Add support for CRAN and Bioconductor #1477
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Use the Posit Public Package Manager as an API endpoint to query for package version information TODO: Add Bioconductor support Refs: google#1476 Signed-off-by: Tyler <[email protected]>
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/gcbrun |
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/gcbrun |
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I think this is good to go now - thanks!
I'm going to go ahead and merge this so we can get importing on our staging site.
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Perfect, thanks for the patience @michaelkedar @andrewpollock great feedback, and feel free to reach out if there's anything else you need from me. |
| def test_next_version(self): | ||
| """Test next_version.""" | ||
| ecosystem = ecosystems.get('Bioconductor') | ||
| self.assertEqual('1.18.0', ecosystem.next_version('a4', '1.16.0')) |
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@tylfin this is starting to fail, but I'm not seeing why?
$ GET https://packagemanager.posit.co/__api__/repos/4/packages/a4?bioc_version=1.16.0
{"code":2,"error":"No sources found for Bioconductor 1.16.0","payload":null}
$ GET https://packagemanager.posit.co/__api__/repos/4/packages/a4?bioc_version=1.18.0
{"code":2,"error":"No sources found for Bioconductor 1.18.0","payload":null}
Yet https://bioconductor.org/packages/release/bioc/html/a4.html suggests the package still exists?
Also:
$ GET https://packagemanager.posit.co/__api__/repos/4/packages/a4?bioc_version=1.50.1
{"code":2,"error":"No sources found for Bioconductor 1.50.1","payload":null}
$ GET https://packagemanager.posit.co/__api__/repos/4/packages/a4?bioc_version=1.50.0
{"code":2,"error":"No sources found for Bioconductor 1.50.0","payload":null}
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Sorry, I was driving that wrong, here's what's happening:
$ GET https://packagemanager.posit.co/__api__/repos/4/packages/a4?bioc_version=3.19
{"code":4,"error":"Package 'a4' not found","payload":null}
It seems to work with all of the earlier versions than 3.19, based on a spot check with the bounds of bioc_versions
This pull request adds support for CRAN and Bioconductor from the R advisory database such that they will populate on the osv.dev site, included:
Refs: #1476