Preliminary JATS XML output

[dhimmel]

Supersedes https://github.com/greenelab/manubot-rootstock/pull/51.

• [ ] Update pandoc to 2.0.1 to resolve https://github.com/jgm/pandoc/issues/4020.

[AppVeyorBot]

AppVeyor build 1.0.183 for commit 3918ea7b06ad6a1d0aa32d38fbb7c4f2801516c0 failed.

[AppVeyorBot]

AppVeyor build 1.0.184 for commit f36146af5d4bae346f3178b202a14140f2a6c79a is now complete.

Found 52 potential spelling error(s). Preview:

content/02.delete-me.md:44:adipiscing content/02.delete-me.md:44:aliqua content/02.delete-me.md:44:amet content/02.delete-me.md:44:consectetur content/02.delete-me.md:44:dolore content/02.delete-me.md:44:eiusmod content/02.delete-me.md:44:elit content/02.delete-me.md:44:incididunt content/02.delete-me.md:44:ipsum content/02.delete-me.md:44:labore content/02.delete-me.md:44:Lorem content/02.delete-me.md:44:magna content/02...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.184-f36146a.html
• manuscript-1.0.184-f36146a.pdf
• spelling-errors-1.0.184-f36146a.txt
• spelling-error-locations-1.0.184-f36146a.txt

[dhimmel]

I'd like to load manuscript.xml into a JATS article viewer, to see how it looks. But I can't find any online JATS viewers/editors. I think texture was one, but it appears to be dead https://github.com/substance/texture/issues/1358.

https://github.com/libero/editor-client looks like an alternative, but it seems like a lot of work to set it up. Also noting https://github.com/elifesciences/lens. Looking for a webapp that allows uploading a JATS document and renders it.

[blahah]

@dhimmel I've made a few before - in sciencefair-land/sciencefair for example I modified the unsupported lens and made new adapters: https://github.com/sciencefair-land/sciencefair/tree/master/app/client/lib/lens

Happy to pull a standalone JATS viewer out from sciencefair if that's useful. Just need to understand your requirements.

edit: and some example files would be useful.

[blahah]

Here you go @dhimmel: https://github.com/blahah/scrappylens

Not a webapp exactly but it should suit the basic purpose. lmk if you need something more - or, quite likely, the JATS you have needs a new adapter for lens.

[hubgit]

It has some PMC-specific metadata requirements, but you could try https://www.ncbi.nlm.nih.gov/pmc/tools/article-previewer-intro/

[blahah]

Nice @hubgit (also hello old friend)!