added oncokb_api_request() as underlying util function for all requests
added parse_responses() for general parsing of all API responses
added validate_oncokb_token()
added .check_protein_start_end() utility function for used in mutation API call
major updates to annotation functions (annotate_mutations(), annotate_cna(), annotate_sv() to now use same internal API calling function oncokb_api_request()If there is an GitHub issue associated with this pull request, please provide link.
Ready for Review:
[ ] annotate_cna()
[ ] annotate_sv()
Reviewer Checklist (if item does not apply, mark is as complete)
[ ] PR branch has pulled the most recent updates from master branch. Ensure the pull request branch and your local version match and both have the latest updates from the master branch.
[ ] If a new function was added, function included in _pkgdown.yml
[ ] If a bug was fixed, a unit test was added for the bug check
[ ] Run pkgdown::build_site(run_dont_run = TRUE). Check the R console for errors, and review the rendered website.
[ ] Code coverage is suitable for any new functions/features. Review coverage with withr::with_envvar(new = c("NOT_CRAN" = "true"). Begin in a fresh R session without any packages loaded.
[ ] R CMD Check runs without errors, warnings, and notes
[ ] usethis::use_spell_check() runs with no spelling errors in documentation
When the branch is ready to be merged into master:
[ ] Update NEWS.md with the changes from this pull request under the heading "# cbioportalR (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (see NEWS.md for examples).
What changes are proposed in this pull request?
.check_protein_start_end()utility function for used in mutation API callannotate_mutations(),annotate_cna(),annotate_sv()to now use same internal API calling functiononcokb_api_request()If there is an GitHub issue associated with this pull request, please provide link.Ready for Review:
[ ]
annotate_cna()[ ]
annotate_sv()Reviewer Checklist (if item does not apply, mark is as complete)
[ ] PR branch has pulled the most recent updates from master branch. Ensure the pull request branch and your local version match and both have the latest updates from the master branch.
[ ] If a new function was added, function included in
_pkgdown.yml[ ] If a bug was fixed, a unit test was added for the bug check
[ ] Run
pkgdown::build_site(run_dont_run = TRUE). Check the R console for errors, and review the rendered website.[ ] Code coverage is suitable for any new functions/features. Review coverage with
withr::with_envvar(new = c("NOT_CRAN" = "true"). Begin in a fresh R session without any packages loaded.[ ] R CMD Check runs without errors, warnings, and notes
[ ]
usethis::use_spell_check()runs with no spelling errors in documentationWhen the branch is ready to be merged into master:
NEWS.mdwith the changes from this pull request under the heading "# cbioportalR (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (seeNEWS.mdfor examples).codemetar::write_codemeta()usethis::use_spell_check()again