properties.js

Screenshot of three claims on a Wikidata page. Below each property is a link titled "List entities with this property", and below each value a link titled "List entities with this claim".

User:Lagewi/references.js

Sometimes, the data on Wikidata does not answer all your questions. Some types of information are difficult to encode in statements, or simply has not been encoded on Wikidata yet. In such cases, it might be useful to go through the references attached to claims of the entity, for additional information. To simplify this process, this user script lists all unique references based on stated in (P248) and reference URL (P854). The references are listed in a collapsible list below the table of labels and descriptions, collapsed by default to not be obtrusive.

https://www.wikidata.org/wiki/User:Lagewi/references.js

Screenshot of the Wikidata page of Sylvie Deleurance (Q122350848) with, below the list of labels, descriptions, and aliases, a collapsible list titled "Other resources", containing links.

User:Lagewi/bibliography.js

Going a step further than the previous script, this user script appends a full bibliography at the bottom of the page. This uses the (relatively) new citation-js tool hosted on Toolforge (made using Citation.js). Every reference in the list of claims has a footnote link to its entry in the bibliography, and every entry in the bibliography has a list of back-references to the claims where the reference is used, labeled by the property number.

https://www.wikidata.org/wiki/User:Lagewi/bibliography.js

Screenshot of two claims on Wikidata, each with a reference. Both references have a darker grey header containing a link, respectively "[4]" and "[5]".

Screenshot of a numbered list titled "Bibliography". Each item in the list is a formatted reference, and below each reference is a series of links titled with a property number.