try to add in a repo privacy check

[kweav]

Was using the new ottrpal::borrow_chapter in place of the old cow::borrow_chapter and got an error because it expected a token. Hadn't passed one because the documentation made me think I only needed to if I was grabbing content from a private repo (and typically my use cases for borrow_chapter don't). So tried to adjust the logic in the check_git_repo function that borrow_chapter was using so that if the token was NULL and the repo was private, then it would look for a token.

To test if a repo was private, I was using the GItHub API (gh) and grabbing the repo_info. I tried to add in some error handling (wrapping the gh request in a try) in case for some reason we didn't have high enough permissions to be looking into whatever repo it was or the repo name had a typo or what have you. So that's the nested if looking at the repo_info output. If it failed, I knew the repo_info$private wouldn't be accessible and would fail when I added that to the condition checking if the token is NULL.

When testing this, I found that the grepl line errored because if it was a public repo, then the !grepl... was logical(0). So added an isTRUE to maintain the expected function.

Now, my tests are failing with a sink() issue.

I tried to add debugging messages with the message function to the overall borrow_chapter function to see where it is failing, but they didn't display in the logs in my latest test.

[kweav]

I'm wondering if we can simplify this check_git_repo function to use the github api gh function fully and just process its output codes for failures? Because the goal of the function seems to be to check and report if the repo exists. And the API should be able to do that, right? I'm sure there are reasons for not using the API, and perhaps you've got something else in mind for seeing if the repo is private @cansavvy

[kweav]

I should also note that I ran the unit test locally for borrow chapter and it seemed to work. That's why I've been working in a branch and with a dev version on a dev docker image. Related: jhudsl/Adv_Reproducibility_in_Cancer_Informatics#72

[cansavvy]

I'm wondering if we can simplify this check_git_repo function to use the github api gh function fully and just process its output codes for failures? Because the goal of the function seems to be to check and report if the repo exists. And the API should be able to do that, right? I'm sure there are reasons for not using the API, and perhaps you've got something else in mind for seeing if the repo is private @cansavvy

Yes it should be simplified. I wrote it a long time ago and never updated it. But really using gh would be better.

[kweav]

Closing because #19 from @acoffman addresses the issue