Expand pubmed regex to include digits starting from 1 in citoid
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	Mvolz
	Jan 9 2017, 2:51 PM

Description

Pubmed IDs apparently start at 1:
https://www.ncbi.nlm.nih.gov/pubmed/1

However, we currently only recognise a pubmed id if it is 6 or 7 digits long. We should expand the definition in

CitoidService.prototype.addResponseFunction (https://github.com/wikimedia/citoid/blob/master/lib/CitoidService.js) to include these.

Getting Started

citoid is a Node.js application (written in JavaScript) that retrieves information about a webpage, book, journal article, etc. given a URL to the webpage or some other identifier, like DOI (digital_object_identifier). It uses another open source project, Zotero's translation-server, also written in JavaScript, to do a lot of the work.

In order to get citoid working on your computer, you'll need to download both Node version 10.0 (for citoid) and xpcshell version 29.0 (for Zotero) to get both of them working. There are installation instructions and more information available at https://www.mediawiki.org/wiki/Citoid

(For this task, you don't strictly need to install Zotero, but the tests will fail without it installed, so you will need to install it to create the tests.)

Details

	Subject	Repo	Branch	Lines +/-
	Interpret strings of digits between 1 and 8 digits long as PMIDs	mediawiki/services/citoid	master	+27 -39

Customize query in gerrit

Related Objects

Mentioned Here: T115248: Strings of digits currently only search for PMIDs; Add multiple results and include OCLC and PMC in the search

Event Timeline

Mvolz created this task.Jan 9 2017, 2:51 PM

Restricted Application added a project: VisualEditor. · View Herald TranscriptJan 9 2017, 2:51 PM

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Mvolz updated the task description. (Show Details)Jan 9 2017, 2:52 PM

Mvolz renamed this task from Expand pubmed regex to Expand pubmed regex in regex to include digits starting from 1.Jan 9 2017, 2:57 PM

Mvolz added projects: Google-Code-In-2016, good first task.

Mvolz updated the task description. (Show Details)

Restricted Application added a subscriber: TerraCodes. · View Herald TranscriptJan 9 2017, 2:57 PM

Mvolz renamed this task from Expand pubmed regex in regex to include digits starting from 1 to Expand pubmed regex to include digits starting from 1.Jan 9 2017, 2:58 PM

Mvolz renamed this task from Expand pubmed regex to include digits starting from 1 to Expand pubmed regex to include digits starting from 1 in citoid.Jan 9 2017, 3:04 PM

Mvolz updated the task description. (Show Details)

divadsn subscribed.Jan 9 2017, 3:45 PM

Mvolz updated the task description. (Show Details)Jan 9 2017, 3:48 PM

Mvolz updated the task description. (Show Details)Jan 9 2017, 4:51 PM

Imported, needs publishing: https://codein.withgoogle.com/dashboard/tasks/4749295691497472/

Aklapper moved this task from Proposed tasks to Imported in GCI Site on the Google-Code-In-2016 board.Jan 10 2017, 12:41 AM

Sn1per claimed this task.Jan 10 2017, 2:45 AM

Change 331443 had a related patch set uploaded (by Sn1per):
Interpret strings of digits between 1 and 8 digits long as PMIDs

https://gerrit.wikimedia.org/r/331443

gerritbot added a project: Patch-For-Review.Jan 10 2017, 4:52 AM

From the commit message,

"Side effect is that PMCIDs without prefixes are indistinguishable from
and considered PMIDs. Unit tests have been updated accordingly."

Hmm, I hadn't thought about that! This is definitely the preferred behaviour from the previous behaviour, however, we may consider trying and returning both citations if both are found. However, that makes this change much more architecturally complex because instead of handing it off to one function, we'll need to hand it to multiple functions, and concatenate the results, something I think is beyond scope here. Maybe that should be done as part of T115248 as well.

@mobrovac

Mvolz added a comment.Jan 10 2017, 9:36 AM

This comment was removed by Mvolz.

divadsn unsubscribed.Jan 10 2017, 10:33 AM

Agreed @Mvolz . If we can, we should return both, but it's a bit out of scope here. Perhaps create a new ticket that would take that into account for both PM(C)IDs as well as OCLC?

Change 331443 merged by jenkins-bot:
Interpret strings of digits between 1 and 8 digits long as PMIDs

https://gerrit.wikimedia.org/r/331443

Mvolz moved this task from Service to Waiting on Deploy on the Citoid board.Jan 11 2017, 4:25 PM

Mvolz removed a project: Patch-For-Review.

Deployed, resolving.

Jdforrester-WMF set the point value for this task to 0.Feb 3 2017, 9:22 PM

Jdforrester-WMF moved this task from To Triage to External and Administrivia on the VisualEditor board.

Expand pubmed regex to include digits starting from 1 in citoidClosed, ResolvedPublic0 Estimated Story PointsActions