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 

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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