Citoid

Group:	Editing
Start:	2014-05-08
Backlog:	#citoid

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The citoid Node.js service generates citation data given a URL, DOI, ISBN, PMID, PMCID or QID. It has a companion extension, Citoid , which aims to provide use of the citoid service to VisualEditor , but also may be accessible from the wikicode editing palette, if activated.

It is currently deployed in all VisualEditor-enabled WMF-Wikis ^[1], though the extension is only configured on some of them.

Public API

To request metadata about a URL, DOI, PMCID, PMID or QID, you can use the English language API endpoint. Try it! Or, for language localised requests, use your preferred language Wikipedia.

Issue tracker and project management

Bugs, issues, and suggestions for improvement can be added to the Citoid Phabricator project. (Learn more about Phabricator.)

Installation

Best results are obtained if the URLs that are popular on your site are already available in Zotero. If they're not, performance will be better if you create Zotero translators for your popular sites first.

Citoid is a Node.js app that also requires a working installation of Zotero's translation server, which uses the Zotero translators library, and xulrunner.

Install nodejs and npm

Install nodejs and npm. When you are using Ubuntu and depending on OS version you will not end up with the most recent version of nodejs. You are recommended to use nvm to manage nodejs installations. Compatible versions of node are listed in package.json.

sudo apt-get install nodejs npm

Warning:

In order to run the current version of the citoid service, you need the version 20 of node.

For other systems, see:

https://nodejs.org/download/
https://nodejs.org/en/download/package-manager/
(Debian Squeeze, Wheezy) https://gist.github.com/x-Code-x/2562576

Install from scratch

Install and configure Zotero's translation server

For citoid versions 0.5.3 or earlier, see Translation-server installation instructions

For citoid versions 1.0.0 or higher:

Clone the repository git clone --recursive [email protected]:repos/mediawiki/services/zotero.git
1. If you forget the recursive flag, do git submodule init then do git submodule update
Change into the directory cd zotero
Install the librariesnpm install
Run the server: npm start
You should get the following output:

(3)(+0000000): Translators initialized with 528 loaded

(3)(+0000003): Listening on 0.0.0.0:1969

Try a query to verify it's working: curl -d 'https://www.ncbi.nlm.nih.gov/pubmed/?term=crispr' -H 'Content-Type: text/plain' http://127.0.0.1:1969/web

Install and configure citoid service

Get the code

If you want to do an anonymous checkout:

git clone https://gerrit.wikimedia.org/r/mediawiki/services/citoid

Or if you plan to hack citoid, then please follow the Gerrit 'getting started' docs and use an authenticated checkout url instead, such as:

git clone ssh://<user>@gerrit.wikimedia.org:29418/mediawiki/services/citoid

JS dependencies

Install the JS dependencies. Run this command in the citoid directory:

npm install

Modify config.yaml

Config.yaml contains the configuration for the citoid service. The defaults should work out of the box for development, however, they may need to be modified in a deployment set-up.

Run the translation server

You'll first need to run translation-server; see the directions on its github page, but generally from the translation-server directory you should run:

git submodule init
git submodule update
npm i
npm start

Run Citoid server

You should be able to start the citoid web service from the citoid directory using:

node server.js

This will start the citoid service on port 1970. To test it, navigate to http://localhost:1970 in your browser. You'll be able to test sample queries from this page.

Install Citoid extension

See Extension:Citoid for how to download and install the Citoid MediaWiki extension.

Configure Citoid on a Citoid-enabled wiki

The Citoid extension must be configured using special TemplateData maps and a special citoid-specific message. It is currently deployed in all VisualEditor-enabled WMF-Wikis, but it must be configured before it can be used.

Ensure each template to be used in MediaWiki:Citoid-template-type-map.json has an 'citoid' maps value

Warning:

Each template listed in Citoid-template-type-map.json MUST have a citoid maps value! Otherwise completely empty templates will be inserted. If there is no maps value for a given template, it is better to use a different template that does in the MediaWiki message, even if the types don't match well.

Since Citoid has its own set of fields for each document type (for instance, the journal name is called 'publicationTitle' in citoid, but 'journal' in Template:Cite_journal), each Template must have TemplateData defined that creates a map between citoid's fields and the Template's field. Calling the map 'citoid' lets the Citoid extension know which map to look for. If the map 'citoid' doesn't suit your purposes for use with say, a userscript, you may create a citoid service related map that is called something else; an unlimited number of maps with unique keys are allowed in the maps object. Note that you can only see TemplateData maps in edit mode; they are not visible in the TemplateData table.

