Hi Natalie,

Sorry for my delay in responding.

While we don't have APIs for everything that you're interested in doing, it is possible to script those actions from Perl, and we have a couple of installations where users are doing just that. Unfortunately, since it involves poking URLs that we don't consider public APIs, it's more likely to break with new versions of LabKey Server. We don't have much in the way of documentation on this, but the way to determine the magic URL and GET/POST parameters is to go to the HTML form in the standard UI and figure out what needs to be set. Most of them are relatively simple, but will require things like configuring BASIC AUTH to authenticate the user and make sure they have permissions.

It would be great to have client APIs to do things like create folders and initiate pipeline jobs (which can load results, run XTandem and the TPP, etc). Here's some basic information about adding new APIs:

https://www.labkey.org/wiki/home/Documentation/page.view?name=implementActions

The class org.labkey.portal.ProjectController$GetContainersAction might be a good starting point for thinking about an API to create projects and folders.

Please let me know if that's helpful.

Thanks,
Josh