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$ grep -oh "\[http://www.open-bio.org/wiki/.*\]" *.mediawiki 
[http://www.open-bio.org/wiki/Codefest_2010 Codefest session]
[http://www.open-bio.org/wiki/Codefest_2010 Codefest 2010 Report]
[http://www.open-bio.org/wiki/Codefest_2012 Codefest 2012]
[http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation]
[http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation:]  A Community For, By, and Of You ([http://www.slideshare.net/hlapp/obf-address-bosc2013 SlideShare] [http://www.youtube.com/watch?v=DiReTX3FoLM YouTube]
[http://www.open-bio.org/wiki/BOSC_2014_Schedule Complete Schedule]
[http://www.open-bio.org/wiki/EU-Codefest_2014 EU-Codefest 2014]
[http://www.open-bio.org/wiki/BOSC_Abstract_Submission submit your abstract here]
[http://www.open-bio.org/wiki/Main_Page Open Bioinformatics Foundation (OBF) update] ([https://youtu.be/1oSTb8ZAxec video]
[http://www.open-bio.org/wiki/BOSC_2017 BOSC 2017]
[http://www.open-bio.org/wiki/Hackathon Hackathons]
[http://www.open-bio.org/wiki/Hackathon Hackathons]
[http://www.open-bio.org/wiki/Hackathon Hackathons]
[http://www.open-bio.org/wiki/Hackathon Hackathons]
[http://www.open-bio.org/wiki/Hackathon Hackathons]
[http://www.open-bio.org/wiki/EU_Codefest_2012 first one]
[http://www.open-bio.org/wiki/Codefest_2014#Goals goals] as the OBF Codefest, which is usually organized along with the [http://www.open-bio.org/wiki/BOSC BOSC]
[http://www.open-bio.org/wiki/Codefest_2014 OBF Codefest]
[http://www.open-bio.org/wiki/File:BOSC2015-abstract-template.pdf PDF]
[http://www.open-bio.org/wiki/Google_Summer_of_Code_2015_Ideas#Biocaml Project ideas]
[http://www.open-bio.org/wiki/Google_Summer_of_Code_2014#Loris_Cro vcf-mongo ]
[http://www.open-bio.org/wiki/Minutes:2013_Apr_ConfCall April 2013 Board meeting minutes]

We want to turn these into relative links, probably via the mediawiki to markdown script using pandoc.

e.g. https://obf.github.io/wiki/BOSC_2014/BOFs tries to link to https://obf.github.io/wiki/BOSC_2014 but currently links to https://obf.github.io/BOSC_2014 instead.

This looks like bug in the cleanup_markdown function when prefix is empty https://github.com/peterjc/mediawiki_to_git_md/blob/278cbda8cf4b657dcb8da5a46da938a7e5e05e33/mediawiki_to_md.py#L277

There are some HTML snippets left in the post conversion markdown. These need to be reviewed and addressed individually.

e.g. the main page used HTML for the blue donation box layout, with mediawiki text within it. This resulted in Markdown within an HTML block which does not render as expected. This might be best resolved by turning the contents of the blue box into HTML too? Done in 994f421

Spin out from #2, the at-a-glance tables have lost a column each in https://obf.github.io/wiki/BOSC_2017_Schedule compared to https://obf.github.io/wiki/BOSC_2017_Schedule

It looks like pandoc couldn't cope with the nested table design, see https://github.com/OBF/wiki/blob/pre-pandoc/BOSC_2017_Schedule.mediawiki

Simplest fix looks to be make this two separate tables (remove the outer table putting them side by side), which will work better on the slightly narrower page layout in the current theme - and work better on smart phones etc.

Subset of #2, pandoc has output some rather verbose snippets for images.

e.g. from BOSC_2014.mediawiki as on https://open-bio.org/wiki/BOSC_2014 we had:

[[Image:Eagle_logo_2013.jpg|120px|left|Eagle Genomics logo|link=http://www.eaglegenomics.com/]]

This showed the image without a caption below it, clickable, with tool tip "Eagle Genomics logo".

After pandoc in https://github.com/OBF/wiki/edit/main/BOSC_2014.md we currently have:

<figure>
<img src="Eagle_logo_2013.jpg"
title="Eagle Genomics logo|link=http://www.eaglegenomics.com/"
width="120" />
<figcaption>Eagle Genomics logo|link=<a
href="http://www.eaglegenomics.com/">http://www.eaglegenomics.com/</a></figcaption>
</figure>

Sometimes the caption is appropriate, but generally I'd want just something like this:

<a href="http://www.eaglegenomics.com/">
<img src="Eagle_logo_2013.jpg" title="Eagle Genomics logo" alt="[Logo]" width="120" />
</a>

Can we tweak pandoc's settings? Can we adjust the MediaWiki before calling pandoc? Or must we post-process the Markdown?

My first attempt to add the social media icons adds them to the footer in https://github.com/OBF/wiki/blob/main/_layouts/default.html with no CSS or styling attempted.

Also, they are a mix of black and grey as copied from the current WordPress website.

Also, the icons are not hosted locally, which might be best - under assets/images/ perhaps?

This applies to the PDF files etc. e.g. end of https://obf.github.io/wiki//BOSC_2012_Schedule tries to link to media:BOSC2012_schedule.pdf

Currently the file is in the wiki/ directory as BOSC2012_schedule.pdf

We can't / won't match the original URLs. Should we put them under a media/ subdirectory?

File https://github.com/OBF/wiki/blob/main/_layouts/default.html does a crude job of inserting the OBF banner logo into the header, but it takes too much vertical space.

e.g. http://www.open-bio.org/w/images/2/25/Brigham_Circle_-_Countway_Map.pdf from Codefest_2010.mediawiki aka https://github.com/OBF/wiki/blob/main/Codefest_2010.md

$ grep "http://www.open-bio.org/w/" *.mediawiki  | wc -l
27

We don't seem to have this file via the XML dump - but why not?

Since the old site is live could always fetch over HTTP(s) and add to the repository. See also #6 and if we should use a sub-directory.

Update: We do have the files, just need to change the URL

The old MediaWiki install had some inter-wiki shortcuts setup including the bp: prefix for the BioPerl wiki. Those need to be reviewed and replaced.

e.g. Page PISE tries to redirect to bp:PISE, a BioPerl wiki page which no longer exists see https://web.archive.org/web/20160317135452/http://bioperl.org/wiki/PISE and https://github.com/bioperl/bioperl-pise - in this case replace the page with a stub based on the archived text?

e.g. https://open-bio.org/wiki/Codefest_2016 has a an image https://open-bio.org/w/images/2/22/FamiLAB-Logo3.gif

In the current rendering, https://open-bio.org/w/images/2/22/FamiLAB-Logo3.gif tries to show https://obf.github.io/wiki/_FamiLAB-Logo3.gif (not found).

So (a) where is the image, and (b) why the leading underscore?