Fields issn and isbn can have Arrays [] in the citoid map; using them ensures that only one ISBN is in the field. If you do not place the parameter inside an Array (i.e. isbn: "[ISBN]"), multiple ISBNs or ISSNS will be concatenated in the field (i.e. "issn: 1234-5678, 7777-7777'). All 'person' fields, e.g. author, editor, translator, contributor etc, support 2D Arrays [[]] in the citoid map for first name and last name. It also supports a 1D array for full name fields; this will concatenate the name with the first field first, separated by a space. See sample templateData below for examples.

Examples of map objects on English Wikipedia that are compatible with the Citoid extension are:

Configure special MediaWiki namespace Citoid message

Warning:

It is best if you add this message after each template has a template data map as specified in the above section. Otherwise, in the meantime empty templates will be inserted, because each template needs a template data map to be usable.

You'll need to configure a special MediaWiki: namespace message. This message maps the native citoid types (website, book, journalArticle) to the appropriate template (Cite web, Cite book, Cite journal). You should match a template to every single citoid type; there is no default behaviour if no template is matched to a particular type. It's better to have a bad match (there may be some fields in common between video liner notes and a book, or video liner notes and a video, for example) than none at all.

You may consider using en wiki's Template:Citation as a catch-all for types where there is no good type match as it is designed for this situation.

An sample namespace message is found here: Citoid/MediaWiki:Citoid-template-type-map.json

Every available citoid type is listed as a key in the sample namespace message.

Troubleshooting Citoid VisualEditor Extension

Open your browser's console. The Citoid extension will log errors here.

Inspector does not appear in the toolbar

An icon for the inspector should appear in the toolbar menu. This means either citoid is not installed properly or not configured properly. Verify the extension and dependent extensions are installed on the page localhost:/wiki/Special:Version.

If the extensions are installed and the icon does not appear in the toolbar, it most likely means there's a problem with MediaWiki:Citoid-template-type-map.json. If there is no message at that location, or if the JSON is invalid, the inspector will not load. Look at the messages logged to your browser's console to diagnose the specific problem with the message. Alternatively, you may need to refresh your JavaScript cache.

Get "could not make a citation for you" every time

You may consistently get this error if the citation template being inserted contains no maps data, or if the maps data is there but not making it to the MediaWiki API. First, determine the template that the inspector is attempted to insert, for example, Template:Cite web/doc. View source of the template or documentation page to verify that

"maps": {

    "citoid": {

is present and contains fields. Then verify that these data are making it to the MediaWiki API by visiting the API page, i.e. http://localhost/api.php?action=templatedata&titles=Template:Cite%20web/doc&format=jsonfm on your local installation, or https://en.wikipedia.org/w/api.php?action=templatedata&titles=Template:Cite%20web&format=jsonfm on en wiki.

If the maps object is present in TemplateData, but not in the API response, try editing the template where the TemplateData is transcluded i.e. Template:Cite_web (but making no changes) and saving it, a.k.a. a "null edit". There is a known bug with transcluded TemplateData where it can take a long time for the API to update (T52372); null edits force the change.

If the response from the API looks okay, there may be an issue with installation of the citoid service. Open up your browser's debugger to confirm that the responses from the citoid server are OK.

The inspector is still "pending" after a really long time following insertion

This typically means there is a bug. If you open your JavaScript console, you will likely find error messages that will help you debug.

Access date is formatted differently on my wiki

The dates are in ISO format, which is an international standard. On the back-end, we're sticking to ISO and in the future all dates will all be in ISO, not just access date. This is because it is an unambiguous way to present the date in any language. If the community doesn't like the way this looks to the user, it is possible to edit the citation template to format the ISO dates to something that is standard in your language. For instance, you can add logic to the template such that if the date is detected to be in ISO yyyy/mm/dd format, the date is reformatted *to appear* to be dd/mm/yyyy on the page. However, if you do this, the underlying data (i.e. when you edit the wikitext, or the form in VisualEditor) will still remain the same.

Troubleshooting the citoid service

My favourite site isn't recognised by citoid and only gets basic information

The Citoid service relies on the brilliant Zotero community for much of the "magic", as Zotero translators need to be written for each site. You can see a list of all Zotero translators at https://github.com/zotero/translators. Right now, Zotero best supports English-language sources. We need your help to improve coverage of other sites. You can write your own Zotero translator. Start by looking at Citoid/Creating Zotero translators.

Testing for the translators using the "server" option or 'v' flag

To test with translation-server, download and install https://github.com/zotero/translation-server Your translator will need to have the 'v' flag enabled for 'browserSupport'. More here on that: https://www.zotero.org/support/dev/translators As an example, see https://github.com/zotero/translators/blob/master/A%20Contra%20Corriente.js ; you will see there are a bunch of letters, one of which is v, which corresponds to translation-server. If server support is not enabled by testing it/then adding the 'v' flag, we won't be able to use the translator.

