synapser refactor phase a

anngvu commented 6 months ago

"Master" issue: https://github.com/nf-osi/nfportalutils/issues/94
- Covers about 20% of the refactor
- Update tests and access-utils related vignette
Also add vignette for #172
- 30% of the work outlined in this issue

Update:

Currently, have to be very specific about using synapser (>= 1.0.0) and < 2.0, suggesting you use 1.3.0, see linked issue discussion regarding synSetAnnotations. However, by the time everything is refactored, I trust that synapser will have added back synSetAnnotations.
Ignore the one failed MacOS check, I think it is a brew issue upstream that will be resolved eventually, see discussion at https://github.com/r-lib/actions/issues/280
Suggest @allaway can review the low-level code, @cconrad8 can be made aware of the new vignettes.

anngvu commented 6 months ago

There appears to be a synapser issue that has to be resolved upstream of us. So on Linux stable source build, can use synapser::synSetAnnotations just fine. On MacOs and Windows, one gets the error Error: 'synSetAnnotations' is not an exported object from 'namespace:synapser'

allaway commented 6 months ago

@anngvu, should we report this on Sage-Bionetworks/synapser?

anngvu commented 6 months ago

Reported in https://github.com/Sage-Bionetworks/synapser/issues/331. I think for now best solution is to specify synapser (>= 1.0.0) and < 2.0 and update CI workflow.

github-actions[bot] commented 5 months ago

PR Preview Action v1.4.7 :---: :rocket: Deployed preview to https://nf-osi.github.io/nfportalutils/pr-preview/pr-171/ on branch gh-pages at 2024-03-13 00:35 UTC

anngvu commented 5 months ago

Update 2:

176, especially helpful for this PR and upcoming tutorials.
Partial work on #177 as another vignette.

anngvu commented 1 month ago

Merging this into develop-synapser isntead of main develop for now.

nf-osi / nfportalutils

synapser refactor phase a #171

176, especially helpful for this PR and upcoming tutorials.