This repository https://github.com/OBF/wiki is a GitHub pages site rendered at https://obf.github.io/wiki/ using Jekyll.
The content is CC-BY 4.0 licensed, having been exported from the OBF MediaWiki installation which was self-hosted at https://www.open-bio.org/wiki/ and used from December 2005 until May 2019 when the only edits were to guide visitors to the replacement WordPress site at https://www.open-bio.org/ instead.
The conversion was run in February 2024 as folloows, with the final MediaWiki revision from July 2020.
On the MediaWiki server we ran the following, reporting 5314 revisions including files like images:
$ php ~/www/w/maintenance/dumpBackup.php --conf ~/www/w/LocalSettings.php \
--full --include-files --uploads > obf_mediawiki_dump_2024-02-05.xml
$ bzip2 obf_mediawiki_dump_2024-02-05.xml.bz2
We then copied the compressed XML dump to a Linux computer with git and pandoc.
The mediawiki_to_git_md
version 2.0.0 script mediawiki_to_md.py was used to turn the MediaWiki
revisions into a chronological git history, recording each page as a MediaWiki
file (with an extra header containing the page title), and any uploaded files
like images:
$ ./xml_to_git.py -i ./obf_mediawiki_dump_2024-02-05.xml.bz2 -p ""
These commits we all dated as per the MediaWiki history, along with our best effort to map the usernames to their name and email as used on GitHub.
During the import multiple usernames were flagged as spam and the commit
comments labelled as unwanted. This along with searching the history for
reverts allowed the git history to be cleaned up with the interactive git
rebase command (git rebase -i XXXXX --empty=drop). Only a few cases
required manual conflict resolution as most spam was reverted via the
MediaWiki interface.
The mediawiki_to_git_md
version 2.0.0 script ./mediawiki_to_md.py was used to turn the final
MediaWiki files (with custom headers recording their titles) into Markdown
using pandoc.
./mediawiki_to_md.py -i . -p ""
This script also handled internal redirects between pages. For example
BioPython.mediawiki was a redirect to Biopython, while file
Biopython.mediawiki became Biopython.md and included the
redirect-from entry in the header:
redirect_from:
- wiki/BioPython
This required the following in the Jekyll _config.yml file:
plugins:
- jekyll-redirect-from
External redirects done with the inter-wiki addon issue #1 were resolved manually, in many cases the old BioPerl wiki page no longer existed.
There were snippets of HTML left over from the migration issue #2, for example the blue box on the main page. These were addressed by hand.
The GitHub Pages theme and styling was also done separately.