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add bioDBnet REST API support

Open thatRichman opened this issue 6 years ago • 5 comments

Module to implement bioDBnet REST API access

Types of changes

This PR implements the following changes:

  • [x] :sparkles: New feature (A non-breaking change which adds functionality).
  • [ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
  • [ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).

:clipboard: Additional detail

bioDBnet, created and maintained by the Advanced Biomedical Computing Center (ABCC), Frederick National Laboratory for Cancer Research (FNLCR), and National Cancer Institute at Frederick (NCI), is a useful tool for mapping identifiers from various biological, chemical, and pharmacological databases to identifiers in other databases.

I have implemented this module following style and functionality precedence from eutils.jl, as I wished to help maintain consistency between modules as much as possible.

This will be my first contribution to any public project, so I apologize for anything that has been done incorrectly.

:ballot_box_with_check: Checklist

  • [x] :art: The changes implemented is consistent with the julia style guide.
  • [x] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the documentation styleguide.
  • [x] :blue_book: I have added or updated relevant user and developer manuals/documentation in docs/src/.
  • [x] :ok: There are unit tests that cover the code changes I have made.
  • [x] :ok: The unit tests cover my code changes AND they pass.
  • [ ] :pencil: I have added an entry to the [UNRELEASED] section of the manually curated CHANGELOG.md file for this repository.
  • [x] :ok: All changes should be compatible with the latest stable version of Julia.
  • [x] :thought_balloon: I have commented liberally for any complex pieces of internal code.

thatRichman avatar Oct 17 '19 01:10 thatRichman

This will be my first contribution to any public project, so I apologize for anything that has been done incorrectly.

Woo! Welcome to open source :-)

This is a very welcome contribution, but alas I'm not competent to review it.

kescobo avatar Oct 18 '19 20:10 kescobo

@thatRichman - really sorry that this has languished for so long, especially seeing as how it's your first contribution :-(. Seems from your github activity that it didn't slow you down though - I'm glad for that. This package has not been super actively maintained, but I hope to turn that around. Are you willing to rebase this off the current master brach, then I can take a look?

If you're not sure how to rebase, I can help with that.

kescobo avatar Apr 07 '21 14:04 kescobo

@thatRichman - really sorry that this has languished for so long, especially seeing as how it's your first contribution :-(. Seems from your github activity that it didn't slow you down though - I'm glad for that. This package has not been super actively maintained, but I hope to turn that around. Are you willing to rebase this off the current master brach, then I can take a look?

If you're not sure how to rebase, I can help with that.

No worries at all! I've been plenty busy so I almost completely forgot about this. I'll make sure that it hasn't broken over the past year and rebase.

thatRichman avatar Apr 08 '21 14:04 thatRichman

Fantastic! Ping me when it's done and I'll give it a review

kescobo avatar Apr 08 '21 14:04 kescobo

I've confirmed everything still works and I think (hope) I rebased correctly! Happy to fix anything that may have been done incorrectly.

thatRichman avatar Apr 22 '21 21:04 thatRichman