parsing files with parse2.php breaks automated git pulling

[CathyHajo]

Nothing that I have uploaded to XML Queue is turning up in the parse2.php page. It still has the 23 files that had to odd error messages, but never showed the new ones I have committed and synced. Ergh.

[JonathanReeve]

Hm, this sounds like it could be an issue with my automatic git pull script from #65. I logged into the server and noticed that the repo was four commits behind, for some reason. I'll look into this.

[JonathanReeve]

I see what's happening now. Parsing the XML files put the repository into a modified state, since it moves files from xml_added to xml_queue. That makes it so that automated git pulling breaks, since git won't overwrite a repo that has been modified (this is a feature designed so that you won't lose any work).

For now, a workaround is this (you only have to do this after you parse files):

• log into the DigitalOcean console
• change into the directory: cd /var/www/html/sanger
• reset the directory to its last commit (before parsing): sudo -u www-data git reset --hard HEAD. It may ask you for your admin password again here.
• pull in the latest changes: sudo -u www-data git pull.

This is another point for #63, for sure, since moving files between xml_added and xml_queue can really make version control unnecessarily complicated. I'll keep looking into a solution for this.

[CathyHajo]

When I did all that it said that the directory is up to date, which makes me think that you did it earlier.

[JonathanReeve]

Yep, I did it first to make sure it worked.