Investigate the API of labkey

How can we programmatically access data from labkey?

assigned to @boersch

• How can we call the API of labkey?
• What settings do we need to set it up?
• Add script that calls the API

@gypas I wrote a python script that retrieves data from the LabKey (the script is located in the repository "scripts" in the branch called "labkey_api") and wrote a detailed description, how to run the script in README file. I also made a merge request to Alex.

I will close this as !8 (merged) should pretty much answer these questions, as far as I'm concerned. Plus there is already issue #3 (closed) which I think also deals with this (although it's hard to say because it does not contain any description). Let's try to write better issues and not forget to close them. If there is something else to do in this respect (e.g., putting data in to LabKey), we can open a more specific issue for that.

closed

Since we do not want to move (big) files is there a solution that does not require ftp transfer? Something json based would be ideal. I don't like the .netrc solution.

reopened

Another possibility would be to generate an API key, see below https://labkey.scicore.unibas.ch/labkey/home/wiki-page.view?name=security

added Duplicate label

@gypas: not sure what you mean, we don't need to transfer more than a row of metadata for each sample. For this case, a .netrc file is fine to carry credentials and isn't much different from any other auth system (in fact, one of the ways to use the API key is to put it in the .netrc file). Anyway, I'd say that we go ahead with what he have for now and if we run into walls with that approach we can open another issue to fix that.

closed

mentioned in issue #47 (closed)