Hacking citoid

Installation

You can install Citoid with Docker. See: MediaWiki-Docker/Extension/Citoid

After following these instructions, you will further need to add wiki pages to get citoid working. The most expedient way to do this is to export the following pages from en-wiki:

Template:Citation
Template:Cite_web
Template:Cite_news
Template:Cite_journal
Template:Cite_book
MediaWiki:Citoid-template-type-map.json
MediaWiki:Cite-tool-definition.json
MediaWiki:Visualeditor-cite-tool-name-web
MediaWiki:Visualeditor-cite-tool-name-book
MediaWiki:Visualeditor-cite-tool-name-journal
MediaWiki:Visualeditor-cite-tool-name-news

And then import them: localhost:8080/wiki/Special:Import.

After importing the Templates, you may need to navigate to the template, hit the edit button, and then hit save (a "null" edit), in order for the templatedata to propagate to the DB.

(Unfortunately en wiki templates as of 2022 currently also require a file from commons, and if your wiki is not set up to work with commons you will get an error. You can copy this file locally and make a few changes to the CS1 Module.)

Running tests

citoid service

npm test runs eslint and unit tests.

mocha runs the full set of tests. (You can run ./node_modules/mocha/bin/mocha if you only have mocha installed locally)

npm run-script coverage runs the tests and reports code coverage.

In order for all tests to pass, you will need a WorldCat wskey in your config.dev.yaml file, which you can request at here.

Another reason why some tests may fail erroneously is if your DNS will redirect invalid domains to a valid IP (Such as BT Internet's DNS); in some cases, this causes a 520 response instead of a 400 response to be returned. This can be fixed by configuring your internet connection to use OpenDNS or another DNS that does not do this.

Citoid extension

See: Manual:JavaScript unit testing

Formatting the citation output of Citoid

Citoid depends on Extension:TemplateData for mapping variables from a wiki's citation templates to citoid's fields. However, it may not be apparent that the formatting output of citations from Citoid isn't managed explicitly by Citoid but rather by TemplateData. As such, if a particular citation format is required, you'll need to adjust the "format" in your citation templates' TemplateData. Guidance is provided in Help:TemplateData. You may, for example, see "format": "inline" at the bottom of many pre-existing TemplateData Citoid maps, which means the resulting citation output will appear inline. However, this will not put any spacing in the resulting citation text. If the output should have a space before each pipe character but no spaces before or after an equals sign in the citation, one may set "format": "{{_ |_=_}}". The code would typically be placed before closing out with the final curly brace, as such:

<templatedata>
{
    "description": "",
    "params": {
        "1": {
            "label": "",
            "description": "",
            "type": ""
        },
        "2": {
            "label": "",
            "description": "",
            "type": ""
        }
    },
    "paramOrder": [

    ],

	"maps": {
        "citoid": {

		}
	},
	"format": "{{_ |_=_}}"
}
</templatedata>

Consult Help:TemplateData for more formatting options.

It's worth noting that if you want to change this format on a large wiki project, you should probably discuss it somewhere with the community as users may have strong feelings about formatting in citations. Additionally, note that when "format" is changed on an existing wiki, it will cause VisualEditor to update the formatting of each citation whenever someone makes changes to it. On large wikis like Wikipedia, this can cause annoying dirty diffs and even accidental edit wars with bots that maintain citations.

References

↑ CommonSettings.php on phabricator.wikimedia.org (no feature flag set)

[1] CommonSettings.php on phabricator.wikimedia.org (no feature flag set)

[1]

Public API

Issue tracker and project management

Installation

Install nodejs and npm

Install from scratch

Install and configure Zotero's translation server

Install and configure citoid service

Get the code

JS dependencies

Modify config.yaml

Run the translation server

Run Citoid server

Install Citoid extension

Configure Citoid on a Citoid-enabled wiki

Ensure each template to be used in MediaWiki:Citoid-template-type-map.json has an 'citoid' maps value

Configure special MediaWiki namespace Citoid message

Troubleshooting Citoid VisualEditor Extension

Inspector does not appear in the toolbar

Get "could not make a citation for you" every time

The inspector is still "pending" after a really long time following insertion

Access date is formatted differently on my wiki

Troubleshooting the citoid service

My favourite site isn't recognised by citoid and only gets basic information

Testing for the translators using the "server" option or 'v' flag

Hacking citoid

Installation

Running tests

citoid service

Citoid extension

Formatting the citation output of Citoid

See also

References