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lmu-bioinformatics / xmlpipedb

XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources.
http://xmlpipedb.cs.lmu.edu
GNU Lesser General Public License v3.0
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Archive/backup past Biological Database course wikis #38

Open dondi opened 7 years ago

dondi commented 7 years ago

Each offering of the Biological Databases course is housed in a combined MediaWiki installation + underlying database. They are currently on computer science servers and should be backed up into separate archives for safekeeping.

kdahlquist commented 7 years ago

I'm posting the e-mail from @dondi regarding the issue that triggered this one.

Good news---I was able to track down the issue with Fall 2013 [the Fall 2013 BioDB wiki was not displaying page content] and it has been fixed for me. Please check if it works for you now. [It's working for me]

So the problem turned out to be a side effect of an underlying OS library update (queue discussion with GRNmap students, haha). Newer versions of MediaWiki accommodate it, but not the version running Fall 2013. Rather than upgrading in full (a more involved operation because that version is from 2013), I was able to locate a patch that I applied. I then had to purge the MediaWiki cache for the main page, and the content appeared again.

Just for the record, here are some relevant links:

I also found out that if the user tries to Edit a page, the wiki markup still appears. So it really was just this issue of rendering the markup which was introduced by the OS library update ("PCRE"....I will guess that the "RE" stands for "regular expression"). Clicking Edit and seeing the wiki markup gave me assurance that the database was intact.

According to Michele Yeung, we have have unlimited storage on Box (for the moment). If the BioDB database and instance of MediaWiki can somehow be compressed in an archive, we could store the back-ups there for now. It would be great to do this for every instance of the course (but I'm not sure of the status of the earlier ones that were behind a firewall; I can't remember my password for those).