For PMID interwiki, there was probably some sort of caching happening.
Interwiki links are cached for 3 hours by default (
$wgInterwikiExpiry). It will take that long before removing PMID from
the interwiki table will take affect.

For the DB error, that would be odd. They do slightly different
things, but are basically the same. Usually when people encounter
errors its because of different versions between webserver php and
shell php. What is the precise error you got from update.php?

--
Brian

On Mon, Apr 9, 2018 at 3:53 PM, Jim Hu <jim.hu.bio...@gmail.com> wrote:
>
> I’ve been way too slow in updating our wikis to new versions, often because 
> new versions reveal all the places where my custom extensions are poorly 
> coded (by me). One thing that has been a total nightmare for me is that our 
> biology/genetics based wikis are heavily dependent on having pages that have 
> titles based on PMIDs. For example, in GONUTS (https://gowiki.tamu.edu), we 
> use pages like this one https://gowiki.tamu.edu/wiki/index.php/PMID:29370269 
> to gather information related to a specific paper by combining citations 
> within the wiki with information pulled in from an external web service.
>
> This weekend I had to bite the bullet and update GONUTS and I went with 
> 1.29.2 from 1.25, and I was shocked to find that links to those pages and 
> creating pages with those titles was causing bad title exceptions. I traced 
> the problem to the overlap between PMID: and an interwiki namespace, but 
> deleting the pmid row from the interwiki table in the database didn’t fix the 
> problem.
>
> I finally resorted to something that I know is a terrible, terrible idea: I 
> tweaked the code on line 337 of MediaWikiTitleCodec.php to specifically 
> ignore matches to ‘PMID’. It works, but I’m hoping someone can guide me on 
> how to do this without messing with the MW core code.
>
> I also noticed something about the updating process. I made a test copy of my 
> backend database from a SQL dump and ran the web installer pointed at the 
> 1.25-based database. Then I copied LocalSettings.php from the old install and 
> did testing/debugging. When I was satisfied that things were working, I 
> edited LocalSettings.php to point the wiki to the production database and ran 
> maintenance/update.php… and got a fatal error that was addressed in an item I 
> found online:  https://www.mediawiki.org/wiki/Topic:U26n1a1pgo0078tt 
> <https://www.mediawiki.org/wiki/Topic:U26n1a1pgo0078tt>
>
> So, it seems that the update from the shell doesn’t behave quite the same as 
> the update from the web-based system. There might have also been a difference 
> in PMID strings getting magic links, but I’m not sure if the difference was 
> due to shell vs web on that one.
>
> Jim Hu
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