Wikipedia:Bots/Requests for approval/Rfambot

The following discussion is an archived debate. Please do not modify it. Subsequent comments should be made in a new section. The result of the discussion was

Approved.

Rfambot[edit]

Operator: Jennifer_Rfm

Automatic or Manually Assisted: Automatically set to run on a curated list of pages

Programming Language(s): Perl and MediaWiki API

Function Summary: Update values in Rfam and Rfam box templates. Add/fix external database links

Edit period(s) (e.g. Continuous, daily, one time run): Schedule to run once every few weeks/month or so. The exact edits and subset of pages to be edited each time will vary.

Already has a bot flag (Y/N):NO

Function Details: The bot is written in perl and use the Mediawiki API. It downloads the current revision of a page from Wikipedia, parses it, replaces selective content (currently in rfam and rfam_box templates), and writes it back to Wikipedia.

Discussion[edit]

Could you please let me know what this bot does in simple English. :) =Nichalp «Talk»= 08:31, 13 October 2008 (UTC)[reply]

Sorry, a bit of background: Im interested in maintaining a set of pages which are relevant to Molecular Biology, in particular non coding RNA. I was involved in creating a set of pages ~ 600 which are relevant to different kinds (families) of non coding RNA. Please see WikiProject_RNA and WikiProject_Molecular_and_Cellular_Biology for some background on our efforts to improve the RNA pages in Wikipedia.

w.r.t. the purpose of the Rfambot: These ~600 RNA pages primarily contain information obtained from one of the public RNA databases Rfam and also links and references to other RNA database resources for this RNA family. I want to be able to maintain this Rfam data - update it when the Rfam database gets updated and also have an automated means of updating other data fields such as new secondary structure images or fixing or updating the the other database links. The majority of this data is stored in the Rfam database and it would be useful to have a bot to facilitate updates. The exact nature of the edits will probably be different each time- so I understand it may be necessary to submitt a new request each time.

As a first run of the bot I would be happy to restrict the data I want to update to the data used in the Rfam_box and the Rfam template. The Rfam template gives a standard format for the relevant link back to Rfam (where the Wikipedia pages are displayed)e.g U1 spliceosomal RNA. The Rfam_box provides more detailed family information/statistics from Rfam on the accession, description, type, length, sources for the RNA family.

So the bot would:

Be provided with a list of pages to edit. At most the full ~600-700 pages. Otherwise just a subset of them.
Use the media wiki API, download the page text from Wikipedia
Check that the page uses the Rfam or Rfam_box templates.(If not it will leave the page untouched)
If the expected Rfam_box or Rfam template is used, the data used in these templates will be compared with the relevant fields in Rfam and update the values e.g "acc", "description", "abbreviation", "type", "avg_length", "avg_identity", "ss", "se" otherwise if unchnaged the values will be left as is.
write the text back to Wikipedia using the Mediawiki API.

I hope this is a bit clearer. Let me know if I need to elaborate a bit more.Jennifer_Rfm (talk)

Approved for trial (20 edits). Please provide a link to the relevant contributions and/or diffs when the trial is complete. Mr.Z-man 05:15, 16 October 2008 (UTC)[reply]

What's the status on this? Mr.Z-man 03:06, 2 November 2008 (UTC)[reply]

Sorry, Ive just been busy. I was planning to give the trial edits a go this week Jennifer_Rfm (talk) 09:49, 3 November 2008 (UTC)[reply]

Hi, I only got time to look at this today- Im still in the process of fixing/checking my code so test edits will probably be run on Monday (10th). Is there an official expiry date on the trial periods? Jennifer_Rfm (talk) 16:43, 7 November 2008 (UTC)[reply]

Trial complete.

Ive run Rfambot on 20 page editsJennifer_Rfm (talk) 09:18, 12 November 2008 (UTC)[reply]

Approved. BJ^Talk 20:26, 12 November 2008 (UTC)[reply]

The above discussion is preserved as an archive of the debate. Please do not modify it. Subsequent comments should be made in a new